dcmjs 0.30.0 → 0.30.2

package/build/dcmjs.es.js

@@ -8468,6 +8468,11 @@ var ValueRepresentation = /*#__PURE__*/function () {
       }
       return vr;
     }
+  }, {
+    key: "parseUnknownVr",
+    value: function parseUnknownVr(type) {
+      return new ParsedUnknownValue(type);
+    }
   }]);
   return ValueRepresentation;
 }();
@@ -9534,60 +9539,108 @@ var UnknownValue = /*#__PURE__*/function (_BinaryRepresentation) {
   }
   return _createClass(UnknownValue);
 }(BinaryRepresentation);
-var OtherWordString = /*#__PURE__*/function (_BinaryRepresentation2) {
-  _inherits(OtherWordString, _BinaryRepresentation2);
-  var _super30 = _createSuper(OtherWordString);
-  function OtherWordString() {
+var ParsedUnknownValue = /*#__PURE__*/function (_BinaryRepresentation2) {
+  _inherits(ParsedUnknownValue, _BinaryRepresentation2);
+  var _super30 = _createSuper(ParsedUnknownValue);
+  function ParsedUnknownValue(vr) {
     var _this29;
-    _classCallCheck(this, OtherWordString);
-    _this29 = _super30.call(this, "OW");
+    _classCallCheck(this, ParsedUnknownValue);
+    _this29 = _super30.call(this, vr);
     _this29.maxLength = null;
-    _this29.padByte = PADDING_NULL;
+    _this29.padByte = 0;
     _this29.noMultiple = true;
+    _this29._isBinary = true;
+    _this29._allowMultiple = false;
+    _this29._isExplicit = true;
     return _this29;
   }
-  return _createClass(OtherWordString);
+  _createClass(ParsedUnknownValue, [{
+    key: "read",
+    value: function read(stream, length, syntax) {
+      var arrayBuffer = this.readBytes(stream, length, syntax)[0];
+      var streamFromBuffer = new ReadBufferStream(arrayBuffer, true);
+      var vr = ValueRepresentation.createByTypeString(this.type);
+      var values = [];
+      if (vr.isBinary() && length > vr.maxLength && !vr.noMultiple) {
+        var times = length / vr.maxLength,
+          i = 0;
+        while (i++ < times) {
+          values.push(vr.read(streamFromBuffer, vr.maxLength, syntax));
+        }
+      } else {
+        var val = vr.read(streamFromBuffer, length, syntax);
+        if (!vr.isBinary() && singleVRs$1.indexOf(vr.type) == -1) {
+          values = val;
+          if (typeof val === "string") {
+            values = val.split(String.fromCharCode(VM_DELIMITER));
+          }
+        } else if (vr.type == "SQ") {
+          values = val;
+        } else if (vr.type == "OW" || vr.type == "OB") {
+          values = val;
+        } else {
+          Array.isArray(val) ? values = val : values.push(val);
+        }
+      }
+      return values;
+    }
+  }]);
+  return ParsedUnknownValue;
 }(BinaryRepresentation);
-var OtherByteString = /*#__PURE__*/function (_BinaryRepresentation3) {
-  _inherits(OtherByteString, _BinaryRepresentation3);
-  var _super31 = _createSuper(OtherByteString);
-  function OtherByteString() {
+var OtherWordString = /*#__PURE__*/function (_BinaryRepresentation3) {
+  _inherits(OtherWordString, _BinaryRepresentation3);
+  var _super31 = _createSuper(OtherWordString);
+  function OtherWordString() {
     var _this30;
-    _classCallCheck(this, OtherByteString);
-    _this30 = _super31.call(this, "OB");
+    _classCallCheck(this, OtherWordString);
+    _this30 = _super31.call(this, "OW");
     _this30.maxLength = null;
     _this30.padByte = PADDING_NULL;
     _this30.noMultiple = true;
     return _this30;
   }
-  return _createClass(OtherByteString);
+  return _createClass(OtherWordString);
 }(BinaryRepresentation);
-var OtherDoubleString = /*#__PURE__*/function (_BinaryRepresentation4) {
-  _inherits(OtherDoubleString, _BinaryRepresentation4);
-  var _super32 = _createSuper(OtherDoubleString);
-  function OtherDoubleString() {
+var OtherByteString = /*#__PURE__*/function (_BinaryRepresentation4) {
