Merge pull request #322 from rdvincent/rdv-gifti

Fix #321: Add support for GIFTI surfaces and vertex data.
aces · Nov 25, 2016 · 0d3ac3e · 0d3ac3e
2 parents 8ca39ce + 33af6b4
commit 0d3ac3e
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Showing 9 changed files with 13,766 additions and 6 deletions.
diff --git a/Gruntfile.js b/Gruntfile.js
@@ -92,7 +92,10 @@ module.exports = function(grunt) {
           "<%= build_dir %>/workers/freesurferbin.intensity.worker.js": "src/brainbrowser/workers/freesurferbin.intensity.worker.js",
           "<%= build_dir %>/workers/freesurferasc.intensity.worker.js": "src/brainbrowser/workers/freesurferasc.intensity.worker.js",
           "<%= build_dir %>/workers/deindex.worker.js": "src/brainbrowser/workers/deindex.worker.js",
-          "<%= build_dir %>/workers/wireframe.worker.js": "src/brainbrowser/workers/wireframe.worker.js"
+          "<%= build_dir %>/workers/wireframe.worker.js": "src/brainbrowser/workers/wireframe.worker.js",
+          "<%= build_dir %>/workers/gifti.worker.js": "src/brainbrowser/workers/gifti.worker.js",
+          "<%= build_dir %>/workers/gifti-reader.js": "src/brainbrowser/workers/gifti-reader.js"
+
         }
       }
     },
@@ -139,10 +142,14 @@ module.exports = function(grunt) {
           globals: {
             Float32Array: true,
             Uint32Array: true,
+            gifti: true,
             DataView: true
           }
         },
-        src: ["src/brainbrowser/workers/*.js"]
+        src: [
+          "src/brainbrowser/workers/*.js",
+          "!src/brainbrowser/workers/gifti-reader.js"
+        ]
       },
       examples: {
         options: {

diff --git a/examples/surface-viewer-demo.html b/examples/surface-viewer-demo.html
@@ -111,6 +111,7 @@ <h4>Load your own data!</h4>
                   <option value="freesurferasc">Freesurfer ASC</option>
                   <option value="wavefrontobj">Wavefront OBJ</option>
                   <option value="json">JSON</option>
+                  <option value="gifti">GIFTI</option>
                 </select><br>
                 <div class="format-hint"></div>
                 <div id="obj_file_submit_div" class="file-submit-div">
@@ -124,6 +125,7 @@ <h4>Load your own data!</h4>
                   <option value="text">Text</option>
                   <option value="freesurferbin">Freesurfer Binary</option>
                   <option value="freesurferasc">Freesurfer ASC</option>
+                  <option value="gifti">GIFTI</option>
                 </select><br>
                 <div class="format-hint"></div>
                 <div id="data-submit-div" class="file-submit-div">

diff --git a/src/brainbrowser/lib/color-map.js b/src/brainbrowser/lib/color-map.js
@@ -66,15 +66,27 @@
 
     if (data) {
       lines = data.trim().split(/\n/);
-      color_map_colors = new Float32Array(lines.length * 4);
+      color_map_colors = [];
       ic = 0;
 
       for (i = 0, line_count = lines.length; i < line_count; i++) {
-        color = lines[i].trim().split(/\s+/).slice(0, 4);
+        color = lines[i].trim().split(/\s+/).slice(0, 5);
         line_length = color.length;
 
         if (line_length < 3) continue;
 
+        if (line_length > 4) {
+          /* Sparse colour map. The first column gives the
+           * label to associate with the colour, the remaining
+           * 4 columns give the RGBA values to associate with
+           * the label.
+           */
+          ic = parseInt(color[0], 10);
+          ic *= 4;
+          line_length = 4;
+          color = color.slice(1, 5);
+        }
+
         for (j = 0; j < line_length; j++) {
           color_map_colors[ic + j] = parseFloat(color[j]);
         }

diff --git a/src/brainbrowser/lib/utils.js b/src/brainbrowser/lib/utils.js
@@ -126,6 +126,25 @@
       return window.URL.createObjectURL(new Blob([data], {type : mime_type || "text/plain"}));
     },
 
+    /**
+    * @doc function
+    * @name BrainBrowser.utils:getWorkerImportURL
+    *
+    * @description
+    * Assemble an absolute path for possible script imports within
+    * a worker.
+    */
+    getWorkerImportURL: function() {
+      var worker_dir = BrainBrowser.config.get("worker_dir");
+      var import_url = document.location.origin + '/' + worker_dir;
+      var doc_href = document.location.href;
+      var slash_index = doc_href.lastIndexOf('/');
+      if (slash_index >= 0) {
+        import_url = doc_href.substring(0, slash_index + 1) + worker_dir;
+      }
+      return import_url;
+    },
+
     /**
     * @doc function
     * @name BrainBrowser.utils:min

diff --git a/src/brainbrowser/surface-viewer.js b/src/brainbrowser/surface-viewer.js
@@ -573,10 +573,13 @@
   BrainBrowser.config.set("model_types.freesurferbin.worker", "freesurferbin.worker.js");
   BrainBrowser.config.set("model_types.freesurferbin.binary", true);
   BrainBrowser.config.set("model_types.freesurferasc.worker", "freesurferasc.worker.js");
+  BrainBrowser.config.set("model_types.gifti.worker", "gifti.worker.js");
+
   BrainBrowser.config.set("intensity_data_types.text.worker", "text.intensity.worker.js");
   BrainBrowser.config.set("intensity_data_types.freesurferbin.worker", "freesurferbin.intensity.worker.js");
   BrainBrowser.config.set("intensity_data_types.freesurferbin.binary", true);
   BrainBrowser.config.set("intensity_data_types.freesurferasc.worker", "freesurferasc.intensity.worker.js");
+  BrainBrowser.config.set("intensity_data_types.gifti.worker", "gifti.worker.js");
 
   // Build worker URLs and attempt to inline
   // them using Blob URLs if possible.

diff --git a/src/brainbrowser/surface-viewer/lib/parse-intensity-data.js b/src/brainbrowser/surface-viewer/lib/parse-intensity-data.js
@@ -64,5 +64,6 @@ BrainBrowser.SurfaceViewer.parseIntensityData = function(data, type, callback) {
     worker.terminate();
   });
 
-  worker.postMessage({ cmd: "parse", data: data });
+  var url = BrainBrowser.utils.getWorkerImportURL();
+  worker.postMessage({ cmd: "parse", data: data, url: url });
 };
diff --git a/src/brainbrowser/surface-viewer/modules/loading.js b/src/brainbrowser/surface-viewer/modules/loading.js
@@ -399,6 +399,10 @@ BrainBrowser.SurfaceViewer.modules.loading = function(viewer) {
       var min;
       var max;
 
+      if (intensity_data.colors) {
+        loadColorMap(BrainBrowser.createColorMap(intensity_data.colors));
+      }
+
       if (viewer.getAttribute("fix_color_range") &&
           old_range.min !== undefined && old_range.max !== undefined) {
         min = old_range.min;
@@ -518,9 +522,11 @@ BrainBrowser.SurfaceViewer.modules.loading = function(viewer) {
       parse_worker.terminate();
     });
 
+    var import_url = BrainBrowser.utils.getWorkerImportURL();
     parse_worker.postMessage({
       data: data,
-      options: options
+      options: options,
+      url: import_url
     });
 
   }