.hg_archival.txt

 repo: 3959d33612ccaadc0d4d707227fbed09ac35e5fe
-node: 218854b02a71c1ba79b446bf4273179b0098ae48
-branch: Orthanc-1.4.1
+node: afb581263e1d79e67ebf2fc1ca85780f9f3783e5
+branch: Orthanc-1.4.2
 latesttag: dcmtk-3.6.1
-latesttagdistance: 366
-changessincelatesttag: 408
+latesttagdistance: 423
+changessincelatesttag: 465

AUTHORS

@@ -15,6 +15,6 @@ Authors of Orthanc
   Belgium
 
 * Osimis S.A. <info@osimis.io>
-  Rue des Chasseurs Ardennais 3
-  4031 Liege 
+  Rue du Bois Saint-Jean 15/1
+  4102 Seraing
   Belgium

CMakeLists.txt

@@ -125,6 +125,7 @@ if (ENABLE_PLUGINS)
     Plugins/Engine/OrthancPlugins.cpp
     Plugins/Engine/PluginsEnumerations.cpp
     Plugins/Engine/PluginsErrorDictionary.cpp
+    Plugins/Engine/PluginsJob.cpp
     Plugins/Engine/PluginsManager.cpp
     )
 

Core/DicomFormat/DicomMap.cpp

@@ -109,7 +109,16 @@ namespace Orthanc
     DICOM_TAG_TEMPORAL_POSITION_IDENTIFIER,
     DICOM_TAG_SOP_INSTANCE_UID,
     DICOM_TAG_IMAGE_POSITION_PATIENT,    // New in db v6
-    DICOM_TAG_IMAGE_COMMENTS             // New in db v6
+    DICOM_TAG_IMAGE_COMMENTS,            // New in db v6
+
+    /**
+     * Main DICOM tags that are not part of any release of the
+     * database schema yet, and that will be part of future db v7. In
+     * the meantime, the user must call "/tools/reconstruct" once to
+     * access these tags if the corresponding DICOM files where
+     * indexed in the database by an older version of Orthanc.
+     **/
+    DICOM_TAG_IMAGE_ORIENTATION_PATIENT  // New in Orthanc 1.4.2
   };
 
 

Core/DicomNetworking/Internals/CommandDispatcher.cpp

@@ -527,8 +527,6 @@ namespace Orthanc
         transferSyntaxes.push_back(UID_JPEGProcess28TransferSyntax);
         transferSyntaxes.push_back(UID_JPEGProcess29TransferSyntax);
         transferSyntaxes.push_back(UID_JPEGProcess14SV1TransferSyntax);
-        transferSyntaxes.push_back(UID_JPEGLSLosslessTransferSyntax);
-        transferSyntaxes.push_back(UID_JPEGLSLossyTransferSyntax);
       }
 
       if (!server.HasApplicationEntityFilter() ||
@@ -536,15 +534,17 @@ namespace Orthanc
       {
         transferSyntaxes.push_back(UID_JPEG2000LosslessOnlyTransferSyntax);
         transferSyntaxes.push_back(UID_JPEG2000TransferSyntax);
+        transferSyntaxes.push_back(UID_JPEG2000LosslessOnlyTransferSyntax);
+        transferSyntaxes.push_back(UID_JPEG2000TransferSyntax);
+        transferSyntaxes.push_back(UID_JPEG2000Part2MulticomponentImageCompressionLosslessOnlyTransferSyntax);
+        transferSyntaxes.push_back(UID_JPEG2000Part2MulticomponentImageCompressionTransferSyntax);
       }
 
       if (!server.HasApplicationEntityFilter() ||
           server.GetApplicationEntityFilter().IsAllowedTransferSyntax(remoteIp, remoteAet, calledAet, TransferSyntax_JpegLossless))
       {
-        transferSyntaxes.push_back(UID_JPEG2000LosslessOnlyTransferSyntax);
-        transferSyntaxes.push_back(UID_JPEG2000TransferSyntax);
-        transferSyntaxes.push_back(UID_JPEG2000Part2MulticomponentImageCompressionLosslessOnlyTransferSyntax);
-        transferSyntaxes.push_back(UID_JPEG2000Part2MulticomponentImageCompressionTransferSyntax);
+        transferSyntaxes.push_back(UID_JPEGLSLosslessTransferSyntax);
+        transferSyntaxes.push_back(UID_JPEGLSLossyTransferSyntax);
       }
 
       if (!server.HasApplicationEntityFilter() ||

Core/DicomParsing/FromDcmtkBridge.cpp

@@ -1714,11 +1714,32 @@ DCMTK_TO_CTYPE_CONVERTER(DcmtkToFloat64Converter, Float64, DcmFloatingPointDoubl
         {
           std::auto_ptr<DcmItem> item(new DcmItem);
 
+          switch (value[i].type())
+          {
+            case Json::objectValue:
+            {
               Json::Value::Members members = value[i].getMemberNames();
               for (Json::Value::ArrayIndex j = 0; j < members.size(); j++)
               {
                 item->insert(FromJson(ParseTag(members[j]), value[i][members[j]], decodeDataUriScheme, dicomEncoding));
               }
+              break;
+            }
+
+            case Json::arrayValue:
+            {
+              // Lua cannot disambiguate between an empty dictionary
+              // and an empty array
+              if (value[i].size() != 0)
+              {
+                throw OrthancException(ErrorCode_BadParameterType);
+              }
+              break;
+            }
+
+            default:
+              throw OrthancException(ErrorCode_BadParameterType);
+          }
 
           sequence->append(item.release());
         }

Core/DicomParsing/ParsedDicomFile.cpp

@@ -525,6 +525,13 @@ namespace Orthanc
   void ParsedDicomFile::Clear(const DicomTag& tag,
                               bool onlyIfExists)
   {
+    if (tag.GetElement() == 0x0000)
+    {
+      // Prevent manually modifying generic group length tags: This is
+      // handled by DCMTK serialization
+      return;
+    }
+
     InvalidateCache();
 
     DcmItem* dicom = pimpl_->file_->getDataset();
@@ -612,6 +619,13 @@ namespace Orthanc
                                const Json::Value& value,
                                bool decodeDataUriScheme)
   {
+    if (tag.GetElement() == 0x0000)
+    {
+      // Prevent manually modifying generic group length tags: This is
+      // handled by DCMTK serialization
+      return;
+    }
+
     if (pimpl_->file_->getDataset()->tagExists(ToDcmtkBridge::Convert(tag)))
     {
       throw OrthancException(ErrorCode_AlreadyExistingTag);
@@ -724,6 +738,13 @@ namespace Orthanc
                                 bool decodeDataUriScheme,
                                 DicomReplaceMode mode)
   {
+    if (tag.GetElement() == 0x0000)
+    {
+      // Prevent manually modifying generic group length tags: This is
+      // handled by DCMTK serialization
+      return;
+    }
+
     InvalidateCache();
 
     DcmDataset& dicom = *pimpl_->file_->getDataset();
@@ -756,6 +777,13 @@ namespace Orthanc
                                 bool decodeDataUriScheme,
                                 DicomReplaceMode mode)
   {
+    if (tag.GetElement() == 0x0000)
+    {
+      // Prevent manually modifying generic group length tags: This is
+      // handled by DCMTK serialization
+      return;
+    }
+
     InvalidateCache();
 
     DcmDataset& dicom = *pimpl_->file_->getDataset();

Core/Endianness.h

@@ -145,13 +145,18 @@
 
 static inline uint16_t __orthanc_bswap16(uint16_t a)
 {
-  const uint8_t* p = reinterpret_cast<const uint8_t*>(&a);
-  return (static_cast<uint16_t>(p[0]) << 8 |
-          static_cast<uint16_t>(p[1]));
-
-  // WARNING: The implementation below makes LSB (Linux Standard
-  // Base) segfault in release builds. Don't use it!!!
-  // return (a << 8) | (a >> 8);
+  /**
+   * Note that an alternative implementation was included in Orthanc
+   * 1.4.0 and 1.4.1:
+   * 
+   *  # hg log -p -r 2706
+   *
+   * This alternative implementation only hid an underlying problem
+   * with pointer alignment on some architectures, and was thus
+   * reverted. Check out issue #99:
+   * https://bitbucket.org/sjodogne/orthanc/issues/99
+   **/
+  return (a << 8) | (a >> 8);
 }
 
 static inline uint32_t __orthanc_bswap32(uint32_t a)

