Fix support for tiled images and feature vectors

src/Jobs/GenerateFeatureVectors.php

@@ -213,8 +213,8 @@ protected function generateFileInput(VolumeFile $file, Collection $annotations):
 
             if (!$zeroSize) {
                 // Convert width and height to "right" and "bottom" coordinates.
-                $box[2] = $box[0] + $box[2];
-                $box[3] = $box[1] + $box[3];
+                $box[2] += $box[0];
+                $box[3] += $box[1];
 
                 $boxes[$a->id] = $box;
             }

src/Jobs/ProcessAnnotatedImage.php

@@ -12,7 +12,7 @@
 use Illuminate\Database\Eloquent\Collection;
 use Illuminate\Support\Facades\File;
 use Illuminate\Support\Facades\Storage;
-use VipsImage;
+use Jcupitt\Vips\Image as VipsImage;
 
 class ProcessAnnotatedImage extends ProcessAnnotatedFile
 {
@@ -22,7 +22,12 @@ class ProcessAnnotatedImage extends ProcessAnnotatedFile
     public function handleFile(VolumeFile $file, $path)
     {
         if (!$this->skipPatches) {
-            $image = $this->getVipsImage($path);
+            $options = [];
+            // Optimize for extracting only a single patch.
+            if (count($this->only) === 1) {
+                $options['access'] = 'sequential';
+            }
+            $image = $this->getVipsImage($path, $options);
         } else {
             $image = null;
         }
@@ -71,17 +76,65 @@ protected function updateOrCreateFeatureVectors(Collection $annotations, \Genera
         }
     }
 
+    /**
+     * {@inheritdoc}
+     */
+    protected function generateFeatureVectors(Collection $annotations, array|string $filePath): void
+    {
+        // Tiled images cannot be processed directly. Instead, a crop has to be
+        // generated for each annotation.
+        if (!$this->file->tiled) {
+            parent::generateFeatureVectors($annotations, $filePath);
+            return;
+        }
+
+        $boxes = $this->generateFileInput($this->file, $annotations);
+
+        if (empty($boxes)) {
+            return;
+        }
+
+        $inputPath = tempnam(sys_get_temp_dir(), 'largo_feature_vector_input');
+        $outputPath = tempnam(sys_get_temp_dir(), 'largo_feature_vector_output');
+        $tmpFiles = [$inputPath, $outputPath];
+
+        try {
+            $input = [];
+            $options = [];
+            // Optimize for extracting only a single patch.
+            if ($annotations->count() === 1) {
+                $options['access'] = 'sequential';
+            }
+            $image = $this->getVipsImage($filePath, $options);
+
+            foreach ($boxes as $id => $box) {
+                // Convert right and bottom back to width and height.
+                $box[2] -= $box[0];
+                $box[3] -= $box[1];
+
+                $path = tempnam(sys_get_temp_dir(), 'largo_feature_vector_patch');
+                $tmpFiles[] = $path;
+                $image->crop(...$box)->pngsave($path);
+
+                $input[$path] = [$id => [0, 0, $box[2], $box[3]]];
+            }
+
+            File::put($inputPath, json_encode($input));
+            $this->python($inputPath, $outputPath);
+            $output = $this->readOutputCsv($outputPath);
+            $this->updateOrCreateFeatureVectors($annotations, $output);
+        } finally {
+            File::delete($tmpFiles);
+        }
+    }
+
     /**
      * Get the vips image instance.
-     *
-     * @param string $path
-     *
-     * @return \Jcupitt\Vips\Image
      */
-    protected function getVipsImage($path)
+    protected function getVipsImage(string $path, array $options = [])
     {
         // Must not use sequential access because multiple patches could be extracted.
-        return VipsImage::newFromFile($path);
+        return VipsImage::newFromFile($path, $options);
     }
 
     /**

tests/Jobs/ProcessAnnotatedImageTest.php

@@ -3,6 +3,7 @@
 namespace Biigle\Tests\Modules\Largo\Jobs;
 
 use Biigle\FileCache\Exceptions\FileLockedException;
+use Biigle\Image;
 use Biigle\Modules\Largo\ImageAnnotationLabelFeatureVector;
 use Biigle\Modules\Largo\Jobs\ProcessAnnotatedImage;
 use Biigle\Shape;
@@ -12,7 +13,7 @@
 use Exception;
 use File;
 use FileCache;
-use Jcupitt\Vips\Image;
+use Jcupitt\Vips\Image as VipsImage;
 use Log;
 use Mockery;
 use Storage;
@@ -642,6 +643,46 @@ public function testHandleOnlyAnnotations()
         $this->assertEquals(1, ImageAnnotationLabelFeatureVector::count());
     }
 
+    public function testHandleFeatureVectorTiledImage()
+    {
+        $vipsImage = $this->getImageMock(0);
+        $vipsImage->shouldReceive('crop')
+            ->once()
+            ->with(19888, 19888, 224, 224)
+            ->andReturn($vipsImage);
+        $vipsImage->shouldReceive('pngsave')->once()->andReturn($vipsImage);
+
+        $disk = Storage::fake('test');
+        $image = Image::factory()->create([
+            'attrs' => ['width' => 40000, 'height' => 40000],
+            'tiled' => true,
+        ]);
+        $annotation = ImageAnnotationTest::create([
+            'points' => [20000, 20000],
+            'shape_id' => Shape::pointId(),
+            'image_id' => $image->id,
+        ]);
+        ImageAnnotationLabelTest::create(['annotation_id' => $annotation->id]);
+        $job = new ProcessAnnotatedImageStub($image,
+            skipPatches: true,
+            skipSvgs: true
+        );
+        $job->output = [[$annotation->id, '"'.json_encode(range(1, 384)).'"']];
+        $job->mock = $vipsImage;
+
+        $job->handle();
+        $prefix = fragment_uuid_path($annotation->image->uuid);
+        $this->assertEquals(1, ImageAnnotationLabelFeatureVector::count());
+
+        $input = $job->input;
+        $this->assertCount(1, $input);
+        $filename = array_keys($input)[0];
+        $this->assertArrayHasKey($annotation->id, $input[$filename]);
+        $box = $input[$filename][$annotation->id];
+        // These are the coordinates of the cropped image.
+        $this->assertEquals([0, 0, 224, 224], $box);
+    }
+
     protected function getImageMock($times = 1)
     {
         $image = Mockery::mock();
@@ -661,7 +702,7 @@ class ProcessAnnotatedImageStub extends ProcessAnnotatedImage
     public $outputPath;
     public $output = [];
 
-    public function getVipsImage($path)
+    public function getVipsImage(string $path, array $options = [])
     {
         return $this->mock;
     }