.hg_archival.txt

 repo: 3959d33612ccaadc0d4d707227fbed09ac35e5fe
-node: 78e5414d57f8874cfe88997726b97bd3b25e48df
-branch: Orthanc-1.3.2
+node: a2536c0d72deda960f2908e7bdcc56929837a0bf
+branch: Orthanc-1.4.0
 latesttag: dcmtk-3.6.1
-latesttagdistance: 205
-changessincelatesttag: 213
+latesttagdistance: 354
+changessincelatesttag: 396

.hgignore

 syntax: glob
-ThirdPartyDownloads/
\ No newline at end of file
+ThirdPartyDownloads/
+CMakeLists.txt.user
+*.cpp.orig
+*.h.orig

Core/Cache/MemoryCache.cpp

@@ -80,9 +80,12 @@ namespace Orthanc
 
   void MemoryCache::Invalidate(const std::string& id)
   {
-    if (index_.Contains(id))
+    Page* p = NULL;
+    if (index_.Contains(id, p))
     {
       VLOG(1) << "Invalidating a cache page";
+      assert(p != NULL);
+      delete p;
       index_.Invalidate(id);
     }
   }

Core/DicomFormat/DicomTag.cpp

@@ -39,9 +39,32 @@
 #include <iostream>
 #include <iomanip>
 #include <stdio.h>
+#include <string.h>
 
 namespace Orthanc
-{
+{ 
+  static inline uint16_t GetCharValue(char c)
+  {
+    if (c >= '0' && c <= '9')
+      return c - '0';
+    else if (c >= 'a' && c <= 'f')
+      return c - 'a' + 10;
+    else if (c >= 'A' && c <= 'F')
+      return c - 'A' + 10;
+    else
+      return 0;
+  }
+
+
+  static inline uint16_t GetTagValue(const char* c)
+  {
+    return ((GetCharValue(c[0]) << 12) + 
+            (GetCharValue(c[1]) << 8) + 
+            (GetCharValue(c[2]) << 4) + 
+            GetCharValue(c[3]));
+  }
+
+
   bool DicomTag::operator< (const DicomTag& other) const
   {
     if (group_ < other.group_)
@@ -74,6 +97,49 @@ namespace Orthanc
   }
 
 
+  bool DicomTag::ParseHexadecimal(DicomTag& tag,
+                                  const char* value)
+  {
+    size_t length = strlen(value);
+
+    if (length == 9 &&
+        isxdigit(value[0]) &&
+        isxdigit(value[1]) &&
+        isxdigit(value[2]) &&
+        isxdigit(value[3]) &&
+        (value[4] == '-' || value[4] == ',') &&
+        isxdigit(value[5]) &&
+        isxdigit(value[6]) &&
+        isxdigit(value[7]) &&
+        isxdigit(value[8]))        
+    {
+      uint16_t group = GetTagValue(value);
+      uint16_t element = GetTagValue(value + 5);
+      tag = DicomTag(group, element);
+      return true;
+    }
+    else if (length == 8 &&
+             isxdigit(value[0]) &&
+             isxdigit(value[1]) &&
+             isxdigit(value[2]) &&
+             isxdigit(value[3]) &&
+             isxdigit(value[4]) &&
+             isxdigit(value[5]) &&
+             isxdigit(value[6]) &&
+             isxdigit(value[7])) 
+    {
+      uint16_t group = GetTagValue(value);
+      uint16_t element = GetTagValue(value + 4);
+      tag = DicomTag(group, element);
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
   const char* DicomTag::GetMainTagsName() const
   {
     if (*this == DICOM_TAG_ACCESSION_NUMBER)

Core/DicomFormat/DicomTag.h

@@ -88,6 +88,9 @@ namespace Orthanc
 
     std::string Format() const;
 
