dicom-curate 0.38.1 → 0.39.0

package/dist/esm/applyMappingsWorker.js

@@ -86083,14 +86083,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -86183,12 +86185,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");

package/dist/esm/collectMappings.js

@@ -34147,14 +34147,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -34247,12 +34249,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");

package/dist/esm/config/sampleSummaryCurationSpecification.js

@@ -0,0 +1,40 @@
+// src/config/sampleSummaryCurationSpecification.ts
+function sampleSummaryCurationSpecification() {
+  const hostProps = { protocolNumber: "Demo" };
+  return {
+    inputPathPattern: "any",
+    additionalData: {
+      type: "listing",
+      collect: (parser) => ({
+        lookups: {
+          PerSeries: parser.getDicom("SeriesInstanceUID")
+        },
+        info: [
+          ["StudyInstanceUID", parser.getDicom("StudyInstanceUID")],
+          ["SeriesInstanceUID", parser.getDicom("SeriesInstanceUID")],
+          ["SeriesDescription", parser.getDicom("SeriesDescription")],
+          ["FolderX", parser.getFilePathComp(0)],
+          ["FolderY", parser.getFilePathComp(1)],
+          ["SOPInstanceUIDs", parser.getDicom("SOPInstanceUID"), "list"]
+        ],
+        collect: []
+      }),
+      output: {
+        path: "reports/series_summary.csv",
+        rowKey: "PerSeries"
+      }
+      // No `mapping` => single pass, write CSV summary instead of DICOMs.
+    },
+    version: "3.0",
+    hostProps,
+    // No de-identification or header modification in summary mode.
+    dicomPS315EOptions: "Off",
+    modifyDicomHeader: () => ({}),
+    // Unused when consumers run with skipModifications.
+    outputFilePathComponents: () => [],
+    errors: () => []
+  };
+}
+export {
+  sampleSummaryCurationSpecification
+};

package/dist/esm/curateDict.js

@@ -34164,14 +34164,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -34264,12 +34266,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");

package/dist/esm/curateOne.js

@@ -79792,14 +79792,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -79892,12 +79894,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");

package/dist/esm/getParser.js

@@ -32798,14 +32798,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);

package/dist/esm/index.js

@@ -87646,14 +87646,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -87746,12 +87748,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");
@@ -95006,7 +95008,7 @@ async function collectMappingOptions(organizeOptions) {
     ));
   }
   let columnMappings;
-  if (organizeOptions.table && additionalData) {
+  if (organizeOptions.table && additionalData?.mapping) {
     columnMappings = extractColumnMappings(
       organizeOptions.table,
       additionalData.mapping
@@ -95017,6 +95019,11 @@ async function collectMappingOptions(organizeOptions) {
   const skipValidation = organizeOptions.skipValidation ?? false;
   const hashMethod = organizeOptions.hashMethod;
   const hashPartSize = organizeOptions.hashPartSize;
+  if (additionalData?.type === "listing" && additionalData.output && !skipWrite) {
+    throw new Error(
+      "additionalData.output (summary-table mode) requires skipWrite: true \u2014 summary specs produce a CSV summary and no curated output."
+    );
+  }
   const dateOffset = organizeOptions.dateOffset;
   if (requiresDateOffset(deIdOpts) && !dateOffset?.match(iso8601)) {
     throw new Error(

package/dist/esm/mappingWorkerPool.js

@@ -86083,14 +86083,16 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
   function getFrom(source, identifier) {
     return source === "dicom" ? getDicom(identifier) : getFilePathComp(identifier);
   }
-  const getMapping = !additionalData || !columnMappings ? void 0 : (
+  const getMapping = !additionalData || !additionalData.mapping || !columnMappings ? void 0 : (
     // key: one of the keys defined in the `mapping` object
-    function getMapping2(key) {
-      const { mapping } = additionalData;
-      const { value: valueFn } = mapping[key];
-      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-      return getCsvMapping(columnMappings, mapping, key, value);
-    }
+    (() => {
+      const mapping = additionalData.mapping;
+      return function getMapping2(key) {
+        const { value: valueFn } = mapping[key];
+        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+        return getCsvMapping(columnMappings, mapping, key, value);
+      };
+    })()
   );
   function missingDicom(attrName) {
     const value = getDicom(attrName);
@@ -86183,12 +86185,12 @@ function collectMappings(inputFilePath, dicomData, mappingOptions) {
     });
     const cleanedInfo = info.map((item) => {
       if (Array.isArray(item[1]) && item[1].length === 1 && typeof item[1][0] === "object" && "Alphabetic" in item[1][0] && /^\d+$/.test(item[1][0].Alphabetic)) {
-        return [item[0], item[1][0].Alphabetic];
+        return item.length > 2 ? [item[0], item[1][0].Alphabetic, item[2]] : [item[0], item[1][0].Alphabetic];
       } else {
         return item;
       }
     });
-    mapResults.listing = { info: cleanedInfo, collectByValue };
+    mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
   }
   if (!mappingOptions.skipModifications) {
     mapResults.outputFilePath = finalSpec.outputFilePathComponents(parser).join("/");

