Compare commits

...
Author SHA1 Message Date
ohif-bot 2a647fd618 chore(release): publish [skip ci]
- @ohif/extension-dicom-rt@0.2.7
 - @ohif/extension-dicom-segmentation@0.3.4
 - @ohif/extension-vtk@1.6.10
 - @ohif/core@2.9.14
 - @ohif/viewer@4.2.16
2020-08-10 09:21:53 +00:00
James Petts f8fc31bcac [IDC-1670] Better display of derived datasets in side panel. (#1962)
* WIP

* WIP

* WIP

* WIP

* Working click on seg.

* Load SEG if not loaded and set active.

* RTSTRUCT

* feat: 🎸 Display SEG and RTSTRUCT in side panel

* Throw error if dataset not available.

* Add delay in microscopy viewer e2e test.

* Add delay in microscopy viewer e2e test.
2020-08-10 11:20:31 +02:00
ohif-bot b7ab88b0f1 chore(release): publish [skip ci]
- @ohif/extension-cornerstone@2.8.5
 - @ohif/viewer@4.2.15
2020-08-05 09:48:08 +00:00
James Petts 57a30d7c34 [IDC-1956] - Remove loading %age which is always zero. (#1959)
* Remove loading percent.

* fix: 🐛 Remove % loading on cornerstone viewport
2020-08-05 11:46:42 +02:00
ohif-bot cd90665b0e chore(release): publish [skip ci]
- @ohif/extension-dicom-rt@0.2.6
 - @ohif/viewer@4.2.14
2020-08-05 09:03:27 +00:00
James Petts 98c657231e IDC-1897 (#1940)
* show warnings for rt.

* Remove unneeded old code
2020-08-05 11:00:47 +02:00
ohif-bot 14da247318 chore(release): publish [skip ci]
- @ohif/extension-vtk@1.6.9
 - @ohif/ui@1.5.3
 - @ohif/viewer@4.2.13
2020-07-23 07:44:17 +00:00
Erik Ziegler 6a77d6c778 chore: Use same config for branch deploys as for deploy previews (#1893) (#1916) 2020-07-23 09:42:42 +02:00
Sinan 8f1785446b docs: Update readme for end to end test commands (#1774) 2020-07-22 21:52:23 +02:00
39 changed files with 593 additions and 224 deletions

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+13
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@@ -21,6 +21,19 @@ mv platform/viewer/dist/* .netlify/www/pwa -v
# Build && Move script output
# yarn run build:package
# Build && Move Docz Output
# Using local yarn install to prevent Gatsby from needing to access
# node_modules above the platform/ui folder
cd platform/ui
yarn install
yarn run build
cd ../..
mkdir -p ./.netlify/www/ui
mv platform/ui/.docz/dist/* .netlify/www/ui -v
# Cache all of the node_module dependencies in
# extensions, modules, and platform packages
yarn run lerna:cache
echo 'Nothing left to see here. Go home, folks.'
# Build using react-scripts
+8
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@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.8.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.4...@ohif/extension-cornerstone@2.8.5) (2020-08-05)
**Note:** Version bump only for package @ohif/extension-cornerstone
## [2.8.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-cornerstone@2.8.3...@ohif/extension-cornerstone@2.8.4) (2020-07-13)
+2 -2
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-cornerstone",
"version": "2.8.4",
"version": "2.8.5",
"description": "OHIF extension for Cornerstone",
"author": "OHIF",
"license": "MIT",
@@ -51,6 +51,6 @@
"classnames": "^2.2.6",
"lodash.merge": "^4.6.2",
"lodash.throttle": "^4.1.1",
"react-cornerstone-viewport": "2.3.9"
"react-cornerstone-viewport": "4.0.1"
}
}
+16
View File
@@ -3,6 +3,22 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [0.2.7](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.6...@ohif/extension-dicom-rt@0.2.7) (2020-08-10)
**Note:** Version bump only for package @ohif/extension-dicom-rt
## [0.2.6](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.5...@ohif/extension-dicom-rt@0.2.6) (2020-08-05)
**Note:** Version bump only for package @ohif/extension-dicom-rt
## [0.2.5](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-rt@0.2.4...@ohif/extension-dicom-rt@0.2.5) (2020-07-13)
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-rt",
"version": "0.2.5",
"version": "0.2.7",
"description": "OHIF extension for rendering DICOM RTSTRUCTs on top of cornerstone images.",
"author": "OHIF",
"license": "MIT",
@@ -1,5 +1,6 @@
import { MODULE_TYPES, utils, DICOMWeb } from '@ohif/core';
import loadRTStruct from './loadRTStruct';
import getSourceDisplaySet from './getSourceDisplaySet';
import id from './id';
@@ -67,6 +68,10 @@ const OHIFDicomRTStructSopClassHandler = {
}
}
rtStructDisplaySet.getSourceDisplaySet = function(studies) {
return getSourceDisplaySet(studies, rtStructDisplaySet);
};
rtStructDisplaySet.load = function(referencedDisplaySet, studies) {
return loadRTStruct(
rtStructDisplaySet,
@@ -17,7 +17,6 @@ const { studyMetadataManager } = utils;
const refreshViewport = () => {
cornerstone.getEnabledElements().forEach(enabledElement => {
debugger;
if (enabledElement.image) {
cornerstone.updateImage(enabledElement.element);
}
@@ -40,7 +39,6 @@ const RTPanel = ({
activeIndex,
isOpen,
onContourItemClick,
noContoursNotification,
activeContexts = [],
contexts = {},
