Merge pull request #188 from SCIInstitute/nrrd_headers

Nrrd headers

Author: Ayla Khan

src/Application/LayerIO/NrrdLayerExporter.cc

@@ -78,14 +78,17 @@ bool NrrdLayerExporter::export_nrrd( const std::string& file_path )
   DataLayer* temp_handle = dynamic_cast< DataLayer* >( 
     this->layers_[ 0 ].get() );
 
+  bool no_downgrade = PreferencesManager::Instance()->export_nrrd0005_state_->get();
+
   Core::NrrdDataHandle nrrd = Core::NrrdDataHandle( new Core::NrrdData( 
-    temp_handle->get_data_volume()->get_data_block(), temp_handle->get_grid_transform() ) );
+    temp_handle->get_data_volume()->get_data_block(), temp_handle->get_grid_transform(),
+    no_downgrade ) );
 
   bool compress = PreferencesManager::Instance()->compression_state_->get();
   int level = PreferencesManager::Instance()->compression_level_state_->get();
 
   std::string error;
-  if ( !( Core::NrrdData::SaveNrrd( file_path, nrrd, error, compress, level ) ) ) 
+  if ( !( Core::NrrdData::SaveNrrd( file_path, nrrd, error, compress, level ) ) )
   {
     CORE_LOG_ERROR( error );
     return false;

src/Application/PreferencesManager/PreferencesManager.cc

@@ -169,6 +169,7 @@ void PreferencesManager::initialize_states()
   this->add_state( "compression_level", this->compression_level_state_, 2, 0, 9, 1 );
   this->add_state( "slice_step_multiplier", this->slice_step_multiplier_state_, 8 );
   this->add_state( "add_dicom_headers", this->export_dicom_headers_state_, true );
+  this->add_state( "use_nrrd0005_format", this->export_nrrd0005_state_, true );
 
   this->add_state( "axis_labels_option", this->axis_labels_option_state_, "sca", 
     "sca=Sagittal/Coronal/Axial|sct=Sagittal/Coronal/Transverse|"

src/Application/PreferencesManager/PreferencesManager.h

@@ -87,6 +87,7 @@ class PreferencesManager : public Core::StateHandler
   Core::StateBoolHandle generate_osx_project_bundle_state_;
 
   Core::StateBoolHandle export_dicom_headers_state_;
+  Core::StateBoolHandle export_nrrd0005_state_;
 
   //Viewers Preferences
   Core::StateOptionHandle default_viewer_mode_state_;

src/Core/DataBlock/NrrdData.cc

@@ -83,7 +83,7 @@ NrrdData::NrrdData( DataBlockHandle data_block ) :
 }
 
 
-NrrdData::NrrdData( DataBlockHandle data_block, GridTransform transform ) :
+NrrdData::NrrdData( DataBlockHandle data_block, GridTransform transform, bool no_downgrade ) :
   private_( new  NrrdDataPrivate )
 {
   if ( !data_block )
@@ -102,7 +102,7 @@ NrrdData::NrrdData( DataBlockHandle data_block, GridTransform transform ) :
       data_block->get_nx(), data_block->get_ny(),
       data_block->get_nz() );
 
-    set_transform( transform );
+    set_transform( transform, no_downgrade );
   }
 }
 
@@ -264,7 +264,7 @@ GridTransform NrrdData::get_grid_transform() const
   return grid_transform;
 }
 
-void NrrdData::set_transform( GridTransform& transform )
+void NrrdData::set_transform( GridTransform& transform, bool no_downgrade )
 {
   if ( !this->private_->nrrd_ ) return;
 
