2a:T485,sample = (background, input, targetId) => { const bg_image = new Image(); bg_image.src = URL.createObjectURL(background); const image = new Image(); image.src = URL.createObjectURL(input); image.onload = function() { const { cv } = window; // Source and destination images const contour_src = new cv.imread(image); const ct_scan = new cv.imread(bg_image); // Convert to binary cv.cvtColor(contour_src, contour_src, cv.COLOR_RGBA2GRAY, 0); cv.threshold(contour_src, contour_src, 120, 200, cv.THRESH_BINARY); // Find contours let contours = new cv.MatVector(); let hierarchy = new cv.Mat(); cv.findContours(contour_src, contours, hierarchy, cv.RETR_CCOMP, cv.CHAIN_APPROX_SIMPLE); // Draw contours on destination image for (let i = 0; i < contours.size(); ++i) { let color = new cv.Scalar(0, 255, 0, 255); cv.drawContours(ct_scan, contours, i, color, 1, cv.LINE_8, hierarchy, 160); } // Show result and clean up cv.imshow(targetId, ct_scan); contour_src.delete(); ct_scan.delete(); contours.delete(); hierarchy.delete(); }; }2b:T7ed,/*{ allTable.length = 0 Object.entries(dataLola11[selectedRow].metrics).slice(0,7).map((metric, j)=>{ // k = 0 to 55 metric[1].map((dice,k)=>{ allTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } ) llTable.length = 0 rlTable.length = 0 rllTable.length = 0 rmlTable.length = 0 rulTable.length = 0 lllTable.length = 0 lulTable.length = 0 Object.entries(dataLola11[selectedRow].metrics).slice(0,7).map((metric, j)=>{ if(metric[0]=== 'll'){ metric[1].map((dice,k)=>{ // k = 0 to 55 llTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'rl'){ metric[1].map((dice,k)=>{ // k = 0 to 55 rlTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'rll'){ metric[1].map((dice,k)=>{ // k = 0 to 55 rllTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'rml'){ metric[1].map((dice,k)=>{ // k = 0 to 55 rmlTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'rul'){ metric[1].map((dice,k)=>{ // k = 0 to 55 rulTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'lll'){ metric[1].map((dice,k)=>{ // k = 0 to 55 lllTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } else if(metric[0]=== 'lul'){ metric[1].map((dice,k)=>{ // k = 0 to 55 lulTable.push({ subject: k+1, dice: dice, segment: metric[0]}) }) } }) } */2c:[] 29:{"title":"Visualizing FedMix results","cells":[{"id":936,"value":"md `# Visualizing FedMix results`","pinned":true,"hidden":false,"mode":"ojs"},{"id":236,"value":"md`### Import Json data file`","pinned":false,"hidden":false,"mode":"ojs"},{"id":0,"value":"viewof data_in = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":511,"value":"md `Example data from FedMix (Decathlon data).`","pinned":false,"hidden":false,"mode":"ojs"},{"id":3,"value":"results = Files.text(data_in)","pinned":false,"hidden":false,"mode":"ojs"},{"id":842,"value":"// Parse JSON File\ndataFedMix = JSON.parse(results);","pinned":false,"hidden":false,"mode":"ojs"},{"id":1190,"value":"viewof multiFiles = html`` //load segmentation slices for this case","pinned":true,"hidden":false,"mode":"ojs"},{"id":1192,"value":"multiFileList = Array.from(multiFiles);","pinned":true,"hidden":false,"mode":"ojs"},{"id":1195,"value":"multiFileDict = {\n var result = {};\n \n multiFileList.forEach(function(f) { \n var name = f.name;\n var path = f.webkitRelativePath;\n var subdir = f.webkitRelativePath.match(/variations_decathlon_dataset\\/(.*)\\//i)[1];\n var caseNr = parseInt(f.name.match(/Case([0-9]+)_/i)[1]);\n var slice = parseInt(f.name.match(/Case[0-9]+[a-zA-Z_]+([0-9]+)/i)[1]);\n \n if (result[subdir] === undefined) { \n result[subdir] = [];\n }\n if (result[subdir][caseNr] === undefined) {\n result[subdir][caseNr] = [];\n }\n result[subdir][caseNr][slice] = {\n name: name,\n path: subdir,\n file: f\n }; \n })\n return result;\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1199,"value":"numberOfCases = Object.keys(multiFileDict[\"images\"]).length;","pinned":false,"hidden":false,"mode":"ojs"},{"id":1218,"value":"viewof caseSlider = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":1216,"value":"caseNo = Object.keys(multiFileDict.images)[caseSlider];","pinned":false,"hidden":false,"mode":"ojs"},{"id":1205,"value":"numberOfSlices = Object.keys(multiFileDict[\"images\"][caseNo]).length;","pinned":false,"hidden":false,"mode":"ojs"},{"id":1220,"value":"viewof sliceNo = html``","pinned":false,"hidden":false,"mode":"ojs"},{"id":1233,"value":"canvasses = html`\n\n\n

