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chore(prettier): full repo linting and code reformatting once and for all (#3627)

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Alireza authored and GitHub committed 2023-09-01 16:19:39 -04:00
1 parent 01500a2d4c
commit 9045ddaedc
656 files changed
+21737 -20628
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extensions/tmtv/src/Panels/PanelPetSUV.tsx
+10 -24
View File
@@ -24,12 +24,9 @@ const DEFAULT_MEATADATA = {
*/
export default function PanelPetSUV({ servicesManager, commandsManager }) {
const { t } = useTranslation('PanelSUV');
const {
displaySetService,
toolGroupService,
toolbarService,
hangingProtocolService,
} = (servicesManager as ServicesManager).services;
const { displaySetService, toolGroupService, toolbarService, hangingProtocolService } = (
servicesManager as ServicesManager
).services;
const [metadata, setMetadata] = useState(DEFAULT_MEATADATA);
const [ptDisplaySet, setPtDisplaySet] = useState(null);
@@ -127,9 +124,7 @@ export default function PanelPetSUV({ servicesManager, commandsManager }) {
});
toolbarService.state.toggles['Crosshairs'] = false;
toolbarService._broadcastEvent(
toolbarService.EVENTS.TOOL_BAR_STATE_MODIFIED
);
toolbarService._broadcastEvent(toolbarService.EVENTS.TOOL_BAR_STATE_MODIFIED);
// metadata should be dcmjs naturalized
DicomMetadataStore.updateMetadataForSeries(
@@ -139,15 +134,13 @@ export default function PanelPetSUV({ servicesManager, commandsManager }) {
);
// update the displaySets
displaySetService.setDisplaySetMetadataInvalidated(
ptDisplaySet.displaySetInstanceUID
);
displaySetService.setDisplaySetMetadataInvalidated(ptDisplaySet.displaySetInstanceUID);
}
return (
<div className="overflow-x-hidden overflow-y-auto invisible-scrollbar">
<div className="invisible-scrollbar overflow-y-auto overflow-x-hidden">
{
<div className="flex flex-col">
<div className="flex flex-col p-4 space-y-4 bg-primary-dark">
<div className="bg-primary-dark flex flex-col space-y-4 p-4">
<Input
label={t('Patient Sex')}
labelClassName="text-white mb-2"
@@ -174,10 +167,7 @@ export default function PanelPetSUV({ servicesManager, commandsManager }) {
label={t('Total Dose (bq)')}
labelClassName="text-white mb-2"
className="mt-1"
value={
metadata.RadiopharmaceuticalInformationSequence
.RadionuclideTotalDose || ''
}
value={metadata.RadiopharmaceuticalInformationSequence.RadionuclideTotalDose || ''}
onChange={e => {
handleMetadataChange({
RadiopharmaceuticalInformationSequence: {
@@ -190,10 +180,7 @@ export default function PanelPetSUV({ servicesManager, commandsManager }) {
label={t('Half Life (s)')}
labelClassName="text-white mb-2"
className="mt-1"
value={
metadata.RadiopharmaceuticalInformationSequence
.RadionuclideHalfLife || ''
}
value={metadata.RadiopharmaceuticalInformationSequence.RadionuclideHalfLife || ''}
onChange={e => {
handleMetadataChange({
RadiopharmaceuticalInformationSequence: {
@@ -207,8 +194,7 @@ export default function PanelPetSUV({ servicesManager, commandsManager }) {
labelClassName="text-white mb-2"
className="mt-1"
value={
metadata.RadiopharmaceuticalInformationSequence
.RadiopharmaceuticalStartTime || ''
metadata.RadiopharmaceuticalInformationSequence.RadiopharmaceuticalStartTime || ''
}
onChange={e => {
handleMetadataChange({
extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ExportReports.tsx
+9 -3
View File
@@ -8,9 +8,12 @@ function ExportReports({ segmentations, tmtvValue, config, commandsManager }) {
return (
<>
{segmentations?.length ? (
<div className="flex justify-center mt-4 space-x-2">
<div className="mt-4 flex justify-center space-x-2">
