Yolo output

app/Http/Requests/StoreProjectReport.php

@@ -37,6 +37,21 @@ public function rules()
     {
         return array_merge(parent::rules(), [
             'type_id' => 'required|integer|exists:report_types,id',
+            'yolo_image_path' => 'nullable|string',
+            'yolo_split_ratio' => 'nullable|string|regex:/^\d+(\.\d+)? \d+(\.\d+)? \d+(\.\d+)?$/',
+        ]);
+    }
+
+    /**
+     * Get the options for the new report.
+     *
+     * @return array
+     */
+    public function getOptions()
+    {
+        return array_merge(parent::getOptions(), [
+            'yoloImagePath' => $this->input('yolo_image_path'),
+            'yoloSplitRatio' => $this->input('yolo_split_ratio'),
         ]);
     }
 

app/Http/Requests/StoreVolumeReport.php

@@ -42,6 +42,7 @@ public function rules()
                 ReportType::imageAnnotationsCsvId(),
                 ReportType::imageAnnotationsExtendedId(),
                 ReportType::imageAnnotationsCocoId(),
+                ReportType::imageAnnotationsYoloId(),
                 ReportType::imageAnnotationsFullId(),
                 ReportType::imageAnnotationsAbundanceId(),
                 ReportType::imageAnnotationsImageLocationId(),
@@ -62,6 +63,8 @@ public function rules()
         return array_merge(parent::rules(), [
             'type_id' => ['required', Rule::in($types)],
             'annotation_session_id' => "nullable|integer|exists:annotation_sessions,id,volume_id,{$this->volume->id}",
+            'yolo_image_path' => 'nullable|string',
+            'yolo_split_ratio' => 'nullable|string|regex:/^\d+(\.\d+)? \d+(\.\d+)? \d+(\.\d+)?$/',
         ]);
     }
 
@@ -119,8 +122,13 @@ public function withValidator($validator)
      */
     public function getOptions()
     {
-        return array_merge(parent::getOptions(), [
+        \Log::info('StoreVolumeReport input:', $this->all());
+        $options = array_merge(parent::getOptions(), [
             'annotationSession' => $this->input('annotation_session_id'),
+            'yoloImagePath' => $this->input('yolo_image_path'),
+            'yoloSplitRatio' => $this->input('yolo_split_ratio'),
         ]);
+        \Log::info('StoreVolumeReport options:', $options);
+        return $options;
     }
 }

app/ReportType.php

@@ -21,6 +21,8 @@
  * @method static int imageAnnotationsExtendedId()
  * @method static ReportType imageAnnotationsCoco()
  * @method static int imageAnnotationsCocoId()
+ * @method static ReportType imageAnnotationsYolo()
+ * @method static int imageAnnotationsYoloId()
  * @method static ReportType imageAnnotationsFull()
  * @method static int imageAnnotationsFullId()
  * @method static ReportType imageAnnotationsImageLocation()
@@ -57,6 +59,7 @@ class ReportType extends Model
         'imageAnnotationsCsv' => 'ImageAnnotations\Csv',
         'imageAnnotationsExtended' => 'ImageAnnotations\Extended',
         'imageAnnotationsCoco' => 'ImageAnnotations\Coco',
+        'imageAnnotationsYolo' => 'ImageAnnotations\Yolo',
         'imageAnnotationsFull' => 'ImageAnnotations\Full',
         'imageAnnotationsImageLocation' => 'ImageAnnotations\ImageLocation',
         'imageIfdo' => 'ImageIfdo',

app/Services/Reports/Projects/ImageAnnotations/YoloReportGenerator.php

@@ -0,0 +1,29 @@
+<?php
+
+namespace Biigle\Services\Reports\Projects\ImageAnnotations;
+
+use Biigle\Services\Reports\Volumes\ImageAnnotations\YoloReportGenerator as ReportGenerator;
+
+class YoloReportGenerator extends AnnotationReportGenerator
+{
+    /**
+     * The class of the volume report to use for this project report.
+     *
+     * @var string
+     */
+    protected $reportClass = ReportGenerator::class;
+
+    /**
+     * Name of the report for use in text.
+     *
+     * @var string
+     */
+    public $name = 'Yolo image annotation report';
+
+    /**
+     * Name of the report for use as (part of) a filename.
+     *
+     * @var string
+     */
+    public $filename = 'yolo_image_annotation_report';
+}

