@abasb75/dicom-parser 0.0.0-test20 → 0.0.0-test21

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Files changed (11) hide show
  1. package/Dataset.d.ts +3 -0
  2. package/Dataset.js +27 -0
  3. package/Parser.d.ts +1 -0
  4. package/Parser.js +27 -7
  5. package/Value.js +0 -1
  6. package/package.json +1 -1
  7. package/types.d.ts +2 -1
  8. package/utils/PaletteColor.js +13 -17
  9. package/utils/PixelData.d.ts +1 -0
  10. package/utils/PixelData.js +25 -5
  11. package/tsconfig.tsbuildinfo +0 -1
package/Dataset.d.ts CHANGED
@@ -1,5 +1,7 @@
1
1
  import { DicomDate, DicomPatientModule, DicomPixelModule, DicomScalingModule, DicomTime, DicomVOILutModule, Tags } from "./types";
2
2
  declare class Dataset {
3
+ static Float: string;
4
+ static Integer: string;
3
5
  /** duration of parse */
4
6
  start: number;
5
7
  end: number | undefined;
@@ -25,6 +27,7 @@ declare class Dataset {
25
27
  scalingModule: DicomScalingModule;
26
28
  constructor(tags: Tags, dataView: DataView, littleEndian: boolean, start: number, end: number);
27
29
  hasPixelData(): boolean;
30
+ getPixelTypes(): string | null;
28
31
  getPixelData(frame?: number): Promise<DataView>;
29
32
  getVOILutModule(): DicomVOILutModule;
30
33
  getPatientModule(): DicomPatientModule;
package/Dataset.js CHANGED
@@ -201,6 +201,21 @@ var Dataset = /** @class */ (function () {
201
201
  return false;
202
202
  }
203
203
  });
204
+ Object.defineProperty(Dataset.prototype, "getPixelTypes", {
205
+ enumerable: false,
206
+ configurable: true,
207
+ writable: true,
208
+ value: function () {
209
+ if (this.tags['0x7FE00008']
210
+ || this.tags['0x7FE00009']) {
211
+ return Dataset.Float;
212
+ }
213
+ else if (this.tags['0x7FE00010']) {
214
+ return Dataset.Integer;
215
+ }
216
+ return null;
217
+ }
218
+ });
204
219
  Object.defineProperty(Dataset.prototype, "getPixelData", {
205
220
  enumerable: false,
206
221
  configurable: true,
@@ -443,6 +458,18 @@ var Dataset = /** @class */ (function () {
443
458
  return Tag.intTo4digitString(input);
444
459
  }
445
460
  });
461
+ Object.defineProperty(Dataset, "Float", {
462
+ enumerable: true,
463
+ configurable: true,
464
+ writable: true,
465
+ value: "Float"
466
+ });
467
+ Object.defineProperty(Dataset, "Integer", {
468
+ enumerable: true,
469
+ configurable: true,
470
+ writable: true,
471
+ value: "Integer"
472
+ });
446
473
  return Dataset;
447
474
  }());
448
475
  export default Dataset;
package/Parser.d.ts CHANGED
@@ -5,6 +5,7 @@ declare class Parser {
5
5
  private end;
6
6
  private arrayBuffer;
7
7
  private offset;
8
+ private startOfset;
8
9
  private dataView;
9
10
  private tags;
10
11
  private dataSet;
package/Parser.js CHANGED
@@ -28,6 +28,12 @@ var Parser = /** @class */ (function () {
28
28
  writable: true,
29
29
  value: void 0
30
30
  });
31
+ Object.defineProperty(this, "startOfset", {
32
+ enumerable: true,
33
+ configurable: true,
34
+ writable: true,
35
+ value: 132
36
+ });
31
37
  Object.defineProperty(this, "dataView", {
32
38
  enumerable: true,
33
39
  configurable: true,
@@ -124,12 +130,11 @@ var Parser = /** @class */ (function () {
124
130
  this.offset = 132;
125
131
  }
126
132
  else {
127
- // in some image (128 empty byte and DICM) does not exist.
