Consider THUMBNAIL images part of image pyramid

Author: hackermd

src/channel.js

@@ -580,6 +580,7 @@ class _Channel {
     const imageResolutions = []
     const imageOrigins = []
     const imagePixelSpacings = []
+    const physicalSizes = []
     const offset = [0, -1]
     const baseTotalPixelMatrixColumns = image.pyramidBaseMetadata.TotalPixelMatrixColumns
     const baseTotalPixelMatrixRows = image.pyramidBaseMetadata.TotalPixelMatrixRows
@@ -600,6 +601,11 @@ class _Channel {
         nRows
       ])
       imagePixelSpacings.push(pixelSpacing)
+
+      physicalSizes.push([
+        (totalPixelMatrixColumns * pixelSpacing[0]).toFixed(4),
+        (totalPixelMatrixRows * pixelSpacing[1]).toFixed(4)
+      ])
       /*
       * Compute the resolution at each pyramid level, since the zoom
       * factor may not be the same between adjacent pyramid levels.
@@ -619,6 +625,16 @@ class _Channel {
     imageOrigins.reverse()
     imagePixelSpacings.reverse()
 
+    const uniquePhysicalSizes = [
+      ...new Set(physicalSizes.map(v => v.toString()))
+    ].map(v => v.split(','))
+    if (uniquePhysicalSizes.length > 1) {
+      console.warn(
+        'images of the image pyramid have different sizes (in millimeter): ',
+        physicalSizes
+      )
+    }
+
     /** Frames may extend beyond the size of the total pixel matrix.
      * The excess pixels are empty, i.e. have only a padding value.
      * We set the extent to the size of the actual image without taken

src/metadata.js

@@ -162,7 +162,10 @@ function groupColorInstances (metadata) {
     const microscopyImage = new VLWholeSlideMicroscopyImage({
       metadata: metadata[i]
     })
-    if (microscopyImage.ImageType[2] !== 'VOLUME') {
+    if (
+      microscopyImage.ImageType[2] === 'LABEL' ||
+      microscopyImage.ImageType[2] === 'OVERVIEW'
+    ) {
       continue
     }
 

src/viewer.js

@@ -999,7 +999,6 @@ class VolumeImageViewer {
        */
 
       const z = tileCoord[0]
-      console.debug('Pyramid level:', z)
       const y = tileCoord[1] + 1
       const x = tileCoord[2] + 1
       const index = x + '-' + y