diff --git a/.gitignore b/.gitignore index 0c89107..e3b387a 100644 --- a/.gitignore +++ b/.gitignore @@ -134,4 +134,4 @@ _version.py \#* # Ignore topostats/_version.py as per setuptools_scm -topofileformats/_version.py \ No newline at end of file +AFMReader/_version.py \ No newline at end of file diff --git a/AFMReader/__init__.py b/AFMReader/__init__.py index 45679d8..a01d4f8 100644 --- a/AFMReader/__init__.py +++ b/AFMReader/__init__.py @@ -2,5 +2,5 @@ from importlib.metadata import version -release = version("topofileformats") +release = version("AFMReader") __version__ = ".".join(release.split("."[:2])) diff --git a/README.md b/README.md index 0841548..6e41153 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,16 @@ -# topofileformats +# AFMReader
-[![PyPI version](https://badge.fury.io/py/topofileformats.svg)](https://badge.fury.io/py/topofileformats) -![PyPI - Python Version](https://img.shields.io/pypi/pyversions/topofileformats) +[![PyPI version](https://badge.fury.io/py/AFMReader.svg)](https://badge.fury.io/py/AFMReader) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/AFMReader) [![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Code style: flake8](https://img.shields.io/badge/code%20style-flake8-456789.svg)](https://github.com/psf/flake8) - + [![pre-commit.ci -status](https://results.pre-commit.ci/badge/github/AFM-SPM/topofileformats/main.svg)](https://results.pre-commit.ci/latest/github/AFM-SPM/topofileformats/main) +status](https://results.pre-commit.ci/badge/github/AFM-SPM/AFMReader/main.svg)](https://results.pre-commit.ci/latest/github/AFM-SPM/AFMReader/main)
@@ -27,7 +27,7 @@ Supported file formats | `.jpk` | [Bruker](https://www.bruker.com/) | Support for the following additional formats is planned. Some of these are already supported in TopoStats and are -awaiting refactoring to move their functionality into topofileformats these are denoted in bold below. +awaiting refactoring to move their functionality into AFMReader these are denoted in bold below. | File format | Description | Status | |-------------|---------------------------------------------------------|--------------------------------------------| @@ -38,7 +38,7 @@ awaiting refactoring to move their functionality into topofileformats these are ## Usage -If you wish to process AFM images supported by `topofileformats` it is recommend you use +If you wish to process AFM images supported by `AFMReader` it is recommend you use [TopoStats](https://github.com/AFM-SPM/TopoStats) to do so, however the library can be used on its own. ### .spm @@ -48,7 +48,7 @@ channel name that you want to use. (If in doubt use one of the following: "Heigh "Height Sensor"). ```python -from topofileformats.spm import load_spm +from AFMReader.spm import load_spm image, pixel_to_nanometre_scaling_factor = load_spm(file_path="./my_spm_file.spm", channel="Height") ``` @@ -64,7 +64,7 @@ will want to use unless you know you specifically want something else. Other channels: `"ER"` - Error, `"PH"` - Phase ```python -from topofileformats.asd import load_asd +from AFMReader.asd import load_asd frames, pixel_to_nanometre_scaling_factor, metadata = load_asd(file_path="./my_asd_file.asd", channel="TP") ``` @@ -76,7 +76,7 @@ and the channel name that you want to use. (If in doubt, use `HeightTracee` (yes extra 'e'), `ZSensorTrace`, or `ZSensor`). ```python -from topofileformats.ibw import load_ibw +from AFMReader.ibw import load_ibw image, pixel_to_nanometre_scaling_factor = load_ibw(file_path="./my_ibw_file.ibw", channel="HeightTracee") ``` @@ -87,7 +87,7 @@ You can open `.jpk` files using the `load_jpk` function. Just pass in the path to the file and the channel name you want to use. (If in doubt, use `height_trace` or `measuredHeight_trace`). ```python -from topofileformats.jpk import load_jpk +from AFMReader.jpk import load_jpk image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk", channel="height_trace") ``` @@ -95,11 +95,11 @@ image, pixel_to_nanometre_scaling_factor = load_jpk(file_path="./my_jpk_file.jpk ## Contributing Bug reports and feature requests are welcome. Please search for existing issues, if none relating to your bug/feature -are found then feel free to create a new [issue](https://github.com/AFM-SPM/topofileformats/issues/new) detailing what +are found then feel free to create a new [issue](https://github.com/AFM-SPM/AFMReader/issues/new) detailing what went wrong or the feature you would like to see implemented. Pull requests are also welcome, please note that we have a [Code of -Conduct](https://github.com/AFM-SPM/topofileformats/blob/main/CODE_OF_CONDUCT.md). +Conduct](https://github.com/AFM-SPM/AFMReader/blob/main/CODE_OF_CONDUCT.md). ### Setup @@ -112,9 +112,9 @@ dependencies and `pre-commit` as shown below. ``` bash # Activate your virtual environment, this will depend on which system you use e.g. conda or virtualenvwrapper # Clone the repository -git clone git@github.com:AFM-SPM/topofileformats.git +git clone git@github.com:AFM-SPM/AFMReader.git # Change directories into the newly cloned directory -cd topofileformats +cd AFMReader # Install the package along with the optional development (dev) dependencies pip install -e .[dev] # Install pre-commit diff --git a/examples/example_01.ipynb b/examples/example_01.ipynb index bb6cef7..c2762d0 100644 --- a/examples/example_01.ipynb +++ b/examples/example_01.ipynb @@ -15,9 +15,9 @@ "source": [ "from pathlib import Path\n", "\n", - "# Import the load_spm from topofileformats\n", - "from topofileformats.spm import load_spm\n", - "from topofileformats.logging import logger\n", + "# Import the load_spm from AFMReader\n", + "from AFMReader.spm import load_spm\n", + "from AFMReader.logging import logger\n", "\n", "logger.enable(__package__)" ] @@ -60,8 +60,8 @@ "metadata": {}, "outputs": [], "source": [ - "# Import the load_asd from topofileformats\n", - "from topofileformats.asd import load_asd, create_animation" + "# Import the load_asd from AFMReader\n", + "from AFMReader.asd import load_asd, create_animation" ] }, { @@ -114,8 +114,8 @@ "metadata": {}, "outputs": [], "source": [ - "# Import the load_jpk function from topofileformats\n", - "from topofileformats.jpk import load_jpk" + "# Import the load_jpk function from AFMReader\n", + "from AFMReader.jpk import load_jpk" ] }, { @@ -155,8 +155,8 @@ "metadata": {}, "outputs": [], "source": [ - "# Import the load_ibw function from topofileformats\n", - "from topofileformats.ibw import load_ibw" + "# Import the load_ibw function from AFMReader\n", + "from AFMReader.ibw import load_ibw" ] }, { @@ -196,8 +196,8 @@ "metadata": {}, "outputs": [], "source": [ - "# Import the load_ibw function from topofileformats\n", - "from topofileformats.ibw import load_ibw" + "# Import the load_ibw function from AFMReader\n", + "from AFMReader.ibw import load_ibw" ] }, {