fix(src/test): Address lint issues + setup lint/format CI action (#406)

* Address lint issues * fix(src/test): Address lint issues * Add lint workflow and use yarn * Update lint rules * Add prettier check * Run frmat * Update action title
dcmjs-org · Oct 15, 2024 · 158c396 · 158c396
1 parent 96a068e
commit 158c396
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Showing 40 changed files with 811 additions and 688 deletions.
diff --git a/.eslintrc.json b/.eslintrc.json
@@ -14,5 +14,9 @@
   "parserOptions": {
     "ecmaVersion": 11,
     "sourceType": "module"
+  },
+
+  "rules": {
+    "no-loss-of-precision": "off"
   }
 }
diff --git a/.github/workflows/lint-and-format.yml b/.github/workflows/lint-and-format.yml
@@ -0,0 +1,27 @@
+name: Run lint and format check
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  lint-and-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18
+
+      - name: Install packages
+        run: yarn install --frozen-lockfile
+
+      - name: Run ESLint
+        run: yarn lint
+
+      - name: Check Prettier formatting
+        run: yarn format:check
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,7 +18,7 @@ jobs:
           node-version: 18
 
       - name: Install packages
-        uses: bahmutov/npm-install@v1
+        run: yarn install --frozen-lockfile
 
       - name: Run tests
-        run: npm run test
+        run: yarn test
diff --git a/package.json b/package.json
@@ -13,7 +13,8 @@
     "build:examples": "npm run build && npx cpx 'build/**/*.{js,map}' examples/js",
     "start": "rollup -c -w",
     "format": "prettier --write 'src/**/*.js' 'test/**/*.js'",
-    "lint": "eslint --fix ."
+    "format:check": "prettier --check 'src/**/*.js' 'test/**/*.js'",
+    "lint": "eslint --fix 'src/**/*.js' 'test/**/*.js'"
   },
   "repository": {
     "type": "git",

diff --git a/src/BufferStream.js b/src/BufferStream.js
@@ -371,7 +371,9 @@ class ReadBufferStream extends BufferStream {
     }
 
     writeUint8Repeat(value, count) {
-        throw new Error(value, "writeUint8Repeat not implemented");
+        throw new Error(
+            `writeUint8Repeat not implemented (value: ${value}, count: ${count})`
+        );
     }
 
     writeInt8(value) {

diff --git a/src/DicomMessage.js b/src/DicomMessage.js
@@ -277,7 +277,9 @@ class DicomMessage {
 
         // apply VR specific formatting to the original _rawValue and compare to the Value
         const vr = ValueRepresentation.createByTypeString(vrType);
-        const originalValue = tagObject._rawValue.map((val) => vr.applyFormatting(val))
+        const originalValue = tagObject._rawValue.map(val =>
+            vr.applyFormatting(val)
+        );
 
         // if Value has not changed, write _rawValue unformatted back into the file
         if (deepEqual(tagObject.Value, originalValue)) {
@@ -366,18 +368,28 @@ class DicomMessage {
             var times = length / vr.maxLength,
                 i = 0;
             while (i++ < times) {
-                const { rawValue, value } = vr.read(stream, vr.maxLength, syntax, options);
+                const { rawValue, value } = vr.read(
+                    stream,
+                    vr.maxLength,
+                    syntax,
+                    options
+                );
                 rawValues.push(rawValue);
                 values.push(value);
             }
         } else {
-            const { rawValue, value } = vr.read(stream, length, syntax, options);
+            const { rawValue, value } = vr.read(
+                stream,
+                length,
+                syntax,
+                options
+            );
             if (!vr.isBinary() && singleVRs.indexOf(vr.type) == -1) {
                 rawValues = rawValue;
-                values = value
+                values = value;
                 if (typeof value === "string") {
                     const delimiterChar = String.fromCharCode(VM_DELIMITER);
-                    rawValues = vr.dropPadByte(rawValue.split(delimiterChar))
+                    rawValues = vr.dropPadByte(rawValue.split(delimiterChar));
                     values = vr.dropPadByte(value.split(delimiterChar));
                 }
             } else if (vr.type == "SQ") {
@@ -388,7 +400,9 @@ class DicomMessage {
                 values = value;
             } else {
                 Array.isArray(value) ? (values = value) : values.push(value);
-                Array.isArray(rawValue) ? (rawValues = rawValue) : rawValues.push(rawValue);
+                Array.isArray(rawValue)
+                    ? (rawValues = rawValue)
+                    : rawValues.push(rawValue);
             }
         }
         stream.setEndian(oldEndian);

diff --git a/src/adapters/Cornerstone/Bidirectional.js b/src/adapters/Cornerstone/Bidirectional.js
@@ -127,7 +127,6 @@ class Bidirectional {
             isCreating: false,
             longestDiameter,
             shortestDiameter,
-            toolType: "Bidirectional",
             toolName: "Bidirectional",
             visible: true,
             finding: findingGroup

