Merge pull request #262 from KPMP/KPMP-5528_fix_viewconfighelper

Kpmp 5528 fix viewconfighelper
KPMP · Sep 23, 2024 · a1536f0 · a1536f0
2 parents 42ed246 + 300e870
commit a1536f0
Showing 1 changed file with 10 additions and 7 deletions.
diff --git a/src/components/SpatialViewer/viewConfigHelper.js b/src/components/SpatialViewer/viewConfigHelper.js
@@ -19,7 +19,7 @@ export const getViewConfig = (type) => {
             return lmViewConfig;
         case 'Spatial Transcriptomics':
             return stViewConfig;
-        case 'Segmentation':
+        case 'Segmentation Masks & Pathomics Vectors':
             return segmentationConfig;
         default:
             return threeDCytometryViewConfig
@@ -51,14 +51,17 @@ export const populateViewConfig = async (viewConfig, selectedDataset) => {
         let dataUrl = getPublicFileLink(selectedDataset["packageid"], relatedFiles[0]['filename']);
         stringifiedConfig = stringifiedConfig.replace(/<DATA_FILE_URL>/gi, dataUrl);
 
-        if (selectedDataset["configtype"] === "Segmentation") {
-            stringifiedConfig = stringifiedConfig.replace('<SEGMENTATION_MASK_NAME>', relatedFiles[0]['filename']);
-            stringifiedConfig = stringifiedConfig.replace('<SEGMENTATION_MASK_URL>', dataUrl);
-            const loaders = await loadOmeTiff(dataUrl);
-            const physicalSizeX = unit(loaders.metadata.Pixels.PhysicalSizeX, (loaders.metadata.Pixels.PhysicalSizeXUnit.replace('µ', 'u'))).to("um").toNumber();
-            const physicalSizeY = unit(loaders.metadata.Pixels.PhysicalSizeY, (loaders.metadata.Pixels.PhysicalSizeYUnit.replace('µ', 'u'))).to("um").toNumber();
+        if (selectedDataset["configtype"] === "Segmentation Masks & Pathomics Vectors") {
+            stringifiedConfig = stringifiedConfig.replace('<SEGMENTATION_MASK_NAME>', selectedDataset["filename"]);
+            stringifiedConfig = stringifiedConfig.replace('<SEGMENTATION_MASK_URL>', imageUrlResponse.data);
+            let wsiUrl = await getFileLink(relatedFiles[0]['packageid'] + "/" + relatedFiles[0]['filename']);
+            const loaders = await loadOmeTiff(wsiUrl.data);
+            const physicalSizeX = unit(loaders.metadata.Pixels.PhysicalSizeX, (loaders.metadata.Pixels.PhysicalSizeXUnit.replace(/[µ|?]/g, 'u'))).to("um").toNumber();
+            const physicalSizeY = unit(loaders.metadata.Pixels.PhysicalSizeY, (loaders.metadata.Pixels.PhysicalSizeYUnit.replace(/[µ|?]/g, 'u'))).to("um").toNumber();
             stringifiedConfig = stringifiedConfig.replace('"<PHYSICAL_SIZE_X>"', physicalSizeX);
             stringifiedConfig = stringifiedConfig.replace('"<PHYSICAL_SIZE_Y>"', physicalSizeY);
+            selectedDataset = relatedFiles[0]
+            imageUrlResponse = wsiUrl
         }
     }
     stringifiedConfig = stringifiedConfig.replace('<IMAGE_NAME>', selectedDataset["filename"]);