import {Index} from '../math/index';
import {Point3D} from '../math/point';
import {logger} from '../utils/logger';
import {getTypedArray} from '../dicom/dicomParser';
import {ListenerHandler} from '../utils/listen';
import {colourRange} from './iterator';
import {RescaleSlopeAndIntercept} from './rsi';
import {ImageFactory} from './imageFactory';
import {MaskFactory} from './maskFactory';
// doc imports
/* eslint-disable no-unused-vars */
import {Geometry} from './geometry';
import {Matrix33} from '../math/matrix';
/* eslint-enable no-unused-vars */
/**
* Get the slice index of an input slice into a volume geometry.
*
* @param {Geometry} volumeGeometry The volume geometry.
* @param {Geometry} sliceGeometry The slice geometry.
* @returns {Index} The index of the slice in the volume geomtry.
*/
function getSliceIndex(volumeGeometry, sliceGeometry) {
// possible time
const timeId = sliceGeometry.getInitialTime();
// index values
const values = [];
// x, y
values.push(0);
values.push(0);
// z
values.push(volumeGeometry.getSliceIndex(sliceGeometry.getOrigin(), timeId));
// time
if (typeof timeId !== 'undefined') {
values.push(timeId);
}
// return index
return new Index(values);
}
/**
* Create an Image from DICOM elements.
*
* @param {object} elements The DICOM elements.
* @returns {Image} The Image object.
*/
export function createImage(elements) {
const factory = new ImageFactory();
return factory.create(
elements,
elements['7FE00010'].value[0],
1
);
}
/**
* Create a mask Image from DICOM elements.
*
* @param {object} elements The DICOM elements.
* @returns {Image} The mask Image object.
*/
export function createMaskImage(elements) {
const factory = new MaskFactory();
return factory.create(
elements,
elements['7FE00010'].value[0]
);
}
/**
* Image class.
* Usable once created, optional are:
* - rescale slope and intercept (default 1:0),
* - photometric interpretation (default MONOCHROME2),
* - planar configuration (default RGBRGB...).
*
* @example
* // XMLHttpRequest onload callback
* const onload = function (event) {
* // parse the dicom buffer
* const dicomParser = new dwv.DicomParser();
* dicomParser.parse(event.target.response);
* // create the image object
* const image = dwv.createImage(dicomParser.getDicomElements());
* // result div
* const div = document.getElementById('dwv');
* // display the image size
* const size = image.getGeometry().getSize();
* div.appendChild(document.createTextNode(
* 'Size: ' + size.toString() +
* ' (should be 256,256,1)'));
* // break line
* div.appendChild(document.createElement('br'));
* // display a pixel value
* div.appendChild(document.createTextNode(
* 'Pixel @ [128,40,0]: ' +
* image.getRescaledValue(128,40,0) +
* ' (should be 101)'));
* };
* // DICOM file request
* const request = new XMLHttpRequest();
* const url = 'https://raw.githubusercontent.com/ivmartel/dwv/master/tests/data/bbmri-53323851.dcm';
* request.open('GET', url);
* request.responseType = 'arraybuffer';
* request.onload = onload;
* request.send();
*/
export class Image {
/**
* Data geometry.
*
* @type {Geometry}
*/
#geometry;
/**
* List of compatible typed arrays.
*
* @typedef {(
* Uint8Array | Int8Array |
* Uint16Array | Int16Array |
* Uint32Array | Int32Array
* )} TypedArray
*/
/**
* Data buffer.
*
* @type {TypedArray}
*/
#buffer;
/**
* Image UIDs.
*
* @type {Array}
*/
#imageUids;
/**
* Constant rescale slope and intercept (default).
*
* @type {object}
*/
#rsi = new RescaleSlopeAndIntercept(1, 0);
/**
* Varying rescale slope and intercept.
*
* @type {Array}
*/
#rsis = null;
/**
* Flag to know if the RSIs are all identity (1,0).
*
* @type {boolean}
*/
#isIdentityRSI = true;
/**
* Flag to know if the RSIs are all equals.
*
* @type {boolean}
*/
#isConstantRSI = true;
/**
* Photometric interpretation (MONOCHROME, RGB...).
*
* @type {string}
*/
#photometricInterpretation = 'MONOCHROME2';
/**
* Planar configuration for RGB data (0:RGBRGBRGBRGB... or
* 1:RRR...GGG...BBB...).
*
* @type {number}
*/
#planarConfiguration = 0;
/**
* Number of components.
*
* @type {number}
*/
#numberOfComponents;
/**
* Meta information.
*
* @type {object}
*/
#meta = {};
/**
* Data range.
*
* @type {object}
*/
#dataRange = null;
/**
* Rescaled data range.
*
* @type {object}
*/
#rescaledDataRange = null;
/**
* Histogram.
*
* @type {Array}
*/
#histogram = null;
/**
* Listener handler.
*
* @type {object}
*/
#listenerHandler = new ListenerHandler();
/**
* @param {Geometry} geometry The geometry of the image.
* @param {TypedArray} buffer The image data as a one dimensional buffer.