diff --git a/src/adapters/Cornerstone/EllipticalRoi.js b/src/adapters/Cornerstone/EllipticalRoi.js
@@ -1,11 +1,8 @@
 import MeasurementReport from "./MeasurementReport";
 import TID300Ellipse from "../../utilities/TID300/Ellipse";
 import CORNERSTONE_4_TAG from "./cornerstone4Tag";
-import { toArray } from "../helpers.js";
 
 const ELLIPTICALROI = "EllipticalRoi";
-const FINDING = "121071";
-const FINDING_SITE = "G-C0E3";
 
 class EllipticalRoi {
     constructor() {}

diff --git a/src/adapters/Cornerstone/Length.js b/src/adapters/Cornerstone/Length.js
@@ -1,11 +1,8 @@
 import MeasurementReport from "./MeasurementReport.js";
 import TID300Length from "../../utilities/TID300/Length.js";
 import CORNERSTONE_4_TAG from "./cornerstone4Tag";
-import { toArray } from "../helpers.js";
 
 const LENGTH = "Length";
-const FINDING = "121071";
-const FINDING_SITE = "G-C0E3";
 
 class Length {
     constructor() {}

diff --git a/src/adapters/Cornerstone/Segmentation_3X.js b/src/adapters/Cornerstone/Segmentation_3X.js
@@ -415,8 +415,6 @@ function addImageIdSpecificBrushToolState(
 
     const cToolsPixelData = brushDataI.pixelData;
 
-    const [rows, cols] = pixelData2D.shape;
-
     for (let p = 0; p < cToolsPixelData.length; p++) {
         if (pixelData2D.data[p]) {
             cToolsPixelData[p] = 1;

diff --git a/src/adapters/Cornerstone/Segmentation_4X.js b/src/adapters/Cornerstone/Segmentation_4X.js
@@ -6,7 +6,6 @@ import { DicomMessage } from "../../DicomMessage.js";
 import { DicomMetaDictionary } from "../../DicomMetaDictionary.js";
 import { Normalizer } from "../../normalizers.js";
 import { Segmentation as SegmentationDerivation } from "../../derivations/index.js";
-import { mat4 } from "gl-matrix";
 import {
     rotateDirectionCosinesInPlane,
     flipImageOrientationPatient as flipIOP,
@@ -432,177 +431,6 @@ function generateToolState(
     };
 }
 
-function insertPixelDataPerpendicular(
-    segmentsOnFrame,
-    labelmapBuffer,
-    pixelData,
-    multiframe,
-    imageIds,
-    validOrientations,
-    metadataProvider
-) {
-    const {
-        SharedFunctionalGroupsSequence,
-        PerFrameFunctionalGroupsSequence,
-        Rows,
-        Columns
-    } = multiframe;
-
-    const firstImagePlaneModule = metadataProvider.get(
-        "imagePlaneModule",
-        imageIds[0]
-    );
-
-    const lastImagePlaneModule = metadataProvider.get(
-        "imagePlaneModule",
-        imageIds[imageIds.length - 1]
-    );
-
-    console.log(firstImagePlaneModule);
-    console.log(lastImagePlaneModule);
-
-    const corners = [
-        ...getCorners(firstImagePlaneModule),
-        ...getCorners(lastImagePlaneModule)
-    ];
-
-    console.log(`corners:`);
-    console.log(corners);
-
-    const indexToWorld = mat4.create();
-
-    const ippFirstFrame = firstImagePlaneModule.imagePositionPatient;
-    const rowCosines = Array.isArray(firstImagePlaneModule.rowCosines)
-        ? [...firstImagePlaneModule.rowCosines]
-        : [
-              firstImagePlaneModule.rowCosines.x,
-              firstImagePlaneModule.rowCosines.y,
-              firstImagePlaneModule.rowCosines.z
-          ];
-
-    const columnCosines = Array.isArray(firstImagePlaneModule.columnCosines)
-        ? [...firstImagePlaneModule.columnCosines]
-        : [
-              firstImagePlaneModule.columnCosines.x,
-              firstImagePlaneModule.columnCosines.y,
-              firstImagePlaneModule.columnCosines.z
-          ];
-
-    const { pixelSpacing } = firstImagePlaneModule;
-
-    mat4.set(
-        indexToWorld,
-        // Column 1
-        0,
-        0,
-        0,
-        ippFirstFrame[0],
-        // Column 2
-        0,
-        0,
-        0,
-        ippFirstFrame[1],
-        // Column 3
-        0,
-        0,
-        0,
-        ippFirstFrame[2],
-        // Column 4
-        0,
-        0,
-        0,
-        1
-    );
-
-    // TODO -> Get origin and (x,y,z) increments to build a translation matrix:
-    // TODO -> Equation C.7.6.2.1-1
-
-    // | cx*di rx* Xx 0 |  |x|
-    // | cy*di ry Xy 0 |  |y|
-    // | cz*di rz Xz 0 |  |z|
-    // | tx ty tz 1 |  |1|
-
-    // const [
-    //     0, 0 , 0 , 0,
-    //     0, 0 , 0 , 0,
-    //     0, 0 , 0 , 0,
-    //     ipp[0], ipp[1] , ipp[2] , 1,
-    // ]
-
-    // Each frame:
-
-    // Find which corner the first voxel lines up with (one of 8 corners.)
-
-    // Find how i,j,k orient with respect to source volume.
-    // Go through each frame, find location in source to start, and whether to increment +/ix,+/-y,+/-z
-    //   through each voxel.
-
-    // [1,0,0,0,1,0]
-
-    // const [
-
-    // ]
-
-    // Invert transformation matrix to get worldToIndex
-
-    // Apply world to index on each point to fill up the matrix.
-
-    // const sharedImageOrientationPatient = SharedFunctionalGroupsSequence.PlaneOrientationSequence
-    //     ? SharedFunctionalGroupsSequence.PlaneOrientationSequence
-    //           .ImageOrientationPatient
-    //     : undefined;
-    // const sliceLength = Columns * Rows;
-}
-
-function getCorners(imagePlaneModule) {
-    // console.log(imagePlaneModule);
-
-    const {
-        rows,
-        columns,
-        rowCosines,
-        columnCosines,
-        imagePositionPatient: ipp,
-        rowPixelSpacing,
-        columnPixelSpacing
-    } = imagePlaneModule;
-
-    const rowLength = columns * columnPixelSpacing;
-    const columnLength = rows * rowPixelSpacing;
-
-    const entireRowVector = [
-        rowLength * columnCosines[0],
-        rowLength * columnCosines[1],
-        rowLength * columnCosines[2]
-    ];
-
-    const entireColumnVector = [
-        columnLength * rowCosines[0],
-        columnLength * rowCosines[1],
-        columnLength * rowCosines[2]
-    ];
-
-    const topLeft = [ipp[0], ipp[1], ipp[2]];
-    const topRight = [
-        topLeft[0] + entireRowVector[0],
-        topLeft[1] + entireRowVector[1],
-        topLeft[2] + entireRowVector[2]
-    ];
-    const bottomLeft = [
-        topLeft[0] + entireColumnVector[0],
-        topLeft[1] + entireColumnVector[1],
-        topLeft[2] + entireColumnVector[2]
-    ];
-
-    const bottomRight = [
-        bottomLeft[0] + entireRowVector[0],
-        bottomLeft[1] + entireRowVector[1],
-        bottomLeft[2] + entireRowVector[2]
-    ];
-
-    return [topLeft, topRight, bottomLeft, bottomRight];
-}
-
 /**
  * Find the reference frame of the segmentation frame in the source data.
  *
@@ -786,7 +614,7 @@ function checkSEGsOverlapping(
         }
     }
 
