dicom-curate 0.8.4 → 0.9.0

package/README.md

@@ -69,7 +69,7 @@ If `outputDirectory` is omitted, output `Blob`s will be passed to the `onProgres
 You can also call `curateOne` directly and receive a promise with the mapped blob:
 
 ```ts
-import { curateOne, extractColumnMappings, clearCaches } from 'dicom-curate'
+import { curateOne, extractColumnMappings } from 'dicom-curate'
 
 // Data prep responsibility for optional table is with caller
 const columnMappings = extractColumnMappings([
@@ -81,9 +81,6 @@ curateOne({
   fileInfo, // path, name, size, kind, blob
   mappingOptions: { curationSpec, columnMappings },
 })
-
-// Cache clean-up responsibility, e.g. for consistent UID mapping in `retainUIDsOption: 'Off'` is with caller
-clearCaches()
 ```
 
 An example DICOM curation function:
@@ -229,7 +226,7 @@ dicom-curate
   - 'retainLongitudinalTemporalInformationOptions': this considers all temporal attributes (DA, TM, DT), as described as a possible approach in PS3.15E.
     Possible values are 'Full' (keep all temporal info intact), 'Off' (remove all temporal attributes or add defaults per PS3.15E), or 'Offset' (move all temporal attributes by a duration. An ISO-8601 compliant duration `dateOffset` parameter must be passed).
   - 'retainDeviceIdentityOption': true or false. If true, overrides `retainLongitudinalTemporalInformationOptions` for the respective attributes to keep.
-  - 'retainUIDsOption': 'On', 'Off', or 'Hashed'.
+  - 'retainUIDsOption': 'On', 'Hashed'.
     - If 'On', maintain all UIDs.
     - If 'Off', replaces instance UIDs with arbitrary new UIDs, maintaining referential integrity within a single run.
       - maximum protection
@@ -239,6 +236,7 @@ dicom-curate
       - maintains referential integrity even if de-identifying data in separate, or decentralized, batches
       - use if the risk of re-identifying by UID is not bigger than the risk of re-identifying by PixelData
       - do not use if you want to specifically protect UIDs from an auxiliary knowledge attack, e.g. an attacker that knows possible input UIDs
+    - For compatibility, the 'Off' option is now treated the same way as 'Hashed'.
     - There are more instance UIDs in part PS3.06 than described in PS3.15E for protection, therefore this option identifies the following uids for protection: 1. All instance UIDs per PS3.15E, 2. Any additional UIDs with a value not well-known in DICOM, per table PS3.06A (Registry of DICOM Unique Identifiers). This protects instance UIDs but also private class UIDs, which is intentional.
   - 'retainSafePrivateOption': 'Quarantine' or 'Off'. If 'Quarantine', keeps all private tags but creates a quarantine log for manual review
   - 'retainInstitutionIdentityOption': true or false

package/dist/esm/applyMappingsWorker.js

@@ -4559,17 +4559,17 @@ var require_lodash = __commonJS({
           if (typeof func != "function" || resolver != null && typeof resolver != "function") {
             throw new TypeError2(FUNC_ERROR_TEXT);
           }
-          var memoized2 = function() {
-            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized2.cache;
+          var memoized = function() {
+            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized.cache;
             if (cache.has(key)) {
               return cache.get(key);
             }
             var result2 = func.apply(this, args);
-            memoized2.cache = cache.set(key, result2) || cache;
+            memoized.cache = cache.set(key, result2) || cache;
             return result2;
           };
-          memoized2.cache = new (memoize.Cache || MapCache)();
-          return memoized2;
+          memoized.cache = new (memoize.Cache || MapCache)();
+          return memoized;
         }
         memoize.Cache = MapCache;
         function negate2(predicate) {
@@ -25190,82 +25190,6 @@ function hashUid(uid) {
   return uuidBasedUIDPrefix + hashedString;
 }
 
