dcmjs 0.49.3 → 0.50.0

package/test/DicomMetaDictionary.test.js

@@ -1,73 +0,0 @@
-import { DicomMetaDictionary } from "../src/DicomMetaDictionary";
-
-describe("DicomMetaDictionary", () => {
-    describe("static methods", () => {
-        describe("unpunctuateTag", () => {
-            it("returns the unpunctuated tag String", () => {
-                const originalTag = "(0000,0003)";
-                const unpunctuatedTag = "00000003";
-
-                expect(DicomMetaDictionary.unpunctuateTag(originalTag)).toMatch(
-                    unpunctuatedTag
-                );
-            });
-        });
-
-        describe("parseIntFromTag", () => {
-            it("returns the correct Integer of a simple Integer", () => {
-                const originalTag = "(0000,0003)";
-                const integerValue = 3;
-
-                expect(DicomMetaDictionary.parseIntFromTag(originalTag)).toBe(
-                    integerValue
-                );
-            });
-
-            it("returns the correct Integer of a simple hexadecimal String", () => {
-                const originalTag = "(0000,000F)";
-                const integerValue = 15;
-
-                expect(DicomMetaDictionary.parseIntFromTag(originalTag)).toBe(
-                    integerValue
-                );
-            });
-
-            it("returns the correct Integer of a complex hexadecimal String", () => {
-                const originalTag = "(000F,0000)";
-                const integerValue = 983040;
-
-                expect(DicomMetaDictionary.parseIntFromTag(originalTag)).toBe(
-                    integerValue
-                );
-            });
-
-            it("returns NaN if String can not be parsed", () => {
-                const originalTag = "()";
-
-                expect(DicomMetaDictionary.parseIntFromTag(originalTag)).toBe(
-                    NaN
-                );
-            });
-        });
-
-        describe("tagAsIntegerFromName", () => {
-            it("returns undefined if name has no item in dictionary", () => {
-                const tagName = "dummy";
-
-                expect(DicomMetaDictionary.tagAsIntegerFromName(tagName)).toBe(
-                    undefined
-                );
-            });
-
-            describe("tagAsIntegerFromName", () => {
-                it("returns the tag as integer value", () => {
-                    const tagName = "AffectedSOPClassUID";
-
-                    expect(
-                        DicomMetaDictionary.tagAsIntegerFromName(tagName)
-                    ).toBe(2);
-                });
-            });
-        });
-    });
-});

package/test/SequenceOfItems.test.js

@@ -1,86 +0,0 @@
-import {
-    IMPLICIT_LITTLE_ENDIAN,
-    UNDEFINED_LENGTH
-} from "../src/constants/dicom";
-import "../src/index.js";
-import { ValueRepresentation } from "../src/ValueRepresentation";
-import { DicomMessage } from "../src/DicomMessage";
-import { DicomDataReadBufferStreamBuilder } from "./helper/DicomDataReadBufferStreamBuilder";
-
-ValueRepresentation.setDicomMessageClass(DicomMessage);
-
-describe("SequenceOfItems extends ValueRepresentation", () => {
-    const sequenceOfItems = ValueRepresentation.createByTypeString("SQ");
-
-    describe("zero length tests", () => {
-        it("returns an empty elements array", () => {
-            const syntax = IMPLICIT_LITTLE_ENDIAN;
-            const sqLength = 0x0;
-            const streamBuilder = new DicomDataReadBufferStreamBuilder();
-            const stream = streamBuilder.build();
-
-            const elements = sequenceOfItems.readBytes(
-                stream,
-                sqLength,
-                syntax
-            );
-
-            expect(elements.length).toBe(0);
-        });
-    });
-
-    describe("undefined length tests", () => {
-        const sqLength = UNDEFINED_LENGTH;
-        it("returns an empty elements array", () => {
-            const syntax = IMPLICIT_LITTLE_ENDIAN;
-            const streamBuilder = new DicomDataReadBufferStreamBuilder();
-            streamBuilder.addSequenceDelimitationTagAndValue();
-            const stream = streamBuilder.build();
-
-            const elements = sequenceOfItems.readBytes(
-                stream,
-                sqLength,
-                syntax
-            );
-
-            expect(elements.length).toBe(0);
-        });
-
-        it("returns an empty elements array sinnce the item is empty", () => {
-            const syntax = IMPLICIT_LITTLE_ENDIAN;
-            const streamBuilder = new DicomDataReadBufferStreamBuilder();
-            streamBuilder.addUndefinedLengthItem();
-            streamBuilder.addUndefinedLengthItemDelimitation();
-            streamBuilder.addSequenceDelimitationTagAndValue();
-            const stream = streamBuilder.build();
-
-            const elements = sequenceOfItems.readBytes(
-                stream,
-                sqLength,
-                syntax
-            );
-
-            expect(elements.length).toBe(0);
-        });
-
-        it("returns an elements array with one item", () => {
-            const syntax = IMPLICIT_LITTLE_ENDIAN;
-            const streamBuilder = new DicomDataReadBufferStreamBuilder();
-            streamBuilder.addUndefinedLengthItem();
-            streamBuilder.addUlExampleItem();
-            streamBuilder.addUndefinedLengthItemDelimitation();
-            streamBuilder.addSequenceDelimitationTagAndValue();
-            const stream = streamBuilder.build();
-
-            const elements = sequenceOfItems.readBytes(
-                stream,
-                sqLength,
-                syntax
-            );
-
-            expect(elements.length).toBe(1);
-            expect(elements[0]["00020000"].vr).toBe("UL");
-            expect(elements[0]["00020000"].Value[0]).toBe(4);
-        });
-    });
-});

