From 3ee6fa3c4ef9cff46c9fb41028b2e76ac72d239e Mon Sep 17 00:00:00 2001 From: luiz Date: Tue, 29 Oct 2024 17:05:37 +0100 Subject: [PATCH 01/27] basic docs --- docs/README.md | 31 + docs/pydoc-markdown.yml | 14 + docs/requirements-docs.txt | 1 + docs/voluseg-docs-app/.gitignore | 20 + docs/voluseg-docs-app/README.md | 41 + docs/voluseg-docs-app/babel.config.js | 3 + .../blog/2021-08-26-welcome/index.md | 8 + docs/voluseg-docs-app/blog/authors.yml | 5 + docs/voluseg-docs-app/docs/faq.mdx | 15 + .../docs/getting_started/_category_.json | 8 + .../docs/getting_started}/iac_aws_batch.md | 5 +- .../docs/getting_started/installation.md | 30 + .../docs/getting_started/parameters.mdx | 172 + .../docs/getting_started/running.mdx | 85 + .../getting_started/running_container.mdx | 80 + docs/voluseg-docs-app/docs/intro.md | 7 + docs/voluseg-docs-app/docusaurus.config.js | 113 + docs/voluseg-docs-app/package-lock.json | 14514 ++++++++++++++++ docs/voluseg-docs-app/package.json | 44 + docs/voluseg-docs-app/sidebars.js | 22 + .../src/components/HomepageFeatures/index.js | 52 + .../HomepageFeatures/styles.module.css | 13 + docs/voluseg-docs-app/src/css/custom.css | 30 + docs/voluseg-docs-app/src/pages/index.js | 43 + .../src/pages/index.module.css | 23 + .../src/pages/markdown-page.md | 7 + docs/voluseg-docs-app/static/.nojekyll | 0 docs/voluseg-docs-app/yarn.lock | 8349 +++++++++ 28 files changed, 23734 insertions(+), 1 deletion(-) create mode 100644 docs/README.md create mode 100644 docs/pydoc-markdown.yml create mode 100644 docs/requirements-docs.txt create mode 100644 docs/voluseg-docs-app/.gitignore create mode 100644 docs/voluseg-docs-app/README.md create mode 100644 docs/voluseg-docs-app/babel.config.js create mode 100644 docs/voluseg-docs-app/blog/2021-08-26-welcome/index.md create mode 100644 docs/voluseg-docs-app/blog/authors.yml create mode 100644 docs/voluseg-docs-app/docs/faq.mdx create mode 100644 docs/voluseg-docs-app/docs/getting_started/_category_.json rename docs/{ => voluseg-docs-app/docs/getting_started}/iac_aws_batch.md (98%) create mode 100644 docs/voluseg-docs-app/docs/getting_started/installation.md create mode 100644 docs/voluseg-docs-app/docs/getting_started/parameters.mdx create mode 100644 docs/voluseg-docs-app/docs/getting_started/running.mdx create mode 100644 docs/voluseg-docs-app/docs/getting_started/running_container.mdx create mode 100644 docs/voluseg-docs-app/docs/intro.md create mode 100644 docs/voluseg-docs-app/docusaurus.config.js create mode 100644 docs/voluseg-docs-app/package-lock.json create mode 100644 docs/voluseg-docs-app/package.json create mode 100644 docs/voluseg-docs-app/sidebars.js create mode 100644 docs/voluseg-docs-app/src/components/HomepageFeatures/index.js create mode 100644 docs/voluseg-docs-app/src/components/HomepageFeatures/styles.module.css create mode 100644 docs/voluseg-docs-app/src/css/custom.css create mode 100644 docs/voluseg-docs-app/src/pages/index.js create mode 100644 docs/voluseg-docs-app/src/pages/index.module.css create mode 100644 docs/voluseg-docs-app/src/pages/markdown-page.md create mode 100644 docs/voluseg-docs-app/static/.nojekyll create mode 100644 docs/voluseg-docs-app/yarn.lock diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..39613c0 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,31 @@ +# Documentation + +This folder contains the documentation for the Voluseg project. The docs are a docusaurus app that is built and deployed to GitHub Pages. + + +### Automatically generating the API Reference documentation +The API Reference documentation is automatically generated from the docstrings and type annotations in the codebase using [pydoc-markdown](https://github.com/NiklasRosenstein/pydoc-markdown). + +1. Install pydoc-markdown: +First install `pydoc-markdown` package following their guide [here](https://niklasrosenstein.github.io/pydoc-markdown/#installation-). + +2. In the `docs/` directory, run the following command to generate the API Reference documentation: +```bash +pydoc-markdown +``` +This command will generate the API Reference documentation from the project and save it in the `docs/voluseg-docs-app/docs/reference/voluseg` folder. + + +### Running the documentation app locally +To run the documentation app locally, follow these steps: + +1. Install the dependencies: go to the `docs/voluseg-docs-app` directory and run: +```bash +# Be sure using node > 18 +yarn +``` +2. Start the development server: +```bash +yarn start +``` + diff --git a/docs/pydoc-markdown.yml b/docs/pydoc-markdown.yml new file mode 100644 index 0000000..4a074c1 --- /dev/null +++ b/docs/pydoc-markdown.yml @@ -0,0 +1,14 @@ +loaders: + - type: python + search_path: ["../src"] +processors: + - type: filter + skip_empty_modules: true + - type: smart + - type: crossref +renderer: + type: docusaurus + docs_base_path: voluseg-docs-app/docs + relative_output_path: reference + relative_sidebar_path: sidebar.json + sidebar_top_level_label: null diff --git a/docs/requirements-docs.txt b/docs/requirements-docs.txt new file mode 100644 index 0000000..6dcdf89 --- /dev/null +++ b/docs/requirements-docs.txt @@ -0,0 +1 @@ +pydoc-markdown==4.8.2 \ No newline at end of file diff --git a/docs/voluseg-docs-app/.gitignore b/docs/voluseg-docs-app/.gitignore new file mode 100644 index 0000000..b2d6de3 --- /dev/null +++ b/docs/voluseg-docs-app/.gitignore @@ -0,0 +1,20 @@ +# Dependencies +/node_modules + +# Production +/build + +# Generated files +.docusaurus +.cache-loader + +# Misc +.DS_Store +.env.local +.env.development.local +.env.test.local +.env.production.local + +npm-debug.log* +yarn-debug.log* +yarn-error.log* diff --git a/docs/voluseg-docs-app/README.md b/docs/voluseg-docs-app/README.md new file mode 100644 index 0000000..0c6c2c2 --- /dev/null +++ b/docs/voluseg-docs-app/README.md @@ -0,0 +1,41 @@ +# Website + +This website is built using [Docusaurus](https://docusaurus.io/), a modern static website generator. + +### Installation + +``` +$ yarn +``` + +### Local Development + +``` +$ yarn start +``` + +This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server. + +### Build + +``` +$ yarn build +``` + +This command generates static content into the `build` directory and can be served using any static contents hosting service. + +### Deployment + +Using SSH: + +``` +$ USE_SSH=true yarn deploy +``` + +Not using SSH: + +``` +$ GIT_USER= yarn deploy +``` + +If you are using GitHub pages for hosting, this command is a convenient way to build the website and push to the `gh-pages` branch. diff --git a/docs/voluseg-docs-app/babel.config.js b/docs/voluseg-docs-app/babel.config.js new file mode 100644 index 0000000..e00595d --- /dev/null +++ b/docs/voluseg-docs-app/babel.config.js @@ -0,0 +1,3 @@ +module.exports = { + presets: [require.resolve('@docusaurus/core/lib/babel/preset')], +}; diff --git a/docs/voluseg-docs-app/blog/2021-08-26-welcome/index.md b/docs/voluseg-docs-app/blog/2021-08-26-welcome/index.md new file mode 100644 index 0000000..7bf6b1d --- /dev/null +++ b/docs/voluseg-docs-app/blog/2021-08-26-welcome/index.md @@ -0,0 +1,8 @@ +--- +slug: welcome +title: Welcome +authors: [author1] +tags: [blog, voluseg] +--- + +Welcome to Voluseg Blog diff --git a/docs/voluseg-docs-app/blog/authors.yml b/docs/voluseg-docs-app/blog/authors.yml new file mode 100644 index 0000000..cc8de09 --- /dev/null +++ b/docs/voluseg-docs-app/blog/authors.yml @@ -0,0 +1,5 @@ +author1: + name: Mikail Rubinov + title: Maintainer of Voluseg + url: https://github.com/mikarubi/voluseg + image_url: https://avatars.githubusercontent.com/u/10106032?v=4 diff --git a/docs/voluseg-docs-app/docs/faq.mdx b/docs/voluseg-docs-app/docs/faq.mdx new file mode 100644 index 0000000..3bc1845 --- /dev/null +++ b/docs/voluseg-docs-app/docs/faq.mdx @@ -0,0 +1,15 @@ +--- +id: faq +title: FAQ +sidebar_position: 4 +--- + +### Frequently Asked Questions +
+ What is Voluseg? +

+ Voluseg is a software providing a pipeline for automatic volumetric cell segmentation + from calcium imaging recordings. +

+
+ diff --git a/docs/voluseg-docs-app/docs/getting_started/_category_.json b/docs/voluseg-docs-app/docs/getting_started/_category_.json new file mode 100644 index 0000000..14f86c7 --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "Getting Started", + "position": 2, + "link": { + "type": "generated-index", + "description": "Getting Started" + } +} \ No newline at end of file diff --git a/docs/iac_aws_batch.md b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md similarity index 98% rename from docs/iac_aws_batch.md rename to docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md index 4cf51a1..8e1d082 100644 --- a/docs/iac_aws_batch.md +++ b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md @@ -1,4 +1,7 @@ -# Running Voluseg on AWS Batch +--- +title: Running on AWS Batch +sidebar_position: 4 +--- Here we provide instructions for setting up your Voluseg service to run jobs in AWS Batch. First you will need to provision the base AWS Batch infrastructure using CDK. This includes IAM roles, VPC, Security Group, Batch Compute Environments and Batch Job Queues. Next you will need to configure your compute resource controller to submit jobs to AWS Batch. Finally, when you submit jobs from the web interface, you must select aws_batch as the run method. diff --git a/docs/voluseg-docs-app/docs/getting_started/installation.md b/docs/voluseg-docs-app/docs/getting_started/installation.md new file mode 100644 index 0000000..0bc41f3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/installation.md @@ -0,0 +1,30 @@ +--- +title: Installation +sidebar_position: 2 +--- + + +## Installation + +To get started we recommend using [Anaconda](https://www.anaconda.com/distribution/) or [Virtual Environment](https://docs.python.org/3/library/venv.html) with Python 3.11 or higher. + + +### Install with pip +```python +pip install voluseg +``` + + +### Install from Github repository + +1. Clone the Voluseg repository to your local machine by running +```bash +git clone https://github.com/mikarubi/voluseg.git +``` + +2. Install Voluseg from local source +Install Voluseg with pip in your active virtual environment by running +```bash +cd voluseg +pip install . +``` diff --git a/docs/voluseg-docs-app/docs/getting_started/parameters.mdx b/docs/voluseg-docs-app/docs/getting_started/parameters.mdx new file mode 100644 index 0000000..5168781 --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/parameters.mdx @@ -0,0 +1,172 @@ +--- +title: Pipeline Parameters +sidebar_position: 5 +--- + +## Parameters dictionary +To run the Voluseg pipeline, you need to set up the parameters. The parameters are stored in a dictionary and can be modified to fit your specific needs. The parameters are used to control the behavior of the pipeline, such as the type of detrending, registration quality, cell diameter, and resolution. + +**detrending** (str, optional): +
+ Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +
+ +**registration** (str, optional): +
+ Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +
+ +**registration_restrict** (str, optional): +
+ Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +
+ +**diam_cell** (float, optional): +
+ Cell diameter in microns (default is 6.0). +
+ +**dir_ants** (str, optional): +
+ Path to the ANTs directory (default is an empty string). +
+ +**dir_input** (str, optional): +
+ Path to input directories, separate multiple directories with ';' (default is an empty string). +
+ +**dir_output** (str, optional): +
+ Path to the output directory (default is an empty string). +
+ +**dir_transform** (str, optional): +
+ Path to the transform directory (default is an empty string). +
+ +**ds** (int, optional): +
+ Spatial coarse-graining in x-y dimension (default is 2). +
+ +**planes_pad** (int, optional): +
+ Number of planes to pad the volume with for robust registration (default is 0). +
+ +**planes_packed** (bool, optional): +
+ Packed planes in each volume, for single plane imaging with packed planes (default is False). +
+ +**parallel_clean** (bool, optional): +
+ Parallelization of final cleaning (True is fast but memory-intensive, default is True). +
+ +**parallel_volume** (bool, optional): +
+ Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +
+ +**save_volume** (bool, optional): +
+ Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +
+ +**type_timepoints** (str, optional): +
+ Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +
+ +**type_mask** (str, optional): +
+ Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +
+ +**timepoints** (int, optional): +
+ Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +
+ +**f_hipass** (float, optional): +
+ Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +
+ +**f_volume** (float, optional): +
+ Imaging frequency in Hz (default is 2.0). +
+ +**n_cells_block** (int, optional): +
+ Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +
+ +**n_colors** (int, optional): +
+ Number of brain colors (2 in two-color volumes, default is 1). +
+ +**res_x** (float, optional): +
+ X resolution in microns (default is 0.40625). +
+ +**res_y** (float, optional): +
+ Y resolution in microns (default is 0.40625). +
+ +**res_z** (float, optional): +
+ Z resolution in microns (default is 5.0). +
+ +**t_baseline** (int, optional): +
+ Interval for baseline calculation in seconds (default is 300). +
+ +**t_section** (float, optional): +
+ Exposure time in seconds for slice acquisition (default is 0.01). +
+ +**thr_mask** (float, optional): +
+ Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +
+ +**volume_fullnames_input** (list[str], optional): +
+ List of full volume names (default is None). +
+ +**volume_names** (list[str], optional): +
+ List of volume names (default is None). +
+ +**input_dirs** (list[str], optional): +
+ List of input directories (default is None). +
+ +**ext** (str, optional): +
+ File extension (default is None). +
+ +**lt** (int, optional): +
+ Number of volumes (default is None). +
+ +**affine_matrix** (list, optional): +
+ Affine matrix (default is None). +
\ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/getting_started/running.mdx b/docs/voluseg-docs-app/docs/getting_started/running.mdx new file mode 100644 index 0000000..8bd19bd --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/running.mdx @@ -0,0 +1,85 @@ +--- +title: Running Voluseg Pipeline +sidebar_position: 2 +--- + + +## Pipeline Overview +The Voluseg pipeline consists of an initial setup of parameters followed by five consecutive steps: + +1. Process volumes +2. Align volumes +3. Mask volumes +4. Detect cells +5. Clean cells + + +## Running a demo workflow +To get familiar with Voluseg, let's run a simple example with a demo dataset. + + +### Download the necessary resources +To run the demo you will need start by downloading the sample data to your local machine: + +```python +import voluseg + +# Download sample data +voluseg._tools.download_sample_data("/path/to/input/") +``` + +### Setup pipeline parameters +Voluseg provides a dictionary with default parameters that can be modified to fit your specific needs. You can read more about the parameters in the [Parameters](/docs/voluseg-docs-app/docs/getting_started/parameters) section. You can access the default parameters dictionary, edit and process it by running: + +```python +# Set parameters +parameters_0 = voluseg.parameter_dictionary() +parameters_0['dir_ants'] = '/path/to/ants/bin/' +parameters_0['dir_input'] = '/path/to/input/downloaded_data/' +parameters_0['dir_output'] = '/path/to/output/directory/' +parameters_0['registration'] = 'high' +parameters_0['diam_cell'] = 5.0 +parameters_0['f_volume'] = 2.0 + +# Process parameters +parameters = voluseg.step0_process_parameters(parameters_0) +``` + +A parameters file will be saved in the output directory with the name `parameters.json`. + +### Step 1. Process volumes +The first step of the pipeline is to process the input volumes and to save them as nifti files. This step will perform downsampling and padding if specified in parameters. + +```python +voluseg.step1_process_volumes(parameters) +``` + + +#### Step 2. Align volumes +In the second step, the volumes are aligned to a reference volume. This step will generate ANTs transform files (.mat). + +```python +voluseg.step2_align_volumes(parameters) +``` + +### Step 3. Mask volumes +In the third step, the volumes are masked to create an intensity mask from the average registered volume. This step will produce figures with masks and histograms, and will save `mean_timeseries.hdf5` and `volume0.hdf5` files. + +```python +voluseg.step3_mask_volumes(parameters) +``` + +### Step 4. Detect cells +In the fourth step, cells are detected in volumetric blocks. + +```python +voluseg.step4_detect_cells(parameters) +``` + +### Step 5. Clean cells +In the final step, the detected cells are cleaned by removing noisy cells, detrending and detecting a baseline signal. + +```python +voluseg.step5_clean_cells(parameters) +``` + diff --git a/docs/voluseg-docs-app/docs/getting_started/running_container.mdx b/docs/voluseg-docs-app/docs/getting_started/running_container.mdx new file mode 100644 index 0000000..d650038 --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/running_container.mdx @@ -0,0 +1,80 @@ +--- +title: Running from Container +sidebar_position: 3 +--- + +You can easily run the Voluseg pipeline using a container. This is useful if you want to run the pipeline without having to install all the dependencies on your local machine. + +## Using Docker +Pull the image from GHCR: +```bash +docker pull ghcr.io/mikarubi/voluseg/voluseg:latest +``` + +Run with access to your local data and pass user-defined parameters values: +```bash +docker run \ +-v $(pwd)/local_data:/voluseg/data \ +-v $(pwd)/output:/voluseg/output \ +voluseg \ +python3 /voluseg/app/app.py \ +--registration high \ +--diam-cell 5.0 +``` + +To get a list of all available parameters, run: +```bash +docker run voluseg python3 /voluseg/app/app.py --help +``` + +### Example: reading from a remote NWB file +Voluseg can read from remote NWB files stored in S3 buckets. To do this, you should pass the URL of the NWB file to the `--dir-input` parameter: +```bash +docker run \ +-v $(pwd)/output_stream:/voluseg/output \ +voluseg \ +python3 /voluseg/app/app.py \ +--registration high \ +--diam-cell 5.0 \ +--dir-input "https://dandiarchive.s3.amazonaws.com/blobs/057/ecb/057ecbef-e732-4e94-8d99-40ebb74d346e" +``` + + +### For developers +From the repository root, you can build the image locally and run it with hot reload for the voluseg package (useful for development). + +Build the image locally: +```bash +DOCKER_BUILDKIT=1 docker build -t voluseg . +``` + +Run with local data volume mount, default parameters values and hot reload for the voluseg package: +```bash +docker run \ +-v $(pwd)/local_data:/voluseg/data \ +-v $(pwd)/output:/voluseg/output \ +-v $(pwd)/voluseg:/voluseg/voluseg \ +-v $(pwd)/app:/voluseg/app \ +voluseg +``` + +## Using Apptainer + +Pull the image from GHCR and convert it to an Apptainer image: +```bash +apptainer pull docker://ghcr.io/mikarubi/voluseg/voluseg:latest +``` + +Run with access to your local data and pass user-defined parameters values: +```bash +apptainer exec \ +--bind $(pwd)/local_data:/voluseg/data \ +--bind $(pwd)/output:/voluseg/output \ +voluseg_latest.sif \ +python3 /voluseg/app/app.py \ +--registration high \ +--diam-cell 5.0 \ +--no-parallel-volume \ +--no-parallel-clean \ +2>&1 | tee log_file.log +``` \ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/intro.md b/docs/voluseg-docs-app/docs/intro.md new file mode 100644 index 0000000..223775b --- /dev/null +++ b/docs/voluseg-docs-app/docs/intro.md @@ -0,0 +1,7 @@ +--- +title: Introduction +sidebar_position: 1 +--- + +🌟 Welcome to Voluseg, an open-source tool providing a pipeline for automatic volumetric cell segmentation from calcium imaging recordings. + diff --git a/docs/voluseg-docs-app/docusaurus.config.js b/docs/voluseg-docs-app/docusaurus.config.js new file mode 100644 index 0000000..bada349 --- /dev/null +++ b/docs/voluseg-docs-app/docusaurus.config.js @@ -0,0 +1,113 @@ +// @ts-check +// `@type` JSDoc annotations allow editor autocompletion and type checking +// (when paired with `@ts-check`). +// There are various equivalent ways to declare your Docusaurus config. +// See: https://docusaurus.io/docs/api/docusaurus-config + +import { themes as prismThemes } from 'prism-react-renderer'; + +/** @type {import('@docusaurus/types').Config} */ +const config = { + title: 'Voluseg', + tagline: 'Pipeline for volumetric cell segmentation', + // favicon: 'img/favicon.ico', + + // Set the production url of your site here + url: 'https://mikarubi.github.io', + // Set the // pathname under which your site is served + // For GitHub pages deployment, it is often '//' + // baseUrl: '/voluseg/', + baseUrl: "/voluseg/", + + // GitHub pages deployment config. + // If you aren't using GitHub pages, you don't need these. + organizationName: 'facebook', // Usually your GitHub org/user name. + projectName: 'docusaurus', // Usually your repo name. + + onBrokenLinks: 'throw', + onBrokenMarkdownLinks: 'warn', + + // Even if you don't use internationalization, you can use this field to set + // useful metadata like html lang. For example, if your site is Chinese, you + // may want to replace "en" with "zh-Hans". + i18n: { + defaultLocale: 'en', + locales: ['en'], + }, + + presets: [ + [ + 'classic', + /** @type {import('@docusaurus/preset-classic').Options} */ + ({ + docs: { + sidebarPath: './sidebars.js', + }, + blog: { + showReadingTime: true, + }, + theme: { + customCss: './src/css/custom.css', + }, + }), + ], + ], + + themeConfig: + /** @type {import('@docusaurus/preset-classic').ThemeConfig} */ + ({ + // Replace with your project's social card + image: 'img/voluseg_social_card.jpg', + navbar: { + title: 'Voluseg', + items: [ + { + type: 'docSidebar', + sidebarId: 'docsSidebar', + position: 'right', + label: 'Documentation', + }, + { to: '/blog', label: 'Blog', position: 'right' }, + { + href: 'https://github.com/mikarubi/voluseg', + label: 'GitHub', + position: 'right', + }, + ], + }, + footer: { + style: 'dark', + links: [ + { + title: 'Docs', + items: [ + { + label: 'Tutorial', + to: '/docs/intro', + }, + ], + }, + { + title: 'More', + items: [ + { + label: 'Blog', + to: '/blog', + }, + { + label: 'GitHub', + href: 'https://github.com/mikarubi/voluseg', + }, + ], + }, + ], + copyright: `Copyright © ${new Date().getFullYear()} Voluseg, Mikail Rubinov.`, + }, + prism: { + theme: prismThemes.github, + darkTheme: prismThemes.dracula, + }, + }), +}; + +export default config; diff --git a/docs/voluseg-docs-app/package-lock.json b/docs/voluseg-docs-app/package-lock.json new file mode 100644 index 0000000..d297e47 --- /dev/null +++ b/docs/voluseg-docs-app/package-lock.json @@ -0,0 +1,14514 @@ +{ + "name": "docs", + "version": "0.0.0", + "lockfileVersion": 3, + "requires": true, + "packages": { + "": { + "name": "docs", + "version": "0.0.0", + "dependencies": { + "@docusaurus/core": "3.3.2", + "@docusaurus/preset-classic": "3.3.2", + "@mdx-js/react": "^3.0.0", + "clsx": "^2.0.0", + "prism-react-renderer": "^2.3.0", + "react": "^18.0.0", + "react-dom": "^18.0.0" + }, + "devDependencies": { + 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+ }, + "dependencies": { + "@docusaurus/core": "3.3.2", + "@docusaurus/preset-classic": "3.3.2", + "@mdx-js/react": "^3.0.0", + "clsx": "^2.0.0", + "prism-react-renderer": "^2.3.0", + "react": "^18.0.0", + "react-dom": "^18.0.0" + }, + "devDependencies": { + "@docusaurus/module-type-aliases": "3.3.2", + "@docusaurus/types": "3.3.2" + }, + "browserslist": { + "production": [ + ">0.5%", + "not dead", + "not op_mini all" + ], + "development": [ + "last 3 chrome version", + "last 3 firefox version", + "last 5 safari version" + ] + }, + "engines": { + "node": ">=18.0" + } +} diff --git a/docs/voluseg-docs-app/sidebars.js b/docs/voluseg-docs-app/sidebars.js new file mode 100644 index 0000000..e9c5343 --- /dev/null +++ b/docs/voluseg-docs-app/sidebars.js @@ -0,0 +1,22 @@ +/** + * Creating a sidebar enables you to: + - create an ordered group of docs + - render a sidebar for each doc of that group + - provide next/previous navigation + + The sidebars can be generated from the filesystem, or explicitly defined here. + + Create as many sidebars as you want. + */ + +// @ts-check + +/** @type {import('@docusaurus/plugin-content-docs').SidebarsConfig} */ +const sidebars = { + // By default, Docusaurus generates a sidebar from the docs folder structure + docsSidebar: [{type: 'autogenerated', dirName: '.'}], + + +}; + +export default sidebars; diff --git a/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js b/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js new file mode 100644 index 0000000..b7e4493 --- /dev/null +++ b/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js @@ -0,0 +1,52 @@ +import clsx from 'clsx'; +import Heading from '@theme/Heading'; +import styles from './styles.module.css'; + +const FeatureList = [ + { + title: 'Automatic Cell extraction pipeline', + // Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, + description: ( + <> + Voluseg provides advanced algorithms for efficient segemntation of volumetric calcium imaging data. + + ), + }, + { + title: 'Automatic Cell extraction pipeline', + // Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, + description: ( + <> + Voluseg provides advanced algorithms for efficient segemntation of volumetric calcium imaging data. + + ), + }, +]; + +function Feature({ Svg, title, description }) { + return ( +
+ {/*
+ +
*/} +
+ {title} +

{description}

+
+
+ ); +} + +export default function HomepageFeatures() { + return ( +
+
+
+ {FeatureList.map((props, idx) => ( + + ))} +
+
+
+ ); +} diff --git a/docs/voluseg-docs-app/src/components/HomepageFeatures/styles.module.css b/docs/voluseg-docs-app/src/components/HomepageFeatures/styles.module.css new file mode 100644 index 0000000..2d409a9 --- /dev/null +++ b/docs/voluseg-docs-app/src/components/HomepageFeatures/styles.module.css @@ -0,0 +1,13 @@ +.features { + display: flex; + align-items: center; + justify-content: center; + padding: 4rem 0; + /* Increase padding for better spacing */ +} + +.featureSvg { + height: 150px; + /* Adjust height to fit the new images */ + width: auto; +} \ No newline at end of file diff --git a/docs/voluseg-docs-app/src/css/custom.css b/docs/voluseg-docs-app/src/css/custom.css new file mode 100644 index 0000000..2bc6a4c --- /dev/null +++ b/docs/voluseg-docs-app/src/css/custom.css @@ -0,0 +1,30 @@ +/** + * Any CSS included here will be global. The classic template + * bundles Infima by default. Infima is a CSS framework designed to + * work well for content-centric websites. + */ + +/* You can override the default Infima variables here. */ +:root { + --ifm-color-primary: #2e8555; + --ifm-color-primary-dark: #29784c; + --ifm-color-primary-darker: #277148; + --ifm-color-primary-darkest: #205d3b; + --ifm-color-primary-light: #33925d; + --ifm-color-primary-lighter: #359962; + --ifm-color-primary-lightest: #3cad6e; + --ifm-code-font-size: 95%; + --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.1); +} + +/* For readability concerns, you should choose a lighter palette in dark mode. */ +[data-theme='dark'] { + --ifm-color-primary: #25c2a0; + --ifm-color-primary-dark: #21af90; + --ifm-color-primary-darker: #1fa588; + --ifm-color-primary-darkest: #1a8870; + --ifm-color-primary-light: #29d5b0; + --ifm-color-primary-lighter: #32d8b4; + --ifm-color-primary-lightest: #4fddbf; + --docusaurus-highlighted-code-line-bg: rgba(0, 0, 0, 0.3); +} diff --git a/docs/voluseg-docs-app/src/pages/index.js b/docs/voluseg-docs-app/src/pages/index.js new file mode 100644 index 0000000..3572503 --- /dev/null +++ b/docs/voluseg-docs-app/src/pages/index.js @@ -0,0 +1,43 @@ +import clsx from 'clsx'; +import Link from '@docusaurus/Link'; +import useDocusaurusContext from '@docusaurus/useDocusaurusContext'; +import Layout from '@theme/Layout'; +import HomepageFeatures from '@site/src/components/HomepageFeatures'; + +import Heading from '@theme/Heading'; +import styles from './index.module.css'; + +function HomepageHeader() { + const { siteConfig } = useDocusaurusContext(); + return ( +
+
+ + {siteConfig.title} + +

{siteConfig.tagline}

+
+ + Get Started with Voluseg + +
+
+
+ ); +} + +export default function Home() { + const { siteConfig } = useDocusaurusContext(); + return ( + + +
+ +
+ + ); +} diff --git a/docs/voluseg-docs-app/src/pages/index.module.css b/docs/voluseg-docs-app/src/pages/index.module.css new file mode 100644 index 0000000..9f71a5d --- /dev/null +++ b/docs/voluseg-docs-app/src/pages/index.module.css @@ -0,0 +1,23 @@ +/** + * CSS files with the .module.css suffix will be treated as CSS modules + * and scoped locally. + */ + +.heroBanner { + padding: 4rem 0; + text-align: center; + position: relative; + overflow: hidden; +} + +@media screen and (max-width: 996px) { + .heroBanner { + padding: 2rem; + } +} + +.buttons { + display: flex; + align-items: center; + justify-content: center; +} diff --git a/docs/voluseg-docs-app/src/pages/markdown-page.md b/docs/voluseg-docs-app/src/pages/markdown-page.md new file mode 100644 index 0000000..9756c5b --- /dev/null +++ b/docs/voluseg-docs-app/src/pages/markdown-page.md @@ -0,0 +1,7 @@ +--- +title: Markdown page example +--- + +# Markdown page example + +You don't need React to write simple standalone pages. diff --git a/docs/voluseg-docs-app/static/.nojekyll b/docs/voluseg-docs-app/static/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/docs/voluseg-docs-app/yarn.lock b/docs/voluseg-docs-app/yarn.lock new file mode 100644 index 0000000..c1e94b4 --- /dev/null +++ b/docs/voluseg-docs-app/yarn.lock @@ -0,0 +1,8349 @@ +# THIS IS AN AUTOGENERATED FILE. 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6d3b68a6bcd999676b38dbe183a6d65390e6b8d8 Mon Sep 17 00:00:00 2001 From: luiz Date: Tue, 29 Oct 2024 20:54:18 +0100 Subject: [PATCH 02/27] api reference --- .github/workflows/build_publish_docs.yaml | 63 ++++++++++ .../docs/getting_started/running.mdx | 2 +- .../docs/reference/_category_.json | 8 ++ .../docs/reference/sidebar.json | 47 +++++++ .../docs/reference/voluseg/_steps/step0.md | 23 ++++ .../docs/reference/voluseg/_steps/step1.md | 23 ++++ .../docs/reference/voluseg/_steps/step2.md | 23 ++++ .../docs/reference/voluseg/_steps/step3.md | 24 ++++ .../docs/reference/voluseg/_steps/step4.md | 22 ++++ .../docs/reference/voluseg/_steps/step4a.md | 39 ++++++ .../docs/reference/voluseg/_steps/step4b.md | 46 +++++++ .../docs/reference/voluseg/_steps/step4c.md | 53 ++++++++ .../docs/reference/voluseg/_steps/step4d.md | 54 ++++++++ .../docs/reference/voluseg/_steps/step4e.md | 27 ++++ .../docs/reference/voluseg/_steps/step5.md | 22 ++++ .../voluseg/_tools/ants_registration.md | 44 +++++++ .../voluseg/_tools/ants_transformation.md | 38 ++++++ .../docs/reference/voluseg/_tools/aws.md | 36 ++++++ .../docs/reference/voluseg/_tools/ball.md | 25 ++++ .../reference/voluseg/_tools/clean_signal.md | 26 ++++ .../voluseg/_tools/evenly_parallelize.md | 23 ++++ .../voluseg/_tools/get_volume_name.md | 29 +++++ .../reference/voluseg/_tools/load_metadata.md | 28 +++++ .../reference/voluseg/_tools/load_volume.md | 24 ++++ .../docs/reference/voluseg/_tools/nwb.md | 108 ++++++++++++++++ .../voluseg/_tools/parameter_dictionary.md | 119 ++++++++++++++++++ .../reference/voluseg/_tools/parameters.md | 42 +++++++ .../voluseg/_tools/parameters_models.md | 43 +++++++ .../reference/voluseg/_tools/sample_data.md | 68 ++++++++++ .../reference/voluseg/_tools/save_volume.md | 30 +++++ .../reference/voluseg/_tools/sparseness.md | 25 ++++ .../voluseg/_tools/sparseness_projection.md | 29 +++++ .../docs/reference/voluseg/_update.md | 13 ++ 33 files changed, 1225 insertions(+), 1 deletion(-) create mode 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create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md create mode 100644 docs/voluseg-docs-app/docs/reference/voluseg/_update.md diff --git a/.github/workflows/build_publish_docs.yaml b/.github/workflows/build_publish_docs.yaml new file mode 100644 index 0000000..f4fe588 --- /dev/null +++ b/.github/workflows/build_publish_docs.yaml @@ -0,0 +1,63 @@ +name: Build and Publish Docs to GitHub Pages + +on: + push: + branches: + - docs + - master + +jobs: + build-and-publish: + name: Build and Publish Docs + runs-on: ubuntu-latest + permissions: + contents: write + pages: write + id-token: write + steps: + - uses: actions/checkout@v3 + + - name: Set up Python 3.11 + uses: actions/setup-python@v5 + with: + python-version: 3.11 + + - name: Install docs dependencies. + run: pip install -r docs/requirements-docs.txt + + - name: Auto generate API Reference. + run: cd docs && pydoc-markdown + + - uses: actions/setup-node@v3 + with: + node-version: 18 + cache: yarn + working-directory: docs/voluseg-docs-app + cache-dependency-path: docs/voluseg-docs-app/yarn.lock + + - name: Install dependencies + run: cd docs/voluseg-docs-app && yarn install --frozen-lockfile + + - name: Build website + run: cd docs/voluseg-docs-app && yarn build + + - name: Commit pydoc-markdown files + run: | + git config --local user.email "github-actions[bot]@users.noreply.github.com" + git config --local user.name "github-actions[bot]" + GIT_STATUS=$(git status -s) + [[ ! -z "$GIT_STATUS" ]] && git add docs/* && git commit -m "auto-commit-docs" -a || echo "No changes to commit" + + - name: Push changes + uses: ad-m/github-push-action@master + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + branch: ${{ github.ref }} + + # Popular action to deploy to GitHub Pages: + # Docs: https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-docusaurus + - name: Deploy to GitHub Pages + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: ./docs/voluseg-docs-app/build \ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/getting_started/running.mdx b/docs/voluseg-docs-app/docs/getting_started/running.mdx index 8bd19bd..e758d27 100644 --- a/docs/voluseg-docs-app/docs/getting_started/running.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/running.mdx @@ -29,7 +29,7 @@ voluseg._tools.download_sample_data("/path/to/input/") ``` ### Setup pipeline parameters -Voluseg provides a dictionary with default parameters that can be modified to fit your specific needs. You can read more about the parameters in the [Parameters](/docs/voluseg-docs-app/docs/getting_started/parameters) section. You can access the default parameters dictionary, edit and process it by running: +Voluseg provides a dictionary with default parameters that can be modified to fit your specific needs. You can read more about the parameters in the [Parameters](/docs/getting_started/parameters) section. You can access the default parameters dictionary, edit and process it by running: ```python # Set parameters diff --git a/docs/voluseg-docs-app/docs/reference/_category_.json b/docs/voluseg-docs-app/docs/reference/_category_.json new file mode 100644 index 0000000..123b70b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_category_.json @@ -0,0 +1,8 @@ +{ + "label": "API Reference", + "position": 3, + "link": { + "type": "generated-index", + "description": "API Reference" + } +} \ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/reference/sidebar.json b/docs/voluseg-docs-app/docs/reference/sidebar.json new file mode 100644 index 0000000..e77ab6a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/sidebar.json @@ -0,0 +1,47 @@ +{ + "items": [ + { + "items": [ + "reference/voluseg/_steps/step0", + "reference/voluseg/_steps/step1", + "reference/voluseg/_steps/step2", + "reference/voluseg/_steps/step3", + "reference/voluseg/_steps/step4", + "reference/voluseg/_steps/step4a", + "reference/voluseg/_steps/step4b", + "reference/voluseg/_steps/step4c", + "reference/voluseg/_steps/step4d", + "reference/voluseg/_steps/step4e", + "reference/voluseg/_steps/step5" + ], + "label": "voluseg._steps", + "type": "category" + }, + { + "items": [ + "reference/voluseg/_tools/ants_registration", + "reference/voluseg/_tools/ants_transformation", + "reference/voluseg/_tools/aws", + "reference/voluseg/_tools/ball", + "reference/voluseg/_tools/clean_signal", + "reference/voluseg/_tools/evenly_parallelize", + "reference/voluseg/_tools/get_volume_name", + "reference/voluseg/_tools/load_metadata", + "reference/voluseg/_tools/load_volume", + "reference/voluseg/_tools/nwb", + "reference/voluseg/_tools/parameter_dictionary", + "reference/voluseg/_tools/parameters", + "reference/voluseg/_tools/parameters_models", + "reference/voluseg/_tools/sample_data", + "reference/voluseg/_tools/save_volume", + "reference/voluseg/_tools/sparseness", + "reference/voluseg/_tools/sparseness_projection" + ], + "label": "voluseg._tools", + "type": "category" + }, + "reference/voluseg/_update" + ], + "label": "voluseg", + "type": "category" +} \ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md new file mode 100644 index 0000000..826e0e0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md @@ -0,0 +1,23 @@ +--- +sidebar_label: step0 +title: voluseg._steps.step0 +--- + +#### process\_parameters + +```python +def process_parameters(initial_parameters: dict) -> dict +``` + +Process parameters and create parameter file (pickle). + +Parameters +---------- +initial_parameters : dict + Initial parameter dictionary + +Returns +------- +dict + Processed parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md new file mode 100644 index 0000000..70b4c9c --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md @@ -0,0 +1,23 @@ +--- +sidebar_label: step1 +title: voluseg._steps.step1 +--- + +#### process\_volumes + +```python +def process_volumes(parameters: dict) -> None +``` + +Process original volumes and save them to nifti files. +Performs downsampling and padding if specified in parameters. + +Parameters +---------- +parameters : dict + Parameters dictionary. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md new file mode 100644 index 0000000..880eed4 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md @@ -0,0 +1,23 @@ +--- +sidebar_label: step2 +title: voluseg._steps.step2 +--- + +#### align\_volumes + +```python +def align_volumes(parameters: dict) -> None +``` + +Register volumes to a reference volume. +Generates ANTs transforms files (.mat). + +Parameters +---------- +parameters : dict + Parameters dictionary. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md new file mode 100644 index 0000000..6784f38 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md @@ -0,0 +1,24 @@ +--- +sidebar_label: step3 +title: voluseg._steps.step3 +--- + +#### mask\_volumes + +```python +def mask_volumes(parameters: dict) -> None +``` + +Create intensity mask from the average registered volume. +Produces figures with masks and histograms. +Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. + +Parameters +---------- +parameters : dict + Parameters dictionary. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md new file mode 100644 index 0000000..5bb29dd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md @@ -0,0 +1,22 @@ +--- +sidebar_label: step4 +title: voluseg._steps.step4 +--- + +#### detect\_cells + +```python +def detect_cells(parameters: dict) -> None +``` + +Detect cells in volumetric blocks. + +Parameters +---------- +parameters : dict + Parameters dictionary. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md new file mode 100644 index 0000000..e0f6627 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md @@ -0,0 +1,39 @@ +--- +sidebar_label: step4a +title: voluseg._steps.step4a +--- + +#### define\_blocks + +```python +def define_blocks( + lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, + volume_mask: np.ndarray, + volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] +``` + +Get coordinates of individual blocks. + +Parameters +---------- +lx : int + Number of voxels in x-dimension. +ly : int + Number of voxels in y-dimension. +lz : int + Number of voxels in z-dimension. +n_cells_block : int + Number of cells in each block. +n_voxels_cell : int + Number of voxels in each cell. +volume_mask : np.ndarray + Volume mask. +volume_peak : np.ndarray + Volume local intensity maxima (peaks). + +Returns +------- +Tuple[int, bool, np.ndarray, np.ndarray] + Tuple containing: Number of blocks, valid blocks, coordinates of block start, + and coordinates of block end. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md new file mode 100644 index 0000000..f4fd7a2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md @@ -0,0 +1,46 @@ +--- +sidebar_label: step4b +title: voluseg._steps.step4b +--- + +#### process\_block\_data + +```python +def process_block_data( + xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, + color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, + bvolume_peak: h5py.Dataset, timepoints: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Load timeseries in individual blocks, slice-time correct, and find similar timeseries. + +Parameters +---------- +xyz0 : Tuple[int, int, int] + Start coordinates of block. +xyz1 : Tuple[int, int, int] + End coordinates of block. +parameters : dict + Parameters dictionary. +color_i : int + Color index. +lxyz : Tuple[int, int, int] + Number of voxels in x, y, and z dimensions. +rxyz : Tuple[float, float, float] + The resolution of x, y, and z dimensions. +ball_diam : np.ndarray + The diameter of a cell-area sphere. +bvolume_mean : h5py.Dataset + Spark broadcast variable: volume mean. +bvolume_peak : h5py.Dataset + Spark broadcast variable: local intensity maximum volume (peak). +timepoints : np.ndarray + Timepoints at which segmentation will be performed. + +Returns +------- +Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] + Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md new file mode 100644 index 0000000..ea3d610 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md @@ -0,0 +1,53 @@ +--- +sidebar_label: step4c +title: voluseg._steps.step4c +--- + +#### initialize\_block\_cells + +```python +def initialize_block_cells( + n_voxels_cell: int, n_voxels_block: int, n_cells: int, + voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, + peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, + lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Initialize cell positions in individual blocks. + +Parameters +---------- +n_voxels_cell : int + Number of voxels in each cell. +n_voxels_block : int + Number of voxels in block. +n_cells : int + Number of cells. +voxel_xyz : np.ndarray + Voxel coordinates. +voxel_timeseries : np.ndarray + Voxel timeseries. +peak_idx : np.ndarray + Peak indices. +peak_valids : np.ndarray + Valid local-intensity maxima (used to determine number of cells). +voxel_similarity_peak : np.ndarray + Similarity between voxels: defined by the combination of spatial proximity + and temporal similarity (the voxels are neighbors of each other and also + correlated with each other). +lxyz : Tuple[int, int, int] + Number of voxels in x, y, and z dimensions. +rxyz : Tuple[float, float, float] + Resolution of x, y, z dimensions. +ball_diam : np.ndarray + Diameter of a sphere that may defines a cell boundary. +ball_diam_xyz0 : np.ndarray + Midpoint of the sphere. + +Returns +------- +Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] + TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md new file mode 100644 index 0000000..34354a1 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md @@ -0,0 +1,54 @@ +--- +sidebar_label: step4d +title: voluseg._steps.step4d +--- + +#### nnmf\_sparse + +```python +def nnmf_sparse( + V0: np.ndarray, + XYZ0: np.ndarray, + W0: np.ndarray, + B0: np.ndarray, + S0: np.ndarray, + tolfun: float = 1e-4, + miniter: int = 10, + maxiter: int = 100, + timeseries_mean=1.0, + timepoints: np.ndarray = None, + verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] +``` + +Cell detection via nonnegative matrix factorization with sparseness projection. + +Parameters +---------- +V0 : np.ndarray + Voxel timeseries (voxel_timeseries_valid). +XYZ0 : np.ndarray + Voxel coordinates (voxel_xyz_valid). +W0 : np.ndarray + Initial cell weights (cell_weight_init_valid). +B0 : np.ndarray + Cell neighborhood (cell_neighborhood_valid). +S0 : np.ndarray + Cell sparseness (cell_sparseness). +tolfun : float, optional + Tolerance for convergence, by default 1e-4. +miniter : int, optional + Minimum number of iterations, by default 10. +maxiter : int, optional + Maximum number of iterations, by default 100. +timeseries_mean : float, optional + Mean timeseries value, by default 1.0. +timepoints : np.ndarray, optional + Timepoints to use, by default None. +verbosity : bool, optional + Print progress, by default True. + +Returns +------- +Tuple[np.ndarray, np.ndarray, float] + Tuple containing: Spatial footprint, temporal footprint, convergence error. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md new file mode 100644 index 0000000..7ca0fad --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md @@ -0,0 +1,27 @@ +--- +sidebar_label: step4e +title: voluseg._steps.step4e +--- + +#### collect\_blocks + +```python +def collect_blocks( + color_i: int, parameters: dict +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Collect cells across all blocks. + +Parameters +---------- +color_i : int + Color index. +parameters : dict + Parameters dictionary. + +Returns +------- +Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] + Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md new file mode 100644 index 0000000..7bb403f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md @@ -0,0 +1,22 @@ +--- +sidebar_label: step5 +title: voluseg._steps.step5 +--- + +#### clean\_cells + +```python +def clean_cells(parameters: dict) -> None +``` + +Remove noise cells, detrend and detect baseline. + +Parameters +---------- +parameters : dict + Parameters dictionary. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md new file mode 100644 index 0000000..577af96 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md @@ -0,0 +1,44 @@ +--- +sidebar_label: ants_registration +title: voluseg._tools.ants_registration +--- + +#### ants\_registration + +```python +def ants_registration(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + prefix_out_tform: str, + typ: str, + in_tform: str = None, + restrict: str = None) -> str +``` + +ANTs registration. + +Parameters +---------- +dir_ants : str + Path to ANTs directory. +in_nii : str + Input nifti file. +ref_nii : str + Reference nifti file. +out_nii : str + Output nifti file. +prefix_out_tform : str + Prefix for output transformation files. +typ : str + Type of transformation. +in_tform : str (optional) + Initial transformation file. Default is None. +restrict : str (optional) + Restrict deformation. Default is None. + +Returns +------- +str + ANTs registration command. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md new file mode 100644 index 0000000..6be1319 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md @@ -0,0 +1,38 @@ +--- +sidebar_label: ants_transformation +title: voluseg._tools.ants_transformation +--- + +#### ants\_transformation + +```python +def ants_transformation(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + in_tform: str, + interpolation="Linear") -> str +``` + +Application of ANTs transform. + +Parameters +---------- +dir_ants : str + Path to ANTs binaries. +in_nii : str + Path to input nifti file. +ref_nii : str + Path to reference nifti file. +out_nii : str + Path to output nifti file. +in_tform : str + Path to input transform file (.mat). +interpolation : str + Interpolation method. + +Returns +------- +str + ANTs transformation command string. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md new file mode 100644 index 0000000..3bdc582 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md @@ -0,0 +1,36 @@ +--- +sidebar_label: aws +title: voluseg._tools.aws +--- + +#### run\_job\_in\_aws\_batch + +```python +def run_job_in_aws_batch(job_name_prefix: str, + voluseg_kwargs: dict, + aws_local_profile: str = None, + vcpus: int = 32, + memory: int = 65536) +``` + +Submit a Voluseg job to AWS Batch. + +Parameters +---------- +job_name_prefix : str +Job name prefix, it will be concatenated with the current timestamp. +Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" +voluseg_kwargs : dict +Voluseg parameters. +aws_local_profile : str +AWS profile name. Default is None. +vcpus : int +Number of vCPUs. Default is 32. +memory : int +Memory in MB. Default is 65536. + +Returns +------- +dict +Dictionary with the job_name and batch_job_id. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md new file mode 100644 index 0000000..f1c8ae3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md @@ -0,0 +1,25 @@ +--- +sidebar_label: ball +title: voluseg._tools.ball +--- + +#### ball + +```python +def ball(radi: float, affine_matrix: np.ndarray) -> tuple +``` + +Morphological cell balls and midpoints. + +Parameters +---------- +radi : float + Radius of ball. +affine_matrix : np.ndarray + Affine matrix. + +Returns +------- +tuple + Tuple containing: Ball and midpoints. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md new file mode 100644 index 0000000..306e0c3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md @@ -0,0 +1,26 @@ +--- +sidebar_label: clean_signal +title: voluseg._tools.clean_signal +--- + +#### clean\_signal + +```python +def clean_signal(parameters: dict, + timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] +``` + +Detrend, filter, and estimate dynamic baseline for input timeseries. + +Parameters +---------- +parameters : dict + Parameters dictionary. +timeseries : np.ndarray + Input timeseries. + +Returns +------- +Tuple[np.ndarray, np.ndarray] + TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md new file mode 100644 index 0000000..c4e4aeb --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md @@ -0,0 +1,23 @@ +--- +sidebar_label: evenly_parallelize +title: voluseg._tools.evenly_parallelize +--- + +#### evenly\_parallelize + +```python +def evenly_parallelize(input_list: list) -> RDD +``` + +Return evenly partitioned spark resilient distributed dataset (RDD). + +Parameters +---------- +input_list : list + List of input elements. + +Returns +------- +RDD + Spark resilient distributed dataset (RDD). + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md new file mode 100644 index 0000000..3204cb0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md @@ -0,0 +1,29 @@ +--- +sidebar_label: get_volume_name +title: voluseg._tools.get_volume_name +--- + +#### get\_volume\_name + +```python +def get_volume_name(fullname_volume: str, + dir_prefix: str = None, + plane_i: int = None) -> str +``` + +Get name of volume (with directory prefix and plane suffix). + +Parameters +---------- +fullname_volume : str + Full name of volume. +dir_prefix : str (optional) + Prefix for directory. Default is None. +plane_i : int (optional) + Index of plane. Default is None. + +Returns +------- +str + Name of volume. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md new file mode 100644 index 0000000..13b68e6 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md @@ -0,0 +1,28 @@ +--- +sidebar_label: load_metadata +title: voluseg._tools.load_metadata +--- + +#### load\_metadata + +```python +def load_metadata(parameters: dict, filename_channel: str, + filename_stack: str) -> dict +``` + +Fetch z-resolution, exposure time, and stack frequency. + +Parameters +---------- +parameters : dict + Parameters dictionary. +filename_channel : str + Filename XML file containing channel information. +filename_stack : str + Filename of XML file containing stack information. + +Returns +------- +dict + Parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md new file mode 100644 index 0000000..603dea5 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md @@ -0,0 +1,24 @@ +--- +sidebar_label: load_volume +title: voluseg._tools.load_volume +--- + +#### load\_volume + +```python +def load_volume(fullname_ext: str) -> Union[np.ndarray, None] +``` + +Load volume based on input name and extension. +Supports tiff, hdf5, klb, and nifti formats. + +Parameters +---------- +fullname_ext : str + Full name of volume with extension. + +Returns +------- +np.ndarray or None + Volume as numpy array, or None if volume could not be loaded. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md new file mode 100644 index 0000000..8192bbf --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md @@ -0,0 +1,108 @@ +--- +sidebar_label: nwb +title: voluseg._tools.nwb +--- + +#### open\_nwbfile\_local + +```python +@contextmanager +def open_nwbfile_local(file_path: str) +``` + +Context manager to open and close a local NWB file. + +Parameters +---------- +file_path : str + Path to NWB file. + +Yields +------ +pynwb.NWBFile + The opened NWB file. + +#### open\_nwbfile\_remote + +```python +@contextmanager +def open_nwbfile_remote(s3_url: str, output_path: str) +``` + +Context manager to open and close a remote NWB file. + +Parameters +---------- +s3_url : str + S3 URL to NWB file. +output_path : str + Output path to cache the remote file. + +Yields +------ +pynwb.NWBFile + The opened NWB file. + +#### open\_nwbfile + +```python +@contextmanager +def open_nwbfile(input_path: str, remote: bool, output_path: str = None) +``` + +Open and close an NWB file from either a local or remote source. + +Parameters +---------- +input_path : str + Path to the NWB file. This can be a local file path or an S3 URL. +remote : bool + If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. +output_path : str + Output path, only used to cache remote files. + +Yields +------ +pynwb.NWBFile + The opened NWB file. + +#### find\_nwbfile\_volume\_object\_name + +```python +def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str +``` + +Find the name of the `TwoPhotonSeries` volume object in the NWB file. + +Parameters +---------- +nwbfile : pynwb.NWBFile + NWB file. + +Returns +------- +str + Name of the volume object. + +#### get\_nwbfile\_volume + +```python +def get_nwbfile_volume( + nwbfile: pynwb.NWBFile, + acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile +``` + +Get `TwoPhotonSeries` object from NWB file. + +Parameters +---------- +nwbfile : pynwb.NWBFile + NWB file. +acquisition_name : str (default: "TwoPhotonSeries") + Acquisition name. + +Returns +------- +pynwb.NWBFile + NWB file. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md new file mode 100644 index 0000000..335fd0a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md @@ -0,0 +1,119 @@ +--- +sidebar_label: parameter_dictionary +title: voluseg._tools.parameter_dictionary +--- + +#### parameter\_dictionary + +```python +def parameter_dictionary(detrending: str = "standard", + registration: str = "medium", + registration_restrict: str = "", + diam_cell: float = 6.0, + dir_ants: str = "", + dir_input: str = "", + dir_output: str = "", + dir_transform: str = "", + ds: int = 2, + planes_pad: int = 0, + planes_packed: bool = False, + parallel_clean: bool = True, + parallel_volume: bool = True, + save_volume: bool = False, + type_timepoints: str = "dff", + type_mask: str = "geomean", + timepoints: int = 1000, + f_hipass: float = 0, + f_volume: float = 2.0, + n_cells_block: int = 316, + n_colors: int = 1, + res_x: float = 0.40625, + res_y: float = 0.40625, + res_z: float = 5.0, + t_baseline: int = 300, + t_section: float = 0.01, + thr_mask: float = 0.5, + volume_fullnames_input: Union[list[str], None] = None, + volume_names: Union[list[str], None] = None, + input_dirs: Union[list[str], None] = None, + ext: Union[str, None] = None, + lt: Union[int, None] = None, + affine_matrix: Union[list, None] = None) -> dict +``` + +Return a parameter dictionary with specified defaults. + +Parameters +---------- +detrending : str, optional + Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +registration : str, optional + Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +registration_restrict : str, optional + Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +diam_cell : float, optional + Cell diameter in microns (default is 6.0). +dir_ants : str, optional + Path to the ANTs directory (default is an empty string). +dir_input : str, optional + Path to input directories, separate multiple directories with ';' (default is an empty string). +dir_output : str, optional + Path to the output directory (default is an empty string). +dir_transform : str, optional + Path to the transform directory (default is an empty string). +ds : int, optional + Spatial coarse-graining in x-y dimension (default is 2). +planes_pad : int, optional + Number of planes to pad the volume with for robust registration (default is 0). +planes_packed : bool, optional + Packed planes in each volume, for single plane imaging with packed planes (default is False). +parallel_clean : bool, optional + Parallelization of final cleaning (True is fast but memory-intensive, default is True). +parallel_volume : bool, optional + Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +save_volume : bool, optional + Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +type_timepoints : str, optional + Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +type_mask : str, optional + Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +timepoints : int, optional + Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +f_hipass : float, optional + Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +f_volume : float, optional + Imaging frequency in Hz (default is 2.0). +n_cells_block : int, optional + Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +n_colors : int, optional + Number of brain colors (2 in two-color volumes, default is 1). +res_x : float, optional + X resolution in microns (default is 0.40625). +res_y : float, optional + Y resolution in microns (default is 0.40625). +res_z : float, optional + Z resolution in microns (default is 5.0). +t_baseline : int, optional + Interval for baseline calculation in seconds (default is 300). +t_section : float, optional + Exposure time in seconds for slice acquisition (default is 0.01). +thr_mask : float, optional + Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +volume_fullnames_input : list[str], optional + List of full volume names (default is None). +volume_names : list[str], optional + List of volume names (default is None). +input_dirs : list[str], optional + List of input directories (default is None). +ext : str, optional + File extension (default is None). +lt : int, optional + Number of volumes (default is None). +affine_matrix : list, optional + Affine matrix (default is None). + +Returns +------- +dict + A dictionary of validated parameters with their default values. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md new file mode 100644 index 0000000..12f349d --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md @@ -0,0 +1,42 @@ +--- +sidebar_label: parameters +title: voluseg._tools.parameters +--- + +#### load\_parameters + +```python +def load_parameters(filename: str) -> dict +``` + +Load previously saved parameters from filename. + +Parameters +---------- +filename : str + Filename of parameter file. + +Returns +------- +dict + Parameters dictionary. + +#### save\_parameters + +```python +def save_parameters(parameters: dict, filename: str) -> None +``` + +Save parameters to filename. + +Parameters +---------- +parameters : dict + Parameters dictionary. +filename : str + Filename of parameter file. + +Returns +------- +None + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md new file mode 100644 index 0000000..d5a4ae9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md @@ -0,0 +1,43 @@ +--- +sidebar_label: parameters_models +title: voluseg._tools.parameters_models +--- + +## ParametersModel Objects + +```python +class ParametersModel(BaseModel) +``` + +#### convert\_array\_to\_list + +```python +@model_validator(mode="before") +def convert_array_to_list(cls, values) +``` + +Validator to automatically convert NumPy arrays to lists. + +#### model\_dump + +```python +def model_dump(use_np_array: bool = True, *args, **kwargs) +``` + +Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) +and Enums to their values. + +Parameters +---------- +use_np_array : bool, optional + Convert lists to NumPy arrays (default is True) +*args + Positional arguments to pass to the parent class +**kwargs + Keyword arguments to pass to the parent class + +Returns +------- +dict + A dictionary of the model's data + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md new file mode 100644 index 0000000..57d8279 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md @@ -0,0 +1,68 @@ +--- +sidebar_label: sample_data +title: voluseg._tools.sample_data +--- + +#### download\_sample\_data + +```python +def download_sample_data(destination_folder: str = ".", + data_type: str = "h5_dir") -> Union[str, None] +``` + +Download sample data for Voluseg. + +Parameters +---------- +destination_folder : str, optional + Folder where the sample data should be downloaded. If not provided, the data will be downloaded + to the current working directory. +data_type : str, optional + Type of data to download. Options are "h5_dir" and "nwb_file". + +Returns +------- +str or None + Path to the folder or file where the data was downloaded, or None if the download failed. + +#### download\_sample\_data\_nwb\_file + +```python +def download_sample_data_nwb_file( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample NWB file for Voluseg. +Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft + +Parameters +---------- +destination_folder : str, optional + Folder where the sample data should be downloaded. If not provided, the data will be downloaded + to the current working directory. + +Returns +------- +str or None + Path to the downloaded file, or None if the download failed. + +#### download\_sample\_data\_h5\_dir + +```python +def download_sample_data_h5_dir( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample data (h5 directory) for Voluseg. + +Parameters +---------- +destination_folder : str, optional + Folder where the sample data should be downloaded. If not provided, the data will be downloaded + to the current working directory. + +Returns +------- +str or None + Path to the folder where the data was extracted, or None if the download failed. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md new file mode 100644 index 0000000..9573080 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md @@ -0,0 +1,30 @@ +--- +sidebar_label: save_volume +title: voluseg._tools.save_volume +--- + +#### save\_volume + +```python +def save_volume(fullname_ext: str, + volume: np.ndarray, + affine_matrix: np.ndarray = None) -> Union[bool, None] +``` + +Save volume in output format. +Formats currently accepted are: nifti and hdf5. + +Parameters +---------- +fullname_ext : str + Full name of volume with extension. +volume : np.ndarray + Volume as numpy array. +affine_matrix : np.ndarray + Affine matrix for nifti format. + +Returns +------- +bool or None + True if volume was saved successfully, None if volume could not be saved. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md new file mode 100644 index 0000000..2a58c0a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md @@ -0,0 +1,25 @@ +--- +sidebar_label: sparseness +title: voluseg._tools.sparseness +--- + +#### sparseness + +```python +def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray +``` + +Vector sparseness along specified dimension. + +Parameters +---------- +W : np.ndarray + Input array. +dim : int, optional + Dimension along which to compute sparseness, by default 0. + +Returns +------- +np.ndarray + Sparseness of input array along specified dimension. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md new file mode 100644 index 0000000..3da41cd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md @@ -0,0 +1,29 @@ +--- +sidebar_label: sparseness_projection +title: voluseg._tools.sparseness_projection +--- + +#### sparseness\_projection + +```python +def sparseness_projection(Si: np.ndarray, + s: float, + at_least_as_sparse: bool = False) -> np.ndarray +``` + +Hoyer sparseness projection. + +Parameters +---------- +Si : np.ndarray + Input signal. +s : float + Sparseness parameter. +at_least_as_sparse : bool, optional + Enforce at least as sparse, by default False. + +Returns +------- +np.ndarray + Sparse signal. + diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_update.md b/docs/voluseg-docs-app/docs/reference/voluseg/_update.md new file mode 100644 index 0000000..fb6b1ec --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/voluseg/_update.md @@ -0,0 +1,13 @@ +--- +sidebar_label: _update +title: voluseg._update +--- + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From d3093bb52437e644abdffa93da452d676aef53a1 Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 10:43:39 +0100 Subject: [PATCH 03/27] numpy style --- docs/pydoc-markdown.yml | 7 +- .../docs/reference/sidebar.json | 44 +------ .../docs/reference/voluseg/_steps/step0.md | 23 ---- .../docs/reference/voluseg/_steps/step1.md | 23 ---- .../docs/reference/voluseg/_steps/step2.md | 23 ---- .../docs/reference/voluseg/_steps/step3.md | 24 ---- .../docs/reference/voluseg/_steps/step4.md | 22 ---- .../docs/reference/voluseg/_steps/step4a.md | 39 ------ .../docs/reference/voluseg/_steps/step4b.md | 46 ------- .../docs/reference/voluseg/_steps/step4c.md | 53 -------- .../docs/reference/voluseg/_steps/step4d.md | 54 -------- .../docs/reference/voluseg/_steps/step4e.md | 27 ---- .../docs/reference/voluseg/_steps/step5.md | 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voluseg-docs-app/docs diff --git a/docs/voluseg-docs-app/docs/reference/sidebar.json b/docs/voluseg-docs-app/docs/reference/sidebar.json index e77ab6a..27c7e95 100644 --- a/docs/voluseg-docs-app/docs/reference/sidebar.json +++ b/docs/voluseg-docs-app/docs/reference/sidebar.json @@ -1,47 +1,7 @@ { "items": [ - { - "items": [ - "reference/voluseg/_steps/step0", - "reference/voluseg/_steps/step1", - "reference/voluseg/_steps/step2", - "reference/voluseg/_steps/step3", - "reference/voluseg/_steps/step4", - "reference/voluseg/_steps/step4a", - "reference/voluseg/_steps/step4b", - "reference/voluseg/_steps/step4c", - "reference/voluseg/_steps/step4d", - "reference/voluseg/_steps/step4e", - "reference/voluseg/_steps/step5" - ], - "label": "voluseg._steps", - "type": "category" - }, - { - "items": [ - "reference/voluseg/_tools/ants_registration", - "reference/voluseg/_tools/ants_transformation", - "reference/voluseg/_tools/aws", - "reference/voluseg/_tools/ball", - "reference/voluseg/_tools/clean_signal", - "reference/voluseg/_tools/evenly_parallelize", - "reference/voluseg/_tools/get_volume_name", - "reference/voluseg/_tools/load_metadata", - "reference/voluseg/_tools/load_volume", - "reference/voluseg/_tools/nwb", - "reference/voluseg/_tools/parameter_dictionary", - "reference/voluseg/_tools/parameters", - "reference/voluseg/_tools/parameters_models", - "reference/voluseg/_tools/sample_data", - "reference/voluseg/_tools/save_volume", - "reference/voluseg/_tools/sparseness", - "reference/voluseg/_tools/sparseness_projection" - ], - "label": "voluseg._tools", - "type": "category" - }, - "reference/voluseg/_update" + "reference/__init__/__init__" ], - "label": "voluseg", + "label": "__init__", "type": "category" } \ No newline at end of file diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md deleted file mode 100644 index 826e0e0..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step0.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -sidebar_label: step0 -title: voluseg._steps.step0 ---- - -#### process\_parameters - -```python -def process_parameters(initial_parameters: dict) -> dict -``` - -Process parameters and create parameter file (pickle). - -Parameters ----------- -initial_parameters : dict - Initial parameter dictionary - -Returns -------- -dict - Processed parameters dictionary. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md deleted file mode 100644 index 70b4c9c..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step1.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -sidebar_label: step1 -title: voluseg._steps.step1 ---- - -#### process\_volumes - -```python -def process_volumes(parameters: dict) -> None -``` - -Process original volumes and save them to nifti files. -Performs downsampling and padding if specified in parameters. - -Parameters ----------- -parameters : dict - Parameters dictionary. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md deleted file mode 100644 index 880eed4..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step2.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -sidebar_label: step2 -title: voluseg._steps.step2 ---- - -#### align\_volumes - -```python -def align_volumes(parameters: dict) -> None -``` - -Register volumes to a reference volume. -Generates ANTs transforms files (.mat). - -Parameters ----------- -parameters : dict - Parameters dictionary. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md deleted file mode 100644 index 6784f38..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step3.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -sidebar_label: step3 -title: voluseg._steps.step3 ---- - -#### mask\_volumes - -```python -def mask_volumes(parameters: dict) -> None -``` - -Create intensity mask from the average registered volume. -Produces figures with masks and histograms. -Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. - -Parameters ----------- -parameters : dict - Parameters dictionary. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md deleted file mode 100644 index 5bb29dd..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4.md +++ /dev/null @@ -1,22 +0,0 @@ ---- -sidebar_label: step4 -title: voluseg._steps.step4 ---- - -#### detect\_cells - -```python -def detect_cells(parameters: dict) -> None -``` - -Detect cells in volumetric blocks. - -Parameters ----------- -parameters : dict - Parameters dictionary. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md deleted file mode 100644 index e0f6627..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4a.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -sidebar_label: step4a -title: voluseg._steps.step4a ---- - -#### define\_blocks - -```python -def define_blocks( - lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, - volume_mask: np.ndarray, - volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] -``` - -Get coordinates of individual blocks. - -Parameters ----------- -lx : int - Number of voxels in x-dimension. -ly : int - Number of voxels in y-dimension. -lz : int - Number of voxels in z-dimension. -n_cells_block : int - Number of cells in each block. -n_voxels_cell : int - Number of voxels in each cell. -volume_mask : np.ndarray - Volume mask. -volume_peak : np.ndarray - Volume local intensity maxima (peaks). - -Returns -------- -Tuple[int, bool, np.ndarray, np.ndarray] - Tuple containing: Number of blocks, valid blocks, coordinates of block start, - and coordinates of block end. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md deleted file mode 100644 index f4fd7a2..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4b.md +++ /dev/null @@ -1,46 +0,0 @@ ---- -sidebar_label: step4b -title: voluseg._steps.step4b ---- - -#### process\_block\_data - -```python -def process_block_data( - xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, - color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], - ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, - bvolume_peak: h5py.Dataset, timepoints: np.ndarray -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Load timeseries in individual blocks, slice-time correct, and find similar timeseries. - -Parameters ----------- -xyz0 : Tuple[int, int, int] - Start coordinates of block. -xyz1 : Tuple[int, int, int] - End coordinates of block. -parameters : dict - Parameters dictionary. -color_i : int - Color index. -lxyz : Tuple[int, int, int] - Number of voxels in x, y, and z dimensions. -rxyz : Tuple[float, float, float] - The resolution of x, y, and z dimensions. -ball_diam : np.ndarray - The diameter of a cell-area sphere. -bvolume_mean : h5py.Dataset - Spark broadcast variable: volume mean. -bvolume_peak : h5py.Dataset - Spark broadcast variable: local intensity maximum volume (peak). -timepoints : np.ndarray - Timepoints at which segmentation will be performed. - -Returns -------- -Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] - Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md deleted file mode 100644 index ea3d610..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4c.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -sidebar_label: step4c -title: voluseg._steps.step4c ---- - -#### initialize\_block\_cells - -```python -def initialize_block_cells( - n_voxels_cell: int, n_voxels_block: int, n_cells: int, - voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, - peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, - lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], - ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Initialize cell positions in individual blocks. - -Parameters ----------- -n_voxels_cell : int - Number of voxels in each cell. -n_voxels_block : int - Number of voxels in block. -n_cells : int - Number of cells. -voxel_xyz : np.ndarray - Voxel coordinates. -voxel_timeseries : np.ndarray - Voxel timeseries. -peak_idx : np.ndarray - Peak indices. -peak_valids : np.ndarray - Valid local-intensity maxima (used to determine number of cells). -voxel_similarity_peak : np.ndarray - Similarity between voxels: defined by the combination of spatial proximity - and temporal similarity (the voxels are neighbors of each other and also - correlated with each other). -lxyz : Tuple[int, int, int] - Number of voxels in x, y, and z dimensions. -rxyz : Tuple[float, float, float] - Resolution of x, y, z dimensions. -ball_diam : np.ndarray - Diameter of a sphere that may defines a cell boundary. -ball_diam_xyz0 : np.ndarray - Midpoint of the sphere. - -Returns -------- -Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] - TODO - add description - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md deleted file mode 100644 index 34354a1..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4d.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -sidebar_label: step4d -title: voluseg._steps.step4d ---- - -#### nnmf\_sparse - -```python -def nnmf_sparse( - V0: np.ndarray, - XYZ0: np.ndarray, - W0: np.ndarray, - B0: np.ndarray, - S0: np.ndarray, - tolfun: float = 1e-4, - miniter: int = 10, - maxiter: int = 100, - timeseries_mean=1.0, - timepoints: np.ndarray = None, - verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] -``` - -Cell detection via nonnegative matrix factorization with sparseness projection. - -Parameters ----------- -V0 : np.ndarray - Voxel timeseries (voxel_timeseries_valid). -XYZ0 : np.ndarray - Voxel coordinates (voxel_xyz_valid). -W0 : np.ndarray - Initial cell weights (cell_weight_init_valid). -B0 : np.ndarray - Cell neighborhood (cell_neighborhood_valid). -S0 : np.ndarray - Cell sparseness (cell_sparseness). -tolfun : float, optional - Tolerance for convergence, by default 1e-4. -miniter : int, optional - Minimum number of iterations, by default 10. -maxiter : int, optional - Maximum number of iterations, by default 100. -timeseries_mean : float, optional - Mean timeseries value, by default 1.0. -timepoints : np.ndarray, optional - Timepoints to use, by default None. -verbosity : bool, optional - Print progress, by default True. - -Returns -------- -Tuple[np.ndarray, np.ndarray, float] - Tuple containing: Spatial footprint, temporal footprint, convergence error. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md deleted file mode 100644 index 7ca0fad..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step4e.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -sidebar_label: step4e -title: voluseg._steps.step4e ---- - -#### collect\_blocks - -```python -def collect_blocks( - color_i: int, parameters: dict -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Collect cells across all blocks. - -Parameters ----------- -color_i : int - Color index. -parameters : dict - Parameters dictionary. - -Returns -------- -Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] - Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md deleted file mode 100644 index 7bb403f..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_steps/step5.md +++ /dev/null @@ -1,22 +0,0 @@ ---- -sidebar_label: step5 -title: voluseg._steps.step5 ---- - -#### clean\_cells - -```python -def clean_cells(parameters: dict) -> None -``` - -Remove noise cells, detrend and detect baseline. - -Parameters ----------- -parameters : dict - Parameters dictionary. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md deleted file mode 100644 index 577af96..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_registration.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -sidebar_label: ants_registration -title: voluseg._tools.ants_registration ---- - -#### ants\_registration - -```python -def ants_registration(dir_ants: str, - in_nii: str, - ref_nii: str, - out_nii: str, - prefix_out_tform: str, - typ: str, - in_tform: str = None, - restrict: str = None) -> str -``` - -ANTs registration. - -Parameters ----------- -dir_ants : str - Path to ANTs directory. -in_nii : str - Input nifti file. -ref_nii : str - Reference nifti file. -out_nii : str - Output nifti file. -prefix_out_tform : str - Prefix for output transformation files. -typ : str - Type of transformation. -in_tform : str (optional) - Initial transformation file. Default is None. -restrict : str (optional) - Restrict deformation. Default is None. - -Returns -------- -str - ANTs registration command. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md deleted file mode 100644 index 6be1319..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ants_transformation.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -sidebar_label: ants_transformation -title: voluseg._tools.ants_transformation ---- - -#### ants\_transformation - -```python -def ants_transformation(dir_ants: str, - in_nii: str, - ref_nii: str, - out_nii: str, - in_tform: str, - interpolation="Linear") -> str -``` - -Application of ANTs transform. - -Parameters ----------- -dir_ants : str - Path to ANTs binaries. -in_nii : str - Path to input nifti file. -ref_nii : str - Path to reference nifti file. -out_nii : str - Path to output nifti file. -in_tform : str - Path to input transform file (.mat). -interpolation : str - Interpolation method. - -Returns -------- -str - ANTs transformation command string. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md deleted file mode 100644 index 3bdc582..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/aws.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -sidebar_label: aws -title: voluseg._tools.aws ---- - -#### run\_job\_in\_aws\_batch - -```python -def run_job_in_aws_batch(job_name_prefix: str, - voluseg_kwargs: dict, - aws_local_profile: str = None, - vcpus: int = 32, - memory: int = 65536) -``` - -Submit a Voluseg job to AWS Batch. - -Parameters ----------- -job_name_prefix : str -Job name prefix, it will be concatenated with the current timestamp. -Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" -voluseg_kwargs : dict -Voluseg parameters. -aws_local_profile : str -AWS profile name. Default is None. -vcpus : int -Number of vCPUs. Default is 32. -memory : int -Memory in MB. Default is 65536. - -Returns -------- -dict -Dictionary with the job_name and batch_job_id. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md deleted file mode 100644 index f1c8ae3..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/ball.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -sidebar_label: ball -title: voluseg._tools.ball ---- - -#### ball - -```python -def ball(radi: float, affine_matrix: np.ndarray) -> tuple -``` - -Morphological cell balls and midpoints. - -Parameters ----------- -radi : float - Radius of ball. -affine_matrix : np.ndarray - Affine matrix. - -Returns -------- -tuple - Tuple containing: Ball and midpoints. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md deleted file mode 100644 index 306e0c3..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/clean_signal.md +++ /dev/null @@ -1,26 +0,0 @@ ---- -sidebar_label: clean_signal -title: voluseg._tools.clean_signal ---- - -#### clean\_signal - -```python -def clean_signal(parameters: dict, - timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] -``` - -Detrend, filter, and estimate dynamic baseline for input timeseries. - -Parameters ----------- -parameters : dict - Parameters dictionary. -timeseries : np.ndarray - Input timeseries. - -Returns -------- -Tuple[np.ndarray, np.ndarray] - TODO - add description - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md deleted file mode 100644 index c4e4aeb..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/evenly_parallelize.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -sidebar_label: evenly_parallelize -title: voluseg._tools.evenly_parallelize ---- - -#### evenly\_parallelize - -```python -def evenly_parallelize(input_list: list) -> RDD -``` - -Return evenly partitioned spark resilient distributed dataset (RDD). - -Parameters ----------- -input_list : list - List of input elements. - -Returns -------- -RDD - Spark resilient distributed dataset (RDD). - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md deleted file mode 100644 index 3204cb0..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/get_volume_name.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -sidebar_label: get_volume_name -title: voluseg._tools.get_volume_name ---- - -#### get\_volume\_name - -```python -def get_volume_name(fullname_volume: str, - dir_prefix: str = None, - plane_i: int = None) -> str -``` - -Get name of volume (with directory prefix and plane suffix). - -Parameters ----------- -fullname_volume : str - Full name of volume. -dir_prefix : str (optional) - Prefix for directory. Default is None. -plane_i : int (optional) - Index of plane. Default is None. - -Returns -------- -str - Name of volume. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md deleted file mode 100644 index 13b68e6..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_metadata.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -sidebar_label: load_metadata -title: voluseg._tools.load_metadata ---- - -#### load\_metadata - -```python -def load_metadata(parameters: dict, filename_channel: str, - filename_stack: str) -> dict -``` - -Fetch z-resolution, exposure time, and stack frequency. - -Parameters ----------- -parameters : dict - Parameters dictionary. -filename_channel : str - Filename XML file containing channel information. -filename_stack : str - Filename of XML file containing stack information. - -Returns -------- -dict - Parameters dictionary. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md deleted file mode 100644 index 603dea5..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/load_volume.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -sidebar_label: load_volume -title: voluseg._tools.load_volume ---- - -#### load\_volume - -```python -def load_volume(fullname_ext: str) -> Union[np.ndarray, None] -``` - -Load volume based on input name and extension. -Supports tiff, hdf5, klb, and nifti formats. - -Parameters ----------- -fullname_ext : str - Full name of volume with extension. - -Returns -------- -np.ndarray or None - Volume as numpy array, or None if volume could not be loaded. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md deleted file mode 100644 index 8192bbf..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/nwb.md +++ /dev/null @@ -1,108 +0,0 @@ ---- -sidebar_label: nwb -title: voluseg._tools.nwb ---- - -#### open\_nwbfile\_local - -```python -@contextmanager -def open_nwbfile_local(file_path: str) -``` - -Context manager to open and close a local NWB file. - -Parameters ----------- -file_path : str - Path to NWB file. - -Yields ------- -pynwb.NWBFile - The opened NWB file. - -#### open\_nwbfile\_remote - -```python -@contextmanager -def open_nwbfile_remote(s3_url: str, output_path: str) -``` - -Context manager to open and close a remote NWB file. - -Parameters ----------- -s3_url : str - S3 URL to NWB file. -output_path : str - Output path to cache the remote file. - -Yields ------- -pynwb.NWBFile - The opened NWB file. - -#### open\_nwbfile - -```python -@contextmanager -def open_nwbfile(input_path: str, remote: bool, output_path: str = None) -``` - -Open and close an NWB file from either a local or remote source. - -Parameters ----------- -input_path : str - Path to the NWB file. This can be a local file path or an S3 URL. -remote : bool - If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. -output_path : str - Output path, only used to cache remote files. - -Yields ------- -pynwb.NWBFile - The opened NWB file. - -#### find\_nwbfile\_volume\_object\_name - -```python -def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str -``` - -Find the name of the `TwoPhotonSeries` volume object in the NWB file. - -Parameters ----------- -nwbfile : pynwb.NWBFile - NWB file. - -Returns -------- -str - Name of the volume object. - -#### get\_nwbfile\_volume - -```python -def get_nwbfile_volume( - nwbfile: pynwb.NWBFile, - acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile -``` - -Get `TwoPhotonSeries` object from NWB file. - -Parameters ----------- -nwbfile : pynwb.NWBFile - NWB file. -acquisition_name : str (default: "TwoPhotonSeries") - Acquisition name. - -Returns -------- -pynwb.NWBFile - NWB file. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md deleted file mode 100644 index 335fd0a..