diff --git a/.binder/postBuild b/.binder/postBuild deleted file mode 100644 index f68ab1c..0000000 --- a/.binder/postBuild +++ /dev/null @@ -1,6 +0,0 @@ -# fix iopub issues -mkdir $HOME/.jupyter -echo "c.NotebookApp.iopub_data_rate_limit=1e22" >> $HOME/.jupyter/jupyter_notebook_config.py -# add itkwidgets -jupyter nbextension install --py --sys-prefix itkwidgets -jupyter nbextension enable --py --sys-prefix itkwidgets diff --git a/.binder/requirements.txt b/.binder/requirements.txt index 2cb7c73..df8e4f0 100644 --- a/.binder/requirements.txt +++ b/.binder/requirements.txt @@ -1,6 +1,6 @@ tqdm -requests -itk-ioscanco>=0.9.1 -itkwidgets +pooch +itk-ioscanco>=0.10.0 +itkwidgets[all]>=1.0a21 xarray zarr diff --git a/.github/workflows/test-notebooks.yml b/.github/workflows/test-notebooks.yml index 7be13f7..427fb93 100644 --- a/.github/workflows/test-notebooks.yml +++ b/.github/workflows/test-notebooks.yml @@ -8,18 +8,18 @@ jobs: strategy: max-parallel: 3 matrix: - os: [ubuntu-22.04, macos-10.15] + os: [ubuntu-22.04, macos-12, windows-2022] steps: - uses: actions/checkout@v3 - uses: actions/setup-python@v3 with: - python-version: '3.8' + python-version: '3.9' - name: Install build dependencies run: | python -m pip install -r ./.binder/requirements.txt - python -m pip install nbmake[html] - - uses: "treebeardtech/nbmake-action@v0.2" - with: - path: "./examples/" - path-output: . + python -m pip install pytest nbmake + - name: Test notebooks + shell: bash + run: | + pytest --nbmake --nbmake-timeout=3000 examples/*.ipynb diff --git a/README.rst b/README.rst index 0c79baa..73bc698 100644 --- a/README.rst +++ b/README.rst @@ -2,6 +2,12 @@ ITKIOScanco =========== .. image:: https://github.com/KitwareMedical/ITKIOScanco/workflows/Build,%20test,%20package/badge.svg + :target: https://github.com/KitwareMedical/ITKIOScanco/actions/workflows/build-test-package.yml + :alt: Build, test, package + +.. image:: https://github.com/KitwareMedical/ITKIOScanco/actions/workflows/test-notebooks.yml/badge.svg + :target: https://github.com/KitwareMedical/ITKIOScanco/actions/workflows/test-notebooks.yml + :alt: Notebooks tests .. image:: https://img.shields.io/pypi/v/itk-ioscanco.svg :target: https://pypi.python.org/pypi/itk-ioscanco @@ -19,6 +25,8 @@ Overview An `ITK `_ module to read and write Scanco microCT .isq files. +This package is a resource created by `Kitware `_ et. al. for the community for `Open and Reproducible Musculoskeletal Imaging Research (ORMIR) `_. + ITK is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional scientific images. .. image:: https://media.giphy.com/media/W1UCXb57bzGZDOi4kr/giphy.gif diff --git a/app/.gitignore b/app/.gitignore new file mode 100644 index 0000000..bea2f92 --- /dev/null +++ b/app/.gitignore @@ -0,0 +1,3 @@ +node_modules/ +public/ +dist/ diff --git a/app/index.html b/app/index.html new file mode 100644 index 0000000..8d3c9e5 --- /dev/null +++ b/app/index.html @@ -0,0 +1,128 @@ + + + + + + + + + + + ITK IO Scanco + + + + + + +
+ + + + +

ITK IO Scanco

+ Convert and calibrate Scanco microCT volume .isq and .aim files. +

+ + + Volume format conversion + Volume calibration + + + + + Convert Scanco .AIM or .ISQ volumes to an open standard file format.

+ +
+ +
+
+
+ + MetaImage + NIfTI + NRRD + VTK + ITK HDF5 + +
+ +
Load sample + Convert +
+
+ +
+ + +
+ + Download +

+
+ + + + + + + Given a binary or string produced with compress-stringify, decompress and optionally base64 decode.

