Mercurial > hg > orthanc

changeset 1689:26083d84d237

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refactoring
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 07 Oct 2015 16:54:05 +0200
parents 27d70e9ee2e4
children ae09132e4237
files OrthancServer/FromDcmtkBridge.cpp OrthancServer/FromDcmtkBridge.h OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp OrthancServer/ParsedDicomFile.cpp
diffstat 4 files changed, 340 insertions(+), 302 deletions(-) [+]
line wrap: on
line diff
--- a/OrthancServer/FromDcmtkBridge.cpp	Wed Oct 07 15:06:31 2015 +0200
+++ b/OrthancServer/FromDcmtkBridge.cpp	Wed Oct 07 16:54:05 2015 +0200
@@ -95,6 +95,7 @@
 #include <dcmtk/dcmnet/dul.h>
 
 #include <boost/math/special_functions/round.hpp>
+#include <boost/algorithm/string/predicate.hpp>
 #include <dcmtk/dcmdata/dcostrmb.h>
 
 
@@ -1023,4 +1024,321 @@
     }
   }
 
+
+
+  DcmElement* FromDcmtkBridge::CreateElementForTag(const DicomTag& tag)
+  {
+    DcmTag key(tag.GetGroup(), tag.GetElement());
+
+    switch (key.getEVR())
+    {
+      // http://support.dcmtk.org/docs/dcvr_8h-source.html
+
+      /**
+       * TODO.
+       **/
+    
+      case EVR_OB:  // other byte
+      case EVR_OF:  // other float
+      case EVR_OW:  // other word
+      case EVR_AT:  // attribute tag
+        throw OrthancException(ErrorCode_NotImplemented);
+
+      case EVR_UN:  // unknown value representation
+        throw OrthancException(ErrorCode_ParameterOutOfRange);
+
+
+      /**
+       * String types.
+       * http://support.dcmtk.org/docs/classDcmByteString.html
+       **/
+      
+      case EVR_AS:  // age string
+        return new DcmAgeString(key);
+
+      case EVR_AE:  // application entity title
+        return new DcmApplicationEntity(key);
+
+      case EVR_CS:  // code string
+        return new DcmCodeString(key);        
+
+      case EVR_DA:  // date string
+        return new DcmDate(key);
+        
+      case EVR_DT:  // date time string
+        return new DcmDateTime(key);
+
+      case EVR_DS:  // decimal string
+        return new DcmDecimalString(key);
+
+      case EVR_IS:  // integer string
+        return new DcmIntegerString(key);
+
+      case EVR_TM:  // time string
+        return new DcmTime(key);
+
+      case EVR_UI:  // unique identifier
+        return new DcmUniqueIdentifier(key);
+
+      case EVR_ST:  // short text
+        return new DcmShortText(key);
+
+      case EVR_LO:  // long string
+        return new DcmLongString(key);
+
+      case EVR_LT:  // long text
+        return new DcmLongText(key);
+
+      case EVR_UT:  // unlimited text
+        return new DcmUnlimitedText(key);
+
+      case EVR_SH:  // short string
+        return new DcmShortString(key);
+
+      case EVR_PN:  // person name
+        return new DcmPersonName(key);
+
+        
+      /**
+       * Numerical types
+       **/ 
+      
+      case EVR_SL:  // signed long
+        return new DcmSignedLong(key);
+
+      case EVR_SS:  // signed short
+        return new DcmSignedShort(key);
+
+      case EVR_UL:  // unsigned long
+        return new DcmUnsignedLong(key);
+
+      case EVR_US:  // unsigned short
+        return new DcmUnsignedShort(key);
+
+      case EVR_FL:  // float single-precision
+        return new DcmFloatingPointSingle(key);
+
+      case EVR_FD:  // float double-precision
+        return new DcmFloatingPointDouble(key);
+
+
+      /**
+       * Sequence types, should never occur at this point.
+       **/
+
+      case EVR_SQ:  // sequence of items
+        throw OrthancException(ErrorCode_ParameterOutOfRange);
