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Save quantification values, add dicom codes
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@ivmartel
ivmartel committed Jul 23, 2024
1 parent b531afc commit 04e4373
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228 changes: 212 additions & 16 deletions src/dicom/dicomCode.js
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ const TagKeys = {
* DICOM code: item of a basic code sequence.
*
* Ref: {@link https://dicom.nema.org/medical/dicom/2022a/output/chtml/part03/sect_8.8.html}.
* List: {@link https://dicom.nema.org/medical/dicom/2022a/output/chtml/part16/chapter_d.html}.
*/
export class DicomCode {
/**
Expand Down Expand Up @@ -151,30 +150,94 @@ export function getDicomCodeItem(code) {

/**
* DICOM codes.
* List: {@link https://dicom.nema.org/medical/dicom/2022a/output/chtml/part16/chapter_d.html}.
*/
const DcmCodes = {
111030: 'Image Region',
112039: 'Tracking Identifier',
112040: 'Tracking Unique Identifier',
113076: 'Segmentation',
121055: 'Path',
121207: 'Height',
121322: 'Source image for image processing operation',
121324: 'Source Image',
122438: 'Reference Points',
125007: 'Measurement Group',
125309: 'Short label'
125309: 'Short label',
113048: 'Pixel by pixel Maximum',
113049: 'Pixel by pixel mean',
113051: 'Pixel by pixel Minimum',
113061: 'Standard Deviation'
};

/**
* SNOMED-CT codes.
* List: {@link https://browser.ihtsdotools.org}.
*/
const SctCodes = {
1483009: 'Angle',
42798000: 'Area',
103355008: 'Width',
103339001: 'Long axis',
103340004: 'Short axis',
131190003: 'Radius',
261665006: 'Unknown',
410668003: 'Length',
};

/**
* UCUM codes.
* Definition: {@link https://unitsofmeasure.org/ucum}.
* List: {@link https://ucum.nlm.nih.gov/ucum-lhc/demo.html}.
*/
const UcumCodes = {
1: 'No units',
mm: 'Millimeter',
deg: 'Degree - plane angle',
cm2: 'Square centimeter',
'cm2/ml': 'Square centimeter per milliliter',
'/cm': 'Per centimeter',
'g/ml': 'Gram per milliliter',
'mg/ml': 'Milligram per milliliter',
'umol/ml': 'Micromole per milliliter',
'Bq/ml': 'Becquerels per milliliter',
'mg/min/ml': 'Milligrams per minute per milliliter',
'umol/min/ml': 'Micromole per minute per milliliter',
'ml/min/g': 'Milliliter per minute per gram',
'ml/g': 'Milliliter per gram',
'ml/min/ml': 'Milliliter per minute per milliliter',
'ml/ml': 'Milliliter per milliliter',
'%': 'Percentage',
'[hnsf\'U]': 'Hounsfield unit',
'10*23/ml': 'Electron density',
'{counts}': 'Counts',
'{counts}/s': 'Counts per second',
'{propcounts}': 'Proportional to counts',
'{propcounts}/s': 'Proportional to counts per second',
};

/**
* Get a DICOM code from a value (~id).
*
* @param {string} value The code value.
* @returns {DicomCode} The DICOM code.
* @param {string} scheme The scheme designator.
* @returns {DicomCode|undefined} The DICOM code.
*/
function getDicomCode(value) {
const code = new DicomCode(DcmCodes[value]);
code.schemeDesignator = 'DCM';
code.value = value;
function getDicomCode(value, scheme) {
let meaning;
if (scheme === 'DCM') {
meaning = DcmCodes[value];
} else if (scheme === 'SCT') {
meaning = SctCodes[value];
} else if (scheme === 'UCUM') {
meaning = UcumCodes[value];
}
let code;
if (typeof meaning !== 'undefined') {
code = new DicomCode(meaning);
code.schemeDesignator = scheme;
code.value = value;
}
return code;
}