+ +
+ + +

+ parseString - Parse the input string before decompression +

+ +
Load sample inputs + Run

+ +
+ + +
+ + Download +

+
+ + + + + +
+ + + + + diff --git a/app/package.json b/app/package.json new file mode 100644 index 0000000..433bf69 --- /dev/null +++ b/app/package.json @@ -0,0 +1,41 @@ +{ + "name": "itk-io-scanco-app", + "version": "0.1.0", + "description": "Convert and calibrate Scanco microCT volume .isq and .aim files.", + "scripts": { + "start": "pnpm copyShoelaceAssets && pnpm downloadSampleData && vite", + "preview": "pnpm copyShoelaceAssets && pnpm downloadSampleData && vite build && vite preview", + "test": "echo \"tests are not configured\" && exit 1", + "downloadSampleData": "dam download -v public/sample-data public/sample-data.tar.gz bafybeiepwh5ppaeaja7q6kqc25tvzfpkygqomxzqq4csnjfntoxarqtdiq https://w3s.link/ipfs/bafybeihiuinvftya2jqrr7fhdrdf4a5zhx7gnmawwf45mid7j2s5zcn6xi", + "copyShoelaceAssets": "shx mkdir -p public/shoelace && shx cp -r node_modules/@shoelace-style/shoelace/dist/assets public/", + "build": "pnpm copyShoelaceAssets && pnpm downloadSampleData && vite build" + }, + "keywords": [ + "itk", + "wasm", + "scanco", + "isq", + "aim", + "webassembly", + "wasi" + ], + "author": "Matt McCormick ", + "license": "Apache-2.0", + "homepage": "https://github.com/KitwareMedical/ITKIOScanco#readme", + "dependencies": { + "@itk-wasm/image-io": "^0.3.0", + "itk-wasm": "1.0.0-b.149" + }, + "devDependencies": { + "@itk-wasm/dam": "^1.0.1", + "@shoelace-style/shoelace": "^2.5.2", + "@types/node": "^20.2.5", + "shx": "^0.3.4", + "vite": "^4.3.9", + "vite-plugin-static-copy": "^0.14.0" + }, + "repository": { + "type": "git", + "url": "https://github.com/KitwareMedical/ITKIOScanco" + } +} diff --git a/app/pnpm-lock.yaml b/app/pnpm-lock.yaml new file mode 100644 index 0000000..69df66e --- /dev/null +++ b/app/pnpm-lock.yaml @@ -0,0 +1,1400 @@ +lockfileVersion: '6.0' + +settings: + autoInstallPeers: true + excludeLinksFromLockfile: false + +dependencies: + '@itk-wasm/image-io': + specifier: ^0.3.0 + version: 0.3.0 + itk-wasm: + specifier: 1.0.0-b.149 + version: 1.0.0-b.149 + 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this.inputFileName = "scanco-volume" + this.outputFormat = "mha" + this.forceServerSide = false + } + } + + +class ConversionController { + + constructor(loadSampleInputs) { + this.loadSampleInputs = loadSampleInputs + + this.model = new ConversionModel() + const model = this.model + + this.webWorker = null + + if (loadSampleInputs) { + const loadSampleInputsButton = document.querySelector("#conversionInputs [name=loadSampleInputs]") + loadSampleInputsButton.setAttribute('style', 'display: block-inline;') + loadSampleInputsButton.addEventListener('click', (event) => { + loadSampleInputs(model) + }) + } + + // ---------------------------------------------- + // Inputs + const inputVolumeElement = document.querySelector('#conversionInputs input[name=input-volume-file]') + inputVolumeElement.addEventListener('change', (event) => { + const dataTransfer = event.dataTransfer + const files = event.target.files || dataTransfer.files + console.log(files[0]) + + files[0].arrayBuffer().then((arrayBuffer) => { + model.inputVolume = new Uint8Array(arrayBuffer) + const inputVolumeDescription = document.getElementById("input-volume-description") + inputVolumeDescription.innerHTML = `${files[0].name}, ()` + }) + }) + + const outputFormatElement = document.querySelector('#conversionInputs sl-select[name=output-format]') + outputFormatElement.addEventListener('sl-change', (event) => { + model.outputFormat = outputFormatElement.value + console.log(model.outputFormat) + }) + + // // ---------------------------------------------- + // // Options + // const forceServerSideElement = document.querySelector('#conversionInputs sl-checkbox[name=forceServerSide]') + // forceServerSideElement.addEventListener('sl-change', (event) => { + // model.options.set("forceServerSide", forceServerSideElement.checked) + // }) + + // ---------------------------------------------- + // Outputs + const outputOutputDownload = document.querySelector('#conversionOutputs sl-button[name=output-download]') + outputOutputDownload.addEventListener('click', (event) => { + event.preventDefault() + event.stopPropagation() + if (model.outputVolume) { + downloadFile(model.outputVolume, `${model.inputFileName}.${model.outputFormat}`) + } + }) + + const runButton = document.querySelector('#conversionInputs sl-button[name="run"]') + runButton.addEventListener('click', async (event) => { + event.preventDefault() + event.stopPropagation() + + if(!model.inputVolume) { + notify("Required input volume not provided", "Please provide an AIM or ISQ file", "danger", "exclamation-octagon") + return + } + + + try { + runButton.loading = true + const t0 = performance.now() + + const { webWorker, image } = await readImage(this.webWorker, + { data: model.inputVolume.slice(), path: 'volume.isq' } + ) + this.webWorker = webWorker + // Avoid later use of detached buffer + const direction = image.direction.slice() + const { serializedImage } = await writeImage(webWorker, image, `${model.inputFileName}.${model.outputFormat}`) + + const t1 = performance.now() + notify("conversion successfully completed", `in ${t1 - t0} milliseconds.`, "success", "rocket-fill") + + model.outputVolume = new Uint8Array(serializedImage.data) + + outputOutputDownload.variant = "success" + outputOutputDownload.disabled = false + function replacer (key, value) { + if (!!value && value.byteLength !== undefined) { + return String(value.slice(0, 6)) + '...' + } + return value + } + image.direction = direction + image.data = "[...]" + const outputOutput = document.getElementById('output-image-details') + outputOutput.innerHTML = `
${globalThis.escapeHtml(JSON.stringify(image, replacer, 2))}
` + outputOutput.disabled = false + } catch (error) { + notify("Error while running pipeline", error.toString(), "danger", "exclamation-octagon") + throw error + } finally { + runButton.loading = false + } + }) + } +} + +const conversionController = new ConversionController(conversionLoadSampleInputs) diff --git a/app/src/conversion-load-sample-inputs.ts b/app/src/conversion-load-sample-inputs.ts new file mode 100644 index 0000000..b3306ad --- /dev/null +++ b/app/src/conversion-load-sample-inputs.ts @@ -0,0 +1,46 @@ +export default async function conversionLoadSampleInputs (model) { + const progressBar = document.querySelector('#conversionInputs sl-progress-bar[name=progress]') + progressBar.value = 0 + progressBar.setAttribute('style', 'display: block;') + + const inputVolumeDescription = document.getElementById("input-volume-description") + + const url = import.meta.env.DEV ? '/sample-data/AIMIOTestImage.AIM' : 'https://data.kitware.com/api/v1/file/653283f75be10c8fb6ed4efc/download' + const response = await fetch(url) + const contentLength = parseInt(response.headers.get('Content-Length')) + inputVolumeDescription.innerHTML = `Sample AIM volume size: ` + + const reader = response.body.getReader() + + let receivedLength = 0 + const chunks = [] + while(true) { + const {done, value} = await reader.read() + + if (done) { + break + } + + chunks.push(value) + receivedLength += value.length + const percent = receivedLength / contentLength * 100 + progressBar.value = percent + progressBar.textContent = `${percent.toFixed(2)}%` + } + + let inputVolume = new Uint8Array(receivedLength) + let position = 0; + for(let chunk of chunks) { + inputVolume.set(chunk, position); // (4.2) + position += chunk.length; + } + + model.inputVolume = inputVolume + model.inputFileName = 'ITKIOScancoSampleVolume.aim' + progressBar.setAttribute('style', 'display: none;') + progressBar.textContent = '' + progressBar.max = 100 + progressBar.value = 0 + + return model +} diff --git a/app/src/favicon-64x64.png b/app/src/favicon-64x64.png new file mode 100644 index 0000000..e109204 Binary files /dev/null and b/app/src/favicon-64x64.png differ diff --git a/app/src/index.ts b/app/src/index.ts new file mode 100644 index 0000000..21e5cee --- /dev/null +++ b/app/src/index.ts @@ -0,0 +1,8 @@ +import * as imageIo from '@itk-wasm/image-io' + +// Use local, vendored WebAssembly module assets +const pipelinesBaseUrl: string | URL = new URL('/itk/image-io', document.location.origin).href +imageIo.setPipelinesBaseUrl(pipelinesBaseUrl) + +import './conversion-controller.js' +// import './calibration-controller.js' diff --git a/app/src/itkConfig.js b/app/src/itkConfig.js new file mode 100644 index 0000000..0001556 --- /dev/null +++ b/app/src/itkConfig.js @@ -0,0 +1,8 @@ +const itkConfig = { + pipelineWorkerUrl: '/itk/web-workers/min-bundles/pipeline.worker.js', + imageIOUrl: '/itk/image-io', + meshIOUrl: '/itk/mesh-io', + pipelinesUrl: '/itk/pipelines' +} + +export default itkConfig diff --git a/app/src/logo.png b/app/src/logo.png new file mode 100644 index 0000000..c9eaefc Binary files /dev/null and b/app/src/logo.png differ diff --git a/app/src/style.css b/app/src/style.css new file mode 100644 index 0000000..b8d3419 --- /dev/null +++ b/app/src/style.css @@ -0,0 +1,113 @@ +:root { + font-family: Inter, Avenir, Helvetica, Arial, sans-serif; + font-size: 16px; + line-height: 20px; + font-weight: 400; + + color-scheme: light dark; + color: rgba(255, 255, 255, 0.87); + background-color: #242424; + + font-synthesis: none; + text-rendering: optimizeLegibility; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; + -webkit-text-size-adjust: 100%; +} + +a { + font-weight: 500; + color: #646cff; + text-decoration: inherit; +} +a:hover { + color: #535bf2; +} + +body { + margin: 0; + display: flex; + place-items: center; + min-width: 320px; + min-height: 100vh; +} + +h1 { + font-size: 3.2em; + line-height: 1.1; +} + +li { + text-align: left; +} + +#app { + min-width: 640px; + max-width: 1280px; + margin: 0 auto; + padding: 2rem; + text-align: left; +} + +.logo { + height: 10em; + padding: 0.1em; + will-change: filter; +} +.logo:hover { + filter: drop-shadow(0 0 2em #646cffaa); +} +.logo.vanilla:hover { + filter: drop-shadow(0 0 2em #3178c6aa); +} + +.language-logo { + height: 1.0em; + padding-left: 0.6em; +} + +.github-corner { + border-bottom: 0; + position: fixed; + right: 0; + text-decoration: none; + top: 0; + z-index: 1; +} + +.github-corner:hover .octo-arm { + animation:octocat-wave 560ms ease-in-out; +} + +@keyframes octocat-wave { + 0%,100%{transform:rotate(0)} + 20%,60%{transform:rotate(-25deg)} + 40%,80%{transform:rotate(10deg)} +} + +@media (max-width:500px) { + .github-corner:hover .octo-arm{ + animation:none; + } + .github-corner .octo-arm{ + animation:octocat-wave 560ms ease-in-out; + } +} + +@media (prefers-color-scheme: light) { + :root { + color: #213547; + background-color: #ffffff; + } + a:hover { + color: #747bff; + } + button { + background-color: #f9f9f9; + } +} + +.sl-toast-stack { + left: 0; + right: auto; +} \ No newline at end of file diff --git a/app/src/utilities.ts b/app/src/utilities.ts new file mode 100644 index 0000000..5fea7e2 --- /dev/null +++ b/app/src/utilities.ts @@ -0,0 +1,67 @@ +export function downloadFile(content, filename) { + const url = URL.createObjectURL(new Blob([content])) + const a = document.createElement('a') + a.href = url + a.download = filename || 'download' + document.body.appendChild(a) + function clickHandler(event) { + setTimeout(() => { + URL.revokeObjectURL(url) + a.removeEventListener('click', clickHandler) + }, 200) + }; + a.addEventListener('click', clickHandler, false) + a.click() + return a +} + +function escapeHtml(html) { + const div = document.createElement('div'); + div.textContent = html; + const escaped = div.innerHTML; + div.remove() + return escaped +} +globalThis.escapeHtml = escapeHtml + +export function notify(title, message, variant = 'primary', icon = 'info-circle', duration = 3000) { + const slAlert = Object.assign(document.createElement('sl-alert'), { + variant, + closable: true, + duration: duration, + innerHTML: ` + + ${escapeHtml(title)}
+ ${escapeHtml(message)} + ` + }); + + document.body.append(slAlert); + setTimeout(() => slAlert.toast(), 300) +} + +export function disableInputs(inputId) { + document.querySelectorAll(`#${inputId} sl-button`).forEach(button => { + button.disabled = true + }) + document.querySelector(`#${inputId} sl-button[name="run"]`).loading = true + document.querySelectorAll(`#${inputId} sl-checkbox`).forEach(checkbox => { + checkbox.disabled = true + }) + document.querySelectorAll(`#${inputId} sl-input`).forEach(input => { + input.disabled = true + }) +} + +export function enableInputs(inputId) { + document.querySelectorAll(`#${inputId} sl-button`).forEach(button => { + button.disabled = false + }) + document.querySelector(`#${inputId} sl-button[name="run"]`).loading = false + document.querySelectorAll(`#${inputId} sl-checkbox`).forEach(checkbox => { + checkbox.disabled = false + }) + document.querySelectorAll(`#${inputId} sl-input`).forEach(input => { + input.disabled = false + }) +} diff --git a/app/vite.config.js b/app/vite.config.js new file mode 100644 index 0000000..393c02b --- /dev/null +++ b/app/vite.config.js @@ -0,0 +1,26 @@ +import { defineConfig } from 'vite' +import { viteStaticCopy } from 'vite-plugin-static-copy' +import path from 'path' + +const itkConfig = path.resolve(__dirname, 'src', 'itkConfig.js') + +export default defineConfig({ + build: { + outDir: 'dist', + emptyOutDir: true, + }, + worker: { + format: 'es' + }, + optimizeDeps: { + exclude: ['@itk-wasm/image-io'] + }, + plugins: [ + // put lazy loaded JavaScript and Wasm bundles in dist directory + viteStaticCopy({ + targets: [ + { src: 'node_modules/@itk-wasm/image-io/dist/pipelines/*.{js,wasm.zst}', dest: 'itk/image-io' }, + ], + }) + ], +}) diff --git a/examples/ConvertScancoVolumesToOpenStandardFormats.ipynb b/examples/ConvertScancoVolumesToOpenStandardFormats.ipynb index f370c4d..b404953 100644 --- a/examples/ConvertScancoVolumesToOpenStandardFormats.ipynb +++ b/examples/ConvertScancoVolumesToOpenStandardFormats.ipynb @@ -23,7 +23,7 @@ "outputs": [], "source": [ "import sys\n", - "!{sys.executable} -m pip install itk-ioscanco xarray zarr tqdm requests itkwidgets" + "!{sys.executable} -m pip install itk-ioscanco xarray zarr tqdm pooch 'itkwidgets[all]>=1.0a21'" ] }, { @@ -35,13 +35,11 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ - "import requests\n", - "from tqdm.notebook import tqdm\n", - "import os\n", + "import pooch\n", "\n", "from itkwidgets import view\n", "\n", @@ -60,25 +58,14 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ - "def download_data(url, filename):\n", - " if not os.path.exists(filename):\n", - " chunk_size = 32 * 1024\n", - " r = requests.get(url, stream=True)\n", - " total_size = int(r.headers.get('content-length', 0))\n", - " pbar = tqdm(unit=\"B\", unit_scale=True, total=int(total_size))\n", - " with open(filename, 'wb') as f:\n", - " for chunk in r.iter_content(chunk_size=chunk_size): \n", - " if chunk: # filter out keep-alive new chunks\n", - " pbar.update(len(chunk))\n", - " f.write(chunk)\n", - " \n", "file_name = 'C0004255.ISQ'\n", "file_url = 'https://data.kitware.com/api/v1/file/591e56178d777f16d01e0d20/download'\n", - "download_data(file_url, file_name)" + "file_sha256 = 'c2a3750c75826cb077d92093d43976cc0350198b55edecd681265eebabfb438b'\n", + "file_path = pooch.retrieve(file_url, file_sha256, fname=file_name, progressbar=True)" ] }, { @@ -90,12 +77,11 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ - "imageio = itk.ScancoImageIO.New()\n", - "image = itk.imread(file_name, imageio=imageio)" + "image = itk.imread(file_path)" ] }, { @@ -107,7 +93,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -126,22 +112,63 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 12, "metadata": {}, "outputs": [ { "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "1e1e184334524c68903caeec8f6ce966", - "version_major": 2, - "version_minor": 0 - }, + "text/html": [ + "\n", + " \n", + " \n", + " " + ], "text/plain": [ - "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=" ] }, "metadata": {}, "output_type": "display_data" + }, + { + "data": { + "application/javascript": [ + "window.connectPlugin && window.connectPlugin(\"891a74b1-01f7-46d6-8997-c877fc02b4ff\")" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ @@ -159,7 +186,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 13, "metadata": {}, "outputs": [ { @@ -216,7 +243,7 @@ " [-1000, -1000, -1000, ..., -1000, -1000, -1000]]], dtype=int16)" ] }, - "execution_count": 7, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -235,7 +262,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 14, "metadata": {}, "outputs": [ { @@ -275,7 +302,7 @@ " [0., 0., 1.]])}" ] }, - "execution_count": 8, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -302,7 +329,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 15, "metadata": {}, "outputs": [], "source": [ @@ -311,7 +338,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 16, "metadata": {}, "outputs": [ { @@ -352,7 +379,7 @@ " [0., 0., 1.]])}" ] }, - "execution_count": 10, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -373,7 +400,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -382,7 +409,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 18, "metadata": {}, "outputs": [ { @@ -427,7 +454,7 @@ " [0., 0., 1.]])}" ] }, - "execution_count": 12, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -457,7 +484,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 19, "metadata": {}, "outputs": [ { @@ -494,6 +521,7 @@ "}\n", "\n", "html[theme=dark],\n", + "body[data-theme=dark],\n", "body.vscode-dark {\n", " --xr-font-color0: rgba(255, 255, 255, 1);\n", " --xr-font-color2: rgba(255, 255, 255, 0.54);\n", @@ -506,7 +534,7 @@ "}\n", "\n", ".xr-wrap {\n", - " display: block;\n", + " display: block !important;\n", " min-width: 300px;\n", " max-width: 700px;\n", "}\n", @@ -723,6 +751,11 @@ " grid-column: 4;\n", "}\n", "\n", + ".xr-index-preview {\n", + " grid-column: 2 / 5;\n", + " color: var(--xr-font-color2);\n", + "}\n", + "\n", ".xr-var-name,\n", ".xr-var-dims,\n", ".xr-var-dtype,\n", @@ -744,14 +777,16 @@ "}\n", "\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " display: none;\n", " background-color: var(--xr-background-color) !important;\n", " padding-bottom: 5px !important;\n", "}\n", "\n", ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n", - ".xr-var-data-in:checked ~ .xr-var-data {\n", + ".xr-var-data-in:checked ~ .xr-var-data,\n", + ".xr-index-data-in:checked ~ .xr-index-data {\n", " display: block;\n", "}\n", "\n", @@ -761,13 +796,16 @@ "\n", ".xr-var-name span,\n", ".xr-var-data,\n", + ".xr-index-name div,\n", + ".xr-index-data,\n", ".xr-attrs {\n", " padding-left: 25px !important;\n", "}\n", "\n", ".xr-attrs,\n", ".xr-var-attrs,\n", - ".xr-var-data {\n", + ".xr-var-data,\n", + ".xr-index-data {\n", " grid-column: 1 / -1;\n", "}\n", "\n", @@ -805,7 +843,8 @@ "}\n", "\n", ".xr-icon-database,\n", - ".xr-icon-file-text2 {\n", + ".xr-icon-file-text2,\n", + ".xr-no-icon {\n", " display: inline-block;\n", " vertical-align: middle;\n", " width: 1em;\n", @@ -814,7 +853,7 @@ " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", - "
<xarray.DataArray (z: 51, y: 1024, x: 1024)>\n",
+       "
<xarray.DataArray 'image' (z: 51, y: 1024, x: 1024)>\n",
        "array([[[-1000, -1000, -1000, ..., -1000, -1000, -1000],\n",
        "        [-1000, -1000, -1000, ..., -1000, -1000, -1000],\n",
        "        [-1000, -1000, -1000, ..., -1000, -1000, -1000],\n",
@@ -873,7 +912,7 @@
        "    Site:                 5\n",
        "    SliceIncrement:       0.036000000000000004\n",
        "    SliceThickness:       0.036000000000000004\n",
-       "    Version:              CTDATA-HEADER_V1
    • x
      PandasIndex
      PandasIndex(Float64Index([                 0.0, 0.036000000000000004,  0.07200000000000001,\n",
+       "               0.10800000000000001,  0.14400000000000002,  0.18000000000000002,\n",
+       "               0.21600000000000003,                0.252,  0.28800000000000003,\n",
+       "               0.32400000000000007,\n",
+       "              ...\n",
+       "                36.504000000000005,   36.540000000000006,    36.57600000000001,\n",
+       "                            36.612,               36.648,   36.684000000000005,\n",
+       "                36.720000000000006,    36.75600000000001,               36.792,\n",
+       "                            36.828],\n",
+       "             dtype='float64', name='x', length=1024))
    • y
      PandasIndex
      PandasIndex(Float64Index([                 0.0, 0.036000000000000004,  0.07200000000000001,\n",
+       "               0.10800000000000001,  0.14400000000000002,  0.18000000000000002,\n",
+       "               0.21600000000000003,                0.252,  0.28800000000000003,\n",
+       "               0.32400000000000007,\n",
+       "              ...\n",
+       "                36.504000000000005,   36.540000000000006,    36.57600000000001,\n",
+       "                            36.612,               36.648,   36.684000000000005,\n",
+       "                36.720000000000006,    36.75600000000001,               36.792,\n",
+       "                            36.828],\n",
+       "             dtype='float64', name='y', length=1024))
    • z
      PandasIndex
      PandasIndex(Float64Index([                 0.0, 0.036000000000000004,  0.07200000000000001,\n",
+       "               0.10800000000000001,  0.14400000000000002,  0.18000000000000002,\n",
+       "               0.21600000000000003,                0.252,  0.28800000000000003,\n",
+       "               0.32400000000000007,  0.36000000000000004,                0.396,\n",
+       "               0.43200000000000005,   0.4680000000000001,                0.504,\n",
+       "                              0.54,   0.5760000000000001,   0.6120000000000001,\n",
+       "                0.6480000000000001,                0.684,   0.7200000000000001,\n",
+       "                0.7560000000000001,                0.792,   0.8280000000000001,\n",
+       "                0.8640000000000001,   0.9000000000000001,   0.9360000000000002,\n",
+       "                0.9720000000000001,                1.008,                1.044,\n",
+       "                              1.08,                1.116,   1.1520000000000001,\n",
+       "                1.1880000000000002,   1.2240000000000002,   1.2600000000000002,\n",
+       "                1.2960000000000003,                1.332,                1.368,\n",
+       "                1.4040000000000001,   1.4400000000000002,   1.4760000000000002,\n",
+       "                1.5120000000000002,   1.5480000000000003,                1.584,\n",
+       "                              1.62,   1.6560000000000001,   1.6920000000000002,\n",
+       "                1.7280000000000002,   1.7640000000000002,\n",
+       "                1.8000000000000003],\n",
+       "             dtype='float64', name='z'))
  • direction :
    [[1. 0. 0.]\n", " [0. 1. 0.]\n", " [0. 0. 1.]]
