Initial project import

node_modules/three-stdlib/loaders/NRRDLoader.js

@@ -0,0 +1,403 @@
+import { Loader, FileLoader, Vector3, Matrix4 } from "three";
+import { gunzipSync } from "fflate";
+import { Volume } from "../misc/Volume.js";
+class NRRDLoader extends Loader {
+  constructor(manager) {
+    super(manager);
+  }
+  load(url, onLoad, onProgress, onError) {
+    const scope = this;
+    const loader = new FileLoader(scope.manager);
+    loader.setPath(scope.path);
+    loader.setResponseType("arraybuffer");
+    loader.setRequestHeader(scope.requestHeader);
+    loader.setWithCredentials(scope.withCredentials);
+    loader.load(
+      url,
+      function(data) {
+        try {
+          onLoad(scope.parse(data));
+        } catch (e) {
+          if (onError) {
+            onError(e);
+          } else {
+            console.error(e);
+          }
+          scope.manager.itemError(url);
+        }
+      },
+      onProgress,
+      onError
+    );
+  }
+  parse(data) {
+    let _data = data;
+    let _dataPointer = 0;
+    const _nativeLittleEndian = new Int8Array(new Int16Array([1]).buffer)[0] > 0;
+    const _littleEndian = true;
+    const headerObject = {};
+    function scan(type, chunks) {
+      if (chunks === void 0 || chunks === null) {
+        chunks = 1;
+      }
+      let _chunkSize = 1;
+      let _array_type = Uint8Array;
+      switch (type) {
+        case "uchar":
+          break;
+        case "schar":
+          _array_type = Int8Array;
+          break;
+        case "ushort":
+          _array_type = Uint16Array;
+          _chunkSize = 2;
+          break;
+        case "sshort":
+          _array_type = Int16Array;
+          _chunkSize = 2;
+          break;
+        case "uint":
+          _array_type = Uint32Array;
+          _chunkSize = 4;
+          break;
+        case "sint":
+          _array_type = Int32Array;
+          _chunkSize = 4;
+          break;
+        case "float":
+          _array_type = Float32Array;
+          _chunkSize = 4;
+          break;
+        case "complex":
+          _array_type = Float64Array;
+          _chunkSize = 8;
+          break;
+        case "double":
+          _array_type = Float64Array;
+          _chunkSize = 8;
+          break;
+      }
+      let _bytes2 = new _array_type(_data.slice(_dataPointer, _dataPointer += chunks * _chunkSize));
+      if (_nativeLittleEndian != _littleEndian) {
+        _bytes2 = flipEndianness(_bytes2, _chunkSize);
+      }
+      if (chunks == 1) {
+        return _bytes2[0];
+      }
+      return _bytes2;
+    }
+    function flipEndianness(array, chunkSize) {
+      const u8 = new Uint8Array(array.buffer, array.byteOffset, array.byteLength);
+      for (let i2 = 0; i2 < array.byteLength; i2 += chunkSize) {
+        for (let j = i2 + chunkSize - 1, k = i2; j > k; j--, k++) {
+          const tmp = u8[k];
+          u8[k] = u8[j];
+          u8[j] = tmp;
+        }
+      }
+      return array;
+    }
+    function parseHeader(header) {
+      let data2, field, fn, i2, l, m, _i, _len;
+      const lines = header.split(/\r?\n/);
+      for (_i = 0, _len = lines.length; _i < _len; _i++) {
+        l = lines[_i];
+        if (l.match(/NRRD\d+/)) {
+          headerObject.isNrrd = true;
+        } else if (l.match(/^#/))
+          ;
+        else if (m = l.match(/(.*):(.*)/)) {
+          field = m[1].trim();
+          data2 = m[2].trim();
+          fn = _fieldFunctions[field];
+          if (fn) {
+            fn.call(headerObject, data2);
+          } else {
+            headerObject[field] = data2;
+          }
+        }
+      }
+      if (!headerObject.isNrrd) {
+        throw new Error("Not an NRRD file");
+      }
+      if (headerObject.encoding === "bz2" || headerObject.encoding === "bzip2") {
+        throw new Error("Bzip is not supported");
+      }
+      if (!headerObject.vectors) {
+        headerObject.vectors = [new Vector3(1, 0, 0), new Vector3(0, 1, 0), new Vector3(0, 0, 1)];
+        if (headerObject.spacings) {
+          for (i2 = 0; i2 <= 2; i2++) {
+            if (!isNaN(headerObject.spacings[i2])) {
+              headerObject.vectors[i2].multiplyScalar(headerObject.spacings[i2]);
+            }
+          }
+        }
+      }
+    }
+    function parseDataAsText(data2, start, end) {
+      let number = "";
+      start = start || 0;
+      end = end || data2.length;
+      let value;
+      const lengthOfTheResult = headerObject.sizes.reduce(function(previous, current) {
+        return previous * current;
+      }, 1);
+      let base = 10;
+      if (headerObject.encoding === "hex") {
+        base = 16;
+      }
+      const result = new headerObject.__array(lengthOfTheResult);
+      let resultIndex = 0;
+      let parsingFunction = parseInt;
+      if (headerObject.__array === Float32Array || headerObject.__array === Float64Array) {
+        parsingFunction = parseFloat;
+      }
+      for (let i2 = start; i2 < end; i2++) {
+        value = data2[i2];
+        if ((value < 9 || value > 13) && value !== 32) {
+          number += String.fromCharCode(value);
+        } else {
+          if (number !== "") {
+            result[resultIndex] = parsingFunction(number, base);
+            resultIndex++;
+          }
+          number = "";
+        }
+      }
+      if (number !== "") {
+        result[resultIndex] = parsingFunction(number, base);
+        resultIndex++;
+      }
+      return result;
+    }
+    const _bytes = scan("uchar", data.byteLength);
+    const _length = _bytes.length;
+    let _header = null;
+    let _data_start = 0;
+    let i;
+    for (i = 1; i < _length; i++) {
+      if (_bytes[i - 1] == 10 && _bytes[i] == 10) {
+        _header = this.parseChars(_bytes, 0, i - 2);
+        _data_start = i + 1;
+        break;
+      }
+    }
+    parseHeader(_header);
+    _data = _bytes.subarray(_data_start);
+    if (headerObject.encoding.substring(0, 2) === "gz") {
+      _data = gunzipSync(new Uint8Array(_data));
+    } else if (headerObject.encoding === "ascii" || headerObject.encoding === "text" || headerObject.encoding === "txt" || headerObject.encoding === "hex") {
+      _data = parseDataAsText(_data);
+    } else if (headerObject.encoding === "raw") {
+      const _copy = new Uint8Array(_data.length);
+      for (let i2 = 0; i2 < _data.length; i2++) {
+        _copy[i2] = _data[i2];
+      }
+      _data = _copy;
+    }
+    _data = _data.buffer;
+    const volume = new Volume();
+    volume.header = headerObject;
+    volume.data = new headerObject.__array(_data);
+    const min_max = volume.computeMinMax();
+    const min = min_max[0];
+    const max = min_max[1];
+    volume.windowLow = min;
+    volume.windowHigh = max;
+    volume.dimensions = [headerObject.sizes[0], headerObject.sizes[1], headerObject.sizes[2]];
+    volume.xLength = volume.dimensions[0];
+    volume.yLength = volume.dimensions[1];
+    volume.zLength = volume.dimensions[2];
+    const spacingX = new Vector3(
+      headerObject.vectors[0][0],
+      headerObject.vectors[0][1],
+      headerObject.vectors[0][2]
+    ).length();
+    const spacingY = new Vector3(
+      headerObject.vectors[1][0],
+      headerObject.vectors[1][1],
+      headerObject.vectors[1][2]
+    ).length();
+    const spacingZ = new Vector3(
+      headerObject.vectors[2][0],
+      headerObject.vectors[2][1],
+      headerObject.vectors[2][2]
+    ).length();
+    volume.spacing = [spacingX, spacingY, spacingZ];
+    volume.matrix = new Matrix4();
+    let _spaceX = 1;
+    let _spaceY = 1;
+    const _spaceZ = 1;
+    if (headerObject.space == "left-posterior-superior") {
+      _spaceX = -1;
+      _spaceY = -1;
+    } else if (headerObject.space === "left-anterior-superior") {
+      _spaceX = -1;
+    }
+    if (!headerObject.vectors) {
+      volume.matrix.set(_spaceX, 0, 0, 0, 0, _spaceY, 0, 0, 0, 0, _spaceZ, 0, 0, 0, 0, 1);
+    } else {
+      const v = headerObject.vectors;
+      volume.matrix.set(
+        _spaceX * v[0][0],
+        _spaceX * v[1][0],
+        _spaceX * v[2][0],
+        0,
+        _spaceY * v[0][1],
