@radicalimaging/static-wado-creator 1.5.0 → 1.6.11

package/lib/mkdicomwebConfig.js

@@ -1,14 +1,16 @@
-const ConfigPoint = require("config-point");
-const { staticWadoConfig } = require("@radicalimaging/static-wado-util");
-const createMain = require("./createMain");
-const createPart10 = require("./createPart10");
-const deleteMain = require("./deleteMain");
-const rejectMain = require("./rejectMain");
-const instanceMain = require("./instanceMain");
-const indexMain = require("./indexMain");
-const groupMain = require("./groupMain");
-const metadataMain = require("./metadataMain");
-const compressionOptionParser = require("./util/compressionOptionParser");
+const ConfigPoint = require('config-point');
+const { staticWadoConfig } = require('@radicalimaging/static-wado-util');
+const createMain = require('./createMain');
+const createPart10 = require('./createPart10');
+const createThumbnail = require('./createThumbnail');
+const deleteMain = require('./deleteMain');
+const rejectMain = require('./rejectMain');
+const serverMain = require('./serverMain');
+const instanceMain = require('./instanceMain');
+const indexMain = require('./indexMain');
+const groupMain = require('./groupMain');
+const metadataMain = require('./metadataMain');
+const compressionOptionParser = require('./util/compressionOptionParser');
 
