add annotation parsing

biigle · Jul 25, 2024 · a505bd8 · a505bd8
1 parent af35796
commit a505bd8
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Showing 7 changed files with 1,736 additions and 145 deletions.
diff --git a/src/Converter.php b/src/Converter.php
@@ -2,11 +2,18 @@
 namespace Biigle\Modules\MetadataIfdo;
 
 use Biigle\MediaType;
+use Biigle\Services\MetadataParsing\Label;
+use Biigle\Services\MetadataParsing\LabelAndUser;
+use Biigle\Services\MetadataParsing\User;
 use Biigle\Services\MetadataParsing\VolumeMetadata;
+use Biigle\Shape;
+use Illuminate\Support\Arr;
 
 class Converter
 {
     private $acquisitionFormat = '';
+    private $annotators        = [];
+    private $labels            = [];
 
     public function __construct($acquisitionFormat)
     {
@@ -15,10 +22,13 @@ public function __construct($acquisitionFormat)
 
     public function convert($ifdo)
     {
+        $this->annotators = $this->extractIfdoAnnotators($ifdo->getImageSetHeader()['image-annotation-creators']);
+        $this->labels     = $this->extractIfdoLabels($ifdo->getImageSetHeader()['image-annotation-labels']);
+
         $data = new VolumeMetadata($this->mediaType());
         foreach ($ifdo->getImageSetItems() as $name => $items)
         {
-            if ( ! is_array($items))
+            if ( ! array_is_list($items))
             {
                 $items = [$items];
             }
@@ -39,12 +49,18 @@ public function convert($ifdo)
 
                 if ( ! is_null($fileData = $data->getFile($name)) && ! is_null($takenAt))
                 {
-                    $fileData->addFrame(...$params);
+                    $fileData->addFrame(...Arr::except($params, ['name']));
                 }
                 else
                 {
                     $class    = $this->metadataClass();
                     $fileData = new $class(...$params);
+
+                    if (isset($item['image-annotations']))
+                    {
+                        $this->addAnnotations($fileData, $item['image-annotations']);
+                    }
+
                     $data->addFile($fileData);
                 }
 
@@ -62,6 +78,97 @@ protected function maybeCastToFloat(?string $value): ?float
         return (is_null($value) || $value === '') ? null : floatval($value);
     }
 
+    private function addAnnotations($fileData, $ifdoAnnotations)
+    {
+        foreach ($ifdoAnnotations as $ifdoAnnotation)
+        {
+            $fileData->addAnnotation($this->ifdoToBiigleAnnotation($ifdoAnnotation));
+        }
+    }
+
+    private function ifdoToBiigleAnnotation($ifdoAnnotation)
+    {
+        $class  = $this->annotationClass();
+        $params = [
+            $this->ifdoShapeToBiigleShape($ifdoAnnotation['shape']),
+            $ifdoAnnotation['coordinates'],
+            $this->ifdoLabelsToBiigleLabelAndUsers($ifdoAnnotation['labels']),
+        ];
+
+        if (isset($ifdoAnnotation['frames']))
+        {
+            $params[] = $ifdoAnnotation['frames'];
+        }
+
+        $annotation = new $class(...$params);
+
+        return $annotation;
+    }
+
+    private function ifdoLabelsToBiigleLabelAndUsers($ifdoLabels)
+    {
+        return array_map([$this, 'ifdoLabelToBiigleLabelAndUser'], $ifdoLabels);
+    }
+
+    private function ifdoLabelToBiigleLabelAndUser($ifdoLabel)
+    {
+        return new LabelAndUser(
+            $this->labelForId($ifdoLabel['label']),
+            $this->userForId($ifdoLabel['annotator'])
+        );
+    }
+
+    private function extractIfdoLabels($ifdoLabels)
+    {
+        $labels = [];
+        foreach ($ifdoLabels as $ifdoLabel)
+        {
+            $labels[$ifdoLabel['id']] = new Label($ifdoLabel['id'], $ifdoLabel['name']);
+        }
+        return $labels;
+    }
+
+    private function extractIfdoAnnotators($ifdoAnnotators)
+    {
+        $annotators = [];
+        foreach ($ifdoAnnotators as $ifdoAnnotator)
+        {
+            $annotators[$ifdoAnnotator['id']] = new User($ifdoAnnotator['id'], $ifdoAnnotator['name']);
+        }
+        return $annotators;
+    }
+
+    private function userForId($id)
+    {
+        return $this->annotators[$id];
+    }
+
+    private function labelForId($id)
+    {
+        return $this->labels[$id];
+    }
+
+    private function ifdoShapeToBiigleShape($shape)
+    {
+        switch ($shape)
+        {
+        case 'single-pixel':
+            return Shape::point();
+        case 'polyline':
+            return Shape::line();
+        case 'polygon':
+            return Shape::polygon();
+        case 'circle':
+            return Shape::circle();
+        case 'rectangle':
+            return Shape::rectangle();
+        case 'ellipse':
+            return Shape::ellipse();
+        case 'whole-frame':
+            return Shape::wholeFrame();
+        }
+    }
+
     private function mediaType()
     {
         switch ($this->acquisitionFormat)
@@ -84,4 +191,14 @@ private function metadataClass()
         }
     }
 
