demo

imgtools/examples/radcure_simple.py

@@ -1,10 +1,12 @@
+from argparse import ArgumentParser
+
 from ..pipeline import Pipeline
 from ..ops import Resample
 from ..io import ImageDirectoryLoader, read_dicom_series, read_dicom_rtstruct
 
 
 class RADCUREPipeline(Pipeline):
-    def __init__(self, root_directory="/cluster/projects/radiomics/RADCURE_images/", spacing=(1., 1., 1.)):
+    def __init__(self, root_directory="/cluster/projects/radiomics/RADCURE_images/", output_directory="./processed" spacing=(1., 1., 1.)):
         self.root_directory = root_directory
         self.image_loader = ImageDirectoryLoader(self.root_directory, index_by="parent", subdir_path="*/ImageSet_*", reader=read_dicom_series)
         self.structure_set_loader = ImageDirectoryLoader(self.root_directory, index_by="parent", subdir_path="*/structures", reader=read_dicom_rtstruct)
@@ -17,3 +19,12 @@ def process_one_case(self, key):
         mask = structure_set.to_mask(image, roi_names="GTV")
         self.image_writer.add(key, image)
         self.mask_writer.add(key, mask)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser("Example RADCURE processing pipeline.")
+    parser.add_argument("root_directory", type=str)
+    parser.add_argument("output_directory", type=str)
+    parser.add_argument("--spacing", nargs=3, type=float, default=(1., 1., 1.))
+    pipeline = RADCUREPipeline(args.root_directory, output_directory=args.output_directory, spacing=args.spacing)
+    pipeline.run()

imgtools/io/__init__.py

@@ -1,3 +1,3 @@
 from .common import *
-from .readers import *
+from .loaders import *
 from .writers import *

imgtools/io/loaders.py

@@ -95,6 +95,8 @@ def _generate_paths(self):
             if self.subdir_path:
                 path = os.path.join(path, self.subdir_path)
             path = glob.glob(path)[0]
+            if os.path.isdir(path):
+                path = os.path.join(path, "")
             key = self._extract_key_from_path(path)
             paths[key] = path
         return paths

imgtools/io/writers.py

@@ -1,19 +1,9 @@
 import os
-import glob
-import re
-from typing import Optional
-from collections import namedtuple
-from itertools import chain
 
 import numpy as np
-import pandas as pd
 import SimpleITK as sitk
-from pydicom import dcmread
-from pydicom.misc import is_dicom
 
-from .image import physical_point_to_index
-from .segmentation import StructureSet
-from .utils.imageutils import image_to_array
+from ..utils import image_to_array
 
 
 class ImageFileWriter: