Merge pull request #3 from biigle/implement-metadata-parser

Implement metadata parser

.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

composer.json

@@ -20,7 +20,7 @@
       }
     },
     "require": {
-        "biigle/ifdo":"^0.3 || ^1.0"
+        "biigle/ifdo":"^0.4 || ^1.0"
     },
     "extra": {
         "laravel": {

src/Converter.php

@@ -0,0 +1,233 @@
+<?php
+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)
+    {
+        $this->acquisitionFormat = $acquisitionFormat;
+    }
+
+    public function convert($ifdo)
+    {
+        $header = $ifdo->getImageSetHeader();
+        $this->annotators = $this->extractIfdoAnnotators($header['image-annotation-creators']);
+        $this->labels     = $this->extractIfdoLabels($header['image-annotation-labels']);
+
+        $data = new VolumeMetadata(
+            type: $this->mediaType(),
+            name: $header['image-set-name'] ?? null,
+            handle: $this->parseHandle($header['image-set-handle'] ?? null),
+        );
+
+        foreach ($ifdo->getImageSetItems() as $name => $items)
+        {
+            if ( ! array_is_list($items))
+            {
+                $items = [$items];
+            }
+
+            foreach ($items as $item)
+            {
+                $takenAt = $item['image-datetime'] ?? null;
+                $params  = [
+                    'name'             => $name,
+                    'lat'              => $this->maybeCastToFloat($item['image-latitude'] ?? null),
+                    'lng'              => $this->maybeCastToFloat($item['image-longitude'] ?? null),
+                    'takenAt'          => $takenAt,
+                    'area'             => $this->maybeCastToFloat($item['image-area-square-meter'] ?? null),
+                    'distanceToGround' => $this->maybeCastToFloat($item['image-meters-above-ground'] ?? null),
+                    'gpsAltitude'      => $this->maybeCastToFloat($item['image-altitude'] ?? null),
+                    'yaw'              => $this->maybeCastToFloat($item['image-camera-yaw-degrees'] ?? null),
+                ];
+
+                if ( ! is_null($fileData = $data->getFile($name)) && ! is_null($takenAt))
+                {
+                    $fileData->addFrame(...Arr::except($params, ['name']));
+                }
+                else
+                {
+                    $class    = $this->metadataClass();
+                    $fileData = new $class(...$params);
+
+                    if (isset($item['image-annotations']))
+                    {
+                        $this->addAnnotations($fileData, $item['image-annotations']);
+                    }
+
+                    $data->addFile($fileData);
+                }
+
+            }
+        }
+
+        return $data;
+    }
+
+    /**
+     * Cast the value to float if it is not null or an empty string.
+     */
+    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']),
+            $this->ifdoParseCoordinates($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'],
+                $ifdoLabel['color'] ?? null,
+                $ifdoLabel['uuid'] ?? null,
+            );
+        }
+        return $labels;
+    }
+
+    private function extractIfdoAnnotators($ifdoAnnotators)
+    {
+        $annotators = [];
+        foreach ($ifdoAnnotators as $ifdoAnnotator)
+        {
+            $annotators[$ifdoAnnotator['id']] = new User(
+                $ifdoAnnotator['id'],
+                $ifdoAnnotator['name'],
+                $ifdoAnnotator['uuid'] ?? null,
+            );
+        }
+        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 ($this->acquisitionFormat)
+        {
+        case 'photo':
+            return MediaType::image();
+        case 'video':
+            return MediaType::video();
+        }
+    }
+
+    private function metadataClass()
+    {
+        switch ($this->acquisitionFormat)
+        {
+        case 'photo':
+            return 'Biigle\Services\MetadataParsing\ImageMetadata';
+        case 'video':
+            return 'Biigle\Services\MetadataParsing\VideoMetadata';
+        }
+    }
+
+    private function annotationClass()
+    {
+        switch ($this->acquisitionFormat)
+        {
+        case 'photo':
+            return 'Biigle\Services\MetadataParsing\ImageAnnotation';
+        case 'video':
+            return 'Biigle\Services\MetadataParsing\VideoAnnotation';
+        }
+    }
+
+    private function ifdoParseCoordinates($coordinates)
+    {
+        if ($this->acquisitionFormat === 'photo') {
+            return $coordinates[0];
+        }
+
+        return $coordinates;
+    }
+
+    private function parseHandle(?string $handle): ?string
+    {
+        return substr(parse_url($handle ?? '', PHP_URL_PATH) ?? '', 1) ?: null;
+    }
+}

src/IfdoParser.php

@@ -0,0 +1,56 @@
+<?php
+namespace Biigle\Modules\MetadataIfdo;
+
+use Biigle\Ifdo\Ifdo;
+use Biigle\Services\MetadataParsing\MetadataParser;
+use Biigle\Services\MetadataParsing\VolumeMetadata;
+
+class IfdoParser extends MetadataParser
+{
+    private $ifdo = null;
+
+    /**
+     * {@inheritdoc}
+     */
+    public static function getKnownMimeTypes(): array {
+        return [
+            'application/json',
+        ];
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public static function getName(): string
+    {
+        return "iFDO";
+    }
+
+    public function getIfdo(): Ifdo
+    {
+        if ( ! $this->ifdo)
+        {
+            $file       = parent::getFileObject();
+            $this->ifdo = Ifdo::fromFile($file->getRealPath());
+        }
+
+        return $this->ifdo;
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function recognizesFile(): bool
+    {
+        return $this->getIfdo()->isValid();
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function getMetadata(): VolumeMetadata
+    {
+        $converter = new Converter($this->getIfdo()->getImageSetHeader()['image-acquisition']);
+        return $converter->convert($this->getIfdo());
+    }
+}