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| 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 | 34x 34x 34x 34x 34x 34x 34x 34x 34x 34x | import dcmjs from 'dcmjs';
import { classes, Types } from '@ohif/core';
import { cache, metaData } from '@cornerstonejs/core';
import { segmentation as cornerstoneToolsSegmentation } from '@cornerstonejs/tools';
import { adaptersRT, helpers, adaptersSEG } from '@cornerstonejs/adapters';
import { createReportDialogPrompt } from '@ohif/extension-default';
import { DicomMetadataStore } from '@ohif/core';
import PROMPT_RESPONSES from '../../default/src/utils/_shared/PROMPT_RESPONSES';
const { datasetToBlob } = dcmjs.data;
const getTargetViewport = ({ viewportId, viewportGridService }) => {
const { viewports, activeViewportId } = viewportGridService.getState();
const targetViewportId = viewportId || activeViewportId;
const viewport = viewports.get(targetViewportId);
return viewport;
};
const {
Cornerstone3D: {
Segmentation: { generateSegmentation },
},
} = adaptersSEG;
const {
Cornerstone3D: {
RTSS: { generateRTSSFromSegmentations },
},
} = adaptersRT;
const { downloadDICOMData } = helpers;
const commandsModule = ({
servicesManager,
extensionManager,
}: Types.Extensions.ExtensionParams): Types.Extensions.CommandsModule => {
const { segmentationService, displaySetService, viewportGridService, toolGroupService } =
servicesManager.services as AppTypes.Services;
const actions = {
/**
* Loads segmentations for a specified viewport.
* The function prepares the viewport for rendering, then loads the segmentation details.
* Additionally, if the segmentation has scalar data, it is set for the corresponding label map volume.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentations - Array of segmentations to be loaded.
* @param params.viewportId - the target viewport ID.
*
*/
loadSegmentationsForViewport: async ({ segmentations, viewportId }) => {
// Todo: handle adding more than one segmentation
const viewport = getTargetViewport({ viewportId, viewportGridService });
const displaySetInstanceUID = viewport.displaySetInstanceUIDs[0];
const segmentation = segmentations[0];
const segmentationId = segmentation.segmentationId;
const label = segmentation.config.label;
const segments = segmentation.config.segments;
const displaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
await segmentationService.createLabelmapForDisplaySet(displaySet, {
segmentationId,
segments,
label,
});
segmentationService.addOrUpdateSegmentation(segmentation);
await segmentationService.addSegmentationRepresentation(viewport.viewportId, {
segmentationId,
});
return segmentationId;
},
/**
* Generates a segmentation from a given segmentation ID.
* This function retrieves the associated segmentation and
* its referenced volume, extracts label maps from the
* segmentation volume, and produces segmentation data
* alongside associated metadata.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be generated.
* @param params.options - Optional configuration for the generation process.
*
* @returns Returns the generated segmentation data.
*/
generateSegmentation: ({ segmentationId, options = {} }) => {
const segmentation = cornerstoneToolsSegmentation.state.getSegmentation(segmentationId);
const { imageIds } = segmentation.representationData.Labelmap;
const segImages = imageIds.map(imageId => cache.getImage(imageId));
const referencedImages = segImages.map(image => cache.getImage(image.referencedImageId));
const labelmaps2D = [];
let z = 0;
for (const segImage of segImages) {
const segmentsOnLabelmap = new Set();
const pixelData = segImage.getPixelData();
const { rows, columns } = segImage;
// Use a single pass through the pixel data
for (let i = 0; i < pixelData.length; i++) {
const segment = pixelData[i];
Iif (segment !== 0) {
segmentsOnLabelmap.add(segment);
}
}
labelmaps2D[z++] = {
segmentsOnLabelmap: Array.from(segmentsOnLabelmap),
pixelData,
rows,
columns,
};
}
const allSegmentsOnLabelmap = labelmaps2D.map(labelmap => labelmap.segmentsOnLabelmap);
const labelmap3D = {
segmentsOnLabelmap: Array.from(new Set(allSegmentsOnLabelmap.flat())),
metadata: [],
labelmaps2D,
};
const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
const representations = segmentationService.getRepresentationsForSegmentation(segmentationId);
Object.entries(segmentationInOHIF.segments).forEach(([segmentIndex, segment]) => {
// segmentation service already has a color for each segment
Iif (!segment) {
return;
}
const { label } = segment;
const firstRepresentation = representations[0];
const color = segmentationService.getSegmentColor(
firstRepresentation.viewportId,
segmentationId,
segment.segmentIndex
);
const RecommendedDisplayCIELabValue = dcmjs.data.Colors.rgb2DICOMLAB(
color.slice(0, 3).map(value => value / 255)
).map(value => Math.round(value));
const segmentMetadata = {
SegmentNumber: segmentIndex.toString(),
SegmentLabel: label,
SegmentAlgorithmType: segment?.algorithmType || 'MANUAL',
SegmentAlgorithmName: segment?.algorithmName || 'OHIF Brush',
RecommendedDisplayCIELabValue,
SegmentedPropertyCategoryCodeSequence: {
CodeValue: 'T-D0050',
CodingSchemeDesignator: 'SRT',
CodeMeaning: 'Tissue',
},
SegmentedPropertyTypeCodeSequence: {
CodeValue: 'T-D0050',
CodingSchemeDesignator: 'SRT',
CodeMeaning: 'Tissue',
},
};
labelmap3D.metadata[segmentIndex] = segmentMetadata;
});
const generatedSegmentation = generateSegmentation(
referencedImages,
labelmap3D,
metaData,
options
);
return generatedSegmentation;
},
/**
* Downloads a segmentation based on the provided segmentation ID.
