Default DICOM origin to [0, 0, 0]

drivendataorg · Dec 3, 2017 · 28c60c9 · 28c60c9
1 parent 411ae05
commit 28c60c9
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/prediction/src/preprocess/load_ct.py b/prediction/src/preprocess/load_ct.py
@@ -147,6 +147,9 @@ def extract_origin_mhd(self):
         # the default axes order which is used is: (z, y, x)
         return self.meta.GetOrigin()[::-1]
 
+    def extract_origin_dicom(self):
+        return [0]*3
+
     def non_copy_constructor(self, meta_instance):
         self.meta = meta_instance.meta
         self.spacing = meta_instance.spacing
@@ -167,6 +170,7 @@ def __init__(self, meta):
         if dicom_meta:
             # list of methods for DICOM meta
             self.spacing = self.extract_spacing_dcm()
+            self.origin = self.extract_origin_dicom()
         elif mhd_meta:
             # list of methods for MetaImage meta
             self.spacing = self.extract_spacing_mhd()

diff --git a/prediction/src/tests/test_classification.py b/prediction/src/tests/test_classification.py
@@ -6,7 +6,7 @@ def test_classify_predict_load(metaimage_path, model_path):
 
 
 def test_classify_dicom(dicom_paths, nodule_locations, model_path):
-    predicted = trained_model.predict(dicom_paths, nodule_locations, model_path)
+    predicted = trained_model.predict(dicom_paths[0], nodule_locations, model_path)
     assert predicted
     assert 0 <= predicted[0]['p_concerning'] <= 1