Initial updates

requirements.txt

@@ -1 +1,26 @@
 chris_plugin==0.4.0
+
+matplotlib
+monai-weekly
+gdown
+nibabel
+tqdm
+ignite
+
+torch
+pytorch-ignite
+itk
+scikit-image
+scipy
+pillow
+tensorboard
+torchvision
+psutil
+pandas
+lmdb
+einops
+transformers
+mlflow
+pynrrd
+clearml
+

spleenseg_train.py

@@ -3,32 +3,68 @@
 from pathlib import Path
 from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
 
+import os
+from monai.utils import first, set_determinism
+from monai.transforms import (
+    AsDiscrete,
+    AsDiscreted,
+    EnsureChannelFirstd,
+    Compose,
+    CropForegroundd,
+    LoadImaged,
+    Orientationd,
+    RandCropByPosNegLabeld,
+    SaveImaged,
+    ScaleIntensityRanged,
+    Spacingd,
+    Invertd,
+)
+from monai.handlers.utils import from_engine
+from monai.networks.nets import UNet
+from monai.networks.layers import Norm
+from monai.metrics import DiceMetric
+from monai.losses import DiceLoss
+from monai.inferers import sliding_window_inference
+from monai.data import CacheDataset, DataLoader, Dataset, decollate_batch
+from monai.config import print_config
+from monai.apps import download_and_extract
+import torch
+import matplotlib.pyplot as plt
+import tempfile
+import shutil
+import glob
+import pudb
+
 from chris_plugin import chris_plugin, PathMapper
 
-__version__ = '1.0.0'
+__version__ = "1.0.0"
 
 DISPLAY_TITLE = r"""
-       _                                    _             _                                   _             _       
-      | |                                  (_)           | |                                 | |           (_)      
- _ __ | |______ _ __ ___   ___  _ __   __ _ _   ___ _ __ | | ___  ___ _ __  ___  ___  __ _   | |_ _ __ __ _ _ _ __  
-| '_ \| |______| '_ ` _ \ / _ \| '_ \ / _` | | / __| '_ \| |/ _ \/ _ \ '_ \/ __|/ _ \/ _` |  | __| '__/ _` | | '_ \ 
+       _                                    _             _                                   _             _
+      | |                                  (_)           | |                                 | |           (_)
+ _ __ | |______ _ __ ___   ___  _ __   __ _ _   ___ _ __ | | ___  ___ _ __  ___  ___  __ _   | |_ _ __ __ _ _ _ __
+| '_ \| |______| '_ ` _ \ / _ \| '_ \ / _` | | / __| '_ \| |/ _ \/ _ \ '_ \/ __|/ _ \/ _` |  | __| '__/ _` | | '_ \
 | |_) | |      | | | | | | (_) | | | | (_| | | \__ \ |_) | |  __/  __/ | | \__ \  __/ (_| |  | |_| | | (_| | | | | |
 | .__/|_|      |_| |_| |_|\___/|_| |_|\__,_|_| |___/ .__/|_|\___|\___|_| |_|___/\___|\__, |   \__|_|  \__,_|_|_| |_|
-| |                                        ______  | |                                __/ |_____                    
-|_|                                       |______| |_|                               |___/______|                   
+| |                                        ______  | |                                __/ |_____
+|_|                                       |______| |_|                               |___/______|
 """
 
 
-parser = ArgumentParser(description='!!!CHANGE ME!!! An example ChRIS plugin which '
-                                    'counts the number of occurrences of a given '
-                                    'word in text files.',
-                        formatter_class=ArgumentDefaultsHelpFormatter)
-parser.add_argument('-w', '--word', required=True, type=str,
-                    help='word to count')
-parser.add_argument('-p', '--pattern', default='**/*.txt', type=str,
-                    help='input file filter glob')
-parser.add_argument('-V', '--version', action='version',
-                    version=f'%(prog)s {__version__}')
+parser = ArgumentParser(
+    description="""
+A ChRIS DS plugin based on Project MONAI 3D Spleen Segmentation.
+This plugin performs the training component, with some gentle
+refactoring and pervasive type hinting.
+    """,
+    formatter_class=ArgumentDefaultsHelpFormatter,
+)
+parser.add_argument(
+    "-p", "--pattern", default="**/*nii.gz", type=str, help="input file filter glob"
+)
+parser.add_argument(
+    "-V", "--version", action="version", version=f"%(prog)s {__version__}"
+)
 
 
 # The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
@@ -37,11 +73,11 @@
 # documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
 @chris_plugin(
     parser=parser,
-    title='Spleen 3D image segmentation training (MONAI)',
-    category='',                 # ref. https://chrisstore.co/plugins
-    min_memory_limit='100Mi',    # supported units: Mi, Gi
-    min_cpu_limit='1000m',       # millicores, e.g. "1000m" = 1 CPU core
-    min_gpu_limit=0              # set min_gpu_limit=1 to enable GPU
+    title="Spleen 3D image segmentation training (MONAI)",
+    category="",  # ref. https://chrisstore.co/plugins
+    min_memory_limit="100Mi",  # supported units: Mi, Gi
+    min_cpu_limit="1000m",  # millicores, e.g. "1000m" = 1 CPU core
+    min_gpu_limit=0,  # set min_gpu_limit=1 to enable GPU
 )
 def main(options: Namespace, inputdir: Path, outputdir: Path):
     """
@@ -55,6 +91,7 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     """
 
     print(DISPLAY_TITLE)
+    print_config()
 
     # Typically it's easier to think of programs as operating on individual files
     # rather than directories. The helper functions provided by a ``PathMapper``
@@ -63,15 +100,15 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     #
     # Refer to the documentation for more options, examples, and advanced uses e.g.
     # adding a progress bar and parallelism.
-    mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt')
+    mapper = PathMapper.file_mapper(
+        inputdir, outputdir, glob=options.pattern, suffix=".count.txt"
+    )
     for input_file, output_file in mapper:
         # The code block below is a small and easy example of how to use a ``PathMapper``.
         # It is recommended that you put your functionality in a helper function, so that
         # it is more legible and can be unit tested.
-        data = input_file.read_text()
-        frequency = data.count(options.word)
-        output_file.write_text(str(frequency))
+        break
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()