Extend abundance report

app/Http/Requests/StoreReport.php

@@ -24,6 +24,7 @@ public function rules()
             'aggregate_child_labels' => "nullable|boolean",
             'disable_notifications' => "nullable|boolean",
             'strip_ifdo' => "nullable|boolean",
+            'all_labels' => 'nullable|boolean'
         ];
     }
 
@@ -65,6 +66,7 @@ public function getOptions()
             'separateUsers' => boolval($this->input('separate_users', false)),
             'newestLabel' => boolval($this->input('newest_label', false)),
             'onlyLabels' => $this->input('only_labels', []),
+            'allLabels' => boolval($this->input('all_labels', false)),
         ];
 
         if ($this->isAllowedForExportArea()) {

app/Services/Reports/ReportGenerator.php

@@ -265,6 +265,16 @@ protected function shouldSeparateUsers()
         return $this->options->get('separateUsers', false);
     }
 
+    /**
+     * Should this report show all labels?
+     *
+     * @return bool
+     */
+    protected function shouldUseAllLabels()
+    {
+        return $this->options->get('all_labels', false);
+    }
+
     /**
      * Returns the array of label ids to which this report should be restricted.
      *

app/Services/Reports/Volumes/ImageAnnotations/AbundanceReportGenerator.php

@@ -38,33 +38,59 @@ class AbundanceReportGenerator extends AnnotationReportGenerator
      */
     public function generateReport($path)
     {
+        $useAllLabels = $this->shouldUseAllLabels();
         $rows = $this->query()->get();
+        $allLabelsQuery = DB::table('project_volume')
+            ->where('project_volume.volume_id', '=', $this->source->id)
+            ->join('projects', 'project_volume.project_id', '=', 'projects.id')
+            ->join('label_tree_project', 'projects.id', '=', 'label_tree_project.project_id')
+            ->join('label_trees', 'label_tree_project.label_tree_id', '=', 'label_trees.id')
+            ->join('labels', 'label_trees.id', '=', 'labels.label_tree_id')
+            ->select('labels.*');
 
         if ($this->shouldSeparateLabelTrees() && $rows->isNotEmpty()) {
             $rows = $rows->groupBy('label_tree_id');
-            $trees = LabelTree::whereIn('id', $rows->keys())->pluck('name', 'id');
+            $treeIds = $rows->keys()->filter(fn ($k) => $k != null);
+            $trees = LabelTree::whereIn('id', $treeIds)->pluck('name', 'id');
 
             foreach ($trees as $id => $name) {
-                $rowGroup = $rows->get($id);
-                $labels = Label::whereIn('id', $rowGroup->pluck('label_id')->unique())->get();
-                $this->tmpFiles[] = $this->createCsv($rowGroup, $name, $labels);
+                if ($useAllLabels) {
+                    $rowGroup = $rows->flatten();
+                    $labels = (clone $allLabelsQuery)->where('labels.label_tree_id', '=', $id)->get();
+                } else {
+                    $rowGroup = $rows->get($id);
+                    $labels = Label::whereIn('id', $rowGroup->pluck('label_id')->unique())->get();
+                }
+                $this->tmpFiles[] = $this->createCsv($rows->flatten(), $name, $labels);
             }
         } elseif ($this->shouldSeparateUsers() && $rows->isNotEmpty()) {
-            $labels = Label::whereIn('id', $rows->pluck('label_id')->unique())->get();
+            $labels = $allLabelsQuery->get();
+            $allFilenames = $rows->pluck('filename')->unique();
             $rows = $rows->groupBy('user_id');
-            $users = User::whereIn('id', $rows->keys())
+            $userIds = $rows->keys()->filter(fn ($k) => $k != null);
+            $users = User::whereIn('id', $userIds)
                 ->selectRaw("id, concat(firstname, ' ', lastname) as name")
                 ->pluck('name', 'id');
 
             foreach ($users as $id => $name) {
                 $rowGroup = $rows->get($id);
+                $userFilenames = $rowGroup->pluck('filename')->unique();
+                $missingFiles = $allFilenames->diff($userFilenames);
+                // Create empty entries to show all images
+                foreach ($missingFiles as $f) {
+                    $rowGroup->add((object) [
+                        'filename' => $f,
+                        'count' => 0,
+                        'label_id' => null,
+                        'user_id' => $id
+                    ]);
+                }
                 $this->tmpFiles[] = $this->createCsv($rowGroup, $name, $labels);
             }
         } else {
-            $labels = Label::whereIn('id', $rows->pluck('label_id')->unique())->get();
+            $labels = $useAllLabels ? $allLabelsQuery->get() : Label::whereIn('id', $rows->pluck('label_id')->unique())->get();
             $this->tmpFiles[] = $this->createCsv($rows, $this->source->name, $labels);
         }
-
         $this->executeScript('csvs_to_xlsx', $path);
     }
 
