feat: updated focus regions clinical data extraction tool

lucalianas · Aug 31, 2023 · b8da7a3 · b8da7a3
1 parent d655e20
commit b8da7a3
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Showing 2 changed files with 22 additions and 4 deletions.
diff --git a/promort/clinical_annotations_manager/management/commands/get_focus_regions_clinical_data.py b/promort/clinical_annotations_manager/management/commands/get_focus_regions_clinical_data.py
@@ -86,8 +86,12 @@ def _dump_row(self, focus_region_annotation, csv_writer):
                 'hypernephroid_pattern': focus_region_annotation.hypernephroid_pattern,
                 'mucinous': focus_region_annotation.mucinous,
                 'comedo_necrosis': focus_region_annotation.comedo_necrosis,
-                'total_gleason_4_area': focus_region_annotation.get_total_gleason_4_area(),
-                'gleason_4_percentage': focus_region_annotation.get_gleason_4_percentage()
+                'total_gleason_3_area': focus_region_annotation.get_total_gleason_area("G3"),
+                'total_gleason_4_area': focus_region_annotation.get_total_gleason_area("G4"),
+                'total_gleason_5_area': focus_region_annotation.get_total_gleason_area("G5"),
+                'gleason_3_percentage': focus_region_annotation.get_gleason_percentage("G3"),
+                'gleason_4_percentage': focus_region_annotation.get_gleason_percentage("G4"),
+                'gleason_5_percentage': focus_region_annotation.get_gleason_percentage("G5")
             }
         )
 
@@ -96,7 +100,8 @@ def _export_data(self, out_file, page_size):
                   'focus_region_id', 'focus_region_label', 'core_id', 'core_label', 'action_start_time',
                   'action_complete_time', 'creation_date', 'perineural_involvement', 'intraductal_carcinoma',
                   'ductal_carcinoma', 'poorly_formed_glands', 'cribriform_pattern', 'small_cell_signet_ring',
-                  'hypernephroid_pattern', 'mucinous', 'comedo_necrosis', 'total_gleason_4_area', 'gleason_4_percentage']
+                  'hypernephroid_pattern', 'mucinous', 'comedo_necrosis', 'total_gleason_3_area',  'gleason_3_percentage',
+                  'total_gleason_4_area', 'gleason_4_percentage', 'total_gleason_5_area', 'gleason_5_percentage']
         with open(out_file, 'w') as ofile:
             writer = DictWriter(ofile, delimiter=',', fieldnames=header)
             writer.writeheader()

diff --git a/promort/clinical_annotations_manager/models.py b/promort/clinical_annotations_manager/models.py
@@ -289,14 +289,27 @@ def get_gleason_elements(self):
         return gleason_elements_map
 
     def get_gleason_4_elements(self):
-        return self.get_gleason_elements()["G4"]
+        return self.get_gleason_elements().get("G4", [])
+
+    def get_total_gleason_area(self, gleason_pattern):
+        gleason_area = 0
+        for g in self.get_gleason_elements().get(gleason_pattern, []):
+            gleason_area += g.area
+        return gleason_area
 
     def get_total_gleason_4_area(self):
         g4_area = 0
         for g4 in self.get_gleason_4_elements():
             g4_area += g4.area
         return g4_area
 
+    def get_gleason_percentage(self, gleason_pattern):
+        gleason_area = self.get_total_gleason_area(gleason_pattern)
+        try:
+            return (gleason_area / self.focus_region.area) * 100.0
+        except ZeroDivisionError:
+            return -1
+
     def get_gleason_4_percentage(self):
         g4_area = self.get_total_gleason_4_area()
         try: