Chore/kill yalc with fire (#629)

* init * more shifting * Move @babel dependencies up to workspace root * Begin updating dependent libraries to use sync'd webpack builds w/ watches * Commit changes before a long weekend * Split packages into platform and extensions * Consolidate how/where we specify file/module type entrypoints * Make it possible to pass in extensions as App props * Resolve viewer's modules * Target for UMD bundle * Add Webpack Stylus loader * Provide WebPack build options for microscopy, vtk, and ui * Better entrypoint for extensions * Push changes up to switch PCs * Fix ESM symlink build for Viewers * Shift docs to root * Specify additional lerna config props * Begin providing basic readme info * Rename example extension folder * Shift links to bottom of doc * First attempt at a netlify deploy preview * Attempt to fix deploy preview build * push workspace enabled to initial command; remove second yarn install; use npx to call gitbook cli commands * Try to use global gitbook-cli * Export node_modules path * More agressive with modifying PATH * Follow deploy log output advice * try again to set bin path * Try swapping bash with a new shell * Try bash -l instead of exec bash * Annd let's try again * and again * We may have figured it out johnny, boy * We need to pull cornerstone-wado-image-loader files from hoisted node_modules * Attempt to fix ticks/escapes * Change copy syntax; try running tests on viewers from root for circleci * Lower version to match circleci image * Try alternative jest-canvas-mock location and version file syntax * Run version command instead of calling node directly * Try alternative jest transform * Set path and enable workspaces * Add codecov flags * Use cpx so our copying finishes? * Get all platform unit tests to run * Run and report individually and in parallel * Try once relying on codecov yaml to split w/ flags * Add projects to split by flags * Generate separate reports * Trigger codecov after everything has finished running; these may not support flags * Use recommended flags from issue comments for codecov * Fix typo * Remove clear flag * Shift back to calling codecov from root * Generate example for codecov issue * Try fixing paths * Simplify * Try using codecov orb * Bump circleci version * Upload core and viewer * Use full string paths * Remove individual codecov calls * Fix dir * Combine files before upload * Escape anchors * tryfix syntax * Escape string literal * Combine lines to reduce path * long paths * Use home alias * Fix filename * Try to see the contents of our cat'd file * Also upload `core` * Try running with aliased folder * Fix path; split PR and Merge unit tests into separate jobs * Set default threshold * Fix typo * Changing to scoped package names * Adding note * Catch more updates * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.0 - @ohif/extension-dicom-html@0.0.4-alpha.0 - @ohif/extension-dicom-microscopy@0.0.9-alpha.0 - @ohif/extension-dicom-pdf@0.0.8-alpha.0 - @ohif/extension-vtk@0.1.4-alpha.0 - @ohif/core@0.11.1-alpha.0 - @ohif/i18n@0.2.3-alpha.0 - @ohif/ui@0.2.18-alpha.0 - @ohif/viewer@0.0.22-alpha.0 * Clean up primary readme * Support for dev and dev:* commands * Shift build command; satisfy default PWA build * Remove old scripts * Clean up UI to set webpack scripts * Tidy up project links * Clean duplicate code in UI project * Update UI project's docs * Clean up ui and i18n config * Reduce duplicate code in `@ohif/core` * Fix @ohif/ui versions * bump @ohif/core versions * Redux testkit dep * Remove unused/duplicate config files for projects/packages * ohif-core --> @ohif/core * Safer publish command * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.1 - @ohif/extension-dicom-html@0.0.4-alpha.1 - @ohif/extension-dicom-microscopy@0.0.9-alpha.1 - @ohif/extension-dicom-pdf@0.0.8-alpha.1 - @ohif/extension-vtk@0.1.4-alpha.1 - @ohif/core@0.11.1-alpha.1 - @ohif/i18n@0.2.3-alpha.1 - @ohif/ui@0.2.18-alpha.1 - @ohif/viewer@0.0.22-alpha.1 * test version bump * Add global prettier config * chore(release): publish %s [skip ci] - @ohif/viewer@0.0.22-alpha.2 * test lerna publish * Update package.jsons * Fix build scripts * catch changes * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.2 - @ohif/extension-dicom-html@0.0.4-alpha.2 - @ohif/extension-dicom-microscopy@0.0.9-alpha.2 - @ohif/extension-dicom-pdf@0.0.8-alpha.2 - @ohif/extension-vtk@0.1.4-alpha.2 - @ohif/core@0.11.1-alpha.2 - @ohif/i18n@0.2.3-alpha.2 - @ohif/ui@0.2.18-alpha.2 - @ohif/viewer@0.0.22-alpha.3 * fix eslint issues caused by eslint 6 and our react-app config * Publish with canary tag * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.3 - @ohif/extension-dicom-html@0.0.4-alpha.3 - @ohif/extension-dicom-microscopy@0.0.9-alpha.3 - @ohif/extension-dicom-pdf@0.0.8-alpha.3 - @ohif/extension-vtk@0.1.4-alpha.3 - @ohif/core@0.11.1-alpha.3 - @ohif/i18n@0.2.3-alpha.3 - @ohif/ui@0.2.18-alpha.3 - @ohif/viewer@0.0.22-alpha.4 * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.4 - @ohif/extension-dicom-html@0.0.4-alpha.4 - @ohif/extension-dicom-microscopy@0.0.9-alpha.4 - @ohif/extension-dicom-pdf@0.0.8-alpha.4 - @ohif/extension-vtk@0.1.4-alpha.4 - @ohif/core@0.11.1-alpha.4 - @ohif/i18n@0.2.3-alpha.4 - @ohif/ui@0.2.18-alpha.4 - @ohif/viewer@0.0.22-alpha.5 * Simplify build * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.5 - @ohif/extension-dicom-html@0.0.4-alpha.5 - @ohif/extension-dicom-microscopy@0.0.9-alpha.5 - @ohif/extension-dicom-pdf@0.0.8-alpha.5 - @ohif/extension-vtk@0.1.4-alpha.5 - @ohif/core@0.11.1-alpha.5 - @ohif/i18n@0.2.3-alpha.5 - @ohif/ui@0.2.18-alpha.5 - @ohif/viewer@0.0.22-alpha.6 * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.6 - @ohif/extension-dicom-html@0.0.4-alpha.6 - @ohif/extension-dicom-microscopy@0.0.9-alpha.6 - @ohif/extension-dicom-pdf@0.0.8-alpha.6 - @ohif/extension-vtk@0.1.4-alpha.6 - @ohif/core@0.11.1-alpha.6 - @ohif/i18n@0.2.3-alpha.6 - @ohif/ui@0.2.18-alpha.6 - @ohif/viewer@0.0.22-alpha.7 * Split version and publish * chore(release): publish %s [skip ci] - @ohif/extension-cornerstone@0.0.39-alpha.7 - @ohif/extension-dicom-html@0.0.4-alpha.7 - @ohif/extension-dicom-microscopy@0.0.9-alpha.7 - @ohif/extension-dicom-pdf@0.0.8-alpha.7 - @ohif/extension-vtk@0.1.4-alpha.7 - @ohif/core@0.11.1-alpha.7 - @ohif/i18n@0.2.3-alpha.7 - @ohif/ui@0.2.18-alpha.7 - @ohif/viewer@0.0.22-alpha.8 * Try simplify netlify build * react-viewerbase --> @ohif/ui * add test for stylus loader * Try new way to specify publish path * Use an output folder that won't be ignored * Try move command * fiddle with paths * Dig for some information * Make sure we're in root for our commands * Remove discovery * Setup script-tag example * Fix typo * Move config folder * Update cornerstone extension to use shared/root webpack configs * capture changes * Update extension webpack configs * Don't check in docz output * Fix babel runtime resolution issue * Simplify ui build steps * Push in progress * Shift directories * Get viewer dev path to work * Fix viewer commonjs build * Fix build pwa config for viewers * Make sure our package specific command can be called from root * Update notes * Fix imports and misc. merge notes * Bump wado-image-loader version * Switch up commands to remove webworkers copy * Fix CI config * Fix more broken package references * Add react-dropzone * Persist so e2e test can use * Fix lockfile * Use cypress orb to simplify CI * Fix config * Try again * Install yarn latest for orb * Install yarn a different way * Wait on correct port * Run tests in viewer project * Fix cypress config * Make Cypress happier - use default location * Simplify e2e testing * Capture UI changes since fork * Catch core up * Grab latest deps after merge * Fix broken import * Make sure cornerstone-wado-image-loader resolves to 3+ * Note regarding orbs * Fix refresh on 404 routes * Fix odd error for cornerstone-wado-image-loader * Different target for UMD * Simplify dev script * Try to get fancy with netlify output * Let's do it again * Try to fix measurementTools issue * See if we can get our lerna magic to work on merge to monorepo branch
2019-08-13 15:36:46 -04:00
1 parent cac911f08e
commit 08ff214ea6
@@ -0,0 +1,160 @@
+import cornerstone from 'cornerstone-core';
+import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader';
+import * as dcmjs from 'dcmjs';
+
+function datasetsToStudies(datasets) {
+  const StudyInstanceUIDs = new Set();
+  datasets.forEach(ds => {
+    StudyInstanceUIDs.add(ds.StudyInstanceUID);
+  });
+
+  const studies = [];
+  Array.from(StudyInstanceUIDs).forEach(studyInstanceUid => {
+    const studyDatasets = datasets.filter(
+      ds => ds.StudyInstanceUID === studyInstanceUid
+    );
+    const firstDataset = studyDatasets[0];
+    const study = {
+      studyInstanceUid: firstDataset.StudyInstanceUID,
+      studyDate: firstDataset.StudyDate,
