ami.js
Version:
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414 lines (354 loc) • 13.4 kB
JavaScript
;
THREE.TRKLoader = function() {};
Object.assign(THREE.TRKLoader.prototype, THREE.EventDispatcher.prototype, {
constructor: THREE.TRKLoader,
load: function(url, onLoad, onProgress, onError) {
window.console.log(url, onLoad, onProgress, onError);
var scope = this;
var xhr = new XMLHttpRequest();
function onloaded(event) {
if (event.target.status === 200 || event.target.status === 0) {
var geometry = scope.parse(event.target.response || event.target.responseText);
scope.dispatchEvent({
type: 'load',
content: geometry,
});
if (onLoad) {
onLoad(geometry);
}
} else {
scope.dispatchEvent({
type: 'error',
message: 'Couldn\'t load URL [' + url + ']',
response: event.target.statusText,
});
}
}
xhr.addEventListener('load', onloaded, false);
xhr.addEventListener('progress', function(event) {
scope.dispatchEvent({
type: 'progress',
loaded: event.loaded,
total: event.total,
});
}, false);
xhr.addEventListener('error', function() {
scope.dispatchEvent({
type: 'error',
message: 'Couldn\'t load URL [' + url + ']',
});
}, false);
if (xhr.overrideMimeType) {
xhr.overrideMimeType('text/plain; charset=x-user-defined');
}
xhr.open('GET', url, true);
xhr.responseType = 'arraybuffer';
xhr.send(null);
},
littleEndian: function() {
var buffer = new ArrayBuffer(2);
new DataView(buffer).setInt16(0, 256, true);
return new Int16Array(buffer)[0] === 256;
},
scan: function(type, chunks, offset, data) {
window.console.log(type, chunks, offset, data);
},
parse: function(data) {
var littleEndian = this.littleEndian();
var reader = new DataView(data);
// String.fromCharCode
// str.charCodeAt(position)
// ////////////////////////////////////////////
//
// parse all trk header
// http://msdn.microsoft.com/en-us/library/s3f49ktz.aspx
//
// ////////////////////////////////////////////
var offset = 0;
var header = {};
// id_string[6]
// char
// 6
// ID string for track file. The first 5 characters must be "TRACK".
header.ID_STRING = [];
for (var i = 0; i < 6; i++) {
header.ID_STRING.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
// dim[3]
// short int
// 6
// Dimension of the image volume.
header.dim = [];
for (var q = 0; q < 3; q++) {
header.dim.push(reader.getInt16(offset, littleEndian));
offset += 2;
}
// voxel_size[3]
// float
// 12
// Voxel size of the image volume.
header.VOXEL_SIZE = [];
for (var r = 0; r < 3; r++) {
header.VOXEL_SIZE.push(reader.getFloat32(offset, littleEndian));
offset += 4;
}
// origin[3]
// float
// 12
// Origin of the image volume. This field is not yet being used by TrackVis. That means the origin is always (0, 0, 0).
header.origin = [];
for (var s = 0; s < 3; s++) {
header.origin.push(reader.getFloat32(offset, littleEndian));
offset += 4;
}
// n_scalars
// short int
// 2
// Number of scalars saved at each track point (besides x, y and z coordinates).
header.N_SCALARS = [];
for (var t = 0; t < 1; t++) {
header.N_SCALARS.push(reader.getInt16(offset, littleEndian));
offset += 2;
}
// scalar_name[10][20]
// char
// 200
// Name of each scalar. Can not be longer than 20 characters each. Can only store up to 10 names.
header.SCALAR_NAME = [];
for (var u = 0; u < 10; u++) {
header.SCALAR_NAME.push([]);
for (var v = 0; v < 20; v++) {
header.SCALAR_NAME[u].push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
}
// n_propertiess
// short int
// 2
// Number of properties saved at each track.
header.N_PROPERTIES = [];
for (var x = 0; x < 1; x++) {
header.N_PROPERTIES.push(reader.getInt16(offset, littleEndian));
offset += 2;
}
// scalar_name[10][20]
// char
// 200
// Name of each scalar. Can not be longer than 20 characters each. Can only store up to 10 names.
header.PROPERTY_NAME = [];
for (var y = 0; y < 10; y++) {
header.PROPERTY_NAME.push([]);
for (var z = 0; z < 20; z++) {
header.PROPERTY_NAME[y].push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
}
// vox_to_ras[4][4]
// float
// 64
// 4x4 matrix for voxel to RAS (crs to xyz) transformation. If vox_to_ras[3][3] is 0, it means the matrix is not recorded. This field is added from version 2.
header.VOX_TO_RAS = [];
for (var a = 0; a < 4; a++) {
header.VOX_TO_RAS.push([]);
for (var b = 0; b < 4; b++) {
header.VOX_TO_RAS[a].push(reader.getFloat32(offset));
offset += 4;
}
}
// reserved[444]
// char
// 444
// Reserved space for future version.
offset += 444;
// voxel_order[4]
// char
// 4
// Storing order of the original image data.