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameter_dictionary.md +++ /dev/null @@ -1,119 +0,0 @@ ---- -sidebar_label: parameter_dictionary -title: voluseg._tools.parameter_dictionary ---- - -#### parameter\_dictionary - -```python -def parameter_dictionary(detrending: str = "standard", - registration: str = "medium", - registration_restrict: str = "", - diam_cell: float = 6.0, - dir_ants: str = "", - dir_input: str = "", - dir_output: str = "", - dir_transform: str = "", - ds: int = 2, - planes_pad: int = 0, - planes_packed: bool = False, - parallel_clean: bool = True, - parallel_volume: bool = True, - save_volume: bool = False, - type_timepoints: str = "dff", - type_mask: str = "geomean", - timepoints: int = 1000, - f_hipass: float = 0, - f_volume: float = 2.0, - n_cells_block: int = 316, - n_colors: int = 1, - res_x: float = 0.40625, - res_y: float = 0.40625, - res_z: float = 5.0, - t_baseline: int = 300, - t_section: float = 0.01, - thr_mask: float = 0.5, - volume_fullnames_input: Union[list[str], None] = None, - volume_names: Union[list[str], None] = None, - input_dirs: Union[list[str], None] = None, - ext: Union[str, None] = None, - lt: Union[int, None] = None, - affine_matrix: Union[list, None] = None) -> dict -``` - -Return a parameter dictionary with specified defaults. - -Parameters ----------- -detrending : str, optional - Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). -registration : str, optional - Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). -registration_restrict : str, optional - Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). -diam_cell : float, optional - Cell diameter in microns (default is 6.0). -dir_ants : str, optional - Path to the ANTs directory (default is an empty string). -dir_input : str, optional - Path to input directories, separate multiple directories with ';' (default is an empty string). -dir_output : str, optional - Path to the output directory (default is an empty string). -dir_transform : str, optional - Path to the transform directory (default is an empty string). -ds : int, optional - Spatial coarse-graining in x-y dimension (default is 2). -planes_pad : int, optional - Number of planes to pad the volume with for robust registration (default is 0). -planes_packed : bool, optional - Packed planes in each volume, for single plane imaging with packed planes (default is False). -parallel_clean : bool, optional - Parallelization of final cleaning (True is fast but memory-intensive, default is True). -parallel_volume : bool, optional - Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). -save_volume : bool, optional - Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). -type_timepoints : str, optional - Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). -type_mask : str, optional - Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). -timepoints : int, optional - Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). -f_hipass : float, optional - Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). -f_volume : float, optional - Imaging frequency in Hz (default is 2.0). -n_cells_block : int, optional - Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). -n_colors : int, optional - Number of brain colors (2 in two-color volumes, default is 1). -res_x : float, optional - X resolution in microns (default is 0.40625). -res_y : float, optional - Y resolution in microns (default is 0.40625). -res_z : float, optional - Z resolution in microns (default is 5.0). -t_baseline : int, optional - Interval for baseline calculation in seconds (default is 300). -t_section : float, optional - Exposure time in seconds for slice acquisition (default is 0.01). -thr_mask : float, optional - Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). -volume_fullnames_input : list[str], optional - List of full volume names (default is None). -volume_names : list[str], optional - List of volume names (default is None). -input_dirs : list[str], optional - List of input directories (default is None). -ext : str, optional - File extension (default is None). -lt : int, optional - Number of volumes (default is None). -affine_matrix : list, optional - Affine matrix (default is None). - -Returns -------- -dict - A dictionary of validated parameters with their default values. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md deleted file mode 100644 index 12f349d..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -sidebar_label: parameters -title: voluseg._tools.parameters ---- - -#### load\_parameters - -```python -def load_parameters(filename: str) -> dict -``` - -Load previously saved parameters from filename. - -Parameters ----------- -filename : str - Filename of parameter file. - -Returns -------- -dict - Parameters dictionary. - -#### save\_parameters - -```python -def save_parameters(parameters: dict, filename: str) -> None -``` - -Save parameters to filename. - -Parameters ----------- -parameters : dict - Parameters dictionary. -filename : str - Filename of parameter file. - -Returns -------- -None - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md deleted file mode 100644 index d5a4ae9..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/parameters_models.md +++ /dev/null @@ -1,43 +0,0 @@ ---- -sidebar_label: parameters_models -title: voluseg._tools.parameters_models ---- - -## ParametersModel Objects - -```python -class ParametersModel(BaseModel) -``` - -#### convert\_array\_to\_list - -```python -@model_validator(mode="before") -def convert_array_to_list(cls, values) -``` - -Validator to automatically convert NumPy arrays to lists. - -#### model\_dump - -```python -def model_dump(use_np_array: bool = True, *args, **kwargs) -``` - -Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) -and Enums to their values. - -Parameters ----------- -use_np_array : bool, optional - Convert lists to NumPy arrays (default is True) -*args - Positional arguments to pass to the parent class -**kwargs - Keyword arguments to pass to the parent class - -Returns -------- -dict - A dictionary of the model's data - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md deleted file mode 100644 index 57d8279..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sample_data.md +++ /dev/null @@ -1,68 +0,0 @@ ---- -sidebar_label: sample_data -title: voluseg._tools.sample_data ---- - -#### download\_sample\_data - -```python -def download_sample_data(destination_folder: str = ".", - data_type: str = "h5_dir") -> Union[str, None] -``` - -Download sample data for Voluseg. - -Parameters ----------- -destination_folder : str, optional - Folder where the sample data should be downloaded. If not provided, the data will be downloaded - to the current working directory. -data_type : str, optional - Type of data to download. Options are "h5_dir" and "nwb_file". - -Returns -------- -str or None - Path to the folder or file where the data was downloaded, or None if the download failed. - -#### download\_sample\_data\_nwb\_file - -```python -def download_sample_data_nwb_file( - destination_folder: str = ".") -> Union[str, None] -``` - -Download sample NWB file for Voluseg. -Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft - -Parameters ----------- -destination_folder : str, optional - Folder where the sample data should be downloaded. If not provided, the data will be downloaded - to the current working directory. - -Returns -------- -str or None - Path to the downloaded file, or None if the download failed. - -#### download\_sample\_data\_h5\_dir - -```python -def download_sample_data_h5_dir( - destination_folder: str = ".") -> Union[str, None] -``` - -Download sample data (h5 directory) for Voluseg. - -Parameters ----------- -destination_folder : str, optional - Folder where the sample data should be downloaded. If not provided, the data will be downloaded - to the current working directory. - -Returns -------- -str or None - Path to the folder where the data was extracted, or None if the download failed. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md deleted file mode 100644 index 9573080..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/save_volume.md +++ /dev/null @@ -1,30 +0,0 @@ ---- -sidebar_label: save_volume -title: voluseg._tools.save_volume ---- - -#### save\_volume - -```python -def save_volume(fullname_ext: str, - volume: np.ndarray, - affine_matrix: np.ndarray = None) -> Union[bool, None] -``` - -Save volume in output format. -Formats currently accepted are: nifti and hdf5. - -Parameters ----------- -fullname_ext : str - Full name of volume with extension. -volume : np.ndarray - Volume as numpy array. -affine_matrix : np.ndarray - Affine matrix for nifti format. - -Returns -------- -bool or None - True if volume was saved successfully, None if volume could not be saved. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md deleted file mode 100644 index 2a58c0a..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -sidebar_label: sparseness -title: voluseg._tools.sparseness ---- - -#### sparseness - -```python -def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray -``` - -Vector sparseness along specified dimension. - -Parameters ----------- -W : np.ndarray - Input array. -dim : int, optional - Dimension along which to compute sparseness, by default 0. - -Returns -------- -np.ndarray - Sparseness of input array along specified dimension. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md deleted file mode 100644 index 3da41cd..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_tools/sparseness_projection.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -sidebar_label: sparseness_projection -title: voluseg._tools.sparseness_projection ---- - -#### sparseness\_projection - -```python -def sparseness_projection(Si: np.ndarray, - s: float, - at_least_as_sparse: bool = False) -> np.ndarray -``` - -Hoyer sparseness projection. - -Parameters ----------- -Si : np.ndarray - Input signal. -s : float - Sparseness parameter. -at_least_as_sparse : bool, optional - Enforce at least as sparse, by default False. - -Returns -------- -np.ndarray - Sparse signal. - diff --git a/docs/voluseg-docs-app/docs/reference/voluseg/_update.md b/docs/voluseg-docs-app/docs/reference/voluseg/_update.md deleted file mode 100644 index fb6b1ec..0000000 --- a/docs/voluseg-docs-app/docs/reference/voluseg/_update.md +++ /dev/null @@ -1,13 +0,0 @@ ---- -sidebar_label: _update -title: voluseg._update ---- - -#### voluseg\_update - -```python -def voluseg_update() -> None -``` - -Shortcut to update package. - From 379b93d815f27dd8c4e012dd398c5f54d7acad83 Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 10:47:22 +0100 Subject: [PATCH 04/27] docs req --- docs/requirements-docs.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/requirements-docs.txt b/docs/requirements-docs.txt index 6dcdf89..296cd73 100644 --- a/docs/requirements-docs.txt +++ b/docs/requirements-docs.txt @@ -1 +1,2 @@ -pydoc-markdown==4.8.2 \ No newline at end of file +# pydoc-markdown==4.8.2 +git+https://github.com/luiztauffer/pydoc-markdown.git@develop From e3b641b96ff26325ae09c770df2b7f6dc3a9ba81 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 30 Oct 2024 09:48:22 +0000 Subject: [PATCH 05/27] auto-commit-docs --- .../docs/reference/__init__/__init__.md | 29 +++ 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0000000..6619ac0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: _steps +title: _steps +--- + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/_steps/step0.md new file mode 100644 index 0000000..6b623f3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step0.md @@ -0,0 +1,49 @@ +--- +sidebar_label: step0 +title: _steps.step0 +--- + +## os + +## copy + +## json + +## np + +## warn + +## load\_volume + +## get\_volume\_name + +## parameter\_dictionary + +## evenly\_parallelize + +## load\_parameters + +## save\_parameters + +## ParametersModel + +## open\_nwbfile + +## find\_nwbfile\_volume\_object\_name + +#### process\_parameters + +```python +def process_parameters(initial_parameters: dict) -> dict +``` + +Process parameters and create parameter file (pickle). + +**Arguments** + +* **initial_parameters** (`dict`): Initial parameter dictionary + +**Returns** + +* `dict`: Processed parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/_steps/step1.md new file mode 100644 index 0000000..a83feda --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step1.md @@ -0,0 +1,48 @@ +--- +sidebar_label: step1 +title: _steps.step1 +--- + +## os + +## interpolate + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## get\_volume\_name + +## ori + +## ali + +## nii + +## hdf + +## evenly\_parallelize + +## open\_nwbfile + +## get\_nwbfile\_volume + +#### process\_volumes + +```python +def process_volumes(parameters: dict) -> None +``` + +Process original volumes and save them to nifti files. +Performs downsampling and padding if specified in parameters. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/_steps/step2.md new file mode 100644 index 0000000..b372ae7 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step2.md @@ -0,0 +1,54 @@ +--- +sidebar_label: step2 +title: _steps.step2 +--- + +## os + +## h5py + +## shutil + +## np + +## io + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## ori + +## ali + +## nii + +## hdf + +## dtype + +## ants\_registration + +## ants\_transformation + +## evenly\_parallelize + +#### align\_volumes + +```python +def align_volumes(parameters: dict) -> None +``` + +Register volumes to a reference volume. +Generates ANTs transforms files (.mat). + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/_steps/step3.md new file mode 100644 index 0000000..85073bd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step3.md @@ -0,0 +1,61 @@ +--- +sidebar_label: step3 +title: _steps.step3 +--- + +## os + +## h5py + +## pyspark + +## np + +## stats + +## mixture + +## morphology + +## SimpleNamespace + +## median\_filter + +## SparkSession + +## warnings + +## matplotlib + +## plt + +## ball + +## ali + +## hdf + +## load\_volume + +## clean\_signal + +## evenly\_parallelize + +#### mask\_volumes + +```python +def mask_volumes(parameters: dict) -> None +``` + +Create intensity mask from the average registered volume. +Produces figures with masks and histograms. +Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/_steps/step4.md new file mode 100644 index 0000000..8f23d34 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4.md @@ -0,0 +1,47 @@ +--- +sidebar_label: step4 +title: _steps.step4 +--- + +## os + +## h5py + +## time + +## np + +## SimpleNamespace + +## SparkSession + +## define\_blocks + +## process\_block\_data + +## initialize\_block\_cells + +## nnmf\_sparse + +## ball + +## hdf + +## evenly\_parallelize + +#### detect\_cells + +```python +def detect_cells(parameters: dict) -> None +``` + +Detect cells in volumetric blocks. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/_steps/step4a.md new file mode 100644 index 0000000..f44a0dd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4a.md @@ -0,0 +1,37 @@ +--- +sidebar_label: step4a +title: _steps.step4a +--- + +## os + +## Tuple + +## np + +#### define\_blocks + +```python +def define_blocks( + lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, + volume_mask: np.ndarray, + volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] +``` + +Get coordinates of individual blocks. + +**Arguments** + +* **lx** (`int`): Number of voxels in x-dimension. +* **ly** (`int`): Number of voxels in y-dimension. +* **lz** (`int`): Number of voxels in z-dimension. +* **n_cells_block** (`int`): Number of cells in each block. +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **volume_mask** (`np.ndarray`): Volume mask. +* **volume_peak** (`np.ndarray`): Volume local intensity maxima (peaks). + +**Returns** + +* `Tuple[int, bool, np.ndarray, np.ndarray]`: Tuple containing: Number of blocks, valid blocks, coordinates of block start, +and coordinates of block end. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/_steps/step4b.md new file mode 100644 index 0000000..4a09d22 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4b.md @@ -0,0 +1,57 @@ +--- +sidebar_label: step4b +title: _steps.step4b +--- + +## os + +## Tuple + +## np + +## h5py + +## time + +## interpolate + +## morphology + +## SimpleNamespace + +## ali + +## hdf + +## dtype + +#### process\_block\_data + +```python +def process_block_data( + xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, + color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, + bvolume_peak: h5py.Dataset, timepoints: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Load timeseries in individual blocks, slice-time correct, and find similar timeseries. + +**Arguments** + +* **xyz0** (`Tuple[int, int, int]`): Start coordinates of block. +* **xyz1** (`Tuple[int, int, int]`): End coordinates of block. +* **parameters** (`dict`): Parameters dictionary. +* **color_i** (`int`): Color index. +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): The resolution of x, y, and z dimensions. +* **ball_diam** (`np.ndarray`): The diameter of a cell-area sphere. +* **bvolume_mean** (`h5py.Dataset`): Spark broadcast variable: volume mean. +* **bvolume_peak** (`h5py.Dataset`): Spark broadcast variable: local intensity maximum volume (peak). +* **timepoints** (`np.ndarray`): Timepoints at which segmentation will be performed. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/_steps/step4c.md new file mode 100644 index 0000000..7cad9e5 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4c.md @@ -0,0 +1,50 @@ +--- +sidebar_label: step4c +title: _steps.step4c +--- + +## os + +## Tuple + +## np + +## cluster + +## sparseness + +#### initialize\_block\_cells + +```python +def initialize_block_cells( + n_voxels_cell: int, n_voxels_block: int, n_cells: int, + voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, + peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, + lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Initialize cell positions in individual blocks. + +**Arguments** + +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **n_voxels_block** (`int`): Number of voxels in block. +* **n_cells** (`int`): Number of cells. +* **voxel_xyz** (`np.ndarray`): Voxel coordinates. +* **voxel_timeseries** (`np.ndarray`): Voxel timeseries. +* **peak_idx** (`np.ndarray`): Peak indices. +* **peak_valids** (`np.ndarray`): Valid local-intensity maxima (used to determine number of cells). +* **voxel_similarity_peak** (`np.ndarray`): Similarity between voxels: defined by the combination of spatial proximity +and temporal similarity (the voxels are neighbors of each other and also +correlated with each other). +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): Resolution of x, y, z dimensions. +* **ball_diam** (`np.ndarray`): Diameter of a sphere that may defines a cell boundary. +* **ball_diam_xyz0** (`np.ndarray`): Midpoint of the sphere. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/_steps/step4d.md new file mode 100644 index 0000000..df4c35f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4d.md @@ -0,0 +1,56 @@ +--- +sidebar_label: step4d +title: _steps.step4d +--- + +## os + +## Tuple + +## np + +## stats + +## linalg + +## measure + +## sparseness\_projection + +#### nnmf\_sparse + +```python +def nnmf_sparse( + V0: np.ndarray, + XYZ0: np.ndarray, + W0: np.ndarray, + B0: np.ndarray, + S0: np.ndarray, + tolfun: float = 1e-4, + miniter: int = 10, + maxiter: int = 100, + timeseries_mean=1.0, + timepoints: np.ndarray = None, + verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] +``` + +Cell detection via nonnegative matrix factorization with sparseness projection. + +**Arguments** + +* **V0** (`np.ndarray`): Voxel timeseries (voxel_timeseries_valid). +* **XYZ0** (`np.ndarray`): Voxel coordinates (voxel_xyz_valid). +* **W0** (`np.ndarray`): Initial cell weights (cell_weight_init_valid). +* **B0** (`np.ndarray`): Cell neighborhood (cell_neighborhood_valid). +* **S0** (`np.ndarray`): Cell sparseness (cell_sparseness). +* **tolfun** (`float, optional`): Tolerance for convergence, by default 1e-4. +* **miniter** (`int, optional`): Minimum number of iterations, by default 10. +* **maxiter** (`int, optional`): Maximum number of iterations, by default 100. +* **timeseries_mean** (`float, optional`): Mean timeseries value, by default 1.0. +* **timepoints** (`np.ndarray, optional`): Timepoints to use, by default None. +* **verbosity** (`bool, optional`): Print progress, by default True. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, float]`: Tuple containing: Spatial footprint, temporal footprint, convergence error. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/_steps/step4e.md new file mode 100644 index 0000000..b3d4633 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4e.md @@ -0,0 +1,42 @@ +--- +sidebar_label: step4e +title: _steps.step4e +--- + +## os + +## h5py + +## np + +## SimpleNamespace + +## Tuple + +## pyspark + +## SparkSession + +## hdf + +## evenly\_parallelize + +#### collect\_blocks + +```python +def collect_blocks( + color_i: int, parameters: dict +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Collect cells across all blocks. + +**Arguments** + +* **color_i** (`int`): Color index. +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/_steps/step5.md new file mode 100644 index 0000000..485c489 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step5.md @@ -0,0 +1,45 @@ +--- +sidebar_label: step5 +title: _steps.step5 +--- + +## os + +## h5py + +## shutil + +## np + +## SimpleNamespace + +## combinations + +## collect\_blocks + +## hdf + +## dtype + +## clean\_signal + +## evenly\_parallelize + +## SparkSession + +#### clean\_cells + +```python +def clean_cells(parameters: dict) -> None +``` + +Remove noise cells, detrend and detect baseline. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md new file mode 100644 index 0000000..077ce2b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md @@ -0,0 +1,7 @@ +--- +sidebar_label: _tools +title: _tools +--- + +## download\_sample\_data + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md new file mode 100644 index 0000000..5e0ac97 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md @@ -0,0 +1,37 @@ +--- +sidebar_label: ants_registration +title: _tools.ants_registration +--- + +## os + +#### ants\_registration + +```python +def ants_registration(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + prefix_out_tform: str, + typ: str, + in_tform: str = None, + restrict: str = None) -> str +``` + +ANTs registration. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs directory. +* **in_nii** (`str`): Input nifti file. +* **ref_nii** (`str`): Reference nifti file. +* **out_nii** (`str`): Output nifti file. +* **prefix_out_tform** (`str`): Prefix for output transformation files. +* **typ** (`str`): Type of transformation. +* **in_tform** (`str (optional)`): Initial transformation file. Default is None. +* **restrict** (`str (optional)`): Restrict deformation. Default is None. + +**Returns** + +* `str`: ANTs registration command. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md new file mode 100644 index 0000000..5bfcbe7 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md @@ -0,0 +1,33 @@ +--- +sidebar_label: ants_transformation +title: _tools.ants_transformation +--- + +## os + +#### ants\_transformation + +```python +def ants_transformation(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + in_tform: str, + interpolation="Linear") -> str +``` + +Application of ANTs transform. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs binaries. +* **in_nii** (`str`): Path to input nifti file. +* **ref_nii** (`str`): Path to reference nifti file. +* **out_nii** (`str`): Path to output nifti file. +* **in_tform** (`str`): Path to input transform file (.mat). +* **interpolation** (`str`): Interpolation method. + +**Returns** + +* `str`: ANTs transformation command string. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/_tools/aws.md new file mode 100644 index 0000000..beb6fb2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/aws.md @@ -0,0 +1,54 @@ +--- +sidebar_label: aws +title: _tools.aws +--- + +## boto3 + +## datetime + +## timezone + +## JobDefinitionException Objects + +```python +class JobDefinitionException(Exception) +``` + +#### format\_voluseg\_kwargs + +```python +def format_voluseg_kwargs(voluseg_kwargs: dict) -> dict +``` + +#### run\_job\_in\_aws\_batch + +```python +def run_job_in_aws_batch(job_name_prefix: str, + voluseg_kwargs: dict, + aws_local_profile: str = None, + vcpus: int = 32, + memory: int = 65536) +``` + +Submit a Voluseg job to AWS Batch. + +**Arguments** + +* **job_name_prefix** (`str`): Job name prefix, it will be concatenated with the current timestamp. +Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" +* **voluseg_kwargs** (`dict`): Voluseg parameters. +* **aws_local_profile** (`str`): AWS profile name. Default is None. +* **vcpus** (`int`): Number of vCPUs. Default is 32. +* **memory** (`int`): Memory in MB. Default is 65536. + +**Returns** + +* `dict`: Dictionary with the job_name and batch_job_id. + +#### export\_to\_s3 + +```python +def export_to_s3(local_path: str, bucket_name: str, object_name: str) +``` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/_tools/ball.md new file mode 100644 index 0000000..807fedd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ball.md @@ -0,0 +1,24 @@ +--- +sidebar_label: ball +title: _tools.ball +--- + +## np + +#### ball + +```python +def ball(radi: float, affine_matrix: np.ndarray) -> tuple +``` + +Morphological cell balls and midpoints. + +**Arguments** + +* **radi** (`float`): Radius of ball. +* **affine_matrix** (`np.ndarray`): Affine matrix. + +**Returns** + +* `tuple`: Tuple containing: Ball and midpoints. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md new file mode 100644 index 0000000..c98eee8 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md @@ -0,0 +1,39 @@ +--- +sidebar_label: clean_signal +title: _tools.clean_signal +--- + +## os + +## Tuple + +## np + +## pd + +## signal + +## winsorize + +## dtype + +## SimpleNamespace + +#### clean\_signal + +```python +def clean_signal(parameters: dict, + timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] +``` + +Detrend, filter, and estimate dynamic baseline for input timeseries. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **timeseries** (`np.ndarray`): Input timeseries. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/constants.md b/docs/voluseg-docs-app/docs/reference/_tools/constants.md new file mode 100644 index 0000000..b3218c9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/constants.md @@ -0,0 +1,15 @@ +--- +sidebar_label: constants +title: _tools.constants +--- + +#### ori + +#### ali + +#### nii + +#### hdf + +#### dtype + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md new file mode 100644 index 0000000..1408839 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md @@ -0,0 +1,27 @@ +--- +sidebar_label: evenly_parallelize +title: _tools.evenly_parallelize +--- + +## np + +## SparkSession + +## RDD + +#### evenly\_parallelize + +```python +def evenly_parallelize(input_list: list) -> RDD +``` + +Return evenly partitioned spark resilient distributed dataset (RDD). + +**Arguments** + +* **input_list** (`list`): List of input elements. + +**Returns** + +* `RDD`: Spark resilient distributed dataset (RDD). + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md new file mode 100644 index 0000000..1792dda --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md @@ -0,0 +1,27 @@ +--- +sidebar_label: get_volume_name +title: _tools.get_volume_name +--- + +## os + +#### get\_volume\_name + +```python +def get_volume_name(fullname_volume: str, + dir_prefix: str = None, + plane_i: int = None) -> str +``` + +Get name of volume (with directory prefix and plane suffix). + +**Arguments** + +* **fullname_volume** (`str`): Full name of volume. +* **dir_prefix** (`str (optional)`): Prefix for directory. Default is None. +* **plane_i** (`int (optional)`): Index of plane. Default is None. + +**Returns** + +* `str`: Name of volume. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md new file mode 100644 index 0000000..aa404ad --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md @@ -0,0 +1,28 @@ +--- +sidebar_label: load_metadata +title: _tools.load_metadata +--- + +## np + +## ElementTree + +#### load\_metadata + +```python +def load_metadata(parameters: dict, filename_channel: str, + filename_stack: str) -> dict +``` + +Fetch z-resolution, exposure time, and stack frequency. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename_channel** (`str`): Filename XML file containing channel information. +* **filename_stack** (`str`): Filename of XML file containing stack information. + +**Returns** + +* `dict`: Parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md new file mode 100644 index 0000000..5c882c9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md @@ -0,0 +1,32 @@ +--- +sidebar_label: load_volume +title: _tools.load_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### load\_volume + +```python +def load_volume(fullname_ext: str) -> Union[np.ndarray, None] +``` + +Load volume based on input name and extension. +Supports tiff, hdf5, klb, and nifti formats. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. + +**Returns** + +* `np.ndarray or None`: Volume as numpy array, or None if volume could not be loaded. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md new file mode 100644 index 0000000..6c315d4 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md @@ -0,0 +1,98 @@ +--- +sidebar_label: nwb +title: _tools.nwb +--- + +## pynwb + +## contextmanager + +#### open\_nwbfile\_local + +```python +@contextmanager +def open_nwbfile_local(file_path: str) +``` + +Context manager to open and close a local NWB file. + +**Arguments** + +* **file_path** (`str`): Path to NWB file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile\_remote + +```python +@contextmanager +def open_nwbfile_remote(s3_url: str, output_path: str) +``` + +Context manager to open and close a remote NWB file. + +**Arguments** + +* **s3_url** (`str`): S3 URL to NWB file. +* **output_path** (`str`): Output path to cache the remote file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile + +```python +@contextmanager +def open_nwbfile(input_path: str, remote: bool, output_path: str = None) +``` + +Open and close an NWB file from either a local or remote source. + +**Arguments** + +* **input_path** (`str`): Path to the NWB file. This can be a local file path or an S3 URL. +* **remote** (`bool`): If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. +* **output_path** (`str`): Output path, only used to cache remote files. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### find\_nwbfile\_volume\_object\_name + +```python +def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str +``` + +Find the name of the `TwoPhotonSeries` volume object in the NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. + +**Returns** + +* `str`: Name of the volume object. + +#### get\_nwbfile\_volume + +```python +def get_nwbfile_volume( + nwbfile: pynwb.NWBFile, + acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile +``` + +Get `TwoPhotonSeries` object from NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. +* **acquisition_name** (`str (default: "TwoPhotonSeries")`): Acquisition name. + +**Returns** + +* `pynwb.NWBFile`: NWB file. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md new file mode 100644 index 0000000..f0dd2f9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md @@ -0,0 +1,89 @@ +--- +sidebar_label: parameter_dictionary +title: _tools.parameter_dictionary +--- + +## Union + +## ParametersModel + +#### parameter\_dictionary + +```python +def parameter_dictionary(detrending: str = "standard", + registration: str = "medium", + registration_restrict: str = "", + diam_cell: float = 6.0, + dir_ants: str = "", + dir_input: str = "", + dir_output: str = "", + dir_transform: str = "", + ds: int = 2, + planes_pad: int = 0, + planes_packed: bool = False, + parallel_clean: bool = True, + parallel_volume: bool = True, + save_volume: bool = False, + type_timepoints: str = "dff", + type_mask: str = "geomean", + timepoints: int = 1000, + f_hipass: float = 0, + f_volume: float = 2.0, + n_cells_block: int = 316, + n_colors: int = 1, + res_x: float = 0.40625, + res_y: float = 0.40625, + res_z: float = 5.0, + t_baseline: int = 300, + t_section: float = 0.01, + thr_mask: float = 0.5, + volume_fullnames_input: Union[list[str], None] = None, + volume_names: Union[list[str], None] = None, + input_dirs: Union[list[str], None] = None, + ext: Union[str, None] = None, + lt: Union[int, None] = None, + affine_matrix: Union[list, None] = None) -> dict +``` + +Return a parameter dictionary with specified defaults. + +**Arguments** + +* **detrending** (`str, optional`): Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +* **registration** (`str, optional`): Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +* **registration_restrict** (`str, optional`): Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +* **diam_cell** (`float, optional`): Cell diameter in microns (default is 6.0). +* **dir_ants** (`str, optional`): Path to the ANTs directory (default is an empty string). +* **dir_input** (`str, optional`): Path to input directories, separate multiple directories with ';' (default is an empty string). +* **dir_output** (`str, optional`): Path to the output directory (default is an empty string). +* **dir_transform** (`str, optional`): Path to the transform directory (default is an empty string). +* **ds** (`int, optional`): Spatial coarse-graining in x-y dimension (default is 2). +* **planes_pad** (`int, optional`): Number of planes to pad the volume with for robust registration (default is 0). +* **planes_packed** (`bool, optional`): Packed planes in each volume, for single plane imaging with packed planes (default is False). +* **parallel_clean** (`bool, optional`): Parallelization of final cleaning (True is fast but memory-intensive, default is True). +* **parallel_volume** (`bool, optional`): Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +* **save_volume** (`bool, optional`): Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +* **type_timepoints** (`str, optional`): Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +* **type_mask** (`str, optional`): Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +* **timepoints** (`int, optional`): Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +* **f_hipass** (`float, optional`): Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +* **f_volume** (`float, optional`): Imaging frequency in Hz (default is 2.0). +* **n_cells_block** (`int, optional`): Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +* **n_colors** (`int, optional`): Number of brain colors (2 in two-color volumes, default is 1). +* **res_x** (`float, optional`): X resolution in microns (default is 0.40625). +* **res_y** (`float, optional`): Y resolution in microns (default is 0.40625). +* **res_z** (`float, optional`): Z resolution in microns (default is 5.0). +* **t_baseline** (`int, optional`): Interval for baseline calculation in seconds (default is 300). +* **t_section** (`float, optional`): Exposure time in seconds for slice acquisition (default is 0.01). +* **thr_mask** (`float, optional`): Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +* **volume_fullnames_input** (`list[str], optional`): List of full volume names (default is None). +* **volume_names** (`list[str], optional`): List of volume names (default is None). +* **input_dirs** (`list[str], optional`): List of input directories (default is None). +* **ext** (`str, optional`): File extension (default is None). +* **lt** (`int, optional`): Number of volumes (default is None). +* **affine_matrix** (`list, optional`): Affine matrix (default is None). + +**Returns** + +* `dict`: A dictionary of validated parameters with their default values. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters.md new file mode 100644 index 0000000..79a3e8b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameters.md @@ -0,0 +1,44 @@ +--- +sidebar_label: parameters +title: _tools.parameters +--- + +## pickle + +## json + +## ParametersModel + +#### load\_parameters + +```python +def load_parameters(filename: str) -> dict +``` + +Load previously saved parameters from filename. + +**Arguments** + +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `dict`: Parameters dictionary. + +#### save\_parameters + +```python +def save_parameters(parameters: dict, filename: str) -> None +``` + +Save parameters to filename. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md new file mode 100644 index 0000000..5b466cd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md @@ -0,0 +1,171 @@ +--- +sidebar_label: parameters_models +title: _tools.parameters_models +--- + +## Enum + +## np + +## BaseModel + +## Field + +## model\_validator + +## Optional + +## Detrending Objects + +```python +class Detrending(str, Enum) +``` + +#### standard + +#### robust + +#### none + +## Registration Objects + +```python +class Registration(str, Enum) +``` + +#### high + +#### medium + +#### low + +#### none + +## TypeTimepoints Objects + +```python +class TypeTimepoints(str, Enum) +``` + +#### dff + +#### periodic + +#### custom + +## TypeMask Objects + +```python +class TypeMask(str, Enum) +``` + +#### mean + +#### geomean + +#### max + +## ParametersModel Objects + +```python +class ParametersModel(BaseModel) +``` + +#### detrending + +#### registration + +#### registration\_restrict + +#### diam\_cell + +#### dir\_ants + +#### dir\_input + +#### dir\_output + +#### dir\_transform + +#### ds + +#### planes\_pad + +#### planes\_packed + +#### parallel\_clean + +#### parallel\_volume + +#### save\_volume + +#### type\_timepoints + +#### type\_mask + +#### timepoints + +#### f\_hipass + +#### f\_volume + +#### n\_cells\_block + +#### n\_colors + +#### res\_x + +#### res\_y + +#### res\_z + +#### t\_baseline + +#### t\_section + +#### thr\_mask + +#### volume\_fullnames\_input + +#### volume\_names + +#### input\_dirs + +#### ext + +#### lt + +#### affine\_matrix + +#### dim\_order + +#### remote + +#### convert\_array\_to\_list + +```python +@model_validator(mode="before") +def convert_array_to_list(cls, values) +``` + +Validator to automatically convert NumPy arrays to lists. + +#### model\_dump + +```python +def model_dump(use_np_array: bool = True, *args, **kwargs) +``` + +Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) +and Enums to their values. + +**Arguments** + +* **use_np_array** (`bool, optional`): Convert lists to NumPy arrays (default is True) +* ***args**: Positional arguments to pass to the parent class +* ****kwargs**: Keyword arguments to pass to the parent class + +**Returns** + +* `dict`: A dictionary of the model's data + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md new file mode 100644 index 0000000..bd3d6a0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md @@ -0,0 +1,71 @@ +--- +sidebar_label: sample_data +title: _tools.sample_data +--- + +## requests + +## zipfile + +## os + +## Path + +## Union + +#### download\_sample\_data + +```python +def download_sample_data(destination_folder: str = ".", + data_type: str = "h5_dir") -> Union[str, None] +``` + +Download sample data for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. +* **data_type** (`str, optional`): Type of data to download. Options are "h5_dir" and "nwb_file". + +**Returns** + +* `str or None`: Path to the folder or file where the data was downloaded, or None if the download failed. + +#### download\_sample\_data\_nwb\_file + +```python +def download_sample_data_nwb_file( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample NWB file for Voluseg. +Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the downloaded file, or None if the download failed. + +#### download\_sample\_data\_h5\_dir + +```python +def download_sample_data_h5_dir( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample data (h5 directory) for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the folder where the data was extracted, or None if the download failed. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md new file mode 100644 index 0000000..f7c50f6 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md @@ -0,0 +1,36 @@ +--- +sidebar_label: save_volume +title: _tools.save_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### save\_volume + +```python +def save_volume(fullname_ext: str, + volume: np.ndarray, + affine_matrix: np.ndarray = None) -> Union[bool, None] +``` + +Save volume in output format. +Formats currently accepted are: nifti and hdf5. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. +* **volume** (`np.ndarray`): Volume as numpy array. +* **affine_matrix** (`np.ndarray`): Affine matrix for nifti format. + +**Returns** + +* `bool or None`: True if volume was saved successfully, None if volume could not be saved. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md new file mode 100644 index 0000000..28b3c17 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md @@ -0,0 +1,24 @@ +--- +sidebar_label: sparseness +title: _tools.sparseness +--- + +## np + +#### sparseness + +```python +def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray +``` + +Vector sparseness along specified dimension. + +**Arguments** + +* **W** (`np.ndarray`): Input array. +* **dim** (`int, optional`): Dimension along which to compute sparseness, by default 0. + +**Returns** + +* `np.ndarray`: Sparseness of input array along specified dimension. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md new file mode 100644 index 0000000..a734715 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md @@ -0,0 +1,27 @@ +--- +sidebar_label: sparseness_projection +title: _tools.sparseness_projection +--- + +## np + +#### sparseness\_projection + +```python +def sparseness_projection(Si: np.ndarray, + s: float, + at_least_as_sparse: bool = False) -> np.ndarray +``` + +Hoyer sparseness projection. + +**Arguments** + +* **Si** (`np.ndarray`): Input signal. +* **s** (`float`): Sparseness parameter. +* **at_least_as_sparse** (`bool, optional`): Enforce at least as sparse, by default False. + +**Returns** + +* `np.ndarray`: Sparse signal. + diff --git a/docs/voluseg-docs-app/docs/reference/_update.md b/docs/voluseg-docs-app/docs/reference/_update.md new file mode 100644 index 0000000..03ee034 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_update.md @@ -0,0 +1,15 @@ +--- +sidebar_label: _update +title: _update +--- + +## os + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From 1cf998b57cbbbacd5bd832224b386084f7e83e6d Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 30 Oct 2024 10:09:34 +0000 Subject: [PATCH 06/27] auto-commit-docs --- .../docs/reference/_steps/step5.md | 4 ++- .../docs/reference/_tools/nwb.md | 31 +++++++++++++++++++ .../reference/_tools/parameters_models.md | 2 ++ 3 files changed, 36 insertions(+), 1 deletion(-) diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/_steps/step5.md index 485c489..3dd7efb 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step5.md +++ b/docs/voluseg-docs-app/docs/reference/_steps/step5.md @@ -15,6 +15,8 @@ title: _steps.step5 ## combinations +## SparkSession + ## collect\_blocks ## hdf @@ -25,7 +27,7 @@ title: _steps.step5 ## evenly\_parallelize -## SparkSession +## write\_nwbfile #### clean\_cells diff --git a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md index 6c315d4..cee4840 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md +++ b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md @@ -7,6 +7,14 @@ title: _tools.nwb ## contextmanager +## datetime + +## tzlocal + +## uuid4 + +## np + #### open\_nwbfile\_local ```python @@ -96,3 +104,26 @@ Get `TwoPhotonSeries` object from NWB file. * `pynwb.NWBFile`: NWB file. +#### write\_nwbfile + +```python +def write_nwbfile(output_path: str, cell_x: np.ndarray, cell_y: np.ndarray, + cell_z: np.ndarray, cell_weights: np.ndarray, + cell_timeseries: np.ndarray) -> None +``` + +Write results to a local NWB file. + +**Arguments** + +* **output_path** (`str`): Output path. +* **cell_x** (`np.ndarray`): Voxel X coordinates for all cells. +* **cell_y** (`np.ndarray`): Voxel Y coordinates for all cells. +* **cell_z** (`np.ndarray`): Voxel Z coordinates for all cells. +* **cell_weights** (`np.ndarray`): Voxel weights for all cells. +* **cell_timeseries** (`np.ndarray`): Fluorescence timeseries data for all cells. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md index 5b466cd..b358b9f 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md @@ -141,6 +141,8 @@ class ParametersModel(BaseModel) #### remote +#### output\_to\_nwb + #### convert\_array\_to\_list ```python From f16348521d595a67b87fe352d1cff249de12c22e Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 11:09:59 +0100 Subject: [PATCH 07/27] remove files --- .../docs/reference/__init__/__init__.md | 29 --- .../docs/reference/_steps/__init__.md | 5 - .../docs/reference/_steps/step0.md | 49 ----- .../docs/reference/_steps/step1.md | 48 ----- 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+++ /dev/null @@ -1,5 +0,0 @@ ---- -sidebar_label: _steps -title: _steps ---- - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/_steps/step0.md deleted file mode 100644 index 6b623f3..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step0.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -sidebar_label: step0 -title: _steps.step0 ---- - -## os - -## copy - -## json - -## np - -## warn - -## load\_volume - -## get\_volume\_name - -## parameter\_dictionary - -## evenly\_parallelize - -## load\_parameters - -## save\_parameters - -## ParametersModel - -## open\_nwbfile - -## find\_nwbfile\_volume\_object\_name - -#### process\_parameters - -```python -def process_parameters(initial_parameters: dict) -> dict -``` - -Process parameters and create parameter file (pickle). - -**Arguments** - -* **initial_parameters** (`dict`): Initial parameter dictionary - -**Returns** - -* `dict`: Processed parameters dictionary. - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/_steps/step1.md deleted file mode 100644 index a83feda..