loli · loli · Dec 15, 2023 · Dec 15, 2023 · Dec 15, 2023 · Dec 15, 2023
diff --git a/.gitignore b/.gitignore
@@ -1,38 +1,34 @@
 TODO.txt
 
-# Images #
-##########
+# Images
 *.nii
 *.mhd
 *.raw
 
-# DOC dirs #
-############
+# Local virtual envs
+.venv/
+
+# DOC dirs
 doc/build/
 doc/generated/
 doc/source/generated/
 
-# Notebooks dirs #
-##################
+# Notebooks dirs
 .ipynb_checkpoints
 
-# BUILD dirs #
-##############
+# BUILD dirs
 build/
 dist/
 MedPy.egg-info/
 
-# Only locally used, temporary .py scripts. #
-#############################################
+# Only locally used, temporary .py scripts.
 _*.py
 !__init__.py
 
-# Backup files #
-################
+# Backup files
 *.bak
 
-# Compiled source #
-###################
+# Compiled source
 *.com
 *.class
 *.dll
@@ -42,8 +38,7 @@ _*.py
 *.pyc
 *.pyo
 
-# Packages #
-############
+# Packages
 # it's better to unpack these files and commit the raw source
 # git has its own built in compression methods
 *.7z
@@ -55,29 +50,25 @@ _*.py
 *.tar
 *.zip
 
-# Logs and databases #
-######################
+# Logs and databases
 *.log
 *.sql
 *.sqlite
 
-# OS generated files #
-######################
+# OS generated files
 .DS_Store*
 ehthumbs.db
 Icon?
 Thumbs.db
 *~
 
-# Eclipse and PyDev project files #
-###################################
+# Eclipse and PyDev project files
 .project
 .pydevproject
 .settings/
 .metadata/
 
-# Suggestions by GitHub for Python projects #
-#############################################
+# Suggestions by GitHub for Python projects
 # Packages
 *.egg
 *.egg-info

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,34 @@
+default_stages: [commit]
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: debug-statements
+
+  - repo: https://github.com/pycqa/isort
+    rev: "5.13.2"
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--line-length=88"]
+
+  - repo: https://github.com/psf/black
+    rev: 23.12.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/hadialqattan/pycln
+    rev: "v2.4.0"
+    hooks:
+      - id: pycln
+        args: ["--all"]
+
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+      - id: detect-secrets
+        args: ["--exclude-files", ".*\\.ipynb"]
diff --git a/.travis.yml b/.travis.yml
diff --git a/README.md b/README.md
@@ -24,6 +24,12 @@ MedPy is an image processing library and collection of scripts targeted towards
 - Download (development version): https://github.com/loli/medpy
 - HTML documentation and installation instruction (development version): create this from doc/ folder following instructions in contained README file
 
+## Contribute
+
+- Clone `master` branch from [github](https://github.com/loli/medpy)
+- Install [pre-commit] hooks
+- Submit your change as a PR request
+
 ## Python 2 version
 
 Python 2 is no longer supported. But you can still use the older releases `<=0.3.0`.

diff --git a/README_PYPI.md b/README_PYPI.md
@@ -123,7 +123,7 @@ The supported image file formats should include at least the following. Note tha
 * Analyze (plain, SPM99, SPM2) (.hdr/.img, .img.gz)
 * Digital Imaging and Communications in Medicine (DICOM) (.dcm, .dicom)
 * Digital Imaging and Communications in Medicine (DICOM) series (<directory>/)
-* Nearly Raw Raster Data (Nrrd) (.nrrd, .nhdr) 
+* Nearly Raw Raster Data (Nrrd) (.nrrd, .nhdr)
 * Medical Imaging NetCDF (MINC) (.mnc, .MNC)
 * Guys Image Processing Lab (GIPL) (.gipl, .gipl.gz)
 

diff --git a/bin/medpy_anisotropic_diffusion.py b/bin/medpy_anisotropic_diffusion.py
@@ -24,15 +24,16 @@
 import logging
 import os
 
+from medpy.core import Logger
+from medpy.filter.smoothing import anisotropic_diffusion
+
+# own modules
+from medpy.io import get_pixel_spacing, load, save
+
 # third-party modules
 
 # path changes
 
-# own modules
-from medpy.io import load, save, get_pixel_spacing
-from medpy.core import Logger
-from medpy.filter.smoothing import anisotropic_diffusion
-
 