-// node_modules/.pnpm/memize@2.1.1/node_modules/memize/dist/index.js
-function memize(fn, options) {
-  var size = 0;
-  var head;
-  var tail;
-  options = options || {};
-  function memoized2() {
-    var node = head, len2 = arguments.length, args, i;
-    searchCache:
-      while (node) {
-        if (node.args.length !== arguments.length) {
-          node = node.next;
-          continue;
-        }
-        for (i = 0; i < len2; i++) {
-          if (node.args[i] !== arguments[i]) {
-            node = node.next;
-            continue searchCache;
-          }
-        }
-        if (node !== head) {
-          if (node === tail) {
-            tail = node.prev;
-          }
-          node.prev.next = node.next;
-          if (node.next) {
-            node.next.prev = node.prev;
-          }
-          node.next = head;
-          node.prev = null;
-          head.prev = node;
-          head = node;
-        }
-        return node.val;
-      }
-    args = new Array(len2);
-    for (i = 0; i < len2; i++) {
-      args[i] = arguments[i];
-    }
-    node = {
-      args,
-      // Generate the result from original function
-      val: fn.apply(null, args)
-    };
-    if (head) {
-      head.prev = node;
-      node.next = head;
-    } else {
-      tail = node;
-    }
-    if (size === /** @type {MemizeOptions} */
-    options.maxSize) {
-      tail = /** @type {MemizeCacheNode} */
-      tail.prev;
-      tail.next = null;
-    } else {
-      size++;
-    }
-    head = node;
-    return node.val;
-  }
-  memoized2.clear = function() {
-    head = null;
-    tail = null;
-    size = 0;
-  };
-  return memoized2;
-}
-
-// src/replaceUid.ts
-function replaceUid(uid) {
-  return data.DicomMetaDictionary.uid();
-}
-var memoized = memize(replaceUid);
-var replaceUid_default = memoized;
-
 // src/config/dicom/elementNamesToAlwaysKeep.ts
 var elementNamesToAlwaysKeep = [
   "LengthToEnd",
@@ -36199,7 +36123,7 @@ function removeRetiredPrefix(name) {
   return name.startsWith("RETIRED_") ? name.slice(8) : name;
 }
 function protectUid(uid, retainUIDsOption) {
-  return retainUIDsOption === "Hashed" ? hashUid(uid) : replaceUid_default(uid);
+  return hashUid(uid);
 }
 var elementNamesToAlwaysKeepSet = new Set(elementNamesToAlwaysKeep);
 var ps315EElements2 = ps315EElements.map((elm) => {
@@ -36697,43 +36621,9 @@ function getCsvMapping(columnMappings, mapping, mappingKey, value) {
   return mapping[mappingKey].replace(columnMappings.rows[rowIdx]);
 }
 
-// src/UniqueNumbers.ts
-function UniqueNumbers(padding = 5) {
-  let groupCounters = {};
-  function getUniqueNumberInGroup2(groupingId) {
-    groupCounters[groupingId] = groupCounters[groupingId] ? groupCounters[groupingId] + 1 : 1;
-    return groupCounters[groupingId].toString().padStart(padding, "0");
-  }
-  function clearUniqueNumberCache2() {
-    groupCounters = {};
-  }
-  return { getUniqueNumberInGroup: getUniqueNumberInGroup2, clearUniqueNumberCache: clearUniqueNumberCache2 };
-}
-
 // src/getParser.ts
 var FILEBASENAME = Symbol("fileBasename");
 var FILENAME = Symbol("filename");
-var { getUniqueNumberInGroup, clearUniqueNumberCache } = UniqueNumbers(6);
-var { isUniqueInGroup, clearUniqueInGroupCache } = /* @__PURE__ */ function() {
-  let cache = /* @__PURE__ */ new Set();
-  let lastGroupId = "";
-  return {
-    isUniqueInGroup(value, groupId) {
-      if (groupId !== lastGroupId) {
-        cache = /* @__PURE__ */ new Set();
-        lastGroupId = groupId;
-      }
-      if (cache.has(value)) {
-        return false;
-      }
-      cache.add(value);
-      return true;
-    },
-    clearUniqueInGroupCache() {
-      cache = /* @__PURE__ */ new Set();
-    }
-  };
-}();
 function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOptions, columnMappings, additionalData) {
   function protectUid2(uid) {
     let protectedUid = uid;
@@ -36783,13 +36673,6 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
     return typeof value === "undefined" || value === "";
   }
   return {
-    // This function enables errors like:
-    // [
-    //   'Duplicate Instance Number(s)',
-    //   !parser.isUniqueInGroup(instanceNumber, seriesUid),
-    // ],
-    isUniqueInGroup,
-    getUniqueNumberInGroup,
     getFrom,
     getFilePathComp,
     getMapping,