app/Services/Reports/Volumes/ImageAnnotations/YoloReportGenerator.php

@@ -0,0 +1,219 @@
+<?php
+
+namespace Biigle\Services\Reports\Volumes\ImageAnnotations;
+
+use Biigle\LabelTree;
+use Biigle\Services\Reports\CsvFile;
+use Biigle\Services\Reports\MakesZipArchives;
+use Biigle\User;
+use DB;
+
+class YoloReportGenerator extends AnnotationReportGenerator
+{
+    use MakesZipArchives;
+    /**
+     * Name of the report for use in text.
+     *
+     * @var string
+     */
+    public $name = 'yolo image annotation report';
+
+    /**
+     * Name of the report for use as (part of) a filename.
+     *
+     * @var string
+     */
+    public $filename = 'yolo_image_annotation_report';
+
+    /**
+     * File extension of the report file.
+     *
+     * @var string
+     */
+    public $extension = 'zip';
+
+    /**
+     * Generate the report.
+     *
+     * @param string $path Path to the report file that should be generated
+     */
+    public function generateReport($path)
+    {
+        $rows = $this->query()->get();
+
+        // Always create a single unified dataset for YOLO
+        $csv = $this->createCsv($rows);
+        $this->tmpFiles[] = $csv;
+
+        $this->executeScript('to_yolo', $path);
+
+        // Python script creates output directory based on the first CSV file path
+        // Collect all files from that directory for zipping  
+        $firstCsvPath = $this->tmpFiles[0]->getPath();
+        $outputDir = pathinfo($firstCsvPath, PATHINFO_DIRNAME) . '/' . pathinfo($firstCsvPath, PATHINFO_FILENAME) . '_yolo_output';
+
+
+        // Clear the toZip array and rebuild it with files from output directory
+        $toZip = [];
+        if (is_dir($outputDir)) {
+            $this->addDirectoryToZip($outputDir, $toZip);
+        } else {
+            \Log::warning("YOLO: Output directory not found", ['outputDir' => $outputDir]);
+        }
+
+        $this->makeZip($toZip, $path);
+    }
+
+    /**
+     * Override makeZip to handle symlinks properly
+     */
+    protected function makeZip($files, $path)
+    {
+        $zip = \App::make(\ZipArchive::class);
+        $open = $zip->open($path, \ZipArchive::OVERWRITE);
+
+        if ($open !== true) {
+            throw new \Exception("Could not open ZIP file '{$path}'.");
+        }
+
+        try {
+            foreach ($files as $source => $target) {
+                // Check if file is a symlink
+                if (is_link($source)) {
+                    // Add symlink to zip
+                    $linkTarget = readlink($source);
+                    $zip->addFromString($target, $linkTarget);
+                    // Set external attributes to mark as symlink
+                    $zip->setExternalAttributesName($target, \ZipArchive::OPSYS_UNIX, 0120777 << 16);
+                } else {
+                    // Regular file
+                    $zip->addFile($source, $target);
+                }
+            }
+        } finally {
+            $zip->close();
+        }
+    }
+
+    /**
+     * Override executeScript to pass YOLO-specific arguments before CSV files
+     */
+    protected function executeScript($scriptName, $path)
+    {
+        $imagePath = $this->options->get('yoloImagePath', '');
+        $splitRatio = $this->options->get('yoloSplitRatio', '0.7 0.2 0.1');
+
+        // Call parent's pythonScriptRunner directly with custom arguments
+        // Command format: python script.py volumeName path imagePath splitRatio csv1 csv2 ...
+        $python = config('reports.python');
+        $script = config("reports.scripts.{$scriptName}");
+        $csvs = implode(' ', array_map(fn ($csv) => $csv->getPath(), $this->tmpFiles));
+
+        $command = sprintf(
+            "%s %s \"%s\" %s %s %s %s 2>&1",
+            $python,
+            $script,
+            $this->source->name,
+            $path,
+            escapeshellarg($imagePath),
+            escapeshellarg($splitRatio),
+            $csvs
+        );
+
