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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 __cmtkVolumeIO_h_included_
#define __cmtkVolumeIO_h_included_
#include <cmtkconfig.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkAnatomicalOrientation.h>
#include <IO/cmtkFileFormat.h>
#include <IO/cmtkTypedStream.h>
namespace
cmtk
{
/** \addtogroup IO */
//@{
/** Class for input/output of 3-D image data.
* This class is an easy-to-use wrapper around all low-level image readers and
* writers.
*
* An image can be read, for example from a Nifti/Analyze file pair, simply as follows:
* \code
* cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::Read( "image.hdr" ) );
* \endcode
*
* Note that we typically want images to be oriented consistently, so the preferred reader call would be:
* \code
* cmtk::UniformVolume::SmartPtr volume( cmtk::VolumeIO::ReadOriented( "image.hdr" );
* \endcode
*
* Similarly, we can write an image simply by calling
* \code
* cmtk::VolumeIO::Write( volume, "image.hdr" );
* \endcode
*
* The output format is determined automatically from the file name suffix. See
* \see VolumeIO::Write
* for more details.
*/
class VolumeIO
{
public:
/// This class.
typedef VolumeIO Self;
/// Read volume data from filesystem.
static UniformVolume::SmartPtr Read( const std::string& path );
/// Read grid only from filesystem.
static UniformVolume::SmartPtr ReadGrid( const std::string& path );
/// Read grid only from filesystem and bring into standard "RAS" orientation.
static UniformVolume::SmartPtr ReadGridOriented( const std::string& path, const char* orientation );
/// Read grid only from filesystem and bring into standard "RAS" orientation.
static UniformVolume::SmartPtr ReadGridOriented( const std::string& path )
{
return Self::ReadGridOriented( path, AnatomicalOrientation::ORIENTATION_STANDARD );
}
/** Read image from filesystem and reorient to align anatomy with coordinate axes.
*\param path Filesystem path of the image to read.
*\param orientation Three-character orientation code. The image will be brought into the orientation
* specified by this string. Default is "RAS", i.e., the returned image will be oriented so that the
* positive x axis is aligned with the anatomical L/R (left/right) direction, the y axis is aligned
* with the P/A (posterior/anterior) direction, and the y axis is aligned with the I/S (inferior/superior)
* direction.
*/
static UniformVolume::SmartPtr ReadOriented( const std::string& path, const char* orientation );
/** Read image from filesystem and reorient to align anatomy with coordinate axes of standard coordinate system ("RAS").
*\param path Filesystem path of the image to read.
*/
static UniformVolume::SmartPtr ReadOriented( const std::string& path )
{
return Self::ReadOriented( path, AnatomicalOrientation::ORIENTATION_STANDARD );
}
/** Write volume data to filesystem.
*\param volume Image object that is written to disk.
*\param format Selector for output file format.
*\param path Filesystem path of the image to write.
*/
static void Write( const UniformVolume& volume, const FileFormatID format, const std::string& path );
/** Write volume data to filesystem with automatic format parsing.
* The output file format is determined automatically from the output name suffix.
* \note Note that using ".hdr" will write a deprecated Analyze 7.5 hdr/img format pair
* with private extensions and questionable assumptions regarding the anatomical
* orientation of the image. To write a NIFTI hdr/img pair that avoids these problems,
* use the filename suffix ".img" (or write a single-file NIFTI using the ".nii" suffix).
*\param volume Image object that is written to disk.
*\param pathAndFormat Filesystem path of the image to write.
*/
static void Write( const UniformVolume& volume, const std::string& pathAndFormat );
/// Set flag for writing compressed images.
static void SetWriteCompressedOn()
{
Self::WriteCompressedOn = true;
}
/// Clear flag for writing compressed images.
static void SetWriteCompressedOff()
{
Self::WriteCompressedOn = false;
}
/// Get flag for writing compressed images.
static bool GetWriteCompressed()
{
return Self::WriteCompressedOn;
}
private:
/// Global setting: write compressed images.
static bool WriteCompressedOn;
/** Initializer class.
* An object of this class is automatically instantiated when a program is run.
* Its constructor takes care of initializing VolumeIO, e.g., by evaluating the
* IGS_WRITE_UNCOMPRESSED environment variable.
*/
class Initializer
{
private:
/// Default constructor: initialize VolumeIO settings.
Initializer();
/// Instance of the initializer class.
static Initializer Instance;
};
};
//@}
} // namespace cmtk
#endif // #ifndef __cmtkVolumeIO_h_included_
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