package/dist/esm/collectMappings.js

@@ -4559,17 +4559,17 @@ var require_lodash = __commonJS({
           if (typeof func != "function" || resolver != null && typeof resolver != "function") {
             throw new TypeError2(FUNC_ERROR_TEXT);
           }
-          var memoized2 = function() {
-            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized2.cache;
+          var memoized = function() {
+            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized.cache;
             if (cache.has(key)) {
               return cache.get(key);
             }
             var result2 = func.apply(this, args);
-            memoized2.cache = cache.set(key, result2) || cache;
+            memoized.cache = cache.set(key, result2) || cache;
             return result2;
           };
-          memoized2.cache = new (memoize.Cache || MapCache)();
-          return memoized2;
+          memoized.cache = new (memoize.Cache || MapCache)();
+          return memoized;
         }
         memoize.Cache = MapCache;
         function negate2(predicate) {
@@ -18875,82 +18875,6 @@ function hashUid(uid) {
   return uuidBasedUIDPrefix + hashedString;
 }
 
-// node_modules/.pnpm/memize@2.1.1/node_modules/memize/dist/index.js
-function memize(fn, options) {
-  var size = 0;
-  var head;
-  var tail;
-  options = options || {};
-  function memoized2() {
-    var node = head, len2 = arguments.length, args, i;
-    searchCache:
-      while (node) {
-        if (node.args.length !== arguments.length) {
-          node = node.next;
-          continue;
-        }
-        for (i = 0; i < len2; i++) {
-          if (node.args[i] !== arguments[i]) {
-            node = node.next;
-            continue searchCache;
-          }
-        }
-        if (node !== head) {
-          if (node === tail) {
-            tail = node.prev;
-          }
-          node.prev.next = node.next;
-          if (node.next) {
-            node.next.prev = node.prev;
-          }
-          node.next = head;
-          node.prev = null;
-          head.prev = node;
-          head = node;
-        }
-        return node.val;
-      }
-    args = new Array(len2);
-    for (i = 0; i < len2; i++) {
-      args[i] = arguments[i];
-    }
-    node = {
-      args,
-      // Generate the result from original function
-      val: fn.apply(null, args)
-    };
-    if (head) {
-      head.prev = node;
-      node.next = head;
-    } else {
-      tail = node;
-    }
-    if (size === /** @type {MemizeOptions} */
-    options.maxSize) {
-      tail = /** @type {MemizeCacheNode} */
-      tail.prev;
-      tail.next = null;
-    } else {
-      size++;
-    }
-    head = node;
-    return node.val;
-  }
-  memoized2.clear = function() {
-    head = null;
-    tail = null;
-    size = 0;
-  };
-  return memoized2;
-}
-
-// src/replaceUid.ts
-function replaceUid(uid) {
-  return data.DicomMetaDictionary.uid();
-}
-var memoized = memize(replaceUid);
-var replaceUid_default = memoized;
-
 // src/config/dicom/elementNamesToAlwaysKeep.ts
 var elementNamesToAlwaysKeep = [
   "LengthToEnd",
@@ -29870,7 +29794,7 @@ function removeRetiredPrefix(name) {
   return name.startsWith("RETIRED_") ? name.slice(8) : name;
 }
 function protectUid(uid, retainUIDsOption) {
-  return retainUIDsOption === "Hashed" ? hashUid(uid) : replaceUid_default(uid);
+  return hashUid(uid);
 }
 var elementNamesToAlwaysKeepSet = new Set(elementNamesToAlwaysKeep);
 var ps315EElements2 = ps315EElements.map((elm) => {
@@ -30368,43 +30292,9 @@ function getCsvMapping(columnMappings, mapping, mappingKey, value) {
   return mapping[mappingKey].replace(columnMappings.rows[rowIdx]);
 }
 
