Release v0.10.0

crs4 · May 9, 2022 · 8cf494d · 8cf494d
2 parents 051e1e3 + d8c0c6f
commit 8cf494d
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diff --git a/README.md b/README.md
@@ -1,6 +1,8 @@
-# ProMort Image Management System
-The goal of the **ProMort** project is to conduct a large scale epidemiological study of patients that have beendiagnosed 
-with a benign form of prostatic cancer but nevertheless died before expected.
+# CRS4 Digital Pathology Platform
+The Digital Pathology platform developed by CRS4 is a web-based application tailored for interactive annotation of Whole Slide Images in the context of clinical research. It is a multi-component system that integrates [OME Remote Objects (OMERO)](https://www.openmicroscopy.org/omero/), thought the integration of the [ome_seadragon plugin](https://github.com/crs4/ome_seadragon), with a system for annotating tumour tissues, developed entirely at CRS4. 
+The platform was born out of a collaboration with the Karolinska Institutet in Stockholm in the context of the [ProMort](https://academic.oup.com/aje/article/188/6/1165/5320054?login=true) project, where it allowed pathologists to annotate thousands of prostate tissue images.  Its development has continued, incorporating several new functionalities.  Most recently, the ability to apply deep learning models to images for detecting tumour regions in prostate biopsies and for classifying their severity was added (in the [DeepHealth](https://deephealth-project.eu/) project).  The use of the platform for the study of prostate cancer has also been [validated in a collaborative study by CRS4 and KI](https://www.nature.com/articles/s41598-021-82911-z).
 
-The specific goal of the **ProMort Image Management System** is to create a collection of fully annotated images related 
-to biopsies slides.
+## Docker images
+
+* Django based web server: https://hub.docker.com/repository/docker/crs4/promort-web
+* Nginx server with static files: https://hub.docker.com/repository/docker/crs4/promort-nginx
diff --git a/promort/VERSION b/promort/VERSION
@@ -1 +1 @@
-0.9.4-2
+0.10.0
diff --git a/promort/predictions_manager/management/commands/tissue_to_rois.py b/promort/predictions_manager/management/commands/tissue_to_rois.py
@@ -54,6 +54,12 @@ def add_arguments(self, parser):
             default=None,
             help="apply only to ROIs annotation steps assigned to this reviewer",
         )
+        parser.add_argument(
+            "--limit-bounds",
+            dest="limit_bounds",
+            action="store_true",
+            help="apply limit bounds when converting to ROIs",
+        )
 
     def handle(self, *args, **opts):
         logger.info("== Starting import job ==")
@@ -64,19 +70,28 @@ def handle(self, *args, **opts):
 
             for step in annotation_steps:
                 logger.info("Processing ROIs annotation step %s", step.label)
-                latest_prediction = Prediction.objects.filter(
-                    slide=step.slide, type='TISSUE'
-                ).order_by('-creation_date').first()
-
-                fragments_collection = latest_prediction.fragments_collection.order_by('-creation_date').first()
-
+                latest_prediction = (
+                    Prediction.objects.filter(slide=step.slide, type="TISSUE")
+                    .order_by("-creation_date")
+                    .first()
+                )
+
+                fragments_collection = latest_prediction.fragments_collection.order_by(
+                    "-creation_date"
+                ).first()
+
                 if fragments_collection and fragments_collection.fragments.count() > 0:
                     fragments = fragments_collection.fragments.all()
 
-                    slide_bounds = self._get_slide_bounds(step.slide)
+                    if opts["limit_bounds"]:
+                        slide_bounds = self._get_slide_bounds(step.slide)
+                    else:
+                        slide_bounds = {"bounds_x": 0, "bounds_y": 0}
 