}) => {
@@ -126,7 +124,7 @@ const RTPanel = ({
}, [isOpen]);
const toContourItem = (
{ ROINumber, ROIName, RTROIObservations, colorArray, visible },
{ ROINumber, ROIName, RTROIObservations, colorArray, visible, isSupported },
loadedSet
) => {
let interpretedType = '';
@@ -139,6 +137,7 @@ const RTPanel = ({
<StructureSetItem
key={ROINumber}
selected={isSameContour}
isDisabled={!isSupported}
onClick={() => {
setSelectedContour(isSameContour ? null : ROINumber);
@@ -160,12 +159,6 @@ const RTPanel = ({
imageIds
);
if (!imageId) {
noContoursNotification();
return;
}
const frameIndex = imageIds.indexOf(imageId);
const SOPInstanceUID = cornerstone.metaData.get(
'SOPInstanceUID',
@@ -249,7 +242,7 @@ const RTPanel = ({
key={SeriesInstanceUID}
title={metadata.StructureSetLabel}
loading={!isLoaded || !loadedSet}
visible={isLoaded && loadedSet.visible}
visible={isLoaded && loadedSet && loadedSet.visible}
hideVisibleButton={!isLoaded}
expanded={
isLoaded &&
@@ -22,11 +22,6 @@
width: 100%;
}
.dcmrt-structure-set-item.selected .item-actions {
height: 35px;
visibility: visible;
}
.dcmrt-structure-set-item .item-actions {
margin-left: -1px;
background-color: var(--ui-gray-darker);
@@ -47,7 +42,8 @@
transition: all 0.3s ease;
}
.dcmrt-structure-set-item .item-actions .btnAction:hover, .dcmrt-structure-set-item .item-actions .btnAction:active {
.dcmrt-structure-set-item .item-actions .btnAction:hover,
.dcmrt-structure-set-item .item-actions .btnAction:active {
color: var(--text-primary-color);
}
@@ -86,3 +82,12 @@
.dcmrt-structure-set-item .item-label .eye-icon.--visible {
color: var(--default-color);
}
.dcmrt-structure-set-item.isDisabled .item-color-section {
background-color: #e29e4a;
color: #fff;
}
.dcmrt-structure-set-item.isDisabled .item-label {
color: var(--text-disabled-color);
}
@@ -1,6 +1,6 @@
import React, { useState, useEffect } from 'react';
import PropTypes from 'prop-types';
import { TableListItem, Icon } from '@ohif/ui';
import { TableListItem, Icon, Tooltip, OverlayTrigger } from '@ohif/ui';
import './StructureSetItem.css';
@@ -20,6 +20,7 @@ ColoredCircle.propTypes = {
const StructureSetItem = ({
index,
label,
isDisabled,
onClick,
itemClass,
color,
@@ -31,22 +32,44 @@ const StructureSetItem = ({
useEffect(() => {
setIsVisible(visible);
}, [visible])
}, [visible]);
return (
<div className={`dcmrt-structure-set-item ${selected && 'selected'}`}>
<TableListItem
key={index}
itemKey={index}
itemIndex={index}
itemClass={itemClass}
itemMeta={<ColoredCircle color={color} />}
itemMetaClass="item-color-section"
onItemClick={onClick}
>
<div>
<div className="item-label" style={{ marginBottom: 4 }}>
<span>{label}</span>
let dcmrtClassNames = `dcmrt-structure-set-item`;
if (selected) {
dcmrtClassNames += ' selected';
}
if (isDisabled) {
dcmrtClassNames += ' isDisabled';
}
const warningIcon = (
<span>
<Icon name="exclamation-triangle" />
</span>
);
const tableListItem = (
<TableListItem
key={index}
itemKey={index}
itemIndex={index}
itemClass={itemClass}
itemMeta={isDisabled ? warningIcon : <ColoredCircle color={color} />}
itemMetaClass="item-color-section"
onItemClick={() => {
if (isDisabled) {
return;
}
onClick();
}}
>
<div>
<div className="item-label" style={{ marginBottom: 4 }}>
<span>{label}</span>
{!isDisabled && (
<Icon
className={`eye-icon ${isVisible && '--visible'}`}
name={isVisible ? 'eye' : 'eye-closed'}
@@ -54,37 +77,72 @@ const StructureSetItem = ({
height="20px"
onClick={event => {
event.stopPropagation();
if (isDisabled) {
return;
}
const newVisibility = !isVisible;
setIsVisible(newVisibility);
onVisibilityChange(newVisibility);
}}
/>
</div>
{false && <div className="item-info">{'...'}</div>}
{false && (
<div className="item-actions">
<button
className="btnAction"
onClick={() => console.log('Relabelling...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Relabel
</button>
<button
className="btnAction"
onClick={() => console.log('Editing description...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Description
</button>
</div>
)}
</div>
</TableListItem>
{false && <div className="item-info">{'...'}</div>}
{false && (
<div className="item-actions">
<button
className="btnAction"
onClick={() => console.log('Relabelling...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Relabel
</button>
<button
className="btnAction"
onClick={() => console.log('Editing description...')}
>
<span style={{ marginRight: '4px' }}>
<Icon name="edit" width="14px" height="14px" />
</span>
Description
</button>
</div>
)}
</div>
</TableListItem>
);
return (
<div className={dcmrtClassNames}>
<React.Fragment>
{isDisabled ? (
<OverlayTrigger
key={index}
placement="left"
overlay={
<Tooltip
placement="left"
className="in tooltip-warning"
id="tooltip-left"
>
<div className="warningTitle">Unsupported Region</div>
<div className="warningContent">
Contour type currently unsupported.