\n\n

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1235,"value":"loadImage = function(subDir, caseNo, sliceNo) {\n if (multiFileDict[subDir][caseNo] != undefined &&\n multiFileDict[subDir][caseNo][sliceNo] != undefined) {\n var file = multiFileDict[subDir][caseNo][sliceNo].file;\n if (file != undefined) {\n return file;\n }\n }\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1245,"value":"{\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_without_variations\", caseNo, sliceNo), 'swv');\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_with_shifts_5\", caseNo, sliceNo), 'sws');\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_bottom_over_under_segment_10\", caseNo, sliceNo), 'sbo')\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_top_over_under_segment_10\", caseNo, sliceNo), 'sto')\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_with_erosion_dilation_5\", caseNo, sliceNo), 'swe')\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1239,"value":"$2a","pinned":false,"hidden":false,"mode":"ojs"},{"id":1242,"value":"loadOpenCv = {\n return new Promise((resolve, reject) => {\n const script = document.createElement('script');\n script.src = 'https://docs.opencv.org/master/opencv.js';\n script.type = 'text/javascript';\n script.async = true;\n\n script.onabort = () => {\n reject('OpenCV Load failed.');\n };\n\n script.onload = () => {\n if (window.cv !== undefined) {\n resolve('OpenCV Load success.');\n }\n console.log('hallo');\n };\n \n document.body.appendChild(script);\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":978,"value":"md `### One plot in which the lung segment can be selected`","pinned":false,"hidden":false,"mode":"ojs"},{"id":963,"value":"/*viewof selectLungSegment = select({\n title: 'Select Lung Segment',\n options: ['all','ll','lll','lul','rl','rll','rml','rul' ],\n value: 'all'\n})*/","pinned":false,"hidden":false,"mode":"ojs"},{"id":56,"value":"/*vl.markPoint().data(submissionTable).encode(\n vl.x().fieldQ('subject').title('Subject'),\n vl.y().fieldQ('dice').title('Dice').scale({domain: [-1.0, 1.0]}),\n vl.color().field('segment').title('Lung Segment'),\n vl.tooltip(['subject', 'segment', 'dice'])\n).render()*/","pinned":false,"hidden":false,"mode":"ojs"},{"id":969,"value":"md `**Question for James**: *How come there are -1 values in the data for Dice? Subject 44 Rul, Subject 45 lul, Subject 48 rml, in all submissions...*`","pinned":false,"hidden":false,"mode":"ojs"},{"id":991,"value":"md `Initialize submissionTable`","pinned":false,"hidden":false,"mode":"ojs"},{"id":677,"value":"resultsTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":698,"value":"md `⬇️ Fill the submissionTable with data from the selected submission ⬇️`","pinned":false,"hidden":false,"mode":"ojs"},{"id":641,"value":"// only row 0\n// j= 0-8 (ll, rl, ...), discard metrics object\n\n{\n resultsTable.length = 0\n \n //if(selectLungSegment === 'all'){ \n Object.entries(dataFedMix.metrics.head_0.DSC).map((metric, j)=>{ // j = 0 - 12\n // k = 0 to 55\n // metric.value_for_patient\n //[0].DSC.map((dice,k)=>{\n resultsTable.push({ subject: metric[0], dice: metric[0][0]}) \n //})\n }\n )\n //}\n} \n/* \n//else{\n // Filter by Segment\n Object.entries(results.metrics).slice(0,2).map((metric, j)=>{\n metric.head_0.DSC.map((dice,k)=>{ // 12 patients\n //if(metric[0]=== 'head_0'){\n //metric[1].map((dice,k)=>{ // k = 0 to 55\n resultsTable.push({ subject: k+1, dice: dice, segment: metric[0]}) \n })\n }\n //})\n //}\n//}\n*/","pinned":false,"hidden":false,"mode":"ojs"},{"id":988,"value":"md `### Overview of plots with various lung segments`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1007,"value":"/*{\n //const base = vl.markPoint().encode(\n const base = vl.markCircle({size: 15, opacity: 0.9}).encode(\n vl.x().fieldQ('subject').title('Subject'),\n vl.y().fieldQ('dice').title('Dice').scale({domain: [-1.0, 1.0]}),\n vl.color().field('segment').title('Lung Segment'),\n vl.tooltip(['subject', 'segment', 'dice'])\n )\n .width(150)\n .height(130);\n\n const all = base.data(allTable);\n const ll = base.data(llTable);\n const lll = base.data(lllTable);\n const lul = base.data(lulTable);\n const rll = base.data(rllTable);\n const rml = base.data(rmlTable);\n const rul = base.data(rulTable);\n const rl = base.data(rlTable);\n \n return vl.vconcat(\n vl.hconcat(all, ll, lll, lul),\n vl.hconcat(rl, rll, rml, rul)\n ).render();\n // return vl.hconcat(all, ll, rl).render();\n}\n*/","pinned":false,"hidden":false,"mode":"ojs"},{"id":1057,"value":"rulTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1055,"value":"rmlTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1050,"value":"rllTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1048,"value":"lulTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1047,"value":"lllTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1018,"value":"llTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1026,"value":"rlTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1032,"value":"allTable =[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":1020,"value":"$2b","pinned":false,"hidden":false,"mode":"ojs"},{"id":1133,"value":"md `### Overview of plots from various challenge submissions`","pinned":true,"hidden":false,"mode":"ojs"},{"id":1135,"value":"md `\n* Add to comparison button, below the submission slider. \n* Fill overview with multiple submission, with all lung segments.\n* Add the selection of lung segments (change this in all submission plots).\n* And add a clear/reset button.\n`","pinned":true,"hidden":false,"mode":"ojs"},{"id":705,"value":"md `# All Rows`","pinned":false,"hidden":false,"mode":"ojs"},{"id":708,"value":"tableResult=[]","pinned":false,"hidden":false,"mode":"ojs"},{"id":753,"value":"/*viewof selectedSegment = select({\n title: 'View segments',\n options: ['all','ll','lll','lul','rl','rll','rml','rul' ],\n value: 'all'\n})*/\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":724,"value":"/*{\n // Visalization types: markTick, markCircle\n const plot1 = vl.markCircle({size:12}).data(tableResult).encode(\n vl.x().fieldQ('subject'),\n vl.y().fieldQ('dice'),\n vl.color().field('segment'),\n vl.tooltip(['subject', 'segment', 'dice']),\n\n )\n // .width(200)\n // .height(200)\n return vl.vconcat(plot1)\n // .autosize({type: 'fit-x', contains: 'padding'})\n // .repeat({column: ['Acceleration', 'Horsepower', 'Displacement']})\n .render();\n\n\n\n}*/","pinned":true,"hidden":false,"mode":"ojs"},{"id":719,"value":"md `⬇️ Data calculation ⬇️`","pinned":false,"hidden":false,"mode":"ojs"},{"id":715,"value":"/*{\n\n tableResult.length = 0\n \n if(selectedSegment === 'all'){ \n dataLola11.map(\n (row,index) => { // index = 0 to 142\n Object.entries(row.metrics).slice(0,7).map((metric, j)=>{\n metric[1].map((dice,k)=>{ // k = 0 to 55\n tableResult.push({ subject: k+1, dice: dice, segment: metric[0]}) \n })\n })\n }\n )\n }\n else{\n // Filter by Segment\n dataLola11.map(\n (row,index) => { // index = 0 to 142\n Object.entries(row.metrics).slice(0,7).map((metric, j)=>{\n if(metric[0]=== selectedSegment){\n metric[1].map((dice,k)=>{ // k = 0 to 55\n tableResult.push({ subject: k+1, dice: dice, segment: metric[0]}) \n })\n }\n })\n }\n )\n }\n\n}*/","pinned":true,"hidden":false,"mode":"ojs"},{"id":22,"value":"\n\n\n\n\n\n\n\n// printTable(dataLola11.slice(0, 10)) ","pinned":true,"hidden":false,"mode":"ojs"},{"id":142,"value":"//dataLeftLung = dataLola11.map( leftLung => leftLung.metrics.ll )\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":149,"value":"printTable(dataLeftLung.slice(0,10))","pinned":false,"hidden":false,"mode":"ojs"},{"id":163,"value":"dataLeftLung","pinned":true,"hidden":false,"mode":"ojs"},{"id":30,"value":"import {printTable} from '@uwdata/data-utilities'","pinned":false,"hidden":false,"mode":"ojs"},{"id":27,"value":"import {vl} from '@vega/vega-lite-api'","pinned":false,"hidden":false,"mode":"ojs"},{"id":755,"value":"import { slider, select } from '@jashkenas/inputs'\n","pinned":true,"hidden":false,"mode":"ojs"},{"id":895,"value":"vegalite = require(\"@observablehq/vega-lite@0.3\")","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W2c","stdlib":"1","titling":"auto"}