Introduces PTP tab and Job

.github/workflows/test.yml

@@ -57,9 +57,9 @@ jobs:
         docker pull ghcr.io/biigle/worker:latest
 
     - name: Start test database
-      run: docker-compose up -d --no-build database_testing && sleep 5
+      run: docker compose up -d --no-build database_testing && sleep 5
       working-directory: ../core
 
     - name: Run tests
-      run: docker-compose run --rm -u 1001 worker php -d memory_limit=1G vendor/bin/phpunit --random-order --filter 'Biigle\\Tests\\Modules\\'${MODULE_NAME}
+      run: docker compose run --rm -u 1001 worker php -d memory_limit=1G vendor/bin/phpunit --random-order --filter 'Biigle\\Tests\\Modules\\'${MODULE_NAME}
       working-directory: ../core

requirements.txt

@@ -0,0 +1,7 @@
+torch==2.1.*
+git+https://github.com/facebookresearch/segment-anything.git
+numpy==1.24.*
+Pillow==9.3.*
+sahi==0.11.18
+shapely==2.0.6
+pycocotools==2.0.8

src/Console/Commands/Publish.php

@@ -0,0 +1,38 @@
+<?php
+
+namespace Biigle\Modules\Ptp\Console\Commands;
+
+use Biigle\Modules\Ptp\PtpServiceProvider as ServiceProvider;
+use Illuminate\Console\Command;
+
+class Publish extends Command
+{
+    /**
+     * The console command name.
+     *
+     * @var string
+     */
+   protected $name = 'ptp:publish';
+
+    /**
+     * The console command description.
+     *
+     * @var string
+     */
+    protected $description = 'Publish or refresh the public assets of this package';
+
+    /**
+     * Execute the command.
+     *
+     * @return void
+     */
+    public function handle()
+    {
+        $this->call('vendor:publish', [
+            '--provider' => ServiceProvider::class,
+            '--tag' => ['public'],
+            '--force' => true,
+        ]);
+    }
+}
+

src/Database/Factories/PtpExpectedAreaFactory.php

@@ -0,0 +1,32 @@
+<?php
+
+namespace Biigle\Modules\Ptp\Database\Factories;
+
+use Biigle\Label;
+use Biigle\Modules\Ptp\PtpExpectedArea;
+use Biigle\Volume;
+use Illuminate\Database\Eloquent\Factories\Factory;
+
+class PtpExpectedAreaFactory extends Factory
+{
+    /**
+     * The name of the factory's corresponding model.
+     *
+     * @var string
+     */
+    protected $model = PtpExpectedArea::class;
+
+    /**
+     * Define the model's default state.
+     *
+     * @return array
+     */
+    public function definition()
+    {
+        return [
+            'label_id' => Label::factory(),
+            'volume_id' => Volume::factory(),
+            'areas' => json_encode([]),
+        ];
+    }
+}

src/Database/migrations/2024_11_21_091446_create_ptp_expected_areas_table.php

@@ -0,0 +1,32 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Database\Schema\Blueprint;
+use Illuminate\Support\Facades\Schema;
+use Illuminate\Support\Facades\DB;
+
+return new class extends Migration
+{
+    /**
+     * Run the migrations.
+     */
+    public function up(): void
+    {
+        Schema::create('ptp_expected_areas', function (Blueprint $table) {
+            $table->bigIncrements('id');
+            $table->integer('volume_id')->unsigned()->index();
+            $table->foreign('volume_id')->references('id')->on('volumes')->onDelete('cascade');
+            $table->integer('label_id')->unsigned()->index();
+            $table->foreign('label_id')->references('id')->on('labels')->onDelete('cascade');
+            $table->jsonb('areas');
+        });
+    }
+
+    /**
+     * Reverse the migrations.
+     */
+    public function down(): void
+    {
+        Schema::dropIfExists('ptp_expected_areas');
+    }
+};

