dicom-curate 0.23.0 → 0.24.0

package/dist/esm/applyMappingsWorker.js

@@ -79464,6 +79464,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     errors: [],
     quarantine: {}
   };
+  if (mappingOptions.curationSpec === "none") {
+    return [
+      dcmjs4.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict),
+      mapResults
+    ];
+  }
   const naturalData = dcmjs4.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
@@ -79498,6 +79504,8 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
+  } else {
+    mapResults.outputFilePath = inputFilePath;
   }
   const rawModality = naturalData.Modality;
   let modalityStr = "";
@@ -79507,7 +79515,7 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     modalityStr = String(rawModality[0]);
   }
   const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
-  if (finalSpec.dicomPS315EOptions !== "Off") {
+  if (!mappingOptions.skipModifications && finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
       dicomPS315EOptions: finalSpec.dicomPS315EOptions,
@@ -79889,38 +79897,67 @@ async function curateOne({
   if (canSkip && previousSourceFileInfo) {
     return noMapResult();
   }
-  dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
-  dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
-  let dicomData;
-  try {
-    dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
-      ignoreErrors: true
-    });
-  } catch (error2) {
-    console.warn(
-      `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
-      error2
-    );
-    const mapResults = {
-      anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
-      errors: [
-        `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
-      ],
-      sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+  let mappedDicomData;
+  let clonedMapResults;
+  if (mappingOptions.curationSpec !== "none") {
+    dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
+    dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
+    let dicomData;
+    try {
+      dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
+        ignoreErrors: true
+      });
+    } catch (error2) {
+      console.warn(
+        `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
+        error2
+      );
+      const mapResults = {
+        anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
+        errors: [
+          `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
+        ],
+        sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+        fileInfo: {
+          name: fileInfo.name,
+          size: fileInfo.size,
+          path: fileInfo.path,
+          mtime,
+          preMappedHash,
+          parseError: error2 instanceof Error ? error2.message : String(error2)
+        },
+        curationTime: performance.now() - startTime
+      };
+      return mapResults;
+    }
+    ;
+    ({ dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
+      `${fileInfo.path}/${fileInfo.name}`,
+      dicomData,
+      mappingOptions
+    ));
+    clonedMapResults.mappingRequired = true;
+  } else {
+    mappedDicomData = {
+      write: (...args) => fileArrayBuffer
+    };
+    clonedMapResults = {
+      sourceInstanceUID: `passthrough_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+      mappings: {},
+      anomalies: [],
+      errors: [],
+      quarantine: {},
       fileInfo: {
         name: fileInfo.name,
         size: fileInfo.size,
         path: fileInfo.path,
         mtime,
-        preMappedHash,
-        parseError: error2 instanceof Error ? error2.message : String(error2)
+        preMappedHash
       },
-      curationTime: performance.now() - startTime
+      outputFilePath: `${fileInfo.path}/${fileInfo.name}`,
+      mappingRequired: false
     };
-    return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
-  clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {
       preMappedHash = await hash(fileArrayBuffer, hashMethod || "crc64");
@@ -85680,6 +85717,9 @@ var import_acorn_globals = __toESM(require_acorn_globals(), 1);
 // src/serializeMappingOptions.ts
 function deserializeMappingOptions(serializedMappingOptions) {
   const { curationSpecStr, ...rest } = serializedMappingOptions;
+  if (curationSpecStr === "none") {
+    return { ...rest, curationSpec: "none" };
+  }
   const curationSpec = new Function(`return ${curationSpecStr}`)();
   return { ...rest, curationSpec };
 }

package/dist/esm/collectMappings.js

@@ -35458,6 +35458,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     errors: [],
     quarantine: {}
   };
+  if (mappingOptions.curationSpec === "none") {
+    return [
+      dcmjs4.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict),
+      mapResults
+    ];
+  }
   const naturalData = dcmjs4.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
@@ -35492,6 +35498,8 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
+  } else {
+    mapResults.outputFilePath = inputFilePath;
   }
   const rawModality = naturalData.Modality;
   let modalityStr = "";
@@ -35501,7 +35509,7 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     modalityStr = String(rawModality[0]);
   }
   const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
-  if (finalSpec.dicomPS315EOptions !== "Off") {
+  if (!mappingOptions.skipModifications && finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
       dicomPS315EOptions: finalSpec.dicomPS315EOptions,

package/dist/esm/curateDict.js

@@ -35475,6 +35475,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     errors: [],
     quarantine: {}
   };
+  if (mappingOptions.curationSpec === "none") {
+    return [
+      dcmjs4.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict),
+      mapResults
+    ];
+  }
   const naturalData = dcmjs4.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
@@ -35509,6 +35515,8 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
+  } else {
+    mapResults.outputFilePath = inputFilePath;
   }
   const rawModality = naturalData.Modality;
   let modalityStr = "";
@@ -35518,7 +35526,7 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     modalityStr = String(rawModality[0]);
   }
   const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
-  if (finalSpec.dicomPS315EOptions !== "Off") {
+  if (!mappingOptions.skipModifications && finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
       dicomPS315EOptions: finalSpec.dicomPS315EOptions,