+
+
+      /**
+       * Internal to DCMTK.
+       **/ 
+
+      case EVR_ox:  // OB or OW depending on context
+      case EVR_xs:  // SS or US depending on context
+      case EVR_lt:  // US, SS or OW depending on context, used for LUT Data (thus the name)
+      case EVR_na:  // na="not applicable", for data which has no VR
+      case EVR_up:  // up="unsigned pointer", used internally for DICOMDIR suppor
+      case EVR_item:  // used internally for items
+      case EVR_metainfo:  // used internally for meta info datasets
+      case EVR_dataset:  // used internally for datasets
+      case EVR_fileFormat:  // used internally for DICOM files
+      case EVR_dicomDir:  // used internally for DICOMDIR objects
+      case EVR_dirRecord:  // used internally for DICOMDIR records
+      case EVR_pixelSQ:  // used internally for pixel sequences in a compressed image
+      case EVR_pixelItem:  // used internally for pixel items in a compressed image
+      case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
+      case EVR_PixelData:  // used internally for uncompressed pixeld data
+      case EVR_OverlayData:  // used internally for overlay data
+      case EVR_UNKNOWN2B:  // used internally for elements with unknown VR with 2-byte length field in explicit VR
+      default:
+        break;
+    }
+
+    throw OrthancException(ErrorCode_InternalError);          
+  }
+
+
+
+  void FromDcmtkBridge::FillElementWithString(DcmElement& element,
+                                              const DicomTag& tag,
+                                              const std::string& value,
+                                              bool decodeBinaryTags)
+  {
+    std::string binary;
+    const std::string* decoded = &value;
+
+    if (decodeBinaryTags &&
+        boost::starts_with(value, "data:application/octet-stream;base64,"))
+    {
+      std::string mime;
+      Toolbox::DecodeDataUriScheme(mime, binary, value);
+      decoded = &binary;
+    }
+
+
+    if (FromDcmtkBridge::IsPrivateTag(tag) ||
+        FromDcmtkBridge::IsUnknownTag(tag))
+    {
+      if (element.putUint8Array((const Uint8*) decoded->c_str(), decoded->size()).good())
+      {
+        return;
+      }
+      else
+      {
+        throw OrthancException(ErrorCode_InternalError);
+      }
+    }
+
+    DcmTag key(tag.GetGroup(), tag.GetElement());
+    bool ok = false;
+    
+    try
+    {
+      switch (key.getEVR())
+      {
+        // http://support.dcmtk.org/docs/dcvr_8h-source.html
+
+        /**
+         * TODO.
+         **/
+
+        case EVR_OB:  // other byte
+        case EVR_OF:  // other float
+        case EVR_OW:  // other word
+        case EVR_AT:  // attribute tag
+          throw OrthancException(ErrorCode_NotImplemented);
+    
+        case EVR_UN:  // unknown value representation
+          throw OrthancException(ErrorCode_ParameterOutOfRange);
+
+
+        /**
+         * String types.
+         **/
+      
+        case EVR_DS:  // decimal string
+        case EVR_IS:  // integer string
+        case EVR_AS:  // age string
+        case EVR_DA:  // date string
+        case EVR_DT:  // date time string
+        case EVR_TM:  // time string
+        case EVR_AE:  // application entity title
+        case EVR_CS:  // code string
+        case EVR_SH:  // short string
+        case EVR_LO:  // long string
+        case EVR_ST:  // short text
+        case EVR_LT:  // long text
+        case EVR_UT:  // unlimited text
+        case EVR_PN:  // person name
+        case EVR_UI:  // unique identifier
+        {
+          ok = element.putString(decoded->c_str()).good();
+          break;
+        }
+
+        
+        /**
+         * Numerical types
+         **/ 
+      
+        case EVR_SL:  // signed long
+        {
+          ok = element.putSint32(boost::lexical_cast<Sint32>(*decoded)).good();
+          break;
+        }
+
+        case EVR_SS:  // signed short
+        {
+          ok = element.putSint16(boost::lexical_cast<Sint16>(*decoded)).good();
+          break;
+        }
+
+        case EVR_UL:  // unsigned long
+        {
+          ok = element.putUint32(boost::lexical_cast<Uint32>(*decoded)).good();
+          break;
+        }
+
+        case EVR_US:  // unsigned short
+        {
+          ok = element.putUint16(boost::lexical_cast<Uint16>(*decoded)).good();
+          break;
+        }
+
+        case EVR_FL:  // float single-precision
+        {
+          ok = element.putFloat32(boost::lexical_cast<float>(*decoded)).good();
+          break;
+        }
+
+        case EVR_FD:  // float double-precision
+        {
+          ok = element.putFloat64(boost::lexical_cast<double>(*decoded)).good();
+          break;
+        }
+
+
+        /**
+         * Sequence types, should never occur at this point.
+         **/
+
+        case EVR_SQ:  // sequence of items
+        {
+          ok = false;
+          break;
+        }
+
+
+        /**
+         * Internal to DCMTK.
+         **/ 
+
+        case EVR_ox:  // OB or OW depending on context
+        case EVR_xs:  // SS or US depending on context
+        case EVR_lt:  // US, SS or OW depending on context, used for LUT Data (thus the name)
+        case EVR_na:  // na="not applicable", for data which has no VR
+        case EVR_up:  // up="unsigned pointer", used internally for DICOMDIR suppor
+        case EVR_item:  // used internally for items
+        case EVR_metainfo:  // used internally for meta info datasets
+        case EVR_dataset:  // used internally for datasets
+        case EVR_fileFormat:  // used internally for DICOM files
+        case EVR_dicomDir:  // used internally for DICOMDIR objects
+        case EVR_dirRecord:  // used internally for DICOMDIR records
+        case EVR_pixelSQ:  // used internally for pixel sequences in a compressed image
+        case EVR_pixelItem:  // used internally for pixel items in a compressed image
+        case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
+        case EVR_PixelData:  // used internally for uncompressed pixeld data
+        case EVR_OverlayData:  // used internally for overlay data
+        case EVR_UNKNOWN2B:  // used internally for elements with unknown VR with 2-byte length field in explicit VR
+        default:
+          break;
+      }
+    }
+    catch (boost::bad_lexical_cast&)
+    {
+      ok = false;
+    }
+
+    if (!ok)
+    {
+      throw OrthancException(ErrorCode_InternalError);
+    }
+  }
+
+
+  DcmElement* FromDcmtkBridge::FromJson(const Json::Value& value,
+                                        const DicomTag& tag,
+                                        bool decodeBinaryTags)
+  {
+    std::auto_ptr<DcmElement> element;
+
+    if (value.type() == Json::stringValue)
+    {
+      element.reset(CreateElementForTag(tag));
+      FillElementWithString(*element, tag, value.asString(), decodeBinaryTags);
+    }
+
+    return element.release();
+  }
 }
--- a/OrthancServer/FromDcmtkBridge.h	Wed Oct 07 15:06:31 2015 +0200
+++ b/OrthancServer/FromDcmtkBridge.h	Wed Oct 07 16:54:05 2015 +0200
@@ -120,5 +120,16 @@
                                    DcmDataset& dataSet);
 