Expand All @@ -184,7 +247,7 @@ function getDicomCode(value) {
* @returns {DicomCode} The code.
*/
export function getMeasurementGroupCode() {
return getDicomCode('125007');
return getDicomCode('125007', 'DCM');
}

/**
Expand All @@ -193,7 +256,7 @@ export function getMeasurementGroupCode() {
* @returns {DicomCode} The code.
*/
export function getImageRegionCode() {
return getDicomCode('111030');
return getDicomCode('111030', 'DCM');
}

/**
Expand All @@ -202,7 +265,7 @@ export function getImageRegionCode() {
* @returns {DicomCode} The code.
*/
export function getPathCode() {
return getDicomCode('121055');
return getDicomCode('121055', 'DCM');
}

/**
Expand All @@ -211,7 +274,7 @@ export function getPathCode() {
* @returns {DicomCode} The code.
*/
export function getSourceImageCode() {
return getDicomCode('121324');
return getDicomCode('121324', 'DCM');
}

/**
Expand All @@ -220,7 +283,7 @@ export function getSourceImageCode() {
* @returns {DicomCode} The code.
*/
export function getTrackingIdentifierCode() {
return getDicomCode('112039');
return getDicomCode('112039', 'DCM');
}

/**
Expand All @@ -229,7 +292,7 @@ export function getTrackingIdentifierCode() {
* @returns {DicomCode} The code.
*/
export function getSegmentationCode() {
return getDicomCode('113076');
return getDicomCode('113076', 'DCM');
}

/**
Expand All @@ -238,7 +301,7 @@ export function getSegmentationCode() {
* @returns {DicomCode} The code.
*/
export function getSourceImageForProcessingCode() {
return getDicomCode('121322');
return getDicomCode('121322', 'DCM');
}

/**
Expand All @@ -247,7 +310,7 @@ export function getSourceImageForProcessingCode() {
* @returns {DicomCode} The code.
*/
export function getShortLabelCode() {
return getDicomCode('125309');
return getDicomCode('125309', 'DCM');
}

/**
Expand All @@ -256,5 +319,138 @@ export function getShortLabelCode() {
* @returns {DicomCode} The code.
*/
export function getReferencePointsCode() {
return getDicomCode('122438');
return getDicomCode('122438', 'DCM');
}

/**
* Quantification name to dictionary item.
*/
const QuantificationName2DictItem = {
angle: {key: '1483009', scheme: 'SCT'},
length: {key: '410668003', scheme: 'SCT'},
surface: {key: '42798000', scheme: 'SCT'},
height: {key: '121207', scheme: 'DCM'},
width: {key: '103355008', scheme: 'SCT'},
radius: {key: '131190003', scheme: 'SCT'},
a: {key: '103339001', scheme: 'SCT'},
b: {key: '103340004', scheme: 'SCT'},
min: {key: '113051', scheme: 'DCM'},
max: {key: '113048', scheme: 'DCM'},
mean: {key: '113049', scheme: 'DCM'},
stddev: {key: '113061', scheme: 'DCM'},
// median
// 25th percentile
// 75th percentile
};

/**
* Get a concept name DICOM code.
*
* @param {string} name The measurment name as defined
* in a quantification object.
* @returns {DicomCode|undefined} The code.
*/
export function getConceptNameCode(name) {
const item = QuantificationName2DictItem[name];
let code;
if (typeof item !== 'undefined') {
code = getDicomCode(item.key, item.scheme);
}
return code;
}

/**
* Get the DICOM code for a quantification name.
*
* @param {DicomCode} code The Dicom code.
* @returns {string|undefined} The quantification name.
*/
export function getQuantificationName(code) {
let name;
for (const propKey in QuantificationName2DictItem) {
const item = QuantificationName2DictItem[propKey];
if (item.scheme === code.schemeDesignator &&
item.key === code.value) {
name = propKey;
break;
}
}
return name;
}

