dicom-curate 0.22.1 → 0.23.0

package/dist/esm/applyMappingsWorker.js

@@ -79452,7 +79452,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 
 // src/collectMappings.ts
 var import_lodash3 = __toESM(require_lodash(), 1);
-function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function collectMappings(inputFilePath, dicomData, mappingOptions) {
   const mapResults = {
     // original UID for this dicomData
     sourceInstanceUID: "",
@@ -79469,10 +79469,9 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
   const finalSpec = composeSpecs(mappingOptions.curationSpec());
-  const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,
-    finalFilePath,
+    inputFilePath,
     naturalData,
     finalSpec.dicomPS315EOptions,
     mappingOptions.columnMappings,
@@ -79500,6 +79499,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   }
+  const rawModality = naturalData.Modality;
+  let modalityStr = "";
+  if (typeof rawModality === "string") {
+    modalityStr = rawModality;
+  } else if (Array.isArray(rawModality) && rawModality.length > 0) {
+    modalityStr = String(rawModality[0]);
+  }
+  const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -79508,6 +79515,19 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       mapResults,
       originalDicomDict: dicomData.dict
     });
+    const mappedInstanceUID = naturalData.SOPInstanceUID;
+    if (mapResults.outputFilePath && mappedInstanceUID) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mappedInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
+  } else if (mapResults.outputFilePath) {
+    const normaliseFilename = (p4) => p4.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+    if (normaliseFilename(mapResults.outputFilePath) !== normaliseFilename(inputFilePath)) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mapResults.sourceInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
   }
   if (!mappingOptions.skipModifications) {
     const dicomMap = finalSpec.modifyDicomHeader(parser);
@@ -79554,10 +79574,9 @@ function mapMetaheader(metaHeader, newInstanceUid) {
 
 // src/curateDict.ts
 var import_lodash4 = __toESM(require_lodash(), 1);
-function curateDict(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function curateDict(inputFilePath, dicomData, mappingOptions) {
   const [naturalData, mapResults] = collectMappings(
     inputFilePath,
-    inputFileIndex,
     dicomData,
     mappingOptions
   );
@@ -79731,7 +79750,6 @@ async function loadS3Client() {
 // src/curateOne.ts
 async function curateOne({
   fileInfo,
-  fileIndex = 0,
   outputTarget,
   mappingOptions,
   hashMethod,
@@ -79901,12 +79919,7 @@ async function curateOne({
     };
     return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
-    `${fileInfo.path}/${fileInfo.name}`,
-    fileIndex,
-    dicomData,
-    mappingOptions
-  );
+  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
   clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {
@@ -85717,7 +85730,6 @@ fixupNodeWorkerEnvironment().then(() => {
           try {
             curateOne({
               fileInfo,
-              fileIndex: event.data.fileIndex,
               outputTarget: event.data.outputTarget || {},
               hashMethod: event.data.hashMethod,
               mappingOptions,

package/dist/esm/collectMappings.js

@@ -35446,7 +35446,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 
 // src/collectMappings.ts
 var import_lodash3 = __toESM(require_lodash(), 1);
-function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function collectMappings(inputFilePath, dicomData, mappingOptions) {
   const mapResults = {
     // original UID for this dicomData
     sourceInstanceUID: "",
@@ -35463,10 +35463,9 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
   const finalSpec = composeSpecs(mappingOptions.curationSpec());
-  const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,
-    finalFilePath,
+    inputFilePath,
     naturalData,
     finalSpec.dicomPS315EOptions,
     mappingOptions.columnMappings,
@@ -35494,6 +35493,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   }
+  const rawModality = naturalData.Modality;
+  let modalityStr = "";
+  if (typeof rawModality === "string") {
+    modalityStr = rawModality;
+  } else if (Array.isArray(rawModality) && rawModality.length > 0) {
+    modalityStr = String(rawModality[0]);
+  }
+  const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -35502,6 +35509,19 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       mapResults,
       originalDicomDict: dicomData.dict
     });
+    const mappedInstanceUID = naturalData.SOPInstanceUID;
+    if (mapResults.outputFilePath && mappedInstanceUID) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mappedInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
+  } else if (mapResults.outputFilePath) {
+    const normaliseFilename = (p) => p.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+    if (normaliseFilename(mapResults.outputFilePath) !== normaliseFilename(inputFilePath)) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mapResults.sourceInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
   }
   if (!mappingOptions.skipModifications) {
     const dicomMap = finalSpec.modifyDicomHeader(parser);

