dicom-curate 0.6.1 → 0.7.0

package/README.md

@@ -97,8 +97,7 @@ import type { TCurationSpecification } from 'dicom-curate'
  * Curation specification for batch-curating DICOM files.
  */
 export function sampleBatchCurationSpecification(): TCurationSpecification {
-  // Confirm allowed identifiers for this transfer.
-  const identifiers = {
+  const hostProps = {
     protocolNumber: 'Sample_Protocol_Number',
     activityProviderName: 'Sample_CRO',
     centerSubjectId: /^[A-Z]{2}\d{2}-\d{3}$/,
@@ -117,8 +116,8 @@ export function sampleBatchCurationSpecification(): TCurationSpecification {
       // collect from a csv file. A client can use regex to validate the input.
       type: 'load',
       collect: {
-        CURR_ID: identifiers.centerSubjectId,
-        StudyDescription: identifiers.timepointNames,
+        CURR_ID: hostProps.centerSubjectId,
+        StudyDescription: hostProps.timepointNames,
         MAPPED_ID: /BLIND_\d+/,
       },
       // With this, can refer to mappings as parser.getMapping('blindedId')
@@ -132,8 +131,8 @@ export function sampleBatchCurationSpecification(): TCurationSpecification {
       },
     },
 
-    version: '2.0',
-    identifiers,
+    version: '3.0',
+    hostProps,
 
     // This specifies the standardized DICOM de-identification
     dicomPS315EOptions: {
@@ -141,10 +140,10 @@ export function sampleBatchCurationSpecification(): TCurationSpecification {
       cleanDescriptorsExceptions: ['SeriesDescription'],
       retainLongitudinalTemporalInformationOptions: 'Full',
       retainPatientCharacteristicsOption: [
-        'PatientsWeight',
-        'PatientsSize',
-        'PatientsAge',
-        'PatientsSex',
+        'PatientWeight',
+        'PatientSize',
+        'PatientAge',
+        'PatientSex',
         'SelectorASValue',
       ],
       retainDeviceIdentityOption: true,
@@ -153,60 +152,53 @@ export function sampleBatchCurationSpecification(): TCurationSpecification {
       retainInstitutionIdentityOption: true,
     },
 
-    // This section defines the output folder structure and alignment of DICOM headers
-    modifications(parser) {
+    modifyDicomHeader(parser) {
       const scan = parser.getFilePathComp('scan')
       const centerSubjectId = parser.getFilePathComp('centerSubjectId')
 
       return {
-        dicomHeader: {
-          // Align the PatientID DICOM header with the centerSubjectId folder name.
-          PatientID: centerSubjectId,
-          // This example maps PatientIDs based on the mapping CSV file.
-          // PatientID: parser.getMapping('blindedId'),
-          PatientName: centerSubjectId,
-          // Align the StudyDescription DICOM header with the timepoint folder name.
-          StudyDescription: parser.getFilePathComp('timepoint'),
-          // The party responsible for assigning a standard ClinicalTrialSeriesDescription
-          ClinicalTrialCoordinatingCenterName: identifiers.activityProviderName,
-          // Align the ClinicalTrialSeriesDescription DICOM header with the scan folder name.
-          ClinicalTrialSeriesDescription: scan,
-        },
-
-        // This defines the output folder structure.
-        outputFilePathComponents: [
-          parser.getFilePathComp('protocolNumber'),
-          parser.getFilePathComp('activityProvider'),
-          centerSubjectId,
-          parser.getFilePathComp('timepoint'),
-          parser.getFilePathComp('scan') +
-            '=' +
-            parser.getDicom('SeriesNumber'),
-          parser.getFilePathComp(parser.FILEBASENAME) + '.dcm',
-        ],
+        // Align the PatientID DICOM header with the centerSubjectId folder name.
+        PatientID: centerSubjectId,
+        // This example maps PatientIDs based on the mapping CSV file.
+        // PatientID: parser.getMapping('blindedId'),
+        PatientName: centerSubjectId,
+        // Align the StudyDescription DICOM header with the timepoint folder name.
+        StudyDescription: parser.getFilePathComp('timepoint'),
+        // The party responsible for assigning a standard ClinicalTrialSeriesDescription
+        ClinicalTrialCoordinatingCenterName: hostProps.activityProviderName,
+        // Align the ClinicalTrialSeriesDescription DICOM header with the scan folder name.
+        ClinicalTrialSeriesDescription: scan,
       }
     },
 
+    outputFilePathComponents(parser) {
+      const scan = parser.getFilePathComp('scan')
+      const centerSubjectId = parser.getFilePathComp('centerSubjectId')
+
+      return [
+        parser.getFilePathComp('protocolNumber'),
+        parser.getFilePathComp('activityProvider'),
+        centerSubjectId,
+        parser.getFilePathComp('timepoint'),
+        scan + '=' + parser.getDicom('SeriesNumber'),
+        parser.getFilePathComp(parser.FILEBASENAME) + '.dcm',
+      ]
+    },
+
     // This section defines the validation rules for the input DICOMs.
     // The processing continues on errors, but errors will have to be fixed
     // or reviewed between the parties.
-    validation(parser) {
-      const modality = parser.getDicom('Modality')
-      const filename = parser.getFilePathComp(parser.FILEBASENAME)
-      const seriesUid = parser.getDicom('SeriesInstanceUID')
-
-      return {
-        errors: [
-          // File path
-          [
-            'Invalid study folder name',
-            parser.getFilePathComp('protocolNumber') !==
-              identifiers.protocolNumber,
-          ],
-          // DICOM header
-          ['Missing Modality', parser.missingDicom('Modality')],
+    errors(parser) {
+      return [
+        // File path
+        [
+          'Invalid study folder name',
+          parser.getFilePathComp('protocolNumber') !== hostProps.protocolNumber,
         ],
-      }
+        // DICOM header
+        ['Missing Modality', parser.missingDicom('Modality')],
+        ['Missing SOP Class UID', parser.missingDicom('SOPClassUID')],
+      ]
     },
   }
 }

package/dist/esm/applyMappingsWorker.js

@@ -36670,7 +36670,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 }
 
 // src/config/specVersion.ts
-var specVersion = "2.0";
+var specVersion = "3.0";
 
 // src/collectMappings.ts
 var import_lodash2 = __toESM(require_lodash(), 1);
@@ -36693,18 +36693,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   let finalSpec = {
     dicomPS315EOptions: defaultPs315Options,
     inputPathPattern: "",
-    modifications(parser2) {
-      return {
-        dicomHeader: {},
-        outputFilePathComponents: [
-          parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
-          parser2.getFilePathComp(parser2.FILENAME)
-        ]
-      };
-    },
-    validation: () => ({ errors: [] })
+    modifyDicomHeader: () => ({}),
+    outputFilePathComponents: (parser2) => [
+      parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
+      parser2.getFilePathComp(parser2.FILENAME)
+    ],
+    errors: () => []
   };
-  const { modifications, validation, ...restSpec } = mappingOptions.curationSpec();
+  const { modifyDicomHeader, errors, ...restSpec } = mappingOptions.curationSpec();
   if (restSpec.version !== specVersion) {
     throw new Error(
       `Only version ${specVersion} supported in curationSpecification`
@@ -36712,10 +36708,10 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   }
   Object.assign(finalSpec, restSpec);
   if (!mappingOptions.skipModifications) {
-    finalSpec.modifications = modifications;
+    finalSpec.modifyDicomHeader = modifyDicomHeader;
   }
   if (!mappingOptions.skipValidation) {
-    finalSpec.validation = validation;
+    finalSpec.errors = errors;
   }
   const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
@@ -36726,8 +36722,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     mappingOptions.columnMappings,
     finalSpec.additionalData
   );
-  let modificationMap = finalSpec.modifications(parser);
-  mapResults.errors = finalSpec.validation(parser).errors.filter(([, failure]) => failure).map(([message]) => message);
+  mapResults.errors = finalSpec.errors(parser).filter(([, failure]) => failure).map(([message]) => message);
   if (finalSpec.additionalData?.type === "listing") {
     const { lookups, info, collect } = finalSpec.additionalData.collect(parser);
     const collectByValue = collect.map((item) => {
@@ -36744,7 +36739,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     });
     mapResults.listing = { info: cleanedInfo, collectByValue };
   }
-  mapResults.outputFilePath = modificationMap.outputFilePathComponents.join("/");
+  mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -36754,7 +36749,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       originalDicomDict: dicomData.dict
     });
   }
-  const dicomMap = modificationMap.dicomHeader;
+  const dicomMap = finalSpec.modifyDicomHeader(parser);
   for (let attrPath in dicomMap) {
     mapResults.mappings[attrPath] = [
       (0, import_lodash2.get)(naturalData, attrPath),

