Mercurial > hg > orthanc

changeset 784:efd0215736d9

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start of anonymization refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 02 May 2014 15:06:31 +0200
parents a60040857ce6
children 7cbed653476f
files OrthancServer/FromDcmtkBridge.cpp OrthancServer/FromDcmtkBridge.h UnitTestsSources/FromDcmtk.cpp
diffstat 3 files changed, 407 insertions(+), 60 deletions(-) [+]
line wrap: on
line diff
--- a/OrthancServer/FromDcmtkBridge.cpp	Fri May 02 12:59:05 2014 +0200
+++ b/OrthancServer/FromDcmtkBridge.cpp	Fri May 02 15:06:31 2014 +0200
@@ -1732,4 +1732,24 @@
       return false;
     }
   }
+
+
+  void ParsedDicomFile::SaveToFile(const std::string& path)
+  {
+    // TODO Avoid using a temporary memory buffer, write directly on disk
+    std::string content;
+    SaveToMemoryBuffer(content);
+    Toolbox::WriteFile(content, path);
+  }
+
+
+  ParsedDicomFile::ParsedDicomFile()
+  {
+    file_.reset(new DcmFileFormat);
+    Replace(DICOM_TAG_PATIENT_ID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Patient));
+    Replace(DICOM_TAG_STUDY_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Study));
+    Replace(DICOM_TAG_SERIES_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Series));
+    Replace(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Instance));
+  }
+
 }
--- a/OrthancServer/FromDcmtkBridge.h	Fri May 02 12:59:05 2014 +0200
+++ b/OrthancServer/FromDcmtkBridge.h	Fri May 02 15:06:31 2014 +0200
@@ -58,66 +58,6 @@
     DicomReplaceMode_IgnoreIfAbsent
   };
 
-  class ParsedDicomFile : public IDynamicObject
-  {
-  private:
-    std::auto_ptr<DcmFileFormat> file_;
-
-    ParsedDicomFile(DcmFileFormat& other) :
-      file_(dynamic_cast<DcmFileFormat*>(other.clone()))
-    {
-    }
-
-    void Setup(const char* content,
-               size_t size);
-
-  public:
-    ParsedDicomFile(const char* content,
-                    size_t size)
-    {
-      Setup(content, size);
-    }
-
-    ParsedDicomFile(const std::string& content)
-    {
-      if (content.size() == 0)
-        Setup(NULL, 0);
-      else
-        Setup(&content[0], content.size());
-    }
-
-    DcmFileFormat& GetDicom()
-    {
-      return *file_;
-    }
-
-    ParsedDicomFile* Clone()
-    {
-      return new ParsedDicomFile(*file_);
-    }
-
-    void SendPathValue(RestApiOutput& output,
-                       const UriComponents& uri);
-
-    void Answer(RestApiOutput& output);
-
-    void Remove(const DicomTag& tag);
-
-    void Insert(const DicomTag& tag,
-                const std::string& value);
-
-    void Replace(const DicomTag& tag,
-                 const std::string& value,
-                 DicomReplaceMode mode);
-
-    void RemovePrivateTags();
-
-    bool GetTagValue(std::string& value,
-                     const DicomTag& tag);
-
-    DicomInstanceHasher GetHasher();
-  };
-
   class FromDcmtkBridge
   {
   public:
@@ -184,4 +124,74 @@
     static bool SaveToMemoryBuffer(std::string& buffer,
                                    DcmDataset* dataSet);
   };
+
+  class ParsedDicomFile : public IDynamicObject
+  {
+  private:
+    std::auto_ptr<DcmFileFormat> file_;
+
+    ParsedDicomFile(DcmFileFormat& other) :
+      file_(dynamic_cast<DcmFileFormat*>(other.clone()))
+    {
+    }
+
+    void Setup(const char* content,
+               size_t size);
+
+  public:
+    ParsedDicomFile();  // Create a minimal DICOM instance
+
+    ParsedDicomFile(const char* content,
+                    size_t size)
+    {
+      Setup(content, size);
+    }
+
+    ParsedDicomFile(const std::string& content)
+    {
+      if (content.size() == 0)
+        Setup(NULL, 0);
+      else
+        Setup(&content[0], content.size());
+    }
+
+    DcmFileFormat& GetDicom()
+    {
+      return *file_;
+    }
+
+    ParsedDicomFile* Clone()
+    {
+      return new ParsedDicomFile(*file_);
+    }
+
+    void SendPathValue(RestApiOutput& output,
+                       const UriComponents& uri);
+
+    void Answer(RestApiOutput& output);
+
+    void Remove(const DicomTag& tag);
+
+    void Insert(const DicomTag& tag,
+                const std::string& value);
+
+    void Replace(const DicomTag& tag,
+                 const std::string& value,
+                 DicomReplaceMode mode = DicomReplaceMode_InsertIfAbsent);
+
+    void RemovePrivateTags();
+
+    bool GetTagValue(std::string& value,
+                     const DicomTag& tag);
+
+    DicomInstanceHasher GetHasher();
+
+    void SaveToMemoryBuffer(std::string& buffer)
+    {
+      FromDcmtkBridge::SaveToMemoryBuffer(buffer, file_->getDataset());
+    }
+
+    void SaveToFile(const std::string& path);
+  };
+
 }
--- a/UnitTestsSources/FromDcmtk.cpp	Fri May 02 12:59:05 2014 +0200
+++ b/UnitTestsSources/FromDcmtk.cpp	Fri May 02 15:06:31 2014 +0200
@@ -2,6 +2,7 @@
 
