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modified-dicom-pacs

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A modified version of DICOM PACS implementation

github.com/knopkem/dicomweb-pacs

knopkem/dicomweb-pacs

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B.utilities.segmentation.rectangleROIThresholdVolumeByRange(m,d,[{volume:f,lower:S,upper:b},{volume:y,lower:T,upper:w}],{overwrite:!0,segmentIndex:n})},calculateSuvPeak:async({labelmap:e,segmentIndex:t})=>{ie.registerWorker("suv-peak-worker",ce,se);const{referencedVolumeId:n}=e,a=$.cache.getVolume(n),o=g(oe).map((e=>B.annotation.state.getAnnotation(e))),r={dimensions:e.dimensions,origin:e.origin,direction:e.direction,spacing:e.spacing,scalarData:e.scalarData,metadata:e.metadata},i={dimensions:a.dimensions,origin:a.origin,direction:a.direction,spacing:a.spacing,scalarData:a.scalarData,metadata:a.metadata},s=o.map((e=>({...e,metadata:{...e.metadata,enabledElement:{...e.metadata.enabledElement,viewport:null,renderingEngine:null,element:null}}}))),c=await 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n=B.utilities.segmentation.createMergedLabelmapForIndex(e,t,"mergedLabelmap"),{imageData:a,spacing:o}=n;return.001*a.getPointData().getScalars().getData().reduce(((e,t)=>t>0?e+1:e),0)*o[0]*o[1]*o[2]}(t)},exportTMTVReportCSV:({segmentations:e,tmtv:n,config:a,options:o})=>{const r=t.runCommand("getSegmentationCSVReport",{segmentations:e}),i=[{key:"Total Lesion Glycolysis",value:{tlg:f.getTotalLesionGlycolysis({segmentations:e}).toFixed(4)}},{key:"Threshold Configuration",value:{...a}}];void 0!==n&&i.unshift({key:"Total Metabolic Tumor Volume",value:{tmtv:n}}),function(e,t,n={}){const a=e[Object.keys(e)[0]],o=Object.keys(a),r=[o.join(",")];Object.values(e).forEach((e=>{const t=[];o.forEach((n=>{t.push(Array.isArray(e[n])?e[n].join(" "):e[n])})),r.push(t.join(","))})),r.push(""),r.push(""),r.push(""),r.push(`Patient ID,${a.PatientID}`),r.push(`Study Date,${a.StudyDate}`),r.push(""),t.forEach((({key:e,value:t})=>{const n=[];n.push(`${e}`),Object.keys(t).forEach((e=>{n.push(`${e}`),n.push(`${t[e]}`)})),r.push(n.join(","))}));const i=new Blob([r.join("\n")],{type:"text/csv;charset=utf-8"}),s=URL.createObjectURL(i),c=document.createElement("a");c.href=s,c.download=n.filename??`${a.PatientID}_tmtv.csv`,c.click()}(r,i,o)},getTotalLesionGlycolysis:({segmentations:e})=>{const t=e.map((e=>l.getLabelmapVolume(e.id)));let n;try{n=B.utilities.segmentation.createMergedLabelmapForIndex(t)}catch(e){return void console.error("commandsModule::getTotalLesionGlycolysis",e)}const{referencedVolumeId:a,spacing:o}=t[0];a||console.error("commandsModule::getTotalLesionGlycolysis:No referencedVolumeId found");const r=$.cache.getVolume(a),i=n.getScalarData();i.length!==r.getScalarData().length&&console.error("commandsModule::getTotalLesionGlycolysis:Labelmap and ptVolume are not the same size");let s=0,c=0;for(let e=0;e<i.length;e++)0!