+    private function annotationClass()
+    {
+        switch ($this->acquisitionFormat)
+        {
+        case 'photo':
+            return 'Biigle\Services\MetadataParsing\ImageAnnotation';
+        case 'video':
+            return 'Biigle\Services\MetadataParsing\VideoAnnotation';
+        }
+    }
 }
diff --git a/src/MetadataIfdoServiceProvider.php b/src/MetadataIfdoServiceProvider.php
@@ -18,7 +18,7 @@ public function boot(Modules $modules)
         $this->loadViewsFrom(__DIR__ . '/resources/views', 'metadata-ifdo');
 
         ParserFactory::extend(IfdoParser::class, 'image');
-        ParserFactory::extend(VideoIfdoParser::class, 'video');
+        ParserFactory::extend(IfdoParser::class, 'video');
         $modules->register('metadata-ifdo', [
             'viewMixins' => [
                 'metadataParsers',

diff --git a/src/VideoIfdoParser.php b/src/VideoIfdoParser.php
diff --git a/tests/IfdoParserTest.php b/tests/IfdoParserTest.php
@@ -27,5 +27,34 @@ public function testGetMetadata()
         $this->assertEquals(2.1, $file->distanceToGround);
         $this->assertEquals(5.1, $file->area);
         $this->assertEquals(21, $file->yaw);
+
+        $this->assertCount(7, $file->getAnnotations());
+        $annotation = array_pop($file->annotations);
+
+        $this->assertEquals(3, $annotation->shape->id);
+        $this->assertEquals('Hans Wurst', $annotation->labels[0]->user->name);
+    }
+
+    public function testGetVideoMetadata()
+    {
+        $file   = new File(__DIR__ . "/files/video-example-1.json");
+        $parser = new IfdoParser($file);
+        $data   = $parser->getMetadata();
+        $this->assertEquals(MediaType::videoId(), $data->type->id);
+        $this->assertNull($data->name);
+        $this->assertNull($data->url);
+        $this->assertNull($data->handle);
+        $this->assertCount(1, $data->getFiles());
+        $file = $data->getFiles()->last();
+        $this->assertEquals('SO242_2_163-1_LowerHD.mp4', $file->name);
+        $this->assertEquals('2019-04-06 04:29:27.000000', $file->takenAt);
+        $this->assertEquals(-117.0214286, $file->lng);
+        $this->assertEquals(11.8582192, $file->lat);
+        $this->assertEquals(-4129.6, $file->gpsAltitude);
+        $this->assertEquals(2.1, $file->distanceToGround);
+        $this->assertEquals(5.1, $file->area);
+        $this->assertEquals(21, $file->yaw);
+
+        // var_dump($file);
     }
 }
diff --git a/tests/MetadataIfdoServiceProviderTest.php b/tests/MetadataIfdoServiceProviderTest.php
@@ -1,11 +1,11 @@
 <?php
-
 namespace Biigle\Tests\Modules\MetadataIfdo;
 
 use Biigle\Modules\MetadataIfdo\ImageIfdoParser;
 use Biigle\Modules\MetadataIfdo\MetadataIfdoServiceProvider;
 use Biigle\Modules\MetadataIfdo\VideoIfdoParser;
 use Biigle\Services\MetadataParsing\ParserFactory;
+use Symfony\Component\HttpFoundation\File\File;
 use TestCase;
 
 class MetadataIfdoServiceProviderTest extends TestCase
@@ -19,7 +19,7 @@ public function testGetImageIfdo()
     {
         $this->markTestIncomplete('implement metadata parser');
 
-        $file = new File(__DIR__."/files/image-ifdo.json");
+        $file   = new File(__DIR__ . "/files/image-ifdo.json");
         $parser = ParserFactory::getParserForFile($file, 'image');
         $this->assertInstanceOf(ImageIfdoParser::class, $parser);
     }
@@ -28,7 +28,7 @@ public function testGetVideoIfdo()
     {
         $this->markTestIncomplete('implement metadata parser');
 
-        $file = new File(__DIR__."/files/video-ifdo.json");
+        $file   = new File(__DIR__ . "/files/video-ifdo.json");
         $parser = ParserFactory::getParserForFile($file, 'video');
         $this->assertInstanceOf(VideoIfdoParser::class, $parser);
     }