fix(dicomImageLoader): use calibrated pixel spacing (if available) when loading DICOM images via WADO-RS

packages/core/src/utilities/getPixelSpacingInformation.ts

@@ -117,6 +117,7 @@ function calculateUSPixelSpacing(instance) {
 
   return {
     PixelSpacing: USPixelSpacing,
+    type: null,
   };
 }
 

packages/core/src/utilities/index.ts

@@ -102,6 +102,7 @@ import { calculateNeighborhoodStats } from './calculateNeighborhoodStats';
 import getPixelSpacingInformation from './getPixelSpacingInformation';
 import { asArray } from './asArray';
 export { updatePlaneRestriction } from './updatePlaneRestriction';
+export * from './toNumber';
 
 const getViewportModality = (viewport: IViewport, volumeId?: string) =>
   _getViewportModality(viewport, volumeId, cache.getVolume);

packages/core/src/utilities/toNumber.js

@@ -0,0 +1,15 @@
+/**
+ * Returns the values as an array of javascript numbers
+ *
+ * @param val - The javascript object for the specified element in the metadata
+ * @returns {*}
+ */
+export function toNumber(val) {
+  if (Array.isArray(val)) {
+    return [...val].map((v) => (v !== undefined ? Number(v) : v));
+  } else {
+    return val !== undefined ? Number(val) : val;
+  }
+}
+
+export default toNumber;

packages/dicomImageLoader/src/imageLoader/getInstanceModule.ts

@@ -1,3 +1,4 @@
+import { capitalizeTag } from '../shared/tagCase';
 /**
  * Retrieves metadata from a DICOM image and returns it as an object with capitalized keys.
  * @param imageId - the imageId
@@ -29,9 +30,6 @@ function getInstanceModule(imageId, metaDataProvider, types) {
   return result;
 }
 
-const capitalizeTag = (tag: string) =>
-  tag.charAt(0).toUpperCase() + tag.slice(1);
-
 const instanceModuleNames = [
   'multiframeModule',
   'generalSeriesModule',

packages/dicomImageLoader/src/imageLoader/wadors/metaData/metaDataProvider.ts

@@ -22,10 +22,12 @@ import {
   instanceModuleNames,
 } from '../../getInstanceModule';
 import { getUSEnhancedRegions } from './USHelpers';
+import { Modules } from '../../../shared/Tags';
+const { calibratedPixelSpacingMetadataProvider } = utilities;
 
-function metaDataProvider(type, imageId) {
-  const { MetadataModules } = Enums;
+const { MetadataModules } = Enums;
 
+function metaDataProvider(type, imageId) {
   if (type === MetadataModules.MULTIFRAME) {
     // the get function removes the PerFrameFunctionalGroupsSequence
     const { metadata, frame } = retrieveMultiframeMetadataImageId(imageId);
@@ -66,6 +68,10 @@ function metaDataProvider(type, imageId) {
     return;
   }
 
+  if (Modules[type]) {
+    return Modules[type].fromMetadata(metaData);
+  }
+
   if (type === MetadataModules.GENERAL_STUDY) {
     return {
       studyDescription: getValue<string>(metaData['00081030']),
@@ -97,16 +103,6 @@ function metaDataProvider(type, imageId) {
     };
   }
 
-  if (type === MetadataModules.GENERAL_IMAGE) {
-    return {
-      sopInstanceUID: getValue<string>(metaData['00080018']),
-      instanceNumber: getNumberValue(metaData['00200013']),
-      lossyImageCompression: getValue<string>(metaData['00282110']),
-      lossyImageCompressionRatio: getNumberValue(metaData['00282112']),
-      lossyImageCompressionMethod: getValue<string>(metaData['00282114']),
-    };
-  }
-
   if (type === MetadataModules.PATIENT) {
     return {
       patientID: getValue<string>(metaData['00100020']),
@@ -142,73 +138,6 @@ function metaDataProvider(type, imageId) {
     };
   }
 
-  if (type === MetadataModules.IMAGE_PLANE) {
-    //metaData = fixNMMetadata(metaData);
-    let imageOrientationPatient = extractOrientationFromMetadata(metaData);
-    let imagePositionPatient = extractPositionFromMetadata(metaData);
-    const pixelSpacing = getNumberValues(metaData['00280030'], 2);
-
-    let columnPixelSpacing = null;
-    let rowPixelSpacing = null;
-    let rowCosines = null;
-    let columnCosines = null;
-
-    let usingDefaultValues = false;
-    if (pixelSpacing) {
-      rowPixelSpacing = pixelSpacing[0];
-      columnPixelSpacing = pixelSpacing[1];
-    } else {
-      usingDefaultValues = true;
-      rowPixelSpacing = 1;
-      columnPixelSpacing = 1;
-    }
-
-    if (imageOrientationPatient) {
-      rowCosines = [
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[0]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[1]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[2]),
-      ];
-      columnCosines = [
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[3]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[4]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[5]),
-      ];
-    } else {
-      rowCosines = [1, 0, 0];
-      columnCosines = [0, 1, 0];
-      usingDefaultValues = true;
-      imageOrientationPatient = [...rowCosines, ...columnCosines];
-    }
-
-    if (!imagePositionPatient) {
-      imagePositionPatient = [0, 0, 0];
-      usingDefaultValues = true;
-    }
-
-    return {
-      frameOfReferenceUID: getValue<string>(metaData['00200052']),
-      rows: getNumberValue(metaData['00280010']),
-      columns: getNumberValue(metaData['00280011']),
-      imageOrientationPatient,
-      rowCosines,
-      columnCosines,
-      imagePositionPatient,
-      sliceThickness: getNumberValue(metaData['00180050']),
-      sliceLocation: getNumberValue(metaData['00201041']),
-      pixelSpacing,
-      rowPixelSpacing,
-      columnPixelSpacing,
-      usingDefaultValues,
-    };
-  }
-
   if (type === MetadataModules.ULTRASOUND_ENHANCED_REGION) {
     return getUSEnhancedRegions(metaData);
   }
@@ -279,13 +208,6 @@ function metaDataProvider(type, imageId) {
     };
   }
 
-  if (type === MetadataModules.SOP_COMMON) {
-    return {
-      sopClassUID: getValue<string>(metaData['00080016']),
-      sopInstanceUID: getValue<string>(metaData['00080018']),
-    };
-  }
-
   if (type === MetadataModules.PET_ISOTOPE) {
     const radiopharmaceuticalInfo = getValue(metaData['00540016']);
 

packages/dicomImageLoader/src/imageLoader/wadouri/metaData/metaDataProvider.ts

@@ -22,6 +22,7 @@ import {
   instanceModuleNames,
 } from '../../getInstanceModule';
 import { getUSEnhancedRegions } from './USHelpers';
+import { Modules } from '../../../shared/Tags';
 
 function metaDataProvider(type, imageId) {
   const { MetadataModules } = Enums;
@@ -65,12 +66,16 @@ function metaDataProvider(type, imageId) {
   return metadataForDataset(type, imageId, dataSet);
 }
 
+const { MetadataModules } = Enums;
+
 export function metadataForDataset(
   type,
   imageId,
   dataSet: dicomParser.DataSet
 ) {
-  const { MetadataModules } = Enums;
+  if (Modules[type]) {
+    return Modules[type].fromDataset(dataSet);
+  }
 
   if (type === MetadataModules.GENERAL_STUDY) {
     return {
@@ -139,66 +144,6 @@ export function metadataForDataset(
     };
   }
 
-  if (type === MetadataModules.IMAGE_PLANE) {
-    const imageOrientationPatient = extractOrientationFromDataset(dataSet);
-    const imagePositionPatient = extractPositionFromDataset(dataSet);
-    const pixelSpacing = extractSpacingFromDataset(dataSet);
-    const sliceThickness = extractSliceThicknessFromDataset(dataSet);
-
-    let columnPixelSpacing = null;
-
-    let rowPixelSpacing = null;
-
-    let usingDefaultValues = false;
-    if (pixelSpacing) {
-      rowPixelSpacing = pixelSpacing[0];
-      columnPixelSpacing = pixelSpacing[1];
-    } else {
-      usingDefaultValues = true;
-      rowPixelSpacing = 1;
-      columnPixelSpacing = 1;
-    }
-
-    let rowCosines = null;
-
-    let columnCosines = null;
-
-    if (imageOrientationPatient) {
-      rowCosines = [
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[0]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[1]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[2]),
-      ];
-      columnCosines = [
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[3]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[4]),
-        // @ts-expect-error
-        parseFloat(imageOrientationPatient[5]),
-      ];
-    }
-
-    return {
-      frameOfReferenceUID: dataSet.string('x00200052'),
-      rows: dataSet.uint16('x00280010'),
-      columns: dataSet.uint16('x00280011'),
-      imageOrientationPatient,
-      rowCosines,
-      columnCosines,
-      imagePositionPatient,
-      sliceThickness,
-      sliceLocation: dataSet.floatString('x00201041'),
-      pixelSpacing,
-      rowPixelSpacing,
-      columnPixelSpacing,
-      usingDefaultValues,
-    };
-  }
-
   if (type === MetadataModules.CINE) {
     return {
       frameTime: dataSet.floatString('x00181063'),
@@ -237,10 +182,7 @@ export function metadataForDataset(
   }
 
   if (type === MetadataModules.SOP_COMMON) {
-    return {
-      sopClassUID: dataSet.string('x00080016'),
-      sopInstanceUID: dataSet.string('x00080018'),
-    };
+    return Modules[MetadataModules.SOP_COMMON].fromDataset(dataSet);
   }
 
   if (type === MetadataModules.PET_ISOTOPE) {

packages/dicomImageLoader/src/index.ts

@@ -22,6 +22,7 @@ import * as constants from './constants';
 import type * as Types from './types';
 import { decodeImageFrame } from './decodeImageFrameWorker';
 import { initializers } from './shared/decoders';
+import * as utilities from './shared';
 
 const cornerstoneDICOMImageLoader = {
   constants,
@@ -33,6 +34,7 @@ const cornerstoneDICOMImageLoader = {
   wadouri,
   wadors,
   init,
+  utilities,
   convertColorSpace,
   createImage,
   decodeJPEGBaseline8BitColor,
@@ -55,6 +57,7 @@ export {
   convertPALETTECOLOR,
   wadouri,
   wadors,
+  utilities,
   init,
   convertColorSpace,
   createImage,