                     slide_mpp = step.slide.image_microns_per_pixel
-                    all_shapes = [json.loads(fragment.shape_json) for fragment in fragments]
+                    all_shapes = [
+                        json.loads(fragment.shape_json) for fragment in fragments
+                    ]
                     grouped_shapes = self._group_nearest_cores(all_shapes)
                     for idx, shapes in enumerate(grouped_shapes):
                         slice_label = idx + 1
@@ -89,7 +104,7 @@ def handle(self, *args, **opts):
                             step,
                             user,
                             slide_bounds,
-                            fragments_collection
+                            fragments_collection,
                         )
                         logger.info("Slice saved with ID %d", slice_obj.id)
                         for core_index, core in enumerate(shapes):
@@ -107,13 +122,14 @@ def handle(self, *args, **opts):
                                 core_index + 1,
                                 user,
                                 slide_bounds,
-                                fragments_collection
+                                fragments_collection,
                             )
                             logger.info("Core saved with ID %d", core_obj.id)
                 else:
                     logger.info(
                         "Skipping prediction %s for step %s, no tissue fragment found",
-                        latest_prediction.label, step.label,
+                        latest_prediction.label,
+                        step.label,
                     )
                     continue
         else:
@@ -174,7 +190,7 @@ def _create_slice(
         annotation_step,
         user,
         slide_bounds,
-        collection
+        collection,
     ):
         slice_coordinates = self._adjust_roi_coordinates(
             slice_coordinates, slide_bounds
@@ -189,7 +205,7 @@ def _create_slice(
             author=user,
             roi_json=json.dumps(roi_json),
             total_cores=cores_count,
-            source_collection=collection
+            source_collection=collection,
         )
         slice_.save()
         return slice_
@@ -204,7 +220,7 @@ def _create_core(
         core_id,
         user,
         slide_bounds,
-        collection
+        collection,
     ):
         core_coordinates = self._adjust_roi_coordinates(core_coordinates, slide_bounds)
         roi_json = self._create_roi_json(
@@ -217,7 +233,7 @@ def _create_core(
             roi_json=json.dumps(roi_json),
             length=core_length,
             area=core_area,
-            source_collection=collection
+            source_collection=collection,
         )
         core.save()
         return core

diff --git a/promort/predictions_manager/views.py b/promort/predictions_manager/views.py
@@ -20,6 +20,8 @@
 import json
 import logging
 
+from distutils.util import strtobool
+
 from predictions_manager.models import (Prediction, TissueFragment,
                                         TissueFragmentsCollection)
 from predictions_manager.serializers import (
@@ -46,6 +48,31 @@ class PredictionDetail(GenericDetailView):
     permission_classes = (permissions.IsAuthenticated, )
 
 
+class PredictionDetailBySlide(APIView):
+    model_serializer = PredictionSerializer
+    permission_classes = (permissions.IsAuthenticated, )
+
+    def _find_predictions_by_slide_id(self, slide_id, type=None, fetch_latest=False):
+        if type is None:
+            predictions = Prediction.objects.filter(slide__id=slide_id)
+        else:
+            predictions = Prediction.objects.filter(slide__id=slide_id, type=type)
+        if fetch_latest:
+            return predictions.order_by('-creation_date').first()
+        return predictions.all()
+
+
+    def get(self, request, pk, format=None):
+        fetch_latest = strtobool(request.GET.get('latest', 'false'))
+        prediction_type = request.GET.get('type')
+        predictions = self._find_predictions_by_slide_id(pk, prediction_type, fetch_latest)
+        if (fetch_latest and predictions is None) or (not fetch_latest and len(predictions) == 0):
+            raise NotFound(f'No predictions found for the required query')
+        else:
+            serializer = self.model_serializer(predictions, many = not fetch_latest)
+            return Response(serializer.data, status=status.HTTP_200_OK)
+
+
 class PredictionRequireReview(APIView):
     permission_classes = (permissions.IsAuthenticated, )
 

diff --git a/promort/promort/urls.py b/promort/promort/urls.py
@@ -100,6 +100,7 @@ def to_url(self, value):
     path('api/cases/<slug:pk>/', CaseDetail.as_view()),
     path('api/slides/', SlideList.as_view()),
     path('api/slides/<slug:pk>/', SlideDetail.as_view()),
+    path('api/slides/<slug:pk>/predictions/', pmv.PredictionDetailBySlide.as_view()),
     path('api/slides_set/', SlidesSetList.as_view()),
     path('api/slides_set/<slug:pk>/', SlidesSetDetail.as_view()),
 

diff --git a/promort/src/js/ome_seadragon_viewer/viewer.controllers.js b/promort/src/js/ome_seadragon_viewer/viewer.controllers.js
@@ -247,32 +247,74 @@
 