</div>
</Tooltip>
}
>
<div>{tableListItem}</div>
</OverlayTrigger>
) : (
<React.Fragment>{tableListItem} </React.Fragment>
)}
</React.Fragment>
</div>
);
};
@@ -99,7 +157,7 @@ StructureSetItem.propTypes = {
StructureSetItem.defaultProps = {
itemClass: '',
onClick: () => { },
onClick: () => {},
};
export default StructureSetItem;
@@ -0,0 +1,38 @@
export default function getSourceDisplaySet(studies, rtStructDisplaySet) {
const referencedDisplaySet = _getReferencedDisplaySet(
rtStructDisplaySet,
studies
);
rtStructDisplaySet.load(referencedDisplaySet, studies);
return referencedDisplaySet;
}
const _getReferencedDisplaySet = (rtStructDisplaySet, studies) => {
let allDisplaySets = [];
studies.forEach(study => {
allDisplaySets = allDisplaySets.concat(study.displaySets);
});
const otherDisplaySets = allDisplaySets.filter(
ds => ds.displaySetInstanceUID !== rtStructDisplaySet.displaySetInstanceUID
);
const ReferencedSeriesSequence = Array.isArray(
rtStructDisplaySet.metadata.ReferencedSeriesSequence
)
? rtStructDisplaySet.metadata.ReferencedSeriesSequence
: [rtStructDisplaySet.metadata.ReferencedSeriesSequence];
const referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
ReferencedSeries => ReferencedSeries.SeriesInstanceUID
);
const referencedDisplaySet = otherDisplaySets.find(ds =>
referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
);
return referencedDisplaySet;
};
-12
View File
@@ -21,20 +21,9 @@ export default {
init({ servicesManager, configuration });
},
getPanelModule({ commandsManager, servicesManager, api }) {
const { UINotificationService } = servicesManager.services;
const ExtendedRTPanel = props => {
const { activeContexts } = api.hooks.useAppContext();
const noContoursNotificationHandler = () => {
UINotificationService.show({
title: 'ROI Contour empty',
message: 'The ROI contour has no structure set data.',
type: 'error',
autoClose: false,
});
};
const contourItemClickHandler = contourData => {
commandsManager.runCommand('jumpToImage', contourData);
};
@@ -45,7 +34,6 @@ export default {
onContourItemClick={contourItemClickHandler}
activeContexts={activeContexts}
contexts={api.contexts}
noContoursNotification={noContoursNotificationHandler}
/>
);
};
+15 -8
View File
@@ -74,12 +74,7 @@ export default async function loadRTStruct(
continue;
}
_setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour
);
const isSupported = false;
for (let c = 0; c < ContourSequence.length; c++) {
const {
@@ -91,10 +86,12 @@ export default async function loadRTStruct(
if (ContourGeometricType !== 'CLOSED_PLANAR') {
// TODO: Do we want to visualise types other than closed planar?
// We could easily do open planar.
// We could easily do open planar and point.
continue;
}
isSupported = true;
const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID;
const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID);
const imageIdSpecificToolData = _getOrCreateImageIdSpecificToolData(
@@ -126,6 +123,14 @@ export default async function loadRTStruct(
imageIdSpecificToolData.push(measurementData);
}
_setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour,
isSupported
);
}
_setToolEnabledIfNotEnabled(rtStructDisplayToolName);
@@ -155,7 +160,8 @@ function _setROIContourMetadata(
structureSet,
StructureSetROISequence,
RTROIObservationsSequence,
ROIContour
ROIContour,
isSupported
) {
const StructureSetROI = StructureSetROISequence.find(
structureSetROI =>
@@ -167,6 +173,7 @@ function _setROIContourMetadata(
ROIName: StructureSetROI.ROIName,
ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm,
ROIDescription: StructureSetROI.ROIDescription,
isSupported,
visible: true,
};
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [0.3.4](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.3...@ohif/extension-dicom-segmentation@0.3.4) (2020-08-10)
**Note:** Version bump only for package @ohif/extension-dicom-segmentation
## [0.3.3](https://github.com/OHIF/Viewers/compare/@ohif/extension-dicom-segmentation@0.3.2...@ohif/extension-dicom-segmentation@0.3.3) (2020-07-13)
**Note:** Version bump only for package @ohif/extension-dicom-segmentation
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-dicom-segmentation",
"version": "0.3.3",
"version": "0.3.4",
"description": "OHIF extension for viewing segmentations in the 2D MPR view",
"author": "OHIF",
"license": "MIT",
@@ -6,6 +6,9 @@ import moment from 'moment';
import { utils, log } from '@ohif/core';
import { ScrollableArea, TableList, Icon } from '@ohif/ui';
import setActiveLabelmap from '../../utils/setActiveLabelMap';
import refreshViewports from '../../utils/refreshViewports';
import {
BrushColorSelector,
BrushRadius,
@@ -19,12 +22,6 @@ import SegmentationSettings from '../SegmentationSettings/SegmentationSettings';
const { studyMetadataManager } = utils;
const refreshViewport = () => {
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
};
/**
* SegmentationPanel component
*
@@ -68,8 +65,7 @@ const SegmentationPanel = ({
*/
const [state, setState] = useState({
brushRadius: DEFAULT_BRUSH_RADIUS,
brushColor:
'rgba(221, 85, 85, 1)',
brushColor: 'rgba(221, 85, 85, 1)',
selectedSegment: null,
selectedSegmentation: null,
showSegmentationSettings: false,
@@ -78,7 +74,7 @@ const SegmentationPanel = ({
segmentList: [],
cachedSegmentsProperties: [],
isLoading: false,
isDisabled: true
isDisabled: true,
});
useEffect(() => {
@@ -112,7 +108,10 @@ const SegmentationPanel = ({
* allows us to easily watch the module or the segmentations loading process in any other component
* without subscribing to external events.