Core/Enumerations.h

@@ -509,7 +509,10 @@ namespace Orthanc
   enum DicomFromJsonFlags
   {
     DicomFromJsonFlags_DecodeDataUriScheme = (1 << 0),
-    DicomFromJsonFlags_GenerateIdentifiers = (1 << 1)
+    DicomFromJsonFlags_GenerateIdentifiers = (1 << 1),
+
+    // Some predefined combinations
+    DicomFromJsonFlags_None = 0
   };
   
   enum DicomVersion
@@ -567,6 +570,15 @@ namespace Orthanc
     JobStepCode_Retry
   };
 
+  enum JobStopReason
+  {
+    JobStopReason_Paused,
+    JobStopReason_Canceled,
+    JobStopReason_Success,
+    JobStopReason_Failure,
+    JobStopReason_Retry
+  };
+
 
   /**
    * WARNING: Do not change the explicit values in the enumerations

Core/FileStorage/MemoryStorageArea.cpp

@@ -35,6 +35,7 @@
 #include "MemoryStorageArea.h"
 
 #include "../OrthancException.h"
+#include "../Logging.h"
 
 namespace Orthanc
 {
@@ -54,6 +55,9 @@ namespace Orthanc
                                  size_t size,
                                  FileContentType type)
   {
+    LOG(INFO) << "Creating attachment \"" << uuid << "\" of \"" << static_cast<int>(type)
+              << "\" type (size: " << (size / (1024 * 1024) + 1) << "MB)";
+
     boost::mutex::scoped_lock lock(mutex_);
 
     if (size != 0 &&
@@ -76,6 +80,9 @@ namespace Orthanc
                                const std::string& uuid,
                                FileContentType type)
   {
+    LOG(INFO) << "Reading attachment \"" << uuid << "\" of \""
+              << static_cast<int>(type) << "\" content type";
+
     boost::mutex::scoped_lock lock(mutex_);
 
     Content::const_iterator found = content_.find(uuid);
@@ -98,6 +105,8 @@ namespace Orthanc
   void MemoryStorageArea::Remove(const std::string& uuid,
                                  FileContentType type)
   {
+    LOG(INFO) << "Deleting attachment \"" << uuid << "\" of type " << static_cast<int>(type);
+
     boost::mutex::scoped_lock lock(mutex_);
 
     Content::iterator found = content_.find(uuid);

Core/HttpClient.cpp

@@ -95,10 +95,12 @@ namespace Orthanc
     std::string     httpsCACertificates_;
     std::string     proxy_;
     long            timeout_;
+    bool            verbose_;
 
     GlobalParameters() : 
       httpsVerifyPeers_(true),
-      timeout_(0)
+      timeout_(0),
+      verbose_(false)
     {
     }
 
@@ -173,6 +175,16 @@ namespace Orthanc
       Pkcs11::Initialize(module, pin, verbose);
     }
 #endif
+
+    bool IsDefaultVerbose() const
+    {
+      return verbose_;
+    }
+
+    void SetDefaultVerbose(bool verbose) 
+    {
+      verbose_ = verbose;
+    }
   };
 
 
@@ -184,7 +196,7 @@ namespace Orthanc
   };
 
 
-  static void ThrowException(HttpStatus status)
+  void HttpClient::ThrowException(HttpStatus status)
   {
     switch (status)
     {
@@ -240,6 +252,36 @@ namespace Orthanc
   }
 