package/dist/types/config/sampleSummaryCurationSpecification.d.ts

@@ -0,0 +1,2 @@
+import type { TCurationSpecification } from '../types';
+export declare function sampleSummaryCurationSpecification(): TCurationSpecification;

package/dist/types/types.d.ts

@@ -189,6 +189,9 @@ export type TMapResults = {
     listing?: {
         info: TMappingTwoPassInfo[];
         collectByValue: [...TMappingTwoPassCollect, string | number][];
+        lookups: {
+            [lookupField: string]: string;
+        };
     };
     mappedBlob?: Blob;
     outputUpload?: {
@@ -236,13 +239,19 @@ export type TPostExcludeParser = TParser & {
 type TMappingInputDirect = {
     type: 'load';
     collect: Record<string, RegExp | string[]>;
+    mapping: TMappedValues;
 };
-type TMappingTwoPassInfo = [name: string, value: string];
+type TMappingTwoPassInfoMode = 'list';
+type TMappingTwoPassInfo = [name: string, value: string] | [name: string, value: string, mode: TMappingTwoPassInfoMode];
 type TMappingTwoPassCollect = [
     value: string,
     format: RegExp | string[],
     lookupField: string
 ];
+type TSummaryOutput = {
+    path: string;
+    rowKey: string;
+};
 type TMappingInputTwoPass = {
     type: 'listing';
     collect: (parser: Pick<TParser, 'getDicom' | 'getFilePathComp' | 'getFrom'>) => {
@@ -252,7 +261,13 @@ type TMappingInputTwoPass = {
         info: TMappingTwoPassInfo[];
         collect: TMappingTwoPassCollect[];
     };
-};
+} & ({
+    mapping: TMappedValues;
+    output?: never;
+} | {
+    output: TSummaryOutput;
+    mapping?: never;
+});
 type HPPrimitive = string | number | boolean | null | RegExp | ((...args: any[]) => any);
 export type HPValue = HPPrimitive | {
     [k: string]: HPValue;
@@ -269,9 +284,7 @@ export type TCurationSpecification<THost extends HostProps = HostProps> = {
     dicomPS315EOptions: TPs315Options | 'Off';
     inputPathPattern: string;
     hostProps: THost;
-    additionalData?: {
-        mapping: TMappedValues;
-    } & (TMappingInputDirect | TMappingInputTwoPass);
+    additionalData?: TMappingInputDirect | TMappingInputTwoPass;
     excludedFiletypes?: string[];
     preExclude?: (parser: TParser) => boolean;
     postExclude?: (parser: TPostExcludeParser) => boolean;

