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Add ability to parse untilTag and to stopAfterTag with namified or Group,Element syntax #149

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Add ability to parse untilTag and to stopAfterTag with namified or Group,Element syntax #149

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d6b624d
Add ability to parse `untilTag` and to `stopAfterTag` with namified o…
jmhmd Sep 7, 2020
a7310a1
Add ability to parse `untilTag` and to `stopAfterTag` with namified o…
jmhmd Sep 7, 2020
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22 changes: 21 additions & 1 deletion src/DicomMessage.js
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,29 @@ const encapsulatedSyntaxes = [
class DicomMessage {
static read(bufferStream, syntax, ignoreErrors) {
var dict = {};
var untilTagNormalized = Tag.fromDirtyString(untilTag);
var stopAfterTagNormalized = Tag.fromDirtyString(stopAfterTag);

try {
while (!bufferStream.end()) {
var readInfo = DicomMessage.readTag(bufferStream, syntax);
if (breakOnNextLoop === true) {
break;
}
const readInfo = DicomMessage.readTag(bufferStream, syntax);
const cleanTagString = readInfo.tag.toCleanString();

if (
untilTagNormalized &&
untilTagNormalized.toCleanString() === cleanTagString
) {
break;
}
if (
stopAfterTagNormalized &&
stopAfterTagNormalized.toCleanString() === cleanTagString
) {
breakOnNextLoop = true;
}

dict[readInfo.tag.toCleanString()] = {
vr: readInfo.vr.type,
Expand Down
32 changes: 32 additions & 0 deletions src/Tag.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@ import { paddingLeft } from "./ValueRepresentation.js";
import { ValueRepresentation } from "./ValueRepresentation.js";
import { DicomMessage } from "./DicomMessage.js";
import { WriteBufferStream } from "./BufferStream.js";
import { findByName } from "./dictionary.js";

var IMPLICIT_LITTLE_ENDIAN = "1.2.840.10008.1.2";
var EXPLICIT_LITTLE_ENDIAN = "1.2.840.10008.1.2.1";
Expand Down Expand Up @@ -64,6 +65,37 @@ class Tag {
return this.is(0x7fe00010);
}

static fromDirtyString(str) {
if (!str || str.length < 1) {
return null;
}
/**
* Check first for Group,Element format.
*
* Matches various formats for string representation of tags:
* (0028,7017)
* [0028,7017]
* 0028,7017
* 00287017
* x00287017
*/
const matcher = /^x?[\[\(]?([A-Z0-9]{4}),?([A-Z0-9]{4})[\)\]]?$/;
const matches = str.match(matcher);
if (matches && matches.length > 2) {
// For given string (0028,7017), should return array like: ["(0028,7017)", "0028", "7017"]
return Tag.fromString(matches[1] + matches[2]);
} else {
/**
* If no match on Group,Element try to match on dictionary name.
*/
const match = findByName(str);
if (match) {
return Tag.fromPString(match.tag);
}
}
return null;
}

static fromString(str) {
var group = parseInt(str.substring(0, 4), 16),
element = parseInt(str.substring(4), 16);
Expand Down
9 changes: 9 additions & 0 deletions src/dictionary.js
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Expand Up @@ -48060,3 +48060,12 @@ const dictionary = {
};

export default dictionary;
export function findByName(tagName) {
const keys = Object.keys(dictionary);
for (let i = 0; i < keys.length; i += 1) {
if (dictionary[keys[i]].name === tagName) {
return dictionary[keys[i]];
}
}
return null;
}
129 changes: 102 additions & 27 deletions test/test_data.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ const expect = require('chai').expect;
const dcmjs = require('../build/dcmjs');

const fs = require("fs");
const {http, https} = require("follow-redirects");
const { http, https } = require("follow-redirects");
const os = require("os");
const path = require("path");
const unzipper = require("unzipper");
Expand All @@ -14,34 +14,34 @@ fileMetaInformationVersionArray[1] = 1;