 # information
 __author__ = "Oskar Maier"
@@ -42,61 +43,106 @@
 __description__ = """
                   Executes gradient anisotropic diffusion filter over an image.
                   This smoothing algorithm is edges preserving.
-                  
+
                   Note that the images voxel-spacing will be taken into account.
-                                  
+
                   Copyright (C) 2013 Oskar Maier
                   This program comes with ABSOLUTELY NO WARRANTY; This is free software,
                   and you are welcome to redistribute it under certain conditions; see
-                  the LICENSE file or <http://www.gnu.org/licenses/> for details.   
+                  the LICENSE file or <http://www.gnu.org/licenses/> for details.
                   """
 
+
 # code
 def main():
     # parse cmd arguments
     parser = getParser()
     parser.parse_args()
     args = getArguments(parser)
-    
+
     # prepare logger
     logger = Logger.getInstance()
-    if args.debug: logger.setLevel(logging.DEBUG)
-    elif args.verbose: logger.setLevel(logging.INFO)
-
+    if args.debug:
+        logger.setLevel(logging.DEBUG)
+    elif args.verbose:
+        logger.setLevel(logging.INFO)
+
     # check if output image exists (will also be performed before saving, but as the smoothing might be very time intensity, a initial check can save frustration)
     if not args.force:
         if os.path.exists(args.output):
-            raise parser.error('The output image {} already exists.'.format(args.output))
-
+            raise parser.error(
+                "The output image {} already exists.".format(args.output)
+            )
+
     # loading image
     data_input, header_input = load(args.input)
-    
+
     # apply the watershed
-    logger.info('Applying anisotropic diffusion with settings: niter={} / kappa={} / gamma={}...'.format(args.iterations, args.kappa, args.gamma))
-    data_output = anisotropic_diffusion(data_input, args.iterations, args.kappa, args.gamma, get_pixel_spacing(header_input))
+    logger.info(
+        "Applying anisotropic diffusion with settings: niter={} / kappa={} / gamma={}...".format(
+            args.iterations, args.kappa, args.gamma
+        )
+    )
+    data_output = anisotropic_diffusion(
+        data_input,
+        args.iterations,
+        args.kappa,
+        args.gamma,
+        get_pixel_spacing(header_input),
+    )
 
     # save file
     save(data_output, args.output, header_input, args.force)
-
-    logger.info('Successfully terminated.')
+
+    logger.info("Successfully terminated.")
+
 
 def getArguments(parser):
     "Provides additional validation of the arguments collected by argparse."
     return parser.parse_args()
 
+
 def getParser():
     "Creates and returns the argparse parser object."
     parser = argparse.ArgumentParser(description=__description__)
-    parser.add_argument('input', help='Source volume.')
-    parser.add_argument('output', help='Target volume.')
-    parser.add_argument('-i', '--iterations', type=int, default=1, help='The number of smoothing iterations. Strong parameter.')
-    parser.add_argument('-k', '--kappa', type=int, default=50, help='The algorithms kappa parameter. The higher the more edges are smoothed over.')
-    parser.add_argument('-g', '--gamma', type=float, default=0.1, help='The algorithms gamma parameter. The higher, the stronger the plateaus between edges are smeared.')
-    parser.add_argument('-v', dest='verbose', action='store_true', help='Display more information.')
-    parser.add_argument('-d', dest='debug', action='store_true', help='Display debug information.')
-    parser.add_argument('-f', dest='force', action='store_true', help='Silently override existing output images.')
-
+    parser.add_argument("input", help="Source volume.")
+    parser.add_argument("output", help="Target volume.")
+    parser.add_argument(
+        "-i",
+        "--iterations",
+        type=int,
+        default=1,
+        help="The number of smoothing iterations. Strong parameter.",
+    )
+    parser.add_argument(
+        "-k",
+        "--kappa",
+        type=int,
+        default=50,
+        help="The algorithms kappa parameter. The higher the more edges are smoothed over.",
+    )
+    parser.add_argument(
+        "-g",
+            "--gamma",
+        type=float,
+        default=0.1,
+        help="The algorithms gamma parameter. The higher, the stronger the plateaus between edges are smeared.",
+    )
+    parser.add_argument(
+        "-v", dest="verbose", action="store_true", help="Display more information."
+    )
+    parser.add_argument(
+        "-d", dest="debug", action="store_true", help="Display debug information."
+    )
+    parser.add_argument(
+        "-f",
+        dest="force",
+        action="store_true",
+        help="Silently override existing output images.",
+    )
+
     return parser
-
+
+
 if __name__ == "__main__":
     main()