{/* TODO Revisit design of ButtonGroup later - for now use LegacyButton for its children.*/}
<ButtonGroup color="black" size="inherit">
<ButtonGroup
color="black"
size="inherit"
>
<LegacyButton
className="px-2 py-2 text-base"
disabled={tmtvValue === null}
@@ -25,7 +28,10 @@ function ExportReports({ segmentations, tmtvValue, config, commandsManager }) {
{t('Export CSV')}
</LegacyButton>
</ButtonGroup>
<ButtonGroup color="black" size="inherit">
<ButtonGroup
color="black"
size="inherit"
>
<LegacyButton
className="px-2 py-2 text-base"
onClick={() => {
extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/PanelROIThresholdSegmentation.tsx
+12 -26
View File
@@ -5,9 +5,7 @@ import { SegmentationTable, Button, Icon } from '@ohif/ui';
import { useTranslation } from 'react-i18next';
import segmentationEditHandler from './segmentationEditHandler';
import ExportReports from './ExportReports';
import ROIThresholdConfiguration, {
ROI_STAT,
} from './ROIThresholdConfiguration';
import ROIThresholdConfiguration, { ROI_STAT } from './ROIThresholdConfiguration';
const LOWER_CT_THRESHOLD_DEFAULT = -1024;
const UPPER_CT_THRESHOLD_DEFAULT = 1024;
@@ -44,19 +42,14 @@ function reducer(state, action) {
}
}
export default function PanelRoiThresholdSegmentation({
servicesManager,
commandsManager,
}) {
export default function PanelRoiThresholdSegmentation({ servicesManager, commandsManager }) {
const { segmentationService } = servicesManager.services;
const { t } = useTranslation('PanelSUV');
const [showConfig, setShowConfig] = useState(false);
const [labelmapLoading, setLabelmapLoading] = useState(false);
const [selectedSegmentationId, setSelectedSegmentationId] = useState(null);
const [segmentations, setSegmentations] = useState(() =>
segmentationService.getSegmentations()
);
const [segmentations, setSegmentations] = useState(() => segmentationService.getSegmentations());
const [config, dispatch] = useReducer(reducer, {
strategy: DEFAULT_STRATEGY,
@@ -95,9 +88,7 @@ export default function PanelRoiThresholdSegmentation({
const lesionGlyoclysisStats = lesionStats.volume * lesionStats.meanValue;
// update segDetails with the suv peak for the active segmentation
const segmentation = segmentationService.getSegmentation(
selectedSegmentationId
);
const segmentation = segmentationService.getSegmentation(selectedSegmentationId);
const cachedStats = {
lesionStats,
@@ -178,8 +169,8 @@ export default function PanelRoiThresholdSegmentation({
return (
<>
<div className="flex flex-col">
<div className="overflow-x-hidden overflow-y-auto invisible-scrollbar">
<div className="flex mx-4 my-4 mb-4 space-x-4">
<div className="invisible-scrollbar overflow-y-auto overflow-x-hidden">
<div className="mx-4 my-4 mb-4 flex space-x-4">
<Button
onClick={() => {
setLabelmapLoading(true);
@@ -196,14 +187,12 @@ export default function PanelRoiThresholdSegmentation({
<Button onClick={handleROIThresholding}>Run</Button>
</div>
<div
className="flex items-center justify-around h-8 mb-2 border-t outline-none cursor-pointer select-none bg-secondary-dark first:border-0 border-secondary-light"
className="bg-secondary-dark border-secondary-light mb-2 flex h-8 cursor-pointer select-none items-center justify-around border-t outline-none first:border-0"
onClick={() => {
setShowConfig(!showConfig);
}}
>
<div className="px-4 text-base text-white">
{t('ROI Threshold Configuration')}
</div>
<div className="px-4 text-base text-white">{t('ROI Threshold Configuration')}</div>
</div>
{showConfig && (
<ROIThresholdConfiguration
@@ -246,8 +235,8 @@ export default function PanelRoiThresholdSegmentation({
) : null}
</div>
{tmtvValue !== null ? (
<div className="flex items-baseline justify-between px-2 py-1 mt-4 bg-secondary-dark">
<span className="text-base font-bold tracking-widest text-white uppercase">
<div className="bg-secondary-dark mt-4 flex items-baseline justify-between px-2 py-1">
<span className="text-base font-bold uppercase tracking-widest text-white">
{'TMTV:'}
</span>
<div className="text-white">{`${tmtvValue} mL`}</div>
@@ -262,13 +251,10 @@ export default function PanelRoiThresholdSegmentation({
</div>
</div>
<div
className="opacity-50 hover:opacity-80 flex items-center justify-center text-blue-400 mt-auto cursor-pointer mb-4"
className="mt-auto mb-4 flex cursor-pointer items-center justify-center text-blue-400 opacity-50 hover:opacity-80"
onClick={() => {
// navigate to a url in a new tab
window.open(
'https://github.com/OHIF/Viewers/blob/master/modes/tmtv/README.md',
'_blank'
);
window.open('https://github.com/OHIF/Viewers/blob/master/modes/tmtv/README.md', '_blank');
}}
>
<Icon
extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx
+24 -18
View File
@@ -14,18 +14,15 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
const { t } = useTranslation('ROIThresholdConfiguration');
return (
<div className="flex flex-col px-4 space-y-4 bg-primary-dark py-2">
<div className="bg-primary-dark flex flex-col space-y-4 px-4 py-2">
<div className="flex items-end space-x-2">
<div className="flex flex-col w-1/2">
<div className="flex w-1/2 flex-col">
<Select
label={t('Strategy')}
closeMenuOnSelect={true}
className="mr-2 bg-black border-primary-main text-white "
className="border-primary-main mr-2 bg-black text-white "
options={options}
placeholder={
options.find(option => option.value === config.strategy)
.placeHolder
}
placeholder={options.find(option => option.value === config.strategy).placeHolder}
value={config.strategy}
onChange={({ value }) => {
dispatch({
@@ -66,7 +63,7 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
<Input
label={t('Percentage of Max SUV')}
labelClassName="text-white"
className="mt-2 bg-black border-primary-main"
className="border-primary-main mt-2 bg-black"
type="text"
containerClassName="mr-2"
value={config.weight}
@@ -81,11 +78,14 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
/>
)}
{config.strategy !== ROI_STAT && (
<div className="text-sm mr-2">
<div className="mr-2 text-sm">
<table>
<tbody>
<tr className="mt-2">
<td className="pr-4 pt-2" colSpan="3">
<td
className="pr-4 pt-2"
colSpan="3"
>
<Label
className="text-white"
text="Lower & Upper Ranges"
@@ -93,15 +93,18 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
</td>
</tr>
<tr className="mt-2">
<td className="text-center pr-4 pt-2">
<Label className="text-white" text="CT"></Label>
<td className="pr-4 pt-2 text-center">
<Label
className="text-white"
text="CT"
></Label>
</td>
<td>
<div className="flex justify-between">
<Input
label={t('')}
labelClassName="text-white"
className="mt-2 bg-black border-primary-main"
className="border-primary-main mt-2 bg-black"
type="text"
containerClassName="mr-2"
value={config.ctLower}
@@ -117,7 +120,7 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
<Input
label={t('')}
labelClassName="text-white"
className="mt-2 bg-black border-primary-main"
className="border-primary-main mt-2 bg-black"
type="text"
containerClassName="mr-2"
value={config.ctUpper}
@@ -134,15 +137,18 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
</td>
</tr>
<tr>
<td className="text-center pr-4 pt-2">
<Label className="text-white" text="PT"></Label>
<td className="pr-4 pt-2 text-center">
<Label
className="text-white"
text="PT"
></Label>
</td>
<td>
<div className="flex justify-between">
<Input
label={t('')}
labelClassName="text-white"
className="mt-2 bg-black border-primary-main"
className="border-primary-main mt-2 bg-black"
type="text"
containerClassName="mr-2"
value={config.ptLower}
@@ -158,7 +164,7 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) {
<Input
label={t('')}
labelClassName="text-white"
className="mt-2 bg-black border-primary-main"
className="border-primary-main mt-2 bg-black"
type="text"
containerClassName="mr-2"
value={config.ptUpper}
extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/segmentationEditHandler.tsx
+1 -1
View File
@@ -46,7 +46,7 @@ function segmentationItemEditHandler({ id, servicesManager }) {
return (
<Input
autoFocus
className="bg-black border-primary-main"
className="border-primary-main bg-black"
type="text"
containerClassName="mr-2"
value={value.label}
extensions/tmtv/src/commandsModule.js
+20 -63
View File
@@ -14,11 +14,7 @@ const metadataProvider = classes.MetadataProvider;
const RECTANGLE_ROI_THRESHOLD_MANUAL = 'RectangleROIStartEndThreshold';
const LABELMAP = csTools.Enums.SegmentationRepresentations.Labelmap;
const commandsModule = ({
servicesManager,
commandsManager,
extensionManager,
}) => {
const commandsModule = ({ servicesManager, commandsManager, extensionManager }) => {
const {
viewportGridService,
uiNotificationService,
@@ -74,9 +70,7 @@ const commandsModule = ({
continue;
}
ptDisplaySet = displaySets.find(
displaySet => displaySet.Modality === 'PT'
);
ptDisplaySet = displaySets.find(displaySet => displaySet.Modality === 'PT');
if (ptDisplaySet) {
break;
@@ -102,17 +96,13 @@ const commandsModule = ({
PatientWeight: instance.PatientWeight,
RadiopharmaceuticalInformationSequence: {
RadionuclideTotalDose:
instance.RadiopharmaceuticalInformationSequence[0]
.RadionuclideTotalDose,
instance.RadiopharmaceuticalInformationSequence[0].RadionuclideTotalDose,
RadionuclideHalfLife:
instance.RadiopharmaceuticalInformationSequence[0]
.RadionuclideHalfLife,
instance.RadiopharmaceuticalInformationSequence[0].RadionuclideHalfLife,
RadiopharmaceuticalStartTime:
instance.RadiopharmaceuticalInformationSequence[0]
.RadiopharmaceuticalStartTime,
instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartTime,
RadiopharmaceuticalStartDateTime:
instance.RadiopharmaceuticalInformationSequence[0]
.RadiopharmaceuticalStartDateTime,
instance.RadiopharmaceuticalInformationSequence[0].RadiopharmaceuticalStartDateTime,
},
};
@@ -148,10 +138,7 @@ const commandsModule = ({
representationType
);
segmentationService.setActiveSegmentationForToolGroup(
segmentationId,
toolGroupId
);
segmentationService.setActiveSegmentationForToolGroup(segmentationId, toolGroupId);
}
return segmentationId;
@@ -160,21 +147,14 @@ const commandsModule = ({
const toolGroupIds = _getMatchedViewportsToolGroupIds();
toolGroupIds.forEach(toolGroupId => {
segmentationService.setActiveSegmentationForToolGroup(
segmentationId,
toolGroupId
);
segmentationService.setActiveSegmentationForToolGroup(segmentationId, toolGroupId);
});
},
thresholdSegmentationByRectangleROITool: ({ segmentationId, config }) => {
const segmentation = csTools.segmentation.state.getSegmentation(
segmentationId
);
const segmentation = csTools.segmentation.state.getSegmentation(segmentationId);
const { representationData } = segmentation;
const {
displaySetMatchDetails: matchDetails,
} = hangingProtocolService.getMatchDetails();
const { displaySetMatchDetails: matchDetails } = hangingProtocolService.getMatchDetails();
const volumeLoaderScheme = 'cornerstoneStreamingImageVolume'; // Loader id which defines which volume loader to use
const ctDisplaySet = matchDetails.get('ctDisplaySet');
@@ -248,9 +228,7 @@ const commandsModule = ({
getLesionStats: ({ labelmap, segmentIndex = 1 }) => {
const { scalarData, spacing } = labelmap;
const { scalarData: referencedScalarData } = cs.cache.getVolume(
labelmap.referencedVolumeId
);
const { scalarData: referencedScalarData } = cs.cache.getVolume(labelmap.referencedVolumeId);
let segmentationMax = -Infinity;
let segmentationMin = Infinity;
@@ -292,9 +270,7 @@ const commandsModule = ({
};
},
calculateTMTV: ({ segmentations }) => {
const labelmaps = segmentations.map(s =>
segmentationService.getLabelmapVolume(s.id)
);
const labelmaps = segmentations.map(s => segmentationService.getLabelmapVolume(s.id));
if (!labelmaps.length) {
return;
@@ -317,17 +293,14 @@ const commandsModule = ({
createAndDownloadTMTVReport(segReport, additionalReportRows);
},
getTotalLesionGlycolysis: ({ segmentations }) => {
const labelmapVolumes = segmentations.map(s =>
segmentationService.getLabelmapVolume(s.id)
);
const labelmapVolumes = segmentations.map(s => segmentationService.getLabelmapVolume(s.id));
let mergedLabelmap;
// merge labelmap will through an error if labels maps are not the same size
// or same direction or ....
try {
mergedLabelmap = csTools.utilities.segmentation.createMergedLabelmapForIndex(
labelmapVolumes
);
mergedLabelmap =
csTools.utilities.segmentation.createMergedLabelmapForIndex(labelmapVolumes);
} catch (e) {
console.error('commandsModule::getTotalLesionGlycolysis', e);
return;
@@ -337,9 +310,7 @@ const commandsModule = ({
const { referencedVolumeId, spacing } = labelmapVolumes[0];
if (!referencedVolumeId) {
console.error(
'commandsModule::getTotalLesionGlycolysis:No referencedVolumeId found'
);
console.error('commandsModule::getTotalLesionGlycolysis:No referencedVolumeId found');
}
const ptVolume = cs.cache.getVolume(referencedVolumeId);
@@ -365,14 +336,7 @@ const commandsModule = ({
const averageSuv = suv / totalLesionVoxelCount;
// total Lesion Glycolysis [suv * ml]
return (
averageSuv *
totalLesionVoxelCount *
spacing[0] *
spacing[1] *
spacing[2] *
1e-3
);
return averageSuv * totalLesionVoxelCount * spacing[0] * spacing[1] * spacing[2] * 1e-3;
},
setStartSliceForROIThresholdTool: () => {
const { viewport } = _getActiveViewportsEnabledElement();
@@ -488,9 +452,7 @@ const commandsModule = ({
const referencedVolumeId = labelmapVolume.referencedVolumeId;
segReport.referencedVolumeId = referencedVolumeId;
const referencedVolume = segmentationService.getLabelmapVolume(
referencedVolumeId
);
const referencedVolume = segmentationService.getLabelmapVolume(referencedVolumeId);
if (!referencedVolume) {
report[id] = segReport;
@@ -503,10 +465,7 @@ const commandsModule = ({
}
const firstImageId = referencedVolume.imageIds[0];
const instance = OHIF.classes.MetadataProvider.get(
'instance',
firstImageId
);
const instance = OHIF.classes.MetadataProvider.get('instance', firstImageId);
if (!instance) {
report[id] = segReport;
@@ -559,9 +518,7 @@ const commandsModule = ({
},
});
viewports.push(
cornerstoneViewportService.getCornerstoneViewport(viewportId)
);
viewports.push(cornerstoneViewportService.getCornerstoneViewport(viewportId));
});
viewports.forEach(viewport => {
extensions/tmtv/src/getPanelModule.tsx
+1 -5
View File
@@ -6,11 +6,7 @@ import { PanelPetSUV, PanelROIThresholdSegmentation } from './Panels';
// - cancel promises when component is destroyed
// - show errors in UI for thumbnails if promise fails
function getPanelModule({
commandsManager,
extensionManager,
servicesManager,
}) {
function getPanelModule({ commandsManager, extensionManager, servicesManager }) {
const wrappedPanelPetSuv = () => {
return (
<PanelPetSUV
extensions/tmtv/src/index.tsx
+1 -6
View File
@@ -12,12 +12,7 @@ const tmtvExtension = {
* Only required property. Should be a unique value across all extensions.
*/
id,
preRegistration({
servicesManager,
commandsManager,
extensionManager,
configuration = {},
}) {
preRegistration({ servicesManager, commandsManager, extensionManager, configuration = {} }) {
init({ servicesManager, commandsManager, extensionManager, configuration });
},
getPanelModule,
extensions/tmtv/src/init.js
+3 -9
View File
@@ -1,7 +1,4 @@
import {
addTool,
RectangleROIStartEndThresholdTool,
} from '@cornerstonejs/tools';
import { addTool, RectangleROIStartEndThresholdTool } from '@cornerstonejs/tools';
import { utilities } from '@cornerstonejs/core';
import measurementServiceMappingsFactory from './utils/measurementServiceMappings/measurementServiceMappingsFactory';
@@ -18,11 +15,8 @@ const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1';
* @param {Object|Array} configuration.csToolsConfig
*/
export default function init({ servicesManager, extensionManager }) {
const {
measurementService,
displaySetService,
cornerstoneViewportService,
} = servicesManager.services;
const { measurementService, displaySetService, cornerstoneViewportService } =
servicesManager.services;
addTool(RectangleROIStartEndThresholdTool);
extensions/tmtv/src/utils/calculateSUVPeak.ts
+7 -29
View File
@@ -41,21 +41,12 @@ function calculateSuvPeak(
}
if (labelmap.scalarData.length !== referenceVolume.scalarData.length) {
throw new Error(
'labelmap and referenceVolume must have the same number of pixels'
);
throw new Error('labelmap and referenceVolume must have the same number of pixels');
}
const {
scalarData: labelmapData,
dimensions,
imageData: labelmapImageData,
} = labelmap;
const { scalarData: labelmapData, dimensions, imageData: labelmapImageData } = labelmap;
const {
scalarData: referenceVolumeData,
imageData: referenceVolumeImageData,
} = referenceVolume;
const { scalarData: referenceVolumeData, imageData: referenceVolumeImageData } = referenceVolume;
let boundsIJK;
// Todo: using the first annotation for now
@@ -69,10 +60,7 @@ function calculateSuvPeak(
return ijk as Types.Point3;
});
boundsIJK = utilities.boundingBox.getBoundingBoxAroundShape(
rectangleCornersIJK,
dimensions
);
boundsIJK = utilities.boundingBox.getBoundingBoxAroundShape(rectangleCornersIJK, dimensions);
}
let max = 0;
@@ -96,16 +84,9 @@ function calculateSuvPeak(
}
};
utilities.pointInShapeCallback(
labelmapImageData,
() => true,
callback,
boundsIJK
);
utilities.pointInShapeCallback(labelmapImageData, () => true, callback, boundsIJK);
const direction = labelmapImageData
.getDirection()
.slice(0, 3) as Types.Point3;
const direction = labelmapImageData.getDirection().slice(0, 3) as Types.Point3;
/**
* 2. Find the bottom and top of the great circle for the second sphere (1cc sphere)
@@ -120,10 +101,7 @@ function calculateSuvPeak(
referenceVolumeImageData.indexToWorld(maxIJK as vec3, secondaryCircleWorld);
vec3.scaleAndAdd(bottomWorld, secondaryCircleWorld, direction, -diameter / 2);
vec3.scaleAndAdd(topWorld, secondaryCircleWorld, direction, diameter / 2);
const suvPeakCirclePoints = [bottomWorld, topWorld] as [
Types.Point3,
Types.Point3
];
const suvPeakCirclePoints = [bottomWorld, topWorld] as [Types.Point3, Types.Point3];
/**
* 3. Find the Mean and Max of the 1cc sphere centered on the suv Max of the previous
extensions/tmtv/src/utils/calculateTMTV.ts
+2 -8
View File
@@ -11,10 +11,7 @@ import { utilities } from '@cornerstonejs/tools';
* @param {number} segmentIndex
* @returns {number} TMTV in ml
*/
function calculateTMTV(
labelmaps: Array<Types.IImageVolume>,
segmentIndex = 1
): number {
function calculateTMTV(labelmaps: Array<Types.IImageVolume>, segmentIndex = 1): number {
const volumeId = 'mergedLabelmap';
const mergedLabelmap = utilities.segmentation.createMergedLabelmapForIndex(
@@ -24,10 +21,7 @@ function calculateTMTV(
);
const { imageData, spacing } = mergedLabelmap;
const values = imageData
.getPointData()
.getScalars()
.getData();
const values = imageData.getPointData().getScalars().getData();
// count non-zero values inside the outputData, this would
// consider the overlapping regions to be only counted once
extensions/tmtv/src/utils/colormaps/index.js
+1498 -9216
View File
File diff suppressed because it is too large. Load diff
extensions/tmtv/src/utils/createAndDownloadTMTVReport.js
+2 -7
View File
@@ -1,7 +1,4 @@
export default function createAndDownloadTMTVReport(
segReport,
additionalReportRows
) {
export default function createAndDownloadTMTVReport(segReport, additionalReportRows) {
const firstReport = segReport[Object.keys(segReport)[0]];
const columns = Object.keys(firstReport);
const csv = [columns.join(',')];
@@ -11,9 +8,7 @@ export default function createAndDownloadTMTVReport(
columns.forEach(column => {
// if it is array then we need to replace , with space to avoid csv parsing error
row.push(
Array.isArray(segmentation[column])
? segmentation[column].join(' ')
: segmentation[column]
Array.isArray(segmentation[column]) ? segmentation[column].join(' ') : segmentation[column]
);
});
csv.push(row.join(','));
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/RTSSReport.js
+9 -36
View File
@@ -98,15 +98,9 @@ function initializeDataset(annotations, metadataProvider) {
const rtSOPInstanceUID = DicomMetaDictionary.uid();
// get the first annotation data
const {
referencedImageId: imageId,
FrameOfReferenceUID,
} = annotations[0].metadata;
const { referencedImageId: imageId, FrameOfReferenceUID } = annotations[0].metadata;
const { studyInstanceUID } = metadataProvider.get(
'generalSeriesModule',
imageId
);
const { studyInstanceUID } = metadataProvider.get('generalSeriesModule', imageId);
const patientModule = getPatientModule(imageId, metadataProvider);
const rtSeriesModule = getRTSeriesModule(imageId, metadataProvider);
@@ -136,23 +130,11 @@ function initializeDataset(annotations, metadataProvider) {
}
function getPatientModule(imageId, metadataProvider) {
const generalSeriesModule = metadataProvider.get(
'generalSeriesModule',
imageId
);
const generalStudyModule = metadataProvider.get(
'generalStudyModule',
imageId
);
const patientStudyModule = metadataProvider.get(
'patientStudyModule',
imageId
);
const generalSeriesModule = metadataProvider.get('generalSeriesModule', imageId);
const generalStudyModule = metadataProvider.get('generalStudyModule', imageId);
const patientStudyModule = metadataProvider.get('patientStudyModule', imageId);
const patientModule = metadataProvider.get('patientModule', imageId);
const patientDemographicModule = metadataProvider.get(
'patientDemographicModule',
imageId
);
const patientDemographicModule = metadataProvider.get('patientDemographicModule', imageId);
return {
Modality: generalSeriesModule.modality,
@@ -169,11 +151,7 @@ function getPatientModule(imageId, metadataProvider) {
};
}
function getReferencedFrameOfReferenceSequence(
toolData,
metadataProvider,
dataset
) {
function getReferencedFrameOfReferenceSequence(toolData, metadataProvider, dataset) {
const { referencedImageId: imageId, FrameOfReferenceUID } = toolData.metadata;
const instance = metadataProvider.get('instance', imageId);
const { SeriesInstanceUID } = instance;
@@ -190,9 +168,7 @@ function getReferencedFrameOfReferenceSequence(
RTReferencedSeriesSequence: [
{
SeriesInstanceUID,
ContourImageSequence: [