* @param {Array} [imageUids] An array of Uids indexed to slice number.
*/
constructor(geometry, buffer, imageUids) {
this.#geometry = geometry;
this.#buffer = buffer;
this.#imageUids = imageUids;
this.#numberOfComponents = this.#buffer.length / (
this.#geometry.getSize().getTotalSize());
}
/**
* Get the image UID at a given index.
*
* @param {Index} [index] The index at which to get the id.
* @returns {string} The UID.
*/
getImageUid(index) {
let uid = this.#imageUids[0];
if (this.#imageUids.length !== 1 && typeof index !== 'undefined') {
uid = this.#imageUids[this.getSecondaryOffset(index)];
}
return uid;
}
/**
* Get the geometry of the image.
*
* @returns {Geometry} The geometry.
*/
getGeometry() {
return this.#geometry;
}
/**
* Get the data buffer of the image.
*
* @todo dangerous...
* @returns {TypedArray} The data buffer of the image.
*/
getBuffer() {
return this.#buffer;
}
/**
* Can the image values be quantified?
*
* @returns {boolean} True if only one component.
*/
canQuantify() {
return this.getNumberOfComponents() === 1;
}
/**
* Can window and level be applied to the data?
*
* @returns {boolean} True if the data is monochrome.
*/
canWindowLevel() {
return this.getPhotometricInterpretation()
.match(/MONOCHROME/) !== null;
}
/**
* Can the data be scrolled?
*
* @param {Matrix33} viewOrientation The view orientation.
* @returns {boolean} True if the data has a third dimension greater than one
* after applying the view orientation.
*/
canScroll(viewOrientation) {
const size = this.getGeometry().getSize();
// also check the numberOfFiles in case we are in the middle of a load
let nFiles = 1;
if (typeof this.#meta.numberOfFiles !== 'undefined') {
nFiles = this.#meta.numberOfFiles;
}
return size.canScroll(viewOrientation) || nFiles !== 1;
}
/**
* Get the secondary offset max.
*
* @returns {number} The maximum offset.
*/
#getSecondaryOffsetMax() {
return this.#geometry.getSize().getTotalSize(2);
}
/**
* Get the secondary offset: an offset that takes into account
* the slice and above dimension numbers.
*
* @param {Index} index The index.
* @returns {number} The offset.
*/
getSecondaryOffset(index) {
return this.#geometry.getSize().indexToOffset(index, 2);
}
/**
* Get the rescale slope and intercept.
*
* @param {Index} [index] The index (only needed for non constant rsi).
* @returns {object} The rescale slope and intercept.
*/
getRescaleSlopeAndIntercept(index) {
let res = this.#rsi;
if (!this.isConstantRSI()) {
if (typeof index === 'undefined') {
throw new Error('Cannot get non constant RSI with empty slice index.');
}
const offset = this.getSecondaryOffset(index);
if (typeof this.#rsis[offset] !== 'undefined') {
res = this.#rsis[offset];
} else {
logger.warn('undefined non constant rsi at ' + offset);
}
}
return res;
}
/**
* Get the rsi at a specified (secondary) offset.
*
* @param {number} offset The desired (secondary) offset.
* @returns {object} The coresponding rsi.
*/
#getRescaleSlopeAndInterceptAtOffset(offset) {
return this.#rsis[offset];
}
/**
* Set the rescale slope and intercept.
*
* @param {object} inRsi The input rescale slope and intercept.
* @param {number} [offset] The rsi offset (only needed for non constant rsi).
*/
setRescaleSlopeAndIntercept(inRsi, offset) {
// update identity flag
this.#isIdentityRSI = this.#isIdentityRSI && inRsi.isID();
// update constant flag
if (!this.#isConstantRSI) {
if (typeof offset === 'undefined') {
throw new Error(
'Cannot store non constant RSI with empty slice index.');
}
this.#rsis.splice(offset, 0, inRsi);
} else {
if (!this.#rsi.equals(inRsi)) {
if (typeof offset === 'undefined') {
// no slice index, replace existing
this.#rsi = inRsi;
} else {
// first non constant rsi
this.#isConstantRSI = false;
// switch to non constant mode
this.#rsis = [];
// initialise RSIs
for (let i = 0, leni = this.#getSecondaryOffsetMax(); i < leni; ++i) {
this.#rsis.push(i);
}
// store
this.#rsi = null;
this.#rsis.splice(offset, 0, inRsi);
}
}
}
}
/**
* Are all the RSIs identity (1,0).
*
* @returns {boolean} True if they are.
*/
isIdentityRSI() {
return this.#isIdentityRSI;
}
/**
* Are all the RSIs equal.
*
* @returns {boolean} True if they are.
*/
isConstantRSI() {
return this.#isConstantRSI;
}
/**
* Get the photometricInterpretation of the image.
*
* @returns {string} The photometricInterpretation of the image.
*/
getPhotometricInterpretation() {
return this.#photometricInterpretation;
}
/**
* Set the photometricInterpretation of the image.