package/dist/esm/curateDict.js

@@ -35463,7 +35463,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 
 // src/collectMappings.ts
 var import_lodash3 = __toESM(require_lodash(), 1);
-function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function collectMappings(inputFilePath, dicomData, mappingOptions) {
   const mapResults = {
     // original UID for this dicomData
     sourceInstanceUID: "",
@@ -35480,10 +35480,9 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
   const finalSpec = composeSpecs(mappingOptions.curationSpec());
-  const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,
-    finalFilePath,
+    inputFilePath,
     naturalData,
     finalSpec.dicomPS315EOptions,
     mappingOptions.columnMappings,
@@ -35511,6 +35510,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   }
+  const rawModality = naturalData.Modality;
+  let modalityStr = "";
+  if (typeof rawModality === "string") {
+    modalityStr = rawModality;
+  } else if (Array.isArray(rawModality) && rawModality.length > 0) {
+    modalityStr = String(rawModality[0]);
+  }
+  const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -35519,6 +35526,19 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       mapResults,
       originalDicomDict: dicomData.dict
     });
+    const mappedInstanceUID = naturalData.SOPInstanceUID;
+    if (mapResults.outputFilePath && mappedInstanceUID) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mappedInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
+  } else if (mapResults.outputFilePath) {
+    const normaliseFilename = (p) => p.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+    if (normaliseFilename(mapResults.outputFilePath) !== normaliseFilename(inputFilePath)) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mapResults.sourceInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
   }
   if (!mappingOptions.skipModifications) {
     const dicomMap = finalSpec.modifyDicomHeader(parser);
@@ -35565,10 +35585,9 @@ function mapMetaheader(metaHeader, newInstanceUid) {
 
 // src/curateDict.ts
 var import_lodash4 = __toESM(require_lodash(), 1);
-function curateDict(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function curateDict(inputFilePath, dicomData, mappingOptions) {
   const [naturalData, mapResults] = collectMappings(
     inputFilePath,
-    inputFileIndex,
     dicomData,
     mappingOptions
   );

package/dist/esm/curateOne.js

@@ -73161,7 +73161,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 
 // src/collectMappings.ts
 var import_lodash3 = __toESM(require_lodash(), 1);
-function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function collectMappings(inputFilePath, dicomData, mappingOptions) {
   const mapResults = {
     // original UID for this dicomData
     sourceInstanceUID: "",
@@ -73178,10 +73178,9 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
   const finalSpec = composeSpecs(mappingOptions.curationSpec());
-  const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,
-    finalFilePath,
+    inputFilePath,
     naturalData,
     finalSpec.dicomPS315EOptions,
     mappingOptions.columnMappings,
@@ -73209,6 +73208,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   }
+  const rawModality = naturalData.Modality;
+  let modalityStr = "";
+  if (typeof rawModality === "string") {
+    modalityStr = rawModality;
+  } else if (Array.isArray(rawModality) && rawModality.length > 0) {
+    modalityStr = String(rawModality[0]);
+  }
+  const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -73217,6 +73224,19 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       mapResults,
       originalDicomDict: dicomData.dict
     });
+    const mappedInstanceUID = naturalData.SOPInstanceUID;
+    if (mapResults.outputFilePath && mappedInstanceUID) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mappedInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
+  } else if (mapResults.outputFilePath) {
+    const normaliseFilename = (p4) => p4.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+    if (normaliseFilename(mapResults.outputFilePath) !== normaliseFilename(inputFilePath)) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mapResults.sourceInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
   }
   if (!mappingOptions.skipModifications) {
     const dicomMap = finalSpec.modifyDicomHeader(parser);
@@ -73263,10 +73283,9 @@ function mapMetaheader(metaHeader, newInstanceUid) {
 
 // src/curateDict.ts
 var import_lodash4 = __toESM(require_lodash(), 1);
-function curateDict(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function curateDict(inputFilePath, dicomData, mappingOptions) {
   const [naturalData, mapResults] = collectMappings(
     inputFilePath,
-    inputFileIndex,
     dicomData,
     mappingOptions
   );
@@ -73440,7 +73459,6 @@ async function loadS3Client() {
 // src/curateOne.ts
 async function curateOne({
   fileInfo,
-  fileIndex = 0,
   outputTarget,
   mappingOptions,
   hashMethod,
@@ -73610,12 +73628,7 @@ async function curateOne({
     };
     return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
-    `${fileInfo.path}/${fileInfo.name}`,
-    fileIndex,
-    dicomData,
-    mappingOptions
-  );
+  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
   clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {

package/dist/esm/index.js

@@ -81012,7 +81012,7 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
 
 // src/collectMappings.ts
 var import_lodash3 = __toESM(require_lodash(), 1);
-function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function collectMappings(inputFilePath, dicomData, mappingOptions) {
   const mapResults = {
     // original UID for this dicomData
     sourceInstanceUID: "",
@@ -81029,10 +81029,9 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   );
   mapResults.sourceInstanceUID = naturalData.SOPInstanceUID;
   const finalSpec = composeSpecs(mappingOptions.curationSpec());
-  const finalFilePath = finalSpec.dicomPS315EOptions === "Off" ? inputFilePath : inputFilePath.slice(0, inputFilePath.lastIndexOf("/") + 1) + `${String(inputFileIndex + 1).padStart(5, "0")}.dcm`;
   const parser = getParser(
     finalSpec.inputPathPattern,
-    finalFilePath,
+    inputFilePath,
     naturalData,
     finalSpec.dicomPS315EOptions,
     mappingOptions.columnMappings,
@@ -81060,6 +81059,14 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
   }
+  const rawModality = naturalData.Modality;
+  let modalityStr = "";
+  if (typeof rawModality === "string") {
+    modalityStr = rawModality;
+  } else if (Array.isArray(rawModality) && rawModality.length > 0) {
+    modalityStr = String(rawModality[0]);
+  }
+  const modality = modalityStr.trim().replace(/\W/g, "") || "OT";
   if (finalSpec.dicomPS315EOptions !== "Off") {
     deidentifyPS315E({
       naturalData,
@@ -81068,6 +81075,19 @@ function collectMappings(inputFilePath, inputFileIndex, dicomData, mappingOption
       mapResults,
       originalDicomDict: dicomData.dict
     });
+    const mappedInstanceUID = naturalData.SOPInstanceUID;
+    if (mapResults.outputFilePath && mappedInstanceUID) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mappedInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
+  } else if (mapResults.outputFilePath) {
+    const normaliseFilename = (p4) => p4.replace(/\/+/g, "/").replace(/^\/|\/$/g, "");
+    if (normaliseFilename(mapResults.outputFilePath) !== normaliseFilename(inputFilePath)) {
+      const parts = mapResults.outputFilePath.split("/");
+      parts[parts.length - 1] = `${modality}_${mapResults.sourceInstanceUID}.dcm`;
+      mapResults.outputFilePath = parts.join("/");
+    }
   }
   if (!mappingOptions.skipModifications) {
     const dicomMap = finalSpec.modifyDicomHeader(parser);
@@ -81114,10 +81134,9 @@ function mapMetaheader(metaHeader, newInstanceUid) {
 
 // src/curateDict.ts
 var import_lodash4 = __toESM(require_lodash(), 1);
-function curateDict(inputFilePath, inputFileIndex, dicomData, mappingOptions) {
+function curateDict(inputFilePath, dicomData, mappingOptions) {
   const [naturalData, mapResults] = collectMappings(
     inputFilePath,
-    inputFileIndex,
     dicomData,
     mappingOptions
   );
@@ -81291,7 +81310,6 @@ async function loadS3Client() {
 // src/curateOne.ts
 async function curateOne({
   fileInfo,
-  fileIndex = 0,
   outputTarget,
   mappingOptions,
   hashMethod,
@@ -81461,12 +81479,7 @@ async function curateOne({
     };
     return mapResults;
   }
-  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(
-    `${fileInfo.path}/${fileInfo.name}`,
-    fileIndex,
-    dicomData,
-    mappingOptions
-  );
+  const { dicomData: mappedDicomData, mapResults: clonedMapResults } = curateDict(`${fileInfo.path}/${fileInfo.name}`, dicomData, mappingOptions);
   clonedMapResults.mappingRequired = true;
   if (!preMappedHash) {
     try {
@@ -87356,9 +87369,8 @@ async function initializeFileListWorker() {
     (event) => {
       switch (event.data.response) {
         case "file": {
-          const { fileIndex, fileInfo, previousFileInfo } = event.data;
+          const { fileInfo, previousFileInfo } = event.data;
           filesToProcess.push({
-            fileIndex,
             fileInfo,
             scanAnomalies: [],
             // Files sent to processing have no scan anomalies
@@ -87493,7 +87505,7 @@ async function getHttpOutputHeaders(outputTarget) {
 }
 async function dispatchMappingJobs() {
   while (filesToProcess.length > 0 && availableMappingWorkers.length > 0) {
-    const { fileInfo, fileIndex, previousFileInfo } = filesToProcess.pop();
+    const { fileInfo, previousFileInfo } = filesToProcess.pop();
     const mappingWorker = availableMappingWorkers.pop();
     const { outputTarget, hashMethod, ...mappingOptions } = (
       // Not partial anymore.
@@ -87502,7 +87514,6 @@ async function dispatchMappingJobs() {
     mappingWorker.postMessage({
       request: "apply",
       fileInfo: await getHttpInputHeaders(fileInfo),
-      fileIndex,
       outputTarget: await getHttpOutputHeaders(outputTarget),
       previousFileInfo,
       hashMethod,
@@ -87583,7 +87594,7 @@ async function collectMappingOptions(organizeOptions) {
   };
 }
 function queueFilesForMapping(organizeOptions) {
-  organizeOptions.inputFiles.forEach((inputFile, fileIndex) => {
+  organizeOptions.inputFiles.forEach((inputFile) => {
     const fileInfo = {
       path: "",
       name: inputFile.name,
@@ -87593,14 +87604,13 @@ function queueFilesForMapping(organizeOptions) {
     };
     filesToProcess.push({
       fileInfo,
-      fileIndex,
       scanAnomalies: []
     });
   });
   dispatchMappingJobs();
 }
 function queueUrlsForMapping(organizeOptions) {
-  organizeOptions.inputUrls.forEach((inputUrl, fileIndex) => {
+  organizeOptions.inputUrls.forEach((inputUrl) => {
     const fileInfo = {
       kind: "http",
       url: inputUrl,
@@ -87611,7 +87621,6 @@ function queueUrlsForMapping(organizeOptions) {
     };
     filesToProcess.push({
       fileInfo,
-      fileIndex,
       scanAnomalies: []
     });
   });

package/dist/esm/scanDirectoryWorker.js

@@ -37299,7 +37299,6 @@ async function scanS3Bucket(bucketOptions) {
       forcePathStyle: bucketOptions.forcePathStyle
     });
     let continuationToken = void 0;
-    let fileIndex = 0;
     do {
       const listCommand = new s32.ListObjectsV2Command({
         Bucket: bucketOptions.bucketName,
@@ -37314,7 +37313,6 @@ async function scanS3Bucket(bucketOptions) {
             const prev = previousIndex ? previousIndex[item.Key] : void 0;
             globalThis.postMessage({
               response: "file",
-              fileIndex: fileIndex++,
               fileInfo: {
                 size: item.Size,
                 name: item.Key,
@@ -37325,12 +37323,10 @@ async function scanS3Bucket(bucketOptions) {
               },
               previousFileInfo: prev
             });
-            fileIndex += 1;
           } else if (fileAnomalies.length > 0) {
             const prev = previousIndex ? previousIndex[item.Key] : void 0;
             globalThis.postMessage({
               response: "scanAnomalies",
-              fileIndex: fileIndex++,
               fileInfo: {
                 size: item.Size,
                 name: item.Key,
@@ -37359,26 +37355,17 @@ async function scanS3Bucket(bucketOptions) {
 }
 async function scanDirectory(dir) {
   async function traverse(dir2, prefix) {
-    const entries = [];
     for await (const entry of dir2.values()) {
-      entries.push(entry);
-    }
-    entries.sort((a4, b4) => a4.name.localeCompare(b4.name));
-    let fileIndex = 0;
-    for (const entry of entries) {
-      if (entry.kind === "file" && keepScanning) {
+      if (!keepScanning)
+        return;
+      if (entry.kind === "file") {
         const file = await entry.getFile();
         const fileAnomalies = [];
-        if (await shouldProcessFile(
-          file,
-          fileAnomalies,
-          `${prefix}/${entry.name}`
-        )) {
+        if (await shouldProcessFile(file, fileAnomalies, `${prefix}/${entry.name}`)) {
           const key = `${prefix}/${entry.name}`;
           const prev = previousIndex ? previousIndex[key] : void 0;
           globalThis.postMessage({
             response: "file",
-            fileIndex: fileIndex++,
             fileInfo: {
               path: prefix,
               name: entry.name,
@@ -37393,7 +37380,6 @@ async function scanDirectory(dir) {
           const prev = previousIndex ? previousIndex[key] : void 0;
           globalThis.postMessage({
             response: "scanAnomalies",
-            fileIndex: fileIndex++,
             fileInfo: {
               path: prefix,
               name: entry.name,
@@ -37405,7 +37391,7 @@ async function scanDirectory(dir) {
             previousFileInfo: prev
           });
         }
-      } else if (entry.kind === "directory" && keepScanning) {
+      } else if (entry.kind === "directory") {
         await traverse(
           entry,
           prefix + "/" + entry.name
@@ -37430,10 +37416,10 @@ async function scanDirectoryNode(dirPath) {
   const path = await import("path");
   async function traverse(currentPath, prefix) {
     const entries = await fs.readdir(currentPath, { withFileTypes: true });
-    entries.sort((a4, b4) => a4.name.localeCompare(b4.name));
-    let fileIndex = 0;
     for (const entry of entries) {
-      if (entry.isFile() && keepScanning) {
+      if (!keepScanning)
+        return;
+      if (entry.isFile()) {
         const filePath = path.join(currentPath, entry.name);
         const stats = await fs.stat(filePath);
         const fileAnomalies = [];
@@ -37446,7 +37432,6 @@ async function scanDirectoryNode(dirPath) {
         )) {
           globalThis.postMessage({
             response: "file",
-            fileIndex: fileIndex++,
             fileInfo: {
               path: prefix,
               name: entry.name,
@@ -37458,7 +37443,6 @@ async function scanDirectoryNode(dirPath) {
         } else if (fileAnomalies.length > 0) {
           globalThis.postMessage({
             response: "scanAnomalies",
-            fileIndex: fileIndex++,
             fileInfo: {
               path: prefix,
               name: entry.name,
@@ -37469,7 +37453,7 @@ async function scanDirectoryNode(dirPath) {
             anomalies: fileAnomalies
           });
         }
-      } else if (entry.isDirectory() && keepScanning) {
+      } else if (entry.isDirectory()) {
         await traverse(
           path.join(currentPath, entry.name),
           prefix + "/" + entry.name

package/dist/types/applyMappingsWorker.d.ts

@@ -2,7 +2,6 @@ import { type TFileInfo, type TSerializedMappingOptions, type THTTPOptions, type
 export type MappingRequest = {
     request: 'apply';
     fileInfo: TFileInfo;
-    fileIndex: number;
     outputTarget?: {
         http?: THTTPOptions;
         directory?: FileSystemDirectoryHandle | string;

package/dist/types/collectMappings.d.ts

@@ -1,3 +1,3 @@
 import type { TMappingOptions, TMapResults } from './types';
 import type { TDicomData, TNaturalData } from 'dcmjs';
-export default function collectMappings(inputFilePath: string, inputFileIndex: number, dicomData: TDicomData, mappingOptions: TMappingOptions): [TNaturalData, TMapResults];
+export default function collectMappings(inputFilePath: string, dicomData: TDicomData, mappingOptions: TMappingOptions): [TNaturalData, TMapResults];

package/dist/types/curateDict.d.ts

@@ -1,7 +1,7 @@
 import * as dcmjs from 'dcmjs';
 import type { TDicomData } from 'dcmjs';
 import type { TMappingOptions } from './types';
-export default function curateDict(inputFilePath: string, inputFileIndex: number, dicomData: TDicomData, mappingOptions: TMappingOptions): {
+export default function curateDict(inputFilePath: string, dicomData: TDicomData, mappingOptions: TMappingOptions): {
     dicomData: dcmjs.data.DicomDict;
     mapResults: import("./types").TMapResults;
 };

package/dist/types/curateOne.d.ts

@@ -1,7 +1,6 @@
 import type { TFileInfo, THashMethod, THTTPOptions, TMappingOptions, TMapResults, TS3BucketOptions } from './types';
 export type TCurateOneArgs = {
     fileInfo: TFileInfo;
-    fileIndex?: number;
     outputTarget: {
         http?: THTTPOptions;
         s3?: TS3BucketOptions;
@@ -18,6 +17,6 @@ export type TCurateOneArgs = {
         postMappedHash?: string;
     } | undefined;
 };
-export declare function curateOne({ fileInfo, fileIndex, outputTarget, mappingOptions, hashMethod, previousSourceFileInfo, previousMappedFileInfo, }: TCurateOneArgs): Promise<Omit<Partial<TMapResults>, 'anomalies'> & {
+export declare function curateOne({ fileInfo, outputTarget, mappingOptions, hashMethod, previousSourceFileInfo, previousMappedFileInfo, }: TCurateOneArgs): Promise<Omit<Partial<TMapResults>, 'anomalies'> & {
     anomalies: TMapResults['anomalies'];
 }>;

package/dist/types/scanDirectoryWorker.d.ts

@@ -2,7 +2,6 @@ import type { TFileInfo, TFileInfoIndex, TS3BucketOptions } from './types';
 export {};
 export type FileScanMsg = {
     response: 'file';
-    fileIndex: number;
     fileInfo: TFileInfo;
     previousFileInfo?: {
         size?: number;
@@ -11,7 +10,6 @@ export type FileScanMsg = {
     };
 } | {
     response: 'scanAnomalies';
-    fileIndex: number;
     fileInfo: TFileInfo;
     anomalies: string[];
     previousFileInfo?: {