*/
document.addEventListener('extensiondicomsegmentationsegloaded', refreshSegmentations);
document.addEventListener(
'extensiondicomsegmentationsegloaded',
refreshSegmentations
);
/*
* These are specific to each element;
@@ -127,7 +126,10 @@ const SegmentationPanel = ({
);
return () => {
document.removeEventListener('extensiondicomsegmentationsegloaded', refreshSegmentations);
document.removeEventListener(
'extensiondicomsegmentationsegloaded',
refreshSegmentations
);
cornerstoneTools.store.state.enabledElements.forEach(enabledElement =>
enabledElement.removeEventListener(
'cornerstonetoolslabelmapmodified',
@@ -169,26 +171,29 @@ const SegmentationPanel = ({
selectedSegmentation: brushStackState.activeLabelmapIndex,
labelmapList,
segmentList,
isDisabled
isDisabled,
}));
} else {
setState(state => ({
...state,
labelmapList: [],
segmentList: [],
isDisabled
isDisabled,
}));
}
}
}, [
viewports,
activeIndex,
state.isLoading
]);
}, [viewports, activeIndex, state.isLoading]);
useEffect(() => {
refreshSegmentations();
}, [viewports, activeIndex, isOpen, state.selectedSegmentation, activeContexts, state.isLoading]);
}, [
viewports,
activeIndex,
isOpen,
state.selectedSegmentation,
activeContexts,
state.isLoading,
]);
/* Handle open/closed panel behaviour */
useEffect(() => {
@@ -223,12 +228,10 @@ const SegmentationPanel = ({
title: displayDescription,
description: displayDate,
onClick: async () => {
const activatedLabelmapIndex = await _setActiveLabelmap(
const activatedLabelmapIndex = await setActiveLabelmap(
activeViewport,
studies,
displaySet,
firstImageId,
brushStackState.activeLabelmapIndex,
() => onSelectedSegmentationChange(),
onDisplaySetLoadFailure
);
@@ -376,9 +379,13 @@ const SegmentationPanel = ({
return !segmentsHidden[segmentIndex];
};
const cachedSegmentProperties = state.cachedSegmentsProperties[segmentNumber];
const cachedSegmentProperties =
state.cachedSegmentsProperties[segmentNumber];
let visible = isSegmentVisible();
if (cachedSegmentProperties && cachedSegmentProperties.visible !== visible) {
if (
cachedSegmentProperties &&
cachedSegmentProperties.visible !== visible
) {
toggleSegmentVisibility();
}
@@ -406,8 +413,10 @@ const SegmentationPanel = ({
onSegmentVisibilityChange(segmentNumber, newVisibility);
}
updateCachedSegmentsProperties(segmentNumber, { visible: newVisibility });
refreshViewport();
updateCachedSegmentsProperties(segmentNumber, {
visible: newVisibility,
});
refreshViewports();
}}
/>
);
@@ -429,10 +438,9 @@ const SegmentationPanel = ({
const segmentsProperties = state.cachedSegmentsProperties;
const segmentProperties = state.cachedSegmentsProperties[segmentNumber];
segmentsProperties[segmentNumber] =
segmentProperties ?
{ ...segmentProperties, ...properties } :
properties;
segmentsProperties[segmentNumber] = segmentProperties
? { ...segmentProperties, ...properties }
: properties;
updateState('cachedSegmentsProperties', segmentsProperties);
};
@@ -499,10 +507,13 @@ const SegmentationPanel = ({
configuration.fillAlphaInactive = newConfiguration.fillAlphaInactive;
configuration.outlineAlphaInactive = newConfiguration.outlineAlphaInactive;
onConfigurationChange(newConfiguration);
refreshViewport();
refreshViewports();
};
const disabledConfigurationFields = ['outlineAlpha', 'shouldRenderInactiveLabelmaps'];
const disabledConfigurationFields = [
'outlineAlpha',
'shouldRenderInactiveLabelmaps',
];
if (state.showSegmentationSettings) {
return (
<SegmentationSettings
@@ -514,7 +525,10 @@ const SegmentationPanel = ({
);
} else {
return (
<div className={`dcmseg-segmentation-panel ${state.isDisabled && 'disabled'}`}>
<div
className={`dcmseg-segmentation-panel ${state.isDisabled &&
'disabled'}`}
>
<Icon
className="cog-icon"
name="cog"
@@ -613,57 +627,6 @@ const _getReferencedSegDisplaysets = (StudyInstanceUID, SeriesInstanceUID) => {
return referencedDisplaysets;
};
/**
*
*
* @param {*} viewportSpecificData
* @param {*} studies
* @param {*} displaySet
* @param {*} firstImageId
* @param {*} activeLabelmapIndex
* @returns
*/
const _setActiveLabelmap = async (
viewportSpecificData,
studies,
displaySet,
firstImageId,
activeLabelmapIndex,
callback = () => { },
onDisplaySetLoadFailure
) => {
if (displaySet.labelmapIndex === activeLabelmapIndex) {
log.warn(`${activeLabelmapIndex} is already the active labelmap`);
return displaySet.labelmapIndex;
}
if (!displaySet.isLoaded) {
// What props does this expect `viewportSpecificData` to have?
// TODO: Should this return the `labelmapIndex`?
const loadPromise = displaySet.load(viewportSpecificData, studies);
loadPromise.catch(error => {
onDisplaySetLoadFailure(error);
// Return old index.
return activeLabelmapIndex;
});
await loadPromise;
}
const { state } = cornerstoneTools.getModule('segmentation');
const brushStackState = state.series[firstImageId];
brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
refreshViewport();
callback();
return displaySet.labelmapIndex;
};
/**
*
* @param {*} firstImageId
@@ -683,7 +646,7 @@ const _setActiveSegment = (firstImageId, segmentIndex, activeSegmentIndex) => {
brushStackState.labelmaps3D[brushStackState.activeLabelmapIndex];
labelmap3D.activeSegmentIndex = segmentIndex;
refreshViewport();
refreshViewports();
return segmentIndex;
};
@@ -1,5 +1,6 @@
import { MODULE_TYPES, utils } from '@ohif/core';
import loadSegmentation from './loadSegmentation';
import getSourceDisplaySet from './getSourceDisplaySet';
// TODO: Should probably use dcmjs for this
const SOP_CLASS_UIDS = {
@@ -54,6 +55,10 @@ export default function getSopClassHandlerModule({ servicesManager }) {
SeriesDescription,
};
segDisplaySet.getSourceDisplaySet = function(studies) {
return getSourceDisplaySet(studies, segDisplaySet);
};
segDisplaySet.load = function(referencedDisplaySet, studies) {
return loadSegmentation(segDisplaySet, referencedDisplaySet, studies);
};
@@ -0,0 +1,37 @@
import setActiveLabelmap from './utils/setActiveLabelMap';
export default function getSourceDisplaySet(studies, segDisplaySet) {
const referencedDisplaySet = _getReferencedDisplaySet(segDisplaySet, studies);
setActiveLabelmap(referencedDisplaySet, studies, segDisplaySet);
return referencedDisplaySet;
}
const _getReferencedDisplaySet = (segDisplaySet, studies) => {
let allDisplaySets = [];
studies.forEach(study => {
allDisplaySets = allDisplaySets.concat(study.displaySets);
});
const otherDisplaySets = allDisplaySets.filter(
ds => ds.displaySetInstanceUID !== segDisplaySet.displaySetInstanceUID
);
const ReferencedSeriesSequence = Array.isArray(
segDisplaySet.metadata.ReferencedSeriesSequence
)
? segDisplaySet.metadata.ReferencedSeriesSequence
: [segDisplaySet.metadata.ReferencedSeriesSequence];
const referencedSeriesInstanceUIDs = ReferencedSeriesSequence.map(
ReferencedSeries => ReferencedSeries.SeriesInstanceUID
);
const referencedDisplaySet = otherDisplaySets.find(ds =>
referencedSeriesInstanceUIDs.includes(ds.SeriesInstanceUID)
);
return referencedDisplaySet;
};
@@ -0,0 +1,5 @@
export default function refreshViewports() {
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
}
@@ -0,0 +1,67 @@
import { utils, log } from '@ohif/core';
import cornerstoneTools from 'cornerstone-tools';
import refreshViewports from './refreshViewports';
const { studyMetadataManager } = utils;
/**
*
*
* @param {*} viewportSpecificData
* @param {*} studies
* @param {*} displaySet
* @param {*} firstImageId
* @param {*} activeLabelmapIndex
* @returns
*/
export default async function setActiveLabelmap(
referencedDisplaySet,
studies,
displaySet,
callback = () => {},
onDisplaySetLoadFailure = err => {
throw new Error(err.message);
}
) {
const studyMetadata = studyMetadataManager.get(
referencedDisplaySet.StudyInstanceUID
);
const firstImageId = studyMetadata.getFirstImageId(
referencedDisplaySet.displaySetInstanceUID
);
let { state } = cornerstoneTools.getModule('segmentation');
let brushStackState = state.series[firstImageId];
const activeLabelmapIndex = brushStackState
? brushStackState.activeLabelmapIndex
: undefined;
if (displaySet.labelmapIndex === activeLabelmapIndex) {
log.warn(`${activeLabelmapIndex} is already the active labelmap`);
return displaySet.labelmapIndex;
}
if (!displaySet.isLoaded) {
const loadPromise = displaySet.load(referencedDisplaySet, studies);
loadPromise.catch(error => {
onDisplaySetLoadFailure(error);
// Return old index.
return activeLabelmapIndex;
});
await loadPromise;
}
// This might have just been created, so need to use the non-cached value.