+      studyTime: firstDataset.StudyTime,
+      accessionNumber: firstDataset.AccessionNumber,
+      referringPhysicianName: firstDataset.ReferringPhysicianName,
+      patientName: firstDataset.PatientName,
+      patientId: firstDataset.PatientID,
+      patientBirthdate: firstDataset.PatientBirthDate,
+      patientSex: firstDataset.PatientSex,
+      studyId: firstDataset.StudyID,
+      studyDescription: firstDataset.StudyDescription,
+      //numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
+      //numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
+      // modality: DICOMWeb.getString(study['00080060']),
+      // modalitiesInStudy: DICOMWeb.getString(study['00080061']),
+      //modalities:
+      seriesList: [],
+    };
+
+    const SeriesInstanceUIDs = new Set();
+    studyDatasets.forEach(ds => {
+      SeriesInstanceUIDs.add(ds.SeriesInstanceUID);
+    });
+
+    Array.from(SeriesInstanceUIDs).forEach(seriesInstanceUid => {
+      const seriesDatasets = studyDatasets.filter(
+        ds => ds.SeriesInstanceUID === seriesInstanceUid
+      );
+
+      const SOPInstanceUIDs = new Set();
+      seriesDatasets.forEach(ds => {
+        SOPInstanceUIDs.add(ds.SOPInstanceUID);
+
+        study.seriesList.push({
+          seriesInstanceUid: ds.SeriesInstanceUID,
+          seriesDescription: ds.SeriesDescription,
+          seriesNumber: ds.SeriesNumber,
+          instances: [],
+        });
+      });
+
+      Array.from(SOPInstanceUIDs).forEach(sopInstanceUid => {
+        const instance = seriesDatasets.find(
+          a => a.SOPInstanceUID === sopInstanceUid
+        );
+        const series = study.seriesList.find(
+          a => a.seriesInstanceUid === seriesInstanceUid
+        );
+
+        series.instances.push({
+          sopInstanceUid: instance.SOPInstanceUID,
+          sopClassUid: instance.SOPClassUID,
+          rows: instance.Rows,
+          columns: instance.Columns,
+          numberOfFrames: instance.NumberOfFrames,
+          instanceNumber: instance.InstanceNumber,
+          getImageId: () => instance.imageId, // TODO: Change getImageId to check for instance.imageId property first.
+          /*imageType: DICOMWeb.getString(instance['00080008']),
+          modality: DICOMWeb.getString(instance['00080060']),
+          instanceNumber: DICOMWeb.getNumber(instance['00200013']),
+          imagePositionPatient: DICOMWeb.getString(instance['00200032']),
+          imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
+          frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
+          sliceLocation: DICOMWeb.getNumber(instance['00201041']),
+          samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
+          photometricInterpretation: DICOMWeb.getString(instance['00280004']),
+          planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
+          pixelSpacing: DICOMWeb.getString(instance['00280030']),
+          pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
+          bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
+          bitsStored: DICOMWeb.getNumber(instance['00280101']),
+          highBit: DICOMWeb.getNumber(instance['00280102']),
+          pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
+          smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
+          largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
+          windowCenter: DICOMWeb.getString(instance['00281050']),
+          windowWidth: DICOMWeb.getString(instance['00281051']),
+          rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
+          rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
+          rescaleType: DICOMWeb.getNumber(instance['00281054']),
+          sourceImageInstanceUid: getSourceImageInstanceUid(instance),
+          laterality: DICOMWeb.getString(instance['00200062']),
+          viewPosition: DICOMWeb.getString(instance['00185101']),
+          acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
+          frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
+          frameTime: DICOMWeb.getNumber(instance['00181063']),
+          frameTimeVector: parseFloatArray(
+            DICOMWeb.getString(instance['00181065'])
+          ),
+          sliceThickness: DICOMWeb.getNumber(instance['00180050']),
+          spacingBetweenSlices: DICOMWeb.getString(instance['00180088']),
+          lossyImageCompression: DICOMWeb.getString(instance['00282110']),