     AnnotationsViewerController.$inject = ['$scope', '$rootScope', '$location', '$log', 'ngDialog',
         'ViewerService', 'AnnotationsViewerService', 'ROIsAnnotationStepManagerService',
-        'CurrentSlideDetailsService', 'CurrentAnnotationStepsDetailsService'];
+        'CurrentSlideDetailsService', 'CurrentAnnotationStepsDetailsService',
+        'HeatmapViewerService', 'CurrentPredictionDetailsService'];
 
     function AnnotationsViewerController($scope, $rootScope, $location, $log, ngDialog, ViewerService,
                                          AnnotationsViewerService, ROIsAnnotationStepManagerService,
-                                         CurrentSlideDetailsService, CurrentAnnotationStepsDetailsService) {
+                                         CurrentSlideDetailsService, CurrentAnnotationStepsDetailsService,
+                                         HeatmapViewerService, CurrentPredictionDetailsService) {
         var vm = this;
+        vm.ome_base_url = undefined;
         vm.slide_id = undefined;
+        vm.prediction_id = undefined;
         vm.annotation_step_label = undefined;
         vm.slide_details = undefined;
+        vm.prediction_details = undefined;
         vm.dzi_url = undefined;
         vm.static_files_url = undefined;
+        vm.loading_tiled_images = undefined;
+        vm.current_opacity = undefined;
         vm.getDZIURL = getDZIURL;
+        vm.enableHeatmapLayer = enableHeatmapLayer;
+        vm.getDatasetDZIURL = getDatasetDZIURL;
         vm.getStaticFilesURL = getStaticFilesURL;
         vm.getSlideMicronsPerPixel = getSlideMicronsPerPixel;
         vm.registerComponents = registerComponents;
+        vm.registerHeatmapComponents = registerHeatmapComponents;
+        vm.setOverlayOpacity = setOverlayOpacity;
+        vm.updateOverlayOpacity = updateOverlayOpacity;
 
         activate();
 
         function activate() {
+            var dialog = undefined;
+
             vm.slide_id = CurrentSlideDetailsService.getSlideId();
+            vm.prediction_id = CurrentPredictionDetailsService.getPredictionId();
             vm.annotation_step_label = CurrentAnnotationStepsDetailsService.getROIsAnnotationStepLabel();
+
+            vm.loading_tiled_images = 0;
+
+            $scope.$on('viewer.tiledimage.added', function() {
+                if (vm.loading_tiled_images == 0) {
+                    dialog = ngDialog.open({
+                        template: '/static/templates/dialogs/heatmap_loading.html',
+                        showClose: false,
+                        closeByEscape: false,
+                        closeByNavigation: false,
+                        closeByDocument: false
+                    });
+                }
+                vm.loading_tiled_images += 1;
+            });
+
+            $scope.$on('viewer.tiledimage.loaded', function() {
+                if (vm.loading_tiled_images > 0) {
+                    vm.loading_tiled_images -= 1;
+                    if (vm.loading_tiled_images === 0) {
+                        dialog.close();
+                    }
+                } else {
+                    console.log('Nothing to do...');
+                }
+            });
+
             ViewerService.getOMEBaseURLs()
                 .then(OMEBaseURLSuccessFn, OMEBaseURLErrorFn);
 
             function OMEBaseURLSuccessFn(response) {
-                var base_url = response.data.base_url;
+                vm.ome_base_url = response.data.base_url;
                 vm.static_files_url = response.data.static_files_url + '/ome_seadragon/img/openseadragon/';
 
