Merge remote-tracking branch 'origin/master' into dev-tests

.gitignore

@@ -3,7 +3,6 @@ __pycache__/
 *.pyc
 *.egg-info
 
-
 # Python coverage files
 .coverage
 .coverage.*

README-docker.md

@@ -0,0 +1,21 @@
+# Voluseg container
+
+Build the image:
+```bash
+DOCKER_BUILDKIT=1 docker build -t voluseg .
+```
+
+Run with local data volume mount:
+```bash
+docker run -v $(pwd)/data:/voluseg/data voluseg
+```
+
+Run with local data volume mount and hot reload for the voluseg package:
+```bash
+docker run \
+-v $(pwd)/sample_data:/voluseg/data \
+-v $(pwd)/output:/voluseg/output \
+-v $(pwd)/voluseg:/voluseg/voluseg \
+-v $(pwd)/app:/voluseg/app \
+voluseg
+```

README.md

@@ -38,7 +38,7 @@ Contact: Mika Rubinov, `mika.rubinov at vanderbilt.edu`
 
 # example code
 
-```
+```python
 # set up
 import os
 import pprint

app/app.py

@@ -1,23 +1,20 @@
-# set up
 import os
 import pprint
 import voluseg
 
-# check for updates
-# voluseg.update()
 
 # set and save parameters
 parameters0 = voluseg.parameter_dictionary()
-parameters0['dir_ants'] = '/ants-2.5.3/bin/'
-parameters0['dir_input'] = '/voluseg/data/'
-parameters0['dir_output'] = '/voluseg/output/'
-parameters0['registration'] = 'high'
-parameters0['diam_cell'] = 5.0
-parameters0['f_volume'] = 2.0
+parameters0["dir_ants"] = "/ants-2.5.3/bin/"
+parameters0["dir_input"] = "/voluseg/data/"
+parameters0["dir_output"] = "/voluseg/output/"
+parameters0["registration"] = "high"
+parameters0["diam_cell"] = 5.0
+parameters0["f_volume"] = 2.0
 voluseg.step0_process_parameters(parameters0)
 
 # load and print parameters
-filename_parameters = os.path.join(parameters0['dir_output'], 'parameters.pickle')
+filename_parameters = os.path.join(parameters0["dir_output"], "parameters.pickle")
 parameters = voluseg.load_parameters(filename_parameters)
 pprint.pprint(parameters)
 
@@ -34,4 +31,4 @@
 voluseg.step4_detect_cells(parameters)
 
 print("clean cells.")
-voluseg.step5_clean_cells(parameters)
+voluseg.step5_clean_cells(parameters)

requirements-docker.txt

@@ -7,4 +7,4 @@ matplotlib==3.9.2
 numpy==2.1.0
 pandas==2.2.2
 pyspark==3.4.0
-pynwb==2.8.1
+pynwb==2.8.1

setup.py

@@ -1,32 +1,28 @@
-'''volumetric segmentation pipeline'''
+"""volumetric segmentation pipeline"""
 
 import setuptools
 
-with open('README.md', 'r') as fh:
+with open("README.md", "r") as fh:
     README = fh.read()
 
 # with open('requirements.txt', 'r') as fh:
 #     install_requires = fh.read().split('\n')
 
 setuptools.setup(
-    name='voluseg',
-    version='2023.12',
-    author='Mika Rubinov',
-    author_email='mika.rubinov@vanderbilt.edu',
-    description='pipeline for volumetric segmentation of calcium imaging data',
+    name="voluseg",
+    version="2023.12",
+    author="Mika Rubinov",
+    author_email="mika.rubinov@vanderbilt.edu",
+    description="pipeline for volumetric segmentation of calcium imaging data",
     long_description=README,
-    long_description_content_type='text/markdown',
-    url='https://github.com/mikarubi/voluseg',
-    packages=[
-        'voluseg',
-        'voluseg._steps',
-        'voluseg._tools'
-    ],
+    long_description_content_type="text/markdown",
+    url="https://github.com/mikarubi/voluseg",
+    packages=["voluseg", "voluseg._steps", "voluseg._tools"],
     classifiers=[
-        'Programming Language :: Python :: 3',
-        'License :: OSI Approved :: MIT License',
-        'Operating System :: OS Independent',
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
     ],
-    python_requires='>=3.5',
+    python_requires=">=3.5",
     # install_requires=install_requires
 )