package/dist/esm/curateOne.js

@@ -73173,6 +73173,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     errors: [],
     quarantine: {}
   };
+  if (mappingOptions.curationSpec === "none") {
+    return [
+      dcmjs4.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict),
+      mapResults
+    ];
+  }
   const naturalData = dcmjs4.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
@@ -73207,6 +73213,8 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
+  } else {
+    mapResults.outputFilePath = inputFilePath;
   }
   const rawModality = naturalData.Modality;
   let modalityStr = "";
@@ -73216,7 +73224,7 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     modalityStr = String(rawModality[0]);
   }
   const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
-  if (finalSpec.dicomPS315EOptions !== "Off") {
+  if (!mappingOptions.skipModifications && finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
       dicomPS315EOptions: finalSpec.dicomPS315EOptions,
@@ -73598,38 +73606,67 @@ async function curateOne({
   if (canSkip && previousSourceFileInfo) {
     return noMapResult();
   }
-  dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
-  dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
-  let dicomData;
-  try {
-    dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
-      ignoreErrors: true
-    });
-  } catch (error2) {
-    console.warn(
-      `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
-      error2
-    );
-    const mapResults = {
-      anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
-      errors: [
-        `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
-      ],
-      sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+  let mappedDicomData;
+  let clonedMapResults;
+  if (mappingOptions.curationSpec !== "none") {
+    dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
+    dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
+    let dicomData;
+    try {
+      dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
+        ignoreErrors: true
+      });
+    } catch (error2) {
+      console.warn(
+        `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
+        error2
+      );
+      const mapResults = {
+        anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
+        errors: [
+          `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
+        ],
+        sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+        fileInfo: {
+          name: fileInfo.name,
+          size: fileInfo.size,
+          path: fileInfo.path,
+          mtime,
+          preMappedHash,
+          parseError: error2 instanceof Error ? error2.message : String(error2)
+        },
+        curationTime: performance.now() - startTime
+      };
+      return mapResults;
+    }
+    ;
+    ({ dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
+      `${fileInfo.path}/${fileInfo.name}`,
+      dicomData,
+      mappingOptions
+    ));
+    clonedMapResults.mappingRequired = true;
+  } else {
+    mappedDicomData = {
+      write: (...args) => fileArrayBuffer
+    };
+    clonedMapResults = {
+      sourceInstanceUID: `passthrough_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+      mappings: {},
+      anomalies: [],
+      errors: [],
+      quarantine: {},
       fileInfo: {
         name: fileInfo.name,
         size: fileInfo.size,
         path: fileInfo.path,
         mtime,
-        preMappedHash,
-        parseError: error2 instanceof Error ? error2.message : String(error2)
+        preMappedHash
       },
-      curationTime: performance.now() - startTime
+      outputFilePath: `${fileInfo.path}/${fileInfo.name}`,
+      mappingRequired: false
     };
-    return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
-  clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {
       preMappedHash = await hash(fileArrayBuffer, hashMethod || "crc64");

package/dist/esm/index.js

@@ -81024,6 +81024,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     errors: [],
     quarantine: {}
   };
+  if (mappingOptions.curationSpec === "none") {
+    return [
+      dcmjs4.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict),
+      mapResults
+    ];
+  }
   const naturalData = dcmjs4.data.DicomMetaDictionary.naturalizeDataset(
     dicomData.dict
   );
@@ -81058,6 +81064,8 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
+  } else {
+    mapResults.outputFilePath = inputFilePath;
   }
   const rawModality = naturalData.Modality;
   let modalityStr = "";
@@ -81067,7 +81075,7 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     modalityStr = String(rawModality[0]);
   }
   const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
-  if (finalSpec.dicomPS315EOptions !== "Off") {
+  if (!mappingOptions.skipModifications && finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
       dicomPS315EOptions: finalSpec.dicomPS315EOptions,
@@ -81449,38 +81457,67 @@ async function curateOne({
   if (canSkip && previousSourceFileInfo) {
     return noMapResult();
   }
-  dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
-  dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
-  let dicomData;
-  try {
-    dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
-      ignoreErrors: true
-    });
-  } catch (error2) {
-    console.warn(
-      `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
-      error2
-    );
-    const mapResults = {
-      anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
-      errors: [
-        `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
-      ],
-      sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+  let mappedDicomData;
+  let clonedMapResults;
+  if (mappingOptions.curationSpec !== "none") {
+    dcmjs7.log.setLevel(dcmjs7.log.levels.ERROR);
+    dcmjs7.log.getLogger("validation.dcmjs").setLevel(dcmjs7.log.levels.SILENT);
+    let dicomData;
+    try {
+      dicomData = dcmjs7.data.DicomMessage.readFile(fileArrayBuffer, {
+        ignoreErrors: true
+      });
+    } catch (error2) {
+      console.warn(
+        `[dicom-curate] Could not parse ${fileInfo.name} as DICOM data:`,
+        error2
+      );
+      const mapResults = {
+        anomalies: [`Could not parse ${fileInfo.name} as DICOM data`],
+        errors: [
+          `File ${fileInfo.name} is not a valid DICOM file or is corrupted`
+        ],
+        sourceInstanceUID: `invalid_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+        fileInfo: {
+          name: fileInfo.name,
+          size: fileInfo.size,
+          path: fileInfo.path,
+          mtime,
+          preMappedHash,
+          parseError: error2 instanceof Error ? error2.message : String(error2)
+        },
+        curationTime: performance.now() - startTime
+      };
+      return mapResults;
+    }
+    ;
+    ({ dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
+      `${fileInfo.path}/${fileInfo.name}`,
+      dicomData,
+      mappingOptions
+    ));
+    clonedMapResults.mappingRequired = true;
+  } else {
+    mappedDicomData = {
+      write: (...args) => fileArrayBuffer
+    };
+    clonedMapResults = {
+      sourceInstanceUID: `passthrough_${fileInfo.name.replace(/[^a-zA-Z0-9]/g, "_")}`,
+      mappings: {},
+      anomalies: [],
+      errors: [],
+      quarantine: {},
       fileInfo: {
         name: fileInfo.name,
         size: fileInfo.size,
         path: fileInfo.path,
         mtime,
-        preMappedHash,
-        parseError: error2 instanceof Error ? error2.message : String(error2)
+        preMappedHash
       },
-      curationTime: performance.now() - startTime
+      outputFilePath: `${fileInfo.path}/${fileInfo.name}`,
+      mappingRequired: false
     };
-    return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
-  clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {
       preMappedHash = await hash(fileArrayBuffer, hashMethod || "crc64");
@@ -87282,7 +87319,9 @@ function assertNoClosure(fn) {
 
