fix: Multiple Slim issues regarding ANN visualization (#185)

* Improve logging

* CR Updates: Update scoord3d conditionals around first/last point

* Bump dcmjs

* Disable measurements fetching

* Lint

* Add zoom to roi

* Address issue where icc profile failed request would block image rendering

* Address icc profile issues with dcm4chee

* Fix getExtendedROI for annotation groups

* Improve tile error messag

* Remove resolution so we can have full image even without thumbnails

* Lint

* Add check for overview map while disposing

* Update zoom to roi to use scale

Author: igoroctaviano

package.json

@@ -83,7 +83,7 @@
     "@cornerstonejs/codec-openjph": "^2.4.5",
     "dicomweb-client": "^0.10.3",
     "colormap": "^2.3",
-    "dcmjs": "^0.38.1",
+    "dcmjs": "^0.41.0",
     "dicomicc": "^0.1",
     "image-type": "^4.1",
     "mathjs": "^11.2",

src/bulkAnnotations/getExtendedROI.js

@@ -6,13 +6,14 @@ import dcmjs from 'dcmjs'
  * @param {Object} options.feature - The feature object.
  * @param {Object} options.roi - The ROI object.
  * @param {Object} options.metadata - The metadata object.
+ * @param {Object} options.annotationGroup - The annotation group object.
  * @returns {Object} The extended ROI.
  */
-const getExtendedROI = ({ feature, roi, metadata }) => {
+const getExtendedROI = ({ feature, roi, metadata, annotationGroup }) => {
   const annotationGroupUID = feature.get('annotationGroupUID')
   const annotationGroupMetadata = metadata.AnnotationGroupSequence.find(
     (item) => item.AnnotationGroupUID === annotationGroupUID
-  )
+  ) || annotationGroup
 
   if (annotationGroupUID == null || annotationGroupMetadata == null) {
     throw new Error(

src/pyramid.js

@@ -12,36 +12,50 @@ import { are1DArraysAlmostEqual, are2DArraysAlmostEqual, _fetchBulkdata } from '
  *
  * @param {Array<metadata.VLWholeSlideMicroscopyImage>} pyramid - Metadata of
  * VL Whole Slide Microscopy Image instances
- * @param {object} client - dicom web client
+ * @param {object} options - options object
+ * @param {object} options.metadata - metadata of VL Whole Slide Microscopy Image instances
+ * @param {object} options.client - dicom web client
+ * @param {function} options.onError - function to call when an error occurs
  *
- * @returns {Promise<Array<TypedArray>>} image array with ICC profiles
+ * @returns {Promise<Array<TypedArray>>} image array with ICC profiles (only for images with SamplesPerPixel === 3 and ICCProfile present)
  *
  * @private
  */
-async function _getIccProfiles (metadata, client) {
-  const profiles = []
-  for (let i = 0; i < metadata.length; i++) {
-    const image = metadata[i]
+async function _getIccProfiles ({ metadata, client, onError }) {
+  const fetchPromises = metadata.map(image => {
     if (image.SamplesPerPixel === 3) {
-      if (image.bulkdataReferences.OpticalPathSequence == null) {
-        console.warn(
-          `no ICC Profile was not found for image "${image.SOPInstanceUID}"`
-        )
-        continue
+      let iccProfile = false
+      const metadataItem = image.OpticalPathSequence[0]
+      if (metadataItem.ICCProfile == null) {
+        if ('OpticalPathSequence' in image.bulkdataReferences) {
+          const bulkdataItem = image.bulkdataReferences.OpticalPathSequence[0]
+          if ('ICCProfile' in bulkdataItem) {
+            iccProfile = bulkdataItem.ICCProfile
+          }
+        }
+      } else {
+        iccProfile = metadataItem.ICCProfile
+      }
+      if (!iccProfile) {
+        console.warn(`ICC Profile was not found for image "${image.SOPInstanceUID}"`)
+        return null
+      } else if ('BulkDataURI' in iccProfile) {
+        console.debug(`fetching ICC Profile for image "${image.SOPInstanceUID}"`, iccProfile)
+        return _fetchBulkdata({
+          client,
+          reference: iccProfile
+        }).catch(onError)
+      } else {
+        return iccProfile
       }
-      const bulkdata = await _fetchBulkdata({
-        client,
-        reference: (
-          image
-            .bulkdataReferences
-            .OpticalPathSequence[0]
-            .ICCProfile
-        )
-      })
-      profiles.push(bulkdata)
     }
-  }
-  return profiles
+    return null
+  })
+  const validPromises = fetchPromises.filter(Boolean)
+  const results = await Promise.allSettled(validPromises)
+  return results
+    .filter(result => result.status === 'fulfilled' && result.value != null)
+    .map(result => result.value)
 }
 
 /**

src/scoord3d.js

@@ -208,7 +208,6 @@ class Polyline extends Scoord3D {
 /**
  * POLYGON graphic denoted by multiple, ordered, coplaner (x, y, z) coordinates
  * that represent vertices of connected line segments.
- * The first and last coordinate should be identical.
  *
  * @class
  * @extends scoord3d.Scoord3D
@@ -234,12 +233,17 @@ class Polygon extends Scoord3D {
     if (options.coordinates.find(c => c.some(item => item < 0))) {
       console.warn('coordinates of Polygon contain negative numbers')
     }
-    const n = options.coordinates.length
-    if ((options.coordinates[0][0] !== options.coordinates[n - 1][0]) ||
-       (options.coordinates[0][1] !== options.coordinates[n - 1][1]) ||
-       (options.coordinates[0][2] !== options.coordinates[n - 1][2])) {
-      throw new Error('First and last coordinate of Polygon must be the same.')
-    }
+    // Note: the POLYGON GraphicType value for ANN specifies that the
+    // first and last points are implicitly joined, so the first point
+    // should not be repeated at the end (unlike other uses in other IODs).
+    // Reference: https://github.com/ImagingDataCommons/slim/issues/298#issuecomment-2959241315
+    //
+    // const n = options.coordinates.length
+    // if ((options.coordinates[0][0] !== options.coordinates[n - 1][0]) ||
+    //    (options.coordinates[0][1] !== options.coordinates[n - 1][1]) ||
+    //    (options.coordinates[0][2] !== options.coordinates[n - 1][2])) {
+    //   throw new Error('First and last coordinate of Polygon must be the same.')
+    // }
     super({
       coordinates: options.coordinates,
       frameOfReferenceUID: options.frameOfReferenceUID,