package/test/adapters.test.js

@@ -1,43 +0,0 @@
-import fs from "fs";
-import "../src/index.js";
-import Segmentation_4X from "../src/adapters/Cornerstone/Segmentation_4X";
-import { getTestDataset } from "./testUtils.js";
-
-const mockMetadataProvider = {
-    get: (type, imageId) => {
-        // Unlike CT, is missing coordinate system such as frameOfReferenceUID or rowCosines attributes
-        if (imageId === "mg://1") {
-            return {
-                seriesInstanceUID:
-                    "1.2.840.113681.167838594.1562401072.4432.2070.71100000",
-                rows: 3328,
-                columns: 2560,
-                pixelSpacing: [0.065238, 0.065238],
-                rowPixelSpacing: 0.065238,
-                columnPixelSpacing: 0.065238,
-                columnCosines: null,
-                frameOfReferenceUID: undefined,
-                imageOrientationPatient: undefined,
-                imagePositionPatient: undefined,
-                rowCosines: null,
-                sliceLocation: undefined,
-                sliceThickness: undefined
-            };
-        }
-    }
-};
-
-it("Can generate tool state (4X) with SEG sourcing MG images without throwing any errors", async () => {
-    const url =
-        "https://github.com/dcmjs-org/data/releases/download/mg-seg/seg-test-SEG.dcm";
-    const dcmPath = await getTestDataset(url, "seg-test-SEG.dcm");
-    const arrayBuffer = fs.readFileSync(dcmPath).buffer;
-
-    expect(() => {
-        Segmentation_4X.generateToolState(
-            ["mg://1"],
-            arrayBuffer,
-            mockMetadataProvider
-        );
-    }).not.toThrowError();
-});