state = cornerstoneTools.getModule('segmentation').state;
brushStackState = state.series[firstImageId];
brushStackState.activeLabelmapIndex = displaySet.labelmapIndex;
refreshViewports();
callback();
return displaySet.labelmapIndex;
}
+16
View File
@@ -3,6 +3,22 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.6.10](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.9...@ohif/extension-vtk@1.6.10) (2020-08-10)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.6.9](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.8...@ohif/extension-vtk@1.6.9) (2020-07-23)
**Note:** Version bump only for package @ohif/extension-vtk
## [1.6.8](https://github.com/OHIF/Viewers/compare/@ohif/extension-vtk@1.6.7...@ohif/extension-vtk@1.6.8) (2020-07-22)
**Note:** Version bump only for package @ohif/extension-vtk
+3 -3
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/extension-vtk",
"version": "1.6.8",
"version": "1.6.10",
"description": "OHIF extension for VTK.js",
"author": "OHIF",
"license": "MIT",
@@ -53,8 +53,8 @@
"react-vtkjs-viewport": "^0.9.0"
},
"devDependencies": {
"@ohif/core": "^2.9.13",
"@ohif/ui": "^1.5.2",
"@ohif/core": "^2.9.14",
"@ohif/ui": "^1.5.3",
"cornerstone-tools": "4.15.1",
"cornerstone-wado-image-loader": "^3.1.0",
"dicom-parser": "^1.8.3",
+26
View File
@@ -0,0 +1,26 @@
#!/bin/sh
NODE_MODULES_CACHE="./node_modules"
LERNA_CACHE="$NODE_MODULES_CACHE/lerna-cache"
echo "Running netlify-lerna-cache.sh"
mkdir -p "$NODE_MODULES_CACHE/lerna-cache"
cache_deps() {
PACKAGES=$(ls -1 $1)
for PKG in $PACKAGES
do
PKG_NODE_MODULES="$1/$PKG/node_modules"
if [ -d $PKG_NODE_MODULES ];
then
mv $PKG_NODE_MODULES $LERNA_CACHE/$PKG
echo "Cached node modules for $PKG"
else
echo "Unable to cache node modules for $PKG"
fi
done
}
cache_deps platform
cache_deps extensions
cache_deps modes
+27
View File
@@ -0,0 +1,27 @@
#!/bin/sh
NODE_MODULES_CACHE="./node_modules"
LERNA_CACHE="$NODE_MODULES_CACHE/lerna-cache"
echo "Running netlify-lerna-restore.sh"
mkdir -p "$NODE_MODULES_CACHE/lerna-cache"
echo "$NODE_MODULES_CACHE/lerna-cache/*"
restore_deps() {
PACKAGES=$(ls -1 $1)
for PKG in $PACKAGES
do
PKG_CACHE="$LERNA_CACHE/$PKG"
if [ -d $PKG_CACHE ];
then
mv $PKG_CACHE $1/$PKG/node_modules
echo "Restored node modules for $PKG"
else
echo "Unable to restore cache for $PKG"
fi
done
}
restore_deps platform
restore_deps extensions
restore_deps modes
+6 -7
View File
@@ -8,6 +8,11 @@
# managed by CircleCI and deployed to our Google Hosting
#
[build]
base = ""
publish = ".netlify/www/"
command = "chmod +x .netlify/build-deploy-preview.sh && .netlify/build-deploy-preview.sh"
# NODE_VERSION in root `.nvmrc` takes priority
# YARN_FLAGS: https://www.netlify.com/docs/build-gotchas/#yarn
[build.environment]
@@ -16,19 +21,13 @@
YARN_VERSION = "1.17.3"
RUBY_VERSION = "2.6.2"
YARN_FLAGS = "--no-ignore-optional --pure-lockfile"
NETLIFY_RESTORE = "1"
# Production context: all deploys from the Production branch set in your site's
# deploy contexts will inherit these settings.
[context.production]
ignore = "exit 0" # Never build production; We'll let our CI do that
# Deploy Preview context: all deploys generated from a pull/merge request will
# inherit these settings.
[context.deploy-preview]
base = ""
publish = ".netlify/www/"
command = "chmod +x .netlify/build-deploy-preview.sh && .netlify/build-deploy-preview.sh"
[[headers]]
# Define which paths this specific [[headers]] block will cover.
for = "/*"
+3
View File
@@ -34,6 +34,9 @@
"see-changed": "lerna changed",
"docs:publish": "chmod +x ./build-and-publish-docs.sh && ./build-and-publish-docs.sh",
"release": "yarn run lerna:version && yarn run lerna:publish",
"lerna:cache": "[ $NETLIFY_RESTORE = 1 ] && ./netlify-lerna-cache.sh || :",
"lerna:restore": "[ $NETLIFY_RESTORE = 1 ] && ./netlify-lerna-restore.sh || :",
"preinstall": "yarn lerna:restore",
"lerna:version": "npx lerna version prerelease --force-publish",
"lerna:publish": "lerna publish from-package --canary --dist-tag canary",
"link-list": "npm ls --depth=0 --link=true"
+8
View File
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [2.9.14](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.13...@ohif/core@2.9.14) (2020-08-10)
**Note:** Version bump only for package @ohif/core
## [2.9.13](https://github.com/OHIF/Viewers/compare/@ohif/core@2.9.12...@ohif/core@2.9.13) (2020-07-22)
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/core",
"version": "2.9.13",
"version": "2.9.14",
"description": "Generic business logic for web-based medical imaging applications",
"author": "OHIF Core Team",
"license": "MIT",
@@ -139,9 +139,11 @@ export class StudyMetadata extends Metadata {
if (displaySet) {
displaySet.sopClassModule = true;
displaySet.isDerived
? this._addDerivedDisplaySet(displaySet)
: displaySets.push(displaySet);
if (displaySet.isDerived) {
this._addDerivedDisplaySet(displaySet);
}
displaySets.push(displaySet);
return displaySets;
}
+8
View File
@@ -3,6 +3,14 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [1.5.3](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.5.2...@ohif/ui@1.5.3) (2020-07-23)
**Note:** Version bump only for package @ohif/ui
## [1.5.2](https://github.com/OHIF/Viewers/compare/@ohif/ui@1.5.1...@ohif/ui@1.5.2) (2020-07-22)
+25
View File
@@ -0,0 +1,25 @@
const path = require('path');
// ~~ Plugins
const PnpWebpackPlugin = require(`pnp-webpack-plugin`); // Required until Webpack@5
exports.onCreateWebpackConfig = args => {
args.actions.setWebpackConfig({
node: { fs: 'empty' },
resolve: {
plugins: [PnpWebpackPlugin],
// Note the '..' in the path because docz gatsby project lives in the '.docz' directory
modules: [
// platform/ui
path.resolve(__dirname, '../node_modules'),
// .docz
'node_modules',
],
// resolve: {
// symlinks: true,
// },
},
resolveLoader: {
plugins: [PnpWebpackPlugin.moduleLoader(module)],
},
});
};
+1 -1
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/ui",
"version": "1.5.2",
"version": "1.5.3",
"description": "A set of React components for Medical Imaging Viewers",
"author": "OHIF Contributors",
"license": "MIT",
+32
View File
@@ -3,6 +3,38 @@
All notable changes to this project will be documented in this file.
