@radicalimaging/static-wado-creator 1.7.4 → 1.7.6

package/dist/createThumbnail.js

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+const { Tags, readBulkData, handleHomeRelative } = require('@radicalimaging/static-wado-util');
+const dcmjs = require('dcmjs');
+
+const StaticWado = require('./StaticWado');
+const adaptProgramOpts = require('./util/adaptProgramOpts');
+const WriteStream = require('./writer/WriteStream');
+
+const UncompressedLEIExplicit = '1.2.840.10008.1.2.1';
+const { DicomDict, DicomMetaDictionary } = dcmjs.data;
+
+const fileMetaInformationVersionArray = new Uint8Array(2);
+fileMetaInformationVersionArray[1] = 1;
+
+const readBulkDataValue = async (studyDir, instance, value, options) => {
+  const { BulkDataURI } = value;
+  value.vr = 'OB';
+  const seriesUid = Tags.getValue(instance, Tags.SeriesInstanceUID);
+  const numberOfFrames = Tags.getValue(instance, Tags.NumberOfFrames) || 1;
+  if (BulkDataURI.indexOf('/frames') !== -1) {
+    const seriesDir = `${studyDir}/series/${seriesUid}`;
+    if (options?.frame === false) {
+      return;
+    }
+    // Really only support a limited number of frames based on memory size
+    value.Value = [];
+    if (typeof options?.frame === 'number') {
+      console.noQuiet('Reading frame', options.frame);
+      const bulk = await readBulkData(seriesDir, BulkDataURI, options.frame);
+      if (!bulk) {
+        return;
+      }
+      value.Value[options.frame - 1] = bulk.binaryData;
+      value.transferSyntaxUid = bulk.transferSyntaxUid;
+      value.contentType = bulk.contentType;
+      return;
+    }
+    console.noQuiet('Reading frames', 1, '...', numberOfFrames);
+    for (let frame = 1; frame <= numberOfFrames; frame++) {
+      const bulk = await readBulkData(seriesDir, BulkDataURI, frame);
+      if (!bulk) break;
+      value.Value.push(bulk.binaryData);
+      value.transferSyntaxUid = bulk.transferSyntaxUid;
+      value.contentType = bulk.contentType;
+    }
+  } else {
+    const bulk = await readBulkData(studyDir, BulkDataURI);
+    value.Value = [new ArrayBuffer(bulk.binaryData)];
+    value.contentType = bulk.contentType;
+  }
+};
+
+const readBinaryData = async (dir, instance, options = { frame: true }) => {
+  for (const tag of Object.keys(instance)) {
+    const v = instance[tag];
+    if (v.BulkDataURI) {
+      await readBulkDataValue(dir, instance, v, options);
+      continue;
+    }
+    if (!v.vr) {
+      const value0 = v.Value?.[0];
+      if (typeof value0 === 'string') {
+        v.vr = 'LT';
+      } else {
+        console.log('Deleting', tag, v.Value, v);
+        delete instance[tag];
+      }
+      continue;
+    }
+    if (v.vr === 'SQ' && v.Values?.length) {
+      await Promise.all(v.Values.map(readBinaryData));
+      continue;
+    }
+  }
+};
+
+module.exports = async function createThumbnail(options, program) {
+  const finalOptions = adaptProgramOpts(options, {
+    ...this,
+    // Instance metadata is the instances/<sopUID>/metadata.gz files
+    isInstance: false,
+    // Deduplicated data is single instance deduplicated data
+    isDeduplicate: false,
+    // Group data is the group file directories
+    isGroup: false,
+    isStudyData: false,
+    isDeleteInstances: false,
+  });
+  const importer = new StaticWado(finalOptions);
+  const studyInstanceUid = program.args[0];
+  const dir = `${importer.options.rootDir}/studies/${studyInstanceUid}`;
+  console.noQuiet('Creating thumbnail for', studyInstanceUid, dir);
+  const study = await importer.callback.scanStudy(studyInstanceUid);
+  const outputPath = `./studies/${studyInstanceUid}`;
+  const { sopInstanceUid, seriesInstanceUid, seriesThumbnail, studyThumbnail } = options;
+  const sops = sopInstanceUid ? new Set() : null;
+  if (sopInstanceUid) {
+    for (const sop of sopInstanceUid.split(',').map(s => s.trim())) {
+      sops.add(sop);
+    }
+  }
+  const promises = [];
+
+  const writeThumbnail = async (id, buffer) => {
+    console.verbose('Write thumbnail', id, buffer);
+    await importer.callback.thumbWriter(id.sopInstanceRootPath, 'thumbnail', buffer);
+    if (seriesThumbnail) {
+      await importer.callback.thumbWriter(id.seriesRootPath, 'thumbnail', buffer);
+    }
+    if (studyThumbnail) {
+      await importer.callback.thumbWriter(id.studyPath, 'thumbnail', buffer);
+    }
+  };
+
+  // TODO - choose middle frame of multiframe and choose middle image of
+  // series for series thumbnail, and first series for study thumbnail
+  const codecOptions = { frame: 1 };
+
+  for (const sop of study.getSopUids()) {
+    if (sops && !sops.has(sop)) {
+      continue;
+    }
+    const instance = await study.recombine(sop);
+
+    if (
+      seriesInstanceUid &&
+      Tags.getValue(instance, Tags.SeriesInstanceUID) !== seriesInstanceUid
+    ) {
+      continue;
+    }
+
+    await readBinaryData(dir, instance, codecOptions);
+
+    const availableTransferSyntaxUID = Tags.getValue(instance, Tags.AvailableTransferSyntaxUID);
+    const pixelData = Tags.getValue(instance, Tags.PixelData);
+    if (!pixelData) {
+      console.warn('No pixel data found in instance');
+      continue;
+    }
+    const transferSyntaxUid =
+      instance[Tags.PixelData].transferSyntaxUid || availableTransferSyntaxUID;
+    const frame = Array.isArray(pixelData.Value) ? pixelData.Value[0] : pixelData;
+    console.verbose('Use transfer syntax uid:', transferSyntaxUid);
+    const id = importer.callback.uids({
+      studyInstanceUid,
+      seriesInstanceUid: Tags.getValue(instance, Tags.SeriesInstanceUID),
+      sopInstanceUid: sop,
+      transferSyntaxUid,
+    });
+
+    const promise = importer.callback.internalGenerateImage(
+      frame,
+      null,
+      instance,
+      id.transferSyntaxUid,
+      writeThumbnail.bind(null, id)
+    );
+    promises.push(promise);
+    if (seriesThumbnail) {
+      break;
+    }
+  }
+  await Promise.all(promises);
+};

package/dist/deleteMain.js

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+const StaticWado = require('./StaticWado');
+const adaptProgramOpts = require('./util/adaptProgramOpts');
+
+module.exports = function deleteMain(options, program) {
+  const finalOptions = adaptProgramOpts(options, {
+    ...this,
+    isGroup: true,
+    isStudyData: true,
+  });
+  const importer = new StaticWado(finalOptions);
+  return importer.delete(program.args);
+};

package/dist/groupMain.js

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+const StaticWado = require('./StaticWado');
+const adaptProgramOpts = require('./util/adaptProgramOpts');
+
+module.exports = function createMain(options, program) {
+  const finalOptions = adaptProgramOpts(options, {
+    ...this,
+    isInstance: false,
+    isDeduplicate: true,
+    isGroup: true,
+    isStudyData: false,
+    scanStudies: true,
+    isDeleteInstances: true,
+  });
+  const importer = new StaticWado(finalOptions);
+  // Either do a scan or on specified studies
+  return importer.executeCommand(program.args);
+};