*
* @param {string} interp The photometricInterpretation of the image.
*/
setPhotometricInterpretation(interp) {
this.#photometricInterpretation = interp;
}
/**
* Get the planarConfiguration of the image.
*
* @returns {number} The planarConfiguration of the image.
*/
getPlanarConfiguration() {
return this.#planarConfiguration;
}
/**
* Set the planarConfiguration of the image.
*
* @param {number} config The planarConfiguration of the image.
*/
setPlanarConfiguration(config) {
this.#planarConfiguration = config;
}
/**
* Get the numberOfComponents of the image.
*
* @returns {number} The numberOfComponents of the image.
*/
getNumberOfComponents() {
return this.#numberOfComponents;
}
/**
* Get the meta information of the image.
*
* @returns {object} The meta information of the image.
*/
getMeta() {
return this.#meta;
}
/**
* Set the meta information of the image.
*
* @param {object} rhs The meta information of the image.
*/
setMeta(rhs) {
this.#meta = rhs;
}
/**
* Get value at offset. Warning: No size check...
*
* @param {number} offset The desired offset.
* @returns {number} The value at offset.
*/
getValueAtOffset(offset) {
return this.#buffer[offset];
}
/**
* Get the offsets where the buffer equals the input value.
* Loops through the whole volume, can get long for big data...
*
* @param {number|object} value The value to check.
* @returns {Array} The list of offsets.
*/
getOffsets(value) {
// value to array
if (this.#numberOfComponents === 1) {
value = [value];
} else if (this.#numberOfComponents === 3 &&
typeof value.r !== 'undefined') {
value = [value.r, value.g, value.b];
}
// main loop
const offsets = [];
let equal;
for (let i = 0; i < this.#buffer.length; i = i + this.#numberOfComponents) {
equal = true;
for (let j = 0; j < this.#numberOfComponents; ++j) {
if (this.#buffer[i + j] !== value[j]) {
equal = false;
break;
}
}
if (equal) {
offsets.push(i);
}
}
return offsets;
}
/**
* Check if the input values are in the buffer.
* Could loop through the whole volume, can get long for big data...
*
* @param {Array} values The values to check.
* @returns {Array} A list of booleans for each input value,
* set to true if the value is present in the buffer.
*/
hasValues(values) {
// check input
if (typeof values === 'undefined' ||
values.length === 0) {
return [];
}
// final array value
const finalValues = [];
for (let v1 = 0; v1 < values.length; ++v1) {
if (this.#numberOfComponents === 1) {
finalValues.push([values[v1]]);
} else if (this.#numberOfComponents === 3) {
finalValues.push([
values[v1].r,
values[v1].g,
values[v1].b
]);
}
}
// find callback
let equalFunc;
if (this.#numberOfComponents === 1) {
equalFunc = function (a, b) {
return a[0] === b[0];
};
} else if (this.#numberOfComponents === 3) {
equalFunc = function (a, b) {
return a[0] === b[0] &&
a[1] === b[1] &&
a[2] === b[2];
};
}
const getEqualCallback = function (value) {
return function (item) {
return equalFunc(item, value);
};
};
// main loop
const res = new Array(values.length);
res.fill(false);
const valuesToFind = finalValues.slice();
let equal;
let indicesToRemove;
for (let i = 0, leni = this.#buffer.length;
i < leni; i = i + this.#numberOfComponents) {
indicesToRemove = [];
for (let v = 0; v < valuesToFind.length; ++v) {
equal = true;
// check value(s)
for (let j = 0; j < this.#numberOfComponents; ++j) {
if (this.#buffer[i + j] !== valuesToFind[v][j]) {
equal = false;
break;
}
}
// if found, store answer and add to indices to remove
if (equal) {
const valIndex = finalValues.findIndex(
getEqualCallback(valuesToFind[v]));
res[valIndex] = true;
indicesToRemove.push(v);
}
}
// remove found values
for (let r = 0; r < indicesToRemove.length; ++r) {
valuesToFind.splice(indicesToRemove[r], 1);
}
// exit if no values to find
if (valuesToFind.length === 0) {
break;
}
}
// return
return res;
}
/**
* Clone the image.
*
* @returns {Image} A clone of this image.
*/
clone() {
// clone the image buffer
const clonedBuffer = this.#buffer.slice(0);
// create the image copy
const copy = new Image(this.getGeometry(), clonedBuffer, this.#imageUids);
// copy the RSI(s)
if (this.isConstantRSI()) {
copy.setRescaleSlopeAndIntercept(this.getRescaleSlopeAndIntercept());
} else {
for (let i = 0; i < this.#getSecondaryOffsetMax(); ++i) {
copy.setRescaleSlopeAndIntercept(
this.#getRescaleSlopeAndInterceptAtOffset(i), i);
}
}
// copy extras
copy.setPhotometricInterpretation(this.getPhotometricInterpretation());
copy.setPlanarConfiguration(this.getPlanarConfiguration());
copy.setMeta(this.getMeta());
// return
return copy;
}
/**
* Re-allocate buffer memory to an input size.
