From 4ba2af3de85d038c3c35c50eb478d40033bd12ce Mon Sep 17 00:00:00 2001
From: Nathan <nx33@drexel.edu>
Date: Thu, 4 Aug 2022 23:46:36 -0400
Subject: [PATCH 1/2] added feature extraction

---
 feature_extraction.py | 25 +++++++++++++++++++++++++
 requirements.txt      | 13 +++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 feature_extraction.py
 create mode 100644 requirements.txt

diff --git a/feature_extraction.py b/feature_extraction.py
new file mode 100644
index 0000000..8dacc35
--- /dev/null
+++ b/feature_extraction.py
@@ -0,0 +1,25 @@
+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
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..7404f59
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,13 @@
+docopt==0.6.2
+numpy==1.23.1
+pandas==1.4.3
+pydicom==2.3.0
+pykwalify==1.8.0
+pyradiomics==3.0.1
+python-dateutil==2.8.2
+pytz==2022.1
+PyWavelets==1.3.0
+ruamel.yaml==0.17.21
+ruamel.yaml.clib==0.2.6
+SimpleITK==2.1.1.2
+six==1.16.0

From 16193ddde37891812eaa29cb23d5269fe3393300 Mon Sep 17 00:00:00 2001
From: Nathan <nx33@drexel.edu>
Date: Thu, 4 Aug 2022 23:51:49 -0400
Subject: [PATCH 2/2] removed unnecessary imports

---
 requirements.txt | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 7404f59..07c2453 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,11 +1,8 @@
 docopt==0.6.2
 numpy==1.23.1
-pandas==1.4.3
-pydicom==2.3.0
 pykwalify==1.8.0
 pyradiomics==3.0.1
 python-dateutil==2.8.2
-pytz==2022.1
 PyWavelets==1.3.0
 ruamel.yaml==0.17.21
 ruamel.yaml.clib==0.2.6