35:null 36:["$","title",null,{"children":"Loading local image files examples | Pushpanjali | Observable"}] 3c: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(); }; }3d:Tca4,surfaceDiceHighlight = (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); cv.imshow(targetId, ct_scan); // 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 let contour_img_for_distance = cv.Mat.ones(contour_src.cols, contour_src.rows, cv.CV_8UC1); let contour_img_for_coloring = new cv.Mat(contour_src.cols, contour_src.rows, cv.CV_8UC4, new cv.Scalar(0,0,0,255)); let color = new cv.Scalar(0, 255, 0, 255); let color2 = new cv.Scalar(0); let color3 = new cv.Scalar(255, 255, 255, 255); cv.drawContours(ct_scan, contours, -1, color, 1, cv.LINE_8, hierarchy, 160); cv.drawContours(contour_img_for_distance, contours, -1, color2, 1, cv.LINE_8, hierarchy, 160); cv.drawContours(contour_img_for_coloring, contours, -1, color3, 1, cv.LINE_8, hierarchy, 160); // Calculate distance transform let dist = new cv.Mat(contour_src.cols, contour_src.rows, cv.CV_8UC1); cv.distanceTransform(contour_img_for_distance, dist, cv.DIST_L2, 3); let threshold = new cv.Mat(contour_src.cols, contour_src.rows, cv.CV_8UC1); cv.threshold(dist, threshold, distance_threshold, 255, cv.THRESH_BINARY_INV); let imgNormalize = new cv.Mat(contour_src.cols, contour_src.rows, cv.CV_8UC1); console.log(type2str(imgNormalize.type())); cv.normalize(threshold, imgNormalize, 0, 1.0, cv.NORM_MINMAX); console.log(type2str(imgNormalize.type())); imgNormalize.convertTo(imgNormalize, cv.CV_8UC4); console.log(type2str(imgNormalize.type())); cv.cvtColor(imgNormalize, imgNormalize, cv.COLOR_GRAY2RGB); console.log(type2str(imgNormalize.type())); let diff = new cv.Mat(contour_src.cols, contour_src.rows, cv.CV_8UC4, new cv.Scalar(0,0,0,255)); // console.log(type2str(contour_img_for_coloring.type())); // cv.cvtColor(contour_img_for_coloring, contour_img_for_coloring, cv.COLOR_RGB2RGBA); // console.log(type2str(contour_img_for_coloring.type())); // cv.cvtColor(imgNormalize, imgNormalize, cv.COLOR_GRAY2RGB); // console.log(type2str(imgNormalize.type())); // cv.absdiff(contour_img_for_coloring, imgNormalize, diff); // Show result and clean up cv.imshow(targetId, contour_img_for_coloring); contour_src.delete(); ct_scan.delete(); contours.delete(); hierarchy.delete(); contour_img_for_distance.delete(); dist.delete(); threshold.delete(); imgNormalize.delete(); diff.delete(); // mask.delete(); contour_img_for_coloring.delete(); }; }3e:[] 3a:{"id":"5e599359086e3d1c","slug":"loading-local-image-files-examples/4","title":"Loading local image files examples","thumbnail":"7e6c11bffca04f5fe8c64d1fc0923f3918e03ed674a92a317dc1d3e789e00ae5","access_level":"public","create_time":"$D2020-07-08T19:27:24.375Z","update_time":"$D2020-07-10T08:41:20.743Z","view_time":null,"first_public_time":"$D2020-07-08T19:29:10.022Z","has_unpublished_edits":null,"fork":{"id":"d77f991fa3df60a5","slug":"loading-local-image-files-examples","title":"Loading local image files examples","owner":{"id":"137e4289e70da9fc","login":"maartenvm","name":"Maarten van Meersbergen"}},"stars":0,"starred":false,"owner":{"type":"team","id":"4c86536cb4c6cf1e","login":"pushpanjalip","name":"Pushpanjali","avatar_url":"https://avatars-next.observableusercontent.com/5c58cbda843aeb048387834410ec87153d06081424e76fca4d88ba373ffc4322","tier":"starter_2024","bio":""},"version":820,"publish_version":820,"role":null,"authored":false,"authors":[{"type":"individual","id":"56ae40df9962604e","login":"pushpanjalip","name":"Pushpanjali","avatar_url":"https://avatars-next.observableusercontent.com/5c58cbda843aeb048387834410ec87153d06081424e76fca4d88ba373ffc4322","tier":null,"bio":""}],"members":[{"type":"individual","id":"56ae40df9962604e","login":"pushpanjalip","name":"Pushpanjali","avatar_url":"https://avatars-next.observableusercontent.com/5c58cbda843aeb048387834410ec87153d06081424e76fca4d88ba373ffc4322","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"titling":"auto","title":"Loading local image files examples","cells":[{"id":46,"value":"md`# Loading local image files examples`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":33,"value":"md`## Load all files in folder`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":298,"value":"viewof multiFiles = html`` //load segmentation slices for this case","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":300,"value":"multiFileList = Array.from(multiFiles);","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":303,"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","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":111,"value":"numberOfCases = Object.keys(multiFileDict[\"images\"]).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":276,"value":"numberOfSlices = Object.keys(multiFileDict[\"images\"][caseNo]).length","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":194,"value":"viewof caseSlider = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":311,"value":"caseNo = Object.keys(multiFileDict.images)[caseSlider];","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":106,"value":"viewof sliceNo = html``","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":108,"value":"sliceNo\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":460,"value":"gallery = html`\n\n

\n ${Object.keys(multiFileDict).sort().slice(1).map((fileName, index) => {\n sample(loadImage(\"images\", caseNo, sliceNo), loadImage(fileName, caseNo, sliceNo), fileName);\n return setCanvas(fileName, caseNo, sliceNo, true)\n })}\n

\n`\n","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":806,"value":"comparision = html `

\n ${addCheckbox ? \n html`` \n : null}\n

` \n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":763,"value":"function compare(){\n const checkboxes = Array.from(document.getElementsByName('selectScan'))\n const selected = checkboxes.filter(c => c.checked)\n if(selected.length === 2) {\n const selectedIds = selected.map(ch => ch.dataset.id);\n getSelectedCanvas(selectedIds);\n } else {\n console.log(\"You can select only 2 scans to compare\")\n }\n \n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":767,"value":"function getSelectedCanvas(selectedCanvas) {\n const canvasContainer = document.getElementById('comparision');\n canvasContainer.innerHTML='';\n selectedCanvas.map(canvas => {\n const canvasData = canvas.split(\"/\"); // To separate id, caseNo and SliceNo\n sample(loadImage(\"images\", canvasData[1], canvasData[2]), loadImage(canvasData[0], canvasData[1], canvasData[2]), 'selected'+canvasData[0]);\n const canvasToCompare = setCanvas('selected'+canvasData[0], canvasData[1], canvasData[2], false)\n canvasContainer.appendChild(canvasToCompare)\n })\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":374,"value":"loadImage = function(subDir, caseNo, sliceNo) {\n if (multiFileDict[subDir][caseNo] != undefined &&\n multiFileDict[subDir][caseNo][sliceNo] != undefined) {\n var file = multiFileDict[subDir][caseNo][sliceNo].file;\n if (file != undefined) {\n return file;\n }\n }\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":372,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":616,"value":"html`

`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":623,"value":"distance_threshold = 1","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":619,"value":"surfaceDiceHighlight(loadImage(\"images\", caseNo, sliceNo), loadImage(\"segmentations_without_variations\", caseNo, sliceNo), 'surfaceDice')","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":612,"value":"$3d","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":715,"value":"type2str = function(type) {\n const { cv } = window;\n \n let r;\n\n let depth = type & cv.CV_MAT_DEPTH_MASK;\n let chans = 1 + (type >> cv.CV_CN_SHIFT);\n\n switch ( depth ) {\n case cv.CV_8U: r = \"8U\"; break;\n case cv.CV_8S: r = \"8S\"; break;\n case cv.CV_16U: r = \"16U\"; break;\n case cv.CV_16S: r = \"16S\"; break;\n case cv.CV_32S: r = \"32S\"; break;\n case cv.CV_32F: r = \"32F\"; break;\n case cv.CV_64F: r = \"64F\"; break;\n default: r = \"User\"; break;\n }\n\n r += \"C\";\n r += (chans+'0');\n\n return r;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":760,"value":"html`\n`","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":369,"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","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":814,"value":"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"},{"id":817,"value":"import {html, svg} from \"@observablehq/htl\"","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","tool":"$undefined","providerMetadata":"$undefined","attachments":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W3e","stdlib":"1"}} 3b:"$3a:body"