    CalibrationData :
    45 kVp, 0.5mm Al, BH: 1200mg HA/ccm, Scaling 4096
    CreationDate :
    5-JUN-2015 11:09:18.880
    DataRange :
    (-2813.0, 32767.0)
    Energy :
    45.0
    Intensity :
    0.177
    MeasurementIndex :
    4937
    ModificationDate :
    5-JUN-2015 11:09:18.880
    MuScaling :
    4096.0
    MuWater :
    0.7032999992370605
    NumberOfProjections :
    500
    NumberOfSamples :
    1024
    PatientIndex :
    78
    PatientName :
    COLE-BPBP
    ReconstructionAlg :
    3
    ReferenceLine :
    0.0
    RescaleIntercept :
    -1000.0
    RescaleSlope :
    0.34713582434927287
    RescaleType :
    2
    RescaleUnits :
    mg HA/ccm
    SampleTime :
    400.0
    ScanDistance :
    36.864000000000004
    ScannerID :
    2135
    ScannerType :
    10
    Site :
    5
    SliceIncrement :
    0.036000000000000004
    SliceThickness :
    0.036000000000000004
    Version :
    CTDATA-HEADER_V1
    • " ], "text/plain": [ - "\n", + "\n", "array([[[-1000, -1000, -1000, ..., -1000, -1000, -1000],\n", " [-1000, -1000, -1000, ..., -1000, -1000, -1000],\n", " [-1000, -1000, -1000, ..., -1000, -1000, -1000],\n", @@ -987,7 +1062,7 @@ " Version: CTDATA-HEADER_V1" ] }, - "execution_count": 13, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } @@ -999,7 +1074,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 20, "metadata": {}, "outputs": [], "source": [ @@ -1010,7 +1085,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 21, "metadata": {}, "outputs": [], "source": [ @@ -1019,7 +1094,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 22, "metadata": {}, "outputs": [ { @@ -1058,7 +1133,7 @@ " [0., 0., 1.]])}" ] }, - "execution_count": 16, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } @@ -1071,7 +1146,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1085,9 +1160,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.2" + "version": "3.10.8" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 } diff --git a/examples/ReadISQ.ipynb b/examples/ReadISQ.ipynb index d2522c5..3c3ddfc 100644 --- a/examples/ReadISQ.ipynb +++ b/examples/ReadISQ.ipynb @@ -8,7 +8,7 @@ "source": [ "# Install notebook dependencies\n", "import sys\n", - "!{sys.executable} -m pip install itk-ioscanco tqdm requests itkwidgets" + "!{sys.executable} -m pip install itk-ioscanco tqdm pooch 'itkwidgets[all]>=1.0a21'" ] }, { @@ -17,9 +17,7 @@ "metadata": {}, "outputs": [], "source": [ - "import requests\n", - "from tqdm.notebook import tqdm\n", - "import os\n", + "import pooch\n", "\n", "from itkwidgets import view\n", "\n", @@ -32,22 +30,10 @@ "metadata": {}, "outputs": [], "source": [ - "# Download example data\n", - "def download_data(url, filename):\n", - " if not os.path.exists(filename):\n", - " chunk_size = 32 * 1024\n", - " r = requests.get(url, stream=True)\n", - " total_size = int(r.headers.get('content-length', 0))\n", - " pbar = tqdm(unit=\"B\", unit_scale=True, total=int(total_size))\n", - " with open(filename, 'wb') as f:\n", - " for chunk in r.iter_content(chunk_size=chunk_size): \n", - " if chunk: # filter out keep-alive new chunks\n", - " pbar.update(len(chunk))\n", - " f.write(chunk)\n", - " \n", "file_name = 'C0004255.ISQ'\n", "file_url = 'https://data.kitware.com/api/v1/file/591e56178d777f16d01e0d20/download'\n", - "download_data(file_url, file_name)" + "file_sha256 = 'c2a3750c75826cb077d92093d43976cc0350198b55edecd681265eebabfb438b'\n", + "file_path = pooch.retrieve(file_url, file_sha256, fname=file_name, progressbar=True)" ] }, { @@ -56,8 +42,7 @@ "metadata": {}, "outputs": [], "source": [ - "imageio = itk.ScancoImageIO.New()\n", - "image = itk.imread(file_name, imageio=imageio)" + "image = itk.imread(file_path)" ] }, { @@ -67,17 +52,58 @@ "outputs": [ { "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "1dc71affddad4730ba2778e62534c472", - "version_major": 2, - "version_minor": 0 - }, + "text/html": [ + "\n", + " \n", + " \n", + " " + ], "text/plain": [ - "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=" ] }, "metadata": {}, "output_type": "display_data" + }, + { + "data": { + "application/javascript": [ + "window.connectPlugin && window.connectPlugin(\"268f936d-91fb-48a4-af3f-e27de70d428f\")" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
    " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" } ], "source": [ @@ -87,7 +113,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -101,9 +127,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.10.8" } }, "nbformat": 4, - "nbformat_minor": 2 + "nbformat_minor": 4 }