 /**
  * Defines the basic configuration values for the dicomwebserver component.  See the README for more details.
@@ -22,217 +24,310 @@ const { mkdicomwebConfig } = ConfigPoint.register({
     isGroup: true,
     options: [
       {
-        key: "-c <configFile.json5>",
-        description: "Use an alternate configuration file",
-        defaultValue: "~/static-wado.json5",
+        key: '-c <configFile.json5>',
+        description: 'Use an alternate configuration file',
+        defaultValue: '~/static-wado.json5',
       },
       {
-        key: "--clean",
-        description: "Clean the outputs before generating/starting to write new values.",
+        key: '--clean',
+        description: 'Clean the outputs before generating/starting to write new values.',
         defaultValue: false,
       },
       {
-        key: "-d, --deployments <listvalue...>",
-        description: "List of deployments from configuration to deploy to. Separated by space.",
+        key: '-d, --deployments <listvalue...>',
+        description: 'List of deployments from configuration to deploy to. Separated by space.',
         defaultValue: undefined,
       },
       {
-        key: "--no-notifications",
-        description: "Turns off notifications",
+        key: '--no-notifications',
+        description: 'Turns off notifications',
       },
       {
-        key: "--delete",
-        description: "Delete the imported instances",
+        key: '--delete',
+        description: 'Delete the imported instances',
         defaultValue: false,
       },
       {
-        key: "--lossy",
-        description: "Generate lossy instances instead of lossless",
+        key: '--lossy',
+        description: 'Generate lossy instances instead of lossless',
         defaultValue: false,
       },
       {
-        key: "--alternate <type>",
-        description: "Generates an alternate representaton of the image generally in the /lossy sub-directory",
-        choices: ["jhc", "jls", "jhcLossless", "jlsLossless"],
+        key: '--alternate <type>',
+        description:
+          'Generates an alternate representaton of the image generally in the /lossy sub-directory',
+        choices: ['jhc', 'jls', 'jhcLossless', 'jlsLossless'],
       },
       {
-        key: "--alternate-thumbnail",
-        description: "Generates a thumbnail for the alternate representation",
+        key: '--alternate-thumbnail',
+        description: 'Generates a thumbnail for the alternate representation',
       },
       {
-        key: "--alternate-name <dir>",
-        description: "Uses a given sub directory name",
-        defaultValue: "lossy",
+        key: '--alternate-name <dir>',
+        description: 'Uses a given sub directory name',
+        defaultValue: 'lossy',
       },
       {
-        key: "-v, --verbose",
-        description: "Write verbose output",
+        key: '-v, --verbose',
+        description: 'Write verbose output',
         defaultValue: false,
       },
       {
-        key: "-t, --content-type <type>",
-        description: 'Destination type to compress to (choices: "jpeg", "jls", "lei", "jls-lossy", "jhc", "jxl" or DICOM Transfer Syntax UID - default: "jls")',
-        defaultValue: "jls",
+        key: '--show-progress',
+        description: 'Show progress during DICOM file processing',
+      },
+      {
+        key: '-t, --content-type <type>',
+        description:
+          'Destination type to compress to (choices: "jpeg", "jls", "lei", "jls-lossy", "jhc", "jxl" or DICOM Transfer Syntax UID - default: "jls")',
+        defaultValue: 'jls',
         customParser: compressionOptionParser,
       },
       {
-        key: "--encapsulated-image",
-        description: "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
+        key: '--encapsulated-image',
+        description:
+          'Avoid encapsulating the image frame.  Writes with the extension and without multipart',
       },
       {
-        key: "-e, --no-encapsulated-image",
-        description: "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
+        key: '-e, --no-encapsulated-image',
+        description:
+          'Avoid encapsulating the image frame.  Writes with the extension and without multipart',
       },
       {
-        key: "--single-part-image",
-        description: "Writes single part image data",
+        key: '--single-part-image',
+        description: 'Writes single part image data',
       },
       {
-        key: "--no-single-part-image",
-        description: "Writes single part image data",
+        key: '--no-single-part-image',
+        description: 'Writes single part image data',
       },
       {
-        key: "-m, --maximum-inline-public-length <value>",
-        description: "Maximum length of public binary data",
+        key: '-m, --maximum-inline-public-length <value>',
+        description: 'Maximum length of public binary data',
         defaultValue: 128 * 1024 + 2,
       },
       {
-        key: "-M, --maximum-inline-private-length <value>",
-        description: "Maximum length of private binary data",
+        key: '-M, --maximum-inline-private-length <value>',
+        description: 'Maximum length of private binary data',
         defaultValue: 64,
       },
       {
-        key: "-r, --recompress <listvalue...>",
-        description: "List of types to recompress separated by space",
-        defaultValue: ["uncompressed", "jp2", "jls", "jll"],
-        choices: ["uncompressed", "jp2", "jpeg", "jpeglossless", "rle", "jph", "jls", "true", "none"],
+        key: '-r, --recompress <listvalue...>',
+        description: 'List of types to recompress separated by space',
+        defaultValue: ['uncompressed', 'jp2', 'jls', 'jll'],
+        choices: [
+          'uncompressed',
+          'jp2',
+          'jpeg',
+          'jpeglossless',
+          'rle',
+          'jph',
+          'jls',
+          'true',
+          'none',
+        ],
+      },
+      {
+        key: '--recompress-color <listvalue...>',
+        description: 'List of types to recompress for color images, separated by space',
+        defaultValue: ['uncompressed'],
+        choices: [
+          'uncompressed',
+          'jpeg',
+          'jp2',
+          'jpeglossless',
+          'rle',
+          'jph',
+          'jls',
+          'true',
+          'none',
+        ],
+      },
+      {
+        key: '-f, --force',
+        description: 'Force the update even if the SOP exists',
+        defaultValue: false,
       },
       {
-        key: "--recompress-color <listvalue...>",
-        description: "List of types to recompress for color images, separated by space",
-        defaultValue: ["uncompressed"],
-        choices: ["uncompressed", "jpeg", "jp2", "jpeglossless", "rle", "jph", "jls", "true", "none"],
+        key: '--delete-input',
+        description: 'Deletes successful input files',
+        defaultValue: false,
       },
       {
-        key: "-f, --force",
-        description: "Force the update even if the SOP exists",
+        key: '--delete-failed',
+        description: 'Deletes unsuccessful input files',
         defaultValue: false,
       },
       {
-        key: "--recompress-thumb <listvalue...>",
-        description: "List of types to recompress thumb separated by space",
-        defaultValue: ["uncompressed", "jp2"],
-        choices: ["uncompressed", "jp2", "jpeglossless", "rle", "none"],
+        key: '--recompress-thumb <listvalue...>',
+        description: 'List of types to recompress thumb separated by space',
+        defaultValue: ['uncompressed', 'jp2'],
+        choices: ['uncompressed', 'jp2', 'jpeglossless', 'rle', 'none'],
       },
       {
-        key: "--no-recompress",
-        description: "Force no recompression",
+        key: '--no-recompress',
+        description: 'Force no recompression',
         defaultValue: false,
       },
       {
-        key: "--no-recompress-thumb",
-        description: "Force no recompression thumbnail",
+        key: '--no-recompress-thumb',
+        description: 'Force no recompression thumbnail',
         defaultValue: false,
       },
       {
-        key: "--thumb",
-        description: "Generate thumbnails",
+        key: '--no-thumb',
+        description: 'Skip generating thumbnails using CS3D internal render',
+        defaultValue: true,
       },
       {
-        key: "--dcm2jpg",
-        description: "Use dcm2jpg for thumbnail image generation",
+        key: '--dcm2jpg',
+        description: 'Use dcm2jpg for thumbnail image generation',
         defaultValue: false,
       },
       {
-        key: "--rendered",
-        description: "Use dcm2jpg to generate a rendered PNG image",
+        key: '--rendered',
+        description: 'Use dcm2jpg to generate a rendered PNG image',
         defaultValue: false,
       },
       {
-        key: "-T, --color-content-type <value>",
-        description: "Colour content type",
-        defaultValue: "jpeg",
+        key: '-T, --color-content-type <value>',
+        description: 'Colour content type',
+        defaultValue: 'jpeg',
+      },
+      {
+        key: '--path-deduplicated <path>',
+        description: 'Set the deduplicate data directory path (relative to dir)',
+        defaultValue: 'deduplicated',
+      },
+      {
+        key: '--path-instances <path>',
+        description: 'Set the instances directory path (relative to dir)',
+        defaultValue: 'instances',
       },
       {
-        key: "--path-deduplicated <path>",
-        description: "Set the deduplicate data directory path (relative to dir)",
-        defaultValue: "deduplicated",
+        key: '--store-multipart-bulk-data',
+        description: 'Use multipart encoding for non image frame bulkdata',
+        defaultValue: false,
       },
       {
-        key: "--path-instances <path>",
-        description: "Set the instances directory path (relative to dir)",
-        defaultValue: "instances",
+        key: '--prepend-bulk-data-uri <value>',
+        description:
+          'Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)',
+        defaultValue: '',
       },
       {
-        key: "--store-multipart-bulk-data",
-        description: "Use multipart encoding for non image frame bulkdata",
+        key: '--expand-bulk-data-uri',
+        description:
+          'expand bulkdata relative uri to use full relative path (should also be set when using --prepend-bulk-data-uri)',
         defaultValue: false,
       },
       {
-        key: "--prepend-bulk-data-uri <value>",
-        description: "Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)",
-        defaultValue: "",
+        key: '--quiet',
+        description: 'Run quietly, minimizing extraneous output',
+        defaultValue: false,
       },
       {
-        key: "--expand-bulk-data-uri",
-        description: "expand bulkdata relative uri to use full relative path (should also be set when using --prepend-bulk-data-uri)",
+        key: '--multipart',
+        description: 'Add a multipart result output',
         defaultValue: false,
       },
       {
-        key: "-o, --dir <value>",
-        description: "Set output directory",
-        defaultValue: { configOperation: "reference", source: "staticWadoConfig", reference: "rootDir" },
+        key: '--no-verify',
+        description: 'Verify',
+        defaultValue: true,
+      },
+      {
+        key: '-o, --dir <value>',
+        description: 'Set output directory',
+        defaultValue: {
+          configOperation: 'reference',
+          source: 'staticWadoConfig',
+          reference: 'rootDir',
+        },
+      },
+      {
+        key: '--sop-instance-uid <value>',
+        description: 'Choose sop instances to run against (only for instance runs)',
+      },
+      {
+        key: '--series-instance-uid <value>',
+        description: 'Choose series instances to run against (only for instance runs)',
+      },
+
+      {
+        key: '--hash-study-uid-path',
+        description: 'Enable hashing of studyUID folder structure',
+        defaultValue: false,
       },
     ],
     programs: [
       {
-        command: "create",
+        command: 'create',
         isDefault: true,
-        arguments: ["input"],
+        arguments: ['input'],
         main: createMain,
         helpDescription:
-          "Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read\n" +
-          "of deduplicated files each time a study instance UID is found, and only updates\n" +
-          "those studies having at least one ",
+          'Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read\n' +
+          'of deduplicated files each time a study instance UID is found, and only updates\n' +
+          'those studies having at least one ',
       },
       {
-        command: "part10",
-        arguments: ["studyUID"],
+        command: 'server',
+        main: serverMain,
+        helpDescription: 'Run server deploy instances single threaded/separated exec process',
+      },
+      {
+        command: 'part10',
+        arguments: ['studyUID'],
         main: createPart10,
-        helpDescription: "Store the specified study as part 10 data",
+        helpDescription: 'Store the specified study as part 10 data',
       },
       {
-        command: "index",
+        command: 'index',
         main: indexMain,
-        helpDescription: "Recreate the index for the DICOMweb data.",
+        helpDescription: 'Recreate the index for the DICOMweb data.',
+      },
+      {
+        command: 'thumbnail',
+        main: createThumbnail,
+        helpDescription: 'Create a thumbnail for the specified image',
+        options: [
+          {
+            key: '--series-thumbnail',
+            description: 'Generate a series thumbnail instead of instance',
+          },
+        ],
       },
       {
-        command: "instance",
-        arguments: ["input"],
+        command: 'instance',
+        arguments: ['input'],
         main: instanceMain,
-        helpDescription: "Make instance level DICOMweb metadata and bulkdata, but don't group or write series metadata",
+        helpDescription:
+          "Make instance level DICOMweb metadata and bulkdata, but don't group or write series metadata",
       },
       {
-        command: "group",
-        arguments: ["input"],
+        command: 'group',
+        arguments: ['input'],
         main: groupMain,
-        helpDescription: "Group instance level metadata into deduplicated data.\nDeletes instance level deduplicated information once it is confirmed written.",
+        helpDescription:
+          'Group instance level metadata into deduplicated data.\nDeletes instance level deduplicated information once it is confirmed written.',
       },
       {
-        command: "metadata",
-        arguments: ["input"],
+        command: 'metadata',
+        arguments: ['input'],
         main: metadataMain,
-        helpDescription: "Write the metadata object (series and study details) from the grouped deduplicated data.",
+        helpDescription:
+          'Write the metadata object (series and study details) from the grouped deduplicated data.',
       },
       {
-        command: "delete",
+        command: 'delete',
         main: deleteMain,
-        helpDescription: "Delete the given study, series or instance (not yet implemented)",
+        helpDescription: 'Delete the given study, series or instance (not yet implemented)',
       },
       {
-        command: "reject <studyUID...>",
+        command: 'reject <studyUID...>',
         main: rejectMain,
-        helpDescription: "Reject the specified series",
+        helpDescription: 'Reject the specified series',
       },
     ],
   },