src/Http/Controllers/Api/PtpController.php

@@ -0,0 +1,91 @@
+<?php
+
+namespace Biigle\Modules\Ptp\Http\Controllers\Api;
+use Biigle\Http\Controllers\Api\Controller;
+use Biigle\Modules\Ptp\Jobs\PtpJob;
+use Biigle\Modules\Ptp\Jobs\UploadPtpExpectedAreaJob;
+use Biigle\Modules\Ptp\Jobs\UploadConvertedAnnotationsJob;
+use Biigle\Modules\Ptp\PtpExpectedArea;
+use Biigle\ImageAnnotation;
+use Biigle\Volume;
+use Biigle\Label;
+use Illuminate\Http\Request;
+use Illuminate\Support\Facades\Bus;
+
+/**
+ * Controller used for creating a PTP Job Chain
+ */
+class PtpController extends Controller
+{
+    /**
+     * Generate Point to Polygon Job Chain.
+     * This method generates, based on the request. The jobs generated are first for computing and uploading the expected areas of converted polygons.
+     * Then, it generates a job for executing the conversion and then upload the new annotations to the DB
+     *
+     * @param  $request
+     * @return
+     */
+    public function generatePtpJob(Request $request) {
+        $this->validate($request, ['label_id' => 'integer', 'volume_id' => 'integer']);
+        $volume = Volume::findOrFail($request->volume_id);
+        $this->authorize('edit-in', $volume); Label::findOrFail($request->label_id);
+        $imageAnnotationArray = [];
+        $labelId = $request->label_id;
+        $pointShapeId = 1; //Find annotations with selected label in desired volume
+        $annotations = ImageAnnotation::join('image_annotation_labels','image_annotations.id', '=', 'image_annotation_labels.annotation_id')
+            ->join('images','image_annotations.image_id', '=','images.id')
+            ->where('image_annotation_labels.label_id', $labelId)
+            ->where('images.volume_id', $volume->id)
+            ->where('image_annotations.shape_id', $pointShapeId)
+            ->select('image_annotations.id as id', 'images.id as image_id', 'image_annotations.points as points','image_annotations.shape_id as shape_id')
+            ->get();
+        foreach ($annotations as $annotation) {
+            if (!isset($imageAnnotationArray[$annotation->image_id])) {
+                $imageAnnotationArray[$annotation->image_id] = [];
+            }
+            $imageAnnotationArray[$annotation->image_id][] = [
+                'annotation_id' => $annotation->id,
+                'points' => $annotation->points,
+                'shape' => $annotation->shape_id,
+                'image' => $annotation->image_id,
+                'label' => $labelId,
+            ];
+        };
+
+        // INFO: should we batch per small number or annotations? for now, just grouping per
+        // image IDs
+
+        $jobArray = [];
+        $expectedAreaCount = PtpExpectedArea::where('label_id', $labelId)->where('volume_id', $volume->id)->count('id');
+
+        if ($expectedAreaCount == 0){
+            $expectedAreaJobs = [];
+            $outputDir = config('ptp.temp_dir').'/compute-area/'.$volume->id.'/'.$labelId;
+
+            foreach ($imageAnnotationArray as $imageId => $imageAnnotationValues){
+                $outputFile = "$outputDir/".$labelId."_"."$imageId.json";
+                $job = new PtpJob($request->user(), $imageAnnotationValues, 'compute-area', $labelId, $outputFile);
+                array_push($expectedAreaJobs, $job);
+            }
+            array_push($jobArray, Bus::batch($expectedAreaJobs));
+            $uploadJob = new UploadPtpExpectedAreaJob($outputFile, $volume->id, $labelId);
+            array_push($jobArray, $uploadJob);
+        }
+
+        $ptpConversionJobs = [];
+        $outputDir = config('ptp.temp_dir').'/ptp/'.$volume->id.'/'.$labelId;
+
+        foreach ($imageAnnotationArray as $imageId => $imageAnnotationValues){
+            $outputFile = "$outputDir/".$labelId."_"."$imageId.json";
+            $job = new PtpJob($request->user(), $imageAnnotationValues, 'ptp', $labelId, $outputFile) ;
+             array_push($ptpConversionJobs, $job);
+        }
+        $job = new UploadConvertedAnnotationsJob($outputDir, $request->user());
+
+        array_push($jobArray, Bus::batch($ptpConversionJobs), $job);
+
+        Bus::chain($jobArray)->dispatch();
+
+        return ['submitted' => true];
+    }
+}