feat: download dicomweb data to local file system

README.md

@@ -29,7 +29,19 @@ dicomwebjs dump https://d33do7qe4w26qo.cloudfront.net/dicomweb/studies/1.3.6.1.4
 dicomwebjs dump testdata/studies/1.2.276.1.74.1.2.132733202464108492637644434464108492/series/2.16.840.1.113883.3.8467.132733202477512857637644434477512857/metadata.gz
 ```
 
-## File Locations
+## download `url`
+dicomwebjs can be used to download a directory of file locations.  By default it will fetch everything at and below the specified URL, plus referenced bulkdata.  Bulkdata will be
+placed in the `studies/<studyUID>/bulkdata` directory, with metadata references to the bulkdata using the `../../bulkdata/<path>` relative URI locations.
+
+
+
+### Example Commands
+```
+dicomwebjs download https://d33do7qe4w26qo.cloudfront.net/dicomweb/studies/1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627 -d ~/dicomweb
+```
+
+
+### File Locations
 Files dicomweb can be paths to JSON files.  However, tree structure data must follow the Static DICOMweb format, specifically starting at `studies/` relative to the base directory, and containing some/all of the ones below.
 Note that un-compressed files are acceptable as well, but will not be found on a search.
 

bin/dicomwebjs.js

@@ -1,35 +1,64 @@
 #!/usr/bin/env node
-import { Command } from 'commander';
-import { dicomweb, instanceDicom, dumpDicom } from '../src/index.js';
+import { Command } from "commander"
+import { dicomweb, instanceDicom, dumpDicom, utils } from "../src/index.js"
 
-const program = new Command();
+const program = new Command()
+
+program.option(
+  "-s, --study <studyInstanceUID>",
+  "Download a specific study instance UID"
+)
 
 program
-  .name('dicomwebjs')
-  .description('dicomwebjs based tools for manipulation of DICOMweb')
-  .version('0.0.1')
-  .option('--seriesUID <seriesUID>', 'For a specific seriesUID');
+  .name("dicomwebjs")
+  .description("dicomwebjs based tools for manipulation of DICOMweb")
+  .version("0.0.1")
+  .option("--seriesUID <seriesUID>", "For a specific seriesUID")
 
-program.command('dump')
-  .description('Dump a dicomweb file')
-  .argument('<dicomwebUrl>', 'dicomweb URL or file location')
+program
+  .command("dump")
+  .description("Dump a dicomweb file")
+  .argument("<dicomwebUrl>", "dicomweb URL or file location")
+  .option("--debug", "Set debug level logging")
   .action(async (fileName, options) => {
-    const qido = await dicomweb.readDicomWeb(fileName, options);
+    const qido = await dicomweb.readDicomWeb(fileName, options)
     for (const dict of qido) {
-      dumpDicom({ dict });
+      dumpDicom({ dict })
     }
-  });
+  })
 
-program.command('instance')
-  .description('Write the instance data')
-  .argument('<part10>', 'part 10 file')
-  .option('-p, --pretty', 'Pretty print')
+program
+  .command("download")
+  .description("Download dicomweb file(s)")
+  .argument("<dicomwebUrl>", "dicomweb URL to the base DICOMweb service")
+  .option(
+    "-d, --directory <dicomwebdir>",
+    "Download to local DICOMweb directory"
+  )
+  .option("--debug", "Set debug level logging")
   .action(async (fileName, options) => {
-    const qido = await dicomweb.readDicomWeb(fileName, options);
-    for (const dict of qido) {
-      instanceDicom({ dict }, options);
+    utils.logger.setOptions(options)
+    let downloadUrls = [fileName]
+    if (options.study) {
+      downloadUrls = await dicomweb.queryDownloads(fileName, options)
+    }
+    for (const downloadUrl of downloadUrls) {
+      const data = await dicomweb.readDicomWeb(downloadUrl, options)
+      dicomweb.store(downloadUrl, data, options)
     }
   })
 
+program
+  .command("instance")
+  .description("Write the instance data")
+  .argument("<part10>", "part 10 file")
+  .option("-p, --pretty", "Pretty print")
+  .option("--debug", "Set debug level logging")
+  .action(async (fileName, options) => {
+    const qido = await dicomweb.readDicomWeb(fileName, options)
+    for (const dict of qido) {
+      instanceDicom({ dict }, options)
+    }
+  })
 
-program.parse();
