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RGB24 support #15

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RGB24 support #15

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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
node_modules/
coverage/
package-lock.json
examples/data/603_1__ALPHA_Serie_a.nii.gz
examples/data/603_1__ALPHA_Serie_a.nii
package-lock.json
package-lock.json
52 changes: 47 additions & 5 deletions dist/cornerstoneNIFTIImageLoader.js
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
/*! cornerstone-nifti-image-loader - 1.0.0 - 2019-06-19 | (c) 2018 Flywheel Exchange, LLC | https://github.com/flywheel-io/cornerstone-nifti-image-loader */
/*! cornerstone-nifti-image-loader - 1.0.0 - 2020-04-08 | (c) 2018 Flywheel Exchange, LLC | https://github.com/flywheel-io/cornerstone-nifti-image-loader */
(function webpackUniversalModuleDefinition(root, factory) {
if(typeof exports === 'object' && typeof module === 'object')
module.exports = factory();
Expand Down Expand Up @@ -70,6 +70,17 @@ return /******/ (function(modules) { // webpackBootstrap
/******/ // __webpack_public_path__
/******/ __webpack_require__.p = "";
/******/
/******/ // webpack-livereload-plugin
/******/ (function() {
/******/ if (typeof window === "undefined") { return };
/******/ var id = "webpack-livereload-plugin-script";
/******/ if (document.getElementById(id)) { return; }
/******/ var el = document.createElement("script");
/******/ el.id = id;
/******/ el.async = true;
/******/ el.src = "//" + location.hostname + ":45001/livereload.js";
/******/ document.getElementsByTagName("head")[0].appendChild(el);
/******/ }());
/******/ // Load entry module and return exports
/******/ return __webpack_require__(__webpack_require__.s = 41);
/******/ })
Expand Down Expand Up @@ -3407,6 +3418,22 @@ function parseNiftiHeader(fileData) {
};
}

function convert24bito32bit(typedArray8) {
var dview = new DataView(typedArray8.buffer);
var num_pixels = typedArray8.length / 3 * 4;
var image32bit = new Uint32Array(num_pixels);

for (var i = 0; i < num_pixels; i++) {
var b = dview.getUint8(i * 3);
var g = dview.getUint8(i * 3 + 1);
var r = dview.getUint8(i * 3 + 2);

image32bit[i] = (r << 16) + (g << 8) + b + 0xff000000;
}

return image32bit;
}

function parseNiftiFile(fileData, metaData) {
var nifti = _externalModules.external.niftiReader;

Expand All @@ -3424,6 +3451,10 @@ function parseNiftiFile(fileData, metaData) {
imageData = (0, _niftiBigEndianDecoder2.default)(metaData.header.datatypeCode, imageData);
}

if (metaData.header.datatypeCode === nifti.NIFTI1.TYPE_RGB24) {
imageData = convert24bito32bit(imageData);
}

// determines the meta data that depends on the image data
return {
metaData: metaData,
Expand Down Expand Up @@ -3511,15 +3542,15 @@ function getOrientationMatrix(header) {
function niftiDatatypeCodeToTypedArray(nifti, datatypeCode) {
var _typedArrayConstructo;

var typedArrayConstructorMap = (_typedArrayConstructo = {}, _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT8, Uint8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT16, Uint16Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT32, Uint32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT8, Int8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT16, Int16Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT32, Int32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_FLOAT32, Float32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_FLOAT64, Float64Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_RGB, Uint8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_RGBA, Uint8Array), _typedArrayConstructo);
var typedArrayConstructorMap = (_typedArrayConstructo = {}, _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT8, Uint8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT16, Uint16Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_UINT32, Uint32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT8, Int8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT16, Int16Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_INT32, Int32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_FLOAT32, Float32Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_FLOAT64, Float64Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_RGB, Uint8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_RGBA, Uint8Array), _defineProperty(_typedArrayConstructo, nifti.NIFTI1.TYPE_RGB24, Uint32Array), _typedArrayConstructo);

return typedArrayConstructorMap[datatypeCode];
}

function isDataInFloat(nifti, datatypeCode) {
var _isFloatTypeMap;

var isFloatTypeMap = (_isFloatTypeMap = {}, _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT8, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT16, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT32, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT8, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT16, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT32, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_FLOAT32, true), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_FLOAT64, true), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_RGB, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_RGBA, false), _isFloatTypeMap);
var isFloatTypeMap = (_isFloatTypeMap = {}, _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT8, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT16, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_UINT32, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT8, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT16, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_INT32, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_FLOAT32, true), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_FLOAT64, true), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_RGB, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_RGBA, false), _defineProperty(_isFloatTypeMap, nifti.NIFTI1.TYPE_RGB24, false), _isFloatTypeMap);

return isFloatTypeMap[datatypeCode];
}
Expand All @@ -3528,7 +3559,7 @@ function isDataInColors(nifti, dims, datatypeCode) {
var _hasColorsMap;

var samplesPerPixel = getSamplesPerPixel(dims);
var hasColorsMap = (_hasColorsMap = {}, _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT8, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT16, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT8, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT16, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_FLOAT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_FLOAT64, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_RGB, samplesPerPixel === 3), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_RGBA, samplesPerPixel === 4), _hasColorsMap);
var hasColorsMap = (_hasColorsMap = {}, _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT8, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT16, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_UINT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT8, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT16, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_INT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_FLOAT32, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_FLOAT64, false), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_RGB, samplesPerPixel === 3), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_RGBA, samplesPerPixel === 4), _defineProperty(_hasColorsMap, nifti.NIFTI1.TYPE_RGB24, true), _hasColorsMap);

return hasColorsMap[datatypeCode];
}
Expand Down Expand Up @@ -8648,9 +8679,10 @@ function getPhotometricInterpretation(metaData, niftiReader) {
var samplesPerPixel = getSamplesPerPixel(metaData);
var isRGB = dataTypeCode === niftiReader.NIFTI1.TYPE_RGB && samplesPerPixel === 3;
var isRGBA = dataTypeCode === niftiReader.NIFTI1.TYPE_RGBA && samplesPerPixel === 4;
var isRGB24 = dataTypeCode === niftiReader.NIFTI1.TYPE_RGB24;

// we assume 'RGB' if nifti file has RGB or RGBA types and samplesPerPixel matches
if (isRGB || isRGBA) {
if (isRGB || isRGBA || isRGB24) {
return 'RGB';
}

Expand Down Expand Up @@ -16327,6 +16359,16 @@ var Slice = function () {
var cornerstone = _externalModules.external.cornerstone;
var render = volumeMetaData.dataType.isDataInColors ? cornerstone.renderColorImage : cornerstone.renderGrayscaleImage;

if (volumeMetaData.header.datatypeCode === 128) {
this.pixelData = new Uint8Array(this.pixelData.buffer);

// this should probably go elsewhere for RGB24 data
volumeMetaData.windowCenter = 128;
volumeMetaData.windowWidth = 256;
volumeMetaData.minPixelValue = 0;
volumeMetaData.maxPixelValue = 255;
}

return {
imageId: this.imageIdObject.url,
color: volumeMetaData.dataType.isDataInColors,
Expand Down
2 changes: 1 addition & 1 deletion dist/cornerstoneNIFTIImageLoader.js.map
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