DicomFile.getRadiopharmaceuticalTag - Code Metrics - Inspection of "better local dicom parsing" - salimkanoun/GaelO - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — dev ( 86a962...d312fb )

by Salim

created 2020-05-17 14:00 UTC

DicomFile.getRadiopharmaceuticalTag A

↳ Parent: DicomFile

Complexity

Conditions

Size

Total Lines	10
Code Lines	8

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	8
dl	0
loc	10
rs	10
c	0
b	0
f	0
cc	2

/**
 Copyright (C) 2018-2020 KANOUN Salim
 This program is free software; you can redistribute it and/or modify
 it under the terms of the Affero GNU General Public v.3 License as published by
 the Free Software Foundation;
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 Affero GNU General Public Public for more details.
 You should have received a copy of the Affero GNU General Public Public along
 with this program; if not, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 */

class DicomFile {
	constructor(originalFile, dataSet) {
		this.originalFile = originalFile;
		this.dataSet = dataSet;
		this.header = this.retrieveHeaderData(dataSet.byteArray);
		this.removeByteArrayReferences();
	}

	removeByteArrayReferences(dataSet = this.dataSet) {
		// Recursively delete byteArray references
		for (let propName in dataSet) {
			let prop = dataSet[propName];

			// Check inner elements
			if (propName == 'elements') {
				for (let elmt in prop) {
					if (prop[elmt].items !== undefined) {
						for (let it of prop[elmt].items) {
							this.removeByteArrayReferences(it.dataSet);
						}
					}
				}
			}

			if (propName == 'byteArray' || propName == 'byteArrayParser') {
				// Delete reference to the object
				dataSet[propName] = null;
			}

		}
	}

	retrieveHeaderData(byteArray) {
		let pxData = this.dataSet.elements.x7fe00010;
		//If no pixel data return the full byte array
		if(pxData === undefined){
			return byteArray.slice()
		}
		//if pixel data here return only header
		return byteArray.slice(0, pxData.dataOffset-1);
	}

	anonymise(tagsToErase) {
		if (tagsToErase === undefined) {
			tagsToErase = [
				'00101005',	// Patient's Birth Name
				'00100010', // Patient's Name
				'00100020', // Patient's ID
				'00100030',	// Patient's Birth Date
				'00101040', // Patient's Address
				'00080050',	// Accession Number
				'00080080',	// Institution Name
				'00080081',	// Institution Adress
				'00080090',	// Referring Physician's Name
				'00080092',	// Referring Physician's Adress
				'00080094', // Refering Physician's Telephone Number
				'00080096', // Referring Pysician ID Sequence
				'00081040', // Institutional Departement Name
				'00081048', // Physician Of Record
				'00081049', // Physician Of Record ID Sequence
				'00081050', // Performing Physician's Name
				'00081052', // Performing Physicians ID Sequence
				'00081060', // Name Of Physician Reading Study
				'00081062', // Physician Reading Study ID Sequence
				'00081070', // Operators Name
				'00200010', // Study ID
				'0040A123'  // Person Name
			];
		}

		let notFoundTags = [];

		for (let id of tagsToErase) {
			try {
				this.erase(id);
			} catch (e) {
				// Only catch "Can't find tag id" error
				if (e != `Can't find ${id} while erasing.`) {
					throw e;
				}
				notFoundTags.push(id);
			}
		}

		/*console.warn(`Couldn't find ${notFoundTags.toString()}`
			+ ` while anonymising ${this.originalFile.name}`
			+ ` => These tags will be skipped.`);*/
	}

	/**
	 * Write unsignificant content at a specified tag in the dataset
	 */
	erase(id, newContent = '*') {
		id = id.toLowerCase();

		const element = this.dataSet.elements[`x${id}`];

		if (element === undefined) {
			throw `Can't find ${id.toUpperCase()} while erasing.`;
		}

		// Retrieve the index position of the element in the data set array
		const dataOffset = element.dataOffset;

		// Retrieve the length of the element
		const length = element.length;

		// Fill the field with unsignificant values
		for (let i = 0; i < length; i++) {
			// Get charcode of the current char in 'newContent'
			const char = newContent.charCodeAt(i % newContent.length);

