@radicalimaging/static-wado-creator 1.3.2 → 1.6.10

package/lib/instanceMain.js

@@ -9,6 +9,7 @@ module.exports = function createMain(options, program) {
     isDeduplicate: true,
     isGroup: false,
     isStudyData: false,
+    isSkipStudyScan: true,
   });
   const importer = new StaticWado(finalOptions);
   return importer.executeCommand(program.args);

package/lib/mkdicomwebConfig.js

@@ -2,8 +2,10 @@ 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");
@@ -28,12 +30,14 @@ const { mkdicomwebConfig } = ConfigPoint.register({
       },
       {
         key: "--clean",
-        description: "Clean the outputs before generating/starting to write new values.",
+        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.",
+        description:
+          "List of deployments from configuration to deploy to. Separated by space.",
         defaultValue: undefined,
       },
       {
@@ -52,7 +56,8 @@ const { mkdicomwebConfig } = ConfigPoint.register({
       },
       {
         key: "--alternate <type>",
-        description: "Generates an alternate representaton of the image generally in the /lossy sub-directory",
+        description:
+          "Generates an alternate representaton of the image generally in the /lossy sub-directory",
         choices: ["jhc", "jls", "jhcLossless", "jlsLossless"],
       },
       {
@@ -69,19 +74,26 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         description: "Write verbose output",
         defaultValue: false,
       },
+      {
+        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")',
+        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",
+        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",
+        description:
+          "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
       },
       {
         key: "--single-part-image",
@@ -105,19 +117,50 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         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"],
+        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",
+        description:
+          "List of types to recompress for color images, separated by space",
         defaultValue: ["uncompressed"],
-        choices: ["uncompressed", "jpeg", "jp2", "jpeglossless", "rle", "jph", "jls", "true", "none"],
+        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: "--delete-input",
+        description: "Deletes successful input files",
+        defaultValue: false,
+      },
+      {
+        key: "--delete-failed",
+        description: "Deletes unsuccessful input files",
+        defaultValue: false,
+      },
       {
         key: "--recompress-thumb <listvalue...>",
         description: "List of types to recompress thumb separated by space",
@@ -135,8 +178,9 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         defaultValue: false,
       },
       {
-        key: "--thumb",
-        description: "Generate thumbnails",
+        key: "--no-thumb",
+        description: "Skip generating thumbnails using CS3D internal render",
+        defaultValue: true,
       },
       {
         key: "--dcm2jpg",
@@ -155,7 +199,8 @@ const { mkdicomwebConfig } = ConfigPoint.register({
       },
       {
         key: "--path-deduplicated <path>",
-        description: "Set the deduplicate data directory path (relative to dir)",
+        description:
+          "Set the deduplicate data directory path (relative to dir)",
         defaultValue: "deduplicated",
       },
       {
@@ -170,18 +215,55 @@ const { mkdicomwebConfig } = ConfigPoint.register({
       },
       {
         key: "--prepend-bulk-data-uri <value>",
-        description: "Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)",
+        description:
+          "Prepend bulkdata uri (ex. to use absolute Uri like http://host:3000/dicomweb)",
         defaultValue: "",
       },
       {
         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)",
+        description:
+          "expand bulkdata relative uri to use full relative path (should also be set when using --prepend-bulk-data-uri)",
         defaultValue: false,
       },
+      {
+        key: "--quiet",
+        description: "Run quietly, minimizing extraneous output",
+        defaultValue: false,
+      },
+      {
+        key: "--multipart",
+        description: "Add a multipart result output",
+        defaultValue: false,
+      },
+      {
+        key: "--no-verify",
+        description: "Verify",
+        defaultValue: true,
+      },
       {
         key: "-o, --dir <value>",
         description: "Set output directory",
-        defaultValue: { configOperation: "reference", source: "staticWadoConfig", reference: "rootDir" },
+        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: [
@@ -195,6 +277,12 @@ const { mkdicomwebConfig } = ConfigPoint.register({
           "of deduplicated files each time a study instance UID is found, and only updates\n" +
           "those studies having at least one ",
       },
+      {
+        command: "server",
+        main: serverMain,
+        helpDescription:
+          "Run server deploy instances single threaded/separated exec process",
+      },
       {
         command: "part10",
         arguments: ["studyUID"],
@@ -206,28 +294,43 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         main: indexMain,
         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"],
         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"],
         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"],
         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",
         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...>",