+  _inherits(OtherByteString, _BinaryRepresentation4);
+  var _super32 = _createSuper(OtherByteString);
+  function OtherByteString() {
     var _this31;
-    _classCallCheck(this, OtherDoubleString);
-    _this31 = _super32.call(this, "OD");
+    _classCallCheck(this, OtherByteString);
+    _this31 = _super32.call(this, "OB");
     _this31.maxLength = null;
     _this31.padByte = PADDING_NULL;
     _this31.noMultiple = true;
     return _this31;
   }
-  return _createClass(OtherDoubleString);
+  return _createClass(OtherByteString);
 }(BinaryRepresentation);
-var OtherFloatString = /*#__PURE__*/function (_BinaryRepresentation5) {
-  _inherits(OtherFloatString, _BinaryRepresentation5);
-  var _super33 = _createSuper(OtherFloatString);
-  function OtherFloatString() {
+var OtherDoubleString = /*#__PURE__*/function (_BinaryRepresentation5) {
+  _inherits(OtherDoubleString, _BinaryRepresentation5);
+  var _super33 = _createSuper(OtherDoubleString);
+  function OtherDoubleString() {
     var _this32;
-    _classCallCheck(this, OtherFloatString);
-    _this32 = _super33.call(this, "OF");
+    _classCallCheck(this, OtherDoubleString);
+    _this32 = _super33.call(this, "OD");
     _this32.maxLength = null;
     _this32.padByte = PADDING_NULL;
     _this32.noMultiple = true;
     return _this32;
   }
+  return _createClass(OtherDoubleString);
+}(BinaryRepresentation);
+var OtherFloatString = /*#__PURE__*/function (_BinaryRepresentation6) {
+  _inherits(OtherFloatString, _BinaryRepresentation6);
+  var _super34 = _createSuper(OtherFloatString);
+  function OtherFloatString() {
+    var _this33;
+    _classCallCheck(this, OtherFloatString);
+    _this33 = _super34.call(this, "OF");
+    _this33.maxLength = null;
+    _this33.padByte = PADDING_NULL;
+    _this33.noMultiple = true;
+    return _this33;
+  }
   return _createClass(OtherFloatString);
 }(BinaryRepresentation); // these VR instances are precreate and are reused for each requested vr/tag
 var VRinstances = {
@@ -10213,7 +10266,12 @@ var DicomMessage = /*#__PURE__*/function () {
         vr = ValueRepresentation.createByTypeString(vrType);
       } else {
         vrType = stream.readVR();
-        vr = ValueRepresentation.createByTypeString(vrType);
+        if (vrType === "UN" && DicomMessage.lookupTag(tag) && DicomMessage.lookupTag(tag).vr) {
+          vrType = DicomMessage.lookupTag(tag).vr;
+          vr = ValueRepresentation.parseUnknownVr(vrType);
+        } else {
+          vr = ValueRepresentation.createByTypeString(vrType);
+        }
         if (vr.isExplicit()) {
           stream.increment(2);
           length = stream.readUint32();
@@ -17410,13 +17468,18 @@ function generateToolState$1(imageIds, arrayBuffer, metadataProvider) {
   var imagePlaneModule = metadataProvider.get("imagePlaneModule", imageIds[0]);
   var generalSeriesModule = metadataProvider.get("generalSeriesModule", imageIds[0]);
   var SeriesInstanceUID = generalSeriesModule.seriesInstanceUID;
-  if (!imagePlaneModule) {
-    console.warn("Insufficient metadata, imagePlaneModule missing.");
-  }
-  var ImageOrientationPatient = Array.isArray(imagePlaneModule.rowCosines) ? [].concat(_toConsumableArray(imagePlaneModule.rowCosines), _toConsumableArray(imagePlaneModule.columnCosines)) : [imagePlaneModule.rowCosines.x, imagePlaneModule.rowCosines.y, imagePlaneModule.rowCosines.z, imagePlaneModule.columnCosines.x, imagePlaneModule.columnCosines.y, imagePlaneModule.columnCosines.z];
+  var ImageOrientationPatient;
+  var validOrientations;
+  var hasCoordinateSystem = ("FrameOfReferenceUID" in multiframe);
+  if (hasCoordinateSystem) {
+    if (!imagePlaneModule) {
+      console.warn("Insufficient metadata, imagePlaneModule missing.");
+    }
+    ImageOrientationPatient = Array.isArray(imagePlaneModule.rowCosines) ? [].concat(_toConsumableArray(imagePlaneModule.rowCosines), _toConsumableArray(imagePlaneModule.columnCosines)) : [imagePlaneModule.rowCosines.x, imagePlaneModule.rowCosines.y, imagePlaneModule.rowCosines.z, imagePlaneModule.columnCosines.x, imagePlaneModule.columnCosines.y, imagePlaneModule.columnCosines.z];
 
-  // Get IOP from ref series, compute supported orientations:
-  var validOrientations = getValidOrientations(ImageOrientationPatient);
+    // Get IOP from ref series, compute supported orientations:
+    validOrientations = getValidOrientations(ImageOrientationPatient);
+  }
   var sliceLength = multiframe.Columns * multiframe.Rows;
   var segMetadata = getSegmentMetadata(multiframe, SeriesInstanceUID);
   var TransferSyntaxUID = multiframe._meta.TransferSyntaxUID.Value[0];
@@ -17434,7 +17497,12 @@ function generateToolState$1(imageIds, arrayBuffer, metadataProvider) {
       throw new Error("Fractional segmentations are not yet supported");
     }
   }
-  var orientation = checkOrientation(multiframe, validOrientations, [imagePlaneModule.rows, imagePlaneModule.columns, imageIds.length], tolerance);
+  var orientation;
+  if (hasCoordinateSystem) {
+    orientation = checkOrientation(multiframe, validOrientations, [imagePlaneModule.rows, imagePlaneModule.columns, imageIds.length], tolerance);
+  } else {
+    orientation = "Planar";
+  }
   var overlapping = false;
   if (!skipOverlapping) {
     overlapping = checkSEGsOverlapping(pixelData, multiframe, imageIds, validOrientations, metadataProvider, tolerance);
@@ -17505,9 +17573,7 @@ function findReferenceSourceImageId(multiframe, frameSegment, imageIds, metadata
     return imageId;
   }
   var frameSourceImageSequence = undefined;
-  if (SourceImageSequence && SourceImageSequence.length !== 0) {
-    frameSourceImageSequence = SourceImageSequence[frameSegment];
-  } else if (PerFrameFunctionalGroup.DerivationImageSequence) {
+  if (PerFrameFunctionalGroup.DerivationImageSequence) {
     var DerivationImageSequence = PerFrameFunctionalGroup.DerivationImageSequence;
     if (Array.isArray(DerivationImageSequence)) {
       if (DerivationImageSequence.length !== 0) {
@@ -17526,6 +17592,8 @@ function findReferenceSourceImageId(multiframe, frameSegment, imageIds, metadata
         }
       }
     }
+  } else if (SourceImageSequence && SourceImageSequence.length !== 0) {
+    frameSourceImageSequence = SourceImageSequence[frameSegment];
   }
   if (frameSourceImageSequence) {
     imageId = getImageIdOfSourceImagebySourceImageSequence(frameSourceImageSequence, imageIds, metadataProvider);
@@ -17603,9 +17671,15 @@ function checkSEGsOverlapping(pixelData, multiframe, imageIds, validOrientations
       for (var i = 0; i < role.length; ++i) {
         var _frameSegment = role[i];
         var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[_frameSegment];
-        var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
         var pixelDataI2D = ndarray$1(new Uint8Array(pixelData.buffer, _frameSegment * sliceLength, sliceLength), [Rows, Columns]);
-        var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+        var alignedPixelDataI = void 0;
+        var hasCoordinateSystem = ("FrameOfReferenceUID" in multiframe);
+        if (hasCoordinateSystem) {
+          var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+          alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+        } else {
+          alignedPixelDataI = pixelDataI2D;
+        }
         if (!alignedPixelDataI) {
           console.warn("Individual SEG frames are out of plane with respect to the first SEG frame, this is not yet supported, skipping this frame.");
           continue;