-// src/UniqueNumbers.ts
-function UniqueNumbers(padding = 5) {
-  let groupCounters = {};
-  function getUniqueNumberInGroup2(groupingId) {
-    groupCounters[groupingId] = groupCounters[groupingId] ? groupCounters[groupingId] + 1 : 1;
-    return groupCounters[groupingId].toString().padStart(padding, "0");
-  }
-  function clearUniqueNumberCache2() {
-    groupCounters = {};
-  }
-  return { getUniqueNumberInGroup: getUniqueNumberInGroup2, clearUniqueNumberCache: clearUniqueNumberCache2 };
-}
-
 // src/getParser.ts
 var FILEBASENAME = Symbol("fileBasename");
 var FILENAME = Symbol("filename");
-var { getUniqueNumberInGroup, clearUniqueNumberCache } = UniqueNumbers(6);
-var { isUniqueInGroup, clearUniqueInGroupCache } = /* @__PURE__ */ function() {
-  let cache = /* @__PURE__ */ new Set();
-  let lastGroupId = "";
-  return {
-    isUniqueInGroup(value, groupId) {
-      if (groupId !== lastGroupId) {
-        cache = /* @__PURE__ */ new Set();
-        lastGroupId = groupId;
-      }
-      if (cache.has(value)) {
-        return false;
-      }
-      cache.add(value);
-      return true;
-    },
-    clearUniqueInGroupCache() {
-      cache = /* @__PURE__ */ new Set();
-    }
-  };
-}();
 function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOptions, columnMappings, additionalData) {
   function protectUid2(uid) {
     let protectedUid = uid;
@@ -30454,13 +30344,6 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
     return typeof value === "undefined" || value === "";
   }
   return {
-    // This function enables errors like:
-    // [
-    //   'Duplicate Instance Number(s)',
-    //   !parser.isUniqueInGroup(instanceNumber, seriesUid),
-    // ],
-    isUniqueInGroup,
-    getUniqueNumberInGroup,
     getFrom,
     getFilePathComp,
     getMapping,

package/dist/esm/composeSpecs.js

@@ -4559,17 +4559,17 @@ var require_lodash = __commonJS({
           if (typeof func != "function" || resolver != null && typeof resolver != "function") {
             throw new TypeError2(FUNC_ERROR_TEXT);
           }
-          var memoized2 = function() {
-            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized2.cache;
+          var memoized = function() {
+            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized.cache;
             if (cache.has(key)) {
               return cache.get(key);
             }
             var result2 = func.apply(this, args);
-            memoized2.cache = cache.set(key, result2) || cache;
+            memoized.cache = cache.set(key, result2) || cache;
             return result2;
           };
-          memoized2.cache = new (memoize.Cache || MapCache)();
-          return memoized2;
+          memoized.cache = new (memoize.Cache || MapCache)();
+          return memoized;
         }
         memoize.Cache = MapCache;
         function negate2(predicate) {
@@ -18813,81 +18813,6 @@ Tag.setDicomMessageClass(DicomMessage);
 // src/hashUid.ts
 var import_js_sha256 = __toESM(require_sha256(), 1);
 