package/dist/umd/dicom-curate.umd.js

@@ -53836,15 +53836,17 @@
                   ? getDicom(identifier)
                   : getFilePathComp(identifier);
           }
-          const getMapping = !additionalData || !columnMappings
+          const getMapping = !additionalData || !additionalData.mapping || !columnMappings
               ? undefined
               : // key: one of the keys defined in the `mapping` object
-                  function getMapping(key) {
-                      const { mapping } = additionalData;
-                      const { value: valueFn } = mapping[key];
-                      const value = valueFn({ getDicom, getFilePathComp, getFrom });
-                      return getCsvMapping(columnMappings, mapping, key, value);
-                  };
+                  (() => {
+                      const mapping = additionalData.mapping;
+                      return function getMapping(key) {
+                          const { value: valueFn } = mapping[key];
+                          const value = valueFn({ getDicom, getFilePathComp, getFrom });
+                          return getCsvMapping(columnMappings, mapping, key, value);
+                      };
+                  })();
           function missingDicom(attrName) {
               const value = getDicom(attrName);
               return typeof value === 'undefined' || value === '';
@@ -53933,20 +53935,23 @@
                   const lookupValue = lookups[lookupField];
                   return [...item, lookupValue];
               });
-              // FIXME: Bug in dcmjs
+              // FIXME: Bug in dcmjs. Flatten single-element PN arrays, preserving any
+              // optional aggregation mode marker (3rd tuple element) untouched.
               const cleanedInfo = info.map((item) => {
                   if (Array.isArray(item[1]) &&
                       item[1].length === 1 &&
                       typeof item[1][0] === 'object' &&
                       'Alphabetic' in item[1][0] &&
                       /^\d+$/.test(item[1][0].Alphabetic)) {
-                      return [item[0], item[1][0].Alphabetic];
+                      return (item.length > 2
+                          ? [item[0], item[1][0].Alphabetic, item[2]]
+                          : [item[0], item[1][0].Alphabetic]);
                   }
                   else {
                       return item;
                   }
               });
-              mapResults.listing = { info: cleanedInfo, collectByValue };
+              mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
           }
           if (!mappingOptions.skipModifications) {
               mapResults.outputFilePath = finalSpec
@@ -125428,15 +125433,17 @@
                 ? getDicom(identifier)
                 : getFilePathComp(identifier);
         }
-        const getMapping = !additionalData || !columnMappings
+        const getMapping = !additionalData || !additionalData.mapping || !columnMappings
             ? undefined
             : // key: one of the keys defined in the `mapping` object
-                function getMapping(key) {
-                    const { mapping } = additionalData;
-                    const { value: valueFn } = mapping[key];
-                    const value = valueFn({ getDicom, getFilePathComp, getFrom });
-                    return getCsvMapping(columnMappings, mapping, key, value);
-                };
+                (() => {
+                    const mapping = additionalData.mapping;
+                    return function getMapping(key) {
+                        const { value: valueFn } = mapping[key];
+                        const value = valueFn({ getDicom, getFilePathComp, getFrom });
+                        return getCsvMapping(columnMappings, mapping, key, value);
+                    };
+                })();
         function missingDicom(attrName) {
             const value = getDicom(attrName);
             return typeof value === 'undefined' || value === '';
@@ -125525,20 +125532,23 @@
                 const lookupValue = lookups[lookupField];
                 return [...item, lookupValue];
             });
-            // FIXME: Bug in dcmjs
+            // FIXME: Bug in dcmjs. Flatten single-element PN arrays, preserving any
+            // optional aggregation mode marker (3rd tuple element) untouched.
             const cleanedInfo = info.map((item) => {
                 if (Array.isArray(item[1]) &&
                     item[1].length === 1 &&
                     typeof item[1][0] === 'object' &&
                     'Alphabetic' in item[1][0] &&
                     /^\d+$/.test(item[1][0].Alphabetic)) {
-                    return [item[0], item[1][0].Alphabetic];
+                    return (item.length > 2
+                        ? [item[0], item[1][0].Alphabetic, item[2]]
+                        : [item[0], item[1][0].Alphabetic]);
                 }
                 else {
                     return item;
                 }
             });
-            mapResults.listing = { info: cleanedInfo, collectByValue };
+            mapResults.listing = { info: cleanedInfo, collectByValue, lookups };
         }
         if (!mappingOptions.skipModifications) {
             mapResults.outputFilePath = finalSpec
@@ -141144,7 +141154,7 @@
         // The need for mapping can come from additionalData or from the
         // retainLongitudinalTemporalInformationOptions option
         let columnMappings;
-        if (organizeOptions.table && additionalData) {
+        if (organizeOptions.table && additionalData?.mapping) {
             columnMappings = extractColumnMappings(organizeOptions.table, additionalData.mapping);
         }
         const skipWrite = organizeOptions.skipWrite ?? false;
@@ -141152,6 +141162,15 @@
         const skipValidation = organizeOptions.skipValidation ?? false;
         const hashMethod = organizeOptions.hashMethod;
         const hashPartSize = organizeOptions.hashPartSize;
+        // Summary-table mode (additionalData.output set) produces a CSV summary and
+        // no curated DICOMs, so it must run read-only. skipWrite is the option that
+        // actually prevents any file from being written/transferred (skipModifications
+        // only governs whether content is changed). Fail fast on misuse.
+        if (additionalData?.type === 'listing' &&
+            additionalData.output &&
+            !skipWrite) {
+            throw new Error('additionalData.output (summary-table mode) requires skipWrite: true — summary specs produce a CSV summary and no curated output.');
+        }
         const dateOffset = organizeOptions.dateOffset;
         if (requiresDateOffset(deIdOpts) && !dateOffset?.match(iso8601)) {
             throw new Error('When using "Offset" for retainLongitudinalTemporalInformationOptions, an iso8601 compatible dateOffset must be provided.');