const metadata = {
"00020001": {
"Value": [
fileMetaInformationVersionArray.buffer
],
"vr": "OB"
"Value": [
fileMetaInformationVersionArray.buffer
],
"vr": "OB"
},
"00020012": {
"Value": [
"1.2.840.113819.7.1.1997.1.0"
],
"vr": "UI"
"Value": [
"1.2.840.113819.7.1.1997.1.0"
],
"vr": "UI"
},
"00020002": {
"Value": [
"1.2.840.10008.5.1.4.1.1.4"
],
"vr": "UI"
"Value": [
"1.2.840.10008.5.1.4.1.1.4"
],
"vr": "UI"
},
"00020003": {
"Value": [
DicomMetaDictionary.uid()
],
"vr": "UI"
"Value": [
DicomMetaDictionary.uid()
],
"vr": "UI"
},
"00020010": {
"Value": [
"1.2.840.10008.1.2"
],
"vr": "UI"
"Value": [
"1.2.840.10008.1.2"
],
"vr": "UI"
}
};

Expand Down Expand Up @@ -74,7 +74,7 @@ const sequenceMetadata = {
}

function downloadToFile(url, filePath) {
return new Promise( (resolve,reject) => {
return new Promise((resolve, reject) => {
const fileStream = fs.createWriteStream(filePath);
const request = https.get(url, (response) => {
response.pipe(fileStream);
Expand Down Expand Up @@ -152,9 +152,9 @@ const tests = {
const unzipPath = path.join(os.tmpdir(), "test_multiframe_1");

downloadToFile(url, zipFilePath)
.then( () => {
.then(() => {
fs.createReadStream(zipFilePath)
.pipe(unzipper.Extract( {path: unzipPath} )
.pipe(unzipper.Extract({ path: unzipPath })
.on('close', () => {
const mrHeadPath = path.join(unzipPath, "MRHead");
fs.readdir(mrHeadPath, (err, fileNames) => {
Expand Down Expand Up @@ -188,9 +188,9 @@ const tests = {
const segFilePath = path.join(os.tmpdir(), "Lesion1_onesliceSEG.dcm");

downloadToFile(ctPelvisURL, zipFilePath)
.then( () => {
.then(() => {
fs.createReadStream(zipFilePath)
.pipe(unzipper.Extract( {path: unzipPath} )
.pipe(unzipper.Extract({ path: unzipPath })
.on('close', () => {
const ctPelvisPath = path.join(unzipPath, "Series-1.2.840.113704.1.111.1916.1223562191.15");
fs.readdir(ctPelvisPath, (err, fileNames) => {
Expand All @@ -211,7 +211,7 @@ const tests = {
expect(roundedSpacing).to.equal(5);

downloadToFile(segURL, segFilePath)
.then( () => {
.then(() => {
const arrayBuffer = fs.readFileSync(segFilePath).buffer;
const dicomDict = DicomMessage.readFile(arrayBuffer);
const dataset = DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
Expand All @@ -225,6 +225,81 @@ const tests = {
);
});
},

test_untilTag: () => {
const dicomJSON = `
[
{
"00100010": {
"vr": "PN",
"Value": [ "Fake Patient 1" ]
},
"0020000D": {
"vr": "UI",
"Value": [ "1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873" ]
}
}
]`;
const dicomDict = new DicomDict(metadata);
const datasets = JSON.parse(dicomJSON)[0];
dicomDict.dict = datasets;
const part10Buffer = dicomDict.write();

let dicomData;
let natural;

dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer);
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural.StudyInstanceUID).to.equal('1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873');

dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
untilTag: '00100010'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural).to.not.have.property('PatientName');
expect(natural).to.not.have.property('StudyInstanceUID');


dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
stopAfterTag: '0010,0010'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural).to.not.have.property('StudyInstanceUID');

dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
untilTag: '(0020,000D)'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural).to.not.have.property('StudyInstanceUID');


dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
stopAfterTag: 'x0020000D'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural.StudyInstanceUID).to.equal('1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873');

dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
untilTag: 'StudyInstanceUID'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural).to.not.have.property('StudyInstanceUID');


dicomData = dcmjs.data.DicomMessage.readFile(part10Buffer, {
stopAfterTag: 'PatientName'
});
natural = DicomMetaDictionary.naturalizeDataset(dicomData.dict);
expect(natural.PatientName).to.equal('Fake Patient 1');
expect(natural).to.not.have.property('StudyInstanceUID');

console.log("Finished test_untilTag")
}
}


Expand Down