*
* @param {number} size The new size.
*/
#realloc(size) {
// save buffer
let tmpBuffer = this.#buffer;
// create new
this.#buffer = getTypedArray(
this.#buffer.BYTES_PER_ELEMENT * 8,
this.#meta.IsSigned ? 1 : 0,
size);
if (this.#buffer === null) {
throw new Error('Cannot reallocate data for image.');
}
// put old in new
this.#buffer.set(tmpBuffer);
// clean
tmpBuffer = null;
}
/**
* Append a slice to the image.
*
* @param {Image} rhs The slice to append.
*/
appendSlice(rhs) {
// check input
if (rhs === null) {
throw new Error('Cannot append null slice');
}
const rhsSize = rhs.getGeometry().getSize();
let size = this.#geometry.getSize();
if (rhsSize.get(2) !== 1) {
throw new Error('Cannot append more than one slice');
}
if (size.get(0) !== rhsSize.get(0)) {
throw new Error('Cannot append a slice with different number of columns');
}
if (size.get(1) !== rhsSize.get(1)) {
throw new Error('Cannot append a slice with different number of rows');
}
if (!this.#geometry.getOrientation().equals(
rhs.getGeometry().getOrientation(), 0.0001)) {
throw new Error('Cannot append a slice with different orientation');
}
if (this.#photometricInterpretation !==
rhs.getPhotometricInterpretation()) {
throw new Error(
'Cannot append a slice with different photometric interpretation');
}
// all meta should be equal
for (const key in this.#meta) {
if (key === 'windowPresets' || key === 'numberOfFiles' ||
key === 'custom') {
continue;
}
if (this.#meta[key] !== rhs.getMeta()[key]) {
throw new Error('Cannot append a slice with different ' + key);
}
}
// possible time
const timeId = rhs.getGeometry().getInitialTime();
// append frame if needed
let isNewFrame = false;
if (typeof timeId !== 'undefined' &&
!this.#geometry.hasSlicesAtTime(timeId)) {
// update grometry
this.appendFrame(timeId, rhs.getGeometry().getOrigin());
// update size
size = this.#geometry.getSize();
// update flag
isNewFrame = true;
}
// get slice index
const index = getSliceIndex(this.#geometry, rhs.getGeometry());
// calculate slice size
const sliceSize = this.#numberOfComponents * size.getDimSize(2);
// create full buffer if not done yet
if (typeof this.#meta.numberOfFiles === 'undefined') {
throw new Error('Missing number of files for buffer manipulation.');
}
const fullBufferSize = sliceSize * this.#meta.numberOfFiles;
if (this.#buffer.length !== fullBufferSize) {
this.#realloc(fullBufferSize);
}
// slice index
const sliceIndex = index.get(2);
// slice index including possible 4D
let fullSliceIndex = sliceIndex;
if (typeof timeId !== 'undefined') {
fullSliceIndex +=
this.#geometry.getCurrentNumberOfSlicesBeforeTime(timeId);
}
// offset of the input slice
const indexOffset = fullSliceIndex * sliceSize;
const maxOffset =
this.#geometry.getCurrentTotalNumberOfSlices() * sliceSize;
// move content if needed
if (indexOffset < maxOffset) {
this.#buffer.set(
this.#buffer.subarray(indexOffset, maxOffset),
indexOffset + sliceSize
);
}
// add new slice content
this.#buffer.set(rhs.getBuffer(), indexOffset);
// update geometry
if (!isNewFrame) {
this.#geometry.appendOrigin(
rhs.getGeometry().getOrigin(), sliceIndex, timeId);
}
// update rsi
// (rhs should just have one rsi)
this.setRescaleSlopeAndIntercept(
rhs.getRescaleSlopeAndIntercept(), fullSliceIndex);
// current number of images
const numberOfImages = this.#imageUids.length;
// insert sop instance UIDs
this.#imageUids.splice(fullSliceIndex, 0, rhs.getImageUid());
// update window presets
if (typeof this.#meta.windowPresets !== 'undefined') {
const windowPresets = this.#meta.windowPresets;
const rhsPresets = rhs.getMeta().windowPresets;
const keys = Object.keys(rhsPresets);
let pkey = null;
for (let i = 0; i < keys.length; ++i) {
pkey = keys[i];
const rhsPreset = rhsPresets[pkey];
const windowPreset = windowPresets[pkey];
if (typeof windowPreset !== 'undefined') {
// if not set or false, check perslice
if (typeof windowPreset.perslice === 'undefined' ||
windowPreset.perslice === false) {
// if different preset.wl, mark it as perslice
if (!windowPreset.wl[0].equals(rhsPreset.wl[0])) {
windowPreset.perslice = true;
// fill wl array with copy of wl[0]
// (loop on number of images minus the existing one)
for (let j = 0; j < numberOfImages - 1; ++j) {
windowPreset.wl.push(windowPreset.wl[0]);
}
}
}
// store (first) rhs preset.wl if needed
if (typeof windowPreset.perslice !== 'undefined' &&
windowPreset.perslice === true) {
windowPresets[pkey].wl.splice(
fullSliceIndex, 0, rhsPreset.wl[0]);
}
} else {
// if not defined (it should be), store all
windowPresets[pkey] = rhsPresets[pkey];
}
}
}
}
/**
* Append a frame buffer to the image.