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step1.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -sidebar_label: step1 -title: _steps.step1 ---- - -## os - -## interpolate - -## SimpleNamespace - -## load\_volume - -## save\_volume - -## get\_volume\_name - -## ori - -## ali - -## nii - -## hdf - -## evenly\_parallelize - -## open\_nwbfile - -## get\_nwbfile\_volume - -#### process\_volumes - -```python -def process_volumes(parameters: dict) -> None -``` - -Process original volumes and save them to nifti files. -Performs downsampling and padding if specified in parameters. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/_steps/step2.md deleted file mode 100644 index b372ae7..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step2.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -sidebar_label: step2 -title: _steps.step2 ---- - -## os - -## h5py - -## shutil - -## np - -## io - -## SimpleNamespace - -## load\_volume - -## save\_volume - -## ori - -## ali - -## nii - -## hdf - -## dtype - -## ants\_registration - -## ants\_transformation - -## evenly\_parallelize - -#### align\_volumes - -```python -def align_volumes(parameters: dict) -> None -``` - -Register volumes to a reference volume. -Generates ANTs transforms files (.mat). - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/_steps/step3.md deleted file mode 100644 index 85073bd..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step3.md +++ /dev/null @@ -1,61 +0,0 @@ ---- -sidebar_label: step3 -title: _steps.step3 ---- - -## os - -## h5py - -## pyspark - -## np - -## stats - -## mixture - -## morphology - -## SimpleNamespace - -## median\_filter - -## SparkSession - -## warnings - -## matplotlib - -## plt - -## ball - -## ali - -## hdf - -## load\_volume - -## clean\_signal - -## evenly\_parallelize - -#### mask\_volumes - -```python -def mask_volumes(parameters: dict) -> None -``` - -Create intensity mask from the average registered volume. -Produces figures with masks and histograms. -Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/_steps/step4.md deleted file mode 100644 index 8f23d34..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4.md +++ /dev/null @@ -1,47 +0,0 @@ ---- -sidebar_label: step4 -title: _steps.step4 ---- - -## os - -## h5py - -## time - -## np - -## SimpleNamespace - -## SparkSession - -## define\_blocks - -## process\_block\_data - -## initialize\_block\_cells - -## nnmf\_sparse - -## ball - -## hdf - -## evenly\_parallelize - -#### detect\_cells - -```python -def detect_cells(parameters: dict) -> None -``` - -Detect cells in volumetric blocks. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/_steps/step4a.md deleted file mode 100644 index f44a0dd..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -sidebar_label: step4a -title: _steps.step4a ---- - -## os - -## Tuple - -## np - -#### define\_blocks - -```python -def define_blocks( - lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, - volume_mask: np.ndarray, - volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] -``` - -Get coordinates of individual blocks. - -**Arguments** - -* **lx** (`int`): Number of voxels in x-dimension. -* **ly** (`int`): Number of voxels in y-dimension. -* **lz** (`int`): Number of voxels in z-dimension. -* **n_cells_block** (`int`): Number of cells in each block. -* **n_voxels_cell** (`int`): Number of voxels in each cell. -* **volume_mask** (`np.ndarray`): Volume mask. -* **volume_peak** (`np.ndarray`): Volume local intensity maxima (peaks). - -**Returns** - -* `Tuple[int, bool, np.ndarray, np.ndarray]`: Tuple containing: Number of blocks, valid blocks, coordinates of block start, -and coordinates of block end. - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/_steps/step4b.md deleted file mode 100644 index 4a09d22..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -sidebar_label: step4b -title: _steps.step4b ---- - -## os - -## Tuple - -## np - -## h5py - -## time - -## interpolate - -## morphology - -## SimpleNamespace - -## ali - -## hdf - -## dtype - -#### process\_block\_data - -```python -def process_block_data( - xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, - color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], - ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, - bvolume_peak: h5py.Dataset, timepoints: np.ndarray -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Load timeseries in individual blocks, slice-time correct, and find similar timeseries. - -**Arguments** - -* **xyz0** (`Tuple[int, int, int]`): Start coordinates of block. -* **xyz1** (`Tuple[int, int, int]`): End coordinates of block. -* **parameters** (`dict`): Parameters dictionary. -* **color_i** (`int`): Color index. -* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. -* **rxyz** (`Tuple[float, float, float]`): The resolution of x, y, and z dimensions. -* **ball_diam** (`np.ndarray`): The diameter of a cell-area sphere. -* **bvolume_mean** (`h5py.Dataset`): Spark broadcast variable: volume mean. -* **bvolume_peak** (`h5py.Dataset`): Spark broadcast variable: local intensity maximum volume (peak). -* **timepoints** (`np.ndarray`): Timepoints at which segmentation will be performed. - -**Returns** - -* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/_steps/step4c.md deleted file mode 100644 index 7cad9e5..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -sidebar_label: step4c -title: _steps.step4c ---- - -## os - -## Tuple - -## np - -## cluster - -## sparseness - -#### initialize\_block\_cells - -```python -def initialize_block_cells( - n_voxels_cell: int, n_voxels_block: int, n_cells: int, - voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, - peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, - lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], - ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Initialize cell positions in individual blocks. - -**Arguments** - -* **n_voxels_cell** (`int`): Number of voxels in each cell. -* **n_voxels_block** (`int`): Number of voxels in block. -* **n_cells** (`int`): Number of cells. -* **voxel_xyz** (`np.ndarray`): Voxel coordinates. -* **voxel_timeseries** (`np.ndarray`): Voxel timeseries. -* **peak_idx** (`np.ndarray`): Peak indices. -* **peak_valids** (`np.ndarray`): Valid local-intensity maxima (used to determine number of cells). -* **voxel_similarity_peak** (`np.ndarray`): Similarity between voxels: defined by the combination of spatial proximity -and temporal similarity (the voxels are neighbors of each other and also -correlated with each other). -* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. -* **rxyz** (`Tuple[float, float, float]`): Resolution of x, y, z dimensions. -* **ball_diam** (`np.ndarray`): Diameter of a sphere that may defines a cell boundary. -* **ball_diam_xyz0** (`np.ndarray`): Midpoint of the sphere. - -**Returns** - -* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: TODO - add description - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/_steps/step4d.md deleted file mode 100644 index df4c35f..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -sidebar_label: step4d -title: _steps.step4d ---- - -## os - -## Tuple - -## np - -## stats - -## linalg - -## measure - -## sparseness\_projection - -#### nnmf\_sparse - -```python -def nnmf_sparse( - V0: np.ndarray, - XYZ0: np.ndarray, - W0: np.ndarray, - B0: np.ndarray, - S0: np.ndarray, - tolfun: float = 1e-4, - miniter: int = 10, - maxiter: int = 100, - timeseries_mean=1.0, - timepoints: np.ndarray = None, - verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] -``` - -Cell detection via nonnegative matrix factorization with sparseness projection. - -**Arguments** - -* **V0** (`np.ndarray`): Voxel timeseries (voxel_timeseries_valid). -* **XYZ0** (`np.ndarray`): Voxel coordinates (voxel_xyz_valid). -* **W0** (`np.ndarray`): Initial cell weights (cell_weight_init_valid). -* **B0** (`np.ndarray`): Cell neighborhood (cell_neighborhood_valid). -* **S0** (`np.ndarray`): Cell sparseness (cell_sparseness). -* **tolfun** (`float, optional`): Tolerance for convergence, by default 1e-4. -* **miniter** (`int, optional`): Minimum number of iterations, by default 10. -* **maxiter** (`int, optional`): Maximum number of iterations, by default 100. -* **timeseries_mean** (`float, optional`): Mean timeseries value, by default 1.0. -* **timepoints** (`np.ndarray, optional`): Timepoints to use, by default None. -* **verbosity** (`bool, optional`): Print progress, by default True. - -**Returns** - -* `Tuple[np.ndarray, np.ndarray, float]`: Tuple containing: Spatial footprint, temporal footprint, convergence error. - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/_steps/step4e.md deleted file mode 100644 index b3d4633..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md +++ /dev/null @@ -1,42 +0,0 @@ ---- -sidebar_label: step4e -title: _steps.step4e ---- - -## os - -## h5py - -## np - -## SimpleNamespace - -## Tuple - -## pyspark - -## SparkSession - -## hdf - -## evenly\_parallelize - -#### collect\_blocks - -```python -def collect_blocks( - color_i: int, parameters: dict -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] -``` - -Collect cells across all blocks. - -**Arguments** - -* **color_i** (`int`): Color index. -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/_steps/step5.md deleted file mode 100644 index 485c489..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/step5.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -sidebar_label: step5 -title: _steps.step5 ---- - -## os - -## h5py - -## shutil - -## np - -## SimpleNamespace - -## combinations - -## collect\_blocks - -## hdf - -## dtype - -## clean\_signal - -## evenly\_parallelize - -## SparkSession - -#### clean\_cells - -```python -def clean_cells(parameters: dict) -> None -``` - -Remove noise cells, detrend and detect baseline. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md deleted file mode 100644 index 077ce2b..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -sidebar_label: _tools -title: _tools ---- - -## download\_sample\_data - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md deleted file mode 100644 index 5e0ac97..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -sidebar_label: ants_registration -title: _tools.ants_registration ---- - -## os - -#### ants\_registration - -```python -def ants_registration(dir_ants: str, - in_nii: str, - ref_nii: str, - out_nii: str, - prefix_out_tform: str, - typ: str, - in_tform: str = None, - restrict: str = None) -> str -``` - -ANTs registration. - -**Arguments** - -* **dir_ants** (`str`): Path to ANTs directory. -* **in_nii** (`str`): Input nifti file. -* **ref_nii** (`str`): Reference nifti file. -* **out_nii** (`str`): Output nifti file. -* **prefix_out_tform** (`str`): Prefix for output transformation files. -* **typ** (`str`): Type of transformation. -* **in_tform** (`str (optional)`): Initial transformation file. Default is None. -* **restrict** (`str (optional)`): Restrict deformation. Default is None. - -**Returns** - -* `str`: ANTs registration command. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md deleted file mode 100644 index 5bfcbe7..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md +++ /dev/null @@ -1,33 +0,0 @@ ---- -sidebar_label: ants_transformation -title: _tools.ants_transformation ---- - -## os - -#### ants\_transformation - -```python -def ants_transformation(dir_ants: str, - in_nii: str, - ref_nii: str, - out_nii: str, - in_tform: str, - interpolation="Linear") -> str -``` - -Application of ANTs transform. - -**Arguments** - -* **dir_ants** (`str`): Path to ANTs binaries. -* **in_nii** (`str`): Path to input nifti file. -* **ref_nii** (`str`): Path to reference nifti file. -* **out_nii** (`str`): Path to output nifti file. -* **in_tform** (`str`): Path to input transform file (.mat). -* **interpolation** (`str`): Interpolation method. - -**Returns** - -* `str`: ANTs transformation command string. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/_tools/aws.md deleted file mode 100644 index beb6fb2..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/aws.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -sidebar_label: aws -title: _tools.aws ---- - -## boto3 - -## datetime - -## timezone - -## JobDefinitionException Objects - -```python -class JobDefinitionException(Exception) -``` - -#### format\_voluseg\_kwargs - -```python -def format_voluseg_kwargs(voluseg_kwargs: dict) -> dict -``` - -#### run\_job\_in\_aws\_batch - -```python -def run_job_in_aws_batch(job_name_prefix: str, - voluseg_kwargs: dict, - aws_local_profile: str = None, - vcpus: int = 32, - memory: int = 65536) -``` - -Submit a Voluseg job to AWS Batch. - -**Arguments** - -* **job_name_prefix** (`str`): Job name prefix, it will be concatenated with the current timestamp. -Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" -* **voluseg_kwargs** (`dict`): Voluseg parameters. -* **aws_local_profile** (`str`): AWS profile name. Default is None. -* **vcpus** (`int`): Number of vCPUs. Default is 32. -* **memory** (`int`): Memory in MB. Default is 65536. - -**Returns** - -* `dict`: Dictionary with the job_name and batch_job_id. - -#### export\_to\_s3 - -```python -def export_to_s3(local_path: str, bucket_name: str, object_name: str) -``` - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/_tools/ball.md deleted file mode 100644 index 807fedd..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/ball.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -sidebar_label: ball -title: _tools.ball ---- - -## np - -#### ball - -```python -def ball(radi: float, affine_matrix: np.ndarray) -> tuple -``` - -Morphological cell balls and midpoints. - -**Arguments** - -* **radi** (`float`): Radius of ball. -* **affine_matrix** (`np.ndarray`): Affine matrix. - -**Returns** - -* `tuple`: Tuple containing: Ball and midpoints. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md deleted file mode 100644 index c98eee8..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -sidebar_label: clean_signal -title: _tools.clean_signal ---- - -## os - -## Tuple - -## np - -## pd - -## signal - -## winsorize - -## dtype - -## SimpleNamespace - -#### clean\_signal - -```python -def clean_signal(parameters: dict, - timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] -``` - -Detrend, filter, and estimate dynamic baseline for input timeseries. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. -* **timeseries** (`np.ndarray`): Input timeseries. - -**Returns** - -* `Tuple[np.ndarray, np.ndarray]`: TODO - add description - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/constants.md b/docs/voluseg-docs-app/docs/reference/_tools/constants.md deleted file mode 100644 index b3218c9..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/constants.md +++ /dev/null @@ -1,15 +0,0 @@ ---- -sidebar_label: constants -title: _tools.constants ---- - -#### ori - -#### ali - -#### nii - -#### hdf - -#### dtype - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md deleted file mode 100644 index 1408839..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -sidebar_label: evenly_parallelize -title: _tools.evenly_parallelize ---- - -## np - -## SparkSession - -## RDD - -#### evenly\_parallelize - -```python -def evenly_parallelize(input_list: list) -> RDD -``` - -Return evenly partitioned spark resilient distributed dataset (RDD). - -**Arguments** - -* **input_list** (`list`): List of input elements. - -**Returns** - -* `RDD`: Spark resilient distributed dataset (RDD). - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md deleted file mode 100644 index 1792dda..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -sidebar_label: get_volume_name -title: _tools.get_volume_name ---- - -## os - -#### get\_volume\_name - -```python -def get_volume_name(fullname_volume: str, - dir_prefix: str = None, - plane_i: int = None) -> str -``` - -Get name of volume (with directory prefix and plane suffix). - -**Arguments** - -* **fullname_volume** (`str`): Full name of volume. -* **dir_prefix** (`str (optional)`): Prefix for directory. Default is None. -* **plane_i** (`int (optional)`): Index of plane. Default is None. - -**Returns** - -* `str`: Name of volume. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md deleted file mode 100644 index aa404ad..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -sidebar_label: load_metadata -title: _tools.load_metadata ---- - -## np - -## ElementTree - -#### load\_metadata - -```python -def load_metadata(parameters: dict, filename_channel: str, - filename_stack: str) -> dict -``` - -Fetch z-resolution, exposure time, and stack frequency. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. -* **filename_channel** (`str`): Filename XML file containing channel information. -* **filename_stack** (`str`): Filename of XML file containing stack information. - -**Returns** - -* `dict`: Parameters dictionary. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md deleted file mode 100644 index 5c882c9..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -sidebar_label: load_volume -title: _tools.load_volume ---- - -## h5py - -## nibabel - -## np - -## Union - -## dtype - -#### load\_volume - -```python -def load_volume(fullname_ext: str) -> Union[np.ndarray, None] -``` - -Load volume based on input name and extension. -Supports tiff, hdf5, klb, and nifti formats. - -**Arguments** - -* **fullname_ext** (`str`): Full name of volume with extension. - -**Returns** - -* `np.ndarray or None`: Volume as numpy array, or None if volume could not be loaded. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md deleted file mode 100644 index 6c315d4..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md +++ /dev/null @@ -1,98 +0,0 @@ ---- -sidebar_label: nwb -title: _tools.nwb ---- - -## pynwb - -## contextmanager - -#### open\_nwbfile\_local - -```python -@contextmanager -def open_nwbfile_local(file_path: str) -``` - -Context manager to open and close a local NWB file. - -**Arguments** - -* **file_path** (`str`): Path to NWB file. - -**Yields** - -* `pynwb.NWBFile`: The opened NWB file. - -#### open\_nwbfile\_remote - -```python -@contextmanager -def open_nwbfile_remote(s3_url: str, output_path: str) -``` - -Context manager to open and close a remote NWB file. - -**Arguments** - -* **s3_url** (`str`): S3 URL to NWB file. -* **output_path** (`str`): Output path to cache the remote file. - -**Yields** - -* `pynwb.NWBFile`: The opened NWB file. - -#### open\_nwbfile - -```python -@contextmanager -def open_nwbfile(input_path: str, remote: bool, output_path: str = None) -``` - -Open and close an NWB file from either a local or remote source. - -**Arguments** - -* **input_path** (`str`): Path to the NWB file. This can be a local file path or an S3 URL. -* **remote** (`bool`): If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. -* **output_path** (`str`): Output path, only used to cache remote files. - -**Yields** - -* `pynwb.NWBFile`: The opened NWB file. - -#### find\_nwbfile\_volume\_object\_name - -```python -def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str -``` - -Find the name of the `TwoPhotonSeries` volume object in the NWB file. - -**Arguments** - -* **nwbfile** (`pynwb.NWBFile`): NWB file. - -**Returns** - -* `str`: Name of the volume object. - -#### get\_nwbfile\_volume - -```python -def get_nwbfile_volume( - nwbfile: pynwb.NWBFile, - acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile -``` - -Get `TwoPhotonSeries` object from NWB file. - -**Arguments** - -* **nwbfile** (`pynwb.NWBFile`): NWB file. -* **acquisition_name** (`str (default: "TwoPhotonSeries")`): Acquisition name. - -**Returns** - -* `pynwb.NWBFile`: NWB file. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md deleted file mode 100644 index f0dd2f9..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md +++ /dev/null @@ -1,89 +0,0 @@ ---- -sidebar_label: parameter_dictionary -title: _tools.parameter_dictionary ---- - -## Union - -## ParametersModel - -#### parameter\_dictionary - -```python -def parameter_dictionary(detrending: str = "standard", - registration: str = "medium", - registration_restrict: str = "", - diam_cell: float = 6.0, - dir_ants: str = "", - dir_input: str = "", - dir_output: str = "", - dir_transform: str = "", - ds: int = 2, - planes_pad: int = 0, - planes_packed: bool = False, - parallel_clean: bool = True, - parallel_volume: bool = True, - save_volume: bool = False, - type_timepoints: str = "dff", - type_mask: str = "geomean", - timepoints: int = 1000, - f_hipass: float = 0, - f_volume: float = 2.0, - n_cells_block: int = 316, - n_colors: int = 1, - res_x: float = 0.40625, - res_y: float = 0.40625, - res_z: float = 5.0, - t_baseline: int = 300, - t_section: float = 0.01, - thr_mask: float = 0.5, - volume_fullnames_input: Union[list[str], None] = None, - volume_names: Union[list[str], None] = None, - input_dirs: Union[list[str], None] = None, - ext: Union[str, None] = None, - lt: Union[int, None] = None, - affine_matrix: Union[list, None] = None) -> dict -``` - -Return a parameter dictionary with specified defaults. - -**Arguments** - -* **detrending** (`str, optional`): Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). -* **registration** (`str, optional`): Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). -* **registration_restrict** (`str, optional`): Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). -* **diam_cell** (`float, optional`): Cell diameter in microns (default is 6.0). -* **dir_ants** (`str, optional`): Path to the ANTs directory (default is an empty string). -* **dir_input** (`str, optional`): Path to input directories, separate multiple directories with ';' (default is an empty string). -* **dir_output** (`str, optional`): Path to the output directory (default is an empty string). -* **dir_transform** (`str, optional`): Path to the transform directory (default is an empty string). -* **ds** (`int, optional`): Spatial coarse-graining in x-y dimension (default is 2). -* **planes_pad** (`int, optional`): Number of planes to pad the volume with for robust registration (default is 0). -* **planes_packed** (`bool, optional`): Packed planes in each volume, for single plane imaging with packed planes (default is False). -* **parallel_clean** (`bool, optional`): Parallelization of final cleaning (True is fast but memory-intensive, default is True). -* **parallel_volume** (`bool, optional`): Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). -* **save_volume** (`bool, optional`): Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). -* **type_timepoints** (`str, optional`): Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). -* **type_mask** (`str, optional`): Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). -* **timepoints** (`int, optional`): Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). -* **f_hipass** (`float, optional`): Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). -* **f_volume** (`float, optional`): Imaging frequency in Hz (default is 2.0). -* **n_cells_block** (`int, optional`): Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). -* **n_colors** (`int, optional`): Number of brain colors (2 in two-color volumes, default is 1). -* **res_x** (`float, optional`): X resolution in microns (default is 0.40625). -* **res_y** (`float, optional`): Y resolution in microns (default is 0.40625). -* **res_z** (`float, optional`): Z resolution in microns (default is 5.0). -* **t_baseline** (`int, optional`): Interval for baseline calculation in seconds (default is 300). -* **t_section** (`float, optional`): Exposure time in seconds for slice acquisition (default is 0.01). -* **thr_mask** (`float, optional`): Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). -* **volume_fullnames_input** (`list[str], optional`): List of full volume names (default is None). -* **volume_names** (`list[str], optional`): List of volume names (default is None). -* **input_dirs** (`list[str], optional`): List of input directories (default is None). -* **ext** (`str, optional`): File extension (default is None). -* **lt** (`int, optional`): Number of volumes (default is None). -* **affine_matrix** (`list, optional`): Affine matrix (default is None). - -**Returns** - -* `dict`: A dictionary of validated parameters with their default values. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters.md deleted file mode 100644 index 79a3e8b..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -sidebar_label: parameters -title: _tools.parameters ---- - -## pickle - -## json - -## ParametersModel - -#### load\_parameters - -```python -def load_parameters(filename: str) -> dict -``` - -Load previously saved parameters from filename. - -**Arguments** - -* **filename** (`str`): Filename of parameter file. - -**Returns** - -* `dict`: Parameters dictionary. - -#### save\_parameters - -```python -def save_parameters(parameters: dict, filename: str) -> None -``` - -Save parameters to filename. - -**Arguments** - -* **parameters** (`dict`): Parameters dictionary. -* **filename** (`str`): Filename of parameter file. - -**Returns** - -* `None` - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md deleted file mode 100644 index 5b466cd..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md +++ /dev/null @@ -1,171 +0,0 @@ ---- -sidebar_label: parameters_models -title: _tools.parameters_models ---- - -## Enum - -## np - -## BaseModel - -## Field - -## model\_validator - -## Optional - -## Detrending Objects - -```python -class Detrending(str, Enum) -``` - -#### standard - -#### robust - -#### none - -## Registration Objects - -```python -class Registration(str, Enum) -``` - -#### high - -#### medium - -#### low - -#### none - -## TypeTimepoints Objects - -```python -class TypeTimepoints(str, Enum) -``` - -#### dff - -#### periodic - -#### custom - -## TypeMask Objects - -```python -class TypeMask(str, Enum) -``` - -#### mean - -#### geomean - -#### max - -## ParametersModel Objects - -```python -class ParametersModel(BaseModel) -``` - -#### detrending - -#### registration - -#### registration\_restrict - -#### diam\_cell - -#### dir\_ants - -#### dir\_input - -#### dir\_output - -#### dir\_transform - -#### ds - -#### planes\_pad - -#### planes\_packed - -#### parallel\_clean - -#### parallel\_volume - -#### save\_volume - -#### type\_timepoints - -#### type\_mask - -#### timepoints - -#### f\_hipass - -#### f\_volume - -#### n\_cells\_block - -#### n\_colors - -#### res\_x - -#### res\_y - -#### res\_z - -#### t\_baseline - -#### t\_section - -#### thr\_mask - -#### volume\_fullnames\_input - -#### volume\_names - -#### input\_dirs - -#### ext - -#### lt - -#### affine\_matrix - -#### dim\_order - -#### remote - -#### convert\_array\_to\_list - -```python -@model_validator(mode="before") -def convert_array_to_list(cls, values) -``` - -Validator to automatically convert NumPy arrays to lists. - -#### model\_dump - -```python -def model_dump(use_np_array: bool = True, *args, **kwargs) -``` - -Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) -and Enums to their values. - -**Arguments** - -* **use_np_array** (`bool, optional`): Convert lists to NumPy arrays (default is True) -* ***args**: Positional arguments to pass to the parent class -* ****kwargs**: Keyword arguments to pass to the parent class - -**Returns** - -* `dict`: A dictionary of the model's data - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md deleted file mode 100644 index bd3d6a0..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md +++ /dev/null @@ -1,71 +0,0 @@ ---- -sidebar_label: sample_data -title: _tools.sample_data ---- - -## requests - -## zipfile - -## os - -## Path - -## Union - -#### download\_sample\_data - -```python -def download_sample_data(destination_folder: str = ".", - data_type: str = "h5_dir") -> Union[str, None] -``` - -Download sample data for Voluseg. - -**Arguments** - -* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded -to the current working directory. -* **data_type** (`str, optional`): Type of data to download. Options are "h5_dir" and "nwb_file". - -**Returns** - -* `str or None`: Path to the folder or file where the data was downloaded, or None if the download failed. - -#### download\_sample\_data\_nwb\_file - -```python -def download_sample_data_nwb_file( - destination_folder: str = ".") -> Union[str, None] -``` - -Download sample NWB file for Voluseg. -Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft - -**Arguments** - -* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded -to the current working directory. - -**Returns** - -* `str or None`: Path to the downloaded file, or None if the download failed. - -#### download\_sample\_data\_h5\_dir - -```python -def download_sample_data_h5_dir( - destination_folder: str = ".") -> Union[str, None] -``` - -Download sample data (h5 directory) for Voluseg. - -**Arguments** - -* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded -to the current working directory. - -**Returns** - -* `str or None`: Path to the folder where the data was extracted, or None if the download failed. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md deleted file mode 100644 index f7c50f6..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -sidebar_label: save_volume -title: _tools.save_volume ---- - -## h5py - -## nibabel - -## np - -## Union - -## dtype - -#### save\_volume - -```python -def save_volume(fullname_ext: str, - volume: np.ndarray, - affine_matrix: np.ndarray = None) -> Union[bool, None] -``` - -Save volume in output format. -Formats currently accepted are: nifti and hdf5. - -**Arguments** - -* **fullname_ext** (`str`): Full name of volume with extension. -* **volume** (`np.ndarray`): Volume as numpy array. -* **affine_matrix** (`np.ndarray`): Affine matrix for nifti format. - -**Returns** - -* `bool or None`: True if volume was saved successfully, None if volume could not be saved. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md deleted file mode 100644 index 28b3c17..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -sidebar_label: sparseness -title: _tools.sparseness ---- - -## np - -#### sparseness - -```python -def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray -``` - -Vector sparseness along specified dimension. - -**Arguments** - -* **W** (`np.ndarray`): Input array. -* **dim** (`int, optional`): Dimension along which to compute sparseness, by default 0. - -**Returns** - -* `np.ndarray`: Sparseness of input array along specified dimension. - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md deleted file mode 100644 index a734715..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -sidebar_label: sparseness_projection -title: _tools.sparseness_projection ---- - -## np - -#### sparseness\_projection - -```python -def sparseness_projection(Si: np.ndarray, - s: float, - at_least_as_sparse: bool = False) -> np.ndarray -``` - -Hoyer sparseness projection. - -**Arguments** - -* **Si** (`np.ndarray`): Input signal. -* **s** (`float`): Sparseness parameter. -* **at_least_as_sparse** (`bool, optional`): Enforce at least as sparse, by default False. - -**Returns** - -* `np.ndarray`: Sparse signal. - diff --git a/docs/voluseg-docs-app/docs/reference/_update.md b/docs/voluseg-docs-app/docs/reference/_update.md deleted file mode 100644 index 03ee034..0000000 --- a/docs/voluseg-docs-app/docs/reference/_update.md +++ /dev/null @@ -1,15 +0,0 @@ ---- 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step1\_process\_volumes + +## step2\_align\_volumes + +## step3\_mask\_volumes + +## step4\_detect\_cells + +## step5\_clean\_cells + +## parameter\_dictionary + +## load\_parameters + +## save\_parameters + +## load\_metadata + +## update + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/__init__.md b/docs/voluseg-docs-app/docs/reference/_steps/__init__.md new file mode 100644 index 0000000..6619ac0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: _steps +title: _steps +--- + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/_steps/step0.md new file mode 100644 index 0000000..6b623f3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step0.md @@ -0,0 +1,49 @@ +--- +sidebar_label: step0 +title: _steps.step0 +--- + +## os + +## copy + +## json + +## np + +## warn + +## load\_volume + +## get\_volume\_name + +## parameter\_dictionary + +## evenly\_parallelize + +## load\_parameters + +## save\_parameters + +## ParametersModel + +## open\_nwbfile + +## find\_nwbfile\_volume\_object\_name + +#### process\_parameters + +```python +def process_parameters(initial_parameters: dict) -> dict +``` + +Process parameters and create parameter file (pickle). + +**Arguments** + +* **initial_parameters** (`dict`): Initial parameter dictionary + +**Returns** + +* `dict`: Processed parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/_steps/step1.md new file mode 100644 index 0000000..a83feda --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step1.md @@ -0,0 +1,48 @@ +--- +sidebar_label: step1 +title: _steps.step1 +--- + +## os + +## interpolate + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## get\_volume\_name + +## ori + +## ali + +## nii + +## hdf + +## evenly\_parallelize + +## open\_nwbfile + +## get\_nwbfile\_volume + +#### process\_volumes + +```python +def process_volumes(parameters: dict) -> None +``` + +Process original volumes and save them to nifti files. +Performs downsampling and padding if specified in parameters. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/_steps/step2.md new file mode 100644 index 0000000..b372ae7 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step2.md @@ -0,0 +1,54 @@ +--- +sidebar_label: step2 +title: _steps.step2 +--- + +## os + +## h5py + +## shutil + +## np + +## io + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## ori + +## ali + +## nii + +## hdf + +## dtype + +## ants\_registration + +## ants\_transformation + +## evenly\_parallelize + +#### align\_volumes + +```python +def align_volumes(parameters: dict) -> None +``` + +Register volumes to a reference volume. +Generates ANTs transforms files (.mat). + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/_steps/step3.md new file mode 100644 index 0000000..85073bd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step3.md @@ -0,0 +1,61 @@ +--- +sidebar_label: step3 +title: _steps.step3 +--- + +## os + +## h5py + +## pyspark + +## np + +## stats + +## mixture + +## morphology + +## SimpleNamespace + +## median\_filter + +## SparkSession + +## warnings + +## matplotlib + +## plt + +## ball + +## ali + +## hdf + +## load\_volume + +## clean\_signal + +## evenly\_parallelize + +#### mask\_volumes + +```python +def mask_volumes(parameters: dict) -> None +``` + +Create intensity mask from the average registered volume. +Produces figures with masks and histograms. +Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/_steps/step4.md new file mode 100644 index 0000000..8f23d34 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4.md @@ -0,0 +1,47 @@ +--- +sidebar_label: step4 +title: _steps.step4 +--- + +## os + +## h5py + +## time + +## np + +## SimpleNamespace + +## SparkSession + +## define\_blocks + +## process\_block\_data + +## initialize\_block\_cells + +## nnmf\_sparse + +## ball + +## hdf + +## evenly\_parallelize + +#### detect\_cells + +```python +def detect_cells(parameters: dict) -> None +``` + +Detect cells in volumetric blocks. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/_steps/step4a.md new file mode 100644 index 0000000..f44a0dd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4a.md @@ -0,0 +1,37 @@ +--- +sidebar_label: step4a +title: _steps.step4a +--- + +## os + +## Tuple + +## np + +#### define\_blocks + +```python +def define_blocks( + lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, + volume_mask: np.ndarray, + volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] +``` + +Get coordinates of individual blocks. + +**Arguments** + +* **lx** (`int`): Number of voxels in x-dimension. +* **ly** (`int`): Number of voxels in y-dimension. +* **lz** (`int`): Number of voxels in z-dimension. +* **n_cells_block** (`int`): Number of cells in each block. +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **volume_mask** (`np.ndarray`): Volume mask. +* **volume_peak** (`np.ndarray`): Volume local intensity maxima (peaks). + +**Returns** + +* `Tuple[int, bool, np.ndarray, np.ndarray]`: Tuple containing: Number of blocks, valid blocks, coordinates of block start, +and coordinates of block end. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/_steps/step4b.md new file mode 100644 index 0000000..4a09d22 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4b.md @@ -0,0 +1,57 @@ +--- +sidebar_label: step4b +title: _steps.step4b +--- + +## os + +## Tuple + +## np + +## h5py + +## time + +## interpolate + +## morphology + +## SimpleNamespace + +## ali + +## hdf + +## dtype + +#### process\_block\_data + +```python +def process_block_data( + xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, + color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, + bvolume_peak: h5py.Dataset, timepoints: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Load timeseries in individual blocks, slice-time correct, and find similar timeseries. + +**Arguments** + +* **xyz0** (`Tuple[int, int, int]`): Start coordinates of block. +* **xyz1** (`Tuple[int, int, int]`): End coordinates of block. +* **parameters** (`dict`): Parameters dictionary. +* **color_i** (`int`): Color index. +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): The resolution of x, y, and z dimensions. +* **ball_diam** (`np.ndarray`): The diameter of a cell-area sphere. +* **bvolume_mean** (`h5py.Dataset`): Spark broadcast variable: volume mean. +* **bvolume_peak** (`h5py.Dataset`): Spark broadcast variable: local intensity maximum volume (peak). +* **timepoints** (`np.ndarray`): Timepoints at which segmentation will be performed. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/_steps/step4c.md new file mode 100644 index 0000000..7cad9e5 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4c.md @@ -0,0 +1,50 @@ +--- +sidebar_label: step4c +title: _steps.step4c +--- + +## os + +## Tuple + +## np + +## cluster + +## sparseness + +#### initialize\_block\_cells + +```python +def initialize_block_cells( + n_voxels_cell: int, n_voxels_block: int, n_cells: int, + voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, + peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, + lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Initialize cell positions in individual blocks. + +**Arguments** + +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **n_voxels_block** (`int`): Number of voxels in block. +* **n_cells** (`int`): Number of cells. +* **voxel_xyz** (`np.ndarray`): Voxel coordinates. +* **voxel_timeseries** (`np.ndarray`): Voxel timeseries. +* **peak_idx** (`np.ndarray`): Peak indices. +* **peak_valids** (`np.ndarray`): Valid local-intensity maxima (used to determine number of cells). +* **voxel_similarity_peak** (`np.ndarray`): Similarity between voxels: defined by the combination of spatial proximity +and temporal similarity (the voxels are neighbors of each other and also +correlated with each other). +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): Resolution of x, y, z dimensions. +* **ball_diam** (`np.ndarray`): Diameter of a sphere that may defines a cell boundary. +* **ball_diam_xyz0** (`np.ndarray`): Midpoint of the sphere. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/_steps/step4d.md new file mode 100644 index 0000000..df4c35f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4d.md @@ -0,0 +1,56 @@ +--- +sidebar_label: step4d +title: _steps.step4d +--- + +## os + +## Tuple + +## np + +## stats + +## linalg + +## measure + +## sparseness\_projection + +#### nnmf\_sparse + +```python +def nnmf_sparse( + V0: np.ndarray, + XYZ0: np.ndarray, + W0: np.ndarray, + B0: np.ndarray, + S0: np.ndarray, + tolfun: float = 1e-4, + miniter: int = 10, + maxiter: int = 100, + timeseries_mean=1.0, + timepoints: np.ndarray = None, + verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] +``` + +Cell detection via nonnegative matrix factorization with sparseness projection. + +**Arguments** + +* **V0** (`np.ndarray`): Voxel timeseries (voxel_timeseries_valid). +* **XYZ0** (`np.ndarray`): Voxel coordinates (voxel_xyz_valid). +* **W0** (`np.ndarray`): Initial cell weights (cell_weight_init_valid). +* **B0** (`np.ndarray`): Cell neighborhood (cell_neighborhood_valid). +* **S0** (`np.ndarray`): Cell sparseness (cell_sparseness). +* **tolfun** (`float, optional`): Tolerance for convergence, by default 1e-4. +* **miniter** (`int, optional`): Minimum number of iterations, by default 10. +* **maxiter** (`int, optional`): Maximum number of iterations, by default 100. +* **timeseries_mean** (`float, optional`): Mean timeseries value, by default 1.0. +* **timepoints** (`np.ndarray, optional`): Timepoints to use, by default None. +* **verbosity** (`bool, optional`): Print progress, by default True. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, float]`: Tuple containing: Spatial footprint, temporal footprint, convergence error. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/_steps/step4e.md new file mode 100644 index 0000000..b3d4633 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step4e.md @@ -0,0 +1,42 @@ +--- +sidebar_label: step4e +title: _steps.step4e +--- + +## os + +## h5py + +## np + +## SimpleNamespace + +## Tuple + +## pyspark + +## SparkSession + +## hdf + +## evenly\_parallelize + +#### collect\_blocks + +```python +def collect_blocks( + color_i: int, parameters: dict +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Collect cells across all blocks. + +**Arguments** + +* **color_i** (`int`): Color index. +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/_steps/step5.md new file mode 100644 index 0000000..3dd7efb --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_steps/step5.md @@ -0,0 +1,47 @@ +--- +sidebar_label: step5 +title: _steps.step5 +--- + +## os + +## h5py + +## shutil + +## np + +## SimpleNamespace + +## combinations + +## SparkSession + +## collect\_blocks + +## hdf + +## dtype + +## clean\_signal + +## evenly\_parallelize + +## write\_nwbfile + +#### clean\_cells + +```python +def clean_cells(parameters: dict) -> None +``` + +Remove noise cells, detrend and detect baseline. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md new file mode 100644 index 0000000..077ce2b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md @@ -0,0 +1,7 @@ +--- +sidebar_label: _tools +title: _tools +--- + +## download\_sample\_data + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md new file mode 100644 index 0000000..5e0ac97 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md @@ -0,0 +1,37 @@ +--- +sidebar_label: ants_registration +title: _tools.ants_registration +--- + +## os + +#### ants\_registration + +```python +def ants_registration(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + prefix_out_tform: str, + typ: str, + in_tform: str = None, + restrict: str = None) -> str +``` + +ANTs registration. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs directory. +* **in_nii** (`str`): Input nifti file. +* **ref_nii** (`str`): Reference nifti file. +* **out_nii** (`str`): Output nifti file. +* **prefix_out_tform** (`str`): Prefix for output transformation files. +* **typ** (`str`): Type of transformation. +* **in_tform** (`str (optional)`): Initial transformation file. Default is None. +* **restrict** (`str (optional)`): Restrict deformation. Default is None. + +**Returns** + +* `str`: ANTs registration command. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md new file mode 100644 index 0000000..5bfcbe7 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md @@ -0,0 +1,33 @@ +--- +sidebar_label: ants_transformation +title: _tools.ants_transformation +--- + +## os + +#### ants\_transformation + +```python +def ants_transformation(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + in_tform: str, + interpolation="Linear") -> str +``` + +Application of ANTs transform. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs binaries. +* **in_nii** (`str`): Path to input nifti file. +* **ref_nii** (`str`): Path to reference nifti file. +* **out_nii** (`str`): Path to output nifti file. +* **in_tform** (`str`): Path to input transform file (.mat). +* **interpolation** (`str`): Interpolation method. + +**Returns** + +* `str`: ANTs transformation command string. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/_tools/aws.md new file mode 100644 index 0000000..beb6fb2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/aws.md @@ -0,0 +1,54 @@ +--- +sidebar_label: aws +title: _tools.aws +--- + +## boto3 + +## datetime + +## timezone + +## JobDefinitionException Objects + +```python +class JobDefinitionException(Exception) +``` + +#### format\_voluseg\_kwargs + +```python +def format_voluseg_kwargs(voluseg_kwargs: dict) -> dict +``` + +#### run\_job\_in\_aws\_batch + +```python +def run_job_in_aws_batch(job_name_prefix: str, + voluseg_kwargs: dict, + aws_local_profile: str = None, + vcpus: int = 32, + memory: int = 65536) +``` + +Submit a Voluseg job to AWS Batch. + +**Arguments** + +* **job_name_prefix** (`str`): Job name prefix, it will be concatenated with the current timestamp. +Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" +* **voluseg_kwargs** (`dict`): Voluseg parameters. +* **aws_local_profile** (`str`): AWS profile name. Default is None. +* **vcpus** (`int`): Number of vCPUs. Default is 32. +* **memory** (`int`): Memory in MB. Default is 65536. + +**Returns** + +* `dict`: Dictionary with the job_name and batch_job_id. + +#### export\_to\_s3 + +```python +def export_to_s3(local_path: str, bucket_name: str, object_name: str) +``` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/_tools/ball.md new file mode 100644 index 0000000..807fedd --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/ball.md @@ -0,0 +1,24 @@ +--- +sidebar_label: ball +title: _tools.ball +--- + +## np + +#### ball + +```python +def ball(radi: float, affine_matrix: np.ndarray) -> tuple +``` + +Morphological cell balls and midpoints. + +**Arguments** + +* **radi** (`float`): Radius of ball. +* **affine_matrix** (`np.ndarray`): Affine matrix. + +**Returns** + +* `tuple`: Tuple containing: Ball and midpoints. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md new file mode 100644 index 0000000..c98eee8 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md @@ -0,0 +1,39 @@ +--- +sidebar_label: clean_signal +title: _tools.clean_signal +--- + +## os + +## Tuple + +## np + +## pd + +## signal + +## winsorize + +## dtype + +## SimpleNamespace + +#### clean\_signal + +```python +def clean_signal(parameters: dict, + timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] +``` + +Detrend, filter, and estimate dynamic baseline for input timeseries. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **timeseries** (`np.ndarray`): Input timeseries. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/constants.md b/docs/voluseg-docs-app/docs/reference/_tools/constants.md new file mode 100644 index 0000000..b3218c9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/constants.md @@ -0,0 +1,15 @@ +--- +sidebar_label: constants +title: _tools.constants +--- + +#### ori + +#### ali + +#### nii + +#### hdf + +#### dtype + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md new file mode 100644 index 0000000..1408839 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md @@ -0,0 +1,27 @@ +--- +sidebar_label: evenly_parallelize +title: _tools.evenly_parallelize +--- + +## np + +## SparkSession + +## RDD + +#### evenly\_parallelize + +```python +def evenly_parallelize(input_list: list) -> RDD +``` + +Return evenly partitioned spark resilient distributed dataset (RDD). + +**Arguments** + +* **input_list** (`list`): List of input elements. + +**Returns** + +* `RDD`: Spark resilient distributed dataset (RDD). + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md new file mode 100644 index 0000000..1792dda --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md @@ -0,0 +1,27 @@ +--- +sidebar_label: get_volume_name +title: _tools.get_volume_name +--- + +## os + +#### get\_volume\_name + +```python +def get_volume_name(fullname_volume: str, + dir_prefix: str = None, + plane_i: int = None) -> str +``` + +Get name of volume (with directory prefix and plane suffix). + +**Arguments** + +* **fullname_volume** (`str`): Full name of volume. +* **dir_prefix** (`str (optional)`): Prefix for directory. Default is None. +* **plane_i** (`int (optional)`): Index of plane. Default is None. + +**Returns** + +* `str`: Name of volume. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md new file mode 100644 index 0000000..aa404ad --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md @@ -0,0 +1,28 @@ +--- +sidebar_label: load_metadata +title: _tools.load_metadata +--- + +## np + +## ElementTree + +#### load\_metadata + +```python +def load_metadata(parameters: dict, filename_channel: str, + filename_stack: str) -> dict +``` + +Fetch z-resolution, exposure time, and stack frequency. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename_channel** (`str`): Filename XML file containing channel information. +* **filename_stack** (`str`): Filename of XML file containing stack information. + +**Returns** + +* `dict`: Parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md new file mode 100644 index 0000000..5c882c9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md @@ -0,0 +1,32 @@ +--- +sidebar_label: load_volume +title: _tools.load_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### load\_volume + +```python +def load_volume(fullname_ext: str) -> Union[np.ndarray, None] +``` + +Load volume based on input name and extension. +Supports tiff, hdf5, klb, and nifti formats. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. + +**Returns** + +* `np.ndarray or None`: Volume as numpy array, or None if volume could not be loaded. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md new file mode 100644 index 0000000..cee4840 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/nwb.md @@ -0,0 +1,129 @@ +--- +sidebar_label: nwb +title: _tools.nwb +--- + +## pynwb + +## contextmanager + +## datetime + +## tzlocal + +## uuid4 + +## np + +#### open\_nwbfile\_local + +```python +@contextmanager +def open_nwbfile_local(file_path: str) +``` + +Context manager to open and close a local NWB file. + +**Arguments** + +* **file_path** (`str`): Path to NWB file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile\_remote + +```python +@contextmanager +def open_nwbfile_remote(s3_url: str, output_path: str) +``` + +Context manager to open and close a remote NWB file. + +**Arguments** + +* **s3_url** (`str`): S3 URL to NWB file. +* **output_path** (`str`): Output path to cache the remote file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile + +```python +@contextmanager +def open_nwbfile(input_path: str, remote: bool, output_path: str = None) +``` + +Open and close an NWB file from either a local or remote source. + +**Arguments** + +* **input_path** (`str`): Path to the NWB file. This can be a local file path or an S3 URL. +* **remote** (`bool`): If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. +* **output_path** (`str`): Output path, only used to cache remote files. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### find\_nwbfile\_volume\_object\_name + +```python +def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str +``` + +Find the name of the `TwoPhotonSeries` volume object in the NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. + +**Returns** + +* `str`: Name of the volume object. + +#### get\_nwbfile\_volume + +```python +def get_nwbfile_volume( + nwbfile: pynwb.NWBFile, + acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile +``` + +Get `TwoPhotonSeries` object from NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. +* **acquisition_name** (`str (default: "TwoPhotonSeries")`): Acquisition name. + +**Returns** + +* `pynwb.NWBFile`: NWB file. + +#### write\_nwbfile + +```python +def write_nwbfile(output_path: str, cell_x: np.ndarray, cell_y: np.ndarray, + cell_z: np.ndarray, cell_weights: np.ndarray, + cell_timeseries: np.ndarray) -> None +``` + +Write results to a local NWB file. + +**Arguments** + +* **output_path** (`str`): Output path. +* **cell_x** (`np.ndarray`): Voxel X coordinates for all cells. +* **cell_y** (`np.ndarray`): Voxel Y coordinates for all cells. +* **cell_z** (`np.ndarray`): Voxel Z coordinates for all cells. +* **cell_weights** (`np.ndarray`): Voxel weights for all cells. +* **cell_timeseries** (`np.ndarray`): Fluorescence timeseries data for all cells. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md new file mode 100644 index 0000000..f0dd2f9 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md @@ -0,0 +1,89 @@ +--- +sidebar_label: parameter_dictionary +title: _tools.parameter_dictionary +--- + +## Union + +## ParametersModel + +#### parameter\_dictionary + +```python +def parameter_dictionary(detrending: str = "standard", + registration: str = "medium", + registration_restrict: str = "", + diam_cell: float = 6.0, + dir_ants: str = "", + dir_input: str = "", + dir_output: str = "", + dir_transform: str = "", + ds: int = 2, + planes_pad: int = 0, + planes_packed: bool = False, + parallel_clean: bool = True, + parallel_volume: bool = True, + save_volume: bool = False, + type_timepoints: str = "dff", + type_mask: str = "geomean", + timepoints: int = 1000, + f_hipass: float = 0, + f_volume: float = 2.0, + n_cells_block: int = 316, + n_colors: int = 1, + res_x: float = 0.40625, + res_y: float = 0.40625, + res_z: float = 5.0, + t_baseline: int = 300, + t_section: float = 0.01, + thr_mask: float = 0.5, + volume_fullnames_input: Union[list[str], None] = None, + volume_names: Union[list[str], None] = None, + input_dirs: Union[list[str], None] = None, + ext: Union[str, None] = None, + lt: Union[int, None] = None, + affine_matrix: Union[list, None] = None) -> dict +``` + +Return a parameter dictionary with specified defaults. + +**Arguments** + +* **detrending** (`str, optional`): Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +* **registration** (`str, optional`): Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +* **registration_restrict** (`str, optional`): Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +* **diam_cell** (`float, optional`): Cell diameter in microns (default is 6.0). +* **dir_ants** (`str, optional`): Path to the ANTs directory (default is an empty string). +* **dir_input** (`str, optional`): Path to input directories, separate multiple directories with ';' (default is an empty string). +* **dir_output** (`str, optional`): Path to the output directory (default is an empty string). +* **dir_transform** (`str, optional`): Path to the transform directory (default is an empty string). +* **ds** (`int, optional`): Spatial coarse-graining in x-y dimension (default is 2). +* **planes_pad** (`int, optional`): Number of planes to pad the volume with for robust registration (default is 0). +* **planes_packed** (`bool, optional`): Packed planes in each volume, for single plane imaging with packed planes (default is False). +* **parallel_clean** (`bool, optional`): Parallelization of final cleaning (True is fast but memory-intensive, default is True). +* **parallel_volume** (`bool, optional`): Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +* **save_volume** (`bool, optional`): Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +* **type_timepoints** (`str, optional`): Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +* **type_mask** (`str, optional`): Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +* **timepoints** (`int, optional`): Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +* **f_hipass** (`float, optional`): Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +* **f_volume** (`float, optional`): Imaging frequency in Hz (default is 2.0). +* **n_cells_block** (`int, optional`): Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +* **n_colors** (`int, optional`): Number of brain colors (2 in two-color volumes, default is 1). +* **res_x** (`float, optional`): X resolution in microns (default is 0.40625). +* **res_y** (`float, optional`): Y resolution in microns (default is 0.40625). +* **res_z** (`float, optional`): Z resolution in microns (default is 5.0). +* **t_baseline** (`int, optional`): Interval for baseline calculation in seconds (default is 300). +* **t_section** (`float, optional`): Exposure time in seconds for slice acquisition (default is 0.01). +* **thr_mask** (`float, optional`): Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +* **volume_fullnames_input** (`list[str], optional`): List of full volume names (default is None). +* **volume_names** (`list[str], optional`): List of volume names (default is None). +* **input_dirs** (`list[str], optional`): List of input directories (default is None). +* **ext** (`str, optional`): File extension (default is None). +* **lt** (`int, optional`): Number of volumes (default is None). +* **affine_matrix** (`list, optional`): Affine matrix (default is None). + +**Returns** + +* `dict`: A dictionary of validated parameters with their default values. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters.md new file mode 100644 index 0000000..79a3e8b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameters.md @@ -0,0 +1,44 @@ +--- +sidebar_label: parameters +title: _tools.parameters +--- + +## pickle + +## json + +## ParametersModel + +#### load\_parameters + +```python +def load_parameters(filename: str) -> dict +``` + +Load previously saved parameters from filename. + +**Arguments** + +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `dict`: Parameters dictionary. + +#### save\_parameters + +```python +def save_parameters(parameters: dict, filename: str) -> None +``` + +Save parameters to filename. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md new file mode 100644 index 0000000..b358b9f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md @@ -0,0 +1,173 @@ +--- +sidebar_label: parameters_models +title: _tools.parameters_models +--- + +## Enum + +## np + +## BaseModel + +## Field + +## model\_validator + +## Optional + +## Detrending Objects + +```python +class Detrending(str, Enum) +``` + +#### standard + +#### robust + +#### none + +## Registration Objects + +```python +class Registration(str, Enum) +``` + +#### high + +#### medium + +#### low + +#### none + +## TypeTimepoints Objects + +```python +class TypeTimepoints(str, Enum) +``` + +#### dff + +#### periodic + +#### custom + +## TypeMask Objects + +```python +class TypeMask(str, Enum) +``` + +#### mean + +#### geomean + +#### max + +## ParametersModel Objects + +```python +class ParametersModel(BaseModel) +``` + +#### detrending + +#### registration + +#### registration\_restrict + +#### diam\_cell + +#### dir\_ants + +#### dir\_input + +#### dir\_output + +#### dir\_transform + +#### ds + +#### planes\_pad + +#### planes\_packed + +#### parallel\_clean + +#### parallel\_volume + +#### save\_volume + +#### type\_timepoints + +#### type\_mask + +#### timepoints + +#### f\_hipass + +#### f\_volume + +#### n\_cells\_block + +#### n\_colors + +#### res\_x + +#### res\_y + +#### res\_z + +#### t\_baseline + +#### t\_section + +#### thr\_mask + +#### volume\_fullnames\_input + +#### volume\_names + +#### input\_dirs + +#### ext + +#### lt + +#### affine\_matrix + +#### dim\_order + +#### remote + +#### output\_to\_nwb + +#### convert\_array\_to\_list + +```python +@model_validator(mode="before") +def convert_array_to_list(cls, values) +``` + +Validator to automatically convert NumPy arrays to lists. + +#### model\_dump + +```python +def model_dump(use_np_array: bool = True, *args, **kwargs) +``` + +Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) +and Enums to their values. + +**Arguments** + +* **use_np_array** (`bool, optional`): Convert lists to NumPy arrays (default is True) +* ***args**: Positional arguments to pass to the parent class +* ****kwargs**: Keyword arguments to pass to the parent class + +**Returns** + +* `dict`: A dictionary of the model's data + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md new file mode 100644 index 0000000..bd3d6a0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md @@ -0,0 +1,71 @@ +--- +sidebar_label: sample_data +title: _tools.sample_data +--- + +## requests + +## zipfile + +## os + +## Path + +## Union + +#### download\_sample\_data + +```python +def download_sample_data(destination_folder: str = ".", + data_type: str = "h5_dir") -> Union[str, None] +``` + +Download sample data for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. +* **data_type** (`str, optional`): Type of data to download. Options are "h5_dir" and "nwb_file". + +**Returns** + +* `str or None`: Path to the folder or file where the data was downloaded, or None if the download failed. + +#### download\_sample\_data\_nwb\_file + +```python +def download_sample_data_nwb_file( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample NWB file for Voluseg. +Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the downloaded file, or None if the download failed. + +#### download\_sample\_data\_h5\_dir + +```python +def download_sample_data_h5_dir( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample data (h5 directory) for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the folder where the data was extracted, or None if the download failed. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md new file mode 100644 index 0000000..f7c50f6 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md @@ -0,0 +1,36 @@ +--- +sidebar_label: save_volume +title: _tools.save_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### save\_volume + +```python +def save_volume(fullname_ext: str, + volume: np.ndarray, + affine_matrix: np.ndarray = None) -> Union[bool, None] +``` + +Save volume in output format. +Formats currently accepted are: nifti and hdf5. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. +* **volume** (`np.ndarray`): Volume as numpy array. +* **affine_matrix** (`np.ndarray`): Affine matrix for nifti format. + +**Returns** + +* `bool or None`: True if volume was saved successfully, None if volume could not be saved. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md new file mode 100644 index 0000000..28b3c17 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md @@ -0,0 +1,24 @@ +--- +sidebar_label: sparseness +title: _tools.sparseness +--- + +## np + +#### sparseness + +```python +def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray +``` + +Vector sparseness along specified dimension. + +**Arguments** + +* **W** (`np.ndarray`): Input array. +* **dim** (`int, optional`): Dimension along which to compute sparseness, by default 0. + +**Returns** + +* `np.ndarray`: Sparseness of input array along specified dimension. + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md new file mode 100644 index 0000000..a734715 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md @@ -0,0 +1,27 @@ +--- +sidebar_label: sparseness_projection +title: _tools.sparseness_projection +--- + +## np + +#### sparseness\_projection + +```python +def sparseness_projection(Si: np.ndarray, + s: float, + at_least_as_sparse: bool = False) -> np.ndarray +``` + +Hoyer sparseness projection. + +**Arguments** + +* **Si** (`np.ndarray`): Input signal. +* **s** (`float`): Sparseness parameter. +* **at_least_as_sparse** (`bool, optional`): Enforce at least as sparse, by default False. + +**Returns** + +* `np.ndarray`: Sparse signal. + diff --git a/docs/voluseg-docs-app/docs/reference/_update.md b/docs/voluseg-docs-app/docs/reference/_update.md new file mode 100644 index 0000000..03ee034 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/_update.md @@ -0,0 +1,15 @@ +--- +sidebar_label: _update +title: _update +--- + +## os + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From 5a4120add515127dced074a764f62ee09ca5fd8f Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 11:14:54 +0100 Subject: [PATCH 09/27] rename modules --- README.md | 2 +- app/app.py | 2 +- .../docs/getting_started/iac_aws_batch.md | 2 +- .../docs/getting_started/running.mdx | 2 +- src/voluseg/__init__.py | 20 +++++++++---------- src/voluseg/{_steps => steps}/__init__.py | 0 src/voluseg/{_steps => steps}/step0.py | 14 ++++++------- src/voluseg/{_steps => steps}/step1.py | 12 +++++------ src/voluseg/{_steps => steps}/step2.py | 12 +++++------ src/voluseg/{_steps => steps}/step3.py | 10 +++++----- src/voluseg/{_steps => steps}/step4.py | 14 ++++++------- src/voluseg/{_steps => steps}/step4a.py | 0 src/voluseg/{_steps => steps}/step4b.py | 2 +- src/voluseg/{_steps => steps}/step4c.py | 2 +- src/voluseg/{_steps => steps}/step4d.py | 2 +- src/voluseg/{_steps => steps}/step4e.py | 4 ++-- src/voluseg/{_steps => steps}/step5.py | 10 +++++----- src/voluseg/{_tools => tools}/__init__.py | 0 .../{_tools => tools}/ants_registration.py | 0 .../{_tools => tools}/ants_transformation.py | 0 src/voluseg/{_tools => tools}/aws.py | 0 src/voluseg/{_tools => tools}/ball.py | 0 src/voluseg/{_tools => tools}/clean_signal.py | 2 +- src/voluseg/{_tools => tools}/constants.py | 0 .../{_tools => tools}/evenly_parallelize.py | 0 .../{_tools => tools}/get_volume_name.py | 0 .../{_tools => tools}/load_metadata.py | 0 src/voluseg/{_tools => tools}/load_volume.py | 2 +- src/voluseg/{_tools => tools}/nwb.py | 0 .../{_tools => tools}/parameter_dictionary.py | 2 +- src/voluseg/{_tools => tools}/parameters.py | 2 +- .../{_tools => tools}/parameters_models.py | 0 src/voluseg/{_tools => tools}/sample_data.py | 0 src/voluseg/{_tools => tools}/save_volume.py | 2 +- src/voluseg/{_tools => tools}/sparseness.py | 0 .../sparseness_projection.py | 0 src/voluseg/{_update.py => update.py} | 0 tests/test_voluseg.py | 4 ++-- 38 files changed, 62 insertions(+), 62 deletions(-) rename src/voluseg/{_steps => steps}/__init__.py (100%) rename src/voluseg/{_steps => steps}/step0.py (95%) rename src/voluseg/{_steps => steps}/step1.py (94%) rename src/voluseg/{_steps => steps}/step2.py (94%) rename src/voluseg/{_steps => steps}/step3.py (97%) rename src/voluseg/{_steps => steps}/step4.py (96%) rename src/voluseg/{_steps => steps}/step4a.py (100%) rename src/voluseg/{_steps => steps}/step4b.py (98%) rename src/voluseg/{_steps => steps}/step4c.py (98%) rename src/voluseg/{_steps => steps}/step4d.py (98%) rename src/voluseg/{_steps => steps}/step4e.py (97%) rename src/voluseg/{_steps => steps}/step5.py (96%) rename src/voluseg/{_tools => tools}/__init__.py (100%) rename src/voluseg/{_tools => tools}/ants_registration.py (100%) rename src/voluseg/{_tools => tools}/ants_transformation.py (100%) rename src/voluseg/{_tools => tools}/aws.py (100%) rename src/voluseg/{_tools => tools}/ball.py (100%) rename src/voluseg/{_tools => tools}/clean_signal.py (98%) rename src/voluseg/{_tools => tools}/constants.py (100%) rename src/voluseg/{_tools => tools}/evenly_parallelize.py (100%) rename src/voluseg/{_tools => tools}/get_volume_name.py (100%) rename src/voluseg/{_tools => tools}/load_metadata.py (100%) rename src/voluseg/{_tools => tools}/load_volume.py (97%) rename src/voluseg/{_tools => tools}/nwb.py (100%) rename src/voluseg/{_tools => tools}/parameter_dictionary.py (98%) rename src/voluseg/{_tools => tools}/parameters.py (96%) rename src/voluseg/{_tools => tools}/parameters_models.py (100%) rename src/voluseg/{_tools => tools}/sample_data.py (100%) rename src/voluseg/{_tools => tools}/save_volume.py (96%) rename src/voluseg/{_tools => tools}/sparseness.py (100%) rename src/voluseg/{_tools => tools}/sparseness_projection.py (100%) rename src/voluseg/{_update.py => update.py} (100%) diff --git a/README.md b/README.md index f36cbae..79978ca 100755 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ import voluseg voluseg.update() # Download sample data -voluseg._tools.download_sample_data("/path/to/input/") +voluseg.tools.download_sample_data("/path/to/input/") # set and save parameters parameters0 = voluseg.parameter_dictionary() diff --git a/app/app.py b/app/app.py index 557d68e..a59c8d4 100644 --- a/app/app.py +++ b/app/app.py @@ -2,7 +2,7 @@ import typer from typing_extensions import Annotated import voluseg -from voluseg._tools.aws import export_to_s3 +from voluseg.tools.aws import export_to_s3 app = typer.Typer() diff --git a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md index 8e1d082..41890c6 100644 --- a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md +++ b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md @@ -53,7 +53,7 @@ This deployment will create the following AWS resources in your account: Voluseg provides an utility function to submit jobs to AWS Batch. You can use this function to submit jobs from your local machine. You must provide the url of the remote file stored in S3, plus any other voluseg arguments you want to pass to the job. Example: ```python -from voluseg._tools.aws import run_job_in_aws_batch +from voluseg.tools.aws import run_job_in_aws_batch r = run_job_in_aws_batch( job_name="my-voluseg-job", diff --git a/docs/voluseg-docs-app/docs/getting_started/running.mdx b/docs/voluseg-docs-app/docs/getting_started/running.mdx index e758d27..d245fe3 100644 --- a/docs/voluseg-docs-app/docs/getting_started/running.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/running.mdx @@ -25,7 +25,7 @@ To run the demo you will need start by downloading the sample data to your local import voluseg # Download sample data -voluseg._tools.download_sample_data("/path/to/input/") +voluseg.tools.download_sample_data("/path/to/input/") ``` ### Setup pipeline parameters diff --git a/src/voluseg/__init__.py b/src/voluseg/__init__.py index f834840..aa0d323 100644 --- a/src/voluseg/__init__.py +++ b/src/voluseg/__init__.py @@ -1,14 +1,14 @@ """initialization""" -from voluseg._steps.step0 import process_parameters as step0_process_parameters -from voluseg._steps.step1 import process_volumes as step1_process_volumes -from voluseg._steps.step2 import align_volumes as step2_align_volumes -from voluseg._steps.step3 import mask_volumes as step3_mask_volumes -from voluseg._steps.step4 import detect_cells as step4_detect_cells -from voluseg._steps.step5 import clean_cells as step5_clean_cells +from voluseg.steps.step0 import process_parameters as step0_process_parameters +from voluseg.steps.step1 import process_volumes as step1_process_volumes +from voluseg.steps.step2 import align_volumes as step2_align_volumes +from voluseg.steps.step3 import mask_volumes as step3_mask_volumes +from voluseg.steps.step4 import detect_cells as step4_detect_cells +from voluseg.steps.step5 import clean_cells as step5_clean_cells -from voluseg._tools.parameter_dictionary import parameter_dictionary -from voluseg._tools.parameters import load_parameters, save_parameters -from voluseg._tools.load_metadata import load_metadata +from voluseg.tools.parameter_dictionary import parameter_dictionary +from voluseg.tools.parameters import load_parameters, save_parameters +from voluseg.tools.load_metadata import load_metadata -from voluseg._update import voluseg_update as update +from src.voluseg.update import voluseg_update as update diff --git a/src/voluseg/_steps/__init__.py b/src/voluseg/steps/__init__.py similarity index 100% rename from src/voluseg/_steps/__init__.py rename to src/voluseg/steps/__init__.py diff --git a/src/voluseg/_steps/step0.py b/src/voluseg/steps/step0.py similarity index 95% rename from src/voluseg/_steps/step0.py rename to src/voluseg/steps/step0.py index 57a3949..3cb1270 100644 --- a/src/voluseg/_steps/step0.py +++ b/src/voluseg/steps/step0.py @@ -3,13 +3,13 @@ import json import numpy as np from warnings import warn -from voluseg._tools.load_volume import load_volume -from voluseg._tools.get_volume_name import get_volume_name -from voluseg._tools.parameter_dictionary import parameter_dictionary -from voluseg._tools.evenly_parallelize import evenly_parallelize -from voluseg._tools.parameters import load_parameters, save_parameters -from voluseg._tools.parameters_models import ParametersModel -from voluseg._tools.nwb import open_nwbfile, find_nwbfile_volume_object_name +from voluseg.tools.load_volume import load_volume +from voluseg.tools.get_volume_name import get_volume_name +from voluseg.tools.parameter_dictionary import parameter_dictionary +from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.parameters import load_parameters, save_parameters +from voluseg.tools.parameters_models import ParametersModel +from voluseg.tools.nwb import open_nwbfile, find_nwbfile_volume_object_name def process_parameters(initial_parameters: dict) -> dict: diff --git a/src/voluseg/_steps/step1.py b/src/voluseg/steps/step1.py similarity index 94% rename from src/voluseg/_steps/step1.py rename to src/voluseg/steps/step1.py index 1043637..acbcbee 100644 --- a/src/voluseg/_steps/step1.py +++ b/src/voluseg/steps/step1.py @@ -1,12 +1,12 @@ import os from scipy import interpolate from types import SimpleNamespace -from voluseg._tools.load_volume import load_volume -from voluseg._tools.save_volume import save_volume -from voluseg._tools.get_volume_name import get_volume_name -from voluseg._tools.constants import ori, ali, nii, hdf -from voluseg._tools.evenly_parallelize import evenly_parallelize -from voluseg._tools.nwb import open_nwbfile, get_nwbfile_volume +from voluseg.tools.load_volume import load_volume +from voluseg.tools.save_volume import save_volume +from voluseg.tools.get_volume_name import get_volume_name +from voluseg.tools.constants import ori, ali, nii, hdf +from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.nwb import open_nwbfile, get_nwbfile_volume def process_volumes(parameters: dict) -> None: diff --git a/src/voluseg/_steps/step2.py b/src/voluseg/steps/step2.py similarity index 94% rename from src/voluseg/_steps/step2.py rename to src/voluseg/steps/step2.py index 25cedde..880f27d 100644 --- a/src/voluseg/_steps/step2.py +++ b/src/voluseg/steps/step2.py @@ -4,12 +4,12 @@ import numpy as np from scipy import io from types import SimpleNamespace -from voluseg._tools.load_volume import load_volume -from voluseg._tools.save_volume import save_volume -from voluseg._tools.constants import ori, ali, nii, hdf, dtype -from voluseg._tools.ants_registration import ants_registration -from voluseg._tools.ants_transformation import ants_transformation -from voluseg._tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.load_volume import load_volume +from voluseg.tools.save_volume import save_volume +from voluseg.tools.constants import ori, ali, nii, hdf, dtype +from voluseg.tools.ants_registration import ants_registration +from voluseg.tools.ants_transformation import ants_transformation +from voluseg.tools.evenly_parallelize import evenly_parallelize def align_volumes(parameters: dict) -> None: diff --git a/src/voluseg/_steps/step3.py b/src/voluseg/steps/step3.py similarity index 97% rename from src/voluseg/_steps/step3.py rename to src/voluseg/steps/step3.py index d299490..8476700 100644 --- a/src/voluseg/_steps/step3.py +++ b/src/voluseg/steps/step3.py @@ -16,11 +16,11 @@ matplotlib.use("Agg") import matplotlib.pyplot as plt -from voluseg._tools.ball import ball -from voluseg._tools.constants import ali, hdf -from voluseg._tools.load_volume import load_volume -from voluseg._tools.clean_signal import clean_signal -from voluseg._tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.ball import ball +from voluseg.tools.constants import ali, hdf +from voluseg.tools.load_volume import load_volume +from voluseg.tools.clean_signal import clean_signal +from voluseg.tools.evenly_parallelize import evenly_parallelize def mask_volumes(parameters: dict) -> None: diff --git a/src/voluseg/_steps/step4.py b/src/voluseg/steps/step4.py similarity index 96% rename from src/voluseg/_steps/step4.py rename to src/voluseg/steps/step4.py index cc44976..e693e63 100644 --- a/src/voluseg/_steps/step4.py +++ b/src/voluseg/steps/step4.py @@ -5,13 +5,13 @@ from types import SimpleNamespace from pyspark.sql.session import SparkSession -from voluseg._steps.step4a import define_blocks -from voluseg._steps.step4b import process_block_data -from voluseg._steps.step4c import initialize_block_cells -from voluseg._steps.step4d import nnmf_sparse -from voluseg._tools.ball import ball -from voluseg._tools.constants import hdf -from voluseg._tools.evenly_parallelize import evenly_parallelize +from voluseg.steps.step4a import define_blocks +from voluseg.steps.step4b import process_block_data +from voluseg.steps.step4c import initialize_block_cells +from voluseg.steps.step4d import nnmf_sparse +from voluseg.tools.ball import ball +from voluseg.tools.constants import hdf +from voluseg.tools.evenly_parallelize import evenly_parallelize def detect_cells(parameters: dict) -> None: diff --git a/src/voluseg/_steps/step4a.py b/src/voluseg/steps/step4a.py similarity index 100% rename from src/voluseg/_steps/step4a.py rename to src/voluseg/steps/step4a.py diff --git a/src/voluseg/_steps/step4b.py b/src/voluseg/steps/step4b.py similarity index 98% rename from src/voluseg/_steps/step4b.py rename to src/voluseg/steps/step4b.py index a9e8c96..30ebcbb 100644 --- a/src/voluseg/_steps/step4b.py +++ b/src/voluseg/steps/step4b.py @@ -14,7 +14,7 @@ from scipy import interpolate from skimage import morphology from types import SimpleNamespace -from voluseg._tools.constants import ali, hdf, dtype +from voluseg.tools.constants import ali, hdf, dtype def process_block_data( diff --git a/src/voluseg/_steps/step4c.py b/src/voluseg/steps/step4c.py similarity index 98% rename from src/voluseg/_steps/step4c.py rename to src/voluseg/steps/step4c.py index e0ecabd..5089780 100644 --- a/src/voluseg/_steps/step4c.py +++ b/src/voluseg/steps/step4c.py @@ -10,7 +10,7 @@ import numpy as np from sklearn import cluster -from voluseg._tools.sparseness import sparseness +from voluseg.tools.sparseness import sparseness def initialize_block_cells( diff --git a/src/voluseg/_steps/step4d.py b/src/voluseg/steps/step4d.py similarity index 98% rename from src/voluseg/_steps/step4d.py rename to src/voluseg/steps/step4d.py index 9964d8f..cfe0a96 100644 --- a/src/voluseg/_steps/step4d.py +++ b/src/voluseg/steps/step4d.py @@ -12,7 +12,7 @@ from scipy import stats from scipy import linalg from skimage import measure -from voluseg._tools.sparseness_projection import sparseness_projection +from voluseg.tools.sparseness_projection import sparseness_projection def nnmf_sparse( diff --git a/src/voluseg/_steps/step4e.py b/src/voluseg/steps/step4e.py similarity index 97% rename from src/voluseg/_steps/step4e.py rename to src/voluseg/steps/step4e.py index 0e62991..00fcfe6 100644 --- a/src/voluseg/_steps/step4e.py +++ b/src/voluseg/steps/step4e.py @@ -6,8 +6,8 @@ import pyspark from pyspark.sql.session import SparkSession -from voluseg._tools.constants import hdf -from voluseg._tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.constants import hdf +from voluseg.tools.evenly_parallelize import evenly_parallelize def collect_blocks( diff --git a/src/voluseg/_steps/step5.py b/src/voluseg/steps/step5.py similarity index 96% rename from src/voluseg/_steps/step5.py rename to src/voluseg/steps/step5.py index 695e1fd..30954de 100644 --- a/src/voluseg/_steps/step5.py +++ b/src/voluseg/steps/step5.py @@ -6,11 +6,11 @@ from itertools import combinations from pyspark.sql.session import SparkSession -from voluseg._steps.step4e import collect_blocks -from voluseg._tools.constants import hdf, dtype -from voluseg._tools.clean_signal import clean_signal -from voluseg._tools.evenly_parallelize import evenly_parallelize -from voluseg._tools.nwb import write_nwbfile +from voluseg.steps.step4e import collect_blocks +from voluseg.tools.constants import hdf, dtype +from voluseg.tools.clean_signal import clean_signal +from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.nwb import write_nwbfile def clean_cells(parameters: dict) -> None: diff --git a/src/voluseg/_tools/__init__.py b/src/voluseg/tools/__init__.py similarity index 100% rename from src/voluseg/_tools/__init__.py rename to src/voluseg/tools/__init__.py diff --git a/src/voluseg/_tools/ants_registration.py b/src/voluseg/tools/ants_registration.py similarity index 100% rename from src/voluseg/_tools/ants_registration.py rename to src/voluseg/tools/ants_registration.py diff --git a/src/voluseg/_tools/ants_transformation.py b/src/voluseg/tools/ants_transformation.py similarity index 100% rename from src/voluseg/_tools/ants_transformation.py rename to src/voluseg/tools/ants_transformation.py diff --git a/src/voluseg/_tools/aws.py b/src/voluseg/tools/aws.py similarity index 100% rename from src/voluseg/_tools/aws.py rename to src/voluseg/tools/aws.py diff --git a/src/voluseg/_tools/ball.py b/src/voluseg/tools/ball.py similarity index 100% rename from src/voluseg/_tools/ball.py rename to src/voluseg/tools/ball.py diff --git a/src/voluseg/_tools/clean_signal.py b/src/voluseg/tools/clean_signal.py similarity index 98% rename from src/voluseg/_tools/clean_signal.py rename to src/voluseg/tools/clean_signal.py index 870ddd2..39a241c 100644 --- a/src/voluseg/_tools/clean_signal.py +++ b/src/voluseg/tools/clean_signal.py @@ -12,7 +12,7 @@ import pandas as pd from scipy import signal from scipy.stats.mstats import winsorize -from voluseg._tools.constants import dtype +from voluseg.tools.constants import dtype from types import SimpleNamespace diff --git a/src/voluseg/_tools/constants.py b/src/voluseg/tools/constants.py similarity index 100% rename from src/voluseg/_tools/constants.py rename to src/voluseg/tools/constants.py diff --git a/src/voluseg/_tools/evenly_parallelize.py b/src/voluseg/tools/evenly_parallelize.py similarity index 100% rename from src/voluseg/_tools/evenly_parallelize.py rename to src/voluseg/tools/evenly_parallelize.py diff --git a/src/voluseg/_tools/get_volume_name.py b/src/voluseg/tools/get_volume_name.py similarity index 100% rename from src/voluseg/_tools/get_volume_name.py rename to src/voluseg/tools/get_volume_name.py diff --git a/src/voluseg/_tools/load_metadata.py b/src/voluseg/tools/load_metadata.py similarity index 100% rename from src/voluseg/_tools/load_metadata.py rename to src/voluseg/tools/load_metadata.py diff --git a/src/voluseg/_tools/load_volume.py b/src/voluseg/tools/load_volume.py similarity index 97% rename from src/voluseg/_tools/load_volume.py rename to src/voluseg/tools/load_volume.py index f0341ce..38deeae 100644 --- a/src/voluseg/_tools/load_volume.py +++ b/src/voluseg/tools/load_volume.py @@ -12,7 +12,7 @@ import pyklb except: pass -from voluseg._tools.constants import dtype +from voluseg.tools.constants import dtype def load_volume(fullname_ext: str) -> Union[np.ndarray, None]: diff --git a/src/voluseg/_tools/nwb.py b/src/voluseg/tools/nwb.py similarity index 100% rename from src/voluseg/_tools/nwb.py rename to src/voluseg/tools/nwb.py diff --git a/src/voluseg/_tools/parameter_dictionary.py b/src/voluseg/tools/parameter_dictionary.py similarity index 98% rename from src/voluseg/_tools/parameter_dictionary.py rename to src/voluseg/tools/parameter_dictionary.py index 882772e..39aa860 100644 --- a/src/voluseg/_tools/parameter_dictionary.py +++ b/src/voluseg/tools/parameter_dictionary.py @@ -1,5 +1,5 @@ from typing import Union -from voluseg._tools.parameters_models import ParametersModel +from voluseg.tools.parameters_models import ParametersModel def parameter_dictionary( diff --git a/src/voluseg/_tools/parameters.py b/src/voluseg/tools/parameters.py similarity index 96% rename from src/voluseg/_tools/parameters.py rename to src/voluseg/tools/parameters.py index d900b71..ad73b0f 100644 --- a/src/voluseg/_tools/parameters.py +++ b/src/voluseg/tools/parameters.py @@ -1,6 +1,6 @@ import pickle import json -from voluseg._tools.parameters_models import ParametersModel +from voluseg.tools.parameters_models import ParametersModel def load_parameters(filename: str) -> dict: diff --git a/src/voluseg/_tools/parameters_models.py b/src/voluseg/tools/parameters_models.py similarity index 100% rename from src/voluseg/_tools/parameters_models.py rename to src/voluseg/tools/parameters_models.py diff --git a/src/voluseg/_tools/sample_data.py b/src/voluseg/tools/sample_data.py similarity index 100% rename from src/voluseg/_tools/sample_data.py rename to src/voluseg/tools/sample_data.py diff --git a/src/voluseg/_tools/save_volume.py b/src/voluseg/tools/save_volume.py similarity index 96% rename from src/voluseg/_tools/save_volume.py rename to src/voluseg/tools/save_volume.py index 1eaac12..66cfc3c 100644 --- a/src/voluseg/_tools/save_volume.py +++ b/src/voluseg/tools/save_volume.py @@ -2,7 +2,7 @@ import nibabel import numpy as np from typing import Union -from voluseg._tools.constants import dtype +from voluseg.tools.constants import dtype def save_volume( diff --git a/src/voluseg/_tools/sparseness.py b/src/voluseg/tools/sparseness.py similarity index 100% rename from src/voluseg/_tools/sparseness.py rename to src/voluseg/tools/sparseness.py diff --git a/src/voluseg/_tools/sparseness_projection.py b/src/voluseg/tools/sparseness_projection.py similarity index 100% rename from src/voluseg/_tools/sparseness_projection.py rename to src/voluseg/tools/sparseness_projection.py diff --git a/src/voluseg/_update.py b/src/voluseg/update.py similarity index 100% rename from src/voluseg/_update.py rename to src/voluseg/update.py diff --git a/tests/test_voluseg.py b/tests/test_voluseg.py index e957281..d6823d6 100644 --- a/tests/test_voluseg.py +++ b/tests/test_voluseg.py @@ -1,6 +1,6 @@ import os import voluseg -from voluseg._tools import download_sample_data +from voluseg.tools import download_sample_data import pytest from pathlib import Path import numpy as np @@ -361,7 +361,7 @@ def test_save_result_as_nwb(setup_parameters): """ Test saving results as an NWB file. """ - from voluseg._tools.nwb import write_nwbfile + from voluseg.tools.nwb import write_nwbfile clean_cells_file = Path(setup_parameters["dir_output"]) / "cells0_clean.hdf5" hdf_h5 = h5py.File(clean_cells_file, "r") From fec122dcd6a5322928f5e7b7fb9cc0b1a14db406 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 30 Oct 2024 10:17:35 +0000 Subject: [PATCH 10/27] auto-commit-docs --- .../docs/reference/steps/__init__.md | 5 + .../docs/reference/steps/step0.md | 49 +++++ .../docs/reference/steps/step1.md | 48 +++++ .../docs/reference/steps/step2.md | 54 ++++++ .../docs/reference/steps/step3.md | 61 ++++++ .../docs/reference/steps/step4.md | 47 +++++ .../docs/reference/steps/step4a.md | 37 ++++ .../docs/reference/steps/step4b.md | 57 ++++++ .../docs/reference/steps/step4c.md | 50 +++++ .../docs/reference/steps/step4d.md | 56 ++++++ .../docs/reference/steps/step4e.md | 42 +++++ .../docs/reference/steps/step5.md | 47 +++++ .../docs/reference/tools/__init__.md | 7 + 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b/docs/voluseg-docs-app/docs/reference/steps/step0.md @@ -0,0 +1,49 @@ +--- +sidebar_label: step0 +title: steps.step0 +--- + +## os + +## copy + +## json + +## np + +## warn + +## load\_volume + +## get\_volume\_name + +## parameter\_dictionary + +## evenly\_parallelize + +## load\_parameters + +## save\_parameters + +## ParametersModel + +## open\_nwbfile + +## find\_nwbfile\_volume\_object\_name + +#### process\_parameters + +```python +def process_parameters(initial_parameters: dict) -> dict +``` + +Process parameters and create parameter file (pickle). + +**Arguments** + +* **initial_parameters** (`dict`): Initial parameter dictionary + +**Returns** + +* `dict`: Processed parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step1.md b/docs/voluseg-docs-app/docs/reference/steps/step1.md new file mode 100644 index 0000000..d889470 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step1.md @@ -0,0 +1,48 @@ +--- +sidebar_label: step1 +title: steps.step1 +--- + +## os + +## interpolate + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## get\_volume\_name + +## ori + +## ali + +## nii + +## hdf + +## evenly\_parallelize + +## open\_nwbfile + +## get\_nwbfile\_volume + +#### process\_volumes + +```python +def process_volumes(parameters: dict) -> None +``` + +Process original volumes and save them to nifti files. +Performs downsampling and padding if specified in parameters. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step2.md b/docs/voluseg-docs-app/docs/reference/steps/step2.md new file mode 100644 index 0000000..2f55a5a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step2.md @@ -0,0 +1,54 @@ +--- +sidebar_label: step2 +title: steps.step2 +--- + +## os + +## h5py + +## shutil + +## np + +## io + +## SimpleNamespace + +## load\_volume + +## save\_volume + +## ori + +## ali + +## nii + +## hdf + +## dtype + +## ants\_registration + +## ants\_transformation + +## evenly\_parallelize + +#### align\_volumes + +```python +def align_volumes(parameters: dict) -> None +``` + +Register volumes to a reference volume. +Generates ANTs transforms files (.mat). + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step3.md b/docs/voluseg-docs-app/docs/reference/steps/step3.md new file mode 100644 index 0000000..810b75e --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step3.md @@ -0,0 +1,61 @@ +--- +sidebar_label: step3 +title: steps.step3 +--- + +## os + +## h5py + +## pyspark + +## np + +## stats + +## mixture + +## morphology + +## SimpleNamespace + +## median\_filter + +## SparkSession + +## warnings + +## matplotlib + +## plt + +## ball + +## ali + +## hdf + +## load\_volume + +## clean\_signal + +## evenly\_parallelize + +#### mask\_volumes + +```python +def mask_volumes(parameters: dict) -> None +``` + +Create intensity mask from the average registered volume. +Produces figures with masks and histograms. +Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4.md b/docs/voluseg-docs-app/docs/reference/steps/step4.md new file mode 100644 index 0000000..9b482be --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4.md @@ -0,0 +1,47 @@ +--- +sidebar_label: step4 +title: steps.step4 +--- + +## os + +## h5py + +## time + +## np + +## SimpleNamespace + +## SparkSession + +## define\_blocks + +## process\_block\_data + +## initialize\_block\_cells + +## nnmf\_sparse + +## ball + +## hdf + +## evenly\_parallelize + +#### detect\_cells + +```python +def detect_cells(parameters: dict) -> None +``` + +Detect cells in volumetric blocks. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4a.md b/docs/voluseg-docs-app/docs/reference/steps/step4a.md new file mode 100644 index 0000000..21b3c83 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4a.md @@ -0,0 +1,37 @@ +--- +sidebar_label: step4a +title: steps.step4a +--- + +## os + +## Tuple + +## np + +#### define\_blocks + +```python +def define_blocks( + lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, + volume_mask: np.ndarray, + volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] +``` + +Get coordinates of individual blocks. + +**Arguments** + +* **lx** (`int`): Number of voxels in x-dimension. +* **ly** (`int`): Number of voxels in y-dimension. +* **lz** (`int`): Number of voxels in z-dimension. +* **n_cells_block** (`int`): Number of cells in each block. +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **volume_mask** (`np.ndarray`): Volume mask. +* **volume_peak** (`np.ndarray`): Volume local intensity maxima (peaks). + +**Returns** + +* `Tuple[int, bool, np.ndarray, np.ndarray]`: Tuple containing: Number of blocks, valid blocks, coordinates of block start, +and coordinates of block end. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4b.md b/docs/voluseg-docs-app/docs/reference/steps/step4b.md new file mode 100644 index 0000000..6078dae --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4b.md @@ -0,0 +1,57 @@ +--- +sidebar_label: step4b +title: steps.step4b +--- + +## os + +## Tuple + +## np + +## h5py + +## time + +## interpolate + +## morphology + +## SimpleNamespace + +## ali + +## hdf + +## dtype + +#### process\_block\_data + +```python +def process_block_data( + xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, + color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, + bvolume_peak: h5py.Dataset, timepoints: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Load timeseries in individual blocks, slice-time correct, and find similar timeseries. + +**Arguments** + +* **xyz0** (`Tuple[int, int, int]`): Start coordinates of block. +* **xyz1** (`Tuple[int, int, int]`): End coordinates of block. +* **parameters** (`dict`): Parameters dictionary. +* **color_i** (`int`): Color index. +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): The resolution of x, y, and z dimensions. +* **ball_diam** (`np.ndarray`): The diameter of a cell-area sphere. +* **bvolume_mean** (`h5py.Dataset`): Spark broadcast variable: volume mean. +* **bvolume_peak** (`h5py.Dataset`): Spark broadcast variable: local intensity maximum volume (peak). +* **timepoints** (`np.ndarray`): Timepoints at which segmentation will be performed. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4c.md b/docs/voluseg-docs-app/docs/reference/steps/step4c.md new file mode 100644 index 0000000..c4bd65e --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4c.md @@ -0,0 +1,50 @@ +--- +sidebar_label: step4c +title: steps.step4c +--- + +## os + +## Tuple + +## np + +## cluster + +## sparseness + +#### initialize\_block\_cells + +```python +def initialize_block_cells( + n_voxels_cell: int, n_voxels_block: int, n_cells: int, + voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, + peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, + lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Initialize cell positions in individual blocks. + +**Arguments** + +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **n_voxels_block** (`int`): Number of voxels in block. +* **n_cells** (`int`): Number of cells. +* **voxel_xyz** (`np.ndarray`): Voxel coordinates. +* **voxel_timeseries** (`np.ndarray`): Voxel timeseries. +* **peak_idx** (`np.ndarray`): Peak indices. +* **peak_valids** (`np.ndarray`): Valid local-intensity maxima (used to determine number of cells). +* **voxel_similarity_peak** (`np.ndarray`): Similarity between voxels: defined by the combination of spatial proximity +and temporal similarity (the voxels are neighbors of each other and also +correlated with each other). +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): Resolution of x, y, z dimensions. +* **ball_diam** (`np.ndarray`): Diameter of a sphere that may defines a cell boundary. +* **ball_diam_xyz0** (`np.ndarray`): Midpoint of the sphere. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4d.md b/docs/voluseg-docs-app/docs/reference/steps/step4d.md new file mode 100644 index 0000000..1273b9f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4d.md @@ -0,0 +1,56 @@ +--- +sidebar_label: step4d +title: steps.step4d +--- + +## os + +## Tuple + +## np + +## stats + +## linalg + +## measure + +## sparseness\_projection + +#### nnmf\_sparse + +```python +def nnmf_sparse( + V0: np.ndarray, + XYZ0: np.ndarray, + W0: np.ndarray, + B0: np.ndarray, + S0: np.ndarray, + tolfun: float = 1e-4, + miniter: int = 10, + maxiter: int = 100, + timeseries_mean=1.0, + timepoints: np.ndarray = None, + verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] +``` + +Cell detection via nonnegative matrix factorization with sparseness projection. + +**Arguments** + +* **V0** (`np.ndarray`): Voxel timeseries (voxel_timeseries_valid). +* **XYZ0** (`np.ndarray`): Voxel coordinates (voxel_xyz_valid). +* **W0** (`np.ndarray`): Initial cell weights (cell_weight_init_valid). +* **B0** (`np.ndarray`): Cell neighborhood (cell_neighborhood_valid). +* **S0** (`np.ndarray`): Cell sparseness (cell_sparseness). +* **tolfun** (`float, optional`): Tolerance for convergence, by default 1e-4. +* **miniter** (`int, optional`): Minimum number of iterations, by default 10. +* **maxiter** (`int, optional`): Maximum number of iterations, by default 100. +* **timeseries_mean** (`float, optional`): Mean timeseries value, by default 1.0. +* **timepoints** (`np.ndarray, optional`): Timepoints to use, by default None. +* **verbosity** (`bool, optional`): Print progress, by default True. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, float]`: Tuple containing: Spatial footprint, temporal footprint, convergence error. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4e.md b/docs/voluseg-docs-app/docs/reference/steps/step4e.md new file mode 100644 index 0000000..be2a9ac --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4e.md @@ -0,0 +1,42 @@ +--- +sidebar_label: step4e +title: steps.step4e +--- + +## os + +## h5py + +## np + +## SimpleNamespace + +## Tuple + +## pyspark + +## SparkSession + +## hdf + +## evenly\_parallelize + +#### collect\_blocks + +```python +def collect_blocks( + color_i: int, parameters: dict +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Collect cells across all blocks. + +**Arguments** + +* **color_i** (`int`): Color index. +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step5.md b/docs/voluseg-docs-app/docs/reference/steps/step5.md new file mode 100644 index 0000000..b6924c6 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step5.md @@ -0,0 +1,47 @@ +--- +sidebar_label: step5 +title: steps.step5 +--- + +## os + +## h5py + +## shutil + +## np + +## SimpleNamespace + +## combinations + +## SparkSession + +## collect\_blocks + +## hdf + +## dtype + +## clean\_signal + +## evenly\_parallelize + +## write\_nwbfile + +#### clean\_cells + +```python +def clean_cells(parameters: dict) -> None +``` + +Remove noise cells, detrend and detect baseline. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/__init__.md b/docs/voluseg-docs-app/docs/reference/tools/__init__.md new file mode 100644 index 0000000..c7641f3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/__init__.md @@ -0,0 +1,7 @@ +--- +sidebar_label: tools +title: tools +--- + +## download\_sample\_data + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md new file mode 100644 index 0000000..a9f1dab --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md @@ -0,0 +1,37 @@ +--- +sidebar_label: ants_registration +title: tools.ants_registration +--- + +## os + +#### ants\_registration + +```python +def ants_registration(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + prefix_out_tform: str, + typ: str, + in_tform: str = None, + restrict: str = None) -> str +``` + +ANTs registration. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs directory. +* **in_nii** (`str`): Input nifti file. +* **ref_nii** (`str`): Reference nifti file. +* **out_nii** (`str`): Output nifti file. +* **prefix_out_tform** (`str`): Prefix for output transformation files. +* **typ** (`str`): Type of transformation. +* **in_tform** (`str (optional)`): Initial transformation file. Default is None. +* **restrict** (`str (optional)`): Restrict deformation. Default is None. + +**Returns** + +* `str`: ANTs registration command. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md new file mode 100644 index 0000000..f3b88b8 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md @@ -0,0 +1,33 @@ +--- +sidebar_label: ants_transformation +title: tools.ants_transformation +--- + +## os + +#### ants\_transformation + +```python +def ants_transformation(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + in_tform: str, + interpolation="Linear") -> str +``` + +Application of ANTs transform. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs binaries. +* **in_nii** (`str`): Path to input nifti file. +* **ref_nii** (`str`): Path to reference nifti file. +* **out_nii** (`str`): Path to output nifti file. +* **in_tform** (`str`): Path to input transform file (.mat). +* **interpolation** (`str`): Interpolation method. + +**Returns** + +* `str`: ANTs transformation command string. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/aws.md b/docs/voluseg-docs-app/docs/reference/tools/aws.md new file mode 100644 index 0000000..261734f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/aws.md @@ -0,0 +1,54 @@ +--- +sidebar_label: aws +title: tools.aws +--- + +## boto3 + +## datetime + +## timezone + +## JobDefinitionException Objects + +```python +class JobDefinitionException(Exception) +``` + +#### format\_voluseg\_kwargs + +```python +def format_voluseg_kwargs(voluseg_kwargs: dict) -> dict +``` + +#### run\_job\_in\_aws\_batch + +```python +def run_job_in_aws_batch(job_name_prefix: str, + voluseg_kwargs: dict, + aws_local_profile: str = None, + vcpus: int = 32, + memory: int = 65536) +``` + +Submit a Voluseg job to AWS Batch. + +**Arguments** + +* **job_name_prefix** (`str`): Job name prefix, it will be concatenated with the current timestamp. +Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" +* **voluseg_kwargs** (`dict`): Voluseg parameters. +* **aws_local_profile** (`str`): AWS profile name. Default is None. +* **vcpus** (`int`): Number of vCPUs. Default is 32. +* **memory** (`int`): Memory in MB. Default is 65536. + +**Returns** + +* `dict`: Dictionary with the job_name and batch_job_id. + +#### export\_to\_s3 + +```python +def export_to_s3(local_path: str, bucket_name: str, object_name: str) +``` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ball.md b/docs/voluseg-docs-app/docs/reference/tools/ball.md new file mode 100644 index 0000000..53c0565 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ball.md @@ -0,0 +1,24 @@ +--- +sidebar_label: ball +title: tools.ball +--- + +## np + +#### ball + +```python +def ball(radi: float, affine_matrix: np.ndarray) -> tuple +``` + +Morphological cell balls and midpoints. + +**Arguments** + +* **radi** (`float`): Radius of ball. +* **affine_matrix** (`np.ndarray`): Affine matrix. + +**Returns** + +* `tuple`: Tuple containing: Ball and midpoints. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md new file mode 100644 index 0000000..91e6787 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md @@ -0,0 +1,39 @@ +--- +sidebar_label: clean_signal +title: tools.clean_signal +--- + +## os + +## Tuple + +## np + +## pd + +## signal + +## winsorize + +## dtype + +## SimpleNamespace + +#### clean\_signal + +```python +def clean_signal(parameters: dict, + timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] +``` + +Detrend, filter, and estimate dynamic baseline for input timeseries. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **timeseries** (`np.ndarray`): Input timeseries. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/tools/constants.md b/docs/voluseg-docs-app/docs/reference/tools/constants.md new file mode 100644 index 0000000..7f720df --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/constants.md @@ -0,0 +1,15 @@ +--- +sidebar_label: constants +title: tools.constants +--- + +#### ori + +#### ali + +#### nii + +#### hdf + +#### dtype + diff --git a/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md new file mode 100644 index 0000000..440faf4 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md @@ -0,0 +1,27 @@ +--- +sidebar_label: evenly_parallelize +title: tools.evenly_parallelize +--- + +## np + +## SparkSession + +## RDD + +#### evenly\_parallelize + +```python +def evenly_parallelize(input_list: list) -> RDD +``` + +Return evenly partitioned spark resilient distributed dataset (RDD). + +**Arguments** + +* **input_list** (`list`): List of input elements. + +**Returns** + +* `RDD`: Spark resilient distributed dataset (RDD). + diff --git a/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md new file mode 100644 index 0000000..0315d39 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md @@ -0,0 +1,27 @@ +--- +sidebar_label: get_volume_name +title: tools.get_volume_name +--- + +## os + +#### get\_volume\_name + +```python +def get_volume_name(fullname_volume: str, + dir_prefix: str = None, + plane_i: int = None) -> str +``` + +Get name of volume (with directory prefix and plane suffix). + +**Arguments** + +* **fullname_volume** (`str`): Full name of volume. +* **dir_prefix** (`str (optional)`): Prefix for directory. Default is None. +* **plane_i** (`int (optional)`): Index of plane. Default is None. + +**Returns** + +* `str`: Name of volume. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md new file mode 100644 index 0000000..38c388c --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md @@ -0,0 +1,28 @@ +--- +sidebar_label: load_metadata +title: tools.load_metadata +--- + +## np + +## ElementTree + +#### load\_metadata + +```python +def load_metadata(parameters: dict, filename_channel: str, + filename_stack: str) -> dict +``` + +Fetch z-resolution, exposure time, and stack frequency. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename_channel** (`str`): Filename XML file containing channel information. +* **filename_stack** (`str`): Filename of XML file containing stack information. + +**Returns** + +* `dict`: Parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md new file mode 100644 index 0000000..359771c --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md @@ -0,0 +1,32 @@ +--- +sidebar_label: load_volume +title: tools.load_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### load\_volume + +```python +def load_volume(fullname_ext: str) -> Union[np.ndarray, None] +``` + +Load volume based on input name and extension. +Supports tiff, hdf5, klb, and nifti formats. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. + +**Returns** + +* `np.ndarray or None`: Volume as numpy array, or None if volume could not be loaded. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/nwb.md b/docs/voluseg-docs-app/docs/reference/tools/nwb.md new file mode 100644 index 0000000..10aa1ec --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/nwb.md @@ -0,0 +1,129 @@ +--- +sidebar_label: nwb +title: tools.nwb +--- + +## pynwb + +## contextmanager + +## datetime + +## tzlocal + +## uuid4 + +## np + +#### open\_nwbfile\_local + +```python +@contextmanager +def open_nwbfile_local(file_path: str) +``` + +Context manager to open and close a local NWB file. + +**Arguments** + +* **file_path** (`str`): Path to NWB file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile\_remote + +```python +@contextmanager +def open_nwbfile_remote(s3_url: str, output_path: str) +``` + +Context manager to open and close a remote NWB file. + +**Arguments** + +* **s3_url** (`str`): S3 URL to NWB file. +* **output_path** (`str`): Output path to cache the remote file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile + +```python +@contextmanager +def open_nwbfile(input_path: str, remote: bool, output_path: str = None) +``` + +Open and close an NWB file from either a local or remote source. + +**Arguments** + +* **input_path** (`str`): Path to the NWB file. This can be a local file path or an S3 URL. +* **remote** (`bool`): If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. +* **output_path** (`str`): Output path, only used to cache remote files. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### find\_nwbfile\_volume\_object\_name + +```python +def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str +``` + +Find the name of the `TwoPhotonSeries` volume object in the NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. + +**Returns** + +* `str`: Name of the volume object. + +#### get\_nwbfile\_volume + +```python +def get_nwbfile_volume( + nwbfile: pynwb.NWBFile, + acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile +``` + +Get `TwoPhotonSeries` object from NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. +* **acquisition_name** (`str (default: "TwoPhotonSeries")`): Acquisition name. + +**Returns** + +* `pynwb.NWBFile`: NWB file. + +#### write\_nwbfile + +```python +def write_nwbfile(output_path: str, cell_x: np.ndarray, cell_y: np.ndarray, + cell_z: np.ndarray, cell_weights: np.ndarray, + cell_timeseries: np.ndarray) -> None +``` + +Write results to a local NWB file. + +**Arguments** + +* **output_path** (`str`): Output path. +* **cell_x** (`np.ndarray`): Voxel X coordinates for all cells. +* **cell_y** (`np.ndarray`): Voxel Y coordinates for all cells. +* **cell_z** (`np.ndarray`): Voxel Z coordinates for all cells. +* **cell_weights** (`np.ndarray`): Voxel weights for all cells. +* **cell_timeseries** (`np.ndarray`): Fluorescence timeseries data for all cells. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md new file mode 100644 index 0000000..8a8728a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md @@ -0,0 +1,89 @@ +--- +sidebar_label: parameter_dictionary +title: tools.parameter_dictionary +--- + +## Union + +## ParametersModel + +#### parameter\_dictionary + +```python +def parameter_dictionary(detrending: str = "standard", + registration: str = "medium", + registration_restrict: str = "", + diam_cell: float = 6.0, + dir_ants: str = "", + dir_input: str = "", + dir_output: str = "", + dir_transform: str = "", + ds: int = 2, + planes_pad: int = 0, + planes_packed: bool = False, + parallel_clean: bool = True, + parallel_volume: bool = True, + save_volume: bool = False, + type_timepoints: str = "dff", + type_mask: str = "geomean", + timepoints: int = 1000, + f_hipass: float = 0, + f_volume: float = 2.0, + n_cells_block: int = 316, + n_colors: int = 1, + res_x: float = 0.40625, + res_y: float = 0.40625, + res_z: float = 5.0, + t_baseline: int = 300, + t_section: float = 0.01, + thr_mask: float = 0.5, + volume_fullnames_input: Union[list[str], None] = None, + volume_names: Union[list[str], None] = None, + input_dirs: Union[list[str], None] = None, + ext: Union[str, None] = None, + lt: Union[int, None] = None, + affine_matrix: Union[list, None] = None) -> dict +``` + +Return a parameter dictionary with specified defaults. + +**Arguments** + +* **detrending** (`str, optional`): Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +* **registration** (`str, optional`): Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +* **registration_restrict** (`str, optional`): Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +* **diam_cell** (`float, optional`): Cell diameter in microns (default is 6.0). +* **dir_ants** (`str, optional`): Path to the ANTs directory (default is an empty string). +* **dir_input** (`str, optional`): Path to input directories, separate multiple directories with ';' (default is an empty string). +* **dir_output** (`str, optional`): Path to the output directory (default is an empty string). +* **dir_transform** (`str, optional`): Path to the transform directory (default is an empty string). +* **ds** (`int, optional`): Spatial coarse-graining in x-y dimension (default is 2). +* **planes_pad** (`int, optional`): Number of planes to pad the volume with for robust registration (default is 0). +* **planes_packed** (`bool, optional`): Packed planes in each volume, for single plane imaging with packed planes (default is False). +* **parallel_clean** (`bool, optional`): Parallelization of final cleaning (True is fast but memory-intensive, default is True). +* **parallel_volume** (`bool, optional`): Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +* **save_volume** (`bool, optional`): Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +* **type_timepoints** (`str, optional`): Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +* **type_mask** (`str, optional`): Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +* **timepoints** (`int, optional`): Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +* **f_hipass** (`float, optional`): Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +* **f_volume** (`float, optional`): Imaging frequency in Hz (default is 2.0). +* **n_cells_block** (`int, optional`): Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +* **n_colors** (`int, optional`): Number of brain colors (2 in two-color volumes, default is 1). +* **res_x** (`float, optional`): X resolution in microns (default is 0.40625). +* **res_y** (`float, optional`): Y resolution in microns (default is 0.40625). +* **res_z** (`float, optional`): Z resolution in microns (default is 5.0). +* **t_baseline** (`int, optional`): Interval for baseline calculation in seconds (default is 300). +* **t_section** (`float, optional`): Exposure time in seconds for slice acquisition (default is 0.01). +* **thr_mask** (`float, optional`): Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +* **volume_fullnames_input** (`list[str], optional`): List of full volume names (default is None). +* **volume_names** (`list[str], optional`): List of volume names (default is None). +* **input_dirs** (`list[str], optional`): List of input directories (default is None). +* **ext** (`str, optional`): File extension (default is None). +* **lt** (`int, optional`): Number of volumes (default is None). +* **affine_matrix** (`list, optional`): Affine matrix (default is None). + +**Returns** + +* `dict`: A dictionary of validated parameters with their default values. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameters.md b/docs/voluseg-docs-app/docs/reference/tools/parameters.md new file mode 100644 index 0000000..eca4159 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters.md @@ -0,0 +1,44 @@ +--- +sidebar_label: parameters +title: tools.parameters +--- + +## pickle + +## json + +## ParametersModel + +#### load\_parameters + +```python +def load_parameters(filename: str) -> dict +``` + +Load previously saved parameters from filename. + +**Arguments** + +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `dict`: Parameters dictionary. + +#### save\_parameters + +```python +def save_parameters(parameters: dict, filename: str) -> None +``` + +Save parameters to filename. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md new file mode 100644 index 0000000..7b742ce --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md @@ -0,0 +1,173 @@ +--- +sidebar_label: parameters_models +title: tools.parameters_models +--- + +## Enum + +## np + +## BaseModel + +## Field + +## model\_validator + +## Optional + +## Detrending Objects + +```python +class Detrending(str, Enum) +``` + +#### standard + +#### robust + +#### none + +## Registration Objects + +```python +class Registration(str, Enum) +``` + +#### high + +#### medium + +#### low + +#### none + +## TypeTimepoints Objects + +```python +class TypeTimepoints(str, Enum) +``` + +#### dff + +#### periodic + +#### custom + +## TypeMask Objects + +```python +class TypeMask(str, Enum) +``` + +#### mean + +#### geomean + +#### max + +## ParametersModel Objects + +```python +class ParametersModel(BaseModel) +``` + +#### detrending + +#### registration + +#### registration\_restrict + +#### diam\_cell + +#### dir\_ants + +#### dir\_input + +#### dir\_output + +#### dir\_transform + +#### ds + +#### planes\_pad + +#### planes\_packed + +#### parallel\_clean + +#### parallel\_volume + +#### save\_volume + +#### type\_timepoints + +#### type\_mask + +#### timepoints + +#### f\_hipass + +#### f\_volume + +#### n\_cells\_block + +#### n\_colors + +#### res\_x + +#### res\_y + +#### res\_z + +#### t\_baseline + +#### t\_section + +#### thr\_mask + +#### volume\_fullnames\_input + +#### volume\_names + +#### input\_dirs + +#### ext + +#### lt + +#### affine\_matrix + +#### dim\_order + +#### remote + +#### output\_to\_nwb + +#### convert\_array\_to\_list + +```python +@model_validator(mode="before") +def convert_array_to_list(cls, values) +``` + +Validator to automatically convert NumPy arrays to lists. + +#### model\_dump + +```python +def model_dump(use_np_array: bool = True, *args, **kwargs) +``` + +Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) +and Enums to their values. + +**Arguments** + +* **use_np_array** (`bool, optional`): Convert lists to NumPy arrays (default is True) +* ***args**: Positional arguments to pass to the parent class +* ****kwargs**: Keyword arguments to pass to the parent class + +**Returns** + +* `dict`: A dictionary of the model's data + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md new file mode 100644 index 0000000..7398409 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md @@ -0,0 +1,71 @@ +--- +sidebar_label: sample_data +title: tools.sample_data +--- + +## requests + +## zipfile + +## os + +## Path + +## Union + +#### download\_sample\_data + +```python +def download_sample_data(destination_folder: str = ".", + data_type: str = "h5_dir") -> Union[str, None] +``` + +Download sample data for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. +* **data_type** (`str, optional`): Type of data to download. Options are "h5_dir" and "nwb_file". + +**Returns** + +* `str or None`: Path to the folder or file where the data was downloaded, or None if the download failed. + +#### download\_sample\_data\_nwb\_file + +```python +def download_sample_data_nwb_file( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample NWB file for Voluseg. +Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the downloaded file, or None if the download failed. + +#### download\_sample\_data\_h5\_dir + +```python +def download_sample_data_h5_dir( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample data (h5 directory) for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the folder where the data was extracted, or None if the download failed. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md new file mode 100644 index 0000000..1800ca2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md @@ -0,0 +1,36 @@ +--- +sidebar_label: save_volume +title: tools.save_volume +--- + +## h5py + +## nibabel + +## np + +## Union + +## dtype + +#### save\_volume + +```python +def save_volume(fullname_ext: str, + volume: np.ndarray, + affine_matrix: np.ndarray = None) -> Union[bool, None] +``` + +Save volume in output format. +Formats currently accepted are: nifti and hdf5. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. +* **volume** (`np.ndarray`): Volume as numpy array. +* **affine_matrix** (`np.ndarray`): Affine matrix for nifti format. + +**Returns** + +* `bool or None`: True if volume was saved successfully, None if volume could not be saved. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md new file mode 100644 index 0000000..3a48972 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md @@ -0,0 +1,24 @@ +--- +sidebar_label: sparseness +title: tools.sparseness +--- + +## np + +#### sparseness + +```python +def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray +``` + +Vector sparseness along specified dimension. + +**Arguments** + +* **W** (`np.ndarray`): Input array. +* **dim** (`int, optional`): Dimension along which to compute sparseness, by default 0. + +**Returns** + +* `np.ndarray`: Sparseness of input array along specified dimension. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md new file mode 100644 index 0000000..e7d0413 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md @@ -0,0 +1,27 @@ +--- +sidebar_label: sparseness_projection +title: tools.sparseness_projection +--- + +## np + +#### sparseness\_projection + +```python +def sparseness_projection(Si: np.ndarray, + s: float, + at_least_as_sparse: bool = False) -> np.ndarray +``` + +Hoyer sparseness projection. + +**Arguments** + +* **Si** (`np.ndarray`): Input signal. +* **s** (`float`): Sparseness parameter. +* **at_least_as_sparse** (`bool, optional`): Enforce at least as sparse, by default False. + +**Returns** + +* `np.ndarray`: Sparse signal. + diff --git a/docs/voluseg-docs-app/docs/reference/update.md b/docs/voluseg-docs-app/docs/reference/update.md new file mode 100644 index 0000000..5c4b56f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/update.md @@ -0,0 +1,15 @@ +--- +sidebar_label: update +title: update +--- + +## os + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From 521ac9b448b75a1271875bb9f76203880f940d08 Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 12:20:07 +0100 Subject: [PATCH 11/27] fixed api reference --- .../docs/reference/__init__/__init__.md | 22 ---------- .../docs/reference/_steps/__init__.md | 5 --- .../docs/reference/_tools/__init__.md | 7 ---- .../docs/reference/steps/__init__.md | 5 +++ .../docs/reference/{_steps => steps}/step0.md | 30 +------------- .../docs/reference/{_steps => steps}/step1.md | 28 +------------ .../docs/reference/{_steps => steps}/step2.md | 34 +--------------- .../docs/reference/{_steps => steps}/step3.md | 40 +------------------ .../docs/reference/{_steps => steps}/step4.md | 28 +------------ .../reference/{_steps => steps}/step4a.md | 8 +--- .../reference/{_steps => steps}/step4b.md | 24 +---------- .../reference/{_steps => steps}/step4c.md | 12 +----- 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+----- .../{_tools => tools}/save_volume.md | 12 +----- .../reference/{_tools => tools}/sparseness.md | 4 +- .../sparseness_projection.md | 4 +- .../voluseg-docs-app/docs/reference/update.md | 13 ++++++ 35 files changed, 52 insertions(+), 417 deletions(-) delete mode 100644 docs/voluseg-docs-app/docs/reference/_steps/__init__.md delete mode 100644 docs/voluseg-docs-app/docs/reference/_tools/__init__.md create mode 100644 docs/voluseg-docs-app/docs/reference/steps/__init__.md rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step0.md (54%) rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step1.md (59%) rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step2.md (55%) rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step3.md (57%) rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step4.md (51%) rename docs/voluseg-docs-app/docs/reference/{_steps => steps}/step4a.md (95%) rename docs/voluseg-docs-app/docs/reference/{_steps => 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docs/voluseg-docs-app/docs/reference/{_tools => tools}/get_volume_name.md (93%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/load_metadata.md (90%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/load_volume.md (84%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/nwb.md (96%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/parameter_dictionary.md (98%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/parameters.md (89%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/parameters_models.md (94%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/sample_data.md (95%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/save_volume.md (88%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/sparseness.md (92%) rename docs/voluseg-docs-app/docs/reference/{_tools => tools}/sparseness_projection.md (92%) create mode 100644 docs/voluseg-docs-app/docs/reference/update.md diff --git a/docs/voluseg-docs-app/docs/reference/__init__/__init__.md b/docs/voluseg-docs-app/docs/reference/__init__/__init__.md index ffd2d78..9d5a153 100644 --- a/docs/voluseg-docs-app/docs/reference/__init__/__init__.md +++ b/docs/voluseg-docs-app/docs/reference/__init__/__init__.md @@ -5,25 +5,3 @@ title: __init__ initialization -## step0\_process\_parameters - -## step1\_process\_volumes - -## step2\_align\_volumes - -## step3\_mask\_volumes - -## step4\_detect\_cells - -## step5\_clean\_cells - -## parameter\_dictionary - -## load\_parameters - -## save\_parameters - -## load\_metadata - -## update - diff --git a/docs/voluseg-docs-app/docs/reference/_steps/__init__.md b/docs/voluseg-docs-app/docs/reference/_steps/__init__.md deleted file mode 100644 index 6619ac0..0000000 --- a/docs/voluseg-docs-app/docs/reference/_steps/__init__.md +++ /dev/null @@ -1,5 +0,0 @@ ---- -sidebar_label: _steps -title: _steps ---- - diff --git a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md b/docs/voluseg-docs-app/docs/reference/_tools/__init__.md deleted file mode 100644 index 077ce2b..0000000 --- a/docs/voluseg-docs-app/docs/reference/_tools/__init__.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -sidebar_label: _tools -title: _tools ---- - -## download\_sample\_data - diff --git a/docs/voluseg-docs-app/docs/reference/steps/__init__.md b/docs/voluseg-docs-app/docs/reference/steps/__init__.md new file mode 100644 index 0000000..57c3b04 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: steps +title: steps +--- + diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step0.md b/docs/voluseg-docs-app/docs/reference/steps/step0.md similarity index 54% rename from docs/voluseg-docs-app/docs/reference/_steps/step0.md rename to docs/voluseg-docs-app/docs/reference/steps/step0.md index 6b623f3..5113143 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step0.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step0.md @@ -1,36 +1,8 @@ --- sidebar_label: step0 -title: _steps.step0 +title: steps.step0 --- -## os - -## copy - -## json - -## np - -## warn - -## load\_volume - -## get\_volume\_name - -## parameter\_dictionary - -## evenly\_parallelize - -## load\_parameters - -## save\_parameters - -## ParametersModel - -## open\_nwbfile - -## find\_nwbfile\_volume\_object\_name - #### process\_parameters ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step1.md b/docs/voluseg-docs-app/docs/reference/steps/step1.md similarity index 59% rename from docs/voluseg-docs-app/docs/reference/_steps/step1.md rename to docs/voluseg-docs-app/docs/reference/steps/step1.md index a83feda..eefbce8 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step1.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step1.md @@ -1,34 +1,8 @@ --- sidebar_label: step1 -title: _steps.step1 +title: steps.step1 --- -## os - -## interpolate - -## SimpleNamespace - -## load\_volume - -## save\_volume - -## get\_volume\_name - -## ori - -## ali - -## nii - -## hdf - -## evenly\_parallelize - -## open\_nwbfile - -## get\_nwbfile\_volume - #### process\_volumes ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step2.md b/docs/voluseg-docs-app/docs/reference/steps/step2.md similarity index 55% rename from docs/voluseg-docs-app/docs/reference/_steps/step2.md rename to docs/voluseg-docs-app/docs/reference/steps/step2.md index b372ae7..e410734 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step2.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step2.md @@ -1,40 +1,8 @@ --- sidebar_label: step2 -title: _steps.step2 +title: steps.step2 --- -## os - -## h5py - -## shutil - -## np - -## io - -## SimpleNamespace - -## load\_volume - -## save\_volume - -## ori - -## ali - -## nii - -## hdf - -## dtype - -## ants\_registration - -## ants\_transformation - -## evenly\_parallelize - #### align\_volumes ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step3.md b/docs/voluseg-docs-app/docs/reference/steps/step3.md similarity index 57% rename from docs/voluseg-docs-app/docs/reference/_steps/step3.md rename to docs/voluseg-docs-app/docs/reference/steps/step3.md index 85073bd..ea7489b 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step3.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step3.md @@ -1,46 +1,8 @@ --- sidebar_label: step3 -title: _steps.step3 +title: steps.step3 --- -## os - -## h5py - -## pyspark - -## np - -## stats - -## mixture - -## morphology - -## SimpleNamespace - -## median\_filter - -## SparkSession - -## warnings - -## matplotlib - -## plt - -## ball - -## ali - -## hdf - -## load\_volume - -## clean\_signal - -## evenly\_parallelize - #### mask\_volumes ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4.md b/docs/voluseg-docs-app/docs/reference/steps/step4.md similarity index 51% rename from docs/voluseg-docs-app/docs/reference/_steps/step4.md rename to docs/voluseg-docs-app/docs/reference/steps/step4.md index 8f23d34..223742a 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4.md @@ -1,34 +1,8 @@ --- sidebar_label: step4 -title: _steps.step4 +title: steps.step4 --- -## os - -## h5py - -## time - -## np - -## SimpleNamespace - -## SparkSession - -## define\_blocks - -## process\_block\_data - -## initialize\_block\_cells - -## nnmf\_sparse - -## ball - -## hdf - -## evenly\_parallelize - #### detect\_cells ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md b/docs/voluseg-docs-app/docs/reference/steps/step4a.md similarity index 95% rename from docs/voluseg-docs-app/docs/reference/_steps/step4a.md rename to docs/voluseg-docs-app/docs/reference/steps/step4a.md index f44a0dd..5817294 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4a.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4a.md @@ -1,14 +1,8 @@ --- sidebar_label: step4a -title: _steps.step4a +title: steps.step4a --- -## os - -## Tuple - -## np - #### define\_blocks ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md b/docs/voluseg-docs-app/docs/reference/steps/step4b.md similarity index 90% rename from docs/voluseg-docs-app/docs/reference/_steps/step4b.md rename to docs/voluseg-docs-app/docs/reference/steps/step4b.md index 4a09d22..ba394f4 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4b.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4b.md @@ -1,30 +1,8 @@ --- sidebar_label: step4b -title: _steps.step4b +title: steps.step4b --- -## os - -## Tuple - -## np - -## h5py - -## time - -## interpolate - -## morphology - -## SimpleNamespace - -## ali - -## hdf - -## dtype - #### process\_block\_data ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md b/docs/voluseg-docs-app/docs/reference/steps/step4c.md similarity index 95% rename from docs/voluseg-docs-app/docs/reference/_steps/step4c.md rename to docs/voluseg-docs-app/docs/reference/steps/step4c.md index 7cad9e5..9f184ea 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4c.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4c.md @@ -1,18 +1,8 @@ --- sidebar_label: step4c -title: _steps.step4c +title: steps.step4c --- -## os - -## Tuple - -## np - -## cluster - -## sparseness - #### initialize\_block\_cells ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md b/docs/voluseg-docs-app/docs/reference/steps/step4d.md similarity index 93% rename from docs/voluseg-docs-app/docs/reference/_steps/step4d.md rename to docs/voluseg-docs-app/docs/reference/steps/step4d.md index df4c35f..d0d1f2c 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4d.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4d.md @@ -1,22 +1,8 @@ --- sidebar_label: step4d -title: _steps.step4d +title: steps.step4d --- -## os - -## Tuple - -## np - -## stats - -## linalg - -## measure - -## sparseness\_projection - #### nnmf\_sparse ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md b/docs/voluseg-docs-app/docs/reference/steps/step4e.md similarity index 78% rename from docs/voluseg-docs-app/docs/reference/_steps/step4e.md rename to docs/voluseg-docs-app/docs/reference/steps/step4e.md index b3d4633..48e4804 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step4e.