                 ViewerService.getSlideInfo(vm.slide_id)
@@ -281,11 +323,28 @@
                 function SlideInfoSuccessFn(response) {
                     vm.slide_details = response.data;
                     if (vm.slide_details.image_type === 'MIRAX') {
-                        vm.dzi_url = base_url + 'mirax/deepzoom/get/' + vm.slide_details.id + '.dzi';
+                        vm.dzi_url = vm.ome_base_url + 'mirax/deepzoom/get/' + vm.slide_details.id + '.dzi';
                     } else {
-                        vm.dzi_url = base_url + 'deepzoom/get/' + vm.slide_details.omero_id + '.dzi';
+                        vm.dzi_url = vm.ome_base_url + 'deepzoom/get/' + vm.slide_details.omero_id + '.dzi';
+                    }
+
+                    if (typeof(vm.prediction_id) !== 'undefined') {
+                        HeatmapViewerService.getPredictionInfo(vm.prediction_id)
+                            .then(PredictionInfoSuccessFn, PredictionInfoErrorFn);
+
+                        function PredictionInfoSuccessFn(response) {
+                            vm.prediction_details = response.data;
+
+                            $rootScope.$broadcast('viewer.controller_initialized');
+                        }
+
+                        function PredictionInfoErrorFn(response) {
+                            $log.error(response.error);
+                            $location.url('404');
+                        }
+                    } else {
+                        $rootScope.$broadcast('viewer.controller_initialized');
                     }
-                    $rootScope.$broadcast('viewer.controller_initialized');
                 }
 
                 function SlideInfoErrorFn(response) {
@@ -298,8 +357,9 @@
                 $log.error(response.error);
             }
 
-            $scope.$on('viewerctrl.components.registered',
+            $scope.$on('rois_viewerctrl.components.registered',
                 function(event, rois_read_only, clinical_annotation_step_label) {
+                    console.log(event);
                     var dialog = ngDialog.open({
                         template: '/static/templates/dialogs/rois_loading.html',
                         showClose: false,
@@ -312,6 +372,8 @@
                         .then(getROIsSuccessFn, getROIsErrorFn);
 
                     function getROIsSuccessFn(response) {
+                        $log.info('Loaded ROIS');
+
                         for (var sl in response.data.slices) {
                             var slice = response.data.slices[sl];
                             AnnotationsViewerService.drawShape($.parseJSON(slice.roi_json));
@@ -375,6 +437,14 @@
             return vm.dzi_url;
         }
 
+        function enableHeatmapLayer() {
+            return (typeof(vm.prediction_id) !== 'undefined');
+        }
+
+        function getDatasetDZIURL(color_palette) {
+            return HeatmapViewerService.getDatasetBaseUrl() + '?palette=' + color_palette;
+        }
+
         function getStaticFilesURL() {
             return vm.static_files_url;
         }
@@ -384,6 +454,7 @@
         }
 
         function registerComponents(viewer_manager, annotations_manager, tools_manager, rois_read_only) {
+            $log.info('Registering components');
             AnnotationsViewerService.registerComponents(viewer_manager,
                 annotations_manager, tools_manager);
             $log.debug('--- VERIFY ---');
@@ -393,9 +464,24 @@
                 clinical_annotation_step_label =
                     CurrentAnnotationStepsDetailsService.getClinicalAnnotationStepLabel();
             }
-            $rootScope.$broadcast('viewerctrl.components.registered', rois_read_only,
+            $rootScope.$broadcast('rois_viewerctrl.components.registered', rois_read_only,
                 clinical_annotation_step_label);
         }
+
+        function registerHeatmapComponents(viewer_manager) {
+            HeatmapViewerService.registerComponents(viewer_manager, vm.ome_base_url, vm.prediction_details);
+        }
+
+        function setOverlayOpacity(opacity, update) {
+            this.current_opacity = opacity;
+            if (typeof(update) !== 'undefined' && update === true) {
+                this.updateOverlayOpacity();
+            }
+        }
+
+        function updateOverlayOpacity() {
+            HeatmapViewerService.setOverlayOpacity(this.current_opacity);
+        }
     }
 
     SlidesSequenceViewerController.$inject = ['$scope', '$routeParams', '$rootScope', '$location', '$log',