 // src/serializeMappingOptions.ts
 function serializeMappingOptions(mappingOptions) {
-  assertNoClosure(mappingOptions.curationSpec);
+  if (typeof mappingOptions.curationSpec === "function") {
+    assertNoClosure(mappingOptions.curationSpec);
+  }
   const { curationSpec, ...rest } = mappingOptions;
   const curationSpecStr = curationSpec.toString();
   return { ...rest, curationSpecStr };
@@ -87564,7 +87603,12 @@ async function collectMappingOptions(organizeOptions) {
     outputTarget.directory = organizeOptions.outputDirectory;
   }
   const curationSpec = organizeOptions.curationSpec;
-  const { dicomPS315EOptions: deIdOpts, additionalData } = composeSpecs(curationSpec());
+  let additionalData;
+  let deIdOpts = "Off";
+  if (typeof curationSpec === "function") {
+    ;
+    ({ dicomPS315EOptions: deIdOpts, additionalData } = composeSpecs(curationSpec()));
+  }
   let columnMappings;
   if (organizeOptions.table && additionalData) {
     columnMappings = extractColumnMappings(
@@ -87649,8 +87693,16 @@ async function curateMany(organizeOptions, onProgress) {
       );
       if (organizeOptions.inputType === "directory" || organizeOptions.inputType === "path" || organizeOptions.inputType === "s3") {
         const fileListWorker = await initializeFileListWorker();
-        const curationSpec = composeSpecs(organizeOptions.curationSpec());
-        const specExcludedFiletypes = curationSpec.excludedFiletypes;
+        let specExcludedFiletypes;
+        let noDicomSignatureCheck = false;
+        let noDefaultExclusions = false;
+        if (organizeOptions.curationSpec === "none") {
+          noDicomSignatureCheck = true;
+          noDefaultExclusions = true;
+        } else {
+          const curationSpec = composeSpecs(organizeOptions.curationSpec());
+          specExcludedFiletypes = curationSpec.excludedFiletypes;
+        }
         const excludedPathRegexes = organizeOptions.excludedPathGlobs?.map(
           (glob) => import_picomatch.default.makeRe(glob).source
         );
@@ -87660,6 +87712,8 @@ async function curateMany(organizeOptions, onProgress) {
             directoryHandle: organizeOptions.inputDirectory,
             excludedFiletypes: specExcludedFiletypes,
             excludedPathRegexes,
+            noDicomSignatureCheck,
+            noDefaultExclusions,
             fileInfoIndex: organizeOptions.fileInfoIndex
           });
         } else if (organizeOptions.inputType === "s3") {
@@ -87668,7 +87722,9 @@ async function curateMany(organizeOptions, onProgress) {
             bucketOptions: organizeOptions.inputS3Bucket,
             excludedFiletypes: specExcludedFiletypes,
             excludedPathRegexes,
-            fileInfoIndex: organizeOptions.fileInfoIndex
+            fileInfoIndex: organizeOptions.fileInfoIndex,
+            noDicomSignatureCheck,
+            noDefaultExclusions
           });
         } else {
           fileListWorker.postMessage({
@@ -87676,7 +87732,9 @@ async function curateMany(organizeOptions, onProgress) {
             path: organizeOptions.inputDirectory,
             excludedFiletypes: specExcludedFiletypes,
             excludedPathRegexes,
-            fileInfoIndex: organizeOptions.fileInfoIndex
+            fileInfoIndex: organizeOptions.fileInfoIndex,
+            noDicomSignatureCheck,
+            noDefaultExclusions
           });
         }
       } else if (organizeOptions.inputType === "files") {