 
+  /*static int CurlDebugCallback(CURL *handle,
+                               curl_infotype type,
+                               char *data,
+                               size_t size,
+                               void *userptr)
+  {
+    switch (type)
+    {
+      case CURLINFO_TEXT:
+      case CURLINFO_HEADER_IN:
+      case CURLINFO_HEADER_OUT:
+      case CURLINFO_SSL_DATA_IN:
+      case CURLINFO_SSL_DATA_OUT:
+      case CURLINFO_END:
+      case CURLINFO_DATA_IN:
+      case CURLINFO_DATA_OUT:
+      {
+        std::string s(data, size);
+        LOG(INFO) << "libcurl: " << s;
+        break;
+      }
+
+      default:
+        break;
+    }
+
+    return 0;
+    }*/
+
+
   struct CurlHeaderParameters
   {
     bool lowerCase_;
@@ -314,7 +356,7 @@ namespace Orthanc
     url_ = "";
     method_ = HttpMethod_Get;
     lastStatus_ = HttpStatus_200_Ok;
-    SetVerbose(false);
+    SetVerbose(GlobalParameters::GetInstance().IsDefaultVerbose());
     timeout_ = GlobalParameters::GetInstance().GetDefaultTimeout();
     GlobalParameters::GetInstance().GetDefaultProxy(proxy_);
     GlobalParameters::GetInstance().GetSslConfiguration(verifyPeers_, caCertificates_);    
@@ -358,6 +400,13 @@ namespace Orthanc
     SetPkcs11Enabled(service.IsPkcs11Enabled());
 
     SetUrl(service.GetUrl() + uri);
+
+    for (WebServiceParameters::Dictionary::const_iterator 
+           it = service.GetHttpHeaders().begin();
+         it != service.GetHttpHeaders().end(); ++it)
+    {
+      AddHeader(it->first, it->second);
+    }
   }
 
 
@@ -376,6 +425,7 @@ namespace Orthanc
     if (isVerbose_)
     {
       CheckCode(curl_easy_setopt(pimpl_->curl_, CURLOPT_VERBOSE, 1));
+      //CheckCode(curl_easy_setopt(pimpl_->curl_, CURLOPT_DEBUGFUNCTION, &CurlDebugCallback));
     }
     else
     {
@@ -613,6 +663,14 @@ namespace Orthanc
       code = GetHttpStatus(curl_easy_perform(pimpl_->curl_), pimpl_->curl_, &status);
     }
 
+    LOG(INFO) << "HTTP status code " << status << " after "
+              << EnumerationToString(method_) << " request on: " << url_;
+
+    if (isVerbose_)
+    {
+      LOG(INFO) << "cURL status code: " << code;
+    }
+
     CheckCode(code);
 
     if (status == 0)
@@ -711,6 +769,12 @@ namespace Orthanc
   }
   
 
+  void HttpClient::SetDefaultVerbose(bool verbose)
+  {
+    GlobalParameters::GetInstance().SetDefaultVerbose(verbose);
+  }
+
+
   void HttpClient::SetDefaultProxy(const std::string& proxy)
   {
     GlobalParameters::GetInstance().SetDefaultProxy(proxy);

Core/HttpClient.h

@@ -275,6 +275,8 @@ namespace Orthanc
     static void ConfigureSsl(bool httpsVerifyPeers,
                              const std::string& httpsCACertificates);
 
+    static void SetDefaultVerbose(bool verbose);
+
     static void SetDefaultProxy(const std::string& proxy);
 
     static void SetDefaultTimeout(long timeout);
@@ -288,5 +290,7 @@ namespace Orthanc
 
     void ApplyAndThrowException(Json::Value& answerBody,
                                 HttpHeaders& answerHeaders);
+
+    static void ThrowException(HttpStatus status);
   };
 }

Core/HttpServer/HttpOutput.cpp

@@ -432,16 +432,44 @@ namespace Orthanc
     {
       if (!Toolbox::StartsWith(*it, "Set-Cookie: "))
       {
-        LOG(ERROR) << "The only headers that can be set in multipart answers are Set-Cookie (here: " << *it << " is set)";
+        LOG(ERROR) << "The only headers that can be set in multipart answers "
+                   << "are Set-Cookie (here: " << *it << " is set)";
         throw OrthancException(ErrorCode_BadSequenceOfCalls);
       }
 