*
* @param {object} frameBuffer The frame buffer to append.
* @param {number} frameIndex The frame index.
*/
appendFrameBuffer(frameBuffer, frameIndex) {
// create full buffer if not done yet
const size = this.#geometry.getSize();
const frameSize = this.#numberOfComponents * size.getDimSize(2);
if (typeof this.#meta.numberOfFiles === 'undefined') {
throw new Error('Missing number of files for frame buffer manipulation.');
}
const fullBufferSize = frameSize * this.#meta.numberOfFiles;
if (this.#buffer.length !== fullBufferSize) {
this.#realloc(fullBufferSize);
}
// check index
if (frameIndex >= this.#meta.numberOfFiles) {
logger.warn('Ignoring frame at index ' + frameIndex +
' (size: ' + this.#meta.numberOfFiles + ')');
return;
}
// append
this.#buffer.set(frameBuffer, frameSize * frameIndex);
// update geometry
this.appendFrame(frameIndex, new Point3D(0, 0, 0));
}
/**
* Append a frame to the image.
*
* @param {number} time The frame time value.
* @param {Point3D} origin The origin of the frame.
*/
appendFrame(time, origin) {
this.#geometry.appendFrame(origin, time);
this.#fireEvent({type: 'appendframe'});
// memory will be updated at the first appendSlice or appendFrameBuffer
}
/**
* Get the data range.
*
* @returns {object} The data range.
*/
getDataRange() {
if (!this.#dataRange) {
this.#dataRange = this.calculateDataRange();
}
return this.#dataRange;
}
/**
* Get the rescaled data range.
*
* @returns {object} The rescaled data range.
*/
getRescaledDataRange() {
if (!this.#rescaledDataRange) {
this.#rescaledDataRange = this.calculateRescaledDataRange();
}
return this.#rescaledDataRange;
}
/**
* Get the histogram.
*
* @returns {Array} The histogram.
*/
getHistogram() {
if (!this.#histogram) {
const res = this.calculateHistogram();
this.#dataRange = res.dataRange;
this.#rescaledDataRange = res.rescaledDataRange;
this.#histogram = res.histogram;
}
return this.#histogram;
}
/**
* Add an event listener to this class.
*
* @param {string} type The event type.
* @param {Function} callback The function associated with the provided
* event type, will be called with the fired event.
*/
addEventListener(type, callback) {
this.#listenerHandler.add(type, callback);
}
/**
* Remove an event listener from this class.
*
* @param {string} type The event type.
* @param {Function} callback The function associated with the provided
* event type.
*/
removeEventListener(type, callback) {
this.#listenerHandler.remove(type, callback);
}
/**
* Fire an event: call all associated listeners with the input event object.
*
* @param {object} event The event to fire.
*/
#fireEvent = (event) => {
this.#listenerHandler.fireEvent(event);
};
// ****************************************
// image data modifiers... carefull...
// ****************************************
/**
* Set the inner buffer values at given offsets.
*
* @param {Array} offsets List of offsets where to set the data.
* @param {object} value The value to set at the given offsets.
* @fires Image#imagechange
*/
setAtOffsets(offsets, value) {
let offset;
for (let i = 0, leni = offsets.length; i < leni; ++i) {
offset = offsets[i];
this.#buffer[offset] = value.r;
this.#buffer[offset + 1] = value.g;
this.#buffer[offset + 2] = value.b;
}
// fire imagechange
this.#fireEvent({type: 'imagechange'});
}
/**
* Set the inner buffer values at given offsets.
*
* @param {Array} offsetsLists List of offset lists where to set the data.
* @param {object} value The value to set at the given offsets.
* @returns {Array} A list of objects representing the original values before
* replacing them.
* @fires Image#imagechange
*/
setAtOffsetsAndGetOriginals(offsetsLists, value) {
const originalColoursLists = [];
// update and store
for (let j = 0; j < offsetsLists.length; ++j) {
const offsets = offsetsLists[j];
// first colour
let offset = offsets[0] * 3;
let previousColour = {
r: this.#buffer[offset],
g: this.#buffer[offset + 1],
b: this.#buffer[offset + 2]
};
// original value storage
const originalColours = [];
originalColours.push({
index: 0,
colour: previousColour
});
for (let i = 0; i < offsets.length; ++i) {
offset = offsets[i] * 3;
const currentColour = {
r: this.#buffer[offset],
g: this.#buffer[offset + 1],
b: this.#buffer[offset + 2]
};
// check if new colour
if (previousColour.r !== currentColour.r ||
previousColour.g !== currentColour.g ||
previousColour.b !== currentColour.b) {
// store new colour
originalColours.push({
index: i,
colour: currentColour
});
previousColour = currentColour;
}
// write update colour
this.#buffer[offset] = value.r;
this.#buffer[offset + 1] = value.g;
this.#buffer[offset + 2] = value.b;
}
originalColoursLists.push(originalColours);
}
// fire imagechange
this.#fireEvent({type: 'imagechange'});
return originalColoursLists;
}
/**
* Set the inner buffer values at given offsets.