==i[e]&&(s+=r.getScalarData()[e],c+=1);return s/c*c*o[0]*o[1]*o[2]*.001},setStartSliceForROIThresholdTool:()=>{const{viewport:e}=m(),{focalPoint:t,viewPlaneNormal:n}=e.getCamera(),a=g(oe)[0],o=B.annotation.state.getAnnotation(a),{handles:r}=o.data,{points:i}=r,s=e.getCurrentImageIdIndex();o.data.startSlice=s;const c=i.map((e=>{const a=K.vec3.create();K.vec3.subtract(a,t,e);const o=K.vec3.dot(a,n),r=K.vec3.create();return K.vec3.scaleAndAdd(r,e,n,o),r}));r.points=c,o.invalidated=!0,e.render()},setEndSliceForROIThresholdTool:()=>{const{viewport:e}=m(),t=g(oe)[0],n=B.annotation.state.getAnnotation(t),a=e.getCurrentImageIdIndex();n.data.endSlice=a,n.invalidated=!0,e.render()},createTMTVRTReport:()=>{const e=B.annotation.state.getAnnotationManager(),n=[];Object.keys(e.annotations).forEach((t=>{const a=e.annotations[t],o=oe.reduce(((e,t)=>[...e,...a[t]??[]]),[]);n.push(...o)})),t.runCommand("exportRTReportForAnnotations",{annotations:n})},getSegmentationCSVReport:({segmentations:e})=>{e&&e.length||(e=l.getSegmentations());let t={};for(const n of e){const{id:e,label:a,cachedStats:o}=n,r={id:e,label:a};if(!o){t[e]=r;continue}Object.keys(o).forEach((e=>{"object"!=typeof o[e]?r[e]=o[e]:Object.keys(o[e]).forEach((t=>{r[`${e}_${t}`]=o[e][t]}))}));const i=l.getLabelmapVolume(e);if(!i){t[e]=r;continue}const s=i.referencedVolumeId;r.referencedVolumeId=s;const c=l.getLabelmapVolume(s);if(!c){t[e]=r;continue}if(!c.imageIds||!c.imageIds.length){t[e]=r;continue}const u=c.imageIds[0],p=S().classes.MetadataProvider.get("instance",u);t[e]=p?{...r,PatientID:p.PatientID??"000000",PatientName:p.PatientName.Alphabetic,StudyInstanceUID:p.StudyInstanceUID,SeriesInstanceUID:p.SeriesInstanceUID,StudyDate:p.StudyDate}:r}return t},exportRTReportForAnnotations:({annotations:e})=>{!function(e){const t=ee.adaptersRT.Cornerstone3D.RTSS.generateRTSSFromAnnotations(e,ne,v.DicomMetadataStore),n=te(t);var a=URL.createObjectURL(n);window.location.assign(a)}(e)},setFusionPTColormap:({toolGroupId:e,colormap:n})=>{const a=s.getToolGroup(e),{viewportMatchDetails:o}=i.getMatchDetails(),r=f.getMatchingPTDisplaySet({viewportMatchDetails:o});if(!r)return;const l=a.getViewportIds();let u=[];l.forEach((e=>{t.runCommand("setViewportColormap",{viewportId:e,displaySetInstanceUID:r.displaySetInstanceUID,colormap:{name:n}}),u.push(c.getCornerstoneViewport(e))})),u.forEach((e=>{e.render()}))}},y={setEndSliceForROIThresholdTool:{commandFn:f.setEndSliceForROIThresholdTool},setStartSliceForROIThresholdTool:{commandFn:f.setStartSliceForROIThresholdTool},getMatchingPTDisplaySet:{commandFn:f.getMatchingPTDisplaySet},getPTMetadata:{commandFn:f.getPTMetadata},createNewLabelmapFromPT:{commandFn:f.createNewLabelmapFromPT},setSegmentationActiveForToolGroups:{commandFn:f.setSegmentationActiveForToolGroups},thresholdSegmentationByRectangleROITool:{commandFn:f.thresholdSegmentationByRectangleROITool},getTotalLesionGlycolysis:{commandFn:f.getTotalLesionGlycolysis},calculateSuvPeak:{commandFn:f.calculateSuvPeak},getLesionStats:{commandFn:f.getLesionStats},calculateTMTV:{commandFn:f.calculateTMTV},exportTMTVReportCSV:{commandFn:f.exportTMTVReportCSV},createTMTVRTReport:{commandFn:f.createTMTVRTReport},getSegmentationCSVReport:{commandFn:f.getSegmentationCSVReport},exportRTReportForAnnotations:{commandFn:f.exportRTReportForAnnotations},setFusionPTColormap:{commandFn:f.setFusionPTColormap}};return{actions:f,definitions:y,defaultContext:"TMTV:CORNERSTONE"}},ue="roi_stat",pe=[{value:ue,label:"Max",placeHolder:"Max"},{value:"range",label:"Range",placeHolder:"Range"}],me=function({config:e,dispatch:t,runCommand:n}){const{t:a}=q("ROIThresholdConfiguration");return g.createElement("div",{className:"bg-primary-dark flex flex-col space-y-4"},g.createElement("div",{className:"flex items-end space-x-2"},g.createElement("div",{className:"flex w-1/2 flex-col"},g.createElement(h.Select,{label:a("Strategy"),closeMenuOnSelect:!0,className:"border-primary-main mr-2 bg-black text-white ",options:pe,placeholder:pe.find((t=>t.value===e.strategy)).placeHolder,value:e.strategy,onChange:({value:e})=>{t({type:"setStrategy",payload:{strategy:e}})}})),g.createElement("div",{className:"w-1/2"},g.createElement(h.LegacyButtonGroup,null,g.createElement(h.LegacyButton,{size:"initial",className:"px-2 py-2 text-base text-white",color:"primaryLight",variant:"outlined",onClick:()=>n("setStartSliceForROIThresholdTool")},a("Start")),g.createElement(h.LegacyButton,{size:"initial",color:"primaryLight",variant:"outlined",className:"px-2 py-2 text-base text-white",onClick:()=>n("setEndSliceForROIThresholdTool")},a("End"))))),e.strategy===ue&&g.createElement(h.Input,{label:a("Percentage of Max SUV"),labelClassName:"text-[13px] font-inter text-white",className:"border-primary-main bg-black",type:"text",containerClassName:"mr-2",value:e.weight,onChange:e=>{t({type:"setWeight",payload:{weight:e.target.value}})}}),e.strategy!==ue&&g.createElement("div",{className:"mr-2 text-sm"},g.createElement("table",null,g.createElement("tbody",null,g.createElement("tr",{className:"mt-2"},g.createElement("td",{className:"pr-4",colSpan:"3"},g.createElement(h.Label,{className:"font-inter text-[13px] text-white",text:"Lower & Upper Ranges"}))),g.createElement("tr",{className:"mt-2"},g.createElement("td",{className:"pr-4 pt-2 text-center"},g.createElement(h.Label,{className:"text-white",text:"CT"})),g.createElement("td",null,g.createElement("div",{className:"flex justify-between"},g.createElement(h.Input,{label:a(""),labelClassName:"text-white",className:"border-primary-main mt-2 bg-black",type:"text",containerClassName:"mr-2",value:e.ctLower,onChange:e=>{t({type:"setThreshold",payload:{ctLower:e.target.value}})}}),g.createElement(h.Input,{label:a(""),labelClassName:"text-white",className:"border-primary-main mt-2 bg-black",type:"text",containerClassName:"mr-2",value:e.ctUpper,onChange:e=>{t({type:"setThreshold",payload:{ctUpper:e.target.value}})}})))),g.createElement("tr",null,g.createElement("td",{className:"pr-4 pt-2 text-center"},g.createElement(h.Label,{className:"text-white",text:"PT"})),g.createElement("td",null,g.createElement("div",{className:"flex justify-between"},g.createElement(h.Input,{label:a(""),labelClassName:"text-white",className:"border-primary-main mt-2 bg-black",type:"text",containerClassName:"mr-2",value:e.ptLower,onChange:e=>{t({type:"setThreshold",payload:{ptLower:e.target.value}})}}),g.createElement(h.Input,{label:a(""),labelClassName:"text-white",className:"border-primary-main mt-2 bg-black",type:"text",containerClassName:"mr-2",value:e.ptUpper,onChange:e=>{t({type:"setThreshold",payload:{ptUpper:e.target.value}})}}))))))))},de=ue;function ge(e,t){const{payload:n}=t,{strategy:a,ctLower:o,ctUpper:r,ptLower:i,ptUpper:s,weight:c}=n;switch(t.type){case"setStrategy":return{...e,strategy:a};case"setThreshold":return{...e,ctLower:o||e.ctLower,ctUpper:r||e.ctUpper,ptLower:i||e.ptLower,ptUpper:s||e.ptUpper};case"setWeight":return{...e,weight:c};default:return e}}const fe={id:e,preRegistration({servicesManager:e,commandsManager:t,extensionManager:n,configuration:a={}}){!function({servicesManager:e}){const{measurementService:t,displaySetService:n,cornerstoneViewportService:a}=e.services;(0,B.addTool)(B.RectangleROIStartEndThresholdTool);const{RectangleROIStartEndThreshold:o}=((e,t,n)=>({RectangleROIStartEndThreshold:{toAnnotation:Y.toAnnotation,toMeasurement:e=>Y.toMeasurement(e,t,n),matchingCriteria:[{valueType:e.VALUE_TYPES.ROI_THRESHOLD_MANUAL}]}}))(t,n,a),r=t.getSource("Cornerstone3DTools","0.1");t.addMapping(r,"RectangleROIStartEndThreshold",o.matchingCriteria,o.toAnnotation,o.toMeasurement)}({servicesManager:e,commandsManager:t,extensionManager:n,configuration:a})},getToolbarModule:function({commandsManager:e,servicesManager:t}){return[{name:"tmtv.RectangleROIThresholdOptions",defaultComponent:()=>function({servicesManager:e,commandsManager:t}){const{segmentationService:n}=e.services,[a,o]=(0,g.useState)(null),r=(0,g.useCallback)(((e,n={})=>t.runCommand(e,n)),[t]),[i,s]=(0,g.useReducer)(ge,{strategy:de,ctLower:-1024,ctUpper:1024,ptLower:2.5,ptUpper:100,weight:.41}),c=(0,g.useCallback)((()=>{const e=a,t=B.segmentation.segmentIndex.getActiveSegmentIndex(e);r("thresholdSegmentationByRectangleROITool",{segmentationId:e,config:i,segmentIndex:t})}),[a,i]);return(0,g.useEffect)((()=>{const e=n.getSegmentations();if(!e.length)return;const t=e.find((e=>e.isActive));o(t.id)}),[]),(0,g.useEffect)((()=>{const e=n.EVENTS.SEGMENTATION_ADDED,t=n.EVENTS.SEGMENTATION_UPDATED,a=[];return[e,t].forEach((e=>{const{unsubscribe:t}=n.subscribe(e,(()=>{const e=n.getSegmentations();if(!e.length)return;const t=e.find((e=>e.isActive));o(t.id)}));a.push(t)})),()=>{a.forEach((e=>{e()}))}}),[]),g.createElement("div",{className:"invisible-scrollbar mb-2 flex flex-col overflow-y-auto overflow-x-hidden"},g.createElement(me,{config:i,dispatch:s,runCommand:r}),null!==a&&g.createElement(h.Button,{className:"mt-2 !h-[26px] !w-[75px]",onClick:c},"Run"))}({commandsManager:e,servicesManager:t})}]},getPanelModule:function({commandsManager:e,extensionManager:t,servicesManager:n}){return[{name:"petSUV",iconName:"tab-patient-info",iconLabel:"