-// node_modules/.pnpm/memize@2.1.1/node_modules/memize/dist/index.js
-function memize(fn, options) {
-  var size = 0;
-  var head;
-  var tail;
-  options = options || {};
-  function memoized2() {
-    var node = head, len2 = arguments.length, args, i;
-    searchCache:
-      while (node) {
-        if (node.args.length !== arguments.length) {
-          node = node.next;
-          continue;
-        }
-        for (i = 0; i < len2; i++) {
-          if (node.args[i] !== arguments[i]) {
-            node = node.next;
-            continue searchCache;
-          }
-        }
-        if (node !== head) {
-          if (node === tail) {
-            tail = node.prev;
-          }
-          node.prev.next = node.next;
-          if (node.next) {
-            node.next.prev = node.prev;
-          }
-          node.next = head;
-          node.prev = null;
-          head.prev = node;
-          head = node;
-        }
-        return node.val;
-      }
-    args = new Array(len2);
-    for (i = 0; i < len2; i++) {
-      args[i] = arguments[i];
-    }
-    node = {
-      args,
-      // Generate the result from original function
-      val: fn.apply(null, args)
-    };
-    if (head) {
-      head.prev = node;
-      node.next = head;
-    } else {
-      tail = node;
-    }
-    if (size === /** @type {MemizeOptions} */
-    options.maxSize) {
-      tail = /** @type {MemizeCacheNode} */
-      tail.prev;
-      tail.next = null;
-    } else {
-      size++;
-    }
-    head = node;
-    return node.val;
-  }
-  memoized2.clear = function() {
-    head = null;
-    tail = null;
-    size = 0;
-  };
-  return memoized2;
-}
-
-// src/replaceUid.ts
-function replaceUid(uid) {
-  return data.DicomMetaDictionary.uid();
-}
-var memoized = memize(replaceUid);
-
 // src/config/dicom/elementNamesToAlwaysKeep.ts
 var elementNamesToAlwaysKeep = [
   "LengthToEnd",

package/dist/esm/config/sample2PassCurationSpecification.js

@@ -139,10 +139,6 @@ function sample2PassCurationSpecification() {
         // 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")

package/dist/esm/config/sampleCompositeSpecification.js

@@ -125,10 +125,6 @@ function composedSpec() {
               // 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")

package/dist/esm/curateDict.js

@@ -4559,17 +4559,17 @@ var require_lodash = __commonJS({
           if (typeof func != "function" || resolver != null && typeof resolver != "function") {
             throw new TypeError2(FUNC_ERROR_TEXT);
           }
-          var memoized2 = function() {
-            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized2.cache;
+          var memoized = function() {
+            var args = arguments, key = resolver ? resolver.apply(this, args) : args[0], cache = memoized.cache;
             if (cache.has(key)) {
               return cache.get(key);
             }
             var result2 = func.apply(this, args);
-            memoized2.cache = cache.set(key, result2) || cache;
+            memoized.cache = cache.set(key, result2) || cache;
             return result2;
           };
-          memoized2.cache = new (memoize.Cache || MapCache)();
-          return memoized2;
+          memoized.cache = new (memoize.Cache || MapCache)();
+          return memoized;
         }
         memoize.Cache = MapCache;
         function negate2(predicate) {
@@ -18875,82 +18875,6 @@ function hashUid(uid) {
   return uuidBasedUIDPrefix + hashedString;
 }
 