+    static bool ParseHexadecimal(DicomTag& tag,
+                                 const char* value);
+
     friend std::ostream& operator<< (std::ostream& o, const DicomTag& tag);
 
     static void AddTagsForModule(std::set<DicomTag>& target,

Core/DicomNetworking/DicomUserConnection.cpp

@@ -264,8 +264,6 @@ namespace Orthanc
                                          const std::string& moveOriginatorAET,
                                          uint16_t moveOriginatorID)
   {
-    CheckIsOpen();
-
     DcmFileFormat dcmff;
     Check(dcmff.read(is, EXS_Unknown, EGL_noChange, DCM_MaxReadLength));
 
@@ -284,23 +282,36 @@ namespace Orthanc
     bool isGeneric = IsGenericTransferSyntax(syntax);
 
     bool renegotiate;
-    if (isGeneric)
+
+    if (!IsOpen())
+    {
+      renegotiate = true;
+    }
+    else if (isGeneric)
     {
       // Are we making a generic-to-specific or specific-to-generic change of
       // the transfer syntax? If this is the case, renegotiate the connection.
       renegotiate = !IsGenericTransferSyntax(connection.GetPreferredTransferSyntax());
+
+      if (renegotiate)
+      {
+        LOG(INFO) << "Use of non-generic transfer syntax: the C-Store associated must be renegotiated";
+      }
     }
     else
     {
       // We are using a specific transfer syntax. Renegotiate if the
       // current connection does not match this transfer syntax.
       renegotiate = (syntax != connection.GetPreferredTransferSyntax());
+
+      if (renegotiate)
+      {
+        LOG(INFO) << "Change in the transfer syntax: the C-Store associated must be renegotiated";
+      }
     }
 
     if (renegotiate)
     {
-      LOG(INFO) << "Change in the transfer syntax: the C-Store associated must be renegotiated";
-
       if (isGeneric)
       {
         connection.ResetPreferredTransferSyntax();
@@ -313,7 +324,6 @@ namespace Orthanc
 
     if (!connection.IsOpen())
     {
-      LOG(INFO) << "Renegotiating a C-Store association due to a change in the parameters";
       connection.Open();
     }
 
@@ -785,13 +795,12 @@ namespace Orthanc
   }
 
 
-  DicomUserConnection::DicomUserConnection() : 
-    pimpl_(new PImpl),
-    preferredTransferSyntax_(DEFAULT_PREFERRED_TRANSFER_SYNTAX),
-    localAet_("STORESCU"),
-    remoteAet_("ANY-SCP"),
-    remoteHost_("127.0.0.1")
+  void DicomUserConnection::DefaultSetup()
   {
+    preferredTransferSyntax_ = DEFAULT_PREFERRED_TRANSFER_SYNTAX;
+    localAet_ = "STORESCU";
+    remoteAet_ = "ANY-SCP";
+    remoteHost_ = "127.0.0.1";
     remotePort_ = 104;
     manufacturer_ = ModalityManufacturer_Generic;
 
@@ -809,6 +818,24 @@ namespace Orthanc
 
     ResetStorageSOPClasses();
   }
+   
+
+  DicomUserConnection::DicomUserConnection() : 
+    pimpl_(new PImpl)
+  {
+    DefaultSetup();
+  }
+  
+
+  DicomUserConnection::DicomUserConnection(const std::string& localAet,
+                                           const RemoteModalityParameters& remote) : 
+    pimpl_(new PImpl)
+  {
+    DefaultSetup();
+    SetLocalApplicationEntityTitle(localAet);
+    SetRemoteModality(remote);
+  }
+
 
   DicomUserConnection::~DicomUserConnection()
   {
@@ -820,7 +847,7 @@ namespace Orthanc
   {
     SetRemoteApplicationEntityTitle(parameters.GetApplicationEntityTitle());
     SetRemoteHost(parameters.GetHost());
-    SetRemotePort(parameters.GetPort());
+    SetRemotePort(parameters.GetPortNumber());
     SetRemoteManufacturer(parameters.GetManufacturer());
   }
 