tests/test_voluseg.py

@@ -9,14 +9,20 @@
 def setup_parameters(tmp_path):
     # Define parameters and paths
     parameters0 = voluseg.parameter_dictionary()
-    parameters0['dir_ants'] = "/home/luiz/Downloads/ants-2.5.2/bin"  # Change this to your actual ANTs bin path
+    parameters0["dir_ants"] = (
+        "/home/luiz/Downloads/ants-2.5.2/bin"  # Change this to your actual ANTs bin path
+    )
     # parameters0['dir_input'] = str((Path(".").resolve().parent / "sample_data"))
-    parameters0['dir_input'] = "/mnt/shared_storage/taufferconsulting/client_catalystneuro/project_voluseg/sample_data"
+    parameters0["dir_input"] = (
+        "/mnt/shared_storage/taufferconsulting/client_catalystneuro/project_voluseg/sample_data"
+    )
     # parameters0['dir_output'] = str(tmp_path)  # Use pytest's tmp_path fixture for output
-    parameters0['dir_output'] = "/mnt/shared_storage/taufferconsulting/client_catalystneuro/project_voluseg/output"
-    parameters0['registration'] = 'high'
-    parameters0['diam_cell'] = 5.0
-    parameters0['f_volume'] = 2.0
+    parameters0["dir_output"] = (
+        "/mnt/shared_storage/taufferconsulting/client_catalystneuro/project_voluseg/output"
+    )
+    parameters0["registration"] = "high"
+    parameters0["diam_cell"] = 5.0
+    parameters0["f_volume"] = 2.0
 
     # Save parameters
     voluseg.step0_process_parameters(parameters0)
@@ -26,7 +32,9 @@ def setup_parameters(tmp_path):
 
 
 def test_voluseg_pipeline_h5_dir(setup_parameters):
-    filename_parameters = os.path.join(setup_parameters['dir_output'], 'parameters.pickle')
+    filename_parameters = os.path.join(
+        setup_parameters["dir_output"], "parameters.pickle"
+    )
     parameters = voluseg.load_parameters(filename_parameters)
     pprint.pprint(parameters)
 
@@ -57,15 +65,17 @@ def test_voluseg_pipeline_h5_dir(setup_parameters):
 def test_voluseg_pipeline_nwbfile(setup_parameters):
     from voluseg._tools.nwb import h5_dir_to_nwb_file
 
-    filename_parameters = os.path.join(setup_parameters['dir_output'], 'parameters.pickle')
+    filename_parameters = os.path.join(
+        setup_parameters["dir_output"], "parameters.pickle"
+    )
     parameters = voluseg.load_parameters(filename_parameters)
 
     # Convert a directory of HDF5 files to a single NWB file
-    nwb_file_path = str(os.path.join(parameters['dir_output'], "output.nwb"))
+    nwb_file_path = str(os.path.join(parameters["dir_output"], "output.nwb"))
     h5_dir_to_nwb_file(
-        h5_dir=parameters['dir_input'],
+        h5_dir=parameters["dir_input"],
         acquisition_name="TwoPhotonSeries",
-        output_file_path=nwb_file_path
+        output_file_path=nwb_file_path,
     )
     parameters["nwb_input_local_path"] = nwb_file_path
     parameters["nwb_input_acquisition_name"] = "TwoPhotonSeries"
@@ -87,4 +97,4 @@ def test_voluseg_pipeline_nwbfile(setup_parameters):
     # voluseg.step4_detect_cells(parameters)
 
     # print("Clean cells.")
-    # voluseg.step5_clean_cells(parameters)
+    # voluseg.step5_clean_cells(parameters)

voluseg/__init__.py

@@ -1,4 +1,4 @@
-'''initialization'''
+"""initialization"""
 
 from voluseg._steps.step0 import process_parameters as step0_process_parameters
 from voluseg._steps.step1 import process_volumes as step1_process_volumes

voluseg/_steps/step0.py

@@ -148,8 +148,12 @@ def process_parameters(parameters0: dict) -> None:
         if not acquisition_name:
             raise Exception("nwb_input_acquisition_name is required to read nwb file")
         volume_fullnames_input = [parameters.get("nwb_input_local_path")]
-        volume_names = [parameters.get("nwb_input_local_path").split("/")[-1].split(".nwb")[0]]
-        with open_nwbfile_local(file_path=parameters["nwb_input_local_path"]) as nwbfile:
+        volume_names = [
+            parameters.get("nwb_input_local_path").split("/")[-1].split(".nwb")[0]
+        ]
+        with open_nwbfile_local(
+            file_path=parameters["nwb_input_local_path"]
+        ) as nwbfile:
             lt = nwbfile.acquisition[acquisition_name].data.shape[0]
             if parameters["timepoints"]:
                 lt = min(lt, parameters["timepoints"])

voluseg/_steps/step1.py

@@ -127,7 +127,8 @@ def make_output_volume(name_volume, volume):
                         volume_index=tuple_fullname_volume_input[1],
                     )
                 make_output_volume(
-                    name_volume=p.volume_names[0] + f"_{tuple_fullname_volume_input[1]}",
+                    name_volume=p.volume_names[0]
+                    + f"_{tuple_fullname_volume_input[1]}",
                     volume=volume,
                 )
             else:
@@ -136,7 +137,9 @@ def make_output_volume(name_volume, volume):
                 if len(p.input_dirs) == 1:
                     dir_prefix = None
                 else:
-                    dir_prefix = os.path.basename(os.path.split(fullname_volume_input)[0])
+                    dir_prefix = os.path.basename(
+                        os.path.split(fullname_volume_input)[0]
+                    )
 
                 # process output volumes
                 if p.planes_packed: