30:T1632,dump = (dataSet, options) => { let opts = { sort: true, verbose: false, ...options }; // extract single string or an array of strings let extractStr = (dataSet, element) => { let str = dataSet.string(element.tag); if (str === undefined) return undefined; let a = str.split('\\'); if (a.length > 1) return a; else return str; }; // extract single number or an array of numbers let extractNr = (dataSetParser, dataTypeLength, element) => { var a = []; for (var i = 0; i < element.length / dataTypeLength; i++) { a.push(dataSetParser(element.tag, i)); } if (a.length > 1) return a; else return a[0]; }; // extract byte array let extractBytes = (dataSet, element) => { var a = []; // TODO: better performance? for (var i = 0; i < element.length; i++) { a.push(dataSet.byteArray[element.dataOffset + i]); } return a; }; // display uid with human readable description let displayUid = (dataSet, element) => { var str = extractStr(dataSet, element); if (str === undefined) return undefined; let lookup = uid => (dicom_uids[uid] ? dicom_uids[uid].name : undefined); if (Array.isArray(str)) return str.map(s => lookup(s)); else return lookup(str); }; // http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.2.3.html // http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_6.2.html let displayVr = { UI: (dataSet, element) => displayUid(dataSet, element) }; let extractVr = { AE: (dataSet, element) => extractStr(dataSet, element), AS: (dataSet, element) => extractStr(dataSet, element), AT: (dataSet, element) => extractStr(dataSet, element), CS: (dataSet, element) => extractStr(dataSet, element), DA: (dataSet, element) => extractStr(dataSet, element), DS: (dataSet, element) => extractStr(dataSet, element), DT: (dataSet, element) => extractStr(dataSet, element), FD: (dataSet, element) => extractNr((t, i) => dataSet.double(t, i), 8, element), FL: (dataSet, element) => extractNr((t, i) => dataSet.float(t, i), 4, element), IS: (dataSet, element) => extractStr(dataSet, element), LO: (dataSet, element) => extractStr(dataSet, element), LT: (dataSet, element) => extractStr(dataSet, element), OB: (dataSet, element) => extractBytes(dataSet, element), OD: (dataSet, element) => extractBytes(dataSet, element), OF: (dataSet, element) => extractBytes(dataSet, element), OL: (dataSet, element) => extractBytes(dataSet, element), OV: (dataSet, element) => extractBytes(dataSet, element), OW: (dataSet, element) => extractBytes(dataSet, element), PN: (dataSet, element) => extractStr(dataSet, element), SH: (dataSet, element) => extractStr(dataSet, element), SL: (dataSet, element) => extractNr((t, i) => dataSet.int32(t, i), 4, element), // SQ => nested data structure SS: (dataSet, element) => extractNr((t, i) => dataSet.int16(t, i), 2, element), ST: (dataSet, element) => extractStr(dataSet, element), SV: (dataSet, element) => extractStr(dataSet, element), TM: (dataSet, element) => extractStr(dataSet, element), UC: (dataSet, element) => extractStr(dataSet, element), UI: (dataSet, element) => extractStr(dataSet, element), UL: (dataSet, element) => extractNr((t, i) => dataSet.uint32(t, i), 4, element), UN: (dataSet, element) => extractBytes(dataSet, element), UR: (dataSet, element) => extractStr(dataSet, element), US: (dataSet, element) => extractNr((t, i) => dataSet.uint16(t, i), 2, element), UT: (dataSet, element) => extractStr(dataSet, element), UV: (dataSet, element) => extractStr(dataSet, element) }; // dump let _dump = (dataSet, output) => { let tags = Object.keys(dataSet.elements); if (opts.sort) tags = tags.sort(); for (const tag of tags) { if (tag === "xfffee00d") continue; let element = dataSet.elements[tag]; let tagInfo = dicom_tags[tag.substr(1).toUpperCase()]; if (tagInfo === undefined) { tagInfo = { name: undefined, vr: undefined, vm: undefined, keyword: undefined }; } // output object var o = { name: tagInfo.name || "(" + tag.substr(1, 4) + "," + tag.substr(5, 4) + ")" }; if (opts.verbose) { o['tag'] = "(" + tag.substr(1, 4) + "," + tag.substr(5, 4) + ")"; o['vr'] = element.vr || tagInfo.vr; o['vm'] = element.vm || tagInfo.vm; } if (element.items) { // dump sub items recursively o["items"] = []; for (const item of element.items) { var v = {}; _dump(item.dataSet, v); o["items"].push(v); } } else if (element.fragments) { // TODO o["value"] = "[fragment is not implemented yet]"; } else { // interpret value according to 'vr' let vr = element.vr || tagInfo.vr; if (vr in extractVr) { o["value"] = extractVr[vr](dataSet, element); } else { var forced = dataSet.string(element.tag); if (forced !