added feature extraction

feature_extraction.py

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+import numpy as np
+import os
+import radiomics
+import SimpleITK as sitk
+
+from radiomics import featureextractor
+
+def extract_features_from_images(segmented_image_path, raw_image_path):
+    results = {}
+
+    extractor = featureextractor.RadiomicsFeatureExtractor()
+    extractor.enableAllFeatures()
+
+    for segmented_file in os.listdir(segmented_image_path):
+        raw_image = sitk.ReadImage(os.path.join(raw_image_path, segmented_file.replace('segmented_', '')),
+                                   sitk.sitkUInt8)
+        raw_image_arr = sitk.GetArrayFromImage(raw_image)
+        segmented_image = sitk.ReadImage(os.path.join(segmented_image_path, segmented_file), 
+                                         sitk.sitkUInt8)
+
+        mask_arr = sitk.GetArrayFromImage(segmented_image)
+        # mask_arr[0][0] gets the label for the mask
+        featureVector = extractor.execute(raw_image, segmented_image, label=int(mask_arr[0][0]))
+        results[segmented_file] = np.array([(feature, value) for feature, value in featureVector.items()], dtype=object)
+    return results

requirements.txt

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+docopt==0.6.2
+numpy==1.23.1
+pykwalify==1.8.0
+pyradiomics==3.0.1
+python-dateutil==2.8.2
+PyWavelets==1.3.0
+ruamel.yaml==0.17.21
+ruamel.yaml.clib==0.2.6
+SimpleITK==2.1.1.2
+six==1.16.0