+        _spaceY * v[1][1],
+        _spaceY * v[2][1],
+        0,
+        _spaceZ * v[0][2],
+        _spaceZ * v[1][2],
+        _spaceZ * v[2][2],
+        0,
+        0,
+        0,
+        0,
+        1
+      );
+    }
+    volume.inverseMatrix = new Matrix4();
+    volume.inverseMatrix.copy(volume.matrix).invert();
+    volume.RASDimensions = new Vector3(volume.xLength, volume.yLength, volume.zLength).applyMatrix4(volume.matrix).round().toArray().map(Math.abs);
+    if (volume.lowerThreshold === -Infinity) {
+      volume.lowerThreshold = min;
+    }
+    if (volume.upperThreshold === Infinity) {
+      volume.upperThreshold = max;
+    }
+    return volume;
+  }
+  parseChars(array, start, end) {
+    if (start === void 0) {
+      start = 0;
+    }
+    if (end === void 0) {
+      end = array.length;
+    }
+    let output = "";
+    let i = 0;
+    for (i = start; i < end; ++i) {
+      output += String.fromCharCode(array[i]);
+    }
+    return output;
+  }
+}
+const _fieldFunctions = {
+  type: function(data) {
+    switch (data) {
+      case "uchar":
+      case "unsigned char":
+      case "uint8":
+      case "uint8_t":
+        this.__array = Uint8Array;
+        break;
+      case "signed char":
+      case "int8":
+      case "int8_t":
+        this.__array = Int8Array;
+        break;
+      case "short":
+      case "short int":
+      case "signed short":
+      case "signed short int":
+      case "int16":
+      case "int16_t":
+        this.__array = Int16Array;
+        break;
+      case "ushort":
+      case "unsigned short":
+      case "unsigned short int":
+      case "uint16":
+      case "uint16_t":
+        this.__array = Uint16Array;
+        break;
+      case "int":
+      case "signed int":
+      case "int32":
+      case "int32_t":
+        this.__array = Int32Array;
+        break;
+      case "uint":
+      case "unsigned int":
+      case "uint32":
+      case "uint32_t":
+        this.__array = Uint32Array;
+        break;
+      case "float":
+        this.__array = Float32Array;
+        break;
+      case "double":
+        this.__array = Float64Array;
+        break;
+      default:
+        throw new Error("Unsupported NRRD data type: " + data);
+    }
+    return this.type = data;
+  },
+  endian: function(data) {
+    return this.endian = data;
+  },
+  encoding: function(data) {
+    return this.encoding = data;
+  },
+  dimension: function(data) {
+    return this.dim = parseInt(data, 10);
+  },
+  sizes: function(data) {
+    let i;
+    return this.sizes = function() {
+      const _ref = data.split(/\s+/);
+      const _results = [];
+      for (let _i = 0, _len = _ref.length; _i < _len; _i++) {
+        i = _ref[_i];
+        _results.push(parseInt(i, 10));
+      }
+      return _results;
+    }();
+  },
+  space: function(data) {
+    return this.space = data;
+  },
+  "space origin": function(data) {
+    return this.space_origin = data.split("(")[1].split(")")[0].split(",");
+  },
+  "space directions": function(data) {
+    let f, v;
+    const parts = data.match(/\(.*?\)/g);
+    return this.vectors = function() {
+      const _results = [];
+      for (let _i = 0, _len = parts.length; _i < _len; _i++) {
+        v = parts[_i];
+        _results.push(
+          function() {
+            const _ref = v.slice(1, -1).split(/,/);
+            const _results2 = [];
+            for (let _j = 0, _len2 = _ref.length; _j < _len2; _j++) {
+              f = _ref[_j];
+              _results2.push(parseFloat(f));
+            }
+            return _results2;
+          }()
+        );
+      }
+      return _results;
+    }();
+  },
+  spacings: function(data) {
+    let f;
+    const parts = data.split(/\s+/);
+    return this.spacings = function() {
+      const _results = [];
+      for (let _i = 0, _len = parts.length; _i < _len; _i++) {
+        f = parts[_i];
+        _results.push(parseFloat(f));
+      }
+      return _results;
+    }();
+  }
+};
+export {
+  NRRDLoader
+};
+//# sourceMappingURL=NRRDLoader.js.map