added naive dcm series support by converting dcm dir into .nii

.vscode/launch.json

@@ -5,11 +5,14 @@
             "name": "Run Extension",
             "type": "extensionHost",
             "request": "launch",
+            "runtimeExecutable": "${execPath}",
             "args": [
                 "${workspaceFolder}/data",
-                "--extensionDevelopmentPath=${workspaceFolder}",
+                "--extensionDevelopmentPath=${workspaceRoot}",
                 "--disable-extensions"
-            ]
+            ],
+            "sourceMaps": true,
+            "outFiles": ["${workspaceRoot}/dist/**/*.js"]
         },
         {
             "name": "Run Web Extension",

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "editor.indentSize": 2
+}

extension/provider.ts

@@ -1,7 +1,138 @@
 import * as vscode from 'vscode';
 import { Buffer } from 'buffer';
 import { NiftiDocument } from '../extension/document';
+import { dirname } from 'path';
+import daikon from 'daikon';
+import { appendFileSync, readFileSync, renameSync } from 'fs';
+import { v4 } from 'uuid';
+import * as temp from 'temp';
+import { assert } from 'console';
+temp.track();
 
+function toArrayBuffer(buffer: Uint8Array) {
+  const arrayBuffer = new ArrayBuffer(buffer.length);
+  const view = new Uint8Array(arrayBuffer);
+  for (let i = 0; i < buffer.length; ++i) {
+    view[i] = buffer[i];
+  }
+  return arrayBuffer;
+}
+
+async function dcm2nii(uri: vscode.Uri, outUri: vscode.Uri): Promise<vscode.Uri>{
+  const images = (await vscode.workspace.fs.readDirectory(uri).then(async (dcms) => {
+    return dcms.map(async (dcm) => {
+      return daikon.Series.parseImage(new DataView(toArrayBuffer(await vscode.workspace.fs.readFile(vscode.Uri.parse(uri.path + '/' + dcm[0])))));
+    });
+  }).then((promises) => Promise.all(promises))).sort((a, b) => {
+    const a_slic = a.getSliceLocation();
+    const b_slic = b.getSliceLocation();
+    return a_slic < b_slic ? -1 : a_slic > b_slic ? 1 : 0;
+  });
+  const imgPath = outUri.path + "/" + v4();
+  const series = new daikon.Series();
+  let minVal = images[0].getInterpretedData()[0];
+  let maxVal = images[0].getInterpretedData()[0];
+  const l = images[0].getInterpretedData().length;
+  for (const image of images){
+    if (image === null) {
+      console.error(daikon.Series.parserError);
+    } else if (image.hasPixelData()) {
+      const {data, max, maxIndex, min, minIndex, numCols, numRows} = image.getInterpretedData(true, true);
+      if (max > maxVal){maxVal = max;}
+      if (min < minVal){minVal = min;}
+      assert(l === data.length);
+      appendFileSync(imgPath, new Uint8Array(new Float32Array(data).buffer));
+      series.addImage(image);
+    }
+  }
+  series.buildSeries();
+  const ori = images[0].getTag(0x0020,0x0037).value;
+  const firstPos = images[0].getTag(0x0020,0x0032).value;
+  const lastPos = images[images.length - 1].getTag(0x0020,0x0032).value;
+  const thi = images[0].getTag(0x0018,0x0050).value;
+  const n = images.length;
+  // https://brainder.org/2015/04/03/the-nifti-2-file-format/
+  // https://core.ac.uk/download/pdf/79518053.pdf
+  const bytes = [
+    new Uint8Array(new Int32Array([540]).buffer), // sizeof_hdr
+    Buffer.from("n+2"), // magic[0-2]
+    new Uint8Array(5),
+    new Uint8Array(new Int16Array([16]).buffer), // data_type
+    new Uint8Array(new Int16Array([32]).buffer), // bitpix
+    new Uint8Array(new BigInt64Array([