package/lib/model/TagLists.js

@@ -6,8 +6,20 @@ const { Tags } = require("@radicalimaging/static-wado-util");
 const hasher = hashFactory.hasher();
 
 const { PatientID, PatientName, IssuerOfPatientID } = Tags;
-const { StudyDescription, AccessionNumber, StudyInstanceUID, StudyDate, StudyTime } = Tags;
-const { SeriesDescription, SeriesNumber, SeriesInstanceUID, SeriesDate, SeriesTime } = Tags;
+const {
+  StudyDescription,
+  AccessionNumber,
+  StudyInstanceUID,
+  StudyDate,
+  StudyTime,
+} = Tags;
+const {
+  SeriesDescription,
+  SeriesNumber,
+  SeriesInstanceUID,
+  SeriesDate,
+  SeriesTime,
+} = Tags;
 
 const { DeduppedHash, DeduppedRef, DeduppedType } = Tags;
 
@@ -24,7 +36,16 @@ 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];
 

package/lib/model/uids.js

@@ -21,7 +21,11 @@ const uids = {
   "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" },
+  "1.2.840.10008.1.2.4.50": {
+    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" },

package/lib/operation/InstanceDeduplicate.js

@@ -28,7 +28,8 @@ async function deduplicateSingleInstance(id, imageFrame, { force }) {
     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;
@@ -39,7 +40,12 @@ async function deduplicateSingleInstance(id, imageFrame, { force }) {
 
   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);
   }
@@ -78,7 +84,7 @@ const InstanceDeduplicate = (options) =>
     // Notify the existing listeners, if any
     const imageFrame = canonicalize(sourceImageFrame);
     if (options.isInstance) {
-      if (options.verbose) console.log("Writing instance metadata");
+      console.verbose("Writing instance metadata");
       await JSONWriter(id.sopInstanceRootPath, "metadata", imageFrame);
     }
     if (!options.isDeduplicate && !options.isGroup) {
@@ -90,7 +96,11 @@ const InstanceDeduplicate = (options) =>
       this.verbose = options.verbose;
     }
 
-    const deduppedInstance = await this.deduplicateSingleInstance(id, imageFrame, options);
+    const deduppedInstance = await this.deduplicateSingleInstance(
+      id,
+      imageFrame,
+      options,
+    );
     if (deduppedInstance) {
       // this refers to callee
       await this.deduplicated(id, deduppedInstance);

package/lib/operation/ScanStudy.js

@@ -1,14 +1,47 @@
+const {
+  getStudyUIDPathAndSubPath,
+} = require("@radicalimaging/static-wado-util");
+
 const path = require("path");
 
 function ScanStudy(options) {
-  const { directoryName, deduplicatedRoot, deduplicatedInstancesRoot } = options;
+  const {
+    directoryName,
+    deduplicatedRoot,
+    deduplicatedInstancesRoot,
+    hashStudyUidPath,
+  } = options;
 
   return function scanStudy(studyInstanceUid) {
+    const { path: hashPath = "", subpath: hashSubpath = "" } = hashStudyUidPath
+      ? getStudyUIDPathAndSubPath(studyInstanceUid)
+      : {};
+
     console.verbose("scanStudy", studyInstanceUid);
-    const studyPath = path.join(directoryName, "studies", studyInstanceUid);
-    const deduplicatedInstancesPath = path.join(deduplicatedInstancesRoot, studyInstanceUid);
-    const deduplicatedPath = path.join(deduplicatedRoot, studyInstanceUid);
-    console.verbose("Importing", studyInstanceUid, studyPath, deduplicatedInstancesPath, deduplicatedPath);
+
+    if (hashPath && hashSubpath) {
+      console.verbose("hashPath", hashPath);
+      console.verbose("hashSubpath", hashSubpath);
+    }
+
+    const studySubDir = hashStudyUidPath
+      ? path.join(hashPath, hashSubpath, studyInstanceUid)
+      : studyInstanceUid;
+
+    const studyPath = path.join(directoryName, "studies", studySubDir);
+    const deduplicatedInstancesPath = path.join(
+      deduplicatedInstancesRoot,
+      // studyInstanceUid,
+      studySubDir,
+    );
+    const deduplicatedPath = path.join(deduplicatedRoot, studySubDir);
+    console.verbose(
+      "Importing",
+      studyInstanceUid,
+      studyPath,
+      deduplicatedInstancesPath,
+      deduplicatedPath,
+    );
     return this.completeStudy.getCurrentStudyData(this, {
       studyPath,
       deduplicatedPath,