Merge pull request #173 from biigle/issue-125

Sort by similarity

src/Http/Controllers/Api/Projects/SortAnnotationsByOutliersController.php

@@ -4,8 +4,6 @@
 
 use DB;
 use Biigle\Http\Controllers\Api\Controller;
-use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
-use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
 use Biigle\Project;
 
 class SortAnnotationsByOutliersController extends Controller
@@ -30,7 +28,7 @@ public function index($pid, $lid)
         $project = Project::findOrFail($pid);
         $this->authorize('access', $project);
 
-        // This was too complicated with the query builder. Since there is no rist of SQL
+        // This was too complicated with the query builder. Since there is no risk of SQL
         // injection here, we just use raw SQL.
         $sql = <<<SQL
         SELECT "id" FROM (
@@ -67,7 +65,7 @@ public function index($pid, $lid)
 
         $ids = DB::select($sql, ['pid' => $pid, 'lid' => $lid]);
 
-        // Filtering unique IDs is not required here because the UNIQUE in the query
+        // Filtering unique IDs is not required here because the UNION in the query
         // takes care of that.
         return array_map(fn ($v) => $v->id, $ids);
     }

src/Http/Controllers/Api/Projects/SortAnnotationsBySimilarityController.php

@@ -0,0 +1,67 @@
+<?php
+
+namespace Biigle\Modules\Largo\Http\Controllers\Api\Projects;
+
+use Biigle\Http\Controllers\Api\Controller;
+use Biigle\Modules\Largo\Http\Requests\IndexProjectAnnotationsSimilarity;
+use DB;
+
+class SortAnnotationsBySimilarityController extends Controller
+{
+    /**
+     * Sort annotations with specific label by similarity.
+     *
+     * @api {get} projects/:id/annotations/sort/similarity Sort annotations with the same label by similarity
+     * @apiGroup Projects
+     * @apiName ShowProjectsAnnotationsSortSimilarity
+     * @apiParam {Number} id The project ID
+     * @apiParam (Required arguments) {Number} label_id The Label ID
+     * @apiParam (Required arguments) {Number} image_annotation_id The reference image annotation to sort by similarity. This is not required if `video_annotation_id` is provided.
+     * @apiParam (Required arguments) {Number} video_annotation_id The reference video annotation to sort by similarity. This is not required if `image_annotation_id` is provided.
+     * @apiPermission projectMember
+     * @apiDescription Returns a list of image/video annotation IDs with the most similar first (without the reference annotation ID). Image annotation IDs are prefixed with `i` (e.g. `i123`) and video annotation IDs are prefixed with `v` (e.g. `v456`).
+     *
+     * @param  IndexProjectAnnotationsSimilarity  $request
+     */
+    public function index(IndexProjectAnnotationsSimilarity $request)
+    {
+        $r = $request->reference;
+
+        // This was too complicated with the query builder. Since there is no risk of SQL
+        // injection here, we just use raw SQL.
+        $sql = <<<SQL
+        SELECT "id" FROM (
+            (
+              SELECT CONCAT('i', "annotation_id") AS id, "vector"
+              FROM "image_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "annotation_id" != :iid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+           )
+           UNION
+           (
+              SELECT CONCAT('v', "annotation_id") AS id, "vector"
+              FROM "video_annotation_label_feature_vectors"
+              WHERE "label_id" = :lid AND "annotation_id" != :vid AND "volume_id" IN (
+                 SELECT "volume_id" FROM "project_volume" WHERE "project_id" = :pid
+              )
+           )
+        ) AS "temp"
+        ORDER BY "temp"."vector" <=> :vector, id DESC
+        SQL;
+
+        $ids = DB::select($sql, [
+            'pid' => $request->project->id,
+            'lid' => $r->label_id,
+            'vector' => $r->vector,
+            // We need only one at a time but since the ID 0 never exists, we just take
+            // it as the other ID.
+            'iid' => $request->input('image_annotation_id', 0),
+            'vid' => $request->input('video_annotation_id', 0),
+        ]);
+
+        // Filtering unique IDs is not required here because the UNION in the query
+        // takes care of that.
+        return array_map(fn ($v) => $v->id, $ids);
+    }
+}