/**
* Quantification unit to UCUM key. Associated tags:
* - Rescale type {@link https://dicom.innolitics.com/ciods/computed-radiography-image/modality-lut/00281054},
* - Units {@link https://dicom.innolitics.com/ciods/positron-emission-tomography-image/pet-series/00541001}.
*/
const QuantificationUnit2UcumKey = {
'unit.mm': 'mm',
'unit.cm2': 'cm2',
'unit.degree': 'deg',
// OD optical density
HU: '[hnsf\'U]',
US: '1',
MGML: 'mg/ml',
// Z_EFF Effective Atomic Number (i.e., Effective-Z)
ED: '10*23/ml',
// EDW Electron density normalized
// HU_MOD Modified Hounsfield Unit
PCT: '%',
CNTS: '{counts}',
NONE: '1',
CM2: 'cm2',
CM2ML: 'cm2/ml',
PCNT: '%',
CPS: '{counts}/s',
BQML: 'Bq/ml',
MGMINML: 'mg/min/ml',
UMOLMINML: 'umol/min/ml',
MLMING: 'ml/min/g',
MLG: 'ml/g',
'1CM': '/cm',
UMOLML: 'umol/ml',
PROPCNTS: '{propcounts}',
PROPCPS: '{propcounts}/s',
MLMINML: 'ml/min/ml',
MLML: 'ml/ml',
GML: 'g/ml',
//STDDEV
SUV: 'g/ml',
};

/**
* Get a measurement units DICOM code.
*
* @param {string} name The unit name as defined in a quantification object.
* @returns {DicomCode|undefined} The code.
*/
export function getMeasurementUnitsCode(name) {
const key = QuantificationUnit2UcumKey[name];
let code;
if (typeof key !== 'undefined') {
code = getDicomCode(key, 'UCUM');
} else if (typeof key === 'undefined') {
// no unit
code = getDicomCode('1', 'UCUM');
}
return code;
}

/**
* Get a quantification unit name.
*
* @param {DicomCode} code The code to get the unit from.
* @returns {string} The quantification unit.
*/
export function getQuantificationUnit(code) {
let unit;
for (const propKey in QuantificationUnit2UcumKey) {
const item = QuantificationUnit2UcumKey[propKey];
if (code.schemeDesignator === 'UCUM' &&
item.key === code.value) {
unit = propKey;
break;
}
}
return unit;
}
36 changes: 35 additions & 1 deletion src/dicom/dicomSRContent.js
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Original file line number Diff line number Diff line change
@@ -1,10 +1,13 @@
import {
NumericMeasurement,
getNumericMeasurement,
getDicomNumericMeasurementItem
} from './dicomNumericMeasurement';
import {
getCode,
getDicomCodeItem
getDicomCodeItem,
getConceptNameCode,
getMeasurementUnitsCode
} from './dicomCode';
import {
getImageReference,
Expand All @@ -27,6 +30,7 @@ import {
/* eslint-disable no-unused-vars */
import {DataElement} from './dataElement';
import {DicomCode} from './dicomCode';
import {MeasuredValue} from './dicomMeasuredValue';
/* eslint-enable no-unused-vars */

/**
Expand Down Expand Up @@ -331,3 +335,33 @@ export function getDicomSRContentItem(content) {

return contentItem;
}

/**
* Get a DicomSRContent from a value.
*
* @param {string} name The value name.
* @param {object} value The value.
* @param {string} unit The values' unit.
* @returns {DicomSRContent|undefined} The SR content.
*/
export function getSRContentFromValue(name, value, unit) {
const conceptNameCode = getConceptNameCode(name);

if (typeof conceptNameCode === 'undefined') {
return undefined;
}

const content = new DicomSRContent(ValueTypes.num);
content.relationshipType = RelationshipTypes.contains;
content.conceptNameCode = conceptNameCode;

const measure = new MeasuredValue();
measure.numericValue = value;
measure.measurementUnitsCode = getMeasurementUnitsCode(unit);
const numMeasure = new NumericMeasurement();
numMeasure.measuredValue = measure;

content.value = numMeasure;

return content;
}
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