feat: cornerstone3D stack and volume viewports (#2787)

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
2022-07-27 12:39:04 -04:00
1 parent 86dcaf6293
commit bd1c38c00c
@@ -11,8 +11,7 @@ function CallbackPage({ userManager, onRedirectSuccess }) {
    .then(user => onRedirectSuccess(user))
    .catch(error => onRedirectError(error));

-  // todo: add i18n (or return null?)
-  return <div>Redirecting...</div>;
+  return null;
 }

 CallbackPage.propTypes = {
@@ -3,7 +3,7 @@ import React, { useEffect, useState } from 'react';
 import PropTypes from 'prop-types';
 import { MODULE_TYPES } from '@ohif/core';
 //
-import { extensionManager } from '../App.jsx';
+import { extensionManager } from '../App.tsx';
 import { useParams, useLocation } from 'react-router';

 /**
@@ -35,7 +35,7 @@ function DataSourceWrapper(props) {
  // Grabbing first for now - should get active?
  const name = webApiDataSources[0].name;
  // TODO: Why does this return an array?
-  const dataSource = extensionManager.getDataSources(name)[0]
+  const dataSource = extensionManager.getDataSources(name)[0];

  // Route props --> studies.mapParams
  // mapParams --> studies.search
@@ -86,12 +86,13 @@ function DataSourceWrapper(props) {
      const newOffset =
        Math.floor(
          (queryFilterValues.pageNumber * queryFilterValues.resultsPerPage) /
-          STUDIES_LIMIT
+            STUDIES_LIMIT
        ) *
        (STUDIES_LIMIT - 1);
      const isLocationUpdated = data.location !== location;
-      const isDataInvalid = !isSamePage || !isLoading &&
-        (newOffset !== previousOffset || isLocationUpdated);
+      const isDataInvalid =
+        !isSamePage ||
+        (!isLoading && (newOffset !== previousOffset || isLocationUpdated));

      if (isDataInvalid) {
        getData();
@@ -1,14 +1,14 @@
-import React, { useEffect, useRef } from 'react'
-import classnames from 'classnames'
+import React, { useEffect, useRef } from 'react';
+import classnames from 'classnames';
 import { useNavigate } from 'react-router-dom';
-import { MODULE_TYPES } from '@ohif/core'
+import { MODULE_TYPES } from '@ohif/core';

-import Dropzone from 'react-dropzone'
-import filesToStudies from './filesToStudies'
+import Dropzone from 'react-dropzone';
+import filesToStudies from './filesToStudies';

-import { extensionManager } from '../../App.jsx'
+import { extensionManager } from '../../App.tsx';

-import { Icon, Button } from '@ohif/ui'
+import { Icon, Button } from '@ohif/ui';

 const getLoadButton = (onDrop, text, isDir) => {
  return (
@@ -21,7 +21,7 @@ const getLoadButton = (onDrop, text, isDir) => {
            disabled={false}
            endIcon={<Icon name="launch-arrow" />} // launch-arrow | launch-info
            className={classnames('font-bold', 'ml-2')}
-            onClick={() => { }}
+            onClick={() => {}}
          >
            {text}
            {isDir ? (
@@ -36,41 +36,42 @@ const getLoadButton = (onDrop, text, isDir) => {
          </Button>
        </div>
      )}
-    </Dropzone>)
-}
+    </Dropzone>
+  );
+};

 function Local() {
  const navigate = useNavigate();
-  const dropzoneRef = useRef()
+  const dropzoneRef = useRef();

  // Initializing the dicom local dataSource
-  const dataSourceModules = extensionManager.modules[MODULE_TYPES.DATA_SOURCE]
+  const dataSourceModules = extensionManager.modules[MODULE_TYPES.DATA_SOURCE];
  const localDataSources = dataSourceModules.reduce((acc, curr) => {
-    const mods = []
-    curr.module.forEach((mod) => {
+    const mods = [];
+    curr.module.forEach(mod => {
      if (mod.type === 'localApi') {
-        mods.push(mod)
+        mods.push(mod);
      }
-    })
-    return acc.concat(mods)
-  }, [])
+    });
+    return acc.concat(mods);
+  }, []);

-  const firstLocalDataSource = localDataSources[0]
-  const dataSource = firstLocalDataSource.createDataSource({})
+  const firstLocalDataSource = localDataSources[0];
+  const dataSource = firstLocalDataSource.createDataSource({});

-  const onDrop = async (acceptedFiles) => {
-    const studies = await filesToStudies(acceptedFiles, dataSource)
+  const onDrop = async acceptedFiles => {
+    const studies = await filesToStudies(acceptedFiles, dataSource);
    // Todo: navigate to work list and let user select a mode
-    navigate(`/viewer/dicomlocal?StudyInstanceUIDs=${studies[0]}`)
-  }
+    navigate(`/viewer/dicomlocal?StudyInstanceUIDs=${studies[0]}`);
+  };

