Merge pull request #35 from anibalsolon/develop

Deploy

.github/workflows/codeql.yml

@@ -8,7 +8,9 @@ on:
 
 jobs:
   analyze:
-    if: "!startsWith(github.event.head_commit.message, '[RELEASE]')"
+    if: |
+      !startsWith(github.event.head_commit.message, '[RELEASE]') &&
+      !startsWith(github.event.head_commit.message, '[PRERELEASE]')
     name: Analyze
     runs-on: ubuntu-latest
     permissions:

.github/workflows/test-and-deploy.yml

@@ -11,7 +11,10 @@ name: Build
 jobs:
 
   test:
-    if: "!startsWith(github.event.head_commit.message, '[RELEASE]') && !contains(github.event.head_commit.message, '[SKIP:test]')"
+    if: |
+      !startsWith(github.event.head_commit.message, '[RELEASE]') &&
+      !startsWith(github.event.head_commit.message, '[PRERELEASE]') &&
+      !contains(github.event.head_commit.message, '[SKIP:test]')
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -30,14 +33,64 @@ jobs:
           DISPLAY: ':99.0'
       - run: rm -f ./.coveralls.yml
 
+  prerelease:
+    if: |
+      github.event.ref == 'refs/heads/develop' &&
+      !startsWith(github.event.head_commit.message, '[RELEASE]') &&
+      !startsWith(github.event.head_commit.message, '[PRERELEASE]') &&
+      !contains(github.event.head_commit.message, '[SKIP:prerelease]')
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          token: ${{ secrets.GH_TOKEN }}
+      - uses: actions/cache@v3
+        with:
+          path: ~/.npm
+          key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+          restore-keys: |
+            ${{ runner.os }}-node-
+      - run: npm install
+      - run: git config --global user.name `jq -r '.author.name' package.json`
+      - run: git config --global user.email `jq -r '.author.email' package.json`
+      - run: git status
+      - run: |
+          VERSION=$(npm version prerelease --no-git-tag-version)
+          git add package.json package-lock.json
+          git commit -m "[PRERELEASE] ${VERSION}"
+          git push
+
+          npm run vscode:package
+
+          VVERSION=$(echo "$VERSION" | sed 's/^v//g')
+          gh release create ${VERSION} --target develop --prerelease "neuro-viewer-${VVERSION}.vsix"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
   deploy:
-    if: github.event.ref == 'refs/heads/main' && !startsWith(github.event.head_commit.message, '[RELEASE]') && !contains(github.event.head_commit.message, '[SKIP:deploy]')
+    if: |
+      github.event.ref == 'refs/heads/main' &&
+      !startsWith(github.event.head_commit.message, '[RELEASE]') &&
+      !contains(github.event.head_commit.message, '[SKIP:deploy]')
     needs: [test]
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
         with:
           token: ${{ secrets.GH_TOKEN }}
+
+      - run: |
+          npm run vscode:vsce -- verify-pat -p "$PAT"
+        env:
+          PAT: ${{ secrets.VSCE_PAT }}
+
+      # Not yet available
+      # - run: |
+      #     npm run vscode:ovsx -- verify-pat -p "$PAT"
+      #   env:
+      #     PAT: ${{ secrets.VSCE_PAT }}
+
       - uses: actions/cache@v3
         with:
           path: ~/.npm
@@ -47,6 +100,7 @@ jobs:
       - run: npm install
       - run: git config --global user.name `jq -r '.author.name' package.json`
       - run: git config --global user.email `jq -r '.author.email' package.json`
+
       - run: git status
       - run: npm version patch -m "[RELEASE] %s"
       - run: npm run vscode:package

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Change Log
 
+### [0.0.14]
+
+* Better support for code-server, thanks to @TinasheMTapera for input
+* Fix image loading when the affine is zeroed, thanks to @nx10 and @pierre-nedelec for helping debugging it
+* Fix file access when running on Windows, thanks to @nx10 for providing with a fix for it
+
 ### [0.0.13]
 
 * Adjusts colors for high contrast themes

extension/document.ts

@@ -19,7 +19,7 @@ export class NiftiDocument extends Disposable implements vscode.CustomDocument {
     super();
     this._uri = uri;
     this._uuid = v4();
-    this._fd = fd || fs.openSync(uri.path, 'r');
+    this._fd = fd || fs.openSync(uri.fsPath, 'r');
   }
 
   public get uri() { return this._uri; }

extension/formats/nifti/base.ts

@@ -87,7 +87,7 @@ export namespace NiftiDataType {
 export interface NiftiHeader {
     endianness: 'BE' | 'LE',
     dimensions: number[],
-    pixelSizes: number[],
+    voxelSize: number[],
     affine: number[][],
     dataType: NiftiDataType,
     dataOffset: number,
@@ -225,7 +225,7 @@ export abstract class Nifti {
 
     protected abstract _dims(buffer: Buffer): number[];
 
-    protected abstract _pixelSizes(buffer: Buffer, ndims: number): number[];
+    protected abstract _voxelSize(buffer: Buffer, ndims: number): number[];
 
     protected abstract _affine(buffer: Buffer): number[][];
 
@@ -260,7 +260,7 @@ export abstract class Nifti {
       const ndims = dims[0];
       const dimensions = dims.slice(1, 1 + ndims);
 
-      const pixelSizes = this._pixelSizes(buffer, ndims).slice(1, 1 + ndims);
+      const voxelSize = this._voxelSize(buffer, ndims).slice(1, 1 + ndims);
       const affine = this._affine(buffer);
       const qOffset = this._qOffset(buffer);
 
@@ -289,7 +289,7 @@ export abstract class Nifti {
         formCodes,
         orientation,
         intentName,
-        pixelSizes,
+        voxelSize,
         dataType,
         dataOffset: offset,
         dataBits: bits,

extension/formats/nifti/nifti1.ts

@@ -28,13 +28,13 @@ export class Nifti1 extends Nifti {
     return dims;
   }
 
-  protected _pixelSizes(buffer: Buffer, ndims: number): number[] {
-    const pixelSizes = <[number]> new Array(ndims + 1);
+  protected _voxelSize(buffer: Buffer, ndims: number): number[] {
+    const voxelSize = <[number]> new Array(ndims + 1);
     for (let d = 1; d <= ndims; d++) {
       const index = 76 + (d * 4);
-      pixelSizes[d] = this.read(buffer, NiftiDataType.FLOAT32, index);
+      voxelSize[d] = this.read(buffer, NiftiDataType.FLOAT32, index);
     }
-    return pixelSizes;
+    return voxelSize;
   }
 
   protected _affine(buffer: Buffer): number[][] {

extension/formats/nifti/nifti2.ts

@@ -28,13 +28,13 @@ export class Nifti2 extends Nifti {
     return dims;
   }
 
-  protected _pixelSizes(buffer: Buffer, ndims: number): number[] {
-    const pixelSizes = <[number]> new Array(ndims + 1);
+  protected _voxelSize(buffer: Buffer, ndims: number): number[] {
+    const voxelSize = <[number]> new Array(ndims + 1);
     for (let d = 1; d <= ndims; d++) {
       const index = 104 + (d * 8);
-      pixelSizes[d] = this.read(buffer, NiftiDataType.FLOAT64, index);
+      voxelSize[d] = this.read(buffer, NiftiDataType.FLOAT64, index);
     }
-    return pixelSizes;
+    return voxelSize;
   }
 
   protected _affine(buffer: Buffer): number[][] {