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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2013 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit 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.
//
// The Computational Morphometry Toolkit 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 the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include "cmtkStudy.h"
#include <IO/cmtkFileFormat.h>
#include <IO/cmtkVolumeIO.h>
#include <string>
#include <limits.h>
namespace
cmtk
{
/** \addtogroup IO */
//@{
Study::Study()
: m_Modality( NULL ),
m_Volume( NULL ),
m_MinimumValue( 0.0 ),
m_MaximumValue( 0.0 ),
m_Padding( false ),
m_PaddingValue( 0.0 ),
m_HaveUserColorMap( false ),
m_StandardColormap( 0 ),
m_ReverseColormap( false ),
m_Black( 0.0 ),
m_White( 0.0 ),
m_Gamma( 1.0 ),
m_DisplayedImageIndex( -1 ),
m_ZoomFactor( 1 ),
m_SliceNormal( 2 )
{
}
Study::Study( const std::string& fileSystemPath, const std::string& name )
: m_Modality( NULL ),
m_Volume( NULL ),
m_MinimumValue( 0.0 ),
m_MaximumValue( 0.0 ),
m_Padding( false ),
m_PaddingValue( 0.0 ),
m_HaveUserColorMap( false ),
m_StandardColormap( 0 ),
m_ReverseColormap( false ),
m_Black( 0.0 ),
m_White( 0.0 ),
m_Gamma( 1.0 ),
m_DisplayedImageIndex( -1 ),
m_ZoomFactor( 1 ),
m_SliceNormal( 2 )
{
if ( ! fileSystemPath.empty() )
{
this->m_FileSystemPath = fileSystemPath;
this->m_Description = FileFormat::Describe( this->m_FileSystemPath );
// cut trailing '/'s off the study path.
const size_t lastChar = this->m_FileSystemPath.find_last_not_of( "/" );
if ( lastChar != std::string::npos )
{
this->m_FileSystemPath = this->m_FileSystemPath.substr( 0, lastChar+1 );
}
this->SetMakeName( name );
}
}
std::string
Study::SetMakeName( const std::string& name, const int suffix )
{
char suffixStr[10];
snprintf( suffixStr, 9, "<%d>", suffix );
if ( !name.empty() )
{
if ( suffix )
{
this->SetName( name + suffixStr );
}
else
{
this->SetName( name );
}
}
else
{
std::string studyName = name;
const size_t lastChar = studyName.find_last_not_of( "/" );
if ( lastChar != std::string::npos )
{
studyName = studyName.substr( 0, lastChar+1 );
}
const size_t lastSlash = studyName.rfind( "/" );
if ( lastSlash != std::string::npos )
{
studyName = studyName.substr( lastSlash+1 );
}
else
{
studyName = this->m_FileSystemPath;
}
const size_t dot = studyName.find( "." );
if ( dot != std::string::npos )
{
studyName = studyName.substr( 0, dot );
}
if ( suffix )
studyName = studyName + suffixStr;
this->SetName( studyName );
}
return this->m_Name;
}
bool
Study::ReadVolume( const bool reRead, const char* orientation )
{
UniformVolume::SmartPtr oldVolume( NULL );
if ( this->m_Volume && reRead )
{
oldVolume = this->m_Volume;
this->m_Volume = UniformVolume::SmartPtr( NULL );
}
if ( !this->m_Volume )
{
if ( orientation )
this->m_Volume = UniformVolume::SmartPtr( VolumeIO::ReadOriented( this->m_FileSystemPath, orientation ) );
else
this->m_Volume = UniformVolume::SmartPtr( VolumeIO::Read( this->m_FileSystemPath ) );
if ( this->m_Volume )
{
this->m_Dims = this->m_Volume->GetDims();
this->m_DisplayedImageIndex = this->m_Dims[AXIS_Z] / 2 ;
this->m_ZoomFactor = 1;
const TypedArray *dataArray = this->m_Volume->GetData();
if ( dataArray )
{
const Types::DataItemRange range = dataArray->GetRange();
this->m_MinimumValue = range.m_LowerBound;
this->m_MaximumValue = range.m_UpperBound;
this->m_Black = dataArray->GetPercentile( 0.01, 1024 );
this->m_White = dataArray->GetPercentile( 0.99, 1024 );
this->m_StandardColormap = 0;
this->m_ReverseColormap = false;
}
}
}
if ( this->m_Volume && this->m_Volume->GetData() )
{
return true;
}
this->m_Volume = oldVolume;
return false;
}
void
Study::CopyColormap( const Study* other )
{
this->m_MinimumValue = other->m_MinimumValue;
this->m_MaximumValue = other->m_MaximumValue;
this->m_StandardColormap = other->m_StandardColormap;
this->m_ReverseColormap = other->m_ReverseColormap;
this->m_Black = other->m_Black;
this->m_White = other->m_White;
this->m_Gamma = other->m_Gamma;
}
} // namespace cmtk
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