@@ -1217,4 +1244,15 @@ namespace Orthanc
               << seconds << " seconds (0 = no timeout)";
     defaultTimeout_ = seconds;
   }  
+
+
+  bool DicomUserConnection::IsSameAssociation(const std::string& localAet,
+                                              const RemoteModalityParameters& remote) const
+  {
+    return (localAet_ == localAet &&
+            remoteAet_ == remote.GetApplicationEntityTitle() &&
+            remoteHost_ == remote.GetHost() &&
+            remotePort_ == remote.GetPortNumber() &&
+            manufacturer_ == remote.GetManufacturer());
+  }
 }

Core/DicomNetworking/DicomUserConnection.h

@@ -77,11 +77,18 @@ namespace Orthanc
 
     void CheckStorageSOPClassesInvariant() const;
 
+    void DefaultSetup();
+
   public:
     DicomUserConnection();
 
     ~DicomUserConnection();
 
+    // This constructor corresponds to behavior of the old class
+    // "ReusableDicomUserConnection", without the call to "Open()"
+    DicomUserConnection(const std::string& localAet,
+                        const RemoteModalityParameters& remote);
+
     void SetRemoteModality(const RemoteModalityParameters& parameters);
 
     void SetLocalApplicationEntityTitle(const std::string& aet);
@@ -201,5 +208,8 @@ namespace Orthanc
                       ParsedDicomFile& query);
 
     static void SetDefaultTimeout(uint32_t seconds);
+
+    bool IsSameAssociation(const std::string& localAet,
+                           const RemoteModalityParameters& remote) const;
   };
 }

Core/DicomNetworking/IDicomConnectionManager.h

+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#pragma once
+
+#if !defined(ORTHANC_ENABLE_DCMTK_NETWORKING)
+#  error The macro ORTHANC_ENABLE_DCMTK_NETWORKING must be defined
+#endif
+
+#if ORTHANC_ENABLE_DCMTK_NETWORKING == 0
+
+namespace Orthanc
+{
+  // DICOM networking is disabled, this is just a void class
+  class IDicomConnectionManager : public boost::noncopyable
+  {
+  public:
+    virtual ~IDicomConnectionManager()
+    {
+    }
+  };
+}
+
+#else
+
+#include "DicomUserConnection.h"
+
+namespace Orthanc
+{
+  class IDicomConnectionManager : public boost::noncopyable
+  {
+  public:
+    virtual ~IDicomConnectionManager()
+    {
+    }
+
+    class IResource : public boost::noncopyable
+    {
+    public:
+      virtual ~IResource()
+      {
+      }
+
+      virtual DicomUserConnection& GetConnection() = 0;
+    };
+
+    virtual IResource* AcquireConnection(const std::string& localAet,
+                                         const RemoteModalityParameters& remote) = 0;
+  };
+}
+
+#endif

Core/DicomNetworking/Internals/MoveScp.cpp

@@ -93,6 +93,15 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <boost/lexical_cast.hpp>
 
 
+/**
+ * Macro specifying whether to apply the patch suggested in issue 66:
+ * "Orthanc responses C-MOVE with zero Move Originator Message ID"
+ * https://bitbucket.org/sjodogne/orthanc/issues/66/
+ **/
+
+#define APPLY_FIX_ISSUE_66   1
+
+
 namespace Orthanc
 {
   namespace
@@ -112,7 +121,7 @@ namespace Orthanc
     };
 
 
-
+#if APPLY_FIX_ISSUE_66 != 1
     static uint16_t GetMessageId(const DicomMap& message)
     {
       /**
@@ -145,7 +154,7 @@ namespace Orthanc
 
       return 0;
     }
-
+#endif
 
 
     void MoveScpCallback(
@@ -172,8 +181,15 @@ namespace Orthanc
 
         try
         {
+#if APPLY_FIX_ISSUE_66 == 1
+          uint16_t messageId = request->MessageID;
+#else
+          // The line below was the implementation for Orthanc <= 1.3.2
+          uint16_t messageId = GetMessageId(input);
+#endif
+
           data.iterator_.reset(data.handler_->Handle(data.target_, input, *data.remoteIp_, *data.remoteAet_,
-                                                     *data.calledAet_, GetMessageId(input)));
+                                                     *data.calledAet_, messageId));
 
           if (data.iterator_.get() == NULL)
           {

Core/DicomNetworking/RemoteModalityParameters.cpp

@@ -36,6 +36,7 @@
 
 #include "../Logging.h"
 #include "../OrthancException.h"
+#include "../SerializationToolbox.h"
 