       header += *it;
     }
 
+    /**
+     * Fix for issue 54 ("Decide what to do wrt. quoting of multipart
+     * answers"). The "type" parameter in the "Content-Type" HTTP
+     * header must be quoted if it contains a forward slash "/". This
+     * is necessary for DICOMweb compatibility with OsiriX, but breaks
+     * compatibility with old releases of the client in the Orthanc
+     * DICOMweb plugin <= 0.3 (releases >= 0.4 work fine).
+     *
+     * Full history is available at the following locations:
+     * - In changeset 2248:69b0f4e8a49b:
+     *   # hg history -v -r 2248
+     * - https://bitbucket.org/sjodogne/orthanc/issues/54/
+     * - https://groups.google.com/d/msg/orthanc-users/65zhIM5xbKI/TU5Q1_LhAwAJ
+     **/
+    std::string tmp;
+    if (contentType.find('/') == std::string::npos)
+    {
+      // No forward slash in the content type
+      tmp = contentType;
+    }
+    else
+    {
+      // Quote the content type because of the forward slash
+      tmp = "\"" + contentType + "\"";
+    }
+
     multipartBoundary_ = Toolbox::GenerateUuid();
     multipartContentType_ = contentType;
-    header += "Content-Type: multipart/" + subType + "; type=" + contentType + "; boundary=" + multipartBoundary_ + "\r\n\r\n";
+    header += ("Content-Type: multipart/" + subType + "; type=" +
+               tmp + "; boundary=" + multipartBoundary_ + "\r\n\r\n");
 
     stream_.Send(true, header.c_str(), header.size());
     state_ = State_WritingMultipart;

Core/HttpServer/MongooseServer.cpp

@@ -611,7 +611,7 @@ namespace Orthanc
     if (!server.IsRemoteAccessAllowed() &&
         !localhost)
     {
-      output.SendUnauthorized(ORTHANC_REALM);
+      output.SendUnauthorized(server.GetRealm());
       return;
     }
 
@@ -655,7 +655,7 @@ namespace Orthanc
     if (server.IsAuthenticationEnabled() && 
         !IsAccessGranted(server, headers))
     {
-      output.SendUnauthorized(ORTHANC_REALM);
+      output.SendUnauthorized(server.GetRealm());
       return;
     }
 
@@ -682,7 +682,7 @@ namespace Orthanc
       if (!filter->IsAllowed(method, request->uri, remoteIp,
                              username.c_str(), headers, argumentsGET))
       {
-        //output.SendUnauthorized(ORTHANC_REALM);
+        //output.SendUnauthorized(server.GetRealm());
         output.SendStatus(HttpStatus_403_Forbidden);
         return;
       }
@@ -917,6 +917,7 @@ namespace Orthanc
     keepAlive_ = false;
     httpCompression_ = true;
     exceptionFormatter_ = NULL;
+    realm_ = ORTHANC_REALM;
 
 #if ORTHANC_ENABLE_SSL == 1
     // Check for the Heartbleed exploit

Core/HttpServer/MongooseServer.h

@@ -96,6 +96,7 @@ namespace Orthanc
     bool keepAlive_;
     bool httpCompression_;
     IHttpExceptionFormatter* exceptionFormatter_;
+    std::string realm_;
   
     bool IsRunning() const;
 
@@ -188,5 +189,15 @@ namespace Orthanc
     {
       return exceptionFormatter_;
     }
+
+    const std::string& GetRealm() const
+    {
+      return realm_;
+    }
+
+    void SetRealm(const std::string& realm)
+    {
+      realm_ = realm;
+    }
   };
 }

Core/Images/ImageProcessing.cpp

@@ -1219,6 +1219,19 @@ namespace Orthanc
         break;
       }
         
+      case Orthanc::PixelFormat_RGBA32:
+      {
+        PixelTraits<Orthanc::PixelFormat_RGBA32>::PixelType pixel;
+        pixel.red_ = red;
+        pixel.green_ = green;
+        pixel.blue_ = blue;
+        pixel.alpha_ = alpha;
+
+        BresenhamPixelWriter<Orthanc::PixelFormat_RGBA32> writer(image, pixel);
+        writer.DrawSegment(x0, y0, x1, y1);
+        break;
+      }
+        
       case Orthanc::PixelFormat_RGB24:
       {
         PixelTraits<Orthanc::PixelFormat_RGB24>::PixelType pixel;

Core/Images/PamReader.cpp

@@ -209,7 +209,8 @@ namespace Orthanc
       throw OrthancException(ErrorCode_NotImplemented);
     }
     