-    for (let [user, role] of frameSegmentsMapping.entries()) {
+    for (let [, role] of frameSegmentsMapping.entries()) {
         let temp2DArray = new Uint16Array(sliceLength).fill(0);
 
         for (let i = 0; i < role.length; ++i) {

diff --git a/src/adapters/Cornerstone3D/Bidirectional.js b/src/adapters/Cornerstone3D/Bidirectional.js
@@ -7,8 +7,6 @@ import { toArray } from "../helpers.js";
 const BIDIRECTIONAL = "Bidirectional";
 const LONG_AXIS = "Long Axis";
 const SHORT_AXIS = "Short Axis";
-const FINDING = "121071";
-const FINDING_SITE = "G-C0E3";
 const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${BIDIRECTIONAL}`;
 
 class Bidirectional {

diff --git a/src/adapters/Cornerstone3D/EllipticalROI.js b/src/adapters/Cornerstone3D/EllipticalROI.js
@@ -1,11 +1,9 @@
-import { vec2, vec3 } from "gl-matrix";
+import { vec3 } from "gl-matrix";
 import MeasurementReport from "./MeasurementReport";
 import TID300Ellipse from "../../utilities/TID300/Ellipse";
 import CORNERSTONE_3D_TAG from "./cornerstone3DTag";
 
 const ELLIPTICALROI = "EllipticalROI";
-const FINDING = "121071";
-const FINDING_SITE = "G-C0E3";
 const EPSILON = 1e-4;
 
 const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${ELLIPTICALROI}`;

diff --git a/src/adapters/Cornerstone3D/Length.js b/src/adapters/Cornerstone3D/Length.js
@@ -3,8 +3,6 @@ import TID300Length from "../../utilities/TID300/Length.js";
 import CORNERSTONE_3D_TAG from "./cornerstone3DTag";
 
 const LENGTH = "Length";
-const FINDING = "121071";
-const FINDING_SITE = "G-C0E3";
 const trackingIdentifierTextValue = `${CORNERSTONE_3D_TAG}:${LENGTH}`;
 
 class Length {

diff --git a/src/adapters/Cornerstone3D/MeasurementReport.js b/src/adapters/Cornerstone3D/MeasurementReport.js
@@ -379,7 +379,7 @@ export default class MeasurementReport {
             measurementData[key] = [];
         });
 
-        measurementGroups.forEach((measurementGroup, index) => {
+        measurementGroups.forEach(measurementGroup => {
             const measurementGroupContentSequence = toArray(
                 measurementGroup.ContentSequence
             );