See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
## [4.2.16](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.2.15...@ohif/viewer@4.2.16) (2020-08-10)
**Note:** Version bump only for package @ohif/viewer
## [4.2.15](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.2.14...@ohif/viewer@4.2.15) (2020-08-05)
**Note:** Version bump only for package @ohif/viewer
## [4.2.14](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.2.13...@ohif/viewer@4.2.14) (2020-08-05)
**Note:** Version bump only for package @ohif/viewer
## [4.2.13](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.2.12...@ohif/viewer@4.2.13) (2020-07-23)
**Note:** Version bump only for package @ohif/viewer
## [4.2.12](https://github.com/OHIF/Viewers/compare/@ohif/viewer@4.2.11...@ohif/viewer@4.2.12) (2020-07-22)
+3 -3
View File
@@ -115,13 +115,13 @@ Commands to run the tests:
```js
// Open Cypress Dashboard that provides insight into what happened when your tests ran
yarn run cy
yarn test:e2e
// Run all tests using Electron browser headless
yarn run cy:run
yarn test:e2e:local
// Run all tests in CI mode
yarn run cy:run:ci
yarn run test:e2e:ci
```
### Contributing
@@ -12,6 +12,8 @@ describe('OHIF Microscopy Extension', () => {
});
it('drags and drop a SM thumbnail into viewport', () => {
// Waiting for series list to load all displaySets (lots of SRs, before defining which dom element to grab.)
cy.wait(3000);
cy.get('[data-cy="thumbnail-list"]')
.contains('SM')
.drag('.viewport-drop-target');
+7 -7
View File
@@ -1,6 +1,6 @@
{
"name": "@ohif/viewer",
"version": "4.2.12",
"version": "4.2.16",
"description": "OHIF Viewer",
"author": "OHIF Contributors",
"license": "MIT",
@@ -48,18 +48,18 @@
},
"dependencies": {
"@babel/runtime": "^7.5.5",
"@ohif/core": "^2.9.13",
"@ohif/extension-cornerstone": "^2.8.4",
"@ohif/core": "^2.9.14",
"@ohif/extension-cornerstone": "^2.8.5",
"@ohif/extension-dicom-html": "^1.2.4",
"@ohif/extension-dicom-microscopy": "^0.51.0",
"@ohif/extension-dicom-p10-downloader": "^0.1.2",
"@ohif/extension-dicom-pdf": "^1.0.3",
"@ohif/extension-dicom-rt": "^0.2.5",
"@ohif/extension-dicom-segmentation": "^0.3.3",
"@ohif/extension-dicom-rt": "^0.2.7",
"@ohif/extension-dicom-segmentation": "^0.3.4",
"@ohif/extension-lesion-tracker": "^0.2.0",
"@ohif/extension-vtk": "^1.6.8",
"@ohif/extension-vtk": "^1.6.10",
"@ohif/i18n": "^0.52.8",
"@ohif/ui": "^1.5.2",
"@ohif/ui": "^1.5.3",
"@tanem/react-nprogress": "^1.1.25",
"classnames": "^2.2.6",
"core-js": "^3.2.1",
@@ -80,6 +80,7 @@ const ViewportGrid = function(props) {
// - When updating a panel, ensure that the currently enabled plugin
// in the viewport is capable of rendering this display set. If not
// then use the most capable available plugin
const pluginName =
!layout.plugin && displaySet && displaySet.plugin
? displaySet.plugin
@@ -4,6 +4,8 @@ import { StudyBrowser } from '@ohif/ui';
import cloneDeep from 'lodash.clonedeep';
import findDisplaySetByUID from './findDisplaySetByUID';
const { studyMetadataManager } = OHIF.utils;
const { setActiveViewportSpecificData } = OHIF.redux.actions;
// TODO
@@ -39,11 +41,27 @@ const mapStateToProps = (state, ownProps) => {
const mapDispatchToProps = (dispatch, ownProps) => {
return {
onThumbnailClick: displaySetInstanceUID => {
const displaySet = findDisplaySetByUID(
let displaySet = findDisplaySetByUID(
ownProps.studyMetadata,
displaySetInstanceUID
);
if (displaySet.isDerived) {
const { Modality } = displaySet;
displaySet = displaySet.getSourceDisplaySet(ownProps.studyMetadata);
if (!displaySet) {
throw new Error(
`Referenced series for ${Modality} dataset not present.`
);
}
if (!displaySet) {
throw new Error('Source data not present');
}
}
dispatch(setActiveViewportSpecificData(displaySet));
},
};
@@ -133,12 +133,23 @@ class ViewerMain extends Component {
StudyInstanceUID,
displaySetInstanceUID,
}) => {
const displaySet = this.findDisplaySet(
let displaySet = this.findDisplaySet(
this.props.studies,
StudyInstanceUID,
displaySetInstanceUID
);
if (displaySet.isDerived) {
const { Modality } = displaySet;
displaySet = displaySet.getSourceDisplaySet(this.props.studies);
if (!displaySet) {
throw new Error(
