Add base app

spleenseg_train.py

@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+from pathlib import Path
+from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
+
+from chris_plugin import chris_plugin, PathMapper
+
+__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__}')
+
+
+# The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
+# Some metadata about the plugin is specified here. There is more metadata specified in setup.py.
+#
+# 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
+)
+def main(options: Namespace, inputdir: Path, outputdir: Path):
+    """
+    *ChRIS* plugins usually have two positional arguments: an **input directory** containing
+    input files and an **output directory** where to write output files. Command-line arguments
+    are passed to this main method implicitly when ``main()`` is called below without parameters.
+
+    :param options: non-positional arguments parsed by the parser given to @chris_plugin
+    :param inputdir: directory containing (read-only) input files
+    :param outputdir: directory where to write output files
+    """
+
+    print(DISPLAY_TITLE)
+
+    # Typically it's easier to think of programs as operating on individual files
+    # rather than directories. The helper functions provided by a ``PathMapper``
+    # object make it easy to discover input files and write to output files inside
+    # the given paths.
+    #
+    # 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')
+    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))
+
+
+if __name__ == '__main__':
+    main()