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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 $
//
*/
#ifndef __cmtkStudy_h_included_
#define __cmtkStudy_h_included_
#include <cmtkconfig.h>
#include <Base/cmtkMacros.h>
#include <Base/cmtkVolume.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkWarpXform.h>
#include <Base/cmtkLandmarkList.h>
#include <Base/cmtkSegmentationLabel.h>
#include <IO/cmtkFileFormat.h>
#include <string>
namespace
cmtk
{
/** \addtogroup IO */
//@{
/** Constants to identify color table.
*/
enum
{
/// Grayscale color table.
PALETTE_GRAY = 0,
/// Red color table.
PALETTE_RED = 1,
/// Green color table.
PALETTE_GREEN = 2,
/// Blue color table.
PALETTE_BLUE = 3,
/// Rainbow color table.
PALETTE_RAINBOW = 4,
/// Color table for labels.
PALETTE_LABELS = 5
};
/** Class for parameters of a general imaging study.
*/
class Study
{
public:
/// This class.
typedef Study Self;
/// Path of this study in the file system.
cmtkGetSetMacro(std::string,FileSystemPath);
/// Short, memorable name assigned to this study.
cmtkGetSetMacro(std::string,Name);
/// Textual description of study file type.
cmtkGetSetMacro(std::string,Description);
/// Textual description of study file type.
cmtkGetSetMacroString(Modality);
/// Volume data associated with this study.
cmtkGetSetMacro(UniformVolume::SmartPtr,Volume);
/// Landmark list.
cmtkGetSetMacro(LandmarkList::SmartPtr,LandmarkList);
/// Voxel dimensions of the volume image.
DataGrid::IndexType m_Dims;
/// Minimum value.
cmtkGetSetMacro(Types::DataItem,MinimumValue);
/// Maximum value.
cmtkGetSetMacro(Types::DataItem,MaximumValue);
/// Pixel padding value.
cmtkGetSetMacro(bool,Padding);
/// Pixel padding value.
cmtkGetSetMacro(Types::DataItem,PaddingValue);
/// Flag for user-defined colormap.
cmtkGetSetMacro(bool,HaveUserColorMap);
/// Index of colormap.
cmtkGetSetMacro(char,StandardColormap);
/// Is colormap reversed?
cmtkGetSetMacro(bool,ReverseColormap);
/// Value corresponding to "black".
cmtkGetSetMacro(Types::DataItem,Black);
/// Value corresponding to "white".
cmtkGetSetMacro(Types::DataItem,White);
/// Gamma value.
cmtkGetSetMacro(double,Gamma);
/// Index of currently displayed image.
cmtkGetSetMacro(unsigned int,DisplayedImageIndex);
/// Displayed image zoom.
cmtkGetSetMacro(unsigned int,ZoomFactor);
/// Slice normal coordinate axis.
cmtkGetSetMacro(int,SliceNormal);
public:
/// Smart pointer to Study.
typedef SmartPointer<Study> SmartPtr;
/// Default constructor.
Study();
/// Constructor: Construct study from image file.
Study( const std::string& fileSystemPath, const std::string& name = "" );
/// Virtual destructor.
virtual ~Study() {}
/** Read volume data.
*\param reRead If this is false, then the volume is only read if it has not
* been read before. Otherwise, it is re-read in any case.
*\param orientation Optional three-letter anatomical image orientation.
*\return True if reading was successful; the "Volume" field has a pointer to
* the resulting image volume.
*/
bool ReadVolume( const bool reRead = false, const char* orientation = NULL );
/** Set study name; create name if no name given.
* This function sets the name of this study. If no name is given (name
* parameter is NULL pointer), then a name is constructed from the file
* system path of this study.
*/
std::string SetMakeName( const std::string& name = "" /*!< New study name */, const int suffix = 0 /*!< Unique numerical suffix to be added to study name if other studies with the same name exist. */ );
/// Static study reader function.
static Self* Read( const std::string& path )
{
return new Self( path );
}
/** Copy colormap information from another study object.
*/
void CopyColormap( const Self* other );
/** Get colormap from label list.
*/
void SetFromLabelMap( const SegmentationLabelMap& lblMap )
{
this->m_HaveUserColorMap = true;
UserLabelMap = lblMap;
}
/// Get user-defined label map.
const SegmentationLabelMap& GetUserLabelMap() const
{
return UserLabelMap;
}
private:
/// User-defined label and colormap.
SegmentationLabelMap UserLabelMap;
};
//@}
} // namespace cmtk
#endif // #ifndef __cmtkStudy_h_included_
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