*
* @param {Array} offsetsLists List of offset lists where to set the data.
* @param {object|Array} value The value to set at the given offsets.
* @fires Image#imagechange
*/
setAtOffsetsWithIterator(offsetsLists, value) {
for (let j = 0; j < offsetsLists.length; ++j) {
const offsets = offsetsLists[j];
let iterator;
if (typeof value !== 'undefined' &&
typeof value.r !== 'undefined') {
// input value is a simple color
iterator = colourRange(
[{index: 0, colour: value}], offsets.length);
} else {
// input value is a list of iterators
// created by setAtOffsetsAndGetOriginals
iterator = colourRange(
value[j], offsets.length);
}
// set values
let ival = iterator.next();
while (!ival.done) {
const offset = offsets[ival.index] * 3;
this.#buffer[offset] = ival.value.r;
this.#buffer[offset + 1] = ival.value.g;
this.#buffer[offset + 2] = ival.value.b;
ival = iterator.next();
}
}
/**
* Image change event.
*
* @event Image#imagechange
* @type {object}
*/
this.#fireEvent({type: 'imagechange'});
}
/**
* Get the value of the image at a specific coordinate.
*
* @param {number} i The X index.
* @param {number} j The Y index.
* @param {number} k The Z index.
* @param {number} f The frame number.
* @returns {number} The value at the desired position.
* Warning: No size check...
*/
getValue(i, j, k, f) {
const frame = (f || 0);
const index = new Index([i, j, k, frame]);
return this.getValueAtOffset(
this.getGeometry().getSize().indexToOffset(index));
}
/**
* Get the value of the image at a specific index.
*
* @param {Index} index The index.
* @returns {number} The value at the desired position.
* Warning: No size check...
*/
getValueAtIndex(index) {
return this.getValueAtOffset(
this.getGeometry().getSize().indexToOffset(index));
}
/**
* Get the rescaled value of the image at a specific position.
*
* @param {number} i The X index.
* @param {number} j The Y index.
* @param {number} k The Z index.
* @param {number} f The frame number.
* @returns {number} The rescaled value at the desired position.
* Warning: No size check...
*/
getRescaledValue(i, j, k, f) {
if (typeof f === 'undefined') {
f = 0;
}
let val = this.getValue(i, j, k, f);
if (!this.isIdentityRSI()) {
if (this.isConstantRSI()) {
val = this.getRescaleSlopeAndIntercept().apply(val);
} else {
const values = [i, j, k, f];
const index = new Index(values);
val = this.getRescaleSlopeAndIntercept(index).apply(val);
}
}
return val;
}
/**
* Get the rescaled value of the image at a specific index.
*
* @param {Index} index The index.
* @returns {number} The rescaled value at the desired position.
* Warning: No size check...
*/
getRescaledValueAtIndex(index) {
return this.getRescaledValueAtOffset(
this.getGeometry().getSize().indexToOffset(index)
);
}
/**
* Get the rescaled value of the image at a specific offset.
*
* @param {number} offset The desired offset.
* @returns {number} The rescaled value at the desired offset.
* Warning: No size check...
*/
getRescaledValueAtOffset(offset) {
let val = this.getValueAtOffset(offset);
if (!this.isIdentityRSI()) {
if (this.isConstantRSI()) {
val = this.getRescaleSlopeAndIntercept().apply(val);
} else {
const index = this.getGeometry().getSize().offsetToIndex(offset);
val = this.getRescaleSlopeAndIntercept(index).apply(val);
}
}
return val;
}
/**
* Calculate the data range of the image.
* WARNING: for speed reasons, only calculated on the first frame...
*
* @returns {object} The range {min, max}.
*/
calculateDataRange() {
let min = this.getValueAtOffset(0);
let max = min;
let value = 0;
const size = this.getGeometry().getSize();
let leni = size.getTotalSize();
// max to 3D
if (size.length() >= 3) {
leni = size.getDimSize(3);
}
for (let i = 0; i < leni; ++i) {
value = this.getValueAtOffset(i);
if (value > max) {
max = value;
}
if (value < min) {
min = value;
}
}
// return
return {min: min, max: max};
}
/**
* Calculate the rescaled data range of the image.
* WARNING: for speed reasons, only calculated on the first frame...
*
* @returns {object} The range {min, max}.