			// Write this char in the array
			this.header[dataOffset + i] = char;
		}
	}

	getRadiopharmaceuticalTag(tagAddress){
		try{
			let elmt = this.dataSet.elements['x00540016']
			let radioPharmElements = elmt.items[0].dataSet.elements
			return this.string(radioPharmElements['x'+tagAddress])
		}catch ( error ) { 
			console.log(error)

			return undefined 
		}
	}

	getDicomTag(tagAddress){
		let elmt = this.dataSet.elements['x'+tagAddress]
		if ( elmt.length > 0) {
			// Return the value of the dicom attribute
			return this.string(elmt);
		}
		else return undefined
if (a > 0)
    b = 42;
	}

	getAccessionNumber() {
		return this.getDicomTag("00080050");
	}
	getAcquisitionDate() {
		return this.getDicomTag("00080020");
	}
	getInstanceNumber() {
		return this.getDicomTag("00200013");
	}
	getModality() {
		return this.getDicomTag("00080060");
	}
	getPatientBirthDate() {
		return this.getDicomTag("00100030");
	}
	getPatientID() {
		return this.getDicomTag("00100020");
	}
	getPatientName() {
		return this.getDicomTag("00100010");
	}
	getPatientSex() {
		return this.getDicomTag("00100040");
	}
	getSeriesInstanceUID() {
		return this.getDicomTag("0020000e");
	}
	getSeriesDate() {
		return this.getDicomTag("00080021");
	}
	getSeriesDescription() {
		return this.getDicomTag("0008103e");
	}
	getSOPInstanceUID() {
		return this.getDicomTag("00080018");
	}
	getSOPClassUID() {
		return this.getDicomTag("00080016");
	}
	//SK A TESTER : On ne pourrait utiliser que le 0002,0002
	//Ce tag est un duplicat de 00080016 cf https://stackoverflow.com/questions/32689446/is-it-true-that-dicom-media-storage-sop-instance-uid-sop-instance-uid-why
	getMediaStorageSOP(){
		return this.getDicomTag("00020002")
	}
	getSeriesNumber() {
		return this.getDicomTag('00200011')
	}
	getStudyInstanceUID() {
		return this.getDicomTag('0020000d')
	}
	getStudyDate() {
		return this.getDicomTag("00080020");
	}
	getStudyID() {
		return this.getDicomTag("00200010");
	}
	getStudyDescription() {
		return this.getDicomTag("00081030");
	}

	/**
	 * Returns element contain as a string
	 * @param {*} element element from the data set
	 */
	string(element) {
		let position = element.dataOffset;
		let length = element.length;

		if (length < 0) {
			throw 'Negative length';
		}
		if (position + length > this.header.length) {
			throw 'Out of range index';
		}

		var result = '';
		var byte;

		for (var i = 0; i < length; i++) {
			byte = this.header[position + i];
			if (byte === 0) {
				position += length;

				return result.trim();
			}
			result += String.fromCharCode(byte);
		}
		return result.trim();
	}

	isSecondaryCaptureImg() {
		const secondaryCaptureImgValues = [
			'1.2.840.10008.5.1.4.1.1.7',
			'1.2.840.10008.5.1.4.1.1.7.1',
			'1.2.840.10008.5.1.4.1.1.7.2',
			'1.2.840.10008.5.1.4.1.1.7.3',
			'1.2.840.10008.5.1.4.1.1.7.4',
			'1.2.840.10008.5.1.4.1.1.88.11',
			'1.2.840.10008.5.1.4.1.1.88.22',
			'1.2.840.10008.5.1.4.1.1.88.33',
			'1.2.840.10008.5.1.4.1.1.88.40',
			'1.2.840.10008.5.1.4.1.1.88.50',
			'1.2.840.10008.5.1.4.1.1.88.59',
			'1.2.840.10008.5.1.4.1.1.88.65',
			'1.2.840.10008.5.1.4.1.1.88.67'
		];
		return secondaryCaptureImgValues.includes(this.getSOPClassUID());
	}

	isDicomDir(){
		const dicomDirSopValues = [
			'1.2.840.10008.1.3.10'
		]
		return dicomDirSopValues.includes(this.getMediaStorageSOP());
	}