-// node_modules/.pnpm/memize@2.1.1/node_modules/memize/dist/index.js
-function memize(fn, options) {
-  var size = 0;
-  var head;
-  var tail;
-  options = options || {};
-  function memoized2() {
-    var node = head, len2 = arguments.length, args, i;
-    searchCache:
-      while (node) {
-        if (node.args.length !== arguments.length) {
-          node = node.next;
-          continue;
-        }
-        for (i = 0; i < len2; i++) {
-          if (node.args[i] !== arguments[i]) {
-            node = node.next;
-            continue searchCache;
-          }
-        }
-        if (node !== head) {
-          if (node === tail) {
-            tail = node.prev;
-          }
-          node.prev.next = node.next;
-          if (node.next) {
-            node.next.prev = node.prev;
-          }
-          node.next = head;
-          node.prev = null;
-          head.prev = node;
-          head = node;
-        }
-        return node.val;
-      }
-    args = new Array(len2);
-    for (i = 0; i < len2; i++) {
-      args[i] = arguments[i];
-    }
-    node = {
-      args,
-      // Generate the result from original function
-      val: fn.apply(null, args)
-    };
-    if (head) {
-      head.prev = node;
-      node.next = head;
-    } else {
-      tail = node;
-    }
-    if (size === /** @type {MemizeOptions} */
-    options.maxSize) {
-      tail = /** @type {MemizeCacheNode} */
-      tail.prev;
-      tail.next = null;
-    } else {
-      size++;
-    }
-    head = node;
-    return node.val;
-  }
-  memoized2.clear = function() {
-    head = null;
-    tail = null;
-    size = 0;
-  };
-  return memoized2;
-}
-
-// src/replaceUid.ts
-function replaceUid(uid) {
-  return data.DicomMetaDictionary.uid();
-}
-var memoized = memize(replaceUid);
-var replaceUid_default = memoized;
-
 // src/config/dicom/elementNamesToAlwaysKeep.ts
 var elementNamesToAlwaysKeep = [
   "LengthToEnd",
@@ -29884,7 +29808,7 @@ function removeRetiredPrefix(name) {
   return name.startsWith("RETIRED_") ? name.slice(8) : name;
 }
 function protectUid(uid, retainUIDsOption) {
-  return retainUIDsOption === "Hashed" ? hashUid(uid) : replaceUid_default(uid);
+  return hashUid(uid);
 }
 var elementNamesToAlwaysKeepSet = new Set(elementNamesToAlwaysKeep);
 var ps315EElements2 = ps315EElements.map((elm) => {
@@ -30382,43 +30306,9 @@ function getCsvMapping(columnMappings, mapping, mappingKey, value) {
   return mapping[mappingKey].replace(columnMappings.rows[rowIdx]);
 }
 
-// src/UniqueNumbers.ts
-function UniqueNumbers(padding = 5) {
-  let groupCounters = {};
-  function getUniqueNumberInGroup2(groupingId) {
-    groupCounters[groupingId] = groupCounters[groupingId] ? groupCounters[groupingId] + 1 : 1;
-    return groupCounters[groupingId].toString().padStart(padding, "0");
-  }
-  function clearUniqueNumberCache2() {
-    groupCounters = {};
-  }
-  return { getUniqueNumberInGroup: getUniqueNumberInGroup2, clearUniqueNumberCache: clearUniqueNumberCache2 };
-}
-
 // src/getParser.ts
 var FILEBASENAME = Symbol("fileBasename");
 var FILENAME = Symbol("filename");
-var { getUniqueNumberInGroup, clearUniqueNumberCache } = UniqueNumbers(6);
-var { isUniqueInGroup, clearUniqueInGroupCache } = /* @__PURE__ */ function() {
-  let cache = /* @__PURE__ */ new Set();
-  let lastGroupId = "";
-  return {
-    isUniqueInGroup(value, groupId) {
-      if (groupId !== lastGroupId) {
-        cache = /* @__PURE__ */ new Set();
-        lastGroupId = groupId;
-      }
-      if (cache.has(value)) {
-        return false;
-      }
-      cache.add(value);
-      return true;
-    },
-    clearUniqueInGroupCache() {
-      cache = /* @__PURE__ */ new Set();
-    }
-  };
-}();
 function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOptions, columnMappings, additionalData) {
   function protectUid2(uid) {
     let protectedUid = uid;
@@ -30468,13 +30358,6 @@ function getParser(inputPathPattern, inputFilePath, naturalData, dicomPS315EOpti
     return typeof value === "undefined" || value === "";
   }
   return {
-    // This function enables errors like:
-    // [
-    //   'Duplicate Instance Number(s)',
-    //   !parser.isUniqueInGroup(instanceNumber, seriesUid),
-    // ],
-    isUniqueInGroup,
-    getUniqueNumberInGroup,
     getFrom,
     getFilePathComp,
     getMapping,