package/test/anonymizer.test.js

@@ -1,176 +0,0 @@
-import dcmjs from "../src/index.js";
-import fs from "fs";
-import { validationLog } from "./../src/log.js";
-
-// Ignore validation errors
-validationLog.setLevel(5);
-
-const { DicomMessage } = dcmjs.data;
-const { cleanTags, getTagsNameToEmpty } = dcmjs.anonymizer;
-
-it("test_export", () => {
-    expect(typeof cleanTags).toEqual("function");
-});
-
-it("test_anonymization", () => {
-    // given
-    const arrayBuffer = fs.readFileSync("test/sample-dicom.dcm").buffer;
-    const dicomDict = DicomMessage.readFile(arrayBuffer);
-
-    const tagInfo = dcmjs.data.DicomMetaDictionary.nameMap["PatientName"];
-    const tagNumber = tagInfo.tag,
-        tagString = dcmjs.data.Tag.fromPString(tagNumber).toCleanString();
-
-    const patientIDTag = dicomDict.dict[tagString];
-    const patientIDValue = patientIDTag.Value;
-
-    expect(JSON.stringify(patientIDValue)).toEqual(
-        JSON.stringify([{ Alphabetic: "Fall 3" }])
-    );
-    expect(patientIDValue.toString()).toEqual(["Fall 3"].toString());
-
-    // when
-    cleanTags(dicomDict.dict);
-
-    // then
-    expect(JSON.stringify(patientIDTag.Value)).toEqual(
-        JSON.stringify([{ Alphabetic: "ANON^PATIENT" }])
-    );
-    expect(patientIDTag.Value.toString()).toEqual(["ANON^PATIENT"].toString());
-});
-
-it("test_anonymization_no_change_ref", () => {
-    // given
-    const arrayBuffer = fs.readFileSync("test/sample-sr.dcm").buffer;
-    const dicomDict = DicomMessage.readFile(arrayBuffer);
-
-    // multiple value name
-    const tagInfo = dcmjs.data.DicomMetaDictionary.nameMap["OtherPatientNames"];
-    const tagNumber = tagInfo.tag,
-        tagString = dcmjs.data.Tag.fromPString(tagNumber).toCleanString();
-
-    const otherPatientNamesIDTag = dicomDict.dict[tagString];
-    const otherPatientNamesIDValue = otherPatientNamesIDTag.Value;
-    const otherPatientNamesIDValueJSON = JSON.stringify(
-        otherPatientNamesIDValue
-    );
-
-    expect(JSON.stringify(otherPatientNamesIDValue)).toEqual(
-        JSON.stringify([
-            {
-                Alphabetic: "Doe^John",
-                Ideographic: "Johnny",
-                Phonetic: "Jonny"
-            },
-            { Alphabetic: "Doe^Jane", Ideographic: "Janie", Phonetic: "Jayne" }
-        ])
-    );
-    expect(otherPatientNamesIDValue.toString()).toEqual(
-        ["Doe^John=Johnny=Jonny\\Doe^Jane=Janie=Jayne"].toString()
-    );
-
-    // when
-    cleanTags(dicomDict.dict, { "00101001": "ANON^PATIENT" });
-
-    // then
-    expect(JSON.stringify(otherPatientNamesIDTag.Value)).toEqual(
-        JSON.stringify([{ Alphabetic: "ANON^PATIENT" }])
-    );
-    expect(otherPatientNamesIDTag.Value.toString()).toEqual(
-        ["ANON^PATIENT"].toString()
-    );
-
-    expect(JSON.stringify(otherPatientNamesIDValue)).toEqual(
-        otherPatientNamesIDValueJSON
-    );
-});
-
-it("test_anonymization_tagtoreplace_param", () => {
-    // given
-    const arrayBuffer = fs.readFileSync("test/sample-dicom.dcm").buffer;
-    const dicomDict = DicomMessage.readFile(arrayBuffer);
-
-    const tagInfo = dcmjs.data.DicomMetaDictionary.nameMap["PatientName"];
-    const tagNumber = tagInfo.tag,
-        tagString = dcmjs.data.Tag.fromPString(tagNumber).toCleanString();
-
-    const patientNameTag = dicomDict.dict[tagString];
-    const patientNameValue = patientNameTag.Value;
-
-    expect(JSON.stringify(patientNameValue)).toEqual(
-        JSON.stringify([{ Alphabetic: "Fall 3" }])
-    );
-    expect(patientNameValue.toString()).toEqual(["Fall 3"].toString());
-
-    var tagsToReplace = {
-        "00100010": "REPLACE^PATIENT"
-    };
-    // when
-    cleanTags(dicomDict.dict, tagsToReplace);
-
-    // then
-
-    expect(JSON.stringify(patientNameTag.Value)).toEqual(
-        JSON.stringify([{ Alphabetic: "REPLACE^PATIENT" }])
-    );
-    expect(patientNameTag.Value.toString()).toEqual(
-        ["REPLACE^PATIENT"].toString()
-    );
-});
-
-it("test_anonymization_keep_tag", () => {
-    // given
-    const arrayBuffer = fs.readFileSync("test/sample-dicom.dcm").buffer;
-    const dicomDict = DicomMessage.readFile(arrayBuffer);
-
-    const tagInfo = dcmjs.data.DicomMetaDictionary.nameMap["SeriesDescription"];
-    const tagNumber = tagInfo.tag,
-        tagString = dcmjs.data.Tag.fromPString(tagNumber).toCleanString();
-
-    const seriesDescriptionTag = dicomDict.dict[tagString];
-    const seriesDescriptionValue = seriesDescriptionTag.Value;
-
-    expect(seriesDescriptionValue).toEqual(["Oberbauch  *sSSH/FB/4mm"]);
-
-    var tagsToReplace = {};
-    var tagsToKeep = getTagsNameToEmpty();
-    var seriesDescription = "SeriesDescription";
-    if (tagsToKeep.indexOf(seriesDescription) != -1) {
-        tagsToKeep.splice(tagsToKeep.indexOf(seriesDescription), 1);
-    }
-
-    // when
-    cleanTags(dicomDict.dict, tagsToReplace, tagsToKeep);
-
-    // then
-    expect(seriesDescriptionTag.Value).toEqual(["Oberbauch  *sSSH/FB/4mm"]);
-});
-
-it("test_anonymization_anonymize_tag", () => {
-    // given
-    const arrayBuffer = fs.readFileSync("test/sample-dicom.dcm").buffer;
-    const dicomDict = DicomMessage.readFile(arrayBuffer);
-
-    const tagInfo = dcmjs.data.DicomMetaDictionary.nameMap["SeriesInstanceUID"];
-    const tagNumber = tagInfo.tag,
-        tagString = dcmjs.data.Tag.fromPString(tagNumber).toCleanString();
-
-    const SeriesInstanceUIDTag = dicomDict.dict[tagString];
-    const SeriesInstanceUIDValue = SeriesInstanceUIDTag.Value;
-
-    expect(SeriesInstanceUIDValue).toEqual([
-        "1.2.276.0.50.192168001092.11156604.14547392.303"
-    ]);
-
-    var tagsToReplace = {};
-    var tagsToAnon = getTagsNameToEmpty();
-    if (!tagsToAnon.includes("SeriesInstanceUID")) {
-        tagsToAnon.push("SeriesInstanceUID");
-    }
-
-    // when
-    cleanTags(dicomDict.dict, tagsToReplace, tagsToAnon);
-
-    // then
-    expect(SeriesInstanceUIDTag.Value).toEqual([]);
-});