package/lib/model/TagLists.js

@@ -1,5 +1,5 @@
-const hashFactory = require("node-object-hash");
-const { Tags } = require("@radicalimaging/static-wado-util");
+const hashFactory = require('node-object-hash');
+const { Tags } = require('@radicalimaging/static-wado-util');
 
 /* eslint "no-param-reassign": "off" */
 
@@ -24,7 +24,16 @@ const PatientQuery = [
   Tags.PatientIdentityRemoved,
   Tags.DeidentificationMethodCodeSequence,
 ];
-const StudyQuery = [StudyDescription, AccessionNumber, StudyInstanceUID, StudyDate, StudyTime, Tags.StudyStatusID, Tags.StudyPriorityID, Tags.StudyID];
+const StudyQuery = [
+  StudyDescription,
+  AccessionNumber,
+  StudyInstanceUID,
+  StudyDate,
+  StudyTime,
+  Tags.StudyStatusID,
+  Tags.StudyPriorityID,
+  Tags.StudyID,
+];
 
 const PatientStudyQuery = [...PatientQuery, ...StudyQuery];
 
@@ -132,7 +141,7 @@ const TagSets = {
   extract: (data, type, tagSet, options) => {
     const ret = {};
     const { remove, hashRef } = options || {};
-    tagSet.forEach((tag) => {
+    tagSet.forEach(tag => {
       const value = data[tag];
       if (value) {
         ret[tag] = value;

package/lib/model/uids.js

@@ -1,4 +1,4 @@
-const octetStream = "application/octet-stream";
+const octetStream = 'application/octet-stream';
 const uncompressed = {
   uncompressed: true,
   gzip: true,
@@ -8,37 +8,41 @@ const uncompressed = {
 /**
  * @see {@link https://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_8.7.3.3.2.html}
  */
-const jpeg = "image/jpeg";
-const jls = "image/jls";
-const jll = "image/jll";
-const jxl = "image/x-jxl";
-const htj2k = "image/jphc";
-const jp2 = "image/jp2";
-const rle = "image/dicom-rle";
+const jpeg = 'image/jpeg';
+const jls = 'image/jls';
+const jll = 'image/jll';
+const jxl = 'image/x-jxl';
+const htj2k = 'image/jphc';
+const jp2 = 'image/jp2';
+const rle = 'image/dicom-rle';
 
 const uids = {
-  "1.2.840.10008.1.2": uncompressed,
-  "1.2.840.10008.1.2.1": uncompressed,
-  "1.2.840.10008.1.2.1.99": uncompressed,
-  "1.2.840.10008.1.2.2": uncompressed,
-  "1.2.840.10008.1.2.4.50": { contentType: jpeg, lossy: true, extension: ".jpeg" },
-  "1.2.840.10008.1.2.4.51": { contentType: jpeg, lossy: true },
-  "1.2.840.10008.1.2.4.57": { contentType: jpeg },
-  "1.2.840.10008.1.2.4.70": { contentType: jll, extension: ".jll" },
-  "1.2.840.10008.1.2.4.140": { contentType: jxl, extension: ".jxl" },
+  '1.2.840.10008.1.2': uncompressed,
+  '1.2.840.10008.1.2.1': uncompressed,
+  '1.2.840.10008.1.2.1.99': uncompressed,
+  '1.2.840.10008.1.2.2': uncompressed,
+  '1.2.840.10008.1.2.4.50': {
+    contentType: jpeg,
+    lossy: true,
+    extension: '.jpeg',
+  },
+  '1.2.840.10008.1.2.4.51': { contentType: jpeg, lossy: true },
+  '1.2.840.10008.1.2.4.57': { contentType: jpeg },
+  '1.2.840.10008.1.2.4.70': { contentType: jll, extension: '.jll' },
+  '1.2.840.10008.1.2.4.140': { contentType: jxl, extension: '.jxl' },
   // Lossy, original JPEG reconstruction mode
-  "1.2.840.10008.1.2.4.141": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.142": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.80": { contentType: jls, extension: ".jls" },
-  "1.2.840.10008.1.2.4.81": { contentType: jls, lossy: true },
-  "1.2.840.10008.1.2.4.90": { contentType: jp2, extension: ".jp2" },
-  "1.2.840.10008.1.2.4.91": { contentType: jp2 },
+  '1.2.840.10008.1.2.4.141': { contentType: jxl, lossy: true },
+  '1.2.840.10008.1.2.4.142': { contentType: jxl, lossy: true },
+  '1.2.840.10008.1.2.4.80': { contentType: jls, extension: '.jls' },
+  '1.2.840.10008.1.2.4.81': { contentType: jls, lossy: true },
+  '1.2.840.10008.1.2.4.90': { contentType: jp2, extension: '.jp2' },
+  '1.2.840.10008.1.2.4.91': { contentType: jp2 },
   // Private/test transfer syntax for HTJ2K
-  "3.2.840.10008.1.2.4.96": { contentType: htj2k },
-  "1.2.840.10008.1.2.4.201": { contentType: htj2k },
-  "1.2.840.10008.1.2.4.202": { contentType: htj2k, extension: ".jhc" },
-  "1.2.840.10008.1.2.4.203": { contentType: htj2k, lossy: true },
-  "1.2.840.10008.1.2.5": { contentType: rle },
+  '3.2.840.10008.1.2.4.96': { contentType: htj2k },
+  '1.2.840.10008.1.2.4.201': { contentType: htj2k },
+  '1.2.840.10008.1.2.4.202': { contentType: htj2k, extension: '.jhc' },
+  '1.2.840.10008.1.2.4.203': { contentType: htj2k, lossy: true },
+  '1.2.840.10008.1.2.5': { contentType: rle },
   default: {},
 };
 

package/lib/operation/InstanceDeduplicate.js

@@ -1,7 +1,7 @@
 // TODO review returning type of some methods
-const { JSONWriter } = require("@radicalimaging/static-wado-util");
-const { Tags } = require("@radicalimaging/static-wado-util");
-const TagLists = require("../model/TagLists");
+const { JSONWriter } = require('@radicalimaging/static-wado-util');
+const { Tags } = require('@radicalimaging/static-wado-util');
+const TagLists = require('../model/TagLists');
 
 const { getValue, setValue } = Tags;
 
@@ -24,22 +24,27 @@ async function deduplicateSingleInstance(id, imageFrame, { force }) {
   const seriesUID = getValue(imageFrame, Tags.SeriesInstanceUID);
   const sopUID = getValue(imageFrame, Tags.SOPInstanceUID);
   if (!sopUID) {
-    console.warn("No sop instance UID in", imageFrame);
+    console.warn('No sop instance UID in', imageFrame);
     return {};
   }
   if (!force && studyData.sopExists(sopUID)) {
-    if (this.verbose) console.log("SOP Instance UID", sopUID, "already exists, skipping");
+    if (this.verbose) console.log('SOP Instance UID', sopUID, 'already exists, skipping');
     // TODO - allow replace as an option
     // Null value means skip writing this instance
     return null;
   }
 
-  if (this.verbose) console.log("SOP Instance UID", sopUID, "being added");
+  if (this.verbose) console.log('SOP Instance UID', sopUID, 'being added');
   const deduplicated = { ...imageFrame };
 
   if (!this.extractors) this.extractors = extractors;
   for (const key of Object.keys(this.extractors)) {
-    const extracted = TagLists.extract(deduplicated, key, this.extractors[key], TagLists.RemoveExtract);
+    const extracted = TagLists.extract(
+      deduplicated,
+      key,
+      this.extractors[key],
+      TagLists.RemoveExtract
+    );
     const hashKey = getValue(extracted, Tags.DeduppedHash);
     await studyData.addExtracted(this, hashKey, extracted);
   }
@@ -53,13 +58,13 @@ async function deduplicateSingleInstance(id, imageFrame, { force }) {
 }
 
 /** Canonicalize the JSON data, making Values always arrays, remote "undefined" from the tags etc */
-const canonicalize = (json) => {
+const canonicalize = json => {
   if (!json) return undefined;
   if (Array.isArray(json)) {
     return json.map(canonicalize);
   }
-  Object.keys(json).forEach((tag) => {
-    if (!tag || tag === "undefined") {
+  Object.keys(json).forEach(tag => {
+    if (!tag || tag === 'undefined') {
       // console.error('Got an undefined tag:', tag, typeof(tag));
       // TODO check returning value
       return;
@@ -73,13 +78,13 @@ const canonicalize = (json) => {
   return json;
 };
 
-const InstanceDeduplicate = (options) =>
+const InstanceDeduplicate = options =>
   async function run(id, sourceImageFrame) {
     // Notify the existing listeners, if any
     const imageFrame = canonicalize(sourceImageFrame);
     if (options.isInstance) {
-      if (options.verbose) console.log("Writing instance metadata");
-      await JSONWriter(id.sopInstanceRootPath, "metadata", imageFrame);
+      await JSONWriter(id.sopInstanceRootPath, 'metadata', imageFrame);
+      console.verbose('Wrote instance metadata', id.sopInstanceRootPath, 'metadata');
     }
     if (!options.isDeduplicate && !options.isGroup) {
       return;