Implement geo upload

src/Jobs/TileSingleOverlay.php

@@ -66,10 +66,11 @@ public function handle()
     public function generateTiles($file, $path)
     {
         $vipsImage = $this->getVipsImage($path);
-        $min = $vipsImage->min();
+        // 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 || $max > 255) {
+        if($min < 0 || $min > 255 || $max < 0 || $max > 255) {
             $this->imageNormalization($vipsImage, $min, $max)->dzsave($this->tempPath, [
                 'layout' => 'zoomify',
                 'container' => 'fs',
@@ -78,7 +79,6 @@ public function generateTiles($file, $path)
         } else {
             parent::generateTiles($file, $path);
         }
-
     }
 
     /**
@@ -104,7 +104,7 @@ protected function getVipsImage($path)
      */
     protected function imageNormalization($vipsImage, $min, $max)
     {
-        // band intensity normalization x' = (x - $min * (255 / ($max - $min))
+        // band intensity normalization x' = (x - $min) / ($max - $min) * 255
         return $vipsImage->subtract($min)->multiply(255 / ($max - $min));
     }
 }

src/public/assets/scripts/volumes.js.LICENSE.txt

@@ -1,9 +1,3 @@
-/*!
- * Vue.js v2.6.14
- * (c) 2014-2021 Evan You
- * Released under the MIT License.
- */
-
 /**!
  * Sortable 1.10.2
  * @author	RubaXa   <trash@rubaxa.org>

src/public/mix-manifest.json

@@ -1,5 +1,5 @@
 {
-    "/assets/scripts/main.js": "/assets/scripts/main.js?id=96753d36cf46d8eacaa6796d9ee4f4a9",
-    "/assets/scripts/volumes.js": "/assets/scripts/volumes.js?id=571511be8d04bfaea0258ae4ca1a8555",
-    "/assets/styles/main.css": "/assets/styles/main.css?id=bf09d95dc04208c3ee738dafbf8e123c"
+    "/assets/scripts/main.js": "/assets/scripts/main.js?id=5d75e90309015b8aad9b612f52a6979f",
+    "/assets/scripts/volumes.js": "/assets/scripts/volumes.js?id=e3f2145a883f32b9f12c33a39538a345",
+    "/assets/styles/main.css": "/assets/styles/main.css?id=b692ef8518741236ded072068dddeb05"
 }

src/resources/assets/js/geo/components/imageMap.vue

@@ -295,7 +295,9 @@ export default {
         }
 
         Events.$on('sidebar.toggle', function () {
-            this.map.updateSize();
+            if(this.map) {
+                this.map.updateSize();
+            }
         });
 
         // Update once to get the correct map size in case the map is used in combination

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/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/js/volumes/geoOverlayUpload.vue

@@ -3,9 +3,7 @@ import Api from './api/geoOverlays';
 import GeotiffOverlayForm from './components/geotiffOverlayForm';
 import WebmapOverlayForm from './components/webmapOverlayForm';
 import OverlayTable from './components/overlayTable';
-import {handleErrorResponse, LoaderMixin, EditorMixin} from './import';
-import Tabs from 'uiv/dist/Tabs';
-import Tab from 'uiv/dist/Tab';
+import {handleErrorResponse, LoaderMixin, EditorMixin, Tab, Tabs} from './import';
 
 export default {
     mixins: [

src/resources/assets/js/volumes/import.js

@@ -1,5 +1,7 @@
-export let VolumeFilters = biigle.$require('volumes.stores.filters');
-export let LoaderMixin = biigle.$require('core.mixins.loader');
-export let FilterList = biigle.$require('volumes.components.filterListComponent');
 export let EditorMixin = biigle.$require('core.mixins.editor');
-export let handleErrorResponse = biigle.$require('messages').handleErrorResponse;
+export let FilterList = biigle.$require('volumes.components.filterListComponent');
+export let handleErrorResponse = biigle.$require('messages').handleErrorResponse;
+export let LoaderMixin = biigle.$require('core.mixins.loader');
+export let Tab = biigle.$require('uiv.tab');
+export let Tabs = biigle.$require('uiv.tabs');
+export let VolumeFilters = biigle.$require('volumes.stores.filters');

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/manual/tutorials/volume-edit-geo-overlay.blade.php

@@ -13,8 +13,17 @@
     </p>
     <h3>GeoTIFF</h3>
     <p>
-        The first option to upload an overlay is to provide a geoTIFF-file (in .tif format). The upload allows only GeoTIFF's that have projected coordinate reference systems (CRS) and use the common <a href="https://epsg.org/home.html" target="_blank">EPSG Geodetic Parameter Dataset</a> codes (e.g. EPSG:4326 for WGS84 CRS). It does, however, not support user-defined projected CRS.
+        The first option to upload an overlay is to provide a geoTIFF-file (in .tif(f) format). The upload allows only GeoTIFF's that have projected coordinate reference systems (CRS) and use the common <a href="https://epsg.org/home.html" target="_blank">EPSG Geodetic Parameter Dataset</a> codes (e.g. EPSG:4326 for WGS84 CRS). It does, however, not support user-defined projected CRS. <br>
+        Note: When uploaded, the geoTIFF will be tiled into JPGEG files for web-opimization. Therefore, some information that is contained in the original .tiff will be lost. You should take one of the precautionary steps below to ensure the uploaded .tiff is displayed as expected in BIIGLE:
     </p>
+    <ol>
+        <li>
+            Make sure that the color-band of the geoTIFF is normalized to the range of 0 to 255.
+        </li>
+        <li>
+            If the color-band differs (e.g. negative range), the normalization can also be handled by BIIGLE if the NoData values of the geoTIFF are set to -99999.
+        </li>
+    </ol>
     <h3>Web Map Service (WMS)</h3>
     <p>
         The second option to embed an overlay is by providing the URL to a WMS source. If only the base URL of the WMS is provided (e.g. <code>https://maps.org/geoserver/namespace/wms</code>), the first layer of the WMS will be chosen as the overlay. By providing a URL with query parameters (e.g. <code>https://maps.org/geoserver/namespace/wms?service=WMS&version=1.1.0&request=GetMap&layers=LAYER1,LAYER5</code>), it is also possible to specify WHICH layer(s) of the WMS shall be used. The uploaded overlay will contain ALL the layers specified in the layers-parameter of the URL.

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/Http/Controllers/Api/GeoTiffOverlayControllerTest.php

@@ -100,6 +100,7 @@ public function testStoreGeotiff()
         $response->assertJson($overlay->toArray(), $exact=false);
         $this->assertTrue(Storage::disk('geo-overlays')->exists($overlay->path));
 
+
         // 2. testing upload of geoTIFF using the ModelTransform-Tag
         $response = $this->postJson("/api/v1/volumes/{$id}/geo-overlays/geotiff", [
             'geotiff' => $model_transform_gtiff,
@@ -123,6 +124,7 @@ public function testStoreGeotiff()
         $response->assertJson($overlay2->toArray(), $exact=false);
         $this->assertTrue(Storage::disk('geo-overlays')->exists($overlay2->path));
 
+
         // 3. testing upload of geoTIFF with missing PixelScale / ModelTiePoint as well as missing ModelTransform-Tags.
         // Which means there is no way to transform the geotiff from raster- to model-space 
         $response = $this->postJson("/api/v1/volumes/{$id}/geo-overlays/geotiff", [

tests/Jobs/TileSingleOverlayTest.php

@@ -4,6 +4,7 @@
 
 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;
@@ -29,17 +30,19 @@ public function testGenerateOverlayTiles()
             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";
         $job = new TileSingleOverlay($overlay, $disk, $targetPath);
 
-        $tempPath = config('geo.tiles.tmp_dir')."/{$overlay->id}";
         FileCache::getOnce($file, [$job, 'generateTiles']);
     }