Merge pull request FZJ-INM1-BDA#38 from scalableminds/visualize_parce…

…llation_map Visualize parcellation map
scalableminds · Jul 13, 2023 · 89e1e09 · 89e1e09
2 parents a448774 + c105abe
commit 89e1e09
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Showing 7 changed files with 392 additions and 9 deletions.
diff --git a/+siibra/+internal/API.m b/+siibra/+internal/API.m
@@ -66,6 +66,17 @@
             end
             absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink); 
         end
+
+        function absoluteLink = templateForParcellationMap(spaceId, parcellationId)
+            arguments
+                spaceId string
+                parcellationId string
+            end
+            relativeLink = "/map/resampled_template?parcellation_id=" + parcellationId + ...
+                            "&space_id=" + spaceId;
+            absoluteLink = siibra.internal.API.absoluteLinkV3(relativeLink); 
+        end
+
         function absoluteLink = featuresPageForParcellation(atlasId, parcellationId, page, size)
             relativeLink = "/atlases/" + atlasId + ...
                             "/parcellations/" + parcellationId + ...

diff --git a/+siibra/+items/+maps/ParcellationMap.m b/+siibra/+items/+maps/ParcellationMap.m
@@ -33,9 +33,25 @@
             nifti = siibra.items.NiftiImage(obj.CachePath);
         end
 
-        function visualize(obj)
+        function visualize(obj, colorMapName)
+            arguments
+                obj
+                colorMapName string = "lines"
+            end
+
+            template = obj.Space.loadTemplateResampledForParcellation(obj.Parcellation).normalizedData();
             labelVolume = obj.fetch().loadData;
-            volumeViewer(labelVolume, VolumeType="Labels");
+
+            volshow(template, ...
+                "RenderingStyle","GradientOpacity", ...
+                "Alphamap", linspace(0,0.2,256), ...
+                "OverlayData", labelVolume, ...
+                "OverlayRenderingStyle", "LabelOverlay", ...
+                "OverlayAlphamap", linspace(0.3,1.0,256), ...
+                "OverlayColormap", colormap(colorMapName) ...
+                );
+
+
         end
     end
 end

diff --git a/+siibra/+items/Region.m b/+siibra/+items/Region.m
@@ -110,7 +110,7 @@ function visualizeInTemplate(obj, spaceName, colormap_name)
             end
 
             space = obj.matchAgainstSpacesParcellationSupports(spaceName);
-            template = space.loadTemplate().normalizedData();
+            template = space.loadTemplateResampledForParcellation(obj.Parcellation).normalizedData();
             continuousMap = obj.continuousMap(spaceName).fetch().loadData();
 
             fig = uifigure;

diff --git a/+siibra/+items/Space.m b/+siibra/+items/Space.m
@@ -32,5 +32,15 @@
             end
             niftiImage = siibra.items.NiftiImage(cachedPath);
         end
+        function niftiImage = loadTemplateResampledForParcellation(obj, parcellation)
+            cachedPath = siibra.internal.cache(obj.Name + "-" + parcellation.Name + ".nii.gz", "template_cache");
+            if ~isfile(cachedPath)
+                siibra.internal.API.doWebsaveWithLongTimeout( ...
+                    cachedPath, ...
+                    siibra.internal.API.templateForParcellationMap(obj.Id, parcellation.Id) ...
+                    )
+            end
+            niftiImage = siibra.items.NiftiImage(cachedPath);
+        end
     end
 end
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -17,11 +17,6 @@ jobs:
       - name: Run all tests
         uses: matlab-actions/run-tests@v1
 
-      - name: Convert the walkthrough live script into script
-        uses: matlab-actions/run-command@v1
-        with:
-          command: export("walkthrough.mlx", format="m");
-
       - name: Run walkthrough
         uses: matlab-actions/run-command@v1
         with:

diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,3 @@
 *.asv
 screen-shots/
 +siibra/cache/
-walkthrough.m