@@ -17668,9 +17742,15 @@ function insertOverlappingPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray,
         i = _i2;
         return "continue";
       }
-      var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
       var pixelDataI2D = ndarray$1(new Uint8Array(pixelData.buffer, _i2 * sliceLength, sliceLength), [Rows, Columns]);
-      var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+      var alignedPixelDataI = void 0;
+      var hasCoordinateSystem = ("FrameOfReferenceUID" in multiframe);
+      if (hasCoordinateSystem) {
+        var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+        alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+      } else {
+        alignedPixelDataI = pixelDataI2D;
+      }
       if (!alignedPixelDataI) {
         throw new Error("Individual SEG frames are out of plane with respect to the first SEG frame. " + "This is not yet supported. Aborting segmentation loading.");
       }
@@ -17680,8 +17760,8 @@ function insertOverlappingPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray,
         i = _i2;
         return "continue";
       }
-      var sourceImageMetadata = metadataProvider.get("instance", imageId);
-      if (Rows !== sourceImageMetadata.Rows || Columns !== sourceImageMetadata.Columns) {
+      var sourceImageMetadata = metadataProvider.get("imagePixelModule", imageId);
+      if (Rows !== sourceImageMetadata.rows || Columns !== sourceImageMetadata.columns) {
         throw new Error("Individual SEG frames have different geometry dimensions (Rows and Columns) " + "respect to the source image reference frame. This is not yet supported. " + "Aborting segmentation loading. ");
       }
       var imageIdIndex = imageIds.findIndex(function (element) {
@@ -17751,9 +17831,15 @@ function insertPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray, labelmapBu
   var sliceLength = Columns * Rows;
   var _loop5 = function _loop5(groupsLen, _i3) {
     var PerFrameFunctionalGroups = PerFrameFunctionalGroupsSequence[_i3];
-    var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
     var pixelDataI2D = ndarray$1(new Uint8Array(pixelData.buffer, _i3 * sliceLength, sliceLength), [Rows, Columns]);
-    var alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+    var alignedPixelDataI = void 0;
+    var hasCoordinateSystem = ("FrameOfReferenceUID" in multiframe);
+    if (hasCoordinateSystem) {
+      var ImageOrientationPatientI = sharedImageOrientationPatient || PerFrameFunctionalGroups.PlaneOrientationSequence.ImageOrientationPatient;
+      alignedPixelDataI = alignPixelDataWithSourceData(pixelDataI2D, ImageOrientationPatientI, validOrientations, tolerance);
+    } else {
+      alignedPixelDataI = pixelDataI2D;
+    }
     if (!alignedPixelDataI) {
       throw new Error("Individual SEG frames are out of plane with respect to the first SEG frame. " + "This is not yet supported. Aborting segmentation loading.");
     }
@@ -17766,8 +17852,8 @@ function insertPixelDataPlanar(segmentsOnFrame, segmentsOnFrameArray, labelmapBu
       console.warn("Image not present in stack, can't import frame : " + _i3 + ".");
       return "continue";
     }
-    var sourceImageMetadata = metadataProvider.get("instance", imageId);
-    if (Rows !== sourceImageMetadata.Rows || Columns !== sourceImageMetadata.Columns) {
+    var sourceImageMetadata = metadataProvider.get("imagePixelModule", imageId);
+    if (Rows !== sourceImageMetadata.rows || Columns !== sourceImageMetadata.columns) {
       throw new Error("Individual SEG frames have different geometry dimensions (Rows and Columns) " + "respect to the source image reference frame. This is not yet supported. " + "Aborting segmentation loading. ");
     }
     var imageIdIndex = imageIds.findIndex(function (element) {