* This function retrieves the associated segmentation and
* uses it to generate the corresponding DICOM dataset, which
* is then downloaded with an appropriate filename.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be downloaded.
*
*/
downloadSegmentation: ({ segmentationId }) => {
const segmentationInOHIF = segmentationService.getSegmentation(segmentationId);
const generatedSegmentation = actions.generateSegmentation({
segmentationId,
});
downloadDICOMData(generatedSegmentation.dataset, `${segmentationInOHIF.label}`);
},
/**
* Stores a segmentation based on the provided segmentationId into a specified data source.
* The SeriesDescription is derived from user input or defaults to the segmentation label,
* and in its absence, defaults to 'Research Derived Series'.
*
* @param {Object} params - Parameters for the function.
* @param params.segmentationId - ID of the segmentation to be stored.
* @param params.dataSource - Data source where the generated segmentation will be stored.
*
* @returns {Object|void} Returns the naturalized report if successfully stored,
* otherwise throws an error.
*/
storeSegmentation: async ({ segmentationId, dataSource }) => {
const segmentation = segmentationService.getSegmentation(segmentationId);
Iif (!segmentation) {
throw new Error('No segmentation found');
}
const { label } = segmentation;
const defaultDataSource = dataSource ?? extensionManager.getActiveDataSource();
const {
value: reportName,
dataSourceName: selectedDataSource,
action,
} = await createReportDialogPrompt({
servicesManager,
extensionManager,
title: 'Store Segmentation',
});
Iif (action === PROMPT_RESPONSES.CREATE_REPORT) {
try {
const selectedDataSourceConfig = selectedDataSource
? extensionManager.getDataSources(selectedDataSource)[0]
: defaultDataSource;
const generatedData = actions.generateSegmentation({
segmentationId,
options: {
SeriesDescription: reportName || label || 'Research Derived Series',
},
});
Iif (!generatedData || !generatedData.dataset) {
throw new Error('Error during segmentation generation');
}
const { dataset: naturalizedReport } = generatedData;
await selectedDataSourceConfig.store.dicom(naturalizedReport);
// add the information for where we stored it to the instance as well
naturalizedReport.wadoRoot = selectedDataSourceConfig.getConfig().wadoRoot;
DicomMetadataStore.addInstances([naturalizedReport], true);
return naturalizedReport;
} catch (error) {
console.debug('Error storing segmentation:', error);
throw error;
}
}
},
/**
* Converts segmentations into RTSS for download.
* This sample function retrieves all segentations and passes to
* cornerstone tool adapter to convert to DICOM RTSS format. It then
* converts dataset to downloadable blob.
*
*/
downloadRTSS: async ({ segmentationId }) => {
const segmentations = segmentationService.getSegmentation(segmentationId);
// inject colors to the segmentIndex
const firstRepresentation =
segmentationService.getRepresentationsForSegmentation(segmentationId)[0];
Object.entries(segmentations.segments).forEach(([segmentIndex, segment]) => {
segment.color = segmentationService.getSegmentColor(
firstRepresentation.viewportId,
segmentationId,
segmentIndex
);
});
const RTSS = await generateRTSSFromSegmentations(
segmentations,
classes.MetadataProvider,
DicomMetadataStore
);
try {
const reportBlob = datasetToBlob(RTSS);
//Create a URL for the binary.
const objectUrl = URL.createObjectURL(reportBlob);
window.location.assign(objectUrl);
} catch (e) {
console.warn(e);
}
},
};
const definitions = {
loadSegmentationsForViewport: {
commandFn: actions.loadSegmentationsForViewport,
},
generateSegmentation: {
commandFn: actions.generateSegmentation,
},
downloadSegmentation: {
commandFn: actions.downloadSegmentation,
},
storeSegmentation: {
commandFn: actions.storeSegmentation,
},
downloadRTSS: {
commandFn: actions.downloadRTSS,
},
};
return {
actions,
definitions,
defaultContext: 'SEGMENTATION',
};
};
export default commandsModule;
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