@@ -319,32 +319,39 @@ void NrrdData::set_transform( GridTransform& transform )
   if ( nrrd->spaceDim > 0 && nrrd->spaceDim == nrrd->dim )
   {
     bool is_aligned_nrrd = true;
-    for ( size_t j = 0; j < static_cast<size_t>( nrrd->spaceDim ); j++ )
+    if ( no_downgrade )
     {
-      for ( size_t i = 0; i < static_cast<size_t>( nrrd->dim ); i++ )
+      is_aligned_nrrd = false;
+    }
+    else
+    {
+      for ( size_t j = 0; j < static_cast<size_t>( nrrd->spaceDim ); j++ )
       {
-        if ( (i != j) &&
-             ( (nrrd->axis[ i ].spaceDirection[ j ] != 0.0) &&
-               (! IsNan(nrrd->axis[ i ].spaceDirection[ j ])) ) )
+        for ( size_t i = 0; i < static_cast<size_t>( nrrd->dim ); i++ )
         {
-          is_aligned_nrrd = false;
+          if ( (i != j) &&
+               ( (nrrd->axis[ i ].spaceDirection[ j ] != 0.0) &&
+                 (! IsNan(nrrd->axis[ i ].spaceDirection[ j ])) ) )
+          {
+            is_aligned_nrrd = false;
+          }
         }
       }
-    }
 
-    for ( size_t j = 0; j < static_cast<size_t>( nrrd->spaceDim ); j++ )
-    {
-      for ( size_t i = 0; i < static_cast<size_t>( nrrd->spaceDim ); i++ )
+      for ( size_t j = 0; j < static_cast<size_t>( nrrd->spaceDim ); j++ )
       {
-        if ( (i != j) &&
-             ( (nrrd->measurementFrame[ i ][ j ] != 0.0) &&
-               (! IsNan( nrrd->measurementFrame[ i ][ j ])) ) )
+        for ( size_t i = 0; i < static_cast<size_t>( nrrd->spaceDim ); i++ )
         {
-          is_aligned_nrrd = false;
+          if ( (i != j) &&
+               ( (nrrd->measurementFrame[ i ][ j ] != 0.0) &&
+                 (! IsNan( nrrd->measurementFrame[ i ][ j ])) ) )
+          {
+            is_aligned_nrrd = false;
+          }
         }
       }
     }
-
+    
     if ( is_aligned_nrrd )
     {
       // Down grade nrrd

src/Core/DataBlock/NrrdData.h

@@ -80,8 +80,10 @@ class NrrdData : boost::noncopyable
   /// Construct a NrrdData object from an existing DataBlock of data
   /// The datablock handle will be stored internally until the object is deleted
   /// and the memory with the data is shared between the object and the nrrd object.
+  /// no_downgrade specifies whether the nrrd format will be downgraded to NRRD0001 when possible.
+  /// when no_downgrade is true, nrrd format is always NRRD0005.
   NrrdData( DataBlockHandle data_block );
-  NrrdData( DataBlockHandle data_block, GridTransform transform );
+  NrrdData( DataBlockHandle data_block, GridTransform transform, bool no_downgrade = true );
 
   virtual ~NrrdData();
 
@@ -109,7 +111,7 @@ class NrrdData : boost::noncopyable
 
   // SET_TRANSFORM:
   /// Set the transfrom in the nrrd data
-  void set_transform( GridTransform& transform );
+  void set_transform( GridTransform& transform, bool no_downgrade );
 
   // GET_HISTOGRAM:
   /// Get the histogram from the nrrd

src/Interface/Application/PreferencesInterface.cc

@@ -162,6 +162,8 @@ void PreferencesInterface::setup_general_prefs()
     PreferencesManager::Instance()->active_layer_navigation_state_ );
   QtUtils::QtBridge::Connect( this->private_->ui_.export_dicom_headers_,
     PreferencesManager::Instance()->export_dicom_headers_state_ );  
+  QtUtils::QtBridge::Connect( this->private_->ui_.export_nrrd0005_,
+    PreferencesManager::Instance()->export_nrrd0005_state_ );
 
   QtUtils::QtBridge::Connect( this->private_->ui_.enable_compression_checkbox_,
     PreferencesManager::Instance()->compression_state_ );