feat: removed constraints on core clinical annotation creation

promort/clinical_annotations_manager/migrations/0029_auto_20230531_1444.py

@@ -0,0 +1,28 @@
+# Generated by Django 3.1.13 on 2023-05-31 14:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('clinical_annotations_manager', '0028_auto_20221107_1442'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='coreannotation',
+            name='gleason_group',
+            field=models.CharField(choices=[('GG1', 'GRADE_GROUP_1'), ('GG2', 'GRADE_GROUP_2'), ('GG3', 'GRADE_GROUP_3'), ('GG4', 'GRADE_GROUP_4'), ('GG5', 'GRADE_GROUP_5')], default=None, max_length=3, null=True),
+        ),
+        migrations.AlterField(
+            model_name='coreannotation',
+            name='primary_gleason',
+            field=models.IntegerField(default=None, null=True),
+        ),
+        migrations.AlterField(
+            model_name='coreannotation',
+            name='secondary_gleason',
+            field=models.IntegerField(default=None, null=True),
+        ),
+    ]

promort/clinical_annotations_manager/models.py

@@ -23,6 +23,8 @@
 from reviews_manager.models import ClinicalAnnotationStep
 from rois_manager.models import Slice, Core, FocusRegion
 
+from collections import Counter
+
 
 class SliceAnnotation(models.Model):
     author = models.ForeignKey(User, on_delete=models.PROTECT, blank=False)
@@ -95,10 +97,10 @@ class CoreAnnotation(models.Model):
     action_start_time = models.DateTimeField(null=True, default=None)
     action_complete_time = models.DateTimeField(null=True, default=None)
     creation_date = models.DateTimeField(default=timezone.now)
-    primary_gleason = models.IntegerField(blank=False)
-    secondary_gleason = models.IntegerField(blank=False)
+    primary_gleason = models.IntegerField(null=True, default=None)
+    secondary_gleason = models.IntegerField(null=True, default=None)
     gleason_group = models.CharField(
-        max_length=3, choices=GLEASON_GROUP_WHO_16, blank=False
+        max_length=3, choices=GLEASON_GROUP_WHO_16, null=True, default=None
     )
     # acquire ONLY if at least one Cribriform Pattern (under GleasonPattern type 4) exists
     nuclear_grade_size = models.CharField(max_length=1, null=True, default=None)
@@ -119,6 +121,52 @@ class CoreAnnotation(models.Model):
     class Meta:
         unique_together = ('core', 'annotation_step')
 
+    def _get_gleason_elements(self):
+        gleason_elements = list()
+        for fr in self.core.focus_regions.all():
+            gleason_elements.extend(
+                GleasonPattern.objects.filter(
+                    focus_region = fr,
+                    annotation_step = self.annotation_step
+                ).all()
+            )
+        return gleason_elements
+
+    def _get_gleason_coverage(self):
+        g_elems = self._get_gleason_elements()
+        total_gleason_area = 0
+        gleason_patterns_area = Counter()
+        for g_el in g_elems:
+            total_gleason_area += g_el.area
+            gleason_patterns_area[g_el.gleason_type] += g_el.area
+        gleason_coverage = dict()
+        for gp, gpa in gleason_patterns_area.items():
+            gleason_coverage[gp] = (100 * gpa/total_gleason_area)
+        return gleason_coverage
+
+    def _get_primary_and_secondary_gleason(self):
+        gleason_coverage = self._get_gleason_coverage()
+        if len(gleason_coverage) == 0:
+            return None, None
+        primary_gleason = max(gleason_coverage, key=gleason_coverage.get)
+        gleason_coverage.pop(primary_gleason)
+        if len(gleason_coverage) == 0:
+            secondary_gleason = primary_gleason
+        else:
+            secondary_gleason = max(gleason_coverage)
+        return primary_gleason, secondary_gleason
+
+    def get_primary_gleason(self):
+        primary_gleason, _ = self._get_primary_and_secondary_gleason()
+        return primary_gleason
+
+    def get_secondary_gleason(self):
+        _, secondary_gleason = self._get_primary_and_secondary_gleason()
+        return secondary_gleason
+
+    def get_gleason_group(self):
+        pass
+
     def get_gleason_4_total_area(self):
         gleason_4_total_area = 0.0
         for focus_region in self.core.focus_regions.all():
@@ -198,7 +246,7 @@ class Meta:
     def get_gleason_elements(self):
         gleason_elements_map = dict()
         for gp in self.annotation_step.gleason_annotations.filter(focus_region=self.focus_region).all():
-            gleason_elements_map[gp.gleason_type] = gp
+            gleason_elements_map.setdefault(gp.gleason_type, []).append(gp)
         return gleason_elements_map
 
     def get_gleason_4_elements(self):

promort/clinical_annotations_manager/serializers.py

@@ -77,8 +77,7 @@ class CoreAnnotationSerializer(serializers.ModelSerializer):
     class Meta:
         model = CoreAnnotation
         fields = ('id', 'author', 'core', 'annotation_step', 'action_start_time', 'action_complete_time',
-                  'creation_date', 'primary_gleason', 'secondary_gleason', 'gleason_score',
-                  'gleason_4_percentage', 'gleason_group', 'nuclear_grade_size',
+                  'creation_date', 'gleason_score', 'gleason_4_percentage', 'nuclear_grade_size',
                   'intraluminal_acinar_differentiation_grade', 'intraluminal_secretions',
                   'central_maturation', 'extra_cribriform_gleason_score',
                   'largest_confluent_sheet', 'total_cribriform_area', 'predominant_rsg',
@@ -91,7 +90,7 @@ class Meta:
 
     @staticmethod
     def get_gleason_score(obj):
-        return '%d + %d' % (obj.primary_gleason, obj.secondary_gleason)
+        return '{0} + {1}'.format(obj.get_primary_gleason(), obj.get_secondary_gleason())
 
     @staticmethod
     def get_gleason_4_percentage(obj):

promort/src/js/clinical_annotations_manager/clinical_annotations_manager.controllers.js

@@ -573,6 +573,7 @@
                                 break;
                             case 'focus_region':
                                 vm.activateNewFocusRegionAnnotationMode(roi_id);
+                                break;
                         }
                     }
                 } else {
@@ -585,6 +586,7 @@
                             break;
                         case 'focus_region':
                             vm.activateShowFocusRegionAnnotationMode(roi_id);
+                            break;
                     }
                 }
             }
@@ -1259,8 +1261,7 @@
         }
 
         function formValid() {
-            return ((typeof vm.primaryGleason !== 'undefined') &&
-                (typeof vm.secondaryGleason !== 'undefined'));
+            return true;
         }
 
         function destroy() {
@@ -1313,9 +1314,6 @@
                 closeByDocument: false
             });
             var obj_config = {
-                primary_gleason: Number(vm.primaryGleason),
-                secondary_gleason: Number(vm.secondaryGleason),
-                gleason_group: vm.gradeGroupWho,
                 action_start_time: vm.actionStartTime,
                 action_complete_time: new Date(),
                 predominant_rsg: vm.predominant_rsg,