128
- // const {group} = this.getNextGroupAndElement();
129
- // if(group!==0x0002){
130
- // return;
131
- // }
132
133
  this.offset = 0;
134
+ while (Value.getString(this.dataView.buffer.slice(this.offset, this.offset + 1)) === "") {
135
+ this.offset++;
136
+ }
137
+ this.startOfset = this.offset;
133
138
  }
134
139
  this.parse();
135
140
  }
@@ -177,7 +182,8 @@ var Parser = /** @class */ (function () {
177
182
  if (!this.implicit && group !== 0x0002 && this.IMPLICT_TRANSFER_SYNTAXES.includes(this.transferSyntaxUID)) {
178
183
  this.implicit = true;
179
184
  }
180
- if (this.littleEndian && group !== 0x0002 && this.BIG_ENDIAN_TRANSFER_SYNTAXES.includes(this.transferSyntaxUID)) {
185
+ if (this.littleEndian && group !== 0x0002
186
+ && this.BIG_ENDIAN_TRANSFER_SYNTAXES.includes(this.transferSyntaxUID)) {
181
187
  this.littleEndian = false;
182
188
  }
183
189
  if (!this.inflated && group !== 0x0002 && this.DEFLATED_TRANSFER_SYNTAXES.includes(this.transferSyntaxUID)) {
@@ -206,7 +212,7 @@ var Parser = /** @class */ (function () {
206
212
  this.offset += 2;
207
213
  }
208
214
  else if ((!vr || !vr.match(/^[A-Z]{2}$/)) && group === 0x0002 && element === 0x0000) {
209
- this.offset = 132;
215
+ this.offset = this.startOfset;
210
216
  this.tags = {};
211
217
  this.implicit = true;
212
218
  continue;
@@ -219,6 +225,20 @@ var Parser = /** @class */ (function () {
219
225
  if (group === 0x0002 && element === 0x0010) {
220
226
  this.transferSyntaxUID = (Value.getString(new Uint8Array(this.arrayBuffer, this.offset, len))).replace('\0', '');
221
227
  }
228
+ // find dataset thats may be as big endian dicom.
229
+ // if(
230
+ // this.littleEndian
231
+ // && Object.keys(tags)?.length===0
232
+ // && len > this.dataView.byteLength
233
+ // ){
234
+ // console.log({group,element,len,vr});
235
+ // this.littleEndian =false;
236
+ // this.offset = this.startOfset;
237
+ // return this.getElements();
238
+ // }else{
239
+ // console.log({group,element,len,vr});
240
+ // return tags;
241
+ // }
222
242
  var tag = new Tag(group, element, vr, len, this.offset);
223
243
  if (len === 0xFFFFFFFF && group === 0x7FE0 && element === 0x0010) {
224
244
  var _b = this.getNextGroupAndElement(), group_1 = _b.group, element_1 = _b.element;
package/Value.js CHANGED
@@ -132,7 +132,6 @@ var Value = /** @class */ (function () {
132
132
  if (littleEndian === void 0) { littleEndian = true; }
133
133
  if (len === 2) {
134
134
  var value = dataView.getUint16(offset, littleEndian);
135
- console.log({ littleEndian: littleEndian, value: value, v: dataView.getUint16(offset + 2, littleEndian) });
136
135
  return value;
137
136
  }
138
137
  else if (len > 2) {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@abasb75/dicom-parser",
3
- "version": "0.0.0-test20",
3
+ "version": "0.0.0-test21",
4
4
  "description": "a javascript powerfull dicom parser",
5
5
  "main": "index.js",
6
6
  "type": "module",
package/types.d.ts CHANGED
@@ -82,10 +82,11 @@ interface PixelDataDecodeOptions {
82
82
  dataset?: Dataset;
83
83
  }
84
84
  interface PaletteColorDataColor {
85
- data: number[];
85
+ data: Uint8Array[] | Uint16Array[];
86
86
  firstInputValueMapped: number;
87
87
  lutEntries: number;
88
88
  bitsPerEntry: number;
89
+ littleEndian: boolean;
89
90
  }
90
91
  interface PaletteColorData {
91
92
  red: PaletteColorDataColor | undefined;
package/utils/PaletteColor.js CHANGED
@@ -11,10 +11,10 @@ var PaletteColor = /** @class */ (function () {
11
11
  return undefined;
12
12
  }
13
13
  var littleEndian = dataset.littleEndian;
14
- var red = PaletteColor.getData(redPaletteColorLookupTableDescriptor, redPaletteColorLookupTableData, segmentedRedPaletteColorLookupTableData, bitsAllocated, littleEndian);
15