 #include <boost/lexical_cast.hpp>
 #include <stdexcept>
@@ -57,7 +58,7 @@ namespace Orthanc
   {
     SetApplicationEntityTitle(aet);
     SetHost(host);
-    SetPort(port);
+    SetPortNumber(port);
     SetManufacturer(manufacturer);
   }
 
@@ -83,13 +84,13 @@ namespace Orthanc
         throw OrthancException(ErrorCode_ParameterOutOfRange);
       }
 
-      SetPort(static_cast<uint16_t>(tmp));
+      SetPortNumber(static_cast<uint16_t>(tmp));
     }
     catch (std::runtime_error /* error inside JsonCpp */)
     {
       try
       {
-        SetPort(boost::lexical_cast<uint16_t>(portValue.asString()));
+        SetPortNumber(boost::lexical_cast<uint16_t>(portValue.asString()));
       }
       catch (boost::bad_lexical_cast)
       {
@@ -117,12 +118,34 @@ namespace Orthanc
     }
   }
 
+  
   void RemoteModalityParameters::ToJson(Json::Value& value) const
   {
     value = Json::arrayValue;
     value.append(GetApplicationEntityTitle());
     value.append(GetHost());
-    value.append(GetPort());
+    value.append(GetPortNumber());
     value.append(EnumerationToString(GetManufacturer()));
   }
+
+  
+  void RemoteModalityParameters::Serialize(Json::Value& target) const
+  {
+    target = Json::objectValue;
+    target["AET"] = aet_;
+    target["Host"] = host_;
+    target["Port"] = port_;
+    target["Manufacturer"] = EnumerationToString(manufacturer_);
+  }
+
+  
+  RemoteModalityParameters::RemoteModalityParameters(const Json::Value& serialized)
+  {
+    aet_ = SerializationToolbox::ReadString(serialized, "AET");
+    host_ = SerializationToolbox::ReadString(serialized, "Host");
+    port_ = static_cast<uint16_t>
+      (SerializationToolbox::ReadUnsignedInteger(serialized, "Port"));
+    manufacturer_ = StringToModalityManufacturer
+      (SerializationToolbox::ReadString(serialized, "Manufacturer"));
+  }
 }

Core/DicomNetworking/RemoteModalityParameters.h

@@ -52,6 +52,8 @@ namespace Orthanc
   public:
     RemoteModalityParameters();
 
+    RemoteModalityParameters(const Json::Value& serialized);
+
     RemoteModalityParameters(const std::string& aet,
                              const std::string& host,
                              uint16_t port,
@@ -77,12 +79,12 @@ namespace Orthanc
       host_ = host;
     }
     
-    uint16_t GetPort() const
+    uint16_t GetPortNumber() const
     {
       return port_;
     }
 
-    void SetPort(uint16_t port)
+    void SetPortNumber(uint16_t port)
     {
       port_ = port;
     }
@@ -105,5 +107,7 @@ namespace Orthanc
     void FromJson(const Json::Value& modality);
 
     void ToJson(Json::Value& value) const;
+
+    void Serialize(Json::Value& target) const;
   };
 }