src/Http/Controllers/Api/Volumes/SortAnnotationsBySimilarityController.php

@@ -0,0 +1,49 @@
+<?php
+
+namespace Biigle\Modules\Largo\Http\Controllers\Api\Volumes;
+
+use Biigle\Http\Controllers\Api\Controller;
+use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\Http\Requests\IndexVolumeAnnotationsSimilarity;
+
+class SortAnnotationsBySimilarityController extends Controller
+{
+    /**
+     * Sort annotations with specific label by similarity.
+     *
+     * @api {get} volumes/:id/annotations/sort/similarity Sort annotations with the same label by similarity
+     * @apiGroup Volumes
+     * @apiName ShowVolumesAnnotationsSortSimilarity
+     * @apiParam {Number} id The volume ID
+     * @apiParam (Required arguments) {Number} label_id The Label ID
+     * @apiParam (Required arguments) {Number} annotation_id The reference annotation to sort by similarity
+     * @apiPermission projectMember
+     * @apiDescription Returns a list of image/video annotation IDs with the most similar first (without the reference annotation ID).
+     *
+     * @param  IndexVolumeAnnotationsSimilarity  $request
+     */
+    public function index(IndexVolumeAnnotationsSimilarity $request)
+    {
+        $r = $request->reference;
+
+        if ($request->volume->isVideoVolume()) {
+            $query = VideoAnnotationLabelFeatureVector::where('volume_id', $r->volume_id)
+                ->where('label_id', $r->label_id)
+                ->where('id', '!=', $r->id)
+                ->orderByRaw('vector <=> ?, annotation_id DESC', [$r->vector]);
+        } else {
+            $query = ImageAnnotationLabelFeatureVector::where('volume_id', $r->volume_id)
+                ->where('label_id', $r->label_id)
+                ->where('id', '!=', $r->id)
+                ->orderByRaw('vector <=> ?, annotation_id DESC', [$r->vector]);
+        }
+
+        return $query->pluck('annotation_id')
+            // Use distinct/unique *after* fetchig from the DB because otherwise the
+            // vector would need to be selected, too (order by expressions must appear in
+            // the select list). But we don't want to get the huge vectors.
+            ->unique()
+            ->values();
+    }
+}

src/Http/Requests/IndexProjectAnnotationsSimilarity.php

@@ -0,0 +1,87 @@
+<?php
+
+namespace Biigle\Modules\Largo\Http\Requests;
+
+use Biigle\Annotation;
+use Biigle\ImageAnnotation;
+use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
+use Biigle\VideoAnnotation;
+use Biigle\Project;
+use Illuminate\Foundation\Http\FormRequest;
+
+class IndexProjectAnnotationsSimilarity extends FormRequest
+{
+    /**
+     * The project of which to index the annotations.
+     */
+    public Project $project;
+
+    /**
+     * The reference annotation for sorting.
+     */
+    public $reference;
+
+    /**
+     * Determine if the user is authorized to make this request.
+     *
+     * @return bool
+     */
+    public function authorize()
+    {
+        $this->project = Project::findOrFail($this->route('id'));
+
+        return $this->user()->can('access', $this->project);
+    }
+
+    /**
+     * Get the validation rules that apply to the request.
+     *
+     * @return array
+     */
+    public function rules()
+    {
+        return [
+            'label_id' => 'required|bail|integer',
+            'image_annotation_id' => 'required_without:video_annotation_id|bail|integer',
+            'video_annotation_id' => 'required_without:image_annotation_id|bail|integer',
+        ];
+    }
+
+    /**
+     * Configure the validator instance.
+     *
+     * @param  \Illuminate\Validation\Validator  $validator
+     * @return void
+     */
+    public function withValidator($validator)
+    {
+        $validator->after(function ($validator) {
+            if ($validator->errors()->isNotEmpty()) {
+                return;
+            }
+
+            $ids = $this->project->volumes()->pluck('id');
+            if ($this->input('image_annotation_id')) {
+                $this->reference = ImageAnnotationLabelFeatureVector::whereIn('volume_id', $ids)
+                    ->where('label_id', $this->input('label_id'))
+                    ->where('annotation_id', $this->input('image_annotation_id'))
+                    ->first();
+
+                if (is_null($this->reference)) {
+                    $validator->errors()->add('image_annotation_id', 'The annotation does not exist in the project.');
+                }
+            } else {
+                $this->reference = VideoAnnotationLabelFeatureVector::whereIn('volume_id', $ids)
+                    ->where('label_id', $this->input('label_id'))
+                    ->where('annotation_id', $this->input('video_annotation_id'))
+                    ->first();
+
+                if (is_null($this->reference)) {
+                    $validator->errors()->add('video_annotation_id', 'The annotation does not exist in the project.');
+                }
+            }
+
+        });
+    }
+}