+program.parse()

package.json

@@ -49,13 +49,29 @@
   },
   "dependencies": {
     "commander": "^12.1.0",
-    "config-point": ">=0.5.1",
     "dcmjs": "^0.29.5",
     "dcmjs-dimse": "0.1.27",
-    "dicomweb-client": "0.8.4"
+    "dicomweb-client": "0.8.4",
+    "loglevel": "^1.9.2"
   },
   "devDependencies": {
+    "eslint": "^9.6.0",
+    "husky": "^1.3.1",
     "jest": "^29.7.0",
-    "must": "^0.13.4"
-  }
+    "lint-staged": "^13.1.2",
+    "must": "^0.13.4",
+    "prettier": "^3.3.2"
+  },
+  "husky": {
+    "hooks": {
+      "pre-commit": "lint-staged"
+    }
+  },
+  "lint-staged": {
+    "src/**/*.{js,jsx,json,css}": [
+      "prettier --write",
+      "git add"
+    ]
+  },
+  "packageManager": "yarn@1.22.22+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e"
 }

src/dicomweb.js

@@ -1,10 +1,20 @@
-import zlib from 'zlib';
-import fs from 'fs';
+import zlib from "zlib";
+import fs from "fs";
+import dcmjs from "dcmjs";
 
-import { httprequest } from './webRetrieve.js';
+import { httprequest } from "./webRetrieve.js";
+import { logger } from "./utils/index.js";
+
+const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
+
+const log = logger.commandsLog;
+
+/**
+ * The dicomweb support classes for querying and reading various DICOMweb data sources
+ */
 
 export function readDicomWeb(url, options = {}) {
-  if (url.startsWith('http')) {
+  if (url.startsWith("http")) {
     return readDicomWebHttp(url, options);
   }
   return readDicomWebFile(url, options);
@@ -14,11 +24,47 @@ export function readDicomWebHttp(url, options) {
   return httprequest(url, options);
 }
 
-
 export function readDicomWebFile(fileName, _options) {
-  const isGzip = fileName.endsWith('.gz');
+  const isGzip = fileName.endsWith(".gz");
   const arrayBuffer = fs.readFileSync(fileName).buffer;
   const uncompressed = isGzip ? zlib.gunzipSync(arrayBuffer) : arrayBuffer;
   const str = uncompressed.toString();
   return JSON.parse(str);
-}
+}
+
+export function getStudyQuery(wadoUrl, _options, forStudy) {
+  const { StudyInstanceUID } = forStudy;
+  console.log("Querying for study", StudyInstanceUID);
+  return `${wadoUrl}?StudyInstanceUID=${StudyInstanceUID}`;
+}
+
+export function getSeriesQuery(wadoUrl, options, forStudy) {
+  const { StudyInstanceUID } = forStudy;
+  return `${wadoUrl}/studies/${StudyInstanceUID}/series`;
+}
+
+export async function queryDownloads(wadoUrl, options) {
+  const StudyInstanceUID = options.study;
+  const SeriesInstanceUID = options.series || [];
+  const query = { StudyInstanceUID, SeriesInstanceUID };
+  const studyQuery = getStudyQuery(wadoUrl, options);
+  const study = await readDicomWeb(studyQuery)?.[0];
+  const downloaded = [];
+  if (!study) {
+    log.warn("No study found for", options.study);
+    return downloaded;
+  }
+  downloaded.push({
+    relativePath: `studies/${StudyInstanceUID}`,
+    data: [study],
+  });
+
+  const series = await readDicomWeb(getSeriesQuery(wadoUrl, options, query));
+  log.debug("Found series", series);
+  return [];
+}
+
+export function store(path, data, options) {
+  log.info("Storing data", path);
+  log.debug(JSON.stringify(data, null, 2));
+}

src/index.js

@@ -1,7 +1,8 @@
 import fs from "fs";
 import dcmjs from "dcmjs";
 
-export * as dicomweb from './dicomweb.js';
+export * as utils from "./utils/index.js";
+export * as dicomweb from "./dicomweb.js";
 
 const { DicomMessage, DicomMetaDictionary } = dcmjs.data;
 
@@ -20,23 +21,23 @@ export function dumpDicom(dicomDict, options = {}) {
   dumpData(dicomDict.dict, options);
 }
 
-export function dumpData(data, options, indent = '') {
-  if (typeof data !== 'object') {
+export function dumpData(data, options, indent = "") {
+  if (typeof data !== "object") {
     return;
   }
   const keys = Object.keys(data).sort();
   for (const key of keys) {
-    const value = data[key]
+    const value = data[key];
     if (!value) {
       continue;
     }
     const { vr } = value;
     const punctuatedTag = DicomMetaDictionary.punctuateTag(key);
     const entry = DicomMetaDictionary.dictionary[punctuatedTag];
-    const name = entry?.name || '';
-    if (vr === 'SQ') {
+    const name = entry?.name || "";
+    if (vr === "SQ") {
       console.log(indent, key, name);
-      dumpSq(name || key, value, options, indent + '  ');
+      dumpSq(name || key, value, options, indent + "  ");
       continue;
     }
     console.log(indent, key, name, valueToString(value, options));
@@ -46,7 +47,7 @@ export function dumpData(data, options, indent = '') {
 export function valueToString(value, options) {
   const { Value: values, vr, InlineBinary, BulkDataURI } = value;
   if (InlineBinary) {
-    return `Inline Binary ${InlineBinary.substring(0, Math.min(InlineBinary.length, 32))}${InlineBinary.length > 31 ? '...' : ''} (${InlineBinary.length * 3 / 4})`
+    return `Inline Binary ${InlineBinary.substring(0, Math.min(InlineBinary.length, 32))}${InlineBinary.length > 31 ? "..." : ""} (${(InlineBinary.length * 3) / 4})`;
   }
   if (BulkDataURI) {
     return `URL ${BulkDataURI}`;
@@ -56,20 +57,20 @@ export function valueToString(value, options) {
       return vr;
     }
     console.log("***** Value = ", value);
-    return '';
+    return "";
   }
-  if (values.length === 0) return '';
+  if (values.length === 0) return "";
   const [v0] = values;
   if (v0 instanceof ArrayBuffer) {
     return `ArrayBuffer of length ${values.length}`;
   }
-  if (typeof v0 === 'object') {
-    return values.map(it => JSON.stringify(it)).join(', ');
+  if (typeof v0 === "object") {
+    return values.map((it) => JSON.stringify(it)).join(", ");
   }
   if (!Array.isArray(values)) {
     return JSON.stringify(values);
   }
-  return values.map(it => String(it)).join(', ');
+  return values.map((it) => String(it)).join(", ");
 }
 
 export function dumpSq(tag, value, options, indent) {
@@ -80,13 +81,15 @@ export function dumpSq(tag, value, options, indent) {
   }
   for (let i = 0; i < sq.length; i++) {
     console.log(indent, "Item #", i + 1);
-    dumpData(sq[i], options, indent + '  ');
+    dumpData(sq[i], options, indent + "  ");
   }
-  console.log(indent, 'End of', tag, "with", sq.length, 'items');
+  console.log(indent, "End of", tag, "with", sq.length, "items");
 }
 
 export function instanceDicom(dicomDict, options = {}) {
   const { pretty } = options;
-  const result = pretty ? JSON.stringify(dicomDict.dict, null, 2) : JSON.stringify(dicomDict.dict);
-  console.log('', result);
+  const result = pretty
+    ? JSON.stringify(dicomDict.dict, null, 2)
+    : JSON.stringify(dicomDict.dict);
+  console.log("", result);
 }

src/utils/index.js

@@ -0,0 +1 @@
+export * as logger from "./logger.js";

src/utils/logger.js

@@ -0,0 +1,45 @@
+import loglevel from "loglevel";
+
+/**
+ * Gets a logger and adds a getLogger function to id to get child loggers.
+ * This looks like the loggers in the unreleased loglevel 2.0 and is intended
+ * for forwards compatibility.
+ */
+export function getRootLogger(name) {
+  const logger = loglevel.getLogger(name[0]);
+  logger.getLogger = (...names) => {
+    return getRootLogger(`${name}.${names.join(".")}`);
+  };
+  return logger;
+}
+
+/** Gets a nested logger.
+ * This will eventually inherit the level from the parent level, but right now
+ * it doesn't
+ */
+export function getLogger(...name) {
+  return getRootLogger(name.join("."));
+}
+
+/** Pre-setup cateogires for easy logging, by package name */
+export const dcmjsLog = getLogger("dcmjs");
+export const commandsLog = dcmjsLog.getLogger("commands");
+
+/** Dicom issue log is for reporting inconsistencies and issues with DICOM logging */
+export const dicomIssueLog = getLogger("dicom", "issue");
+
+export function setOptions(options) {
+  if (options.loglevel) {
+    loglevel.setLevel(options.loglevel);
+  } else if (options.debug) {
+    console.log("Setting loglevel to debug");
+    loglevel.setLevel("debug");
+    console.log(
+      "commands level is",
+      loglevel.getLogger("dcmjs", "commands").getLevel(),
+    );
+  } else {
+    loglevel.setLevel("info");
+  }
+  loglevel.rebuild();
+}