chore(release): publish [skip ci]

- @ohif/extension-vtk@1.3.4
 - @ohif/core@2.6.3
 - @ohif/viewer@3.8.7

extensions/vtk/CHANGELOG.md

@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [1.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.3...@ohif/extension-vtk@1.3.4) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
+## [1.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.2...@ohif/extension-vtk@1.3.3) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/extension-vtk
+
+
+
+
+
 ## [1.3.2](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.3.1...@ohif/extension-vtk@1.3.2) (2020-03-23)
 
 **Note:** Version bump only for package @ohif/extension-vtk

extensions/vtk/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/extension-vtk",
-  "version": "1.3.2",
+  "version": "1.3.4",
   "description": "OHIF extension for VTK.js",
   "author": "OHIF",
   "license": "MIT",
@@ -53,7 +53,7 @@
     "react-vtkjs-viewport": "^0.8.3"
   },
   "devDependencies": {
-    "@ohif/core": "^2.6.1",
+    "@ohif/core": "^2.6.3",
     "@ohif/ui": "^1.4.1",
     "cornerstone-tools": "4.12.5",
     "cornerstone-wado-image-loader": "^3.0.0",

platform/core/CHANGELOG.md

@@ -3,6 +3,28 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [2.6.3](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.2...@ohif/core@2.6.3) (2020-03-24)
+
+
+### Bug Fixes
+
+* Ensure we take into account pixel spacing fields properly ([#1555](https://github.com/OHIF/Viewers/issues/1555)) ([77ab0ad](https://github.com/OHIF/Viewers/commit/77ab0ad9a14a135b5560741fc1600704df08c141))
+
+
+
+
+
+## [2.6.2](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.1...@ohif/core@2.6.2) (2020-03-24)
+
+
+### Bug Fixes
+
+* OverlayPlane module usage for ArrayBuffer, BulkDataURI, and InlineBinary cases, as well as PaletteColor LUTs for ArrayBuffer (i.e. local drag/drop) case ([#1546](https://github.com/OHIF/Viewers/issues/1546)) ([404d52f](https://github.com/OHIF/Viewers/commit/404d52fe5c0442dd13e4d407bb0687d72fa5f32c))
+
+
+
+
+
 ## [2.6.1](https://github.com/OHIF/Viewers/compare/@ohif/core@2.6.0...@ohif/core@2.6.1) (2020-03-23)
 
 

platform/core/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/core",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "Generic business logic for web-based medical imaging applications",
   "author": "OHIF Core Team",
   "license": "MIT",

platform/core/src/classes/MetadataProvider.js

@@ -1,7 +1,7 @@
 import * as dcmjs from 'dcmjs';
 import queryString from 'query-string';
 import dicomParser from 'dicom-parser';
-import { getFallbackTagFromInstance } from '../utils/metadataProvider/metadataProviderFallbackTags';
+import getPixelSpacingInformation from '../utils/metadataProvider/getPixelSpacingInformation';
 import fetchPaletteColorLookupTableData from '../utils/metadataProvider/fetchPaletteColorLookupTableData';
 import fetchOverlayData from '../utils/metadataProvider/fetchOverlayData';
 
@@ -58,9 +58,7 @@ class MetadataProvider {
 
     Object.assign(instance, naturalizedDataset);
 
-    if (options.server) {
-      await this._checkBulkDataAndInlineBinaries(instance, options.server);
-    }
+    await this._checkBulkDataAndInlineBinaries(instance, options.server);
 
     return instance;
   }
@@ -163,18 +161,6 @@ class MetadataProvider {
       return instance[naturalizedTagOrWADOImageLoaderTag];
     }
 
-    if (options.fallback) {
-      // Perhaps the tag has fallbacks?
-      const fallbackTag = getFallbackTagFromInstance(
-        naturalizedTagOrWADOImageLoaderTag,
-        instance
-      );
-
-      if (fallbackTag) {
-        return fallbackTag;
-      }
-    }
-
     // Maybe its a legacy CornerstoneWADOImageLoader tag then:
     return this._getCornerstoneWADOImageLoaderTag(
       naturalizedTagOrWADOImageLoaderTag,
@@ -220,10 +206,9 @@ class MetadataProvider {
         const { ImageOrientationPatient } = instance;
 
         // Fallback for DX images.
-        const PixelSpacing = getFallbackTagFromInstance(
-          'PixelSpacing',
-          instance
-        );
+        // TODO: We should use the rest of the results of this function
+        // to update the UI somehow
+        const { PixelSpacing } = getPixelSpacingInformation(instance);
 
         let rowPixelSpacing;
         let columnPixelSpacing;
@@ -344,7 +329,7 @@ class MetadataProvider {
 
         break;
       case WADO_IMAGE_LOADER_TAGS.OVERLAY_PLANE_MODULE:
-        metadata = [];
+        const overlays = [];
 
         for (
           let overlayGroup = 0x00;
@@ -389,9 +374,13 @@ class MetadataProvider {
             roiStandardDeviation: instance[ROIStandardDeviationTag],
           };
 
-          metadata.push(overlay);
+          overlays.push(overlay);
         }
 
+        metadata = {
+          overlays
+        };
+
         break;
 
       case WADO_IMAGE_LOADER_TAGS.PATIENT_MODULE:

platform/core/src/utils/metadataProvider/fetchOverlayData.js

@@ -1,5 +1,7 @@
 import { api } from 'dicomweb-client';
 import DICOMWeb from '../../DICOMWeb';
+import str2ab from '../str2ab';
+import unpackOverlay from './unpackOverlay';
 
 export default async function fetchOverlayData(instance, server) {
   const OverlayDataPromises = [];
@@ -15,11 +17,18 @@ export default async function fetchOverlayData(instance, server) {
 
       const OverlayDataTag = `${groupStr}3000`;
 
-      if (instance[OverlayDataTag] && instance[OverlayDataTag].BulkDataURI) {
+      if (instance[OverlayDataTag] && instance[OverlayDataTag].InlineBinary) {
+        const inlineBinaryData = atob(instance[OverlayDataTag].InlineBinary);
+        const arraybuffer = str2ab(inlineBinaryData);
+
+        instance[OverlayDataTag] = unpackOverlay(arraybuffer)
+      } else if (instance[OverlayDataTag] && instance[OverlayDataTag].BulkDataURI) {
         OverlayDataPromises.push(
           _getOverlayData(instance[OverlayDataTag], server)
         );
         OverlayDataTags.push(OverlayDataTag);
+      } else if (instance[OverlayDataTag] && instance[OverlayDataTag] instanceof ArrayBuffer) {
+        instance[OverlayDataTag] = unpackOverlay(instance[OverlayDataTag])
       }
     }
 
@@ -60,19 +69,7 @@ async function _getOverlayData(tag, server) {
   return dicomWeb
     .retrieveBulkData(options)
     .then(result => result[0])
-    .then(_unpackOverlay);
+    .then(unpackOverlay);
 }
 
-function _unpackOverlay(arrayBuffer) {
-  const bitArray = new Uint8Array(arrayBuffer);
-  const byteArray = new Uint8Array(8 * bitArray.length);
 
-  for (let byteIndex = 0; byteIndex < byteArray.length; byteIndex++) {
-    const bitIndex = byteIndex % 8;
-    const bitByteIndex = Math.floor(byteIndex / 8);
-    byteArray[byteIndex] =
-      1 * ((bitArray[bitByteIndex] & (1 << bitIndex)) >> bitIndex);
-  }
-
-  return byteArray;
-}

platform/core/src/utils/metadataProvider/fetchPaletteColorLookupTableData.js

@@ -1,5 +1,6 @@
 import { api } from 'dicomweb-client';
 import DICOMWeb from '../../DICOMWeb';
+import str2ab from '../str2ab';
 
 export default async function fetchPaletteColorLookupTableData(
   instance,
@@ -157,31 +158,12 @@ function _getPaletteColor(server, paletteColorLookupTableData, lutDescriptor) {
       .then(arrayBufferToPaletteColorLUT);
   } else if (paletteColorLookupTableData.InlineBinary) {
     const inlineBinaryData = atob(paletteColorLookupTableData.InlineBinary);
-    const arraybuffer = _str2ab(inlineBinaryData);
+    const arraybuffer = str2ab(inlineBinaryData);
 
     return new Promise(resolve => {
       resolve(arrayBufferToPaletteColorLUT(arraybuffer));
     });
+  } else {
+    return Promise.resolve(arrayBufferToPaletteColorLUT(paletteColorLookupTableData));
   }
-
-  throw new Error(
-    'Palette Color LUT was not provided as InlineBinary or BulkDataURI'
-  );
-}
-
-/**
- * Convert String to ArrayBuffer
- *
- * @param {String} str Input String
- * @return {ArrayBuffer} Output converted ArrayBuffer
- */
-function _str2ab(str) {
-  const strLen = str.length;
-  const bytes = new Uint8Array(strLen);
-
-  for (let i = 0; i < strLen; i++) {
-    bytes[i] = str.charCodeAt(i);
-  }
-
-  return bytes.buffer;
 }

platform/core/src/utils/metadataProvider/getPixelSpacingInformation.js

@@ -0,0 +1,90 @@
+import log from '../../log';
+
+export default function getPixelSpacingInformation(instance) {
+  // See http://gdcm.sourceforge.net/wiki/index.php/Imager_Pixel_Spacing
+
+  // TODO: Add Ultrasound region spacing
+  // TODO: Add manual calibration
+
+  // TODO: Use ENUMS from dcmjs
+  const projectionRadiographSOPClassUIDs = [
+    '1.2.840.10008.5.1.4.1.1.1', //	CR Image Storage
+    '1.2.840.10008.5.1.4.1.1.1.1', //	Digital X-Ray Image Storage – for Presentation
+    '1.2.840.10008.5.1.4.1.1.1.1.1', //	Digital X-Ray Image Storage – for Processing
+    '1.2.840.10008.5.1.4.1.1.1.2', //	Digital Mammography X-Ray Image Storage – for Presentation
+    '1.2.840.10008.5.1.4.1.1.1.2.1', //	Digital Mammography X-Ray Image Storage – for Processing
+    '1.2.840.10008.5.1.4.1.1.1.3', //	Digital Intra – oral X-Ray Image Storage – for Presentation
+    '1.2.840.10008.5.1.4.1.1.1.3.1', //	Digital Intra – oral X-Ray Image Storage – for Processing
+    '1.2.840.10008.5.1.4.1.1.12.1', //	X-Ray Angiographic Image Storage
+    '1.2.840.10008.5.1.4.1.1.12.1.1', //	Enhanced XA Image Storage
+    '1.2.840.10008.5.1.4.1.1.12.2', //	X-Ray Radiofluoroscopic Image Storage
+    '1.2.840.10008.5.1.4.1.1.12.2.1', //	Enhanced XRF Image Storage
+    '1.2.840.10008.5.1.4.1.1.12.3' // X-Ray Angiographic Bi-plane Image Storage	Retired
+  ];
+
+  const { PixelSpacing, ImagerPixelSpacing, SOPClassUID, PixelSpacingCalibrationType, PixelSpacingCalibrationDescription, EstimatedRadiographicMagnificationFactor } = instance;
+  const isProjection = projectionRadiographSOPClassUIDs.includes(SOPClassUID);
+
+  const TYPES = {
+    NOT_APPLICABLE: 'NOT_APPLICABLE',
+    UNKNOWN: 'UNKNOWN',
+    CALIBRATED: 'CALIBRATED',
+    DETECTOR: 'DETECTOR'
+  };
+
+  if (isProjection === false && !ImagerPixelSpacing) {
+    // If only Pixel Spacing is present, and this is not a projection radiograph,
+    // we can stop here
+    return {
+      PixelSpacing,
+      type: TYPES.NOT_APPLICABLE,
+      isProjection
+    };
+  } else if (isProjection && !ImagerPixelSpacing) {
+    // If only Pixel Spacing is present, and this is a projection radiograph,
+    // PixelSpacing should be used, but the user should be informed that
+    // what it means is unknown
+    return {
+      PixelSpacing,
+      type: TYPES.UNKNOWN,
+      isProjection
+    };
+  } else if (PixelSpacing && ImagerPixelSpacing && PixelSpacing === ImagerPixelSpacing) {
+    // If Imager Pixel Spacing and Pixel Spacing are present and they have the same values,
+    // then the user should be informed that the measurements are at the detector plane
+    return {
+      PixelSpacing,
+      type: TYPES.DETECTOR,
+      isProjection
+    };
+  } else if (PixelSpacing && ImagerPixelSpacing && PixelSpacing !== ImagerPixelSpacing) {
+    // If Imager Pixel Spacing and Pixel Spacing are present and they have different values,
+    // then the user should be informed that these are "calibrated"
+    // (in some unknown manner if Pixel Spacing Calibration Type and/or
+    // Pixel Spacing Calibration Description are absent)
+    return {
+      PixelSpacing,
+      type: TYPES.CALIBRATED,
+      isProjection,
+      PixelSpacingCalibrationType,
+      PixelSpacingCalibrationDescription
+    };
+  } else if (!PixelSpacing && ImagerPixelSpacing) {
+    let CorrectedImagerPixelSpacing = ImagerPixelSpacing;
+    if (EstimatedRadiographicMagnificationFactor) {
+      // Note that in IHE Mammo profile compliant displays, the value of Imager Pixel Spacing is required to be corrected by
+      // Estimated Radiographic Magnification Factor and the user informed of that.
+      // TODO: should this correction be done before all of this logic?
+      CorrectedImagerPixelSpacing = ImagerPixelSpacing.map(pixelSpacing => pixelSpacing / EstimatedRadiographicMagnificationFactor);
+    } else {
+      log.info('EstimatedRadiographicMagnificationFactor was not present. Unable to correct ImagerPixelSpacing.');
+    }
+
+    return {
+      PixelSpacing: CorrectedImagerPixelSpacing,
+      isProjection,
+    };
+  }
+
+  log.info('Unknown combination of PixelSpacing and ImagerPixelSpacing identified. Unable to determine spacing.');
+}

platform/core/src/utils/metadataProvider/metadataProviderFallbackTags.js

@@ -1,27 +0,0 @@
-import log from '../../log';
-
-function getFallbackTagFromInstance(tag, instance) {
-  if (instance[tag]) {
-    return instance[tag];
-  }
-
-  const fallbackTags = fallbackTagsMap[tag];
-
-  if (fallbackTags) {
-    for (let i = 0; i < fallbackTags.length; i++) {
-      const fallbackTag = fallbackTags[i];
-
-      if (instance[fallbackTag]) {
-        log.info(`metadata provider fallback tag ${tag} to ${fallbackTag}`);
-
-        return instance[fallbackTag];
-      }
-    }
-  }
-}
-
-const fallbackTagsMap = {
-  PixelSpacing: ['ImagerPixelSpacing'],
-};
-
-export { fallbackTagsMap, getFallbackTagFromInstance };

platform/core/src/utils/metadataProvider/unpackOverlay.js

@@ -0,0 +1,13 @@
+export default function unpackOverlay(arrayBuffer) {
+  const bitArray = new Uint8Array(arrayBuffer);
+  const byteArray = new Uint8Array(8 * bitArray.length);
+
+  for (let byteIndex = 0; byteIndex < byteArray.length; byteIndex++) {
+    const bitIndex = byteIndex % 8;
+    const bitByteIndex = Math.floor(byteIndex / 8);
+    byteArray[byteIndex] =
+      1 * ((bitArray[bitByteIndex] & (1 << bitIndex)) >> bitIndex);
+  }
+
+  return byteArray;
+}

platform/core/src/utils/str2ab.js

@@ -0,0 +1,16 @@
+/**
+ * Convert String to ArrayBuffer
+ *
+ * @param {String} str Input String
+ * @return {ArrayBuffer} Output converted ArrayBuffer
+ */
+export default function str2ab(str) {
+  const strLen = str.length;
+  const bytes = new Uint8Array(strLen);
+
+  for (let i = 0; i < strLen; i++) {
+    bytes[i] = str.charCodeAt(i);
+  }
+
+  return bytes.buffer;
+}

platform/viewer/CHANGELOG.md

@@ -3,6 +3,22 @@
 All notable changes to this project will be documented in this file.
 See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
 
+## [3.8.7](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.6...@ohif/viewer@3.8.7) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
+## [3.8.6](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.5...@ohif/viewer@3.8.6) (2020-03-24)
+
+**Note:** Version bump only for package @ohif/viewer
+
+
+
+
+
 ## [3.8.5](https://github.com/OHIF/Viewers/compare/@ohif/viewer@3.8.4...@ohif/viewer@3.8.5) (2020-03-23)
 
 

platform/viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ohif/viewer",
-  "version": "3.8.5",
+  "version": "3.8.7",
   "description": "OHIF Viewer",
   "author": "OHIF Contributors",
   "license": "MIT",
@@ -48,14 +48,14 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.5.5",
-    "@ohif/core": "^2.6.1",
+    "@ohif/core": "^2.6.3",
     "@ohif/extension-cornerstone": "^2.5.0",
     "@ohif/extension-dicom-html": "^1.1.1",
     "@ohif/extension-dicom-microscopy": "^0.50.7",
     "@ohif/extension-dicom-pdf": "^1.0.2",
     "@ohif/extension-dicom-segmentation": "^0.1.0",
     "@ohif/extension-lesion-tracker": "^0.2.0",
-    "@ohif/extension-vtk": "^1.3.2",
+    "@ohif/extension-vtk": "^1.3.4",
     "@ohif/i18n": "^0.52.7",
     "@ohif/ui": "^1.4.1",
     "@tanem/react-nprogress": "^1.1.25",