     static ValueRepresentation GetValueRepresentation(const DicomTag& tag);
+
+    static DcmElement* CreateElementForTag(const DicomTag& tag);
+    
+    static void FillElementWithString(DcmElement& element,
+                                      const DicomTag& tag,
+                                      const std::string& value,
+                                      bool interpretBinaryTags);
+
+    static DcmElement* FromJson(const Json::Value& element,
+                                const DicomTag& tag,
+                                bool interpretBinaryTags);
   };
 }
--- a/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Wed Oct 07 15:06:31 2015 +0200
+++ b/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Wed Oct 07 16:54:05 2015 +0200
@@ -487,7 +487,7 @@
 
   static void InjectTags(ParsedDicomFile& dicom,
                          const Json::Value& tags,
-                         bool interpretBinaryTags)
+                         bool decodeBinaryTags)
   {
     if (tags.type() != Json::objectValue)
     {
@@ -529,7 +529,7 @@
         {
           throw OrthancException(ErrorCode_CreateDicomUseContent);
         }
-        else if (interpretBinaryTags &&
+        else if (decodeBinaryTags &&
                  boost::starts_with(value, "data:application/octet-stream;base64,"))
         {
           std::string mime, binary;
@@ -548,7 +548,7 @@
   static void CreateSeries(RestApiPostCall& call,
                            ParsedDicomFile& base /* in */,
                            const Json::Value& content,
-                           bool interpretBinaryTags)
+                           bool decodeBinaryTags)
   {
     assert(content.isArray());
     assert(content.size() > 0);
@@ -581,7 +581,7 @@
 
           if (content[i].isMember("Tags"))
           {
-            InjectTags(*dicom, content[i]["Tags"], interpretBinaryTags);
+            InjectTags(*dicom, content[i]["Tags"], decodeBinaryTags);
           }
         }
 
@@ -755,7 +755,7 @@
     }
 
 
-    bool interpretBinaryTags = true;
+    bool decodeBinaryTags = true;
     if (request.isMember("InterpretBinaryTags"))
     {
       const Json::Value& v = request["InterpretBinaryTags"];
@@ -764,7 +764,7 @@
         throw OrthancException(ErrorCode_BadRequest);
       }
 
-      interpretBinaryTags = v.asBool();
+      decodeBinaryTags = v.asBool();
     }
 
     
@@ -794,7 +794,7 @@
     }
 
 
-    InjectTags(dicom, request["Tags"], interpretBinaryTags);
+    InjectTags(dicom, request["Tags"], decodeBinaryTags);
 
 
     // Inject the content (either an image, or a PDF file)
@@ -812,7 +812,7 @@
         if (content.size() > 0)
         {
           // Let's create a series instead of a single instance
-          CreateSeries(call, dicom, content, interpretBinaryTags);
+          CreateSeries(call, dicom, content, decodeBinaryTags);
           return;
         }
       }
--- a/OrthancServer/ParsedDicomFile.cpp	Wed Oct 07 15:06:31 2015 +0200
+++ b/OrthancServer/ParsedDicomFile.cpp	Wed Oct 07 16:54:05 2015 +0200
@@ -519,284 +519,6 @@
   }
 