Core/DicomNetworking/TimeoutDicomConnectionManager.cpp

+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "../PrecompiledHeaders.h"
+#include "TimeoutDicomConnectionManager.h"
+
+#include "../Logging.h"
+#include "../OrthancException.h"
+
+namespace Orthanc
+{
+  static boost::posix_time::ptime GetNow()
+  {
+    return boost::posix_time::microsec_clock::universal_time();
+  }
+
+  class TimeoutDicomConnectionManager::Resource : public IDicomConnectionManager::IResource
+  {
+  private:
+    TimeoutDicomConnectionManager&  that_;
+
+  public:
+    Resource(TimeoutDicomConnectionManager& that) : 
+      that_(that)
+    {
+      if (that_.connection_.get() == NULL)
+      {
+        throw OrthancException(ErrorCode_InternalError);
+      }
+    }
+
+    ~Resource()
+    {
+      that_.Touch();
+    }
+
+    DicomUserConnection& GetConnection()
+    {
+      assert(that_.connection_.get() != NULL);
+      return *that_.connection_;
+    }
+  };
+
+
+  void TimeoutDicomConnectionManager::Touch()
+  {
+    lastUse_ = GetNow();
+  }
+
+
+  void TimeoutDicomConnectionManager::CheckTimeoutInternal()
+  {
+    if (connection_.get() != NULL &&
+        (GetNow() - lastUse_) >= timeout_)
+    {
+      Close();
+    }
+  }
+
+
+  void TimeoutDicomConnectionManager::SetTimeout(unsigned int timeout)
+  {
+    timeout_ = boost::posix_time::milliseconds(timeout);
+    CheckTimeoutInternal();
+  }
+
+
+  unsigned int TimeoutDicomConnectionManager::GetTimeout()
+  {
+    return timeout_.total_milliseconds();
+  }
+
+
+  void TimeoutDicomConnectionManager::Close()
+  {
+    if (connection_.get() != NULL)
+    {
+      LOG(INFO) << "Closing inactive DICOM association with modality: "
+                << connection_->GetRemoteApplicationEntityTitle();
+
+      connection_.reset(NULL);
+    }
+  }
+
+
+  void TimeoutDicomConnectionManager::CheckTimeout()
+  {
+    CheckTimeoutInternal();
+  }
+
+
+  IDicomConnectionManager::IResource* 
+  TimeoutDicomConnectionManager::AcquireConnection(const std::string& localAet,
+                                                   const RemoteModalityParameters& remote)
+  {
+    if (connection_.get() == NULL ||
+        !connection_->IsSameAssociation(localAet, remote))
+    {
+      connection_.reset(new DicomUserConnection(localAet, remote));
+    }
+
+    return new Resource(*this);
+  }
+}

Core/DicomNetworking/TimeoutDicomConnectionManager.h

+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#pragma once
+
+#include "IDicomConnectionManager.h"
+
+#if ORTHANC_ENABLE_DCMTK_NETWORKING == 0
+
+namespace Orthanc
+{
+  class TimeoutDicomConnectionManager : public IDicomConnectionManager
+  {
+  public:
+    void SetTimeout(unsigned int timeout)
+    {
+    }
+
+    unsigned int GetTimeout()
+    {
+      return 0;
+    }
+
+    void Close()
+    {
+    }
+
+    void CheckTimeout()
+    {
+    }
+  };
+}
+
+#else
+
+#include <boost/date_time/posix_time/posix_time.hpp>
+
+namespace Orthanc
+{
+  class TimeoutDicomConnectionManager : public IDicomConnectionManager
+  {
+  private:
+    class Resource;
+
+    std::auto_ptr<DicomUserConnection>   connection_;
+    boost::posix_time::ptime             lastUse_;
+    boost::posix_time::time_duration     timeout_;
+
+    void Touch();
+
+    void CheckTimeoutInternal();
+
+  public:
+    TimeoutDicomConnectionManager() :
+      timeout_(boost::posix_time::milliseconds(1000))
+    {
+    }
+
+    void SetTimeout(unsigned int timeout);
+
+    unsigned int GetTimeout();
+
+    void Close();
+
+    void CheckTimeout();
+
+    virtual IResource* AcquireConnection(const std::string& localAet,
+                                         const RemoteModalityParameters& remote);
+  };
+}
+
+#endif