-    if (Toolbox::DetectEndianness() == Endianness_Little && bytesPerChannel == 2)
+    if (Toolbox::DetectEndianness() == Endianness_Little &&
+        bytesPerChannel == 2)
     {
       for (unsigned int h = 0; h < height; ++h)
       {
@@ -217,7 +218,12 @@ namespace Orthanc
         
         for (unsigned int w = 0; w < GetWidth(); ++w, ++pixel)
         {
-          *pixel = htobe16(*pixel);
+          // memcpy() is necessary to avoid segmentation fault if the
+          // "pixel" pointer is not 16-bit aligned (which is the case
+          // if "offset" is an odd number). Check out issue #99:
+          // https://bitbucket.org/sjodogne/orthanc/issues/99
+          uint16_t v = htobe16(*pixel);
+          memcpy(pixel, &v, sizeof(v));
         }
       }
     }

Core/Images/PamWriter.cpp

@@ -130,7 +130,13 @@ namespace Orthanc
         
         for (unsigned int w = 0; w < width * channelCount; ++w)
         {
-          *q = htobe16(*p);
+          // memcpy() is necessary to avoid segmentation fault if the
+          // "pixel" pointer is not 16-bit aligned (which is the case
+          // if "offset" is an odd number). Check out issue #99:
+          // https://bitbucket.org/sjodogne/orthanc/issues/99
+          uint16_t v = htobe16(*p);
+          memcpy(q, &v, sizeof(uint16_t));
+
           p++;
           q++;
         }

Core/Images/PixelTraits.h

@@ -280,6 +280,67 @@ namespace Orthanc
   };
 
 
+  template <>
+  struct PixelTraits<PixelFormat_RGBA32>
+  {
+    struct PixelType
+    {
+      uint8_t  red_;
+      uint8_t  green_;
+      uint8_t  blue_;
+      uint8_t  alpha_;
+    };
+
+    ORTHANC_FORCE_INLINE
+    static PixelFormat GetPixelFormat()
+    {
+      return PixelFormat_RGBA32;
+    }
+
+    ORTHANC_FORCE_INLINE
+    static void SetZero(PixelType& target)
+    {
+      target.red_ = 0;
+      target.green_ = 0;
+      target.blue_ = 0;
+      target.alpha_ = 0;
+    }
+
+    ORTHANC_FORCE_INLINE
+    static void Copy(PixelType& target,
+                     const PixelType& source)
+    {
+      target.red_ = source.red_;
+      target.green_ = source.green_;
+      target.blue_ = source.blue_;
+      target.alpha_ = source.alpha_;
+    }
+
+    ORTHANC_FORCE_INLINE
+    static bool IsEqual(const PixelType& a,
+                        const PixelType& b)
+    {
+      return (a.red_ == b.red_ &&
+              a.green_ == b.green_ &&
+              a.blue_ == b.blue_ &&
+              a.alpha_ == b.alpha_);
+    }
+
+    ORTHANC_FORCE_INLINE
+    static void FloatToPixel(PixelType& target,
+                             float value)
+    {
+      uint8_t v;
+      PixelTraits<PixelFormat_Grayscale8>::FloatToPixel(v, value);
+
+      target.red_ = v;
+      target.green_ = v;
+      target.blue_ = v;
+      target.alpha_ = 255;      
+    }
+  };
+
+
   template <>
   struct PixelTraits<PixelFormat_Float32>
   {

Core/JobsEngine/IJob.h

@@ -50,12 +50,13 @@ namespace Orthanc
     // Method called once the job enters the jobs engine
     virtual void Start() = 0;
     
-    virtual JobStepResult ExecuteStep() = 0;
+    virtual JobStepResult Step() = 0;
 
     // Method called once the job is resubmitted after a failure
-    virtual void SignalResubmit() = 0;
+    virtual void Reset() = 0;
 
-    virtual void ReleaseResources() = 0;   // For pausing/canceling jobs
+    // For pausing/canceling/ending jobs: This method must release allocated resources
+    virtual void Stop(JobStopReason reason) = 0;
 
     virtual float GetProgress() = 0;