	clearData() {
		this.header = null;
		this.dataSet = null;
	}
}

1			/**
2			Copyright (C) 2018-2020 KANOUN Salim
3			This program is free software; you can redistribute it and/or modify
4			it under the terms of the Affero GNU General Public v.3 License as published by
5			the Free Software Foundation;
6			This program is distributed in the hope that it will be useful,
7			but WITHOUT ANY WARRANTY; without even the implied warranty of
8			MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
9			Affero GNU General Public Public for more details.
10			You should have received a copy of the Affero GNU General Public Public along
11			with this program; if not, write to the Free Software Foundation, Inc.,
12			51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
13			*/
14
15			class DicomFile {
16			constructor(originalFile, dataSet) {
17			this.originalFile = originalFile;
18			this.dataSet = dataSet;
19			this.header = this.retrieveHeaderData(dataSet.byteArray);
20			this.removeByteArrayReferences();
21			}
22
23			removeByteArrayReferences(dataSet = this.dataSet) {
24			// Recursively delete byteArray references
25			for (let propName in dataSet) {
26			let prop = dataSet[propName];
27
28			// Check inner elements
29			if (propName == 'elements') {
30			for (let elmt in prop) {
31			if (prop[elmt].items !== undefined) {
32			for (let it of prop[elmt].items) {
33			this.removeByteArrayReferences(it.dataSet);
34			}
35			}
36			}
37			}
38
39			if (propName == 'byteArray' \|\| propName == 'byteArrayParser') {
40			// Delete reference to the object
41			dataSet[propName] = null;
42			}
43
44			}
45			}
46
47			retrieveHeaderData(byteArray) {
48			let pxData = this.dataSet.elements.x7fe00010;
49			//If no pixel data return the full byte array
50			if(pxData === undefined){
51			return byteArray.slice()
52			}
53			//if pixel data here return only header
54			return byteArray.slice(0, pxData.dataOffset-1);
55			}
56
57			anonymise(tagsToErase) {
58			if (tagsToErase === undefined) {
59			tagsToErase = [
60			'00101005', // Patient's Birth Name
61			'00100010', // Patient's Name
62			'00100020', // Patient's ID
63			'00100030', // Patient's Birth Date
64			'00101040', // Patient's Address
65			'00080050', // Accession Number
66			'00080080', // Institution Name
67			'00080081', // Institution Adress
68			'00080090', // Referring Physician's Name
69			'00080092', // Referring Physician's Adress
70			'00080094', // Refering Physician's Telephone Number
71			'00080096', // Referring Pysician ID Sequence
72			'00081040', // Institutional Departement Name
73			'00081048', // Physician Of Record
74			'00081049', // Physician Of Record ID Sequence
75			'00081050', // Performing Physician's Name
76			'00081052', // Performing Physicians ID Sequence
77			'00081060', // Name Of Physician Reading Study
78			'00081062', // Physician Reading Study ID Sequence
79			'00081070', // Operators Name
80			'00200010', // Study ID
81			'0040A123' // Person Name
82			];
83			}
84
85			let notFoundTags = [];
86
87			for (let id of tagsToErase) {
88			try {
89			this.erase(id);
90			} catch (e) {
91			// Only catch "Can't find tag id" error
92			if (e != `Can't find ${id} while erasing.`) {
93			throw e;
94			}
95			notFoundTags.push(id);
96			}
97			}
98
99			/*console.warn(`Couldn't find ${notFoundTags.toString()}`
100			+ ` while anonymising ${this.originalFile.name}`
101			+ ` => These tags will be skipped.`);*/
102			}
103
104			/**
105			* Write unsignificant content at a specified tag in the dataset
106			*/
107			erase(id, newContent = '*') {
108			id = id.toLowerCase();
109
110			const element = this.dataSet.elements[`x${id}`];
111
112			if (element === undefined) {
113			throw `Can't find ${id.toUpperCase()} while erasing.`;
114			}
115
116			// Retrieve the index position of the element in the data set array
117			const dataOffset = element.dataOffset;
118
119			// Retrieve the length of the element
120			const length = element.length;
121
122			// Fill the field with unsignificant values
123			for (let i = 0; i < length; i++) {
124			// Get charcode of the current char in 'newContent'
125			const char = newContent.charCodeAt(i % newContent.length);
126
127			// Write this char in the array
128			this.header[dataOffset + i] = char;
129			}
130			}
131
132			getRadiopharmaceuticalTag(tagAddress){
133			try{
134			let elmt = this.dataSet.elements['x00540016']
135			let radioPharmElements = elmt.items[0].dataSet.elements
136			return this.string(radioPharmElements['x'+tagAddress])
137			}catch ( error ) {
138			console.log(error)
			0 ignored issues – show Debugging Code introduced 2020-05-17 14:03 UTC by Report Bug Copy Issue Report `console.log` looks like debug code. Are you sure you do not want to remove it? Loading history...
139			return undefined
140			}
141			}
142
143			getDicomTag(tagAddress){
144			let elmt = this.dataSet.elements['x'+tagAddress]
145			if ( elmt.length > 0) {