- var green = PaletteColor.getData(greenPaletteColorLookupTableDescriptor, greenPaletteColorLookupTableData, segmentedGreenPaletteColorLookupTableData, bitsAllocated, littleEndian);
16
- var blue = PaletteColor.getData(bluePaletteColorLookupTableDescriptor, bluePaletteColorLookupTableData, segmentedBluePaletteColorLookupTableData, bitsAllocated, littleEndian);
17
- var alpha = PaletteColor.getData(alphaPaletteColorLookupTableDescriptor, alphaPaletteColorLookupTableData, segmentedAlphaPaletteColorLookupTableData, bitsAllocated, littleEndian);
14
+ var red = PaletteColor.getData(redPaletteColorLookupTableDescriptor, redPaletteColorLookupTableData, segmentedRedPaletteColorLookupTableData, littleEndian);
15
+ var green = PaletteColor.getData(greenPaletteColorLookupTableDescriptor, greenPaletteColorLookupTableData, segmentedGreenPaletteColorLookupTableData, littleEndian);
16
+ var blue = PaletteColor.getData(bluePaletteColorLookupTableDescriptor, bluePaletteColorLookupTableData, segmentedBluePaletteColorLookupTableData, littleEndian);
17
+ var alpha = PaletteColor.getData(alphaPaletteColorLookupTableDescriptor, alphaPaletteColorLookupTableData, segmentedAlphaPaletteColorLookupTableData, littleEndian);
18
18
  return {
19
19
  red: red,
20
20
  green: green,
@@ -27,7 +27,7 @@ var PaletteColor = /** @class */ (function () {
27
27
  enumerable: false,
28
28
  configurable: true,
29
29
  writable: true,
30
- value: function (descriptor, paletteData, segmentedPaletteData, bitsAllocated, littleEndian) {
30
+ value: function (descriptor, paletteData, segmentedPaletteData, littleEndian) {
31
31
  var _a;
32
32
  if (!Array.isArray(descriptor)
33
33
  || descriptor.length < 3) {
@@ -42,12 +42,12 @@ var PaletteColor = /** @class */ (function () {
42
42
  }
43
43
  if (paletteData) {
44
44
  tableDataArray = bitsPerEntry === 16
45
- ? PaletteColor.get16Array(paletteData, bitsAllocated, littleEndian)
45
+ ? PaletteColor.get16Array(paletteData, littleEndian)
46
46
  : PaletteColor.get8Array(paletteData);
47
47
  }
48
48
  else if (segmentedPaletteData) {
49
49
  var segmentedTableDataArray = bitsPerEntry === 16
50
- ? PaletteColor.get16Array(segmentedPaletteData, bitsAllocated, littleEndian)
50
+ ? PaletteColor.get16Array(segmentedPaletteData, littleEndian)
51
51
  : PaletteColor.get8Array(segmentedPaletteData);
52
52
  tableDataArray = (_a = PaletteColor.segmentedDataToData(segmentedTableDataArray, lutEntries)) === null || _a === void 0 ? void 0 : _a.tableData;
53
53
  }
@@ -58,7 +58,8 @@ var PaletteColor = /** @class */ (function () {
58
58
  data: tableDataArray,
59
59
  firstInputValueMapped: firstInputValueMapped,
60
60
  lutEntries: lutEntries,
61
- bitsPerEntry: bitsPerEntry
61
+ bitsPerEntry: bitsPerEntry,
62
+ littleEndian: littleEndian,
62
63
  };
63
64
  }
64
65
  });
@@ -66,15 +67,10 @@ var PaletteColor = /** @class */ (function () {
66
67
  enumerable: false,
67
68
  configurable: true,
68
69
  writable: true,
69
- value: function (paletteData, bitsAllocated, littleEndian) {
70
+ value: function (paletteData, littleEndian) {
70
71
  var array = [];
71
72
  for (var i = 0; i < paletteData.byteLength; i += 2) {
72
- if (bitsAllocated === 8) {
73
- array.push(paletteData.getUint16(i, littleEndian) >> 8);
74
- }
75
- else {
76
- array.push(paletteData.getUint16(i, littleEndian));
77
- }
73
+ array.push(paletteData.getUint16(i, littleEndian));
78
74
  }
79
75
  return array;
80
76
  }
@@ -116,7 +112,7 @@ var PaletteColor = /** @class */ (function () {
116
112
  segmentedDataOffset++;
117
113
  tableDataOffset++;
118
114
  }
119
- lastValue = tableData[segmentedDataOffset - 1] & 0xFFFF;
115
+ lastValue = tableData[segmentedDataOffset - 1] & 0xffff;
120
116
  break;
121
117
  case 1:
122
118
  if (typeof lastValue !== "number") {
@@ -128,7 +124,7 @@ var PaletteColor = /** @class */ (function () {