  // Set body style
  useEffect(() => {
-    document.body.classList.add('bg-black')
+    document.body.classList.add('bg-black');
    return () => {
-      document.body.classList.remove('bg-black')
-    }
-  }, [])
+      document.body.classList.remove('bg-black');
+    };
+  }, []);

  return (
    <Dropzone ref={dropzoneRef} onDrop={onDrop} noClick>
@@ -104,7 +105,7 @@ function Local() {
        </div>
      )}
    </Dropzone>
-  )
+  );
 }

-export default Local
+export default Local;
@@ -61,6 +61,7 @@ export default function ModeRoute({
  dataSourceName,
  extensionManager,
  servicesManager,
+  commandsManager,
  hotkeysManager,
 }) {
  // Parse route params/querystring
@@ -197,16 +198,20 @@ export default function ModeRoute({
      return;
    }
    // TODO: For some reason this is running before the Providers
-    // are calling setServiceImplementationf
-    // TOOD -> iterate through services.
+    // are calling setServiceImplementation
+    // TODO -> iterate through services.

    // Extension

    // Add SOPClassHandlers to a new SOPClassManager.
    DisplaySetService.init(extensionManager, sopClassHandlers);

-    extensionManager.onModeEnter();
-    mode?.onModeEnter({ servicesManager, extensionManager });
+    extensionManager.onModeEnter({
+      servicesManager,
+      extensionManager,
+      commandsManager,
+    });
+    mode?.onModeEnter({ servicesManager, extensionManager, commandsManager });

    // Adding hanging protocols of extensions after onModeEnter since
    // it will reset the protocols
@@ -214,6 +219,7 @@ export default function ModeRoute({
      const hangingProtocolModule = extensionManager.getModuleEntry(
        extensionProtocols
      );
+
      if (hangingProtocolModule?.protocols) {
        HangingProtocolService.addProtocols(hangingProtocolModule.protocols);
      }
@@ -232,8 +238,6 @@ export default function ModeRoute({

      return await defaultRouteInit({
        servicesManager,
-        extensionManager,
-        hotkeysManager,
        studyInstanceUIDs,
        dataSource,
      });
@@ -22,8 +22,7 @@ function SignoutCallbackComponent({ userManager }) {
    .then(user => onRedirectSuccess(user))
    .catch(error => onRedirectError(error));

-  // todo: add i18n
-  return <div>Redirecting...</div>;
+  return null;
 }

 SignoutCallbackComponent.propTypes = {
@@ -12,8 +12,6 @@ import { useAppConfig } from '@state';
 import { useDebounce, useQuery } from '@hooks';
 import { utils, hotkeys } from '@ohif/core';

-const { sortBySeriesDate } = utils;
-
 import {
  Icon,
  StudyListExpandedRow,
@@ -31,6 +29,8 @@ import {

 import i18n from '@ohif/i18n';

+const { sortBySeriesDate } = utils;
+
 const { availableLanguages, defaultLanguage, currentLanguage } = i18n;

 const seriesInStudiesMap = new Map();
@@ -309,6 +309,8 @@ function WorkList({
          gridCol: 4,
        },
      ],
+      // Todo: This is actually running for all rows, even if they are
+      // not clicked on.
      expandedContent: (
        <StudyListExpandedRow
          seriesTableColumns={{
@@ -334,7 +336,6 @@ function WorkList({
            const isFirst = i === 0;

            const isValidMode = mode.isValidMode({ modalities });
-
            // TODO: Modes need a default/target route? We mostly support a single one for now.
            // We should also be using the route path, but currently are not
            // mode.routeName
@@ -27,6 +27,7 @@ export default function buildModeRoutes({
  dataSources,
  extensionManager,
  servicesManager,
+  commandsManager,
  hotkeysManager,
 }) {
  const routes = [];
@@ -58,7 +59,9 @@ export default function buildModeRoutes({
          dataSourceName={dataSourceName}
          extensionManager={extensionManager}
          servicesManager={servicesManager}
+          commandsManager={commandsManager}
          hotkeysManager={hotkeysManager}
+          commandsManager={commandsManager}
        />
      );

@@ -80,7 +83,9 @@ export default function buildModeRoutes({
        dataSourceName={defaultDataSourceName}
        extensionManager={extensionManager}
        servicesManager={servicesManager}
+        commandsManager={commandsManager}
        hotkeysManager={hotkeysManager}
+        commandsManager={commandsManager}
      />
    );

@@ -33,6 +33,7 @@ const createRoutes = ({
  dataSources,
  extensionManager,
  servicesManager,
+  commandsManager,
  hotkeysManager,
  routerBasename,
 }) => {
@@ -42,6 +43,7 @@ const createRoutes = ({
      dataSources,
      extensionManager,
      servicesManager,
+      commandsManager,
      hotkeysManager,
    }) || [];

@@ -67,7 +69,7 @@ const createRoutes = ({
  // Note: PrivateRoutes in react-router-dom 6.x should be defined within
  // a Route element
  return (
-    <Routes basename={routerBasename}>
+    <Routes>
      {allRoutes.map((route, i) => {
        return route.private === true ? (
          <Route