larvitar 0.20.0 → 1.2.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (45) hide show
  1. package/.github/workflows/build-docs.yml +1 -1
  2. package/.github/workflows/deploy.yml +2 -11
  3. package/MIGRATION.md +25 -0
  4. package/README.md +28 -27
  5. package/imaging/dataDictionary.json +21865 -21865
  6. package/imaging/{image_anonymization.js → imageAnonymization.js} +1 -1
  7. package/imaging/{image_colormaps.js → imageColormaps.js} +2 -2
  8. package/imaging/{image_contours.js → imageContours.js} +1 -2
  9. package/imaging/{image_io.js → imageIo.js} +18 -15
  10. package/imaging/{image_layers.js → imageLayers.js} +2 -2
  11. package/imaging/{image_loading.js → imageLoading.js} +9 -6
  12. package/imaging/imageParsing.js +301 -0
  13. package/imaging/{image_presets.js → imagePresets.js} +2 -2
  14. package/imaging/{image_rendering.js → imageRendering.js} +36 -32
  15. package/imaging/imageReslice.js +78 -0
  16. package/imaging/{image_store.js → imageStore.js} +24 -7
  17. package/imaging/{image_tools.js → imageTools.js} +15 -23
  18. package/imaging/{image_utils.js → imageUtils.js} +1 -1
  19. package/imaging/loaders/commonLoader.js +1 -1
  20. package/imaging/loaders/dicomLoader.js +1 -1
  21. package/imaging/loaders/fileLoader.js +2 -2
  22. package/imaging/loaders/multiframeLoader.js +6 -2
  23. package/imaging/loaders/nrrdLoader.js +11 -7
  24. package/imaging/tools/{contourTool.js → custom/contourTool.js} +25 -20
  25. package/imaging/tools/{diameterTool.js → custom/diameterTool.js} +9 -3
  26. package/imaging/tools/{editMaskTool.js → custom/editMaskTool.js} +7 -1
  27. package/imaging/tools/{polylineScissorsTool.js → custom/polylineScissorsTool.js} +12 -5
  28. package/imaging/tools/{seedTool.js → custom/seedTool.js} +3 -3
  29. package/imaging/tools/{thresholdsBrushTool.js → custom/thresholdsBrushTool.js} +7 -1
  30. package/imaging/tools/{tools.default.js → default.js} +9 -2
  31. package/imaging/tools/{tools.interaction.js → interaction.js} +13 -6
  32. package/imaging/tools/{tools.io.js → io.js} +15 -6
  33. package/imaging/tools/{tools.main.js → main.js} +14 -13
  34. package/imaging/tools/polygonSegmentationMixin.js +8 -4
  35. package/imaging/tools/{tools.segmentation.js → segmentation.js} +171 -58
  36. package/imaging/tools/segmentations.md +38 -0
  37. package/imaging/tools/setLabelMap3D.js +248 -0
  38. package/imaging/tools/{tools.state.js → state.js} +7 -1
  39. package/imaging/tools/strategies/eraseFreehand.js +8 -9
  40. package/imaging/tools/strategies/fillFreehand.js +8 -9
  41. package/index.js +41 -39
  42. package/modules/vuex/larvitar.js +2 -1
  43. package/package.json +11 -8
  44. package/imaging/image_parsing.js +0 -307
  45. package/imaging/image_reslice.js +0 -80
package/imaging/image_reslice.js DELETED
@@ -1,80 +0,0 @@
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- /** @module imaging/reslice
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- * @desc This file provides functionalities for
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- * image reslice in orthogonal directions
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- */
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-
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- // external libraries
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- import { v4 as uuidv4 } from "uuid";
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- import { each } from "lodash";
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-
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- // internal libraries
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- import { getReslicedMetadata, getReslicedPixeldata } from "./image_utils";
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- import {
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- getLarvitarImageTracker,
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- getLarvitarManager
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- } from "./loaders/commonLoader";
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- import { larvitar_store } from "./image_store";
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-
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- /*
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- * This module provides the following functions to be exported:
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- * resliceSeries(seriesId, seriesData, orientation, callback)
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- */
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-
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- /**
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- * Reslice a serie from native orientation to coronal or sagittal orientation
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- * @instance
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- * @function resliceSeries
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- * @param {Object} seriesData the original series data
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- * @param {String} orientation the reslice orientation [coronal or sagittal]
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- * @param {String} seriesId the series id
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- * @return {Object} cornerstone data
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- */
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- export function resliceSeries(seriesData, orientation, callback) {
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- let reslicedSeries = {};
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- let reslicedSeriesId = uuidv4();
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- let reslicedMetaData = getReslicedMetadata(
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- reslicedSeriesId,
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- "axial",
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- orientation,
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- seriesData,
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- "resliceLoader"
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- );
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-
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- reslicedSeries.imageIds = reslicedMetaData.imageIds;
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- reslicedSeries.instances = reslicedMetaData.instances;
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-
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- reslicedSeries.currentImageIdIndex = Math.floor(
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- reslicedSeries.imageIds.length / 2
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- );
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-
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- function computeReslice(
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- seriesData,
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- reslicedSeriesId,
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- reslicedSeries,
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- callback
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- ) {
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- let t0 = performance.now();
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- let imageTracker = getLarvitarImageTracker();
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- let manager = getLarvitarManager();
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- each(reslicedSeries.imageIds, function (imageId) {
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- reslicedSeries.instances[imageId].pixelData = getReslicedPixeldata(
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- imageId,
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- seriesData,
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- reslicedSeries
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- );
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- imageTracker[imageId] = reslicedSeriesId;
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- });
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- larvitar_store.addSeriesIds(reslicedSeriesId, reslicedSeries.imageIds);
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- reslicedSeries.numberOfImages = reslicedSeries.imageIds.length;
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- reslicedSeries.seriesUID = reslicedSeriesId;
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- reslicedSeries.seriesDescription = seriesData.seriesDescription;
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- reslicedSeries.orientation = orientation;
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- manager[reslicedSeriesId] = reslicedSeries;
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- manager[seriesData.seriesUID][orientation] = reslicedSeriesId;
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- let t1 = performance.now();
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- console.log(`Call to resliceSeries took ${t1 - t0} milliseconds.`);
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- callback(reslicedSeries);
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- }
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- // reslice the data
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- computeReslice(seriesData, reslicedSeriesId, reslicedSeries, callback);
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- }