+        exec($command, $lines, $code);
+
+        if ($code !== 0) {
+            throw new \Exception("The report script '{$scriptName}' failed with exit code {$code}:\n".implode("\n", $lines));
+        }
+    }
+
+    /**
+     * Recursively add all files from a directory to the zip array
+     */
+    protected function addDirectoryToZip($dir, &$toZip, $basePath = '')
+    {
+        $items = new \DirectoryIterator($dir);
+        foreach ($items as $item) {
+            if ($item->isDot()) continue;
+
+            $relativePath = $basePath ? $basePath . '/' . $item->getFilename() : $item->getFilename();
+
+            if ($item->isDir()) {
+                $this->addDirectoryToZip($item->getPathname(), $toZip, $relativePath);
+            } else {
+                $toZip[$item->getPathname()] = $relativePath;
+            }
+        }
+    }
+
+    /**
+     * Assemble a new DB query for the volume of this report.
+     *
+     * @return \Illuminate\Database\Query\Builder
+     */
+    protected function query()
+    {
+        $query = $this
+            ->initQuery([
+                'image_annotation_labels.id as annotation_label_id',
+                'image_annotation_labels.label_id',
+                'labels.name as label_name',
+                'users.id as user_id',
+                'images.id as image_id',
+                'images.filename',
+                'images.lng as longitude',
+                'images.lat as latitude',
+                'shapes.name as shape_name',
+                'image_annotations.points',
+                'images.attrs',
+            ])
+            ->join('shapes', 'image_annotations.shape_id', '=', 'shapes.id')
+            ->leftJoin('users', 'image_annotation_labels.user_id', '=', 'users.id')
+            ->orderBy('image_annotation_labels.id');
+
+        return $query;
+    }
+
+    /**
+     * Create a CSV file for this report.
+     *
+     * @param \Illuminate\Support\Collection $rows The rows for the CSV
+     * @return CsvFile
+     */
+    protected function createCsv($rows)
+    {
+        $csv = CsvFile::makeTmp();
+        // column headers
+        $csv->putCsv([
+            'annotation_label_id',
+            'label_id',
+            'label_name',
+            'image_id',
+            'filename',
+            'image_longitude',
+            'image_latitude',
+            'shape_name',
+            'points',
+            'attributes',
+        ]);
+
+        foreach ($rows as $row) {
+            $csv->putCsv([
+                $row->annotation_label_id,
+                $row->label_id,
+                $row->label_name,
+                $row->image_id,
+                $row->filename,
+                $row->longitude,
+                $row->latitude,
+                $row->shape_name,
+                $row->points,
+                $row->attrs,
+            ]);
+        }
+
+        $csv->close();
+
+        return $csv;
+    }
+}

config/reports.php

@@ -15,6 +15,7 @@
         'csvs_to_xlsx' => __DIR__.'/../resources/scripts/reports/csvs_to_xlsx.py',
         'full_report' => __DIR__.'/../resources/scripts/reports/full_report.py',
         'to_coco' => __DIR__.'/../resources/scripts/reports/to_coco.py',
+        'to_yolo' => __DIR__.'/../resources/scripts/reports/to_yolo.py',
     ],
 
     /**

database/migrations/2025_11_21_100000_add_yolo_report_type.php

@@ -0,0 +1,29 @@
+<?php
+
+use Illuminate\Database\Migrations\Migration;
+use Illuminate\Support\Facades\DB;
+
+class AddYoloReportType extends Migration
+{
+    /**
+     * Run the migrations.
+     *
+     * @return void
+     */
+    public function up()
+    {
+        DB::table('report_types')->insert([
+            'name' => 'ImageAnnotations\Yolo',
+        ]);
+    }
+
+    /**
+     * Reverse the migrations.
+     *
+     * @return void
+     */
+    public function down()
+    {
+        DB::table('report_types')->where('name', 'ImageAnnotations\Yolo')->delete();
+    }
+}