Core/DicomParsing/DicomDirWriter.cpp

@@ -164,20 +164,23 @@ namespace Orthanc
                                 const DcmTagKey& key)
     {
       DcmElement* element = NULL;
+      result.clear();
 
       if (source.findAndGetElement(key, element).good())
       {
         char* s = NULL;
         if (element->isLeaf() &&
-            element->getString(s).good() &&
-            s != NULL)
+            element->getString(s).good())
         {
-          result = Toolbox::ConvertToUtf8(s, encoding);
+          if (s != NULL)
+          {
+            result = Toolbox::ConvertToUtf8(s, encoding);
+          }
+          
           return true;
         }
       }
 
-      result.clear();
       return false;
     }
 

Core/DicomParsing/DicomModification.cpp

@@ -36,6 +36,7 @@
 
 #include "../Logging.h"
 #include "../OrthancException.h"
+#include "../SerializationToolbox.h"
 #include "FromDcmtkBridge.h"
 #include "ITagVisitor.h"
 
@@ -315,6 +316,7 @@ namespace Orthanc
     keepStudyInstanceUid_(false),
     keepSeriesInstanceUid_(false),
     updateReferencedRelationships_(true),
+    isAnonymization_(false),
     identifierGenerator_(NULL)
   {
   }
@@ -819,6 +821,8 @@ namespace Orthanc
 
   void DicomModification::SetupAnonymization(DicomVersion version)
   {
+    isAnonymization_ = true;
+    
     removals_.clear();
     clearings_.clear();
     ClearReplacements();
@@ -1029,7 +1033,8 @@ namespace Orthanc
       MapDicomTags(toModify, ResourceType_Instance);
     }
 
-    // (6) Update the "referenced" relationships
+    // (6) Update the "referenced" relationships in the case of an anonymization
+    if (isAnonymization_)
     {
       RelationshipsVisitor visitor(*this);
 
@@ -1237,4 +1242,169 @@ namespace Orthanc
     patientNameReplaced = (IsReplaced(DICOM_TAG_PATIENT_NAME) &&
                            GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName);
   }
+
+
+
+
+  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* 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";
+  
+  void DicomModification::Serialize(Json::Value& value) const
+  {
+    if (identifierGenerator_ != NULL)
+    {
+      LOG(ERROR) << "Cannot serialize a DicomModification with a custom identifier generator";
+      throw OrthancException(ErrorCode_InternalError);
+    }
+
+    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[UPDATE_REFERENCED_RELATIONSHIPS] = updateReferencedRelationships_;
+    value[IS_ANONYMIZATION] = isAnonymization_;
+
+    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* tmp = NULL;
+
+      switch (it->first.first)
+      {
+        case ResourceType_Patient:
+          tmp = &mapPatients;
+          break;
+
+        case ResourceType_Study:
+          tmp = &mapStudies;
+          break;
+
+        case ResourceType_Series:
+          tmp = &mapSeries;
+          break;
+
+        case ResourceType_Instance:
+          tmp = &mapInstances;
+          break;
+
+        default:
+          throw OrthancException(ErrorCode_InternalError);
+      }
+
+      assert(tmp != NULL);
+      (*tmp) [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);
+    updateReferencedRelationships_ = SerializationToolbox::ReadBoolean
+      (serialized, UPDATE_REFERENCED_RELATIONSHIPS);
+    isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);
+
+    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);
+  }
 }

Core/DicomParsing/DicomModification.h

@@ -84,6 +84,7 @@ namespace Orthanc
     bool keepStudyInstanceUid_;
     bool keepSeriesInstanceUid_;
     bool updateReferencedRelationships_;
+    bool isAnonymization_;
     DicomMap currentSource_;
 
     IDicomIdentifierGenerator* identifierGenerator_;
@@ -107,9 +108,15 @@ namespace Orthanc
 
     void SetupAnonymization2017c();
 
+    void UnserializeUidMap(ResourceType level,
+                           const Json::Value& serialized,
+                           const char* field);
+
   public:
     DicomModification();
 