+      BigInt(3), // dim[0]
+      BigInt(series.images[0].getRows()), // dim[1]
+      BigInt(series.images[0].getCols()), // dim[2]
+      BigInt(series.images.length), // dim[3]
+      BigInt(1), // dim[4]
+      BigInt(1), // dim[5]
+      BigInt(1), // dim[6]
+      BigInt(1), // dim[7]
+    ]).buffer),
+    new Uint8Array(new Float64Array([
+      0, // intent_p1
+      0, // intent_p2
+      0, // intent_p3
+    ]).buffer),
+    new Uint8Array(new Float64Array([
+      0, // pixdim[0] 
+      ...series.images[0].getPixelSpacing(), // pixdim[1] pixdim[2]
+      series.images[0].getSliceThickness(), // pixdim[3]
+      0, // pixdim[4]
+      0, // pixdim[5]
+      0, // pixdim[6]
+      0, // pixdim[7]
+    ]).buffer),
+    new Uint8Array(new BigInt64Array([BigInt(544)]).buffer), // vox_offset
+    new Uint8Array(new Float64Array([
+      0, //1, // scl_slope
+      0, //0, // scl_inter
+      maxVal, // cal_max
+      minVal, // cal_min
+      0, // slice_duration
+      0, // toffset
+    ]).buffer),
+    new Uint8Array(new BigInt64Array([
+      BigInt(0), // slice_start
+      BigInt(0) // slice_end
+    ]).buffer),
+    new Uint8Array(80), // descrip[80] // some
+    new Uint8Array(24), // aux_file[24] // none
+    new Uint8Array(new Int32Array([
+      0, // qform_code
+      4, // sform_code
+    ]).buffer),
+    new Uint8Array(new Float64Array([
+      0, // quatern_b
+      0, // quatern_c
+      0, // quatern_d
+      ...images[0].getImagePosition(), // qoffset_x qoffset_y qoffset_z
+      //   -ori[0]*thi[0], -ori[3]*thi[1], -(lastPos[0] - firstPos[0]) / (n - 1), -firstPos[0], // srow_x[4]
+      //   -ori[1]*thi[0], -ori[4]*thi[1], -(lastPos[1] - firstPos[1]) / (n - 1), -firstPos[1], // srow_y[4]
+      //    ori[2]*thi[0],  ori[5]*thi[1],  (lastPos[2] - firstPos[2]) / (n - 1),  firstPos[2] // srow_z[4]
+     -1 , 0, 0, 0, // srow_x[4]
+      0 ,-1, 0, 0, // srow_y[4]
+      0 , 0, 1, 0 // srow_z[4]
+    ]).buffer),
+    new Uint8Array(new Int32Array([
+      0, // slice_code
+      2, // xyzt_units
+      0, // intent_code
+    ]).buffer), 
+    new Uint8Array(16), // intent_name[16]
+    new Uint8Array(1), // dim_info
+    new Uint8Array(15), // unused_str[15]
+    new Uint8Array(4), // additional 4 bytes
+  ];
+  const hdrPath = outUri.path + "/" + v4();
+  bytes.map((buf) => appendFileSync(hdrPath, buf));
+//   const outcome = outUri.path + "/" + v4() + ".nii";
+  console.log(new Uint8Array(readFileSync(imgPath)).length);
+  appendFileSync(hdrPath, new Uint8Array(readFileSync(imgPath)));
+  const outcome = hdrPath + ".nii";
+  renameSync(hdrPath, outcome);
+  return vscode.Uri.parse(outcome);
+}
 
 export class NiftiEditorProvider implements vscode.CustomReadonlyEditorProvider<NiftiDocument> {
 
@@ -30,7 +161,12 @@ export class NiftiEditorProvider implements vscode.CustomReadonlyEditorProvider<
     uri: vscode.Uri
   ): Promise<NiftiDocument> {
     console.log(`Open document ${uri}`);
-    const data: Uint8Array = await vscode.workspace.fs.readFile(uri);
+    let data: Uint8Array = await vscode.workspace.fs.readFile(uri);
+    if (uri.path.endsWith(".dcm")){
+      const outDir = temp.mkdirSync(v4());
+      const uriNii = await dcm2nii(vscode.Uri.parse(dirname(uri.path)), vscode.Uri.parse(outDir));
+      data = await vscode.workspace.fs.readFile(uriNii);
+    }
     const document: NiftiDocument = new NiftiDocument(uri, data);
     return document;
   }