 
-  
-
-
-  static DcmElement* CreateElementForTag(const DicomTag& tag)
-  {
-    DcmTag key(tag.GetGroup(), tag.GetElement());
-
-    switch (key.getEVR())
-    {
-      // http://support.dcmtk.org/docs/dcvr_8h-source.html
-
-      /**
-       * TODO.
-       **/
-    
-      case EVR_OB:  // other byte
-      case EVR_OF:  // other float
-      case EVR_OW:  // other word
-      case EVR_AT:  // attribute tag
-        throw OrthancException(ErrorCode_NotImplemented);
-
-      case EVR_UN:  // unknown value representation
-        throw OrthancException(ErrorCode_ParameterOutOfRange);
-
-
-      /**
-       * String types.
-       * http://support.dcmtk.org/docs/classDcmByteString.html
-       **/
-      
-      case EVR_AS:  // age string
-        return new DcmAgeString(key);
-
-      case EVR_AE:  // application entity title
-        return new DcmApplicationEntity(key);
-
-      case EVR_CS:  // code string
-        return new DcmCodeString(key);        
-
-      case EVR_DA:  // date string
-        return new DcmDate(key);
-        
-      case EVR_DT:  // date time string
-        return new DcmDateTime(key);
-
-      case EVR_DS:  // decimal string
-        return new DcmDecimalString(key);
-
-      case EVR_IS:  // integer string
-        return new DcmIntegerString(key);
-
-      case EVR_TM:  // time string
-        return new DcmTime(key);
-
-      case EVR_UI:  // unique identifier
-        return new DcmUniqueIdentifier(key);
-
-      case EVR_ST:  // short text
-        return new DcmShortText(key);
-
-      case EVR_LO:  // long string
-        return new DcmLongString(key);
-
-      case EVR_LT:  // long text
-        return new DcmLongText(key);
-
-      case EVR_UT:  // unlimited text
-        return new DcmUnlimitedText(key);
-
-      case EVR_SH:  // short string
-        return new DcmShortString(key);
-
-      case EVR_PN:  // person name
-        return new DcmPersonName(key);
-
-        
-      /**
-       * Numerical types
-       **/ 
-      
-      case EVR_SL:  // signed long
-        return new DcmSignedLong(key);
-
-      case EVR_SS:  // signed short
-        return new DcmSignedShort(key);
-
-      case EVR_UL:  // unsigned long
-        return new DcmUnsignedLong(key);
-
-      case EVR_US:  // unsigned short
-        return new DcmUnsignedShort(key);
-
-      case EVR_FL:  // float single-precision
-        return new DcmFloatingPointSingle(key);
-
-      case EVR_FD:  // float double-precision
-        return new DcmFloatingPointDouble(key);
-
-
-      /**
-       * Sequence types, should never occur at this point.
-       **/
-
-      case EVR_SQ:  // sequence of items
-        throw OrthancException(ErrorCode_ParameterOutOfRange);
-
-
-      /**
-       * Internal to DCMTK.
-       **/ 
-
-      case EVR_ox:  // OB or OW depending on context
-      case EVR_xs:  // SS or US depending on context
-      case EVR_lt:  // US, SS or OW depending on context, used for LUT Data (thus the name)
-      case EVR_na:  // na="not applicable", for data which has no VR
-      case EVR_up:  // up="unsigned pointer", used internally for DICOMDIR suppor
-      case EVR_item:  // used internally for items
-      case EVR_metainfo:  // used internally for meta info datasets
-      case EVR_dataset:  // used internally for datasets
-      case EVR_fileFormat:  // used internally for DICOM files
-      case EVR_dicomDir:  // used internally for DICOMDIR objects
-      case EVR_dirRecord:  // used internally for DICOMDIR records
-      case EVR_pixelSQ:  // used internally for pixel sequences in a compressed image
-      case EVR_pixelItem:  // used internally for pixel items in a compressed image
-      case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
-      case EVR_PixelData:  // used internally for uncompressed pixeld data
-      case EVR_OverlayData:  // used internally for overlay data
-      case EVR_UNKNOWN2B:  // used internally for elements with unknown VR with 2-byte length field in explicit VR
-      default:
-        break;
-    }
-
-    throw OrthancException(ErrorCode_InternalError);          
-  }
-
-
-
-  static void FillElementWithString(DcmElement& element,
-                                    const DicomTag& tag,
-                                    const std::string& value)
-  {
-    DcmTag key(tag.GetGroup(), tag.GetElement());
-    bool ok = false;
-    
-    try
-    {
-      switch (key.getEVR())
-      {
-        // http://support.dcmtk.org/docs/dcvr_8h-source.html
-
-        /**
-         * TODO.
-         **/
-
-        case EVR_OB:  // other byte
-        case EVR_OF:  // other float
-        case EVR_OW:  // other word
-        case EVR_AT:  // attribute tag
-          throw OrthancException(ErrorCode_NotImplemented);
-    
-        case EVR_UN:  // unknown value representation