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step4e.md @@ -1,26 +1,8 @@ --- sidebar_label: step4e -title: _steps.step4e +title: steps.step4e --- -## os - -## h5py - -## np - -## SimpleNamespace - -## Tuple - -## pyspark - -## SparkSession - -## hdf - -## evenly\_parallelize - #### collect\_blocks ```python diff --git a/docs/voluseg-docs-app/docs/reference/_steps/step5.md b/docs/voluseg-docs-app/docs/reference/steps/step5.md similarity index 54% rename from docs/voluseg-docs-app/docs/reference/_steps/step5.md rename to docs/voluseg-docs-app/docs/reference/steps/step5.md index 3dd7efb..287fdbc 100644 --- a/docs/voluseg-docs-app/docs/reference/_steps/step5.md +++ b/docs/voluseg-docs-app/docs/reference/steps/step5.md @@ -1,34 +1,8 @@ --- sidebar_label: step5 -title: _steps.step5 +title: steps.step5 --- -## os - -## h5py - -## shutil - -## np - -## SimpleNamespace - -## combinations - -## SparkSession - -## collect\_blocks - -## hdf - -## dtype - -## clean\_signal - -## evenly\_parallelize - -## write\_nwbfile - #### clean\_cells ```python diff --git a/docs/voluseg-docs-app/docs/reference/tools/__init__.md b/docs/voluseg-docs-app/docs/reference/tools/__init__.md new file mode 100644 index 0000000..f94abd3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: tools +title: tools +--- + diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md similarity index 95% rename from docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md rename to docs/voluseg-docs-app/docs/reference/tools/ants_registration.md index 5e0ac97..2a99b45 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/ants_registration.md +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md @@ -1,10 +1,8 @@ --- sidebar_label: ants_registration -title: _tools.ants_registration +title: tools.ants_registration --- -## os - #### ants\_registration ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md similarity index 94% rename from docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md rename to docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md index 5bfcbe7..b7221ef 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/ants_transformation.md +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md @@ -1,10 +1,8 @@ --- sidebar_label: ants_transformation -title: _tools.ants_transformation +title: tools.ants_transformation --- -## os - #### ants\_transformation ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/aws.md b/docs/voluseg-docs-app/docs/reference/tools/aws.md similarity index 95% rename from docs/voluseg-docs-app/docs/reference/_tools/aws.md rename to docs/voluseg-docs-app/docs/reference/tools/aws.md index beb6fb2..8d28c12 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/aws.md +++ b/docs/voluseg-docs-app/docs/reference/tools/aws.md @@ -1,14 +1,8 @@ --- sidebar_label: aws -title: _tools.aws +title: tools.aws --- -## boto3 - -## datetime - -## timezone - ## JobDefinitionException Objects ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/ball.md b/docs/voluseg-docs-app/docs/reference/tools/ball.md similarity index 92% rename from docs/voluseg-docs-app/docs/reference/_tools/ball.md rename to docs/voluseg-docs-app/docs/reference/tools/ball.md index 807fedd..61af6f2 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/ball.md +++ b/docs/voluseg-docs-app/docs/reference/tools/ball.md @@ -1,10 +1,8 @@ --- sidebar_label: ball -title: _tools.ball +title: tools.ball --- -## np - #### ball ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md similarity index 79% rename from docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md rename to docs/voluseg-docs-app/docs/reference/tools/clean_signal.md index c98eee8..1dd4c85 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/clean_signal.md +++ b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md @@ -1,24 +1,8 @@ --- sidebar_label: clean_signal -title: _tools.clean_signal +title: tools.clean_signal --- -## os - -## Tuple - -## np - -## pd - -## signal - -## winsorize - -## dtype - -## SimpleNamespace - #### clean\_signal ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/constants.md b/docs/voluseg-docs-app/docs/reference/tools/constants.md similarity index 78% rename from docs/voluseg-docs-app/docs/reference/_tools/constants.md rename to docs/voluseg-docs-app/docs/reference/tools/constants.md index b3218c9..7f720df 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/constants.md +++ b/docs/voluseg-docs-app/docs/reference/tools/constants.md @@ -1,6 +1,6 @@ --- sidebar_label: constants -title: _tools.constants +title: tools.constants --- #### ori diff --git a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md similarity index 83% rename from docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md rename to docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md index 1408839..c32fbf6 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/evenly_parallelize.md +++ b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md @@ -1,14 +1,8 @@ --- sidebar_label: evenly_parallelize -title: _tools.evenly_parallelize +title: tools.evenly_parallelize --- -## np - -## SparkSession - -## RDD - #### evenly\_parallelize ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md similarity index 93% rename from docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md rename to docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md index 1792dda..c30966f 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/get_volume_name.md +++ b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md @@ -1,10 +1,8 @@ --- sidebar_label: get_volume_name -title: _tools.get_volume_name +title: tools.get_volume_name --- -## os - #### get\_volume\_name ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md similarity index 90% rename from docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md rename to docs/voluseg-docs-app/docs/reference/tools/load_metadata.md index aa404ad..8c41212 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/load_metadata.md +++ b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md @@ -1,12 +1,8 @@ --- sidebar_label: load_metadata -title: _tools.load_metadata +title: tools.load_metadata --- -## np - -## ElementTree - #### load\_metadata ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md similarity index 84% rename from docs/voluseg-docs-app/docs/reference/_tools/load_volume.md rename to docs/voluseg-docs-app/docs/reference/tools/load_volume.md index 5c882c9..fdb0f76 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/load_volume.md +++ b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md @@ -1,18 +1,8 @@ --- sidebar_label: load_volume -title: _tools.load_volume +title: tools.load_volume --- -## h5py - -## nibabel - -## np - -## Union - -## dtype - #### load\_volume ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md b/docs/voluseg-docs-app/docs/reference/tools/nwb.md similarity index 96% rename from docs/voluseg-docs-app/docs/reference/_tools/nwb.md rename to docs/voluseg-docs-app/docs/reference/tools/nwb.md index cee4840..4ad3a77 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/nwb.md +++ b/docs/voluseg-docs-app/docs/reference/tools/nwb.md @@ -1,20 +1,8 @@ --- sidebar_label: nwb -title: _tools.nwb +title: tools.nwb --- -## pynwb - -## contextmanager - -## datetime - -## tzlocal - -## uuid4 - -## np - #### open\_nwbfile\_local ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md similarity index 98% rename from docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md rename to docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md index f0dd2f9..5ecd000 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameter_dictionary.md +++ b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md @@ -1,12 +1,8 @@ --- sidebar_label: parameter_dictionary -title: _tools.parameter_dictionary +title: tools.parameter_dictionary --- -## Union - -## ParametersModel - #### parameter\_dictionary ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md b/docs/voluseg-docs-app/docs/reference/tools/parameters.md similarity index 89% rename from docs/voluseg-docs-app/docs/reference/_tools/parameters.md rename to docs/voluseg-docs-app/docs/reference/tools/parameters.md index 79a3e8b..4efb1b0 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameters.md +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters.md @@ -1,14 +1,8 @@ --- sidebar_label: parameters -title: _tools.parameters +title: tools.parameters --- -## pickle - -## json - -## ParametersModel - #### load\_parameters ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md similarity index 94% rename from docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md rename to docs/voluseg-docs-app/docs/reference/tools/parameters_models.md index b358b9f..ce1aad3 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/parameters_models.md +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md @@ -1,20 +1,8 @@ --- sidebar_label: parameters_models -title: _tools.parameters_models +title: tools.parameters_models --- -## Enum - -## np - -## BaseModel - -## Field - -## model\_validator - -## Optional - ## Detrending Objects ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md similarity index 95% rename from docs/voluseg-docs-app/docs/reference/_tools/sample_data.md rename to docs/voluseg-docs-app/docs/reference/tools/sample_data.md index bd3d6a0..01fab2e 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/sample_data.md +++ b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md @@ -1,18 +1,8 @@ --- sidebar_label: sample_data -title: _tools.sample_data +title: tools.sample_data --- -## requests - -## zipfile - -## os - -## Path - -## Union - #### download\_sample\_data ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md similarity index 88% rename from docs/voluseg-docs-app/docs/reference/_tools/save_volume.md rename to docs/voluseg-docs-app/docs/reference/tools/save_volume.md index f7c50f6..2c0d725 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/save_volume.md +++ b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md @@ -1,18 +1,8 @@ --- sidebar_label: save_volume -title: _tools.save_volume +title: tools.save_volume --- -## h5py - -## nibabel - -## np - -## Union - -## dtype - #### save\_volume ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md similarity index 92% rename from docs/voluseg-docs-app/docs/reference/_tools/sparseness.md rename to docs/voluseg-docs-app/docs/reference/tools/sparseness.md index 28b3c17..5a4a724 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/sparseness.md +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md @@ -1,10 +1,8 @@ --- sidebar_label: sparseness -title: _tools.sparseness +title: tools.sparseness --- -## np - #### sparseness ```python diff --git a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md similarity index 92% rename from docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md rename to docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md index a734715..9f92ba2 100644 --- a/docs/voluseg-docs-app/docs/reference/_tools/sparseness_projection.md +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md @@ -1,10 +1,8 @@ --- sidebar_label: sparseness_projection -title: _tools.sparseness_projection +title: tools.sparseness_projection --- -## np - #### sparseness\_projection ```python diff --git a/docs/voluseg-docs-app/docs/reference/update.md b/docs/voluseg-docs-app/docs/reference/update.md new file mode 100644 index 0000000..d622b7d --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/update.md @@ -0,0 +1,13 @@ +--- +sidebar_label: update +title: update +--- + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From 8c1ba20ff0f9ef67405b43046d47eb48ebc8eac8 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 30 Oct 2024 11:23:17 +0000 Subject: [PATCH 12/27] auto-commit-docs --- .../docs/reference/__init__/__init__.md | 7 + .../docs/reference/steps/__init__.md | 5 + .../docs/reference/steps/step0.md | 21 +++ .../docs/reference/steps/step1.md | 22 +++ .../docs/reference/steps/step2.md | 22 +++ .../docs/reference/steps/step3.md | 23 +++ .../docs/reference/steps/step4.md | 21 +++ .../docs/reference/steps/step4a.md | 31 ++++ .../docs/reference/steps/step4b.md | 35 ++++ .../docs/reference/steps/step4c.md | 40 +++++ .../docs/reference/steps/step4d.md | 42 +++++ .../docs/reference/steps/step4e.md | 24 +++ .../docs/reference/steps/step5.md | 21 +++ .../docs/reference/tools/__init__.md | 5 + .../docs/reference/tools/ants_registration.md | 35 ++++ .../reference/tools/ants_transformation.md | 31 ++++ 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b/docs/voluseg-docs-app/docs/reference/steps/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: steps +title: steps +--- + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step0.md b/docs/voluseg-docs-app/docs/reference/steps/step0.md new file mode 100644 index 0000000..5113143 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step0.md @@ -0,0 +1,21 @@ +--- +sidebar_label: step0 +title: steps.step0 +--- + +#### process\_parameters + +```python +def process_parameters(initial_parameters: dict) -> dict +``` + +Process parameters and create parameter file (pickle). + +**Arguments** + +* **initial_parameters** (`dict`): Initial parameter dictionary + +**Returns** + +* `dict`: Processed parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step1.md b/docs/voluseg-docs-app/docs/reference/steps/step1.md new file mode 100644 index 0000000..eefbce8 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step1.md @@ -0,0 +1,22 @@ +--- +sidebar_label: step1 +title: steps.step1 +--- + +#### process\_volumes + +```python +def process_volumes(parameters: dict) -> None +``` + +Process original volumes and save them to nifti files. +Performs downsampling and padding if specified in parameters. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step2.md b/docs/voluseg-docs-app/docs/reference/steps/step2.md new file mode 100644 index 0000000..e410734 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step2.md @@ -0,0 +1,22 @@ +--- +sidebar_label: step2 +title: steps.step2 +--- + +#### align\_volumes + +```python +def align_volumes(parameters: dict) -> None +``` + +Register volumes to a reference volume. +Generates ANTs transforms files (.mat). + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step3.md b/docs/voluseg-docs-app/docs/reference/steps/step3.md new file mode 100644 index 0000000..ea7489b --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step3.md @@ -0,0 +1,23 @@ +--- +sidebar_label: step3 +title: steps.step3 +--- + +#### mask\_volumes + +```python +def mask_volumes(parameters: dict) -> None +``` + +Create intensity mask from the average registered volume. +Produces figures with masks and histograms. +Produces `mean_timeseries.hdf5` and `volume0.hdf5` files. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4.md b/docs/voluseg-docs-app/docs/reference/steps/step4.md new file mode 100644 index 0000000..223742a --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4.md @@ -0,0 +1,21 @@ +--- +sidebar_label: step4 +title: steps.step4 +--- + +#### detect\_cells + +```python +def detect_cells(parameters: dict) -> None +``` + +Detect cells in volumetric blocks. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4a.md b/docs/voluseg-docs-app/docs/reference/steps/step4a.md new file mode 100644 index 0000000..5817294 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4a.md @@ -0,0 +1,31 @@ +--- +sidebar_label: step4a +title: steps.step4a +--- + +#### define\_blocks + +```python +def define_blocks( + lx: int, ly: int, lz: int, n_cells_block: int, n_voxels_cell: int, + volume_mask: np.ndarray, + volume_peak: np.ndarray) -> Tuple[int, bool, np.ndarray, np.ndarray] +``` + +Get coordinates of individual blocks. + +**Arguments** + +* **lx** (`int`): Number of voxels in x-dimension. +* **ly** (`int`): Number of voxels in y-dimension. +* **lz** (`int`): Number of voxels in z-dimension. +* **n_cells_block** (`int`): Number of cells in each block. +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **volume_mask** (`np.ndarray`): Volume mask. +* **volume_peak** (`np.ndarray`): Volume local intensity maxima (peaks). + +**Returns** + +* `Tuple[int, bool, np.ndarray, np.ndarray]`: Tuple containing: Number of blocks, valid blocks, coordinates of block start, +and coordinates of block end. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4b.md b/docs/voluseg-docs-app/docs/reference/steps/step4b.md new file mode 100644 index 0000000..ba394f4 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4b.md @@ -0,0 +1,35 @@ +--- +sidebar_label: step4b +title: steps.step4b +--- + +#### process\_block\_data + +```python +def process_block_data( + xyz0: Tuple[int, int, int], xyz1: Tuple[int, int, int], parameters: dict, + color_i: int, lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, bvolume_mean: h5py.Dataset, + bvolume_peak: h5py.Dataset, timepoints: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Load timeseries in individual blocks, slice-time correct, and find similar timeseries. + +**Arguments** + +* **xyz0** (`Tuple[int, int, int]`): Start coordinates of block. +* **xyz1** (`Tuple[int, int, int]`): End coordinates of block. +* **parameters** (`dict`): Parameters dictionary. +* **color_i** (`int`): Color index. +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): The resolution of x, y, and z dimensions. +* **ball_diam** (`np.ndarray`): The diameter of a cell-area sphere. +* **bvolume_mean** (`h5py.Dataset`): Spark broadcast variable: volume mean. +* **bvolume_peak** (`h5py.Dataset`): Spark broadcast variable: local intensity maximum volume (peak). +* **timepoints** (`np.ndarray`): Timepoints at which segmentation will be performed. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple containing: Voxel coordinates, timeseries, peak indices, and similarity matrix of peaks. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4c.md b/docs/voluseg-docs-app/docs/reference/steps/step4c.md new file mode 100644 index 0000000..9f184ea --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4c.md @@ -0,0 +1,40 @@ +--- +sidebar_label: step4c +title: steps.step4c +--- + +#### initialize\_block\_cells + +```python +def initialize_block_cells( + n_voxels_cell: int, n_voxels_block: int, n_cells: int, + voxel_xyz: np.ndarray, voxel_timeseries: np.ndarray, peak_idx: np.ndarray, + peak_valids: np.ndarray, voxel_similarity_peak: np.ndarray, + lxyz: Tuple[int, int, int], rxyz: Tuple[float, float, float], + ball_diam: np.ndarray, ball_diam_xyz0: np.ndarray +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Initialize cell positions in individual blocks. + +**Arguments** + +* **n_voxels_cell** (`int`): Number of voxels in each cell. +* **n_voxels_block** (`int`): Number of voxels in block. +* **n_cells** (`int`): Number of cells. +* **voxel_xyz** (`np.ndarray`): Voxel coordinates. +* **voxel_timeseries** (`np.ndarray`): Voxel timeseries. +* **peak_idx** (`np.ndarray`): Peak indices. +* **peak_valids** (`np.ndarray`): Valid local-intensity maxima (used to determine number of cells). +* **voxel_similarity_peak** (`np.ndarray`): Similarity between voxels: defined by the combination of spatial proximity +and temporal similarity (the voxels are neighbors of each other and also +correlated with each other). +* **lxyz** (`Tuple[int, int, int]`): Number of voxels in x, y, and z dimensions. +* **rxyz** (`Tuple[float, float, float]`): Resolution of x, y, z dimensions. +* **ball_diam** (`np.ndarray`): Diameter of a sphere that may defines a cell boundary. +* **ball_diam_xyz0** (`np.ndarray`): Midpoint of the sphere. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4d.md b/docs/voluseg-docs-app/docs/reference/steps/step4d.md new file mode 100644 index 0000000..d0d1f2c --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4d.md @@ -0,0 +1,42 @@ +--- +sidebar_label: step4d +title: steps.step4d +--- + +#### nnmf\_sparse + +```python +def nnmf_sparse( + V0: np.ndarray, + XYZ0: np.ndarray, + W0: np.ndarray, + B0: np.ndarray, + S0: np.ndarray, + tolfun: float = 1e-4, + miniter: int = 10, + maxiter: int = 100, + timeseries_mean=1.0, + timepoints: np.ndarray = None, + verbosity: bool = True) -> Tuple[np.ndarray, np.ndarray, float] +``` + +Cell detection via nonnegative matrix factorization with sparseness projection. + +**Arguments** + +* **V0** (`np.ndarray`): Voxel timeseries (voxel_timeseries_valid). +* **XYZ0** (`np.ndarray`): Voxel coordinates (voxel_xyz_valid). +* **W0** (`np.ndarray`): Initial cell weights (cell_weight_init_valid). +* **B0** (`np.ndarray`): Cell neighborhood (cell_neighborhood_valid). +* **S0** (`np.ndarray`): Cell sparseness (cell_sparseness). +* **tolfun** (`float, optional`): Tolerance for convergence, by default 1e-4. +* **miniter** (`int, optional`): Minimum number of iterations, by default 10. +* **maxiter** (`int, optional`): Maximum number of iterations, by default 100. +* **timeseries_mean** (`float, optional`): Mean timeseries value, by default 1.0. +* **timepoints** (`np.ndarray, optional`): Timepoints to use, by default None. +* **verbosity** (`bool, optional`): Print progress, by default True. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, float]`: Tuple containing: Spatial footprint, temporal footprint, convergence error. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step4e.md b/docs/voluseg-docs-app/docs/reference/steps/step4e.md new file mode 100644 index 0000000..48e4804 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step4e.md @@ -0,0 +1,24 @@ +--- +sidebar_label: step4e +title: steps.step4e +--- + +#### collect\_blocks + +```python +def collect_blocks( + color_i: int, parameters: dict +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] +``` + +Collect cells across all blocks. + +**Arguments** + +* **color_i** (`int`): Color index. +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray]`: Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. + diff --git a/docs/voluseg-docs-app/docs/reference/steps/step5.md b/docs/voluseg-docs-app/docs/reference/steps/step5.md new file mode 100644 index 0000000..287fdbc --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/steps/step5.md @@ -0,0 +1,21 @@ +--- +sidebar_label: step5 +title: steps.step5 +--- + +#### clean\_cells + +```python +def clean_cells(parameters: dict) -> None +``` + +Remove noise cells, detrend and detect baseline. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/__init__.md b/docs/voluseg-docs-app/docs/reference/tools/__init__.md new file mode 100644 index 0000000..f94abd3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/__init__.md @@ -0,0 +1,5 @@ +--- +sidebar_label: tools +title: tools +--- + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md new file mode 100644 index 0000000..2a99b45 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_registration.md @@ -0,0 +1,35 @@ +--- +sidebar_label: ants_registration +title: tools.ants_registration +--- + +#### ants\_registration + +```python +def ants_registration(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + prefix_out_tform: str, + typ: str, + in_tform: str = None, + restrict: str = None) -> str +``` + +ANTs registration. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs directory. +* **in_nii** (`str`): Input nifti file. +* **ref_nii** (`str`): Reference nifti file. +* **out_nii** (`str`): Output nifti file. +* **prefix_out_tform** (`str`): Prefix for output transformation files. +* **typ** (`str`): Type of transformation. +* **in_tform** (`str (optional)`): Initial transformation file. Default is None. +* **restrict** (`str (optional)`): Restrict deformation. Default is None. + +**Returns** + +* `str`: ANTs registration command. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md new file mode 100644 index 0000000..b7221ef --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ants_transformation.md @@ -0,0 +1,31 @@ +--- +sidebar_label: ants_transformation +title: tools.ants_transformation +--- + +#### ants\_transformation + +```python +def ants_transformation(dir_ants: str, + in_nii: str, + ref_nii: str, + out_nii: str, + in_tform: str, + interpolation="Linear") -> str +``` + +Application of ANTs transform. + +**Arguments** + +* **dir_ants** (`str`): Path to ANTs binaries. +* **in_nii** (`str`): Path to input nifti file. +* **ref_nii** (`str`): Path to reference nifti file. +* **out_nii** (`str`): Path to output nifti file. +* **in_tform** (`str`): Path to input transform file (.mat). +* **interpolation** (`str`): Interpolation method. + +**Returns** + +* `str`: ANTs transformation command string. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/aws.md b/docs/voluseg-docs-app/docs/reference/tools/aws.md new file mode 100644 index 0000000..8d28c12 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/aws.md @@ -0,0 +1,48 @@ +--- +sidebar_label: aws +title: tools.aws +--- + +## JobDefinitionException Objects + +```python +class JobDefinitionException(Exception) +``` + +#### format\_voluseg\_kwargs + +```python +def format_voluseg_kwargs(voluseg_kwargs: dict) -> dict +``` + +#### run\_job\_in\_aws\_batch + +```python +def run_job_in_aws_batch(job_name_prefix: str, + voluseg_kwargs: dict, + aws_local_profile: str = None, + vcpus: int = 32, + memory: int = 65536) +``` + +Submit a Voluseg job to AWS Batch. + +**Arguments** + +* **job_name_prefix** (`str`): Job name prefix, it will be concatenated with the current timestamp. +Example: "my-voluseg-job" -> "my-voluseg-job-2024-10-01T06-39-10Z00-00" +* **voluseg_kwargs** (`dict`): Voluseg parameters. +* **aws_local_profile** (`str`): AWS profile name. Default is None. +* **vcpus** (`int`): Number of vCPUs. Default is 32. +* **memory** (`int`): Memory in MB. Default is 65536. + +**Returns** + +* `dict`: Dictionary with the job_name and batch_job_id. + +#### export\_to\_s3 + +```python +def export_to_s3(local_path: str, bucket_name: str, object_name: str) +``` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/ball.md b/docs/voluseg-docs-app/docs/reference/tools/ball.md new file mode 100644 index 0000000..61af6f2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/ball.md @@ -0,0 +1,22 @@ +--- +sidebar_label: ball +title: tools.ball +--- + +#### ball + +```python +def ball(radi: float, affine_matrix: np.ndarray) -> tuple +``` + +Morphological cell balls and midpoints. + +**Arguments** + +* **radi** (`float`): Radius of ball. +* **affine_matrix** (`np.ndarray`): Affine matrix. + +**Returns** + +* `tuple`: Tuple containing: Ball and midpoints. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md new file mode 100644 index 0000000..1dd4c85 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/clean_signal.md @@ -0,0 +1,23 @@ +--- +sidebar_label: clean_signal +title: tools.clean_signal +--- + +#### clean\_signal + +```python +def clean_signal(parameters: dict, + timeseries: np.ndarray) -> Tuple[np.ndarray, np.ndarray] +``` + +Detrend, filter, and estimate dynamic baseline for input timeseries. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **timeseries** (`np.ndarray`): Input timeseries. + +**Returns** + +* `Tuple[np.ndarray, np.ndarray]`: TODO - add description + diff --git a/docs/voluseg-docs-app/docs/reference/tools/constants.md b/docs/voluseg-docs-app/docs/reference/tools/constants.md new file mode 100644 index 0000000..7f720df --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/constants.md @@ -0,0 +1,15 @@ +--- +sidebar_label: constants +title: tools.constants +--- + +#### ori + +#### ali + +#### nii + +#### hdf + +#### dtype + diff --git a/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md new file mode 100644 index 0000000..c32fbf6 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/evenly_parallelize.md @@ -0,0 +1,21 @@ +--- +sidebar_label: evenly_parallelize +title: tools.evenly_parallelize +--- + +#### evenly\_parallelize + +```python +def evenly_parallelize(input_list: list) -> RDD +``` + +Return evenly partitioned spark resilient distributed dataset (RDD). + +**Arguments** + +* **input_list** (`list`): List of input elements. + +**Returns** + +* `RDD`: Spark resilient distributed dataset (RDD). + diff --git a/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md new file mode 100644 index 0000000..c30966f --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/get_volume_name.md @@ -0,0 +1,25 @@ +--- +sidebar_label: get_volume_name +title: tools.get_volume_name +--- + +#### get\_volume\_name + +```python +def get_volume_name(fullname_volume: str, + dir_prefix: str = None, + plane_i: int = None) -> str +``` + +Get name of volume (with directory prefix and plane suffix). + +**Arguments** + +* **fullname_volume** (`str`): Full name of volume. +* **dir_prefix** (`str (optional)`): Prefix for directory. Default is None. +* **plane_i** (`int (optional)`): Index of plane. Default is None. + +**Returns** + +* `str`: Name of volume. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md new file mode 100644 index 0000000..8c41212 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/load_metadata.md @@ -0,0 +1,24 @@ +--- +sidebar_label: load_metadata +title: tools.load_metadata +--- + +#### load\_metadata + +```python +def load_metadata(parameters: dict, filename_channel: str, + filename_stack: str) -> dict +``` + +Fetch z-resolution, exposure time, and stack frequency. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename_channel** (`str`): Filename XML file containing channel information. +* **filename_stack** (`str`): Filename of XML file containing stack information. + +**Returns** + +* `dict`: Parameters dictionary. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/load_volume.md b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md new file mode 100644 index 0000000..fdb0f76 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/load_volume.md @@ -0,0 +1,22 @@ +--- +sidebar_label: load_volume +title: tools.load_volume +--- + +#### load\_volume + +```python +def load_volume(fullname_ext: str) -> Union[np.ndarray, None] +``` + +Load volume based on input name and extension. +Supports tiff, hdf5, klb, and nifti formats. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. + +**Returns** + +* `np.ndarray or None`: Volume as numpy array, or None if volume could not be loaded. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/nwb.md b/docs/voluseg-docs-app/docs/reference/tools/nwb.md new file mode 100644 index 0000000..4ad3a77 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/nwb.md @@ -0,0 +1,117 @@ +--- +sidebar_label: nwb +title: tools.nwb +--- + +#### open\_nwbfile\_local + +```python +@contextmanager +def open_nwbfile_local(file_path: str) +``` + +Context manager to open and close a local NWB file. + +**Arguments** + +* **file_path** (`str`): Path to NWB file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile\_remote + +```python +@contextmanager +def open_nwbfile_remote(s3_url: str, output_path: str) +``` + +Context manager to open and close a remote NWB file. + +**Arguments** + +* **s3_url** (`str`): S3 URL to NWB file. +* **output_path** (`str`): Output path to cache the remote file. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### open\_nwbfile + +```python +@contextmanager +def open_nwbfile(input_path: str, remote: bool, output_path: str = None) +``` + +Open and close an NWB file from either a local or remote source. + +**Arguments** + +* **input_path** (`str`): Path to the NWB file. This can be a local file path or an S3 URL. +* **remote** (`bool`): If True, the file is assumed to be remote (S3 URL), otherwise, it is assumed to be a local file. +* **output_path** (`str`): Output path, only used to cache remote files. + +**Yields** + +* `pynwb.NWBFile`: The opened NWB file. + +#### find\_nwbfile\_volume\_object\_name + +```python +def find_nwbfile_volume_object_name(nwbfile: pynwb.NWBFile) -> str +``` + +Find the name of the `TwoPhotonSeries` volume object in the NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. + +**Returns** + +* `str`: Name of the volume object. + +#### get\_nwbfile\_volume + +```python +def get_nwbfile_volume( + nwbfile: pynwb.NWBFile, + acquisition_name: str = "TwoPhotonSeries") -> pynwb.NWBFile +``` + +Get `TwoPhotonSeries` object from NWB file. + +**Arguments** + +* **nwbfile** (`pynwb.NWBFile`): NWB file. +* **acquisition_name** (`str (default: "TwoPhotonSeries")`): Acquisition name. + +**Returns** + +* `pynwb.NWBFile`: NWB file. + +#### write\_nwbfile + +```python +def write_nwbfile(output_path: str, cell_x: np.ndarray, cell_y: np.ndarray, + cell_z: np.ndarray, cell_weights: np.ndarray, + cell_timeseries: np.ndarray) -> None +``` + +Write results to a local NWB file. + +**Arguments** + +* **output_path** (`str`): Output path. +* **cell_x** (`np.ndarray`): Voxel X coordinates for all cells. +* **cell_y** (`np.ndarray`): Voxel Y coordinates for all cells. +* **cell_z** (`np.ndarray`): Voxel Z coordinates for all cells. +* **cell_weights** (`np.ndarray`): Voxel weights for all cells. +* **cell_timeseries** (`np.ndarray`): Fluorescence timeseries data for all cells. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md new file mode 100644 index 0000000..5ecd000 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameter_dictionary.md @@ -0,0 +1,85 @@ +--- +sidebar_label: parameter_dictionary +title: tools.parameter_dictionary +--- + +#### parameter\_dictionary + +```python +def parameter_dictionary(detrending: str = "standard", + registration: str = "medium", + registration_restrict: str = "", + diam_cell: float = 6.0, + dir_ants: str = "", + dir_input: str = "", + dir_output: str = "", + dir_transform: str = "", + ds: int = 2, + planes_pad: int = 0, + planes_packed: bool = False, + parallel_clean: bool = True, + parallel_volume: bool = True, + save_volume: bool = False, + type_timepoints: str = "dff", + type_mask: str = "geomean", + timepoints: int = 1000, + f_hipass: float = 0, + f_volume: float = 2.0, + n_cells_block: int = 316, + n_colors: int = 1, + res_x: float = 0.40625, + res_y: float = 0.40625, + res_z: float = 5.0, + t_baseline: int = 300, + t_section: float = 0.01, + thr_mask: float = 0.5, + volume_fullnames_input: Union[list[str], None] = None, + volume_names: Union[list[str], None] = None, + input_dirs: Union[list[str], None] = None, + ext: Union[str, None] = None, + lt: Union[int, None] = None, + affine_matrix: Union[list, None] = None) -> dict +``` + +Return a parameter dictionary with specified defaults. + +**Arguments** + +* **detrending** (`str, optional`): Type of detrending: 'standard', 'robust', or 'none' (default is 'standard'). +* **registration** (`str, optional`): Quality of registration: 'high', 'medium', 'low' or 'none' (default is 'medium'). +* **registration_restrict** (`str, optional`): Restrict registration (e.g. 1x1x1x1x1x1x0x0x0x1x1x0) (default is an empty string). +* **diam_cell** (`float, optional`): Cell diameter in microns (default is 6.0). +* **dir_ants** (`str, optional`): Path to the ANTs directory (default is an empty string). +* **dir_input** (`str, optional`): Path to input directories, separate multiple directories with ';' (default is an empty string). +* **dir_output** (`str, optional`): Path to the output directory (default is an empty string). +* **dir_transform** (`str, optional`): Path to the transform directory (default is an empty string). +* **ds** (`int, optional`): Spatial coarse-graining in x-y dimension (default is 2). +* **planes_pad** (`int, optional`): Number of planes to pad the volume with for robust registration (default is 0). +* **planes_packed** (`bool, optional`): Packed planes in each volume, for single plane imaging with packed planes (default is False). +* **parallel_clean** (`bool, optional`): Parallelization of final cleaning (True is fast but memory-intensive, default is True). +* **parallel_volume** (`bool, optional`): Parallelization of mean-volume computation (True is fast but memory-intensive, default is True). +* **save_volume** (`bool, optional`): Save registered volumes after segmentation, True keeps a copy of the volumes (default is False). +* **type_timepoints** (`str, optional`): Type of timepoints to use for cell detection: 'dff', 'periodic' or 'custom' (default is 'dff'). +* **type_mask** (`str, optional`): Type of volume averaging for the mask: 'mean', 'geomean' or 'max' (default is 'geomean'). +* **timepoints** (`int, optional`): Number ('dff', 'periodic') or vector ('custom') of timepoints for segmentation (default is 1000). +* **f_hipass** (`float, optional`): Frequency (Hz) for high-pass filtering of cell timeseries (default is 0). +* **f_volume** (`float, optional`): Imaging frequency in Hz (default is 2.0). +* **n_cells_block** (`int, optional`): Number of cells in a block. Small number is fast but can lead to blocky output (default is 316). +* **n_colors** (`int, optional`): Number of brain colors (2 in two-color volumes, default is 1). +* **res_x** (`float, optional`): X resolution in microns (default is 0.40625). +* **res_y** (`float, optional`): Y resolution in microns (default is 0.40625). +* **res_z** (`float, optional`): Z resolution in microns (default is 5.0). +* **t_baseline** (`int, optional`): Interval for baseline calculation in seconds (default is 300). +* **t_section** (`float, optional`): Exposure time in seconds for slice acquisition (default is 0.01). +* **thr_mask** (`float, optional`): Threshold for volume mask: 0 < thr <= 1 (probability) or thr > 1 (intensity) (default is 0.5). +* **volume_fullnames_input** (`list[str], optional`): List of full volume names (default is None). +* **volume_names** (`list[str], optional`): List of volume names (default is None). +* **input_dirs** (`list[str], optional`): List of input directories (default is None). +* **ext** (`str, optional`): File extension (default is None). +* **lt** (`int, optional`): Number of volumes (default is None). +* **affine_matrix** (`list, optional`): Affine matrix (default is None). + +**Returns** + +* `dict`: A dictionary of validated parameters with their default values. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameters.md b/docs/voluseg-docs-app/docs/reference/tools/parameters.md new file mode 100644 index 0000000..4efb1b0 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters.md @@ -0,0 +1,38 @@ +--- +sidebar_label: parameters +title: tools.parameters +--- + +#### load\_parameters + +```python +def load_parameters(filename: str) -> dict +``` + +Load previously saved parameters from filename. + +**Arguments** + +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `dict`: Parameters dictionary. + +#### save\_parameters + +```python +def save_parameters(parameters: dict, filename: str) -> None +``` + +Save parameters to filename. + +**Arguments** + +* **parameters** (`dict`): Parameters dictionary. +* **filename** (`str`): Filename of parameter file. + +**Returns** + +* `None` + diff --git a/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md new file mode 100644 index 0000000..ce1aad3 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/parameters_models.md @@ -0,0 +1,161 @@ +--- +sidebar_label: parameters_models +title: tools.parameters_models +--- + +## Detrending Objects + +```python +class Detrending(str, Enum) +``` + +#### standard + +#### robust + +#### none + +## Registration Objects + +```python +class Registration(str, Enum) +``` + +#### high + +#### medium + +#### low + +#### none + +## TypeTimepoints Objects + +```python +class TypeTimepoints(str, Enum) +``` + +#### dff + +#### periodic + +#### custom + +## TypeMask Objects + +```python +class TypeMask(str, Enum) +``` + +#### mean + +#### geomean + +#### max + +## ParametersModel Objects + +```python +class ParametersModel(BaseModel) +``` + +#### detrending + +#### registration + +#### registration\_restrict + +#### diam\_cell + +#### dir\_ants + +#### dir\_input + +#### dir\_output + +#### dir\_transform + +#### ds + +#### planes\_pad + +#### planes\_packed + +#### parallel\_clean + +#### parallel\_volume + +#### save\_volume + +#### type\_timepoints + +#### type\_mask + +#### timepoints + +#### f\_hipass + +#### f\_volume + +#### n\_cells\_block + +#### n\_colors + +#### res\_x + +#### res\_y + +#### res\_z + +#### t\_baseline + +#### t\_section + +#### thr\_mask + +#### volume\_fullnames\_input + +#### volume\_names + +#### input\_dirs + +#### ext + +#### lt + +#### affine\_matrix + +#### dim\_order + +#### remote + +#### output\_to\_nwb + +#### convert\_array\_to\_list + +```python +@model_validator(mode="before") +def convert_array_to_list(cls, values) +``` + +Validator to automatically convert NumPy arrays to lists. + +#### model\_dump + +```python +def model_dump(use_np_array: bool = True, *args, **kwargs) +``` + +Override the model_dump method to convert lists to NumPy arrays (if use_np_array is True) +and Enums to their values. + +**Arguments** + +* **use_np_array** (`bool, optional`): Convert lists to NumPy arrays (default is True) +* ***args**: Positional arguments to pass to the parent class +* ****kwargs**: Keyword arguments to pass to the parent class + +**Returns** + +* `dict`: A dictionary of the model's data + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sample_data.md b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md new file mode 100644 index 0000000..01fab2e --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sample_data.md @@ -0,0 +1,61 @@ +--- +sidebar_label: sample_data +title: tools.sample_data +--- + +#### download\_sample\_data + +```python +def download_sample_data(destination_folder: str = ".", + data_type: str = "h5_dir") -> Union[str, None] +``` + +Download sample data for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. +* **data_type** (`str, optional`): Type of data to download. Options are "h5_dir" and "nwb_file". + +**Returns** + +* `str or None`: Path to the folder or file where the data was downloaded, or None if the download failed. + +#### download\_sample\_data\_nwb\_file + +```python +def download_sample_data_nwb_file( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample NWB file for Voluseg. +Ref: https://gui-staging.dandiarchive.org/dandiset/215495/draft + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the downloaded file, or None if the download failed. + +#### download\_sample\_data\_h5\_dir + +```python +def download_sample_data_h5_dir( + destination_folder: str = ".") -> Union[str, None] +``` + +Download sample data (h5 directory) for Voluseg. + +**Arguments** + +* **destination_folder** (`str, optional`): Folder where the sample data should be downloaded. If not provided, the data will be downloaded +to the current working directory. + +**Returns** + +* `str or None`: Path to the folder where the data was extracted, or None if the download failed. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/save_volume.md b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md new file mode 100644 index 0000000..2c0d725 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/save_volume.md @@ -0,0 +1,26 @@ +--- +sidebar_label: save_volume +title: tools.save_volume +--- + +#### save\_volume + +```python +def save_volume(fullname_ext: str, + volume: np.ndarray, + affine_matrix: np.ndarray = None) -> Union[bool, None] +``` + +Save volume in output format. +Formats currently accepted are: nifti and hdf5. + +**Arguments** + +* **fullname_ext** (`str`): Full name of volume with extension. +* **volume** (`np.ndarray`): Volume as numpy array. +* **affine_matrix** (`np.ndarray`): Affine matrix for nifti format. + +**Returns** + +* `bool or None`: True if volume was saved successfully, None if volume could not be saved. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sparseness.