Merge branch 'geo_upload' into context_fusion

src/Jobs/TileSingleOverlay.php

@@ -7,6 +7,7 @@
 use FileCache;
 use Biigle\Modules\Geo\GeoOverlay;
 use File;
+use Jcupitt\Vips\Image as VipsImage;
 
 class TileSingleOverlay extends TileSingleObject
 {
@@ -55,4 +56,55 @@ public function handle()
             File::deleteDirectory($this->tempPath);
         }
     }
+
+     /**
+     * Generate tiles for the object and put them to temporary storage.
+     *
+     * @param File $file
+     * @param string $path Path to the cached image file.
+     */
+    public function generateTiles($file, $path)
+    {
+        $vipsImage = $this->getVipsImage($path);
+        // exclude the NoData values (-99999) of the geoTIFF file when searching the min
+        $min = $vipsImage->equal(-99999)->ifthenelse(0, $vipsImage)->min();
+        $max = $vipsImage->max();
+
+        if($min < 0 || $min > 255 || $max < 0 || $max > 255) {
+            $this->imageNormalization($vipsImage, $min, $max)->dzsave($this->tempPath, [
+                'layout' => 'zoomify',
+                'container' => 'fs',
+                'strip' => true,
+            ]);
+        } else {
+            parent::generateTiles($file, $path);
+        }
+    }
+
+    /**
+     * Get the vips image instance.
+     *
+     * @param string $path
+     *
+     * @return \Jcupitt\Vips\Image
+     */
+    protected function getVipsImage($path)
+    {
+        return VipsImage::newFromFile($path);
+    }
+
+    /**
+     * Normalize the image band to 0 to 255
+     * 
+     * @param \Jcupitt\Vips\Image $vipsImage
+     * @param float $min minimum value of color-level of the input image
+     * @param float $max maximum value of color-level of the input image
+     * 
+     * @return \Jcupitt\Vips\Image
+     */
+    protected function imageNormalization($vipsImage, $min, $max)
+    {
+        // band intensity normalization x' = (x - $min) / ($max - $min) * 255
+        return $vipsImage->linear(($vipsImage - $min) / ($max - $min) * 255);
+    }
 }

src/public/mix-manifest.json

@@ -3,4 +3,4 @@
     "/assets/scripts/volumes.js": "/assets/scripts/volumes.js?id=ead6c2afb75060312c61a6d68ad4b28d",
     "/assets/scripts/annotations.js": "/assets/scripts/annotations.js?id=4c1eb02d73360d78996dd306466b2d38",
     "/assets/styles/main.css": "/assets/styles/main.css?id=bf09d95dc04208c3ee738dafbf8e123c"
-}
+}

src/resources/assets/js/volumes/api/geoOverlays.js

@@ -24,10 +24,6 @@ export default Vue.resource('api/v1/geo-overlays{/id}', {}, {
         method: 'POST',
         url: 'api/v1/volumes{/id}/geo-overlays/geotiff',
     },
-    getGeoTiffOverlayUrlTemplate: {
-        method: 'GET',
-        url: 'api/v1/volumes{/id}/geo-overlays/geotiff/url',
-    },
     // WebMap
     saveWebMap: {
         method: 'POST',

src/resources/assets/js/volumes/components/geoMapModal.vue

@@ -39,7 +39,7 @@
         </div>
         <div class="cell cell-content">
             <p class="text-muted">
-                <em>Hint:</em> Select image locations on the volume map by drawing an encompassing rectangle. To do this, press and hold <kbd>Ctrl</kbd> as well as the left mouse button and move the cursor on the map.
+                <em>Hint:</em> Select image locations on the volume map by drawing an encompassing rectangle. To do this, press and hold <kbd>Ctrl</kbd> (<kbd>Cmd &#8984;</kbd> on Mac) as well as the left mouse button and move the cursor on the map.
             </p>
         </div>
     </div>

src/resources/assets/js/volumes/components/geotiffOverlayForm.vue

@@ -1,12 +1,7 @@
 <script>
 import Api from '../api/geoOverlays';
-import {LoaderMixin} from '../import';
-
 
 export default {
-    mixins: [
-        LoaderMixin,
-    ],
     props: {
         volumeId: {
             type: Number,
@@ -16,13 +11,11 @@ export default {
     data() {
         return {
             error: false,
-            success: false,
         };
     },
     methods: {
         handleSuccess(response) {
             this.error = false;
-            this.success = true;
             this.$emit('success', response.data);
         },
         handleError(response) {
@@ -59,7 +52,7 @@ export default {
             data.append('volumeId', this.volumeId);
             this.upload(data)
                 .then(this.handleSuccess, this.handleError)
-                .finally(this.$emit('upload', false));
+                .finally(() => this.$emit('upload', false));
         },
     }
 }

src/resources/assets/js/volumes/components/overlayItem.vue

@@ -128,4 +128,9 @@ td:nth-child(6) {
 td:not(.start) {
     text-align: center;
 }
+
+/* center the delete button */
+.close {
+    float: none;
+}
 </style>

src/resources/assets/js/volumes/components/overlayTable.vue

@@ -1,7 +1,6 @@
 <template>
     <div class="table-responsive">
         <table v-if="overlays.length !== 0" class="table table-sm" v-cloak>
-            <caption><b><slot name="title"></slot></b></caption>
             <thead>
                 <tr>
                     <slot name="header">
@@ -114,6 +113,7 @@ export default {
 