...ReferencedSeriesSequence[0].ReferencedInstanceSequence,
],
ContourImageSequence: [...ReferencedSeriesSequence[0].ReferencedInstanceSequence],
},
],
},
@@ -209,10 +185,7 @@ function getReferencedSeriesSequence(toolData, index, metadataProvider) {
const ReferencedSeriesSequence = [];
if (SeriesInstanceUID) {
const series = DicomMetadataStore.getSeries(
StudyInstanceUID,
SeriesInstanceUID
);
const series = DicomMetadataStore.getSeries(StudyInstanceUID, SeriesInstanceUID);
const ReferencedSeries = {
SeriesInstanceUID,
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/AnnotationToPointData.js
+2 -7
View File
@@ -20,18 +20,13 @@ class AnnotationToPointData {
const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
if (!toolClass) {
throw new Error(
`Unknown tool type: ${toolName}, cannot convert to RTSSReport`
);
throw new Error(`Unknown tool type: ${toolName}, cannot convert to RTSSReport`);
}
// Each toolData should become a list of contours, ContourSequence
// contains a list of contours with their pointData, their geometry
// type and their length.
const ContourSequence = toolClass.getContourSequence(
annotation,
metadataProvider
);
const ContourSequence = toolClass.getContourSequence(annotation, metadataProvider);
// Todo: random rgb color for now, options should be passed in
const color = [
extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/RectangleROIStartEndThreshold.js
+1 -6
View File
@@ -29,12 +29,7 @@ function getPointData(points) {
// Since this is a closed contour, the order of the points is important.
// re-order the points to be in the correct order clockwise
// Spread to make sure Float32Arrays are converted to arrays
const orderedPoints = [
...points[0],
...points[1],
...points[3],
...points[2],
];
const orderedPoints = [...points[0], ...points[1], ...points[3], ...points[2]];
const pointsArray = orderedPoints.flat();
// reduce the precision of the points to 2 decimal places
extensions/tmtv/src/utils/getThresholdValue.ts
+5 -7
View File
@@ -3,10 +3,7 @@ import * as csTools from '@cornerstonejs/tools';
function getRoiStats(referencedVolume, annotations) {
// roiStats
const { imageData } = referencedVolume;
const values = imageData
.getPointData()
.getScalars()
.getData();
const values = imageData.getPointData().getScalars().getData();
// Todo: add support for other strategies
const { fn, baseValue } = _getStrategyFn('max');
@@ -59,9 +56,10 @@ function getThresholdValues(
};
}
function _getStrategyFn(
statistic
): { fn: (a: number, b: number) => number; baseValue: number } {
function _getStrategyFn(statistic): {
fn: (a: number, b: number) => number;
baseValue: number;
} {
const baseValue = -Infinity;
const fn = (number, maxValue) => {
if (number > maxValue) {
extensions/tmtv/src/utils/measurementServiceMappings/RectangleROIStartEndThreshold.js
+2 -10
View File
@@ -10,11 +10,7 @@ const RectangleROIStartEndThreshold = {
* @param {Object} cornerstone Cornerstone event data
* @return {Measurement} Measurement instance
*/
toMeasurement: (
csToolsEventDetail,
displaySetService,
cornerstoneViewportService
) => {
toMeasurement: (csToolsEventDetail, displaySetService, cornerstoneViewportService) => {
const { annotation, viewportId } = csToolsEventDetail;
const { metadata, data, annotationUID } = annotation;
@@ -30,11 +26,7 @@ const RectangleROIStartEndThreshold = {
throw new Error('Tool not supported');
}
const {
SOPInstanceUID,
SeriesInstanceUID,
StudyInstanceUID,
} = getSOPInstanceAttributes(
const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = getSOPInstanceAttributes(
referencedImageId,
cornerstoneViewportService,
viewportId