+    DicomModification(const Json::Value& serialized);
+
     ~DicomModification();
 
     void Keep(const DicomTag& tag);
@@ -172,5 +179,7 @@ namespace Orthanc
     {
       identifierGenerator_ = &generator;
     }
+
+    void Serialize(Json::Value& value) const;
   };
 }

Core/DicomParsing/FromDcmtkBridge.cpp

@@ -57,6 +57,7 @@
 #include <boost/lexical_cast.hpp>
 #include <boost/filesystem.hpp>
 #include <boost/algorithm/string/predicate.hpp>
+#include <boost/algorithm/string/join.hpp>
 
 #include <dcmtk/dcmdata/dcdeftag.h>
 #include <dcmtk/dcmdata/dcdicent.h>
@@ -105,27 +106,6 @@
 
 namespace Orthanc
 {
-  static inline uint16_t GetCharValue(char c)
-  {
-    if (c >= '0' && c <= '9')
-      return c - '0';
-    else if (c >= 'a' && c <= 'f')
-      return c - 'a' + 10;
-    else if (c >= 'A' && c <= 'F')
-      return c - 'A' + 10;
-    else
-      return 0;
-  }
-
-  static inline uint16_t GetTagValue(const char* c)
-  {
-    return ((GetCharValue(c[0]) << 12) + 
-            (GetCharValue(c[1]) << 8) + 
-            (GetCharValue(c[2]) << 4) + 
-            GetCharValue(c[3]));
-  }
-
-
 #if DCMTK_USE_EMBEDDED_DICTIONARIES == 1
   static void LoadEmbeddedDictionary(DcmDataDictionary& dictionary,
                                      EmbeddedResources::FileResourceId resource)
@@ -198,6 +178,56 @@ namespace Orthanc
         return &dictionary_;
       }
     };
+
+    
+#define DCMTK_TO_CTYPE_CONVERTER(converter, cType, dcmtkType, getter) \
+ \
+    struct converter \
+    { \
+      typedef cType CType; \
+ \
+      static bool Apply(CType& result, \
+                        DcmElement& element, \
+                        size_t i) \
+      { \
+        return dynamic_cast<dcmtkType&>(element).getter(result, i).good(); \
+      } \
+    };
+
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint32Converter, Sint32, DcmSignedLong, getSint32)
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToSint16Converter, Sint16, DcmSignedShort, getSint16)
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint32Converter, Uint32, DcmUnsignedLong, getUint32)
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToUint16Converter, Uint16, DcmUnsignedShort, getUint16)
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat32Converter, Float32, DcmFloatingPointSingle, getFloat32)
+DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat64Converter, Float64, DcmFloatingPointDouble, getFloat64)
+
+
+    template <typename F>
+    static DicomValue* ApplyDcmtkToCTypeConverter(DcmElement& element)
+    {
+      F f;
+      typename F::CType value;
+
+      if (element.getLength() > sizeof(typename F::CType)
+          && (element.getLength() % sizeof(typename F::CType)) == 0)
+      {
+        size_t count = element.getLength() / sizeof(typename F::CType);
+        std::vector<std::string> strings;
+        for (size_t i = 0; i < count; i++) {
+          if (f.Apply(value, element, i)) {
+            strings.push_back(boost::lexical_cast<std::string>(value));
+          }
+        }
+        return new DicomValue(boost::algorithm::join(strings, "\\"), false);
+      }
+      else if (f.Apply(value, element, 0)) {
+        return new DicomValue(boost::lexical_cast<std::string>(value), false);
+      }
+      else {
+        return new DicomValue;
+      }
+    }
+
   }
 