`Referenced series for ${Modality} dataset not present.`
);
}
}
this.props.setViewportSpecificData(viewportIndex, displaySet);
};
+6 -31
View File
@@ -1247,34 +1247,13 @@
pirates "^4.0.0"
source-map-support "^0.5.9"
"@babel/runtime@7.1.2":
version "7.1.2"
resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.1.2.tgz#81c89935f4647706fc54541145e6b4ecfef4b8e3"
integrity sha512-Y3SCjmhSupzFB6wcv1KmmFucH6gDVnI30WjOcicV10ju0cZjak3Jcs67YLIXBrmZYw1xCrVeJPbycFwrqNyxpg==
dependencies:
regenerator-runtime "^0.12.0"
"@babel/runtime@7.6.0":
version "7.6.0"
resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.6.0.tgz#4fc1d642a9fd0299754e8b5de62c631cf5568205"
integrity sha512-89eSBLJsxNxOERC0Op4vd+0Bqm6wRMqMbFtV3i0/fbaWw/mJ8Q3eBvgX0G4SyrOOLCtbu98HspF8o09MRT+KzQ==
dependencies:
regenerator-runtime "^0.13.2"
"@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.2.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.0", "@babel/runtime@^7.4.2", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5":
"@babel/runtime@7.1.2", "@babel/runtime@7.5.5", "@babel/runtime@7.6.0", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.2.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.0", "@babel/runtime@^7.4.2", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.6.0", "@babel/runtime@^7.6.3", "@babel/runtime@^7.7.2", "@babel/runtime@^7.8.4", "@babel/runtime@^7.8.7", "@babel/runtime@^7.9.6":
version "7.5.5"
resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.5.5.tgz#74fba56d35efbeca444091c7850ccd494fd2f132"
integrity sha512-28QvEGyQyNkB0/m2B4FU7IEZGK2NUrcMtT6BZEFALTguLk+AUT6ofsHtPk5QyjAdUkpMJ+/Em+quwz4HOt30AQ==
dependencies:
regenerator-runtime "^0.13.2"
"@babel/runtime@^7.6.0", "@babel/runtime@^7.6.3", "@babel/runtime@^7.7.2", "@babel/runtime@^7.8.4", "@babel/runtime@^7.8.7", "@babel/runtime@^7.9.6":
version "7.10.5"
resolved "https://registry.yarnpkg.com/@babel/runtime/-/runtime-7.10.5.tgz#303d8bd440ecd5a491eae6117fd3367698674c5c"
integrity sha512-otddXKhdNn7d0ptoFRHtMLa8LqDxLYwTjB4nYgM1yy5N6gU/MUf8zqyyLltCH3yAVitBzmwK4us+DD0l/MauAg==
dependencies:
regenerator-runtime "^0.13.4"
"@babel/template@^7.0.0", "@babel/template@^7.1.0", "@babel/template@^7.4.0", "@babel/template@^7.4.4", "@babel/template@^7.6.0":
version "7.6.0"
resolved "https://registry.yarnpkg.com/@babel/template/-/template-7.6.0.tgz#7f0159c7f5012230dad64cca42ec9bdb5c9536e6"
@@ -15617,13 +15596,14 @@ react-codemirror2@^6.0.0:
resolved "https://registry.yarnpkg.com/react-codemirror2/-/react-codemirror2-6.0.0.tgz#180065df57a64026026cde569a9708fdf7656525"
integrity sha512-D7y9qZ05FbUh9blqECaJMdDwKluQiO3A9xB+fssd5jKM7YAXucRuEOlX32mJQumUvHUkHRHqXIPBjm6g0FW0Ag==
react-cornerstone-viewport@2.3.9:
version "2.3.9"
resolved "https://registry.yarnpkg.com/react-cornerstone-viewport/-/react-cornerstone-viewport-2.3.9.tgz#f9761da8e536f0a217137c6ca1a983f5882249f9"
integrity sha512-qrhq8CbX/jq6b93cQjV2qC/mhHOvFBpxzxcHlvHzEQZt/rmRMcaYxCqjpNaNbUmmBu61wNkxesUVsggkPTTcqg==
react-cornerstone-viewport@4.0.1:
version "4.0.1"
resolved "https://registry.yarnpkg.com/react-cornerstone-viewport/-/react-cornerstone-viewport-4.0.1.tgz#6a7ec4c01b0626c4ad11552368f3dfa6cd67bdd5"
integrity sha512-47YhFsLS5vCWjiOKS9FwLxtA738HIHuNfdn3EJw6GyWD9jwL5HJQ/Ue1mKATjyHRvb3AyJTJuC/lGl0bsqKbYw==
dependencies:
classnames "^2.2.6"
date-fns "^2.2.1"
lodash.debounce "^4.0.8"
prop-types "^15.7.2"
react-resize-detector "^4.2.1"
@@ -16433,11 +16413,6 @@ regenerator-runtime@^0.11.0, regenerator-runtime@^0.11.1:
resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.11.1.tgz#be05ad7f9bf7d22e056f9726cee5017fbf19e2e9"
integrity sha512-MguG95oij0fC3QV3URf4V2SDYGJhJnJGqvIIgdECeODCT98wSWDAJ94SSuVpYQUoTcGUIL6L4yNB7j1DFFHSBg==
regenerator-runtime@^0.12.0:
version "0.12.1"
resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.12.1.tgz#fa1a71544764c036f8c49b13a08b2594c9f8a0de"
integrity sha512-odxIc1/vDlo4iZcfXqRYFj0vpXFNoGdKMAUieAlFYO6m/nl5e9KR/beGf41z4a1FI+aQgtjhuaSlDxQ0hmkrHg==
regenerator-runtime@^0.13.1, regenerator-runtime@^0.13.2, regenerator-runtime@^0.13.4:
version "0.13.5"
resolved "https://registry.yarnpkg.com/regenerator-runtime/-/regenerator-runtime-0.13.5.tgz#d878a1d094b4306d10b9096484b33ebd55e26697"