package/dist/esm/collectMappings.js

@@ -30341,7 +30341,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 }
 
 // src/config/specVersion.ts
-var specVersion = "2.0";
+var specVersion = "3.0";
 
 // src/collectMappings.ts
 var import_lodash2 = __toESM(require_lodash(), 1);
@@ -30364,18 +30364,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   let finalSpec = {
     dicomPS315EOptions: defaultPs315Options,
     inputPathPattern: "",
-    modifications(parser2) {
-      return {
-        dicomHeader: {},
-        outputFilePathComponents: [
-          parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
-          parser2.getFilePathComp(parser2.FILENAME)
-        ]
-      };
-    },
-    validation: () => ({ errors: [] })
+    modifyDicomHeader: () => ({}),
+    outputFilePathComponents: (parser2) => [
+      parser2.protectUid(parser2.getDicom("SeriesInstanceUID")),
+      parser2.getFilePathComp(parser2.FILENAME)
+    ],
+    errors: () => []
   };
-  const { modifications, validation, ...restSpec } = mappingOptions.curationSpec();
+  const { modifyDicomHeader, errors, ...restSpec } = mappingOptions.curationSpec();
   if (restSpec.version !== specVersion) {
     throw new Error(
       `Only version ${specVersion} supported in curationSpecification`
@@ -30383,10 +30379,10 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   }
   Object.assign(finalSpec, restSpec);
   if (!mappingOptions.skipModifications) {
-    finalSpec.modifications = modifications;
+    finalSpec.modifyDicomHeader = modifyDicomHeader;
   }
   if (!mappingOptions.skipValidation) {
-    finalSpec.validation = validation;
+    finalSpec.errors = errors;
   }
   const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
@@ -30397,8 +30393,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     mappingOptions.columnMappings,
     finalSpec.additionalData
   );
-  let modificationMap = finalSpec.modifications(parser);
-  mapResults.errors = finalSpec.validation(parser).errors.filter(([, failure]) => failure).map(([message]) => message);
+  mapResults.errors = finalSpec.errors(parser).filter(([, failure]) => failure).map(([message]) => message);
   if (finalSpec.additionalData?.type === "listing") {
     const { lookups, info, collect } = finalSpec.additionalData.collect(parser);
     const collectByValue = collect.map((item) => {
@@ -30415,7 +30410,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
     });
     mapResults.listing = { info: cleanedInfo, collectByValue };
   }
-  mapResults.outputFilePath = modificationMap.outputFilePathComponents.join("/");
+  mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -30425,7 +30420,7 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       originalDicomDict: dicomData.dict
     });
   }
-  const dicomMap = modificationMap.dicomHeader;
+  const dicomMap = finalSpec.modifyDicomHeader(parser);
   for (let attrPath in dicomMap) {
     mapResults.mappings[attrPath] = [
       (0, import_lodash2.get)(naturalData, attrPath),

package/dist/esm/config/sample2PassCurationSpecification.js

@@ -1,6 +1,6 @@
 // src/config/sample2PassCurationSpecification.ts
 function sample2PassCurationSpecification() {
-  const identifiers = {
+  const hostProps = {
     protocolNumber: "Sample_Protocol_Number",
     activityProviderName: "Sample_CRO",
     centerSubjectId: /^[A-Z]{2}\d{2}-\d{3}$/,
@@ -24,7 +24,7 @@ function sample2PassCurationSpecification() {
           lookups,
           info: [
             // [label, value]
-            ["Protocol Number", identifiers.protocolNumber],
+            ["Protocol Number", hostProps.protocolNumber],
             ["Patient Name", parser.getDicom("PatientName")],
             ["Patient ID", parser.getDicom("PatientID")],
             ["Study Date", parser.getDicom("StudyDate")],
@@ -37,12 +37,12 @@ function sample2PassCurationSpecification() {
           // PatNamePatId | PatNameIDSeriesDesc | CenterSubjectId | Timepoint | Comment
           // [lookup header, format, lookup value]
           collect: [
-            ["CenterSubjectId", identifiers.centerSubjectId, "PatNamePatId"],
+            ["CenterSubjectId", hostProps.centerSubjectId, "PatNamePatId"],
             // For now, collecting this on Series not Study level.
             // Trade-off is re-use (study level) vs avoiding confusion due to
             // any mismatch on study vs series level (e.g. 2 studies one visit)
-            ["Timepoint", identifiers.timepointNames, "PatNameIDSeriesDesc"],
-            ["ScanName", identifiers.scanNames, "PatNameIDSeriesDesc"],
+            ["Timepoint", hostProps.timepointNames, "PatNameIDSeriesDesc"],
+            ["ScanName", hostProps.scanNames, "PatNameIDSeriesDesc"],
             ["Comment", /.*/, "PatNameIDSeriesDesc"]
           ]
         };
@@ -67,18 +67,18 @@ function sample2PassCurationSpecification() {
         }
       }
     },
-    version: "2.0",
-    identifiers,
+    version: "3.0",
+    hostProps,
     // This specifies the standardized DICOM de-identification
     dicomPS315EOptions: {
       cleanDescriptorsOption: true,
       cleanDescriptorsExceptions: ["SeriesDescription"],
       retainLongitudinalTemporalInformationOptions: "Full",
       retainPatientCharacteristicsOption: [
-        "PatientsWeight",
-        "PatientsSize",
-        "PatientsAge",
-        "PatientsSex",
+        "PatientWeight",
+        "PatientSize",
+        "PatientAge",
+        "PatientSex",
         "SelectorASValue"
       ],
       retainDeviceIdentityOption: true,
@@ -86,77 +86,70 @@ function sample2PassCurationSpecification() {
       retainSafePrivateOption: "Quarantine",
       retainInstitutionIdentityOption: true
     },
-    // This section defines the output folder structure and alignment of DICOM headers
-    modifications(parser) {
+    modifyDicomHeader(parser) {
       const centerSubjectId = String(parser.getMapping("centerSubjectId"));
       const timepoint = String(parser.getMapping("timepoint"));
       const scanName = String(parser.getMapping("scanName"));
       return {
-        dicomHeader: {
-          // Align the PatientID DICOM header with the centerSubjectId folder name.
-          PatientID: centerSubjectId,
-          // This example maps PatientIDs based on the mapping CSV file.
-          // PatientID: parser.getMapping('blindedId'),
-          PatientName: centerSubjectId,
-          // Align the StudyDescription DICOM header with the timepoint folder name.
-          StudyDescription: timepoint,
-          // The party responsible for assigning a standard ClinicalTrialSeriesDescription
-          // ClinicalTrialCoordinatingCenterName: identifiers.activityProviderName,
-          // Align the ClinicalTrialSeriesDescription DICOM header with the scan folder name.
-          ClinicalTrialSeriesDescription: scanName
-        },
-        // This defines the output folder structure.
-        outputFilePathComponents: [
-          identifiers.protocolNumber,
-          centerSubjectId,