 table {
     table-layout: auto;
+    margin-bottom: 0px;
 }
 
 th {

src/resources/assets/js/volumes/components/webmapOverlayForm.vue

@@ -1,6 +1,5 @@
 <script>
 import geoApi from '../api/geoOverlays';
-import {LoaderMixin} from '../import';
 
 export default {
   data() {
@@ -9,9 +8,6 @@ export default {
         success: false,
     };
   },
-  mixins: [
-        LoaderMixin,
-  ],
   props: {
       volumeId: {
           type: Number,
@@ -46,7 +42,7 @@ export default {
         data.append('volumeId', this.volumeId);
         geoApi.saveWebMap({id: this.volumeId}, data)
           .then(this.handleSuccess, this.handleError)
-          .finally(this.$emit('upload', false))
+          .finally(() => this.$emit('upload', false))
       },
     },
 };

src/resources/assets/sass/_volumesEditRight.scss

@@ -10,11 +10,6 @@
     flex: 0;
 }
 
-
-#volume-geo-overlay-upload.panel {
-    margin-bottom: 80px;
-}
-
 .toggle-btn {
     background-color: grey;
     text-decoration: none;

src/resources/views/volumes/edit/geotiffOverlayForm.blade.php

@@ -3,11 +3,8 @@
     <form class="form" v-on:submit.prevent="submitGeoTiff">
         <div class="form-group">
             <input class="hidden" ref="geoTiffInput" type="file" name="file" v-on:change="uploadGeoTiff" accept=".tif,.tiff">
-            <button class="btn btn-default" type="submit" :disabled="loading">Upload geoTIFF</button>
+            <button class="btn btn-default" type="submit">Upload geoTIFF</button>
         </div>
     </form>
     <div class="alert alert-danger" v-if="error" v-text="error" v-cloak></div>
-    <div class="alert alert-success" v-if="success" v-cloak>
-        The geoTIFF-file was successfully uploaded.
-    </div>
 </div>

src/resources/views/volumes/edit/webmapOverlayForm.blade.php

@@ -21,7 +21,4 @@ class="form-control"
         </div>
     </form>
     <div class="alert alert-danger" v-if="error" v-text="error" v-cloak></div>
-    <div class="alert alert-success" v-if="success" v-cloak>
-        The web-map-service was successfully embedded.
-    </div>
 </div>

src/resources/views/volumesEditRight.blade.php

@@ -23,7 +23,6 @@
     </div>
     <div v-if="hasOverlays('geoOverlays')">
         <overlay-table :overlays="geoOverlays" v-on:remove="handleRemove" :volume-id="{{ $volume->id }}" :project-id="{{ $volume->projects->pluck('id')->first() }}" >
-        <template v-slot:title>Geo Overlays</template>
         <template v-slot:header>
             <th></th>
             <th>#</th>

tests/Jobs/TileSingleOverlayTest.php

@@ -4,8 +4,10 @@
 
 use Biigle\Modules\Geo\Jobs\TileSingleOverlay;
 use Biigle\Tests\Modules\Geo\GeoOverlayTest;
+use Biigle\Modules\Geo\GeoOverlay;
 use Biigle\FileCache\GenericFile;
 use File;
+use FileCache;
 use Illuminate\Http\UploadedFile;
 use Illuminate\Support\Facades\Storage;
 use Jcupitt\Vips\Image;
@@ -20,28 +22,28 @@ public function testGenerateOverlayTiles()
         $overlay = GeoOverlayTest::createGeotiffOverlay();
 
         // save fake UploadedFile to geo-overlay storage
-        $overlayFile = UploadedFile::fake()->create($overlay->name, 20, 'image/tiff');
+        // $overlayFile = UploadedFile::fake()->create($overlay->name, 20, 'image/tiff');
+        $overlayFile = new UploadedFile(
+            __DIR__."/../files/geotiff_standardEPSG2013.tif",
+            'standardEPSG2013.tif',
+            'image/tiff',
+            null, 
+            true
+        );
+
+        $disk = config('geo.tiles.overlay_storage_disk');
         $overlay->storeFile($overlayFile);
         $this->assertTrue(Storage::disk('geo-overlays')->exists($overlay->path));
+        // $testCorrectFile = Storage::disk('geo-overlays')->path($overlay->path);
+        // dd("{$disk}://{$overlay->path}", $testCorrectFile);
 
-        // retreive fake UploadedFile from geo-overlay storage and cast to GenericFile
-        $disk = config('geo.tiles.overlay_storage_disk');
-        $file = new GenericFile("{$disk}://{$overlay->path}");
 
+        // retreive UploadedFile from geo-overlay storage and cast to GenericFile
+        $file = new GenericFile("{$disk}://{$overlay->path}");
         $targetPath = "{$overlay->id}/{$overlay->id}_tiles";
-        $job = new TileSingleOverlayStub($overlay, $disk, $targetPath);
-        $mock = Mockery::mock(Image::class);
-        $mock->shouldReceive('dzsave')
-            ->once()
-            ->with($job->tempPath, [
-                'layout' => 'zoomify',
-                'container' => 'fs',
-                'strip' => true,
-            ]);
-
-        $job->mock = $mock;
+        $job = new TileSingleOverlay($overlay, $disk, $targetPath);
 
-        $job->generateTiles($file, '');
+        FileCache::getOnce($file, [$job, 'generateTiles']);
     }
 
     public function testUploadOverlayToStorage()