/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2021 Osimis S.A., Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#include "../PrecompiledHeaders.h"
#include "DicomModification.h"

#include "../Compatibility.h"
#include "../Logging.h"
#include "../OrthancException.h"
#include "../SerializationToolbox.h"
#include "FromDcmtkBridge.h"
#include "ITagVisitor.h"

#include <memory>   // For std::unique_ptr


static const std::string ORTHANC_DEIDENTIFICATION_METHOD_2008 =
  "Orthanc " ORTHANC_VERSION " - PS 3.15-2008 Table E.1-1";

static const std::string ORTHANC_DEIDENTIFICATION_METHOD_2017c =
  "Orthanc " ORTHANC_VERSION " - PS 3.15-2017c Table E.1-1 Basic Profile";

namespace Orthanc
{
  class DicomModification::RelationshipsVisitor : public ITagVisitor
  {
  private:
    DicomModification&  that_;
    
    bool IsEnabled(const DicomTag& tag) const
    {
      return (!that_.IsCleared(tag) &&
              !that_.IsRemoved(tag) &&
              !that_.IsReplaced(tag));
    }

    void RemoveIfEnabled(ParsedDicomFile& dicom,
                         const DicomTag& tag) const
    {
      if (IsEnabled(tag))
      {
        dicom.Remove(tag);
      }
    }
                         

  public:
    explicit RelationshipsVisitor(DicomModification& that) :
      that_(that)
    {
    }

    virtual void VisitNotSupported(const std::vector<DicomTag>& parentTags,
                                   const std::vector<size_t>& parentIndexes,
                                   const DicomTag& tag,
                                   ValueRepresentation vr)
    {
    }

    virtual void VisitEmptySequence(const std::vector<DicomTag>& parentTags,
                                    const std::vector<size_t>& parentIndexes,
                                    const DicomTag& tag)
    {
    }

    virtual void VisitBinary(const std::vector<DicomTag>& parentTags,
                             const std::vector<size_t>& parentIndexes,
                             const DicomTag& tag,
                             ValueRepresentation vr,
                             const void* data,
                             size_t size)
    {
    }

    virtual void VisitIntegers(const std::vector<DicomTag>& parentTags,
                               const std::vector<size_t>& parentIndexes,
                               const DicomTag& tag,
                               ValueRepresentation vr,
                               const std::vector<int64_t>& values)
    {
    }

    virtual void VisitDoubles(const std::vector<DicomTag>& parentTags,
                              const std::vector<size_t>& parentIndexes,
                              const DicomTag& tag,
                              ValueRepresentation vr,
                              const std::vector<double>& value)
    {
    }

    virtual void VisitAttributes(const std::vector<DicomTag>& parentTags,
                                 const std::vector<size_t>& parentIndexes,
                                 const DicomTag& tag,
                                 const std::vector<DicomTag>& value)
    {
    }

    virtual Action VisitString(std::string& newValue,
                               const std::vector<DicomTag>& parentTags,
                               const std::vector<size_t>& parentIndexes,
                               const DicomTag& tag,
                               ValueRepresentation vr,
                               const std::string& value)
    {
      if (!IsEnabled(tag))
      {
        return Action_None;
      }
      else if (parentTags.size() == 2 &&
               parentTags[0] == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_SEQUENCE &&
               parentTags[1] == DICOM_TAG_RT_REFERENCED_STUDY_SEQUENCE &&
               tag == DICOM_TAG_REFERENCED_SOP_INSTANCE_UID)
      {
        // in RT-STRUCT, this ReferencedSOPInstanceUID is actually referencing a StudyInstanceUID !!
        // (observed in many data sets including: https://wiki.cancerimagingarchive.net/display/Public/Lung+CT+Segmentation+Challenge+2017)
        // tested in test_anonymize_relationships_5
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Study);
        return Action_Replace;
      }
      else if (tag == DICOM_TAG_FRAME_OF_REFERENCE_UID ||
               tag == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_UID || 
               tag == DICOM_TAG_REFERENCED_SOP_INSTANCE_UID ||
               tag == DICOM_TAG_RELATED_FRAME_OF_REFERENCE_UID)
      {
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Instance);
        return Action_Replace;
      }
      else if (parentTags.size() == 1 &&
               parentTags[0] == DICOM_TAG_CURRENT_REQUESTED_PROCEDURE_EVIDENCE_SEQUENCE &&
               tag == DICOM_TAG_STUDY_INSTANCE_UID)
      {
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Study);
        return Action_Replace;
      }
      else if (parentTags.size() == 2 &&
               parentTags[0] == DICOM_TAG_CURRENT_REQUESTED_PROCEDURE_EVIDENCE_SEQUENCE &&
               parentTags[1] == DICOM_TAG_REFERENCED_SERIES_SEQUENCE &&
               tag == DICOM_TAG_SERIES_INSTANCE_UID)
      {
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
        return Action_Replace;
      }
      else if (parentTags.size() == 3 &&
               parentTags[0] == DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_SEQUENCE &&
               parentTags[1] == DICOM_TAG_RT_REFERENCED_STUDY_SEQUENCE &&
               parentTags[2] == DICOM_TAG_RT_REFERENCED_SERIES_SEQUENCE &&
               tag == DICOM_TAG_SERIES_INSTANCE_UID)
      {
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
        return Action_Replace;
      }
      else if (parentTags.size() == 1 &&
               parentTags[0] == DICOM_TAG_REFERENCED_SERIES_SEQUENCE &&
               tag == DICOM_TAG_SERIES_INSTANCE_UID)
      {
        newValue = that_.MapDicomIdentifier(Toolbox::StripSpaces(value), ResourceType_Series);
        return Action_Replace;
      }
      else
      {
        return Action_None;
      }
    }