@@ -75,7 +101,15 @@ public function generateReport($path)
      */
     protected function query()
     {
-        $query = $this->initQuery()
+        $query = DB::table('image_annotation_labels')
+            ->join('image_annotations', 'image_annotation_labels.annotation_id', '=', 'image_annotations.id')
+            ->rightJoin('images', 'image_annotations.image_id', '=', 'images.id')
+            ->leftJoin('labels', 'image_annotation_labels.label_id', '=', 'labels.id')
+            ->where('images.volume_id', $this->source->id)
+            ->when($this->isRestrictedToExportArea(), [$this, 'restrictToExportAreaQuery'])
+            ->when($this->isRestrictedToAnnotationSession(), [$this, 'restrictToAnnotationSessionQuery'])
+            ->when($this->isRestrictedToNewestLabel(), fn ($query) => $this->restrictToNewestLabelQuery($query, $this->source))
+            ->when($this->isRestrictedToLabels(), fn ($query) => $this->restrictToLabelsQuery($query, 'image_annotation_labels'))
             ->orderBy('images.filename')
             ->select(DB::raw('images.filename, image_annotation_labels.label_id, count(image_annotation_labels.label_id) as count'))
             ->groupBy('image_annotation_labels.label_id', 'images.id');
@@ -107,7 +141,6 @@ protected function createCsv($rows, $title, $labels)
         if ($this->shouldAggregateChildLabels()) {
             [$rows, $labels] = $this->aggregateChildLabels($rows, $labels);
         }
-
         $labels = $labels->sortBy('id');
 
         $csv = CsvFile::makeTmp();
@@ -118,7 +151,6 @@ protected function createCsv($rows, $title, $labels)
             $columns[] = $label->name;
         }
         $csv->putCsv($columns);
-
         foreach ($rows as $filename => $annotations) {
             $row = [$filename];
             $annotations = $annotations->keyBy('label_id');
@@ -129,7 +161,6 @@ protected function createCsv($rows, $title, $labels)
                     $row[] = 0;
                 }
             }
-
             $csv->putCsv($row);
         }
 
@@ -188,7 +219,7 @@ protected function aggregateChildLabels($rows, $labels)
         foreach ($rows as $filename => $annotations) {
             // Aggregate the number of annotations of child labels to the number of their
             // parent.
-            $annotations = $annotations->keyBy('label_id');
+            $annotations = $annotations->keyBy('label_id')->reject(fn ($a) => is_null($a->label_id));
             foreach ($annotations as $labelId => $annotation) {
                 $parentId = $parentIdMap->get($labelId);
                 if ($parentId) {
@@ -214,9 +245,14 @@ protected function aggregateChildLabels($rows, $labels)
                 ->reject(fn ($annotation) => $parentIdMap->has($annotation->label_id));
         }
 
-        // Remove all labels that did not occur (as parent) in the rows.
-        $presentLabels = $presentLabels->unique()->flip();
-        $labels = $labels->filter(fn ($label) => $presentLabels->has($label->id));
+        if ($this->shouldUseAllLabels()) {
+            // Remove all labels that are not parent labels
+            $labels = $labels->filter(fn ($l) => is_null($l->parent_id));
+        } else {
+            // Remove all labels that did not occur (as parent) in the rows.
+            $presentLabels = $presentLabels->unique()->flip();
+            $labels = $labels->filter(fn ($label) => $presentLabels->has($label->id));
+        }
 
         return [$rows, $labels];
     }

resources/assets/js/reports/mixins/reportForm.vue

@@ -29,6 +29,7 @@ export default {
                 separate_users: false,
                 only_labels: [],
                 aggregate_child_labels: false,
+                all_labels: false,
             },
         };
     },

resources/assets/js/reports/projectForm.vue

@@ -17,6 +17,7 @@ export default {
                     'separate_label_trees',
                     'separate_users',
                     'only_labels',
+                    'all_labels',
                     'aggregate_child_labels',
                 ],
                 'ImageLabels': [

resources/assets/js/reports/volumeForm.vue

@@ -17,6 +17,7 @@ export default {
                     'separate_users',
                     'annotation_session_id',
                     'only_labels',
+                    'all_labels',
                     'aggregate_child_labels',
                 ],
                 'ImageLabels': [

resources/views/projects/reports.blade.php

@@ -94,6 +94,17 @@
                         Annotations that are outside of the export area will be discarded for this report.
                     </div>
                 </div>
+                <div v-cloak v-if="wantsCombination('ImageAnnotations', 'Abundance')" class="form-group" :class="{'has-error': errors.all_labels}">
+                    <div class="checkbox">
+                        <label>
+                            <input type="checkbox" v-model="options.all_labels"> Include all volume labels
+                        </label>
+                    </div>
+                    <div v-if="errors.all_labels" v-cloak class="help-block" v-text="getError('all_labels')"></div>
+                    <div v-else class="help-block">
+                        Include all labels that can be used in a volume.
+                    </div>
+                </div>
                 <div v-cloak v-if="hasOption('newest_label')" :class="{'has-error': errors.newest_label}">
                     <div class="checkbox">
                         <label>

resources/views/volumes/reports.blade.php

@@ -102,6 +102,17 @@
                         </div>
                     </div>
                 @endif
+                <div v-cloak v-if="wantsCombination('ImageAnnotations', 'Abundance')" class="form-group" :class="{'has-error': errors.all_labels}">
+                    <div class="checkbox">
+                        <label>
+                            <input type="checkbox" v-model="options.all_labels"> Include all volume labels
+                        </label>
+                    </div>
+                    <div v-if="errors.all_labels" v-cloak class="help-block" v-text="getError('all_labels')"></div>
+                    <div v-else class="help-block">
+                        Include all labels that can be used in a volume.
+                    </div>
+                </div>
                 <div v-cloak v-if="hasOption('newest_label')" class="form-group" :class="{'has-error': errors.newest_label}">
                     <div class="checkbox">
                         <label>