Release v0.9.4-2

promort/VERSION

@@ -1 +1 @@
-0.9.4
+0.9.4-2

promort/predictions_manager/management/commands/tissue_to_rois.py

@@ -277,17 +277,19 @@ def _get_core_bounds(self, core: Dict) -> Dict:
         except IndexError:
             raise InvalidPolygonError()
 
-    def _group_nearest_cores(self, cores, height_tolerance=0.01):
+    def _group_nearest_cores(self, cores):
         cores_map, sorted_y_coords = self._get_sorted_cores_map(cores)
         cores_groups = list()
-        tolerance = sorted_y_coords[-1][1] * height_tolerance
         current_group = cores_map[sorted_y_coords[0]]
+        cg_max_y = sorted_y_coords[0][1]
         for i, yc in enumerate(sorted_y_coords[1:]):
-            if yc[0] <= sorted_y_coords[i][1] + tolerance:
+            if yc[0] <= cg_max_y:
                 current_group.extend(cores_map[yc])
+                cg_max_y = max([cg_max_y, yc[1]])
             else:
                 cores_groups.append(current_group)
                 current_group = cores_map[yc]
+                cg_max_y = yc[1]
         cores_groups.append(current_group)
         return cores_groups
 

promort/reviews_manager/serializers.py

@@ -18,6 +18,7 @@
 #  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
 from django.contrib.auth.models import User
+from predictions_manager.models import Provenance
 
 from rest_framework import serializers
 
@@ -280,6 +281,7 @@ class PredictionReviewSerializer(serializers.ModelSerializer):
         slug_field='username',
         queryset=User.objects.all()
     )
+    model = serializers.SerializerMethodField()
     started = serializers.SerializerMethodField()
     completed = serializers.SerializerMethodField()
     annotation_type = serializers.SerializerMethodField()
@@ -288,9 +290,16 @@ class PredictionReviewSerializer(serializers.ModelSerializer):
     class Meta:
         model  = PredictionReview
 
-        fields = ('id', 'label', 'annotation_type', 'prediction', 'slide', 'reviewer',
+        fields = ('id', 'label', 'annotation_type', 'prediction', 'slide', 'reviewer', 'model',
                   'creation_date', 'start_date', 'completion_date', 'started', 'completed')
-        read_only_fields = ('id', 'creation_date', 'started', 'completed', 'annotation_type')
+        read_only_fields = ('id', 'creation_date', 'started', 'completed', 'annotation_type', 'model')
+
+    @staticmethod
+    def get_model(obj):
+        try:
+            return Provenance.objects.filter(prediction=obj.prediction).first().model
+        except AttributeError:
+            return None
 
     @staticmethod
     def get_started(obj):

promort/rois_manager/management/commands/extract_focus_regions.py

@@ -44,9 +44,18 @@ def add_arguments(self, parser):
                             help='path of the output folder for the extracted JSON objects')
         parser.add_argument('--limit-bounds', dest='limit_bounds', action='store_true',
                             help='extract ROIs considering only the non-empty slide region')
-
-    def _load_rois_annotation_steps(self):
-        steps = ROIsAnnotationStep.objects.filter(completion_date__isnull=False)
+        parser.add_argument('--reviewer', dest='reviewer', type=str,
+                            help='filter review steps by reviewer username')
+        parser.add_argument('--tissue-type', dest='tissue_type', type=str,
+                            choices=['TUMOR', 'NORMAL'], help='filter focus regions by tissue type')
+
+    def _load_rois_annotation_steps(self, reviewer=None):
+        if reviewer is not None:
+            logger.info(f'Filtering by reviewer: {reviewer}')
+            steps = ROIsAnnotationStep.objects.filter(completion_date__isnull=False,
+                                                      rois_annotation__reviewer__username=reviewer)
+        else:
+            steps = ROIsAnnotationStep.objects.filter(completion_date__isnull=False)
         return steps
 
     def _get_slide_bounds(self, slide):
@@ -112,8 +121,11 @@ def _dump_details(self, details, out_folder):
             writer.writeheader()
             writer.writerows(details)
 
-    def _dump_focus_regions(self, step, out_folder, limit_bounds):
-        focus_regions = step.focus_regions
+    def _dump_focus_regions(self, step, out_folder, limit_bounds, tissue_type=None):
+        if tissue_type is None:
+            focus_regions = step.focus_regions
+        else:
+            focus_regions = [fr for fr in step.focus_regions if fr.tissue_status == tissue_type]
         slide = step.slide
         logger.info('Loading info for slide %s', slide.id)
         if not limit_bounds:
@@ -135,13 +147,13 @@ def _dump_focus_regions(self, step, out_folder, limit_bounds):
                         focus_regions_details.append(frd)
                 self._dump_details(focus_regions_details, out_path)
 
-    def _export_data(self, out_folder, limit_bounds=False):
-        steps = self._load_rois_annotation_steps()
+    def _export_data(self, out_folder, limit_bounds=False, reviewer=None, tissue_type=None):
+        steps = self._load_rois_annotation_steps(reviewer)
         logger.info('Loaded %d ROIs Annotation Steps', len(steps))
         for s in steps:
-            self._dump_focus_regions(s, out_folder, limit_bounds)
+            self._dump_focus_regions(s, out_folder, limit_bounds, tissue_type)
 
     def handle(self, *args, **opts):
         logger.info('=== Starting export job ===')
-        self._export_data(opts['out_folder'], opts['limit_bounds'])
+        self._export_data(opts['out_folder'], opts['limit_bounds'], opts['reviewer'], opts['tissue_type'])
         logger.info('=== Export completed ===')

promort/static_src/templates/worklist/pending_reviews.html

@@ -35,6 +35,9 @@ <h1>WORKLIST - Pending annotations</h1>
                                 <strong>Review ID:</strong> {{ annotation.extended_label }}
                             </p>
                             <p><strong>Review Type:</strong> {{ annotation.annotation_type }}</p>
+                            <p ng-show="wlc.isPredictionReview(annotation)">
+                                <strong>Model:</strong> {{ annotation.model }}
+                            </p>
                             <p ng-show="!wlc.isQuestionnaireRequest(annotation) && !wlc.isPredictionReview(annotation)">
                                 <strong>Slides count:</strong> {{ annotation.steps_count | number:0 }}
                             </p>