header.VOXEL_ORDER = [];
for (var c = 0; c < 4; c++) {
header.VOXEL_ORDER.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
// pad2[4]
// char
// 4
// Paddings.
header.pad2 = [];
for (var d = 0; d < 4; d++) {
header.pad2.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
// image_orientation_patient[6]
// float
// 24
// Image orientation of the original image. As defined in the DICOM header.
header.IMAGE_ORIENTATION_PATIENT = [];
for (var e = 0; e < 6; e++) {
header.IMAGE_ORIENTATION_PATIENT.push(reader.getFloat32(offset, littleEndian));
offset += 4;
}
// pad1[2]
// char
// 2
// Paddings.
header.pad1 = [];
for (var f = 0; f < 2; f++) {
header.pad2.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
// invert_x, invert_y, invert_z, swap_xy, swap_yz, swap_zx
// unsigned_char
// 1
// Inversion/rotation flags used to generate this track file. For internal use only.
header.INVERT_X = [];
for (var g = 0; g < 1; g++) {
header.INVERT_X.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
header.INVERT_Y = [];
for (var h = 0; h < 1; h++) {
header.INVERT_Y.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
header.INVERT_Z = [];
for (var ii = 0; ii < 1; ii++) {
header.INVERT_Z.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
header.SWAP_XY = [];
for (var ij = 0; ij < 1; ij++) {
header.SWAP_XY.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
header.SWAP_YZ = [];
for (var ik = 0; ik < 1; ik++) {
header.SWAP_YZ.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
header.SWAP_ZX = [];
for (var il = 0; il < 1; il++) {
header.SWAP_ZX.push(String.fromCharCode(reader.getUint8(offset)));
offset++;
}
// n_count
// int
// 4
// Number of tracks stored in this track file. 0 means the number was NOT stored.
header.N_COUNT = [];
for (var im = 0; im < 1; im++) {
header.N_COUNT.push(reader.getUint32(offset, littleEndian));
offset += 4;
}
// version
// int
// 4
// Version number. Current version is 2.
header.version = [];
for (var io = 0; io < 1; io++) {
header.version.push(reader.getUint32(offset, littleEndian));
offset += 4;
}
// hdr_size
// int
// 4
// Size of the header. Used to determine byte swap. Should be 1000.
header.HDR_SIZE = [];
for (var ip = 0; ip < 1; ip++) {
header.HDR_SIZE.push(reader.getUint32(offset, littleEndian));
offset += 4;
}
window.console.log(header);
// /////////////////////////////////////
//
// parse the tracts now...!
//
// ////////////////////////////////////
// we should also store each track length
// get the number of points in this track
var tracks = [];
while (offset < reader.byteLength) {
var nbPoints = -1;
nbPoints = reader.getUint32(offset, littleEndian);
offset += 4;
var track = {
'points': [],
'scalars': [],
'properties': [],
'geometry': new THREE.Geometry(),
'xProperties': {},
};
var length = 0;
for (var k = 0; k < nbPoints; k++) {
// first 3 floats are the coordinates
track.points[k] = [];
track.points[k].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.points[k].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.points[k].push(reader.getFloat32(offset, littleEndian));
offset += 4;
// add geometry
//
track.geometry.vertices.push(new THREE.Vector3(track.points[k][0], track.points[k][1], track.points[k][2]));
// then the scalars
track.scalars[k] = [];
for (var l = 0; l < header.N_SCALARS[0]; l++) {
track.scalars[k][l] = [];
track.scalars[k][l].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.scalars[k][l].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.scalars[k][l].push(reader.getFloat32(offset, littleEndian));
offset += 4;
}
if (k !== 0) {
// get previous and current points
var prev = track.points[k - 1];
var cur = track.points[k];
var xDist = cur[0] - prev[0];
var yDist = cur[1] - prev[1];
var zDist = cur[2] - prev[2];
// get distance
var distance = Math.sqrt(Math.pow(xDist, 2) + Math.pow(yDist, 2) + Math.pow(zDist, 2));
// add add to length
length += distance;
}
}
track.xProperties.length = length;
for (var p = 0; p < nbPoints; p++) {
// get previous point if any
var first = track.points[0];
if (p > 1) {
first = track.points[p - 1];
}
// get next point if any
var last = track.points[nbPoints - 1];
if (p < nbPoints - 2) {
last = track.points[p + 1];
}
var diff = [Math.abs(last[0] - first[0]),
Math.abs(last[1] - first[1]),
Math.abs(last[2] - first[2]),
];
var colordistance = Math.sqrt(diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2]);
diff[0] /= colordistance;
diff[1] /= colordistance;
diff[2] /= colordistance;
track.geometry.colors.push(new THREE.Color(diff[0], diff[1], diff[2]));
}
// get the property of this track
for (var o = 0; o < header.N_PROPERTIES[0]; o++) {
track.properties[o] = [];
track.properties[o].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.properties[o].push(reader.getFloat32(offset, littleEndian));
offset += 4;
track.properties[o].push(reader.getFloat32(offset, littleEndian));
offset += 4;
}
tracks.push(track);
}
return tracks;
},
});