128
124
  tableData[tableDataOffset] = (lastValue + ((newValue - lastValue) / len));
129
125
  tableDataOffset++;
130
126
  }
131
- lastValue = newValue & 0xFFFF;
127
+ lastValue = newValue & 0xffff;
132
128
  break;
133
129
  case 2: // untested
134
130
  if (typeof lastValue !== "number") {
package/utils/PixelData.d.ts CHANGED
@@ -9,5 +9,6 @@ declare class PixelData {
9
9
  private static _isJPEG;
10
10
  private static _isJPEG2000;
11
11
  private static _makeFragments;
12
+ private static bitToByte;
12
13
  }
13
14
  export default PixelData;
package/utils/PixelData.js CHANGED
@@ -57,6 +57,7 @@ var PixelData = /** @class */ (function () {
57
57
  configurable: true,
58
58
  writable: true,
59
59
  value: function (dataset, frameIndex) {
60
+ var _a;
60
61
  var pixelDataElement = dataset.tags['0x7FE00010'] || dataset.tags['0x7FE00008'] || dataset.tags['0x7FE00009'];
61
62
  if (!pixelDataElement) {
62
63
  throw new Error("dicom has not pixels");
@@ -66,7 +67,19 @@ var PixelData = /** @class */ (function () {
66
67
  return PixelData._encapsulatePixelDatas(dataset, pixelDataElement, frameIndex);
67
68
  }
68
69
  else {
69
- var frameLen = pixelDataElement.valueLength / numberOfFrames;
70
+ var _b = dataset === null || dataset === void 0 ? void 0 : dataset.pixelModule, columns = _b.columns, rows = _b.rows, samplesPerPixel = _b.samplesPerPixel, bitsAllocated = _b.bitsAllocated;
71
+ var frameLen = 0;
72
+ if ((_a = dataset.pixelModule) === null || _a === void 0 ? void 0 : _a.numberOfFrames) {
73
+ frameLen = pixelDataElement.valueLength / numberOfFrames;
74
+ }
75
+ else if (columns && rows && samplesPerPixel && bitsAllocated) {
76
+ var bytesAllocated = PixelData.bitToByte(bitsAllocated);
77
+ frameLen = rows * columns * bytesAllocated * samplesPerPixel;
78
+ }
79
+ else {
80
+ frameLen = pixelDataElement.valueLength / numberOfFrames;
81
+ }
82
+ frameLen = Math.min(frameLen, pixelDataElement.valueLength);
70
83
  var offset = pixelDataElement.offset + (frameLen * frameIndex);
71
84
  return new DataView(dataset.dataView.buffer.slice(offset, offset + frameLen));
72
85
  }
@@ -179,7 +192,6 @@ var PixelData = /** @class */ (function () {
179
192
  if (PixelData._isJPEG(fragment.offset + 8, dataset.dataView)
180
193
  || PixelData._isJPEG2000(fragment.offset + 8, dataset.dataView)) {
181
194
  basicOffsetTable.push(fragment.offset);
182
- console.log('magics is jpeg/jpeg2000');
183
195
  }
184
196
  }
185
197
  return basicOffsetTable;
@@ -204,10 +216,8 @@ var PixelData = /** @class */ (function () {
204
216
  writable: true,
205
217
  value: function (position, dataView) {
206
218
  var magics2 = [0xFF, 0x4F, 0xFF, 0x51];
207
- console.log('magics2', magics2);
208
219
  for (var i = 0; i < magics2.length; i++) {
209
220
  var finded = dataView.getUint8(position + i);
210
- console.log(finded);
211
221
  if (finded !== magics2[i]) {
212
222
  break;
213
223
  }
@@ -237,7 +247,6 @@ var PixelData = /** @class */ (function () {
237
247
  var offset = basicOffsetIndex;
238
248
  var dataView = dataset.dataView;
239
249
  while (true) {
240
- console.log(offset, dataView.byteLength);
241
250
  if (offset >= dataView.byteLength) {
242
251
  break;
243
252
  }
@@ -260,6 +269,17 @@ var PixelData = /** @class */ (function () {
260
269
  return fragments;
261
270
  }
262
271
  });
272
+ Object.defineProperty(PixelData, "bitToByte", {
273
+ enumerable: false,
274
+ configurable: true,
275
+ writable: true,
276
+ value: function (bit) {
277
+ if (bit <= 8) {
278
+ return bit / 8;
279
+ }
280
+ return Math.ceil(bit / 8);
281
+ }
282
+ });
263
283
  return PixelData;
264
284
  }());
265
285
  export default PixelData;
package/tsconfig.tsbuildinfo DELETED
@@ -1 +0,0 @@
1
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