== undefined) o["value"] = forced; else o["value"] = "[unknown value representation]"; // TODO: do something else? } // extra display of values if (opts.verbose && vr in displayVr) { var display = displayVr[vr](dataSet, element); if (display !== undefined) o["display"] = display; } } // collect result output[tag] = o; } }; var output = {}; _dump(dataSet, output); return output; }31:[{"id":"4396d310ab6af21cc585f66735ccd916d0f7bf50f319c154f37a806d7bc239ab73542c44f1a975c8fb53f9f5d41b72b0875a2096913b7d0b625add210b7cbaca","href":"https://static.observableusercontent.com/files/4396d310ab6af21cc585f66735ccd916d0f7bf50f319c154f37a806d7bc239ab73542c44f1a975c8fb53f9f5d41b72b0875a2096913b7d0b625add210b7cbaca","name":"dicom_tags@2.json","type":"application/json","lastModified":1622797437355.243,"size":510610},{"id":"5da103f7cd708b2253fb35beb733085717f2b27584ec7cd6f96fb7f16b7717b17f07127918538b7f30b54ca2154cfac3751d4307ded45b3f1612f142423292b3","href":"https://static.observableusercontent.com/files/5da103f7cd708b2253fb35beb733085717f2b27584ec7cd6f96fb7f16b7717b17f07127918538b7f30b54ca2154cfac3751d4307ded45b3f1612f142423292b3","name":"dicom_uids@1.json","type":"application/json","lastModified":1622798540091.775,"size":240991}] 2e:{"title":"DICOM Dump","cells":[{"id":122,"value":"md`# DICOM Dump`","pinned":false,"hidden":false,"mode":"ojs"},{"id":517,"value":"Header = md`👍 No file will be *uploaded* to any server. It is processed locally inside the browser.`","pinned":false,"hidden":false,"mode":"ojs"},{"id":28,"value":"viewof fileuploader = fuploader({\n description: md`### (Note: You may use [GDCM](https://sourceforge.net/p/gdcm/gdcm/) to convert any pseudo DICOM file to be P10 compatible. I.e. \\`$ gdcmconv -C from.dcm to.dcm\\`, otherwise a none-P10-compatible file will be parsed with impplicit little endian transfer syntax)`,\n accept: \".dcm\",\n title: \"Select or drop a DICOM file.\"\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1216,"value":"mutable parse_result = md`ⓘ No DICOM file is loaded yet`","pinned":false,"hidden":false,"mode":"ojs"},{"id":669,"value":"md`### Complete dump result ${verbose ? '(including verbose info)' : ''}`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1187,"value":"viewof verbose = Inputs.toggle({\n label: \"verbose:\",\n value: true\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":955,"value":"md`### Overview of Top-level Properties`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1251,"value":"overview_table(dmp)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1349,"value":"md`### Dump Object View`","pinned":false,"hidden":false,"mode":"ojs"},{"id":660,"value":"dmp = dump(dataSet, { verbose: verbose })","pinned":false,"hidden":false,"mode":"ojs"},{"id":665,"value":"md`

`","pinned":false,"hidden":false,"mode":"ojs"},{"id":118,"value":"md`## Appendix`","pinned":false,"hidden":false,"mode":"ojs"},{"id":855,"value":"md`### Internals`","pinned":false,"hidden":false,"mode":"ojs"},{"id":729,"value":"md`parsed data set of the selected DICOM file with dicom-parser`","pinned":false,"hidden":false,"mode":"ojs"},{"id":156,"value":"// parsed DICOM data set\ndataSet = {\n try {\n var ds = parse(await getUint8Array(fileuploader));\n mutable parse_result = md`👍 A DICOM file is sucessfully loaded`;\n return ds;\n } catch (error) {\n mutable parse_result = md`🚫 ${error}`;\n }\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":837,"value":"md`### Utils`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1247,"value":"overview_table = dmp =>\n table(Object.values(dmp), {\n enableFilter: false,\n enableCSVDownload: false,\n columns: [\n {\n key: 'tag',\n name: '',\n render: val => `🏷️`\n },\n {\n key: 'name',\n name: 'tag'\n },\n 'value',\n {\n key: 'display',\n name: '',\n render: (val, i, d) => (val ? `💬` : '')\n }\n ]\n })","pinned":false,"hidden":false,"mode":"ojs"},{"id":842,"value":"md`\n~~~\ndump values of a DICOM data set\n\n@param dataSet raw DICOM data set\n@param options default {sort: true, verbose, false}\n@return