 #include "../OrthancServer/FromDcmtkBridge.h"
 #include "../OrthancServer/OrthancInitialization.h"
+#include "../Core/OrthancException.h"
 
 using namespace Orthanc;
 
@@ -23,3 +24,319 @@
 }
 
 
+namespace Orthanc
+{
+  class DicomModification
+  {
+    /**
+     * Process:
+     * (1) Remove private tags
+     * (2) Remove tags specified by the user
+     * (3) Replace tags
+     **/
+
+  private:
+    typedef std::set<DicomTag> Removals;
+    typedef std::map<DicomTag, std::string> Replacements;
+    typedef std::map< std::pair<DicomRootLevel, std::string>, std::string>  UidMap;
+
+    Removals removals_;
+    Replacements replacements_;
+    bool removePrivateTags_;
+    DicomRootLevel level_;
+    UidMap uidMap_;
+
+    void MapDicomIdentifier(ParsedDicomFile& dicom,
+                            DicomRootLevel level)
+    {
+      std::auto_ptr<DicomTag> tag;
+
+      switch (level)
+      {
+        case DicomRootLevel_Study:
+          tag.reset(new DicomTag(DICOM_TAG_STUDY_INSTANCE_UID));
+          break;
+
+        case DicomRootLevel_Series:
+          tag.reset(new DicomTag(DICOM_TAG_SERIES_INSTANCE_UID));
+          break;
+
+        case DicomRootLevel_Instance:
+          tag.reset(new DicomTag(DICOM_TAG_SOP_INSTANCE_UID));
+          break;
+
+        default:
+          throw OrthancException(ErrorCode_InternalError);
+      }
+
+      std::string original;
+      if (!dicom.GetTagValue(original, *tag))
+      {
+        original = "";
+      }
+
+      std::string mapped;
+      //bool isNew;
+
+      UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original));
+      if (previous == uidMap_.end())
+      {
+        mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level);
+        uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped));
+        //isNew = true;
+      }
+      else
+      {
+        mapped = previous->second;
+        //isNew = false;
+      }    
+
+      dicom.Replace(*tag, mapped);
+
+      //return isNew;
+    }
+
+  public:
+    DicomModification()
+    {
+      removePrivateTags_ = false;
+      level_ = DicomRootLevel_Instance;
+    }
+
+    void Keep(const DicomTag& tag)
+    {
+      removals_.erase(tag);
+    }
+
+    void Remove(const DicomTag& tag)
+    {
+      removals_.insert(tag);
+      replacements_.erase(tag);
+    }
+
+    bool IsRemoved(const DicomTag& tag) const
+    {
+      return removals_.find(tag) != removals_.end();
+    }
+
+    void Replace(const DicomTag& tag,
+                 const std::string& value)
+    {
+      removals_.erase(tag);
+      replacements_[tag] = value;
+    }
+
+    bool IsReplaced(const DicomTag& tag) const
+    {
+      return replacements_.find(tag) != replacements_.end();
+    }
+
+    const std::string& GetReplacement(const DicomTag& tag) const
+    {
+      Replacements::const_iterator it = replacements_.find(tag);
+
+      if (it == replacements_.end())
+      {
+        throw OrthancException(ErrorCode_InexistentItem);
+      }
+      else
+      {
+        return it->second;
+      } 
+    }
+
+    void SetRemovePrivateTags(bool removed)
+    {
+      removePrivateTags_ = removed;
+    }
+
+    bool ArePrivateTagsRemoved() const
+    {
+      return removePrivateTags_;
+    }
+
+    void SetLevel(DicomRootLevel level)
+    {
+      uidMap_.clear();
+      level_ = level;
+    }
+
+    DicomRootLevel GetLevel() const
+    {
+      return level_;
+    }
+
+    void SetupAnonymization()
+    {
+      removals_.clear();
+      replacements_.clear();
+      removePrivateTags_ = true;
+      level_ = DicomRootLevel_Patient;
+      uidMap_.clear();
+
+      // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles
+      removals_.insert(DicomTag(0x0008, 0x0014));  // Instance Creator UID
+      //removals_.insert(DicomTag(0x0008, 0x0018));  // SOP Instance UID => set in Apply()
+      removals_.insert(DicomTag(0x0008, 0x0050));  // Accession Number
+      removals_.insert(DicomTag(0x0008, 0x0080));  // Institution Name
+      removals_.insert(DicomTag(0x0008, 0x0081));  // Institution Address
+      removals_.insert(DicomTag(0x0008, 0x0090));  // Referring Physician's Name 
+      removals_.insert(DicomTag(0x0008, 0x0092));  // Referring Physician's Address 
+      removals_.insert(DicomTag(0x0008, 0x0094));  // Referring Physician's Telephone Numbers 
+      removals_.insert(DicomTag(0x0008, 0x1010));  // Station Name 
+      removals_.insert(DicomTag(0x0008, 0x1030));  // Study Description 
+      removals_.insert(DicomTag(0x0008, 0x103e));  // Series Description 
+      removals_.insert(DicomTag(0x0008, 0x1040));  // Institutional Department Name 
+      removals_.insert(DicomTag(0x0008, 0x1048));  // Physician(s) of Record 
+      removals_.insert(DicomTag(0x0008, 0x1050));  // Performing Physicians' Name 
+      removals_.insert(DicomTag(0x0008, 0x1060));  // Name of Physician(s) Reading Study 
+      removals_.insert(DicomTag(0x0008, 0x1070));  // Operators' Name 
+      removals_.insert(DicomTag(0x0008, 0x1080));  // Admitting Diagnoses Description 
+      removals_.insert(DicomTag(0x0008, 0x1155));  // Referenced SOP Instance UID 
+      removals_.insert(DicomTag(0x0008, 0x2111));  // Derivation Description 
+      //removals_.insert(DicomTag(0x0010, 0x0010));  // Patient's Name => cf. below (*)
+      //removals_.insert(DicomTag(0x0010, 0x0020));  // Patient ID => cf. below (*)
+      removals_.insert(DicomTag(0x0010, 0x0030));  // Patient's Birth Date 
+      removals_.insert(DicomTag(0x0010, 0x0032));  // Patient's Birth Time 
+      removals_.insert(DicomTag(0x0010, 0x0040));  // Patient's Sex 
+      removals_.insert(DicomTag(0x0010, 0x1000));  // Other Patient Ids 
+      removals_.insert(DicomTag(0x0010, 0x1001));  // Other Patient Names 
+      removals_.insert(DicomTag(0x0010, 0x1010));  // Patient's Age 
+      removals_.insert(DicomTag(0x0010, 0x1020));  // Patient's Size 
+      removals_.insert(DicomTag(0x0010, 0x1030));  // Patient's Weight 
+      removals_.insert(DicomTag(0x0010, 0x1090));  // Medical Record Locator 
+      removals_.insert(DicomTag(0x0010, 0x2160));  // Ethnic Group 
+      removals_.insert(DicomTag(0x0010, 0x2180));  // Occupation 
+      removals_.insert(DicomTag(0x0010, 0x21b0));  // Additional Patient's History 
+      removals_.insert(DicomTag(0x0010, 0x4000));  // Patient Comments 
+      removals_.insert(DicomTag(0x0018, 0x1000));  // Device Serial Number 
+      removals_.insert(DicomTag(0x0018, 0x1030));  // Protocol Name 
+      //removals_.insert(DicomTag(0x0020, 0x000d));  // Study Instance UID => set in Apply()
+      //removals_.insert(DicomTag(0x0020, 0x000e));  // Series Instance UID => set in Apply()
+      removals_.insert(DicomTag(0x0020, 0x0010));  // Study ID 
+      removals_.insert(DicomTag(0x0020, 0x0052));  // Frame of Reference UID 
+      removals_.insert(DicomTag(0x0020, 0x0200));  // Synchronization Frame of Reference UID 
+      removals_.insert(DicomTag(0x0020, 0x4000));  // Image Comments 
+      removals_.insert(DicomTag(0x0040, 0x0275));  // Request Attributes Sequence 
+      removals_.insert(DicomTag(0x0040, 0xa124));  // UID
+      removals_.insert(DicomTag(0x0040, 0xa730));  // Content Sequence 
+      removals_.insert(DicomTag(0x0088, 0x0140));  // Storage Media File-set UID 
+      removals_.insert(DicomTag(0x3006, 0x0024));  // Referenced Frame of Reference UID 