src/Http/Requests/IndexVolumeAnnotationsSimilarity.php

@@ -0,0 +1,76 @@
+<?php
+
+namespace Biigle\Modules\Largo\Http\Requests;
+
+use Biigle\Annotation;
+use Biigle\ImageAnnotation;
+use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
+use Biigle\Modules\Largo\VideoAnnotationLabelFeatureVector;
+use Biigle\VideoAnnotation;
+use Biigle\Volume;
+use Illuminate\Foundation\Http\FormRequest;
+
+class IndexVolumeAnnotationsSimilarity extends FormRequest
+{
+    /**
+     * The volume of which to index the annotations.
+     */
+    public Volume $volume;
+
+    /**
+     * The reference annotation for sorting.
+     */
+    public $reference;
+
+    /**
+     * Determine if the user is authorized to make this request.
+     *
+     * @return bool
+     */
+    public function authorize()
+    {
+        $this->volume = Volume::findOrFail($this->route('id'));
+
+        return $this->user()->can('access', $this->volume);
+    }
+
+    /**
+     * Get the validation rules that apply to the request.
+     *
+     * @return array
+     */
+    public function rules()
+    {
+        return [
+            'label_id' => 'required|bail|integer',
+            'annotation_id' => 'required|bail|integer',
+        ];
+    }
+
+    /**
+     * Configure the validator instance.
+     *
+     * @param  \Illuminate\Validation\Validator  $validator
+     * @return void
+     */
+    public function withValidator($validator)
+    {
+        $validator->after(function ($validator) {
+            if ($this->volume->isImageVolume()) {
+                $this->reference = ImageAnnotationLabelFeatureVector::where('volume_id', $this->volume->id)
+                    ->where('label_id', $this->input('label_id'))
+                    ->where('annotation_id', $this->input('annotation_id'))
+                    ->first();
+            } else {
+                $this->reference = VideoAnnotationLabelFeatureVector::where('volume_id', $this->volume->id)
+                    ->where('label_id', $this->input('label_id'))
+                    ->where('annotation_id', $this->input('annotation_id'))
+                    ->first();
+            }
+
+            if (is_null($this->reference)) {
+                $validator->errors()->add('annotation_id', 'The annotation does not exist in the volume.');
+            }
+        });
+    }
+}

src/Http/routes.php

@@ -37,6 +37,10 @@
         'uses' => 'Projects\SortAnnotationsByOutliersController@index',
     ]);
 
+    $router->get('projects/{id}/annotations/sort/similarity', [
+        'uses' => 'Projects\SortAnnotationsBySimilarityController@index',
+    ]);
+
     $router->get('projects/{id}/image-annotations/filter/label/{id2}', [
         'uses' => 'Projects\FilterImageAnnotationsByLabelController@index',
     ]);
@@ -53,6 +57,10 @@
         'uses' => 'Volumes\SortAnnotationsByOutliersController@index',
     ]);
 
+    $router->get('volumes/{id}/annotations/sort/similarity', [
+        'uses' => 'Volumes\SortAnnotationsBySimilarityController@index',
+    ]);
+
     $router->get('volumes/{id}/image-annotations/examples/{id2}', [
         'uses' => 'Volumes\ImageAnnotationExamplesController@index',
     ]);

src/public/mix-manifest.json

@@ -1,4 +1,4 @@
 {
-    "/assets/scripts/main.js": "/assets/scripts/main.js?id=9d428530385ad8ea4cbd82e4600d8cd0",
-    "/assets/styles/main.css": "/assets/styles/main.css?id=f5673570cda3cacb644da42a2840c218"
+    "/assets/scripts/main.js": "/assets/scripts/main.js?id=608af5558117398ca4c3d3598a905abb",
+    "/assets/styles/main.css": "/assets/styles/main.css?id=5295955359904ac00dbeabaf613c5792"
 }

src/resources/assets/js/api/projects.js

@@ -27,4 +27,8 @@ export default Vue.resource('api/v1/projects{/id}/largo', {}, {
         method: 'GET',
         url: 'api/v1/projects{/id}/annotations/sort/outliers{/label_id}',
     },
+    sortAnnotationsBySimilarity: {
+        method: 'GET',
+        url: 'api/v1/projects{/id}/annotations/sort/similarity',
+    },
 });

src/resources/assets/js/api/volumes.js

@@ -35,4 +35,8 @@ export default Vue.resource('api/v1/volumes{/id}/largo', {}, {
         method: 'GET',
         url: 'api/v1/volumes{/id}/annotations/sort/outliers{/label_id}',
     },
+    sortAnnotationsBySimilarity: {
+        method: 'GET',
+        url: 'api/v1/volumes{/id}/annotations/sort/similarity',
+    },
 });