dump object of DICOM file with value representation\n~~~`","pinned":false,"hidden":false,"mode":"ojs"},{"id":263,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":775,"value":"md`\n~~~\nparse DICOM file into raw data set\n\n@param uintArray byte array of incput DICOM file\n@return raw data set without interpretation of tag values\n~~~`","pinned":false,"hidden":false,"mode":"ojs"},{"id":767,"value":"parse = byteArray => \n{\n try {\n dicomParser.readPart10Header(byteArray);\n return dicomParser.parseDicom(byteArray);\n } catch (error) {\n // workaround of missing P10 header \n // https://github.com/cornerstonejs/dicomParser/issues/112#issuecomment-443759299\n var byteStream = new dicomParser.ByteStream(dicomParser.littleEndianByteArrayParser, byteArray, 0);\n var dataSet = new dicomParser.DataSet(byteStream.byteArrayParser, byteStream.byteArray, {});\n dicomParser.parseDicomDataSetImplicit(dataSet, byteStream, byteStream.byteArray.length, {});\n return dataSet;\n }\n}","pinned":true,"hidden":false,"mode":"ojs"},{"id":862,"value":"md`\n~~~\nget byte array from a \\`Blob\\` or a \\`fileuploader\\`\n\n@param blob an object having \\`arrayBuffer()\\`\n@return byte array in Uint8Array\n~~~`","pinned":false,"hidden":false,"mode":"ojs"},{"id":858,"value":"getUint8Array = async blob => {\n var b = await blob.arrayBuffer();\n return new Uint8Array(b);\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":752,"value":"md`DICOM UID list`","pinned":false,"hidden":false,"mode":"ojs"},{"id":296,"value":"dicom_uids = FileAttachment(\"dicom_uids@1.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":290,"value":"/* get the dicom uid list from fo-dicom/fo-dicom */\n/*\ndicom_uids = {\n const res = await soFetch(\n 'https://raw.githubusercontent.com/fo-dicom/fo-dicom/development/DICOM/Dictionaries/DICOM Dictionary.xml'\n );\n const xmlStr = await res.text();\n const parser = new DOMParser();\n const dom = parser.parseFromString(xmlStr, \"application/xml\");\n var uids = {};\n dom.querySelectorAll('uid').forEach(el => {\n uids[el.getAttribute(\"uid\")] = {\n keyword: el.getAttribute(\"keyword\"),\n type: el.getAttribute(\"type\"),\n name: el.textContent\n };\n });\n return uids;\n}\n*/","pinned":true,"hidden":false,"mode":"ojs"},{"id":755,"value":"md`DICOM tag list`","pinned":false,"hidden":false,"mode":"ojs"},{"id":254,"value":"dicom_tags = FileAttachment(\"dicom_tags@2.json\").json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":803,"value":"/* get the dicom tag list from fo-dicom/fo-dicom */\n/*\ndicom_tags = {\n const res = await soFetch(\n 'https://raw.githubusercontent.com/fo-dicom/fo-dicom/development/DICOM/Dictionaries/DICOM Dictionary.xml'\n );\n const xmlStr = await res.text();\n const parser = new DOMParser();\n const dom = parser.parseFromString(xmlStr, \"application/xml\");\n var tags = {};\n dom.querySelectorAll('tag').forEach(el => {\n let group = el.getAttribute(\"group\");\n let element = el.getAttribute(\"element\");\n tags[group + element] = {\n keyword: el.getAttribute(\"keyword\"),\n vr: el.getAttribute(\"vr\"),\n vm: el.getAttribute(\"vm\"),\n name: el.textContent\n };\n });\n return tags;\n}\n*/","pinned":true,"hidden":false,"mode":"ojs"},{"id":153,"value":"md`### Libraries`","pinned":false,"hidden":false,"mode":"ojs"},{"id":0,"value":"dicomParser = require('dicom-parser@1.8.7/dist/dicomParser.js') // or dicomParser.min.js","pinned":false,"hidden":false,"mode":"ojs"},{"id":164,"value":"d3 = require('d3')","pinned":false,"hidden":false,"mode":"ojs"},{"id":169,"value":"import { soFetch } from '@alecglassford/so-fetch'","pinned":false,"hidden":false,"mode":"ojs"},{"id":26,"value":"import { fileuploader as fuploader } from \"@fil/fileuploader\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1005,"value":"import { table } from \"@easz/fancy-table\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":741,"value":"md`### Extra Credit`","pinned":false,"hidden":false,"mode":"ojs"},{"id":745,"value":"md`\n- Inspired by [the example](https://rawgit.com/cornerstonejs/dicomParser/master/examples/dumpWithDataDictionary/index.html) of dicomParser\n- DICOM definition extracted from [fo-dicom](https://github.com/fo-dicom/fo-dicom)`","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}