    void RemoveRelationships(ParsedDicomFile& dicom) const
    {
      // Sequences containing the UID relationships
      RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_IMAGE_SEQUENCE);
      RemoveIfEnabled(dicom, DICOM_TAG_SOURCE_IMAGE_SEQUENCE);
      
      // Individual tags
      RemoveIfEnabled(dicom, DICOM_TAG_FRAME_OF_REFERENCE_UID);

      // The tags below should never occur at the first level of the
      // hierarchy, but remove them anyway
      RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_FRAME_OF_REFERENCE_UID);
      RemoveIfEnabled(dicom, DICOM_TAG_REFERENCED_SOP_INSTANCE_UID);
      RemoveIfEnabled(dicom, DICOM_TAG_RELATED_FRAME_OF_REFERENCE_UID);
    }
  };


  bool DicomModification::CancelReplacement(const DicomTag& tag)
  {
    Replacements::iterator it = replacements_.find(tag);
    
    if (it != replacements_.end())
    {
      delete it->second;
      replacements_.erase(it);
      return true;
    }
    else
    {
      return false;
    }
  }


  void DicomModification::ReplaceInternal(const DicomTag& tag,
                                          const Json::Value& value)
  {
    Replacements::iterator it = replacements_.find(tag);

    if (it != replacements_.end())
    {
      delete it->second;
      it->second = NULL;   // In the case of an exception during the clone
      it->second = new Json::Value(value);  // Clone
    }
    else
    {
      replacements_[tag] = new Json::Value(value);  // Clone
    }
  }


  void DicomModification::ClearReplacements()
  {
    for (Replacements::iterator it = replacements_.begin();
         it != replacements_.end(); ++it)
    {
      delete it->second;
    }

    replacements_.clear();
  }


  void DicomModification::MarkNotOrthancAnonymization()
  {
    Replacements::iterator it = replacements_.find(DICOM_TAG_DEIDENTIFICATION_METHOD);

    if (it != replacements_.end() &&
        (it->second->asString() == ORTHANC_DEIDENTIFICATION_METHOD_2008 ||
         it->second->asString() == ORTHANC_DEIDENTIFICATION_METHOD_2017c))
    {
      delete it->second;
      replacements_.erase(it);
    }
  }

  void DicomModification::RegisterMappedDicomIdentifier(const std::string& original,
                                                        const std::string& mapped,
                                                        ResourceType level)
  {
    UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original));

    if (previous == uidMap_.end())
    {
      uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped));
    }
  }

  std::string DicomModification::MapDicomIdentifier(const std::string& original,
                                                    ResourceType level)
  {
    std::string mapped;

    UidMap::const_iterator previous = uidMap_.find(std::make_pair(level, original));

    if (previous == uidMap_.end())
    {
      if (identifierGenerator_ == NULL)
      {
        mapped = FromDcmtkBridge::GenerateUniqueIdentifier(level);
      }
      else
      {
        if (!identifierGenerator_->Apply(mapped, original, level, currentSource_))
        {
          throw OrthancException(ErrorCode_InternalError,
                                 "Unable to generate an anonymized ID");
        }
      }

      uidMap_.insert(std::make_pair(std::make_pair(level, original), mapped));
    }
    else
    {
      mapped = previous->second;
    }

    return mapped;
  }


  void DicomModification::MapDicomTags(ParsedDicomFile& dicom,
                                       ResourceType level)
  {
    std::unique_ptr<DicomTag> tag;

    switch (level)
    {
      case ResourceType_Study:
        tag.reset(new DicomTag(DICOM_TAG_STUDY_INSTANCE_UID));
        break;

      case ResourceType_Series:
        tag.reset(new DicomTag(DICOM_TAG_SERIES_INSTANCE_UID));
        break;

      case ResourceType_Instance:
        tag.reset(new DicomTag(DICOM_TAG_SOP_INSTANCE_UID));
        break;

      default:
        throw OrthancException(ErrorCode_InternalError);
    }

    std::string original;
    if (!const_cast<const ParsedDicomFile&>(dicom).GetTagValue(original, *tag))
    {
      original = "";
    }

    std::string mapped = MapDicomIdentifier(Toolbox::StripSpaces(original), level);

    dicom.Replace(*tag, mapped, 
                  false /* don't try and decode data URI scheme for UIDs */, 
                  DicomReplaceMode_InsertIfAbsent, privateCreator_);
  }

  
  DicomModification::DicomModification() :
    removePrivateTags_(false),
    level_(ResourceType_Instance),
    allowManualIdentifiers_(true),
    keepStudyInstanceUid_(false),
    keepSeriesInstanceUid_(false),
    keepSopInstanceUid_(false),
    updateReferencedRelationships_(true),
    isAnonymization_(false),
    //privateCreator_("PrivateCreator"),
    identifierGenerator_(NULL)
  {
  }

  DicomModification::~DicomModification()
  {
    ClearReplacements();
  }

  void DicomModification::Keep(const DicomTag& tag)
  {
    bool wasRemoved = IsRemoved(tag);
    bool wasCleared = IsCleared(tag);
    
    removals_.erase(tag);
    clearings_.erase(tag);

    bool wasReplaced = CancelReplacement(tag);

    if (tag == DICOM_TAG_STUDY_INSTANCE_UID)
    {
      keepStudyInstanceUid_ = true;
    }
    else if (tag == DICOM_TAG_SERIES_INSTANCE_UID)
    {
      keepSeriesInstanceUid_ = true;
    }
    else if (tag == DICOM_TAG_SOP_INSTANCE_UID)
    {
      keepSopInstanceUid_ = true;
    }
    else if (tag.IsPrivate())
    {
      privateTagsToKeep_.insert(tag);
    }
    else if (!wasRemoved &&
             !wasReplaced &&
             !wasCleared)
    {
      LOG(WARNING) << "Marking this tag as to be kept has no effect: " << tag.Format();
    }

    MarkNotOrthancAnonymization();
  }

  void DicomModification::Remove(const DicomTag& tag)
  {
    removals_.insert(tag);
    clearings_.erase(tag);
    CancelReplacement(tag);
    privateTagsToKeep_.erase(tag);

    MarkNotOrthancAnonymization();
  }

  void DicomModification::Clear(const DicomTag& tag)
  {
    removals_.erase(tag);
    clearings_.insert(tag);
    CancelReplacement(tag);
    privateTagsToKeep_.erase(tag);

    MarkNotOrthancAnonymization();
  }

  bool DicomModification::IsRemoved(const DicomTag& tag) const
  {
    return removals_.find(tag) != removals_.end();
  }

  bool DicomModification::IsCleared(const DicomTag& tag) const
  {
    return clearings_.find(tag) != clearings_.end();
  }

  void DicomModification::Replace(const DicomTag& tag,
                                  const Json::Value& value,
                                  bool safeForAnonymization)
  {
    clearings_.erase(tag);
    removals_.erase(tag);
    privateTagsToKeep_.erase(tag);
    ReplaceInternal(tag, value);

    if (!safeForAnonymization)
    {
      MarkNotOrthancAnonymization();
    }
  }


  bool DicomModification::IsReplaced(const DicomTag& tag) const
  {
    return replacements_.find(tag) != replacements_.end();
  }

  const Json::Value& DicomModification::GetReplacement(const DicomTag& tag) const
  {
    Replacements::const_iterator it = replacements_.find(tag);

    if (it == replacements_.end())
    {
      throw OrthancException(ErrorCode_InexistentItem);
    }
    else
    {
      return *it->second;
    } 
  }


  std::string DicomModification::GetReplacementAsString(const DicomTag& tag) const
  {
    const Json::Value& json = GetReplacement(tag);

    if (json.type() != Json::stringValue)
    {
      throw OrthancException(ErrorCode_BadParameterType);
    }
    else
    {
      return json.asString();
    }    
  }


  void DicomModification::SetRemovePrivateTags(bool removed)
  {
    removePrivateTags_ = removed;

    if (!removed)
    {
      MarkNotOrthancAnonymization();
    }
  }

  bool DicomModification::ArePrivateTagsRemoved() const
  {
    return removePrivateTags_;
  }

  void DicomModification::SetLevel(ResourceType level)
  {
    uidMap_.clear();
    level_ = level;

    if (level != ResourceType_Patient)
    {
      MarkNotOrthancAnonymization();
    }
  }

  ResourceType DicomModification::GetLevel() const
  {
    return level_;
  }


  void DicomModification::SetupAnonymization2008()
  {
    // This is Table E.1-1 from PS 3.15-2008 - DICOM Part 15: Security and System Management Profiles
    // https://raw.githubusercontent.com/jodogne/dicom-specification/master/2008/08_15pu.pdf
    
    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 => RelationshipsVisitor
    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 => cf. RelationshipsVisitor
    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 => RelationshipsVisitor
    //removals_.insert(DicomTag(0x3006, 0x00c2));  // Related Frame of Reference UID => RelationshipsVisitor

    // 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
    ReplaceInternal(DICOM_TAG_DEIDENTIFICATION_METHOD, ORTHANC_DEIDENTIFICATION_METHOD_2008);
  }
  

  void DicomModification::SetupAnonymization2017c()
  {
    /**
     * This is Table E.1-1 from PS 3.15-2017c (DICOM Part 15: Security
     * and System Management Profiles), "basic profile" column. It was
     * generated automatically by calling:
     * "../../../OrthancServer/Resources/GenerateAnonymizationProfile.py
     * https://raw.githubusercontent.com/jodogne/dicom-specification/master/2017c/part15.xml"
     **/
    
#include "DicomModification_Anonymization2017c.impl.h"
    
    // Set the DeidentificationMethod tag
    ReplaceInternal(DICOM_TAG_DEIDENTIFICATION_METHOD, ORTHANC_DEIDENTIFICATION_METHOD_2017c);
  }
  

  void DicomModification::SetupAnonymization(DicomVersion version)
  {
    isAnonymization_ = true;
    
    removals_.clear();
    clearings_.clear();
    ClearReplacements();
    removePrivateTags_ = true;
    level_ = ResourceType_Patient;
    uidMap_.clear();
    privateTagsToKeep_.clear();

    switch (version)
    {
      case DicomVersion_2008:
        SetupAnonymization2008();
        break;

      case DicomVersion_2017c:
        SetupAnonymization2017c();
        break;

      default:
        throw OrthancException(ErrorCode_ParameterOutOfRange);
    }

    // Set the PatientIdentityRemoved tag
    ReplaceInternal(DicomTag(0x0012, 0x0062), "YES");

    // (*) Choose a random patient name and ID
    std::string patientId = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Patient);
    ReplaceInternal(DICOM_TAG_PATIENT_ID, patientId);
    ReplaceInternal(DICOM_TAG_PATIENT_NAME, patientId);
  }

  void DicomModification::Apply(ParsedDicomFile& toModify)
  {
    // Check the request
    assert(ResourceType_Patient + 1 == ResourceType_Study &&
           ResourceType_Study + 1 == ResourceType_Series &&
           ResourceType_Series + 1 == ResourceType_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);
    }
    

    // Sanity checks at the patient level
    if (level_ == ResourceType_Patient && !IsReplaced(DICOM_TAG_PATIENT_ID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying a patient, her PatientID is required to be modified");
    }

    if (!allowManualIdentifiers_)
    {
      if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a patient, the StudyInstanceUID cannot be manually modified");
      }

      if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a patient, the SeriesInstanceUID cannot be manually modified");
      }

      if (level_ == ResourceType_Patient && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a patient, the SopInstanceUID cannot be manually modified");
      }
    }


    // Sanity checks at the study level
    if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_PATIENT_ID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying a study, the parent PatientID cannot be manually modified");
    }

    if (!allowManualIdentifiers_)
    {
      if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a study, the SeriesInstanceUID cannot be manually modified");
      }

      if (level_ == ResourceType_Study && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a study, the SopInstanceUID cannot be manually modified");
      }
    }


    // Sanity checks at the series level
    if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_PATIENT_ID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying a series, the parent PatientID cannot be manually modified");
    }

    if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying a series, the parent StudyInstanceUID cannot be manually modified");
    }

    if (!allowManualIdentifiers_)
    {
      if (level_ == ResourceType_Series && IsReplaced(DICOM_TAG_SOP_INSTANCE_UID))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "When modifying a series, the SopInstanceUID cannot be manually modified");
      }
    }


    // Sanity checks at the instance level
    if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_PATIENT_ID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying an instance, the parent PatientID cannot be manually modified");
    }

    if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying an instance, the parent StudyInstanceUID cannot be manually modified");
    }

    if (level_ == ResourceType_Instance && IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
    {
      throw OrthancException(ErrorCode_BadRequest,
                             "When modifying an instance, the parent SeriesInstanceUID cannot be manually modified");
    }

    // (0) Create a summary of the source file, if a custom generator
    // is provided
    if (identifierGenerator_ != NULL)
    {
      toModify.ExtractDicomSummary(currentSource_, ORTHANC_MAXIMUM_TAG_LENGTH);
    }

    // (1) Make sure the relationships are updated with the ids that we force too
    // i.e: an RT-STRUCT is referencing its own StudyInstanceUID
    if (isAnonymization_ && updateReferencedRelationships_)
    {
      if (IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
      {
        std::string original;
        std::string replacement = GetReplacementAsString(DICOM_TAG_STUDY_INSTANCE_UID);
        const_cast<const ParsedDicomFile&>(toModify).GetTagValue(original, DICOM_TAG_STUDY_INSTANCE_UID);
        RegisterMappedDicomIdentifier(original, replacement, ResourceType_Study);
      }

      if (IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
      {
        std::string original;
        std::string replacement = GetReplacementAsString(DICOM_TAG_SERIES_INSTANCE_UID);
        const_cast<const ParsedDicomFile&>(toModify).GetTagValue(original, DICOM_TAG_SERIES_INSTANCE_UID);
        RegisterMappedDicomIdentifier(original, replacement, ResourceType_Series);
      }

      if (IsReplaced(DICOM_TAG_SOP_INSTANCE_UID))
      {
        std::string original;
        std::string replacement = GetReplacementAsString(DICOM_TAG_SOP_INSTANCE_UID);
        const_cast<const ParsedDicomFile&>(toModify).GetTagValue(original, DICOM_TAG_SOP_INSTANCE_UID);
        RegisterMappedDicomIdentifier(original, replacement, ResourceType_Instance);
      }
    }


    // (2) Remove the private tags, if need be
    if (removePrivateTags_)
    {
      toModify.RemovePrivateTags(privateTagsToKeep_);
    }

    // (3) Clear the tags specified by the user
    for (SetOfTags::const_iterator it = clearings_.begin(); 
         it != clearings_.end(); ++it)
    {
      toModify.Clear(*it, true /* only clear if the tag exists in the original file */);
    }

    // (4) Remove the tags specified by the user
    for (SetOfTags::const_iterator it = removals_.begin(); 
         it != removals_.end(); ++it)
    {
      toModify.Remove(*it);
    }

    // (5) Replace the tags
    for (Replacements::const_iterator it = replacements_.begin(); 
         it != replacements_.end(); ++it)
    {
      toModify.Replace(it->first, *it->second, true /* decode data URI scheme */,
                       DicomReplaceMode_InsertIfAbsent, privateCreator_);
    }

    // (6) Update the DICOM identifiers
    if (level_ <= ResourceType_Study &&
        !IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
    {
      if (keepStudyInstanceUid_)
      {
        LOG(WARNING) << "Modifying a study while keeping its original StudyInstanceUID: This should be avoided!";
      }
      else
      {
        MapDicomTags(toModify, ResourceType_Study);
      }
    }

    if (level_ <= ResourceType_Series &&
        !IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
    {
      if (keepSeriesInstanceUid_)
      {
        LOG(WARNING) << "Modifying a series while keeping its original SeriesInstanceUID: This should be avoided!";
      }
      else
      {
        MapDicomTags(toModify, ResourceType_Series);
      }
    }

    if (level_ <= ResourceType_Instance &&  // Always true
        !IsReplaced(DICOM_TAG_SOP_INSTANCE_UID))
    {
      if (keepSopInstanceUid_)
      {
        LOG(WARNING) << "Modifying an instance while keeping its original SOPInstanceUID: This should be avoided!";
      }
      else
      {
        MapDicomTags(toModify, ResourceType_Instance);
      }
    }

    // (7) Update the "referenced" relationships in the case of an anonymization
    if (isAnonymization_)
    {
      RelationshipsVisitor visitor(*this);

      if (updateReferencedRelationships_)
      {
        const_cast<const ParsedDicomFile&>(toModify).Apply(visitor);
      }
      else
      {
        visitor.RemoveRelationships(toModify);
      }
    }
  }

  void DicomModification::SetAllowManualIdentifiers(bool check)
  {
    allowManualIdentifiers_ = check;
  }

  bool DicomModification::AreAllowManualIdentifiers() const
  {
    return allowManualIdentifiers_;
  }


  static bool IsDatabaseKey(const DicomTag& tag)
  {
    return (tag == DICOM_TAG_PATIENT_ID ||
            tag == DICOM_TAG_STUDY_INSTANCE_UID ||
            tag == DICOM_TAG_SERIES_INSTANCE_UID ||
            tag == DICOM_TAG_SOP_INSTANCE_UID);
  }


  static void ParseListOfTags(DicomModification& target,
                              const Json::Value& query,
                              DicomModification::TagOperation operation,
                              bool force)
  {
    if (!query.isArray())
    {
      throw OrthancException(ErrorCode_BadRequest);
    }

    for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
    {
      if (query[i].type() != Json::stringValue)
      {
        throw OrthancException(ErrorCode_BadRequest);
      }
      
      std::string name = query[i].asString();

      DicomTag tag = FromDcmtkBridge::ParseTag(name);

      if (!force && IsDatabaseKey(tag))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "Marking tag \"" + name + "\" as to be " +
                               (operation == DicomModification::TagOperation_Keep ? "kept" : "removed") +
                               " requires the \"Force\" option to be set to true");
      }

      switch (operation)
      {
        case DicomModification::TagOperation_Keep:
          target.Keep(tag);
          LOG(TRACE) << "Keep: " << name << " (" << tag.Format() << ")";
          break;

        case DicomModification::TagOperation_Remove:
          target.Remove(tag);
          LOG(TRACE) << "Remove: " << name << " (" << tag.Format() << ")";
          break;

        default:
          throw OrthancException(ErrorCode_InternalError);
      }
    }
  }


  static void ParseReplacements(DicomModification& target,
                                const Json::Value& replacements,
                                bool force)
  {
    if (!replacements.isObject())
    {
      throw OrthancException(ErrorCode_BadRequest);
    }

    Json::Value::Members members = replacements.getMemberNames();
    for (size_t i = 0; i < members.size(); i++)
    {
      const std::string& name = members[i];
      const Json::Value& value = replacements[name];

      DicomTag tag = FromDcmtkBridge::ParseTag(name);

      if (!force && IsDatabaseKey(tag))
      {
        throw OrthancException(ErrorCode_BadRequest,
                               "Marking tag \"" + name + "\" as to be replaced " +
                               "requires the \"Force\" option to be set to true");
      }

      target.Replace(tag, value, false);

      LOG(TRACE) << "Replace: " << name << " (" << tag.Format() 
                 << ") == " << value.toStyledString();
    }
  }


  static bool GetBooleanValue(const std::string& member,
                              const Json::Value& json,
                              bool defaultValue)
  {
    if (!json.isMember(member))
    {
      return defaultValue;
    }
    else if (json[member].type() == Json::booleanValue)
    {
      return json[member].asBool();
    }
    else
    {
      throw OrthancException(ErrorCode_BadFileFormat,
                             "Member \"" + member + "\" should be a Boolean value");
    }
  }


  void DicomModification::ParseModifyRequest(const Json::Value& request)
  {
    if (!request.isObject())
    {
      throw OrthancException(ErrorCode_BadFileFormat);
    }

    bool force = GetBooleanValue("Force", request, false);
      
    if (GetBooleanValue("RemovePrivateTags", request, false))
    {
      SetRemovePrivateTags(true);
    }

    if (request.isMember("Remove"))
    {
      ParseListOfTags(*this, request["Remove"], TagOperation_Remove, force);
    }

    if (request.isMember("Replace"))
    {
      ParseReplacements(*this, request["Replace"], force);
    }

    // The "Keep" operation only makes sense for the tags
    // StudyInstanceUID, SeriesInstanceUID and SOPInstanceUID. Avoid
    // this feature as much as possible, as this breaks the DICOM
    // model of the real world, except if you know exactly what
    // you're doing!
    if (request.isMember("Keep"))
    {
      ParseListOfTags(*this, request["Keep"], TagOperation_Keep, force);
    }

    // New in Orthanc 1.6.0
    if (request.isMember("PrivateCreator"))
    {
      privateCreator_ = SerializationToolbox::ReadString(request, "PrivateCreator");
    }
  }


  void DicomModification::ParseAnonymizationRequest(bool& patientNameReplaced,
                                                    const Json::Value& request)
  {
    if (!request.isObject())
    {
      throw OrthancException(ErrorCode_BadFileFormat);
    }

    bool force = GetBooleanValue("Force", request, false);
      
    // As of Orthanc 1.3.0, the default anonymization is done
    // according to PS 3.15-2017c Table E.1-1 (basic profile)
    DicomVersion version = DicomVersion_2017c;
    if (request.isMember("DicomVersion"))
    {
      if (request["DicomVersion"].type() != Json::stringValue)
      {
        throw OrthancException(ErrorCode_BadFileFormat);
      }
      else
      {
        version = StringToDicomVersion(request["DicomVersion"].asString());
      }
    }
        
    SetupAnonymization(version);

    std::string patientName = GetReplacementAsString(DICOM_TAG_PATIENT_NAME);    

    if (GetBooleanValue("KeepPrivateTags", request, false))
    {
      SetRemovePrivateTags(false);
    }

    if (request.isMember("Remove"))
    {
      ParseListOfTags(*this, request["Remove"], TagOperation_Remove, force);
    }

    if (request.isMember("Replace"))
    {
      ParseReplacements(*this, request["Replace"], force);
    }

    if (request.isMember("Keep"))
    {
      ParseListOfTags(*this, request["Keep"], TagOperation_Keep, force);
    }

    patientNameReplaced = (IsReplaced(DICOM_TAG_PATIENT_NAME) &&
                           GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName);

    // New in Orthanc 1.6.0
    if (request.isMember("PrivateCreator"))
    {
      privateCreator_ = SerializationToolbox::ReadString(request, "PrivateCreator");
    }
  }

  void DicomModification::SetDicomIdentifierGenerator(DicomModification::IDicomIdentifierGenerator &generator)
  {
    identifierGenerator_ = &generator;
  }




  static const char* REMOVE_PRIVATE_TAGS = "RemovePrivateTags";
  static const char* LEVEL = "Level";
  static const char* ALLOW_MANUAL_IDENTIFIERS = "AllowManualIdentifiers";
  static const char* KEEP_STUDY_INSTANCE_UID = "KeepStudyInstanceUID";
  static const char* KEEP_SERIES_INSTANCE_UID = "KeepSeriesInstanceUID";
  static const char* KEEP_SOP_INSTANCE_UID = "KeepSOPInstanceUID";
  static const char* UPDATE_REFERENCED_RELATIONSHIPS = "UpdateReferencedRelationships";
  static const char* IS_ANONYMIZATION = "IsAnonymization";
  static const char* REMOVALS = "Removals";
  static const char* CLEARINGS = "Clearings";
  static const char* PRIVATE_TAGS_TO_KEEP = "PrivateTagsToKeep";
  static const char* REPLACEMENTS = "Replacements";
  static const char* MAP_PATIENTS = "MapPatients";
  static const char* MAP_STUDIES = "MapStudies";
  static const char* MAP_SERIES = "MapSeries";
  static const char* MAP_INSTANCES = "MapInstances";
  static const char* PRIVATE_CREATOR = "PrivateCreator";  // New in Orthanc 1.6.0
  
  void DicomModification::Serialize(Json::Value& value) const
  {
    if (identifierGenerator_ != NULL)
    {
      throw OrthancException(ErrorCode_InternalError,
                             "Cannot serialize a DicomModification with a custom identifier generator");
    }

    value = Json::objectValue;
    value[REMOVE_PRIVATE_TAGS] = removePrivateTags_;
    value[LEVEL] = EnumerationToString(level_);
    value[ALLOW_MANUAL_IDENTIFIERS] = allowManualIdentifiers_;
    value[KEEP_STUDY_INSTANCE_UID] = keepStudyInstanceUid_;
    value[KEEP_SERIES_INSTANCE_UID] = keepSeriesInstanceUid_;
    value[KEEP_SOP_INSTANCE_UID] = keepSopInstanceUid_;
    value[UPDATE_REFERENCED_RELATIONSHIPS] = updateReferencedRelationships_;
    value[IS_ANONYMIZATION] = isAnonymization_;
    value[PRIVATE_CREATOR] = privateCreator_;

    SerializationToolbox::WriteSetOfTags(value, removals_, REMOVALS);
    SerializationToolbox::WriteSetOfTags(value, clearings_, CLEARINGS);
    SerializationToolbox::WriteSetOfTags(value, privateTagsToKeep_, PRIVATE_TAGS_TO_KEEP);

    Json::Value& tmp = value[REPLACEMENTS];

    tmp = Json::objectValue;

    for (Replacements::const_iterator it = replacements_.begin();
         it != replacements_.end(); ++it)
    {
      assert(it->second != NULL);
      tmp[it->first.Format()] = *it->second;
    }