+          derivationDescription: DICOMWeb.getString(instance['00282111']),
+          lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
+          lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
+          echoNumber: DICOMWeb.getString(instance['00180086']),
+          contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
+          radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
+          wadouri: WADOProxy.convertURL(wadouri, server),
+          wadorsuri: WADOProxy.convertURL(wadorsuri, server),*/
+        });
+      });
+    });
+
+    studies.push(study);
+  });
+
+  console.warn(studies);
+
+  return studies;
+}
+
+export default async function filesToStudies(files) {
+  const imagePromises = files.map(file => {
+    const imageId = cornerstoneWADOImageLoader.wadouri.fileManager.add(file);
+    return cornerstone
+      .loadAndCacheImage(imageId)
+      .catch(error => console.warn(error));
+  });
+
+  const images = await Promise.all(imagePromises);
+  const datasets = [];
+
+  images.forEach(image => {
+    if (!image || !image.data) {
+      return;
+    }
+
+    const arrayBuffer = image.data.byteArray.buffer;
+    const dicomData = dcmjs.data.DicomMessage.readFile(arrayBuffer);
+    const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
+      dicomData.dict
+    );
+    dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(
+      dicomData.meta
+    );
+    dataset.imageId = image.imageId;
+
+    datasets.push(dataset);
+  });
+
+  return datasetsToStudies(datasets);
+}
@@ -0,0 +1,33 @@
+import cornerstoneTools from 'cornerstone-tools';
+import updateTableWithNewMeasurementData from './updateTableWithNewMeasurementData';
+
+export default function getMeasurementLocationCallback(
+  eventData,
+  tool,
+  options
+) {
+  const { toolType } = tool;
+  const { element } = eventData;
+  const doneCallback = updateTableWithNewMeasurementData;
+
+  const ToolInstance = cornerstoneTools.getToolForElement(element, toolType);
+
+  if (
+    !ToolInstance ||
+    !ToolInstance.configuration ||
+    !ToolInstance.configuration.getMeasurementLocationCallback
+  ) {
+    console.warn(
+      'Tool instance configuration is missing: getMeasurementLocationCallback'
+    );
+
+    return;
+  }
+
+  ToolInstance.configuration.getMeasurementLocationCallback(
+    tool,
+    eventData,
+    doneCallback,
+    options
+  );
+}
@@ -0,0 +1,29 @@
+import OHIF from "@ohif/core";
+import cornerstone from "cornerstone-core";
+
+export default function updateTableWithNewMeasurementData({
+  toolType,
+  measurementNumber,
+  location,
+  description
+}) {
+  // Update all measurements by measurement number
+  const measurementApi = OHIF.measurements.MeasurementApi.Instance;
+  const measurements = measurementApi.tools[toolType].filter(
+    m => m.measurementNumber === measurementNumber
+  );
+
+  measurements.forEach(measurement => {
+    measurement.location = location;
+    measurement.description = description;
+
+    measurementApi.updateMeasurement(measurement.toolType, measurement);
+  });
+
+  measurementApi.syncMeasurementsAndToolData();
+
+  // Update images in all active viewports
+  cornerstone.getEnabledElements().forEach(enabledElement => {
+    cornerstone.updateImage(enabledElement.element);
+  });
+}
@@ -0,0 +1,46 @@
+export default function bounding(elementRef, currentPosition = {}) {
+  if (!elementRef.current) {
+    return;
+  }
+
+  const currentElement = elementRef.current;
+  const {
+    offsetParent,
+    offsetTop,
+    offsetHeight,
+    offsetLeft,
+    offsetWidth,
+  } = currentElement;
+  let top = currentPosition.top || offsetTop;
+  let left = currentPosition.left || offsetLeft;
+
+  if (!offsetParent) {
+    return;
+  }
+
+  let maxHeight = `${offsetParent.offsetHeight}px`;
+
+  if (offsetHeight + top > offsetParent.offsetHeight) {
+    top = top - (offsetHeight + top - offsetParent.offsetHeight);
+    if (top < 0) {
+      top = 0;
+    }
+  }
+
+  if (left + offsetWidth > offsetParent.offsetWidth) {
+    left = offsetParent.offsetWidth - offsetWidth;
+    if (left < 0) {
+      left = 0;
+    }
+  }
+
+  if (maxHeight && currentElement.style.maxHeight !== maxHeight) {
+    currentElement.style.maxHeight = maxHeight;
+  }
+  if (currentElement.style.top !== `${top}px`) {
+    currentElement.style.top = `${top}px`;
+  }
+  if (currentElement.style.left !== `${left}px`) {
+    currentElement.style.left = `${left}px`;
+  }
+}