+      removals_.insert(DicomTag(0x3006, 0x00c2));  // Related Frame of Reference UID 
+
+      // Some more removals (from the experience of DICOM files at the CHU of Liege)
+      removals_.insert(DicomTag(0x0010, 0x1040));  // Patient's Address
+      removals_.insert(DicomTag(0x0032, 0x1032));  // Requesting Physician
+      removals_.insert(DicomTag(0x0010, 0x2154));  // PatientTelephoneNumbers
+      removals_.insert(DicomTag(0x0010, 0x2000));  // Medical Alerts
+
+      // Set the DeidentificationMethod tag
+      replacements_.insert(std::make_pair(DicomTag(0x0012, 0x0063), "Orthanc " ORTHANC_VERSION " - PS 3.15-2008 Table E.1-1"));
+
+      // Set the PatientIdentityRemoved tag
+      replacements_.insert(std::make_pair(DicomTag(0x0012, 0x0062), "YES"));
+
+      // (*) Choose a random patient name and ID
+      std::string patientId = FromDcmtkBridge::GenerateUniqueIdentifier(DicomRootLevel_Patient);
+      replacements_[DICOM_TAG_PATIENT_ID] = patientId;
+      replacements_[DICOM_TAG_PATIENT_NAME] = patientId;
+    }
+
+    void Apply(ParsedDicomFile& toModify)
+    {
+      // Check the request
+      assert(DicomRootLevel_Patient + 1 == DicomRootLevel_Study &&
+             DicomRootLevel_Study + 1 == DicomRootLevel_Series &&
+             DicomRootLevel_Series + 1 == DicomRootLevel_Instance);
+
+      if (IsRemoved(DICOM_TAG_PATIENT_ID) ||
+          IsRemoved(DICOM_TAG_STUDY_INSTANCE_UID) ||
+          IsRemoved(DICOM_TAG_SERIES_INSTANCE_UID) ||
+          IsRemoved(DICOM_TAG_SOP_INSTANCE_UID))
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+
+      if (level_ == DicomRootLevel_Patient && !IsReplaced(DICOM_TAG_PATIENT_ID))
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+
+      if (level_ > DicomRootLevel_Patient && IsReplaced(DICOM_TAG_PATIENT_ID))
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+
+      if (level_ > DicomRootLevel_Study && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+
+      if (level_ > DicomRootLevel_Series && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
+      {
+        throw OrthancException(ErrorCode_BadRequest);
+      }
+
+      // (1) Remove the private tags, if need be
+      if (removePrivateTags_)
+      {
+        toModify.RemovePrivateTags();
+      }
+
+      // (2) Remove the tags specified by the user
+      for (Removals::const_iterator it = removals_.begin(); 
+           it != removals_.end(); ++it)
+      {
+        toModify.Remove(*it);
+      }
+
+      // (3) Replace the tags
+      for (Replacements::const_iterator it = replacements_.begin(); 
+           it != replacements_.end(); ++it)
+      {
+        toModify.Replace(it->first, it->second, DicomReplaceMode_InsertIfAbsent);
+      }
+
+      // Update the DICOM identifiers
+      if (level_ <= DicomRootLevel_Study)
+      {
+        MapDicomIdentifier(toModify, DicomRootLevel_Study);
+      }
+
+      if (level_ <= DicomRootLevel_Series)
+      {
+        MapDicomIdentifier(toModify, DicomRootLevel_Series);
+      }
+
+      if (level_ <= DicomRootLevel_Instance)  // Always true
+      {
+        MapDicomIdentifier(toModify, DicomRootLevel_Instance);
+      }
+    }
+  };
+}
+
+
+
+TEST(DicomModification, Basic)
+{
+  DicomModification m;
+  m.SetupAnonymization();
+  //m.SetLevel(DicomRootLevel_Study);
+  //m.Replace(DICOM_TAG_PATIENT_ID, "coucou");
+  //m.Replace(DICOM_TAG_PATIENT_NAME, "coucou");
+
+  ParsedDicomFile o;
+  o.SaveToFile("/tmp/tutu.dcm");
+
+  for (int i = 0; i < 10; i++)
+  {
+    char b[1024];
+    sprintf(b, "/tmp/tutu%06d.dcm", i);
+    std::auto_ptr<ParsedDicomFile> f(o.Clone());
+    if (i > 4)
+      o.Replace(DICOM_TAG_SERIES_INSTANCE_UID, "coucou");
+    m.Apply(*f);
+    f->SaveToFile(b);
+  }
+}