 
@@ -572,56 +602,32 @@ namespace Orthanc
       
         case EVR_SL:  // signed long
         {
-          Sint32 f;
-          if (dynamic_cast<DcmSignedLong&>(element).getSint32(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToSint32Converter>(element);
         }
 
         case EVR_SS:  // signed short
         {
-          Sint16 f;
-          if (dynamic_cast<DcmSignedShort&>(element).getSint16(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToSint16Converter>(element);
         }
 
         case EVR_UL:  // unsigned long
         {
-          Uint32 f;
-          if (dynamic_cast<DcmUnsignedLong&>(element).getUint32(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToUint32Converter>(element);
         }
 
         case EVR_US:  // unsigned short
         {
-          Uint16 f;
-          if (dynamic_cast<DcmUnsignedShort&>(element).getUint16(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToUint16Converter>(element);
         }
 
         case EVR_FL:  // float single-precision
         {
-          Float32 f;
-          if (dynamic_cast<DcmFloatingPointSingle&>(element).getFloat32(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToFloat32Converter>(element);
         }
 
         case EVR_FD:  // float double-precision
         {
-          Float64 f;
-          if (dynamic_cast<DcmFloatingPointDouble&>(element).getFloat64(f).good())
-            return new DicomValue(boost::lexical_cast<std::string>(f), false);
-          else
-            return new DicomValue;
+          return ApplyDcmtkToCTypeConverter<DcmtkToFloat64Converter>(element);
         }
 
 
@@ -1034,35 +1040,10 @@ namespace Orthanc
 
   DicomTag FromDcmtkBridge::ParseTag(const char* name)
   {
-    if (strlen(name) == 9 &&
-        isxdigit(name[0]) &&
-        isxdigit(name[1]) &&
-        isxdigit(name[2]) &&
-        isxdigit(name[3]) &&
-        (name[4] == '-' || name[4] == ',') &&
-        isxdigit(name[5]) &&
-        isxdigit(name[6]) &&
-        isxdigit(name[7]) &&
-        isxdigit(name[8]))        
-    {
-      uint16_t group = GetTagValue(name);
-      uint16_t element = GetTagValue(name + 5);
-      return DicomTag(group, element);
-    }
-
-    if (strlen(name) == 8 &&
-        isxdigit(name[0]) &&
-        isxdigit(name[1]) &&
-        isxdigit(name[2]) &&
-        isxdigit(name[3]) &&
-        isxdigit(name[4]) &&
-        isxdigit(name[5]) &&
-        isxdigit(name[6]) &&
-        isxdigit(name[7]))        
-    {
-      uint16_t group = GetTagValue(name);
-      uint16_t element = GetTagValue(name + 4);
-      return DicomTag(group, element);
+    DicomTag parsed(0, 0);
+    if (DicomTag::ParseHexadecimal(parsed, name))
+    {
+      return parsed;
     }
 
 #if 0

Core/DicomParsing/Internals/DicomImageDecoder.cpp

@@ -93,6 +93,7 @@
 #if ORTHANC_ENABLE_JPEG == 1
 #  include "../../Images/JpegWriter.h"
 #endif
+#include "../../Images/PamWriter.h"
 
 #include <boost/lexical_cast.hpp>
 
@@ -952,6 +953,17 @@ namespace Orthanc
   }
 
 
+  void DicomImageDecoder::ExtractPamImage(std::string& result,
+                                          std::auto_ptr<ImageAccessor>& image,
+                                          ImageExtractionMode mode,
+                                          bool invert)
+  {
+    ApplyExtractionMode(image, mode, invert);
+
+    PamWriter writer;
+    writer.WriteToMemory(result, *image);
+  }
+
 #if ORTHANC_ENABLE_PNG == 1
   void DicomImageDecoder::ExtractPngImage(std::string& result,
                                           std::auto_ptr<ImageAccessor>& image,

Core/DicomParsing/Internals/DicomImageDecoder.h

@@ -101,6 +101,11 @@ namespace Orthanc
     static ImageAccessor *Decode(ParsedDicomFile& dicom,
                                  unsigned int frame);
 
+    static void ExtractPamImage(std::string& result,
+                                std::auto_ptr<ImageAccessor>& image,
+                                ImageExtractionMode mode,
+                                bool invert);
+
 #if ORTHANC_ENABLE_PNG == 1
     static void ExtractPngImage(std::string& result,
                                 std::auto_ptr<ImageAccessor>& image,