-          timepoint,
-          scanName + "=" + parser.getDicom("SeriesNumber"),
-          parser.getFilePathComp(parser.FILEBASENAME) + ".dcm"
-        ]
+        // Align the PatientID DICOM header with the centerSubjectId folder name.
+        PatientID: centerSubjectId,
+        // This example maps PatientIDs based on the mapping CSV file.
+        // PatientID: parser.getMapping('blindedId'),
+        PatientName: centerSubjectId,
+        // Align the StudyDescription DICOM header with the timepoint folder name.
+        StudyDescription: timepoint,
+        // The party responsible for assigning a standard ClinicalTrialSeriesDescription
+        // ClinicalTrialCoordinatingCenterName: hostProps.activityProviderName,
+        // Align the ClinicalTrialSeriesDescription DICOM header with the scan folder name.
+        ClinicalTrialSeriesDescription: scanName
       };
     },
+    outputFilePathComponents(parser) {
+      const centerSubjectId = String(parser.getMapping("centerSubjectId"));
+      const timepoint = String(parser.getMapping("timepoint"));
+      const scanName = String(parser.getMapping("scanName"));
+      return [
+        hostProps.protocolNumber,
+        centerSubjectId,
+        timepoint,
+        scanName + "=" + parser.getDicom("SeriesNumber"),
+        parser.getFilePathComp(parser.FILEBASENAME) + ".dcm"
+      ];
+    },
     // This section defines the validation rules for the input DICOMs.
     // The processing continues on errors, but errors will have to be fixed
     // or reviewed between the parties.
-    validation(parser) {
+    errors(parser) {
       const filename = parser.getFilePathComp(parser.FILENAME);
       const seriesUid = parser.getDicom("SeriesInstanceUID");
       const centerSubjectId = String(parser.getMapping("centerSubjectId"));
       const timepoint = String(parser.getMapping("timepoint"));
       const scanName = String(parser.getMapping("scanName"));
-      return {
-        errors: [
-          // File path
-          [
-            "Invalid site-subject format",
-            !centerSubjectId.match(identifiers.centerSubjectId)
-          ],
-          [
-            "Invalid timepoint descriptor",
-            !identifiers.timepointNames.includes(timepoint)
-          ],
-          [
-            "Invalid scan descriptor",
-            !identifiers.scanNames.includes(scanName)
-          ],
-          // DICOM header
-          ["Missing Modality", parser.missingDicom("Modality")],
-          ["Missing SOP Class UID", parser.missingDicom("SOPClassUID")],
-          [
-            "Duplicate File Name(s) in series",
-            !parser.isUniqueInGroup(filename, seriesUid)
-          ],
-          [
-            "Missing Series Instance UID",
-            parser.missingDicom("SeriesInstanceUID")
-          ],
-          [
-            "Missing Study Instance UID",
-            parser.missingDicom("StudyInstanceUID")
-          ],
-          ["Missing SOP Instance UID", parser.missingDicom("SOPInstanceUID")]
-        ]
-      };
+      return [
+        // File path
+        [
+          "Invalid site-subject format",
+          !centerSubjectId.match(hostProps.centerSubjectId)
+        ],
+        [
+          "Invalid timepoint descriptor",
+          !hostProps.timepointNames.includes(timepoint)
+        ],
+        ["Invalid scan descriptor", !hostProps.scanNames.includes(scanName)],
+        // DICOM header
+        ["Missing Modality", parser.missingDicom("Modality")],
+        ["Missing SOP Class UID", parser.missingDicom("SOPClassUID")],
+        [
+          "Duplicate File Name(s) in series",
+          !parser.isUniqueInGroup(filename, seriesUid)
+        ],
+        [
+          "Missing Series Instance UID",
+          parser.missingDicom("SeriesInstanceUID")
+        ],
+        ["Missing Study Instance UID", parser.missingDicom("StudyInstanceUID")],
+        ["Missing SOP Instance UID", parser.missingDicom("SOPInstanceUID")]
+      ];
     }
   };
 }