146			// Return the value of the dicom attribute
147			return this.string(elmt);
148			}
149			else return undefined
			0 ignored issues – show Comprehensibility introduced 2020-05-17 14:03 UTC by Report Bug Copy Issue Report `else` is not necessary here since all `if` branches return, consider removing it to reduce nesting and make code more readable. Loading history... Coding Style Best Practice introduced 2020-05-17 14:03 UTC by Report Bug Copy Issue Report Curly braces around statements make for more readable code and help prevent bugs when you add further statements. Consider adding curly braces around all statements when they are executed conditionally. This is optional if there is only one statement, but leaving them out can lead to unexpected behaviour if another statement is added later. Consider: if (a > 0) b = 42; If you or someone else later decides to put another statement in, only the first statement will be executed. if (a > 0) console.log("a > 0"); b = 42; In this case the statement `b = 42` will always be executed, while the logging statement will be executed conditionally. if (a > 0) { console.log("a > 0"); b = 42; } ensures that the proper code will be executed conditionally no matter how many statements are added or removed. Loading history...
150			}
151
152			getAccessionNumber() {
153			return this.getDicomTag("00080050");
154			}
155			getAcquisitionDate() {
156			return this.getDicomTag("00080020");
157			}
158			getInstanceNumber() {
159			return this.getDicomTag("00200013");
160			}
161			getModality() {
162			return this.getDicomTag("00080060");
163			}
164			getPatientBirthDate() {
165			return this.getDicomTag("00100030");
166			}
167			getPatientID() {
168			return this.getDicomTag("00100020");
169			}
170			getPatientName() {
171			return this.getDicomTag("00100010");
172			}
173			getPatientSex() {
174			return this.getDicomTag("00100040");
175			}
176			getSeriesInstanceUID() {
177			return this.getDicomTag("0020000e");
178			}
179			getSeriesDate() {
180			return this.getDicomTag("00080021");
181			}
182			getSeriesDescription() {
183			return this.getDicomTag("0008103e");
184			}
185			getSOPInstanceUID() {
186			return this.getDicomTag("00080018");
187			}
188			getSOPClassUID() {
189			return this.getDicomTag("00080016");
190			}
191			//SK A TESTER : On ne pourrait utiliser que le 0002,0002
192			//Ce tag est un duplicat de 00080016 cf https://stackoverflow.com/questions/32689446/is-it-true-that-dicom-media-storage-sop-instance-uid-sop-instance-uid-why
193			getMediaStorageSOP(){
194			return this.getDicomTag("00020002")
195			}
196			getSeriesNumber() {
197			return this.getDicomTag('00200011')
198			}
199			getStudyInstanceUID() {
200			return this.getDicomTag('0020000d')
201			}
202			getStudyDate() {
203			return this.getDicomTag("00080020");
204			}
205			getStudyID() {
206			return this.getDicomTag("00200010");
207			}
208			getStudyDescription() {
209			return this.getDicomTag("00081030");
210			}
211
212			/**
213			* Returns element contain as a string
214			* @param {*} element element from the data set
215			*/
216			string(element) {
217			let position = element.dataOffset;
218			let length = element.length;
219
220			if (length < 0) {
221			throw 'Negative length';
222			}
223			if (position + length > this.header.length) {
224			throw 'Out of range index';
225			}
226
227			var result = '';
228			var byte;
229
230			for (var i = 0; i < length; i++) {
231			byte = this.header[position + i];
232			if (byte === 0) {
233			position += length;
			0 ignored issues – show Unused Code introduced 2020-03-31 22:08 UTC by Report Bug Copy Issue Report The assignment to variable `position` seems to be never used. Consider removing it. Loading history...
234			return result.trim();
235			}
236			result += String.fromCharCode(byte);
237			}
238			return result.trim();
239			}
240
241			isSecondaryCaptureImg() {
242			const secondaryCaptureImgValues = [
243			'1.2.840.10008.5.1.4.1.1.7',
244			'1.2.840.10008.5.1.4.1.1.7.1',
245			'1.2.840.10008.5.1.4.1.1.7.2',
246			'1.2.840.10008.5.1.4.1.1.7.3',
247			'1.2.840.10008.5.1.4.1.1.7.4',
248			'1.2.840.10008.5.1.4.1.1.88.11',
249			'1.2.840.10008.5.1.4.1.1.88.22',
250			'1.2.840.10008.5.1.4.1.1.88.33',
251			'1.2.840.10008.5.1.4.1.1.88.40',
252			'1.2.840.10008.5.1.4.1.1.88.50',
253			'1.2.840.10008.5.1.4.1.1.88.59',
254			'1.2.840.10008.5.1.4.1.1.88.65',
255			'1.2.840.10008.5.1.4.1.1.88.67'
256			];
257			return secondaryCaptureImgValues.includes(this.getSOPClassUID());
258			}
259
260			isDicomDir(){
261			const dicomDirSopValues = [
262			'1.2.840.10008.1.3.10'
263			]
264			return dicomDirSopValues.includes(this.getMediaStorageSOP());
265			}
266
267			clearData() {
268			this.header = null;
269			this.dataSet = null;
270			}
271			}

salimkanoun / GaelO

Push — dev ( 86a962...d312fb )

DicomFile.getRadiopharmaceuticalTag A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

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