    Json::Value& mapPatients = value[MAP_PATIENTS];
    Json::Value& mapStudies = value[MAP_STUDIES];
    Json::Value& mapSeries = value[MAP_SERIES];
    Json::Value& mapInstances = value[MAP_INSTANCES];

    mapPatients = Json::objectValue;
    mapStudies = Json::objectValue;
    mapSeries = Json::objectValue;
    mapInstances = Json::objectValue;

    for (UidMap::const_iterator it = uidMap_.begin(); it != uidMap_.end(); ++it)
    {
      Json::Value* tmp2 = NULL;

      switch (it->first.first)
      {
        case ResourceType_Patient:
          tmp2 = &mapPatients;
          break;

        case ResourceType_Study:
          tmp2 = &mapStudies;
          break;

        case ResourceType_Series:
          tmp2 = &mapSeries;
          break;

        case ResourceType_Instance:
          tmp2 = &mapInstances;
          break;

        default:
          throw OrthancException(ErrorCode_InternalError);
      }

      assert(tmp2 != NULL);
      (*tmp2) [it->first.second] = it->second;
    }
  }

  void DicomModification::UnserializeUidMap(ResourceType level,
                                            const Json::Value& serialized,
                                            const char* field)
  {
    if (!serialized.isMember(field) ||
        serialized[field].type() != Json::objectValue)
    {
      throw OrthancException(ErrorCode_BadFileFormat);
    }

    Json::Value::Members names = serialized[field].getMemberNames();
    
    for (Json::Value::Members::const_iterator it = names.begin(); it != names.end(); ++it)
    {
      const Json::Value& value = serialized[field][*it];

      if (value.type() != Json::stringValue)
      {
        throw OrthancException(ErrorCode_BadFileFormat);
      }
      else
      {
        uidMap_[std::make_pair(level, *it)] = value.asString();
      }
    }
  }

  
  DicomModification::DicomModification(const Json::Value& serialized) :
    identifierGenerator_(NULL)
  {
    removePrivateTags_ = SerializationToolbox::ReadBoolean(serialized, REMOVE_PRIVATE_TAGS);
    level_ = StringToResourceType(SerializationToolbox::ReadString(serialized, LEVEL).c_str());
    allowManualIdentifiers_ = SerializationToolbox::ReadBoolean(serialized, ALLOW_MANUAL_IDENTIFIERS);
    keepStudyInstanceUid_ = SerializationToolbox::ReadBoolean(serialized, KEEP_STUDY_INSTANCE_UID);
    keepSeriesInstanceUid_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SERIES_INSTANCE_UID);
    keepSopInstanceUid_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOP_INSTANCE_UID);
    updateReferencedRelationships_ = SerializationToolbox::ReadBoolean
      (serialized, UPDATE_REFERENCED_RELATIONSHIPS);
    isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);

    if (serialized.isMember(PRIVATE_CREATOR))
    {
      privateCreator_ = SerializationToolbox::ReadString(serialized, PRIVATE_CREATOR);
    }

    SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
    SerializationToolbox::ReadSetOfTags(clearings_, serialized, CLEARINGS);
    SerializationToolbox::ReadSetOfTags(privateTagsToKeep_, serialized, PRIVATE_TAGS_TO_KEEP);

    if (!serialized.isMember(REPLACEMENTS) ||
        serialized[REPLACEMENTS].type() != Json::objectValue)
    {
      throw OrthancException(ErrorCode_BadFileFormat);
    }

    Json::Value::Members names = serialized[REPLACEMENTS].getMemberNames();

    for (Json::Value::Members::const_iterator it = names.begin(); it != names.end(); ++it)
    {
      DicomTag tag(0, 0);
      if (!DicomTag::ParseHexadecimal(tag, it->c_str()))
      {
        throw OrthancException(ErrorCode_BadFileFormat);
      }
      else
      {
        const Json::Value& value = serialized[REPLACEMENTS][*it];
        replacements_.insert(std::make_pair(tag, new Json::Value(value)));
      }
    }

    UnserializeUidMap(ResourceType_Patient, serialized, MAP_PATIENTS);
    UnserializeUidMap(ResourceType_Study, serialized, MAP_STUDIES);
    UnserializeUidMap(ResourceType_Series, serialized, MAP_SERIES);
    UnserializeUidMap(ResourceType_Instance, serialized, MAP_INSTANCES);
  }


  void DicomModification::SetPrivateCreator(const std::string &privateCreator)
  {
    privateCreator_ = privateCreator;
  }

  const std::string &DicomModification::GetPrivateCreator() const
  {
    return privateCreator_;
  }
}