*/
calculateRescaledDataRange() {
if (this.isIdentityRSI()) {
return this.getDataRange();
} else if (this.isConstantRSI()) {
const range = this.getDataRange();
const resmin = this.getRescaleSlopeAndIntercept().apply(range.min);
const resmax = this.getRescaleSlopeAndIntercept().apply(range.max);
return {
min: ((resmin < resmax) ? resmin : resmax),
max: ((resmin > resmax) ? resmin : resmax)
};
} else {
let rmin = this.getRescaledValueAtOffset(0);
let rmax = rmin;
let rvalue = 0;
const size = this.getGeometry().getSize();
let leni = size.getTotalSize();
// max to 3D
if (size.length() === 3) {
leni = size.getDimSize(3);
}
for (let i = 0; i < leni; ++i) {
rvalue = this.getRescaledValueAtOffset(i);
if (rvalue > rmax) {
rmax = rvalue;
}
if (rvalue < rmin) {
rmin = rvalue;
}
}
// return
return {min: rmin, max: rmax};
}
}
/**
* Calculate the histogram of the image.
*
* @returns {object} The histogram, data range and rescaled data range.
*/
calculateHistogram() {
const size = this.getGeometry().getSize();
const histo = [];
let min = this.getValueAtOffset(0);
let max = min;
let value = 0;
let rmin = this.getRescaledValueAtOffset(0);
let rmax = rmin;
let rvalue = 0;
for (let i = 0, leni = size.getTotalSize(); i < leni; ++i) {
value = this.getValueAtOffset(i);
if (value > max) {
max = value;
}
if (value < min) {
min = value;
}
rvalue = this.getRescaledValueAtOffset(i);
if (rvalue > rmax) {
rmax = rvalue;
}
if (rvalue < rmin) {
rmin = rvalue;
}
histo[rvalue] = (histo[rvalue] || 0) + 1;
}
// set data range
const dataRange = {min: min, max: max};
const rescaledDataRange = {min: rmin, max: rmax};
// generate data for plotting
const histogram = [];
for (let b = rmin; b <= rmax; ++b) {
histogram.push([b, (histo[b] || 0)]);
}
// return
return {
dataRange: dataRange,
rescaledDataRange: rescaledDataRange,
histogram: histogram
};
}
/**
* Convolute the image with a given 2D kernel.
*
* Note: Uses raw buffer values.
*
* @param {Array} weights The weights of the 2D kernel as a 3x3 matrix.
* @returns {Image} The convoluted image.
*/
convolute2D(weights) {
if (weights.length !== 9) {
throw new Error(
'The convolution matrix does not have a length of 9; it has ' +
weights.length);
}
const newImage = this.clone();
const newBuffer = newImage.getBuffer();
const imgSize = this.getGeometry().getSize();
const dimOffset = imgSize.getDimSize(2) * this.getNumberOfComponents();
for (let k = 0; k < imgSize.get(2); ++k) {
this.convoluteBuffer(weights, newBuffer, k * dimOffset);
}
return newImage;
}
/**
* Convolute an image buffer with a given 2D kernel.
*
* Note: Uses raw buffer values.
*
* @param {Array} weights The weights of the 2D kernel as a 3x3 matrix.
* @param {TypedArray} buffer The buffer to convolute.
* @param {number} startOffset The index to start at.
*/
convoluteBuffer(
weights, buffer, startOffset) {
const imgSize = this.getGeometry().getSize();
const ncols = imgSize.get(0);
const nrows = imgSize.get(1);
const ncomp = this.getNumberOfComponents();
// number of component and planar configuration vars
let factor = 1;
let componentOffset = 1;
if (ncomp === 3) {
if (this.getPlanarConfiguration() === 0) {
factor = 3;
} else {
componentOffset = imgSize.getDimSize(2);
}
}
// allow special indent for matrices
/*jshint indent:false */
// default weight offset matrix
const wOff = [];
wOff[0] = (-ncols - 1) * factor;
wOff[1] = (-ncols) * factor;
wOff[2] = (-ncols + 1) * factor;
wOff[3] = -factor;
wOff[4] = 0;
wOff[5] = 1 * factor;
wOff[6] = (ncols - 1) * factor;
wOff[7] = (ncols) * factor;
wOff[8] = (ncols + 1) * factor;
// border weight offset matrices
// borders are extended (see http://en.wikipedia.org/wiki/Kernel_%28image_processing%29)
// i=0, j=0
const wOff00 = [];
wOff00[0] = wOff[4]; wOff00[1] = wOff[4]; wOff00[2] = wOff[5];
wOff00[3] = wOff[4]; wOff00[4] = wOff[4]; wOff00[5] = wOff[5];
wOff00[6] = wOff[7]; wOff00[7] = wOff[7]; wOff00[8] = wOff[8];
// i=0, j=*