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md new file mode 100644 index 0000000..5a4a724 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness.md @@ -0,0 +1,22 @@ +--- +sidebar_label: sparseness +title: tools.sparseness +--- + +#### sparseness + +```python +def sparseness(W: np.ndarray, dim: int = 0) -> np.ndarray +``` + +Vector sparseness along specified dimension. + +**Arguments** + +* **W** (`np.ndarray`): Input array. +* **dim** (`int, optional`): Dimension along which to compute sparseness, by default 0. + +**Returns** + +* `np.ndarray`: Sparseness of input array along specified dimension. + diff --git a/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md new file mode 100644 index 0000000..9f92ba2 --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/tools/sparseness_projection.md @@ -0,0 +1,25 @@ +--- +sidebar_label: sparseness_projection +title: tools.sparseness_projection +--- + +#### sparseness\_projection + +```python +def sparseness_projection(Si: np.ndarray, + s: float, + at_least_as_sparse: bool = False) -> np.ndarray +``` + +Hoyer sparseness projection. + +**Arguments** + +* **Si** (`np.ndarray`): Input signal. +* **s** (`float`): Sparseness parameter. +* **at_least_as_sparse** (`bool, optional`): Enforce at least as sparse, by default False. + +**Returns** + +* `np.ndarray`: Sparse signal. + diff --git a/docs/voluseg-docs-app/docs/reference/update.md b/docs/voluseg-docs-app/docs/reference/update.md new file mode 100644 index 0000000..d622b7d --- /dev/null +++ b/docs/voluseg-docs-app/docs/reference/update.md @@ -0,0 +1,13 @@ +--- +sidebar_label: update +title: update +--- + +#### voluseg\_update + +```python +def voluseg_update() -> None +``` + +Shortcut to update package. + From ec63c3cf4eb7ba5e1facde0308ed9d73466f06a6 Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 14:24:39 +0100 Subject: [PATCH 13/27] updates --- .../{iac_aws_batch.md => iac_aws_batch.mdx} | 16 +- .../docs/getting_started/installation.md | 9 +- docs/voluseg-docs-app/package.json | 8 +- docs/voluseg-docs-app/yarn.lock | 394 +++++++++--------- 4 files changed, 220 insertions(+), 207 deletions(-) rename docs/voluseg-docs-app/docs/getting_started/{iac_aws_batch.md => iac_aws_batch.mdx} (86%) diff --git a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx similarity index 86% rename from docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md rename to docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx index 41890c6..3d84293 100644 --- a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.md +++ b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx @@ -18,14 +18,16 @@ Here we provide instructions for setting up your Voluseg service to run jobs in AWS CDK is a very convenient tool, it helps automate the provisioning of AWS infrastructure and organizes all created resources in a CloudFormation stack, which can be easily updated or deleted. Follow these steps if you're running the Voluseg CDK stack for the first time: -- go to `cloned_voluseg_repo_path/iac/aws_batch` directory. -- run `pip install -r requirements.txt` to install the required Python packages. -- run `cdk bootstrap` to set up the CDK deployment infrastructure (CKDToolkit) in your AWS account. This only needs to be done once. -- run `cdk deploy` to deploy the stack to your default AWS account/region. -- you will be prompted to confirm the deployment. Review the changes, then type `y` and hit enter. +1. go to `cloned_voluseg_repo_path/iac/aws_batch` directory. +2. run `pip install -r requirements.txt` to install the required Python packages. +3. run `cdk bootstrap` to set up the CDK deployment infrastructure (CKDToolkit) in your AWS account. This only needs to be done once. +4. run `cdk deploy` to deploy the stack to your default AWS account/region. +5. you will be prompted to confirm the deployment. Review the changes, then type `y` and hit enter. If deployment is successful, you will be able to see the stacks in the CloudFormation page in AWS console. +:::tip + Other useful CDK commands: - `cdk ls` - list all stacks in the app. - `cdk synth` to synthesize the CloudFormation template without deploying it. @@ -33,6 +35,10 @@ Other useful CDK commands: - `cdk destroy` - destroy the stack. - `cdk docs` - open CDK documentation. +::: + + + This deployment will create the following AWS resources in your account: - IAM roles: diff --git a/docs/voluseg-docs-app/docs/getting_started/installation.md b/docs/voluseg-docs-app/docs/getting_started/installation.md index 0bc41f3..43219f4 100644 --- a/docs/voluseg-docs-app/docs/getting_started/installation.md +++ b/docs/voluseg-docs-app/docs/getting_started/installation.md @@ -4,9 +4,14 @@ sidebar_position: 2 --- -## Installation +### Prerequisites +In order to use Voluseg you need to have the following dependencies installed on your machine: -To get started we recommend using [Anaconda](https://www.anaconda.com/distribution/) or [Virtual Environment](https://docs.python.org/3/library/venv.html) with Python 3.11 or higher. +- Python >= 3.11 +- Java SE Development Kit 17 +- [ANTs - Advanced Normalization Tools](https://github.com/ANTsX/ANTs) + +It is recommended to install Voluseg in a separate environment, using [Anaconda](https://www.anaconda.com/distribution/) or [Virtual Environment](https://docs.python.org/3/library/venv.html). ### Install with pip diff --git a/docs/voluseg-docs-app/package.json b/docs/voluseg-docs-app/package.json index 4ad1632..61fcfd4 100644 --- a/docs/voluseg-docs-app/package.json +++ b/docs/voluseg-docs-app/package.json @@ -14,8 +14,8 @@ "write-heading-ids": "docusaurus write-heading-ids" }, "dependencies": { - "@docusaurus/core": "3.3.2", - "@docusaurus/preset-classic": "3.3.2", + "@docusaurus/core": "^3.5.2", + "@docusaurus/preset-classic": "^3.5.2", "@mdx-js/react": "^3.0.0", "clsx": "^2.0.0", "prism-react-renderer": "^2.3.0", @@ -23,8 +23,8 @@ "react-dom": "^18.0.0" }, "devDependencies": { - "@docusaurus/module-type-aliases": "3.3.2", - "@docusaurus/types": "3.3.2" + "@docusaurus/module-type-aliases": "^3.5.2", + "@docusaurus/types": "^3.5.2" }, "browserslist": { "production": [ diff --git a/docs/voluseg-docs-app/yarn.lock b/docs/voluseg-docs-app/yarn.lock index c1e94b4..95459ae 100644 --- a/docs/voluseg-docs-app/yarn.lock +++ b/docs/voluseg-docs-app/yarn.lock @@ -1236,10 +1236,10 @@ "@docsearch/css" "3.6.0" algoliasearch "^4.19.1" -"@docusaurus/core@3.3.2": - 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version "0.2.0-alpha.43" - resolved "https://registry.yarnpkg.com/infima/-/infima-0.2.0-alpha.43.tgz#f7aa1d7b30b6c08afef441c726bac6150228cbe0" - integrity sha512-2uw57LvUqW0rK/SWYnd/2rRfxNA5DDNOh33jxF7fy46VWoNhGxiUQyVZHbBMjQ33mQem0cjdDVwgWVAmlRfgyQ== +infima@0.2.0-alpha.44: + version "0.2.0-alpha.44" + resolved "https://registry.yarnpkg.com/infima/-/infima-0.2.0-alpha.44.tgz#9cd9446e473b44d49763f48efabe31f32440861d" + integrity sha512-tuRkUSO/lB3rEhLJk25atwAjgLuzq070+pOW8XcvpHky/YbENnRRdPd85IBkyeTgttmOy5ah+yHYsK1HhUd4lQ== inflight@^1.0.4: version "1.0.6" From 8167b5b95ddada0c4c58fefa414e0aa9c31c6bdb Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 14:28:34 +0100 Subject: [PATCH 14/27] admonition --- docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx index 3d84293..705b8ff 100644 --- a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx @@ -26,9 +26,7 @@ Follow these steps if you're running the Voluseg CDK stack for the first time: If deployment is successful, you will be able to see the stacks in the CloudFormation page in AWS console. -:::tip - -Other useful CDK commands: +:::tip[Other useful CDK commands:] - `cdk ls` - list all stacks in the app. - `cdk synth` to synthesize the CloudFormation template without deploying it. - `cdk diff` - compare deployed stack with current state. From a1b734d38e20d3f278f109a9cd845aa629230caa Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 14:55:29 +0100 Subject: [PATCH 15/27] dandi hub --- .../docs/getting_started/iac_aws_batch.mdx | 2 +- .../docs/getting_started/parameters.mdx | 2 +- .../docs/getting_started/running.mdx | 2 +- .../docs/getting_started/running_dandihub.mdx | 44 +++++++++++++++++++ 4 files changed, 47 insertions(+), 3 deletions(-) create mode 100644 docs/voluseg-docs-app/docs/getting_started/running_dandihub.mdx diff --git a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx index 705b8ff..1866848 100644 --- a/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/iac_aws_batch.mdx @@ -1,6 +1,6 @@ --- title: Running on AWS Batch -sidebar_position: 4 +sidebar_position: 5 --- Here we provide instructions for setting up your Voluseg service to run jobs in AWS Batch. First you will need to provision the base AWS Batch infrastructure using CDK. This includes IAM roles, VPC, Security Group, Batch Compute Environments and Batch Job Queues. Next you will need to configure your compute resource controller to submit jobs to AWS Batch. Finally, when you submit jobs from the web interface, you must select aws_batch as the run method. diff --git a/docs/voluseg-docs-app/docs/getting_started/parameters.mdx b/docs/voluseg-docs-app/docs/getting_started/parameters.mdx index 5168781..312eb06 100644 --- a/docs/voluseg-docs-app/docs/getting_started/parameters.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/parameters.mdx @@ -1,6 +1,6 @@ --- title: Pipeline Parameters -sidebar_position: 5 +sidebar_position: 8 --- ## Parameters dictionary diff --git a/docs/voluseg-docs-app/docs/getting_started/running.mdx b/docs/voluseg-docs-app/docs/getting_started/running.mdx index d245fe3..8b17d16 100644 --- a/docs/voluseg-docs-app/docs/getting_started/running.mdx +++ b/docs/voluseg-docs-app/docs/getting_started/running.mdx @@ -18,7 +18,7 @@ The Voluseg pipeline consists of an initial setup of parameters followed by five To get familiar with Voluseg, let's run a simple example with a demo dataset. -### Download the necessary resources +### Download the sample data To run the demo you will need start by downloading the sample data to your local machine: ```python diff --git a/docs/voluseg-docs-app/docs/getting_started/running_dandihub.mdx b/docs/voluseg-docs-app/docs/getting_started/running_dandihub.mdx new file mode 100644 index 0000000..b61f75e --- /dev/null +++ b/docs/voluseg-docs-app/docs/getting_started/running_dandihub.mdx @@ -0,0 +1,44 @@ +--- +title: Running on DANDI Hub +sidebar_position: 4 +--- + +## DANDI Hub +Neuroscientists registered at [DANDI archive](https://dandiarchive.org/) can use the [DANDI Hub](https://www.dandiarchive.org/handbook/50_hub/) to interact with the data stored in the archive. +DANDI Hub is a JupyterHub instance in the cloud, free to use for exploratory analysis of data on DANDI. + +## Setup +Follow the instructions in the [DANDI Hub Handbook](https://www.dandiarchive.org/handbook/50_hub/) to spin up a Jupyter notebook instance on DANDI Hub. + +Once you have a Jupyter notebook running on DANDI Hub, follow these steps: +1. Open a new terminal +2. Create a folder for your Voluseg run: `mkdir my_voluseg_run` +3. Change to the new directory: `cd my_voluseg_run` + +## Running Voluseg with Apptainer +Pull the image from GHCR and convert it to an Apptainer image: +```bash +apptainer pull docker://ghcr.io/mikarubi/voluseg/voluseg:latest +``` + +You should see a `.sif` file in your working directory, this is the Voluseg image converted to the Apptainer format. + +You can now run the Voluseg pipeline using this Apptainer image. For example: +```bash +apptainer exec \ +--bind $(pwd)/output:/voluseg/output \ +voluseg_latest.sif \ +python3 /voluseg/app/app.py \ +--registration high \ +--diam-cell 5.0 \ +--no-parallel-volume \ +--no-parallel-clean \ +--dir-input "https://dandiarchive.s3.amazonaws.com/blobs/057/ecb/057ecbef-e732-4e94-8d99-40ebb74d346e" \ +2>&1 | tee log_file.log +``` + +The command above will: +- Use the data stored in the S3 path (from DANDI archive) as input +- Run the Voluseg pipeline with the user-specified parameters +- Store the output in the `output` directory +- Save the log output to a file named `log_file.log` \ No newline at end of file From 12d645888fe3ddd40c6d0a86edba90e929504181 Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 15:01:01 +0100 Subject: [PATCH 16/27] landing page --- .../src/components/HomepageFeatures/index.js | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js b/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js index b7e4493..663d844 100644 --- a/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js +++ b/docs/voluseg-docs-app/src/components/HomepageFeatures/index.js @@ -8,16 +8,25 @@ const FeatureList = [ // Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, description: ( <> - Voluseg provides advanced algorithms for efficient segemntation of volumetric calcium imaging data. + Voluseg provides advanced algorithms for automatic segmentation of volumetric calcium imaging data. ), }, { - title: 'Automatic Cell extraction pipeline', + title: 'Efficient for large datasets', + // Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, + description: ( + <> + Voluseg is designed to handle whole brain volumetric data with ease. It is optimized for parallel processing using Spark. + + ), + }, + { + title: 'Open-source and easy to run', // Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, description: ( <> - Voluseg provides advanced algorithms for efficient segemntation of volumetric calcium imaging data. + Voluseg is open-source and easy to run with containers. It can be run on any cloud platform or on-premises. ), }, From 72c2f35043e006febbc3494ca7479a22ec2ec0ad Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 30 Oct 2024 15:02:54 +0100 Subject: [PATCH 17/27] footer --- docs/voluseg-docs-app/docusaurus.config.js | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/voluseg-docs-app/docusaurus.config.js b/docs/voluseg-docs-app/docusaurus.config.js index bada349..18b39f0 100644 --- a/docs/voluseg-docs-app/docusaurus.config.js +++ b/docs/voluseg-docs-app/docusaurus.config.js @@ -82,9 +82,17 @@ const config = { title: 'Docs', items: [ { - label: 'Tutorial', + label: 'Introduction', to: '/docs/intro', }, + { + label: 'Getting Started', + to: '/docs/category/getting-started', + }, + { + label: 'API Reference', + to: '/docs/category/api-reference', + }, ], }, { From 9b46040fde8442801e7f198dac7788070c4ef23f Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 20 Nov 2024 14:22:01 +0100 Subject: [PATCH 18/27] comment to avoid error --- src/voluseg/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/voluseg/__init__.py b/src/voluseg/__init__.py index aa0d323..d181d5c 100644 --- a/src/voluseg/__init__.py +++ b/src/voluseg/__init__.py @@ -11,4 +11,4 @@ from voluseg.tools.parameters import load_parameters, save_parameters from voluseg.tools.load_metadata import load_metadata -from src.voluseg.update import voluseg_update as update +# from src.voluseg.update import voluseg_update as update From 618ac3a41433ec4004675dbda1be11eee88218db Mon Sep 17 00:00:00 2001 From: luiz Date: Wed, 20 Nov 2024 16:27:19 +0100 Subject: [PATCH 19/27] remove root user from dockerfile --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 18c2c4d..110cd66 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,5 @@ FROM python:3.12.4-slim -USER root - WORKDIR /voluseg RUN apt-get update && apt-get install -y wget unzip && \ From 4e97dce72370d2e90bc986cb6f08204fb59f1f8a Mon Sep 17 00:00:00 2001 From: luiz Date: Thu, 21 Nov 2024 19:33:40 +0100 Subject: [PATCH 20/27] try optimal spark allocation --- .github/workflows/run_tests.yaml | 1 + src/voluseg/steps/step3.py | 5 ++- src/voluseg/steps/step4.py | 5 ++- src/voluseg/steps/step4e.py | 5 ++- src/voluseg/steps/step5.py | 5 ++- src/voluseg/tools/evenly_parallelize.py | 6 ++-- src/voluseg/tools/parameters_models.py | 23 ++++++++++++ src/voluseg/tools/spark.py | 48 +++++++++++++++++++++++++ 8 files changed, 83 insertions(+), 15 deletions(-) create mode 100644 src/voluseg/tools/spark.py diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 9fd20ff..732c776 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -4,6 +4,7 @@ on: push: branches: - master + - spark-memory pull_request: branches: - master diff --git a/src/voluseg/steps/step3.py b/src/voluseg/steps/step3.py index 8476700..a1379d1 100644 --- a/src/voluseg/steps/step3.py +++ b/src/voluseg/steps/step3.py @@ -7,7 +7,6 @@ from skimage import morphology from types import SimpleNamespace from scipy.ndimage.filters import median_filter -from pyspark.sql.session import SparkSession import warnings import matplotlib @@ -21,6 +20,7 @@ from voluseg.tools.load_volume import load_volume from voluseg.tools.clean_signal import clean_signal from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.spark import get_spark_context def mask_volumes(parameters: dict) -> None: @@ -38,8 +38,7 @@ def mask_volumes(parameters: dict) -> None: ------- None """ - spark = SparkSession.builder.getOrCreate() - sc = spark.sparkContext + sc = get_spark_context() p = SimpleNamespace(**parameters) diff --git a/src/voluseg/steps/step4.py b/src/voluseg/steps/step4.py index e693e63..9f95f14 100644 --- a/src/voluseg/steps/step4.py +++ b/src/voluseg/steps/step4.py @@ -3,7 +3,6 @@ import time import numpy as np from types import SimpleNamespace -from pyspark.sql.session import SparkSession from voluseg.steps.step4a import define_blocks from voluseg.steps.step4b import process_block_data @@ -12,6 +11,7 @@ from voluseg.tools.ball import ball from voluseg.tools.constants import hdf from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.spark import get_spark_context def detect_cells(parameters: dict) -> None: @@ -27,8 +27,7 @@ def detect_cells(parameters: dict) -> None: ------- None """ - spark = SparkSession.builder.getOrCreate() - sc = spark.sparkContext + sc = get_spark_context() p = SimpleNamespace(**parameters) diff --git a/src/voluseg/steps/step4e.py b/src/voluseg/steps/step4e.py index 00fcfe6..f63e9dc 100644 --- a/src/voluseg/steps/step4e.py +++ b/src/voluseg/steps/step4e.py @@ -4,10 +4,10 @@ from types import SimpleNamespace from typing import Tuple import pyspark -from pyspark.sql.session import SparkSession from voluseg.tools.constants import hdf from voluseg.tools.evenly_parallelize import evenly_parallelize +from voluseg.tools.spark import get_spark_context def collect_blocks( @@ -30,8 +30,7 @@ def collect_blocks( Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. """ - spark = SparkSession.builder.getOrCreate() - sc = spark.sparkContext + sc = get_spark_context() p = SimpleNamespace(**parameters) diff --git a/src/voluseg/steps/step5.py b/src/voluseg/steps/step5.py index 30954de..a436e9b 100644 --- a/src/voluseg/steps/step5.py +++ b/src/voluseg/steps/step5.py @@ -4,13 +4,13 @@ import numpy as np from types import SimpleNamespace from itertools import combinations -from pyspark.sql.session import SparkSession from voluseg.steps.step4e import collect_blocks from voluseg.tools.constants import hdf, dtype from voluseg.tools.clean_signal import clean_signal from voluseg.tools.evenly_parallelize import evenly_parallelize from voluseg.tools.nwb import write_nwbfile +from voluseg.tools.spark import get_spark_context def clean_cells(parameters: dict) -> None: @@ -26,8 +26,7 @@ def clean_cells(parameters: dict) -> None: ------- None """ - spark = SparkSession.builder.getOrCreate() - sc = spark.sparkContext + sc = get_spark_context() p = SimpleNamespace(**parameters) diff --git a/src/voluseg/tools/evenly_parallelize.py b/src/voluseg/tools/evenly_parallelize.py index 609a146..3eb85d9 100644 --- a/src/voluseg/tools/evenly_parallelize.py +++ b/src/voluseg/tools/evenly_parallelize.py @@ -1,7 +1,8 @@ import numpy as np -from pyspark.sql.session import SparkSession from pyspark.rdd import RDD +from voluseg.tools.spark import get_spark_context + def evenly_parallelize(input_list: list) -> RDD: """ @@ -17,8 +18,7 @@ def evenly_parallelize(input_list: list) -> RDD: RDD Spark resilient distributed dataset (RDD). """ - spark = SparkSession.builder.getOrCreate() - sc = spark.sparkContext + sc = get_spark_context() n_input = len(input_list) n_parts = sc.parallelize(input_list).getNumPartitions() diff --git a/src/voluseg/tools/parameters_models.py b/src/voluseg/tools/parameters_models.py index 8dd628b..9b2e10f 100644 --- a/src/voluseg/tools/parameters_models.py +++ b/src/voluseg/tools/parameters_models.py @@ -4,6 +4,25 @@ from typing import Optional +class SparkConfig(BaseModel): + driver_memory: str = Field( + default="4g", + description="Set driver memory", + ) + executor_memory: str = Field( + default="8g", + description="Set executor memory", + ) + executor_cores: str = Field( + default="1", + description="Number of cores per executor", + ) + num_executors: str = Field( + default="4", + description="Total number of executors", + ) + + class Detrending(str, Enum): standard = "standard" robust = "robust" @@ -174,6 +193,10 @@ class ParametersModel(BaseModel): default=False, description="Save results to a new NWB file", ) + spark_config: Optional[SparkConfig] = Field( + default=SparkConfig(), + description="Spark configuration", + ) @model_validator(mode="before") def convert_array_to_list(cls, values): diff --git a/src/voluseg/tools/spark.py b/src/voluseg/tools/spark.py new file mode 100644 index 0000000..41392c4 --- /dev/null +++ b/src/voluseg/tools/spark.py @@ -0,0 +1,48 @@ +from pyspark.sql.session import SparkSession +import psutil + + +def get_spark_context(): + """ + Get or create a Spark context. + + Returns + ------- + SparkContext + Spark context. + """ + # Use (n_cores - 2), minimum 1 core + total_cores = psutil.cpu_count(logical=True) + n_cores_executors = max(total_cores - 2, 1) + + # Get available system memory in GB + available_memory_gb = psutil.virtual_memory().available // (1024 ** 3) + + # Set memory for driver and executors + # 25% of available memory for driver + driver_memory = max(int(available_memory_gb * 0.2), 2) + # 50% split among executors + executor_memory = max(int(available_memory_gb * 0.7 / n_cores_executors), 1) + + print(f"Configuring Spark with:") + print(f"- Total cores: {total_cores}") + print(f"- Executor cores: {n_cores_executors}") + print(f"- Available memory: {available_memory_gb} GB") + print(f"- Driver memory: {driver_memory} GB") + print(f"- Executor memory: {executor_memory} GB per executor") + + # Build Spark session with these configurations + spark = ( + SparkSession.builder + .appName("Voluseg") + .config("spark.driver.memory", f"{driver_memory}g") + .config("spark.executor.memory", f"{executor_memory}g") + .config("spark.executor.cores", n_cores_executors) + .config("spark.num.executors", n_cores_executors) + .config("spark.dynamicAllocation.enabled", "true") + .config("spark.dynamicAllocation.minExecutors", "1") + .config("spark.dynamicAllocation.maxExecutors", n_cores_executors) + .getOrCreate() + ) + + return spark.sparkContext From b2dff18b0846cfd258ed0511a29c795a660c7be1 Mon Sep 17 00:00:00 2001 From: Luiz Tauffer Date: Thu, 21 Nov 2024 19:41:59 +0100 Subject: [PATCH 21/27] Update requirements.txt --- requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index c86fa1c..51cbf8e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,4 +9,5 @@ numpy>=1.13 pandas>=0.2 pydantic>=2.8.0 pynwb>=2.8.0 -loguru==0.7.2 \ No newline at end of file +loguru==0.7.2 +psutil>=6.1.0 From 6b8ff3770d31b2698a10ff50f495292076da8adc Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 08:39:07 +0100 Subject: [PATCH 22/27] tests dev --- .github/workflows/run_tests.yaml | 2 +- src/voluseg/tools/parameters_models.py | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 732c776..8e68ce2 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -4,7 +4,7 @@ on: push: branches: - master - - spark-memory + - dev pull_request: branches: - master diff --git a/src/voluseg/tools/parameters_models.py b/src/voluseg/tools/parameters_models.py index 9b2e10f..603416a 100644 --- a/src/voluseg/tools/parameters_models.py +++ b/src/voluseg/tools/parameters_models.py @@ -5,6 +5,10 @@ class SparkConfig(BaseModel): + auto: bool = Field( + default=True, + description="Automatically configure Spark resources", + ) driver_memory: str = Field( default="4g", description="Set driver memory", From 8ecf4691f709471f8aa7b0a80f2371333da02225 Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 08:58:09 +0100 Subject: [PATCH 23/27] auto or manual mode for spark configuration --- src/voluseg/steps/step0.py | 5 ++- src/voluseg/steps/step1.py | 10 ++++- src/voluseg/steps/step2.py | 5 ++- src/voluseg/steps/step3.py | 12 ++++-- src/voluseg/steps/step4.py | 7 +++- src/voluseg/steps/step4e.py | 7 +++- src/voluseg/steps/step5.py | 15 +++++-- src/voluseg/tools/aws.py | 52 +++++++++++------------ src/voluseg/tools/evenly_parallelize.py | 6 ++- src/voluseg/tools/nwb.py | 23 ++++++----- src/voluseg/tools/parameters_models.py | 2 +- src/voluseg/tools/spark.py | 55 +++++++++++++++++-------- tests/test_voluseg.py | 46 ++++++++++----------- 13 files changed, 149 insertions(+), 96 deletions(-) diff --git a/src/voluseg/steps/step0.py b/src/voluseg/steps/step0.py index 3cb1270..974a9ed 100644 --- a/src/voluseg/steps/step0.py +++ b/src/voluseg/steps/step0.py @@ -197,7 +197,10 @@ def get_plane_names(tuple_fullname_volume_input): ] volume_names_h = ( - evenly_parallelize(volume_fullnames_input_h) + evenly_parallelize( + input_list=volume_fullnames_input_h, + parameters=parameters, + ) .map(get_plane_names) .collect() ) diff --git a/src/voluseg/steps/step1.py b/src/voluseg/steps/step1.py index acbcbee..9f5671b 100644 --- a/src/voluseg/steps/step1.py +++ b/src/voluseg/steps/step1.py @@ -27,9 +27,15 @@ def process_volumes(parameters: dict) -> None: p = SimpleNamespace(**parameters) if parameters.get("ext") == ".nwb": - volume_fullname_inputRDD = evenly_parallelize(p.volume_names) + volume_fullname_inputRDD = evenly_parallelize( + input_list=p.volume_names, + parameters=parameters, + ) else: - volume_fullname_inputRDD = evenly_parallelize(p.volume_fullnames_input) + volume_fullname_inputRDD = evenly_parallelize( + input_list=p.volume_fullnames_input, + parameters=parameters, + ) for color_i in range(p.n_colors): fullname_volmean = os.path.join(p.dir_output, "volume%d" % (color_i)) diff --git a/src/voluseg/steps/step2.py b/src/voluseg/steps/step2.py index 880f27d..d73a312 100644 --- a/src/voluseg/steps/step2.py +++ b/src/voluseg/steps/step2.py @@ -32,7 +32,10 @@ def align_volumes(parameters: dict) -> None: p = SimpleNamespace(**parameters) - volume_nameRDD = evenly_parallelize(p.volume_names) + volume_nameRDD = evenly_parallelize( + input_list=p.volume_names + parameters=parameters, + ) for color_i in range(p.n_colors): fullname_volmean = os.path.join(p.dir_output, "volume%d" % (color_i)) if os.path.isfile(fullname_volmean + hdf): diff --git a/src/voluseg/steps/step3.py b/src/voluseg/steps/step3.py index a1379d1..64b9323 100644 --- a/src/voluseg/steps/step3.py +++ b/src/voluseg/steps/step3.py @@ -38,13 +38,16 @@ def mask_volumes(parameters: dict) -> None: ------- None """ - sc = get_spark_context() + sc = get_spark_context(**parameters.get("spark_config", {})) p = SimpleNamespace(**parameters) # compute mean timeseries and ranked dff fullname_timemean = os.path.join(p.dir_output, "mean_timeseries") - volume_nameRDD = evenly_parallelize(p.volume_names) + volume_nameRDD = evenly_parallelize( + input_list=p.volume_names, + parameters=parameters, + ) if not os.path.isfile(fullname_timemean + hdf): dff_rank = np.zeros(p.lt) mean_timeseries_raw = np.zeros((p.n_colors, p.lt)) @@ -150,7 +153,10 @@ def add_volume(tuple_name_volume): volume_accum.add(volume) if p.parallel_volume: - evenly_parallelize(p.volume_names[timepoints]).foreach(add_volume) + evenly_parallelize( + input_list=p.volume_names[timepoints], + parameters=parameters, + ).foreach(add_volume) else: for name_volume in p.volume_names[timepoints]: add_volume(([], name_volume)) diff --git a/src/voluseg/steps/step4.py b/src/voluseg/steps/step4.py index 9f95f14..4fa9100 100644 --- a/src/voluseg/steps/step4.py +++ b/src/voluseg/steps/step4.py @@ -27,7 +27,7 @@ def detect_cells(parameters: dict) -> None: ------- None """ - sc = get_spark_context() + sc = get_spark_context(**parameters.get("spark_config", {})) p = SimpleNamespace(**parameters) @@ -242,6 +242,9 @@ def detect_cells_block(tuple_i_xyz0_xyz1): file_handle["completion"] = 1 if block_valids.any(): - evenly_parallelize(block_ixyz01).foreach(detect_cells_block) + evenly_parallelize( + input_list=block_ixyz01, + parameters=parameters, + ).foreach(detect_cells_block) # collect_blocks(color_i, parameters, lxyz) diff --git a/src/voluseg/steps/step4e.py b/src/voluseg/steps/step4e.py index f63e9dc..db4b924 100644 --- a/src/voluseg/steps/step4e.py +++ b/src/voluseg/steps/step4e.py @@ -30,7 +30,7 @@ def collect_blocks( Tuple of cell block id, cell xyz, cell weights, cell timeseries, and cell lengths. """ - sc = get_spark_context() + sc = get_spark_context(**parameters.get("spark_config", {})) p = SimpleNamespace(**parameters) @@ -82,7 +82,10 @@ def add_data(tuple_ii): return [cell_block_id, cell_xyz, cell_weights, cell_timeseries] if p.parallel_clean: - evenly_parallelize(np.argwhere(block_valids).T[0]).foreach(add_data) + evenly_parallelize( + input_list=np.argwhere(block_valids).T[0], + parameters=parameters, + ).foreach(add_data) cell_block_id, cell_xyz, cell_weights, cell_timeseries = cell_data.value else: idx_block_valids = np.argwhere(block_valids).T[0] diff --git a/src/voluseg/steps/step5.py b/src/voluseg/steps/step5.py index a436e9b..359a267 100644 --- a/src/voluseg/steps/step5.py +++ b/src/voluseg/steps/step5.py @@ -26,7 +26,7 @@ def clean_cells(parameters: dict) -> None: ------- None """ - sc = get_spark_context() + sc = get_spark_context(**parameters.get("spark_config", {})) p = SimpleNamespace(**parameters) @@ -110,7 +110,14 @@ def get_timebase(timeseries_tuple): if p.parallel_clean: print("Computing baseline in parallel mode... ", end="") - timebase = evenly_parallelize(cell_timeseries).map(get_timebase).collect() + timebase = ( + evenly_parallelize( + input_list=cell_timeseries, + parameters=parameters, + ) + .map(get_timebase) + .collect() + ) else: print("Computing baseline in serial mode... ", end="") timeseries_tuple = zip([[]] * len(cell_timeseries), cell_timeseries) @@ -162,7 +169,9 @@ def get_timebase(timeseries_tuple): if p.output_to_nwb: write_nwbfile( - output_path=os.path.join(p.dir_output, "cells%s_clean" % (color_i) + ".nwb"), + output_path=os.path.join( + p.dir_output, "cells%s_clean" % (color_i) + ".nwb" + ), cell_x=cell_x, cell_y=cell_y, cell_z=cell_z, diff --git a/src/voluseg/tools/aws.py b/src/voluseg/tools/aws.py index 5984b32..ab8f74f 100644 --- a/src/voluseg/tools/aws.py +++ b/src/voluseg/tools/aws.py @@ -79,15 +79,25 @@ def run_job_in_aws_batch( stack_id = "VolusegBatchStack" aws_batch_job_definition = f"{stack_id}-job-definition" - aws_batch_job_queue = f'{stack_id}-job-queue' + aws_batch_job_queue = f"{stack_id}-job-queue" - iso_string = datetime.now(timezone.utc).replace(microsecond=0).isoformat().replace(":", "-").replace("+", "Z") - job_name = f'{job_name_prefix}-{iso_string}' + iso_string = ( + datetime.now(timezone.utc) + .replace(microsecond=0) + .isoformat() + .replace(":", "-") + .replace("+", "Z") + ) + job_name = f"{job_name_prefix}-{iso_string}" - job_def_resp = client.describe_job_definitions(jobDefinitionName=aws_batch_job_definition) - job_defs = job_def_resp['jobDefinitions'] + job_def_resp = client.describe_job_definitions( + jobDefinitionName=aws_batch_job_definition + ) + job_defs = job_def_resp["jobDefinitions"] if len(job_defs) == 0: - raise JobDefinitionException(f'Job definition not found: {aws_batch_job_definition}') + raise JobDefinitionException( + f"Job definition not found: {aws_batch_job_definition}" + ) env_vars = format_voluseg_kwargs(voluseg_kwargs) env_vars["VOLUSEG_DIR_OUTPUT"] = "/tmp/voluseg-jobs" @@ -98,30 +108,18 @@ def run_job_in_aws_batch( jobQueue=aws_batch_job_queue, jobDefinition=aws_batch_job_definition, containerOverrides={ - "environment": [ - { - "name": k, - "value": v - } - for k, v in env_vars.items() - ], + "environment": [{"name": k, "value": v} for k, v in env_vars.items()], "resourceRequirements": [ - { - "type": "MEMORY", - "value": str(memory) - }, - { - "type": "VCPU", - "value": str(vcpus) - }, + {"type": "MEMORY", "value": str(memory)}, + {"type": "VCPU", "value": str(vcpus)}, ], }, ) - batch_job_id = response['jobId'] - print(f'AWS Batch job submitted: {job_name} {batch_job_id}') + batch_job_id = response["jobId"] + print(f"AWS Batch job submitted: {job_name} {batch_job_id}") return { - 'job_name': job_name, - 'batch_job_id': batch_job_id, + "job_name": job_name, + "batch_job_id": batch_job_id, } @@ -130,10 +128,10 @@ def export_to_s3( bucket_name: str, object_name: str, ): - s3 = boto3.client('s3') + s3 = boto3.client("s3") s3.upload_file( Filename=local_path, Bucket=bucket_name, Key=object_name, ) - print(f'File uploaded to s3://{bucket_name}/{object_name}') + print(f"File uploaded to s3://{bucket_name}/{object_name}") diff --git a/src/voluseg/tools/evenly_parallelize.py b/src/voluseg/tools/evenly_parallelize.py index 3eb85d9..b81c35a 100644 --- a/src/voluseg/tools/evenly_parallelize.py +++ b/src/voluseg/tools/evenly_parallelize.py @@ -4,7 +4,7 @@ from voluseg.tools.spark import get_spark_context -def evenly_parallelize(input_list: list) -> RDD: +def evenly_parallelize(input_list: list, parameters: dict) -> RDD: """ Return evenly partitioned spark resilient distributed dataset (RDD). @@ -12,13 +12,15 @@ def evenly_parallelize(input_list: list) -> RDD: ---------- input_list : list List of input elements. + parameters : dict + Parameters dictionary. Returns ------- RDD Spark resilient distributed dataset (RDD). """ - sc = get_spark_context() + sc = get_spark_context(**parameters.get("spark_config", {})) n_input = len(input_list) n_parts = sc.parallelize(input_list).getNumPartitions() diff --git a/src/voluseg/tools/nwb.py b/src/voluseg/tools/nwb.py index 61d8ce0..e0cd9d4 100644 --- a/src/voluseg/tools/nwb.py +++ b/src/voluseg/tools/nwb.py @@ -60,8 +60,8 @@ def open_nwbfile_remote(s3_url: str, output_path: str): io = None try: with fs.open(s3_url, "rb") as f: - file = h5py.File(f, 'r') - io = pynwb.NWBHDF5IO(file=file, mode='r') + file = h5py.File(f, "r") + io = pynwb.NWBHDF5IO(file=file, mode="r") nwbfile = io.read() yield nwbfile except Exception as e: @@ -227,18 +227,19 @@ def write_nwbfile( n_cells = cell_weights.shape[0] for ci in range(0, n_cells): n_valid_voxels = len(np.where(cell_x[ci] != -1)[0]) - voxel_mask = np.array(( - cell_x[ci][0:n_valid_voxels], - cell_y[ci][0:n_valid_voxels], - cell_z[ci][0:n_valid_voxels], - cell_weights[ci][0:n_valid_voxels], - )).T + voxel_mask = np.array( + ( + cell_x[ci][0:n_valid_voxels], + cell_y[ci][0:n_valid_voxels], + cell_z[ci][0:n_valid_voxels], + cell_weights[ci][0:n_valid_voxels], + ) + ).T ps.add_roi(voxel_mask=voxel_mask) # Create response series rt_region = ps.create_roi_table_region( - region=list(range(0, n_cells)), - description="ROIs table region" + region=list(range(0, n_cells)), description="ROIs table region" ) roi_resp_series = pynwb.ophys.RoiResponseSeries( name="RoiResponseSeries", @@ -251,4 +252,4 @@ def write_nwbfile( fl = pynwb.ophys.Fluorescence(roi_response_series=roi_resp_series) ophys_module.add(fl) with pynwb.NWBHDF5IO(output_path, "w") as io: - io.write(nwbfile) \ No newline at end of file + io.write(nwbfile) diff --git a/src/voluseg/tools/parameters_models.py b/src/voluseg/tools/parameters_models.py index 603416a..63dd025 100644 --- a/src/voluseg/tools/parameters_models.py +++ b/src/voluseg/tools/parameters_models.py @@ -193,7 +193,7 @@ class ParametersModel(BaseModel): default=False, description="Remote file", ) - output_to_nwb : Optional[bool] = Field( + output_to_nwb: Optional[bool] = Field( default=False, description="Save results to a new NWB file", ) diff --git a/src/voluseg/tools/spark.py b/src/voluseg/tools/spark.py index 41392c4..92f9e68 100644 --- a/src/voluseg/tools/spark.py +++ b/src/voluseg/tools/spark.py @@ -2,46 +2,65 @@ import psutil -def get_spark_context(): +def get_spark_context( + auto: bool = True, + driver_memory: str = "4g", + executor_memory: str = "8g", + executor_cores: str = "1", + num_executors: str = "4", +): """ Get or create a Spark context. - Returns - ------- + Parameters: + ----------- + auto : bool + Automatically configure Spark resources. + driver_memory : str + Set driver memory. + executor_memory : str + Set executor memory. + executor_cores : str + Number of cores per executor. + num_executors : str + Total number of executors. + + Returns: + -------- SparkContext Spark context. """ - # Use (n_cores - 2), minimum 1 core total_cores = psutil.cpu_count(logical=True) - n_cores_executors = max(total_cores - 2, 1) + if auto: + # Use (n_cores - 2), minimum 1 core + num_executors = max((total_cores - 2) / executor_cores, 1) - # Get available system memory in GB - available_memory_gb = psutil.virtual_memory().available // (1024 ** 3) + # Get available system memory in GB + available_memory_gb = psutil.virtual_memory().available // (1024**3) - # Set memory for driver and executors - # 25% of available memory for driver - driver_memory = max(int(available_memory_gb * 0.2), 2) - # 50% split among executors - executor_memory = max(int(available_memory_gb * 0.7 / n_cores_executors), 1) + # Set memory for driver and executors + # 20% of available memory for driver + driver_memory = max(int(available_memory_gb * 0.2), 2) + # 70% split among executors + executor_memory = max(int(available_memory_gb * 0.7 / num_executors), 1) print(f"Configuring Spark with:") print(f"- Total cores: {total_cores}") - print(f"- Executor cores: {n_cores_executors}") + print(f"- Executor cores: {executor_cores}") print(f"- Available memory: {available_memory_gb} GB") print(f"- Driver memory: {driver_memory} GB") print(f"- Executor memory: {executor_memory} GB per executor") # Build Spark session with these configurations spark = ( - SparkSession.builder - .appName("Voluseg") + SparkSession.builder.appName("Voluseg") .config("spark.driver.memory", f"{driver_memory}g") .config("spark.executor.memory", f"{executor_memory}g") - .config("spark.executor.cores", n_cores_executors) - .config("spark.num.executors", n_cores_executors) + .config("spark.executor.cores", executor_cores) + .config("spark.num.executors", num_executors) .config("spark.dynamicAllocation.enabled", "true") .config("spark.dynamicAllocation.minExecutors", "1") - .config("spark.dynamicAllocation.maxExecutors", n_cores_executors) + .config("spark.dynamicAllocation.maxExecutors", num_executors) .getOrCreate() ) diff --git a/tests/test_voluseg.py b/tests/test_voluseg.py index d6823d6..9db9fc1 100644 --- a/tests/test_voluseg.py +++ b/tests/test_voluseg.py @@ -321,7 +321,6 @@ def compare_results_nwb_and_h5_dir( ), "Different cell weights between NWB and h5 results" - @pytest.mark.order(9) def test_voluseg_h5_dir_step_5(setup_parameters): """ @@ -335,22 +334,22 @@ def test_voluseg_h5_dir_step_5(setup_parameters): hdf_h5 = h5py.File(clean_cells_file, "r") keys = [ - 'background', - 'cell_baseline', - 'cell_block_id', - 'cell_timeseries', - 'cell_timeseries_raw', - 'cell_weights', - 'cell_x', - 'cell_y', - 'cell_z', - 'n', - 't', - 'volume_id', - 'volume_weight', - 'x', - 'y', - 'z' + "background", + "cell_baseline", + "cell_block_id", + "cell_timeseries", + "cell_timeseries_raw", + "cell_weights", + "cell_x", + "cell_y", + "cell_z", + "n", + "t", + "volume_id", + "volume_weight", + "x", + "y", + "z", ] for k in keys: assert k in hdf_h5.keys(), f"Key '{k}' is missing in cleaned cells file" @@ -388,7 +387,9 @@ def test_nwb_remote(tmp_path): parameters = voluseg.parameter_dictionary() # Using this file: https://dandiarchive.org/dandiset/000350/0.240822.1759/files?location=sub-20161022-1&page=1 - parameters["dir_input"] = "https://dandiarchive.s3.amazonaws.com/blobs/057/ecb/057ecbef-e732-4e94-8d99-40ebb74d346e" + parameters["dir_input"] = ( + "https://dandiarchive.s3.amazonaws.com/blobs/057/ecb/057ecbef-e732-4e94-8d99-40ebb74d346e" + ) parameters["dir_ants"] = os.environ.get("ANTS_PATH") # Use pytest's tmp_path fixture for output @@ -398,7 +399,7 @@ def test_nwb_remote(tmp_path): parameters["registration"] = "high" parameters["diam_cell"] = 5.0 parameters["f_volume"] = 2.0 - parameters['timepoints'] = 20 + parameters["timepoints"] = 20 print("Process parameters") parameters = voluseg.step0_process_parameters(parameters) @@ -407,10 +408,9 @@ def test_nwb_remote(tmp_path): voluseg.step1_process_volumes(parameters) output_files = [ - p - for p in (Path(parameters["dir_output"]) / "volumes/0/").glob("*.nii.gz") + p for p in (Path(parameters["dir_output"]) / "volumes/0/").glob("*.nii.gz") ] n_files_output = len(output_files) assert ( - n_files_output == parameters['timepoints'] - ), f"Number of output files ({n_files_output}) does not match number of timepoints ({parameters['timepoints']})" \ No newline at end of file + n_files_output == parameters["timepoints"] + ), f"Number of output files ({n_files_output}) does not match number of timepoints ({parameters['timepoints']})" From 43a9d21573695c59534434d1fa5d0f8ad4dfb583 Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 08:59:45 +0100 Subject: [PATCH 24/27] fix missing comma --- src/voluseg/steps/step2.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/voluseg/steps/step2.py b/src/voluseg/steps/step2.py index d73a312..44d03c9 100644 --- a/src/voluseg/steps/step2.py +++ b/src/voluseg/steps/step2.py @@ -33,7 +33,7 @@ def align_volumes(parameters: dict) -> None: p = SimpleNamespace(**parameters) volume_nameRDD = evenly_parallelize( - input_list=p.volume_names + input_list=p.volume_names, parameters=parameters, ) for color_i in range(p.n_colors): From a9aa133cf81fb548ed79e506b49197d75c7fa647 Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 09:05:26 +0100 Subject: [PATCH 25/27] types --- src/voluseg/tools/parameters_models.py | 20 ++++++++++---------- src/voluseg/tools/spark.py | 16 ++++++++-------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/voluseg/tools/parameters_models.py b/src/voluseg/tools/parameters_models.py index 63dd025..5a20d6b 100644 --- a/src/voluseg/tools/parameters_models.py +++ b/src/voluseg/tools/parameters_models.py @@ -9,20 +9,20 @@ class SparkConfig(BaseModel): default=True, description="Automatically configure Spark resources", ) - driver_memory: str = Field( - default="4g", - description="Set driver memory", + driver_memory: int = Field( + default=4, + description="Set driver memory in GB", ) - executor_memory: str = Field( - default="8g", - description="Set executor memory", + executor_memory: int = Field( + default=8, + description="Set executor memory in GB", ) - executor_cores: str = Field( - default="1", + executor_cores: int = Field( + default=1, description="Number of cores per executor", ) - num_executors: str = Field( - default="4", + num_executors: int = Field( + default=4, description="Total number of executors", ) diff --git a/src/voluseg/tools/spark.py b/src/voluseg/tools/spark.py index 92f9e68..c412696 100644 --- a/src/voluseg/tools/spark.py +++ b/src/voluseg/tools/spark.py @@ -4,10 +4,10 @@ def get_spark_context( auto: bool = True, - driver_memory: str = "4g", - executor_memory: str = "8g", - executor_cores: str = "1", - num_executors: str = "4", + driver_memory: int = 4, + executor_memory: int = 8, + executor_cores: int = 1, + num_executors: int = 4, ): """ Get or create a Spark context. @@ -16,13 +16,13 @@ def get_spark_context( ----------- auto : bool Automatically configure Spark resources. - driver_memory : str + driver_memory : int Set driver memory. - executor_memory : str + executor_memory : int Set executor memory. - executor_cores : str + executor_cores : int Number of cores per executor. - num_executors : str + num_executors : int Total number of executors. Returns: From 030022ca70715c7bf01e570be197f16d7693c7e7 Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 13:59:43 +0100 Subject: [PATCH 26/27] fix maxResultSize error --- src/voluseg/tools/spark.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/voluseg/tools/spark.py b/src/voluseg/tools/spark.py index c412696..495d8e6 100644 --- a/src/voluseg/tools/spark.py +++ b/src/voluseg/tools/spark.py @@ -32,8 +32,8 @@ def get_spark_context( """ total_cores = psutil.cpu_count(logical=True) if auto: - # Use (n_cores - 2), minimum 1 core - num_executors = max((total_cores - 2) / executor_cores, 1) + # Use (n_cores - 2), minimum 1 executor + num_executors = max(int((total_cores - 2) / executor_cores), 1) # Get available system memory in GB available_memory_gb = psutil.virtual_memory().available // (1024**3) @@ -41,6 +41,7 @@ def get_spark_context( # Set memory for driver and executors # 20% of available memory for driver driver_memory = max(int(available_memory_gb * 0.2), 2) + # 70% split among executors executor_memory = max(int(available_memory_gb * 0.7 / num_executors), 1) @@ -61,6 +62,7 @@ def get_spark_context( .config("spark.dynamicAllocation.enabled", "true") .config("spark.dynamicAllocation.minExecutors", "1") .config("spark.dynamicAllocation.maxExecutors", num_executors) + .config("spark.driver.maxResultSize", f"{int(driver_memory * 0.8)}g") # 80% of driver memory .getOrCreate() ) From 5b2b6e222e8a92de0189eb37864e6146ab31bcbb Mon Sep 17 00:00:00 2001 From: luiz Date: Fri, 22 Nov 2024 14:16:40 +0100 Subject: [PATCH 27/27] ci --- .github/workflows/run_tests.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 8e68ce2..77ce9aa 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -4,10 +4,10 @@ on: push: branches: - master - - dev pull_request: branches: - master + - dev jobs: test: