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fix: Ensure we take into account pixel spacing fields properly (#1555)

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* fix: Ensure we take into account pixel spacing fields properly

* Rename to getPixelSpacingInformation
This commit is contained in:
Erik Ziegler 2020-03-24 18:10:58 +01:00 committed by GitHub
parent 1c306dd243
commit 77ab0ad9a1
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GPG Key ID: 4AEE18F83AFDEB23
3 changed files with 94 additions and 44 deletions
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21
platform/core/src/classes/MetadataProvider.js
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@ -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';
@ -161,18 +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,
@ -218,10 +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;

90
platform/core/src/utils/metadataProvider/getPixelSpacingInformation.js Normal file
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@ -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.');
}

27
platform/core/src/utils/metadataProvider/metadataProviderFallbackTags.js
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@ -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 };