-          throw OrthancException(ErrorCode_ParameterOutOfRange);
-
-
-        /**
-         * String types.
-         **/
-      
-        case EVR_DS:  // decimal string
-        case EVR_IS:  // integer string
-        case EVR_AS:  // age string
-        case EVR_DA:  // date string
-        case EVR_DT:  // date time string
-        case EVR_TM:  // time string
-        case EVR_AE:  // application entity title
-        case EVR_CS:  // code string
-        case EVR_SH:  // short string
-        case EVR_LO:  // long string
-        case EVR_ST:  // short text
-        case EVR_LT:  // long text
-        case EVR_UT:  // unlimited text
-        case EVR_PN:  // person name
-        case EVR_UI:  // unique identifier
-        {
-          ok = element.putString(value.c_str()).good();
-          break;
-        }
-
-        
-        /**
-         * Numerical types
-         **/ 
-      
-        case EVR_SL:  // signed long
-        {
-          ok = element.putSint32(boost::lexical_cast<Sint32>(value)).good();
-          break;
-        }
-
-        case EVR_SS:  // signed short
-        {
-          ok = element.putSint16(boost::lexical_cast<Sint16>(value)).good();
-          break;
-        }
-
-        case EVR_UL:  // unsigned long
-        {
-          ok = element.putUint32(boost::lexical_cast<Uint32>(value)).good();
-          break;
-        }
-
-        case EVR_US:  // unsigned short
-        {
-          ok = element.putUint16(boost::lexical_cast<Uint16>(value)).good();
-          break;
-        }
-
-        case EVR_FL:  // float single-precision
-        {
-          ok = element.putFloat32(boost::lexical_cast<float>(value)).good();
-          break;
-        }
-
-        case EVR_FD:  // float double-precision
-        {
-          ok = element.putFloat64(boost::lexical_cast<double>(value)).good();
-          break;
-        }
-
-
-        /**
-         * Sequence types, should never occur at this point.
-         **/
-
-        case EVR_SQ:  // sequence of items
-        {
-          ok = false;
-          break;
-        }
-
-
-        /**
-         * Internal to DCMTK.
-         **/ 
-
-        case EVR_ox:  // OB or OW depending on context
-        case EVR_xs:  // SS or US depending on context
-        case EVR_lt:  // US, SS or OW depending on context, used for LUT Data (thus the name)
-        case EVR_na:  // na="not applicable", for data which has no VR
-        case EVR_up:  // up="unsigned pointer", used internally for DICOMDIR suppor
-        case EVR_item:  // used internally for items
-        case EVR_metainfo:  // used internally for meta info datasets
-        case EVR_dataset:  // used internally for datasets
-        case EVR_fileFormat:  // used internally for DICOM files
-        case EVR_dicomDir:  // used internally for DICOMDIR objects
-        case EVR_dirRecord:  // used internally for DICOMDIR records
-        case EVR_pixelSQ:  // used internally for pixel sequences in a compressed image
-        case EVR_pixelItem:  // used internally for pixel items in a compressed image
-        case EVR_UNKNOWN: // used internally for elements with unknown VR (encoded with 4-byte length field in explicit VR)
-        case EVR_PixelData:  // used internally for uncompressed pixeld data
-        case EVR_OverlayData:  // used internally for overlay data
-        case EVR_UNKNOWN2B:  // used internally for elements with unknown VR with 2-byte length field in explicit VR
-        default:
-          break;
-      }
-    }
-    catch (boost::bad_lexical_cast&)
-    {
-      ok = false;
-    }
-
-    if (!ok)
-    {
-      throw OrthancException(ErrorCode_InternalError);
-    }
-  }
-
-
   void ParsedDicomFile::Remove(const DicomTag& tag)
   {
     DcmTagKey key(tag.GetGroup(), tag.GetElement());
@@ -857,8 +579,6 @@
   }
 
 
-
-
   void ParsedDicomFile::Insert(const DicomTag& tag,
                                const std::string& value)
   {
@@ -876,8 +596,8 @@
     }
     else
     {
-      std::auto_ptr<DcmElement> element(CreateElementForTag(tag));
-      FillElementWithString(*element, tag, value);
+      std::auto_ptr<DcmElement> element(FromDcmtkBridge::CreateElementForTag(tag));
+      FromDcmtkBridge::FillElementWithString(*element, tag, value, false);
 
       cond = pimpl_->file_->getDataset()->insert(element.release(), false, false);
     }
@@ -916,18 +636,7 @@
     }
     else
     {
-      if (FromDcmtkBridge::IsPrivateTag(tag) ||
-          FromDcmtkBridge::IsUnknownTag(tag))
-      {
-        if (!element->putUint8Array((const Uint8*) value.c_str(), value.size()).good())
-        {
-          throw OrthancException(ErrorCode_InternalError);
-        }
-      }
-      else
-      {
-        FillElementWithString(*element, tag, value);
-      }
+      FromDcmtkBridge::FillElementWithString(*element, tag, value, false);
     }