const wOff0x = [];
wOff0x[0] = wOff[1]; wOff0x[1] = wOff[1]; wOff0x[2] = wOff[2];
wOff0x[3] = wOff[4]; wOff0x[4] = wOff[4]; wOff0x[5] = wOff[5];
wOff0x[6] = wOff[7]; wOff0x[7] = wOff[7]; wOff0x[8] = wOff[8];
// i=0, j=nrows
const wOff0n = [];
wOff0n[0] = wOff[1]; wOff0n[1] = wOff[1]; wOff0n[2] = wOff[2];
wOff0n[3] = wOff[4]; wOff0n[4] = wOff[4]; wOff0n[5] = wOff[5];
wOff0n[6] = wOff[4]; wOff0n[7] = wOff[4]; wOff0n[8] = wOff[5];
// i=*, j=0
const wOffx0 = [];
wOffx0[0] = wOff[3]; wOffx0[1] = wOff[4]; wOffx0[2] = wOff[5];
wOffx0[3] = wOff[3]; wOffx0[4] = wOff[4]; wOffx0[5] = wOff[5];
wOffx0[6] = wOff[6]; wOffx0[7] = wOff[7]; wOffx0[8] = wOff[8];
// i=*, j=* -> wOff
// i=*, j=nrows
const wOffxn = [];
wOffxn[0] = wOff[0]; wOffxn[1] = wOff[1]; wOffxn[2] = wOff[2];
wOffxn[3] = wOff[3]; wOffxn[4] = wOff[4]; wOffxn[5] = wOff[5];
wOffxn[6] = wOff[3]; wOffxn[7] = wOff[4]; wOffxn[8] = wOff[5];
// i=ncols, j=0
const wOffn0 = [];
wOffn0[0] = wOff[3]; wOffn0[1] = wOff[4]; wOffn0[2] = wOff[4];
wOffn0[3] = wOff[3]; wOffn0[4] = wOff[4]; wOffn0[5] = wOff[4];
wOffn0[6] = wOff[6]; wOffn0[7] = wOff[7]; wOffn0[8] = wOff[7];
// i=ncols, j=*
const wOffnx = [];
wOffnx[0] = wOff[0]; wOffnx[1] = wOff[1]; wOffnx[2] = wOff[1];
wOffnx[3] = wOff[3]; wOffnx[4] = wOff[4]; wOffnx[5] = wOff[4];
wOffnx[6] = wOff[6]; wOffnx[7] = wOff[7]; wOffnx[8] = wOff[7];
// i=ncols, j=nrows
const wOffnn = [];
wOffnn[0] = wOff[0]; wOffnn[1] = wOff[1]; wOffnn[2] = wOff[1];
wOffnn[3] = wOff[3]; wOffnn[4] = wOff[4]; wOffnn[5] = wOff[4];
wOffnn[6] = wOff[3]; wOffnn[7] = wOff[4]; wOffnn[8] = wOff[4];
// restore indent for rest of method
/*jshint indent:4 */
// loop vars
let pixelOffset = startOffset;
let newValue = 0;
let wOffFinal = [];
for (let c = 0; c < ncomp; ++c) {
// component offset
pixelOffset += c * componentOffset;
for (let j = 0; j < nrows; ++j) {
for (let i = 0; i < ncols; ++i) {
wOffFinal = wOff;
// special border cases
if (i === 0 && j === 0) {
wOffFinal = wOff00;
} else if (i === 0 && j === (nrows - 1)) {
wOffFinal = wOff0n;
} else if (i === (ncols - 1) && j === 0) {
wOffFinal = wOffn0;
} else if (i === (ncols - 1) && j === (nrows - 1)) {
wOffFinal = wOffnn;
} else if (i === 0 && j !== (nrows - 1) && j !== 0) {
wOffFinal = wOff0x;
} else if (i === (ncols - 1) && j !== (nrows - 1) && j !== 0) {
wOffFinal = wOffnx;
} else if (i !== 0 && i !== (ncols - 1) && j === 0) {
wOffFinal = wOffx0;
} else if (i !== 0 && i !== (ncols - 1) && j === (nrows - 1)) {
wOffFinal = wOffxn;
}
// calculate the weighed sum of the source image pixels that
// fall under the convolution matrix
newValue = 0;
for (let wi = 0; wi < 9; ++wi) {
newValue += this.getValueAtOffset(
pixelOffset + wOffFinal[wi]) * weights[wi];
}
buffer[pixelOffset] = newValue;
// increment pixel offset
pixelOffset += factor;
}
}
}
}
/**
* Transform an image using a specific operator.
* WARNING: no size check!
*
* @param {Function} operator The operator to use when transforming.
* @returns {Image} The transformed image.
* Note: Uses the raw buffer values.
*/
transform(operator) {
const newImage = this.clone();
const newBuffer = newImage.getBuffer();
for (let i = 0, leni = newBuffer.length; i < leni; ++i) {
newBuffer[i] = operator(newImage.getValueAtOffset(i));
}
return newImage;
}
/**
* Compose this image with another one and using a specific operator.
* WARNING: no size check!
*
* @param {Image} rhs The image to compose with.
* @param {Function} operator The operator to use when composing.
* @returns {Image} The composed image.
* Note: Uses the raw buffer values.
*/
compose(rhs, operator) {
const newImage = this.clone();
const newBuffer = newImage.getBuffer();
for (let i = 0, leni = newBuffer.length; i < leni; ++i) {
// using the operator on the local buffer, i.e. the
// latest (not original) data
newBuffer[i] = Math.floor(
operator(this.getValueAtOffset(i), rhs.getValueAtOffset(i))
);
}
return newImage;
}
} // class Image