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/* */
/* Copyright 2010 by Joachim Schleicher and Ullrich Koethe */
/* */
/* This file is part of the VIGRA computer vision library. */
/* The VIGRA Website is */
/* http://hci.iwr.uni-heidelberg.de/vigra/ */
/* Please direct questions, bug reports, and contributions to */
/* ullrich.koethe@iwr.uni-heidelberg.de or */
/* vigra@informatik.uni-hamburg.de */
/* */
/* Permission is hereby granted, free of charge, to any person */
/* obtaining a copy of this software and associated documentation */
/* files (the "Software"), to deal in the Software without */
/* restriction, including without limitation the rights to use, */
/* copy, modify, merge, publish, distribute, sublicense, and/or */
/* sell copies of the Software, and to permit persons to whom the */
/* Software is furnished to do so, subject to the following */
/* conditions: */
/* */
/* The above copyright notice and this permission notice shall be */
/* included in all copies or substantial portions of the */
/* Software. */
/* */
/* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND */
/* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES */
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/* OTHER DEALINGS IN THE SOFTWARE. */
/* */
/************************************************************************/
/*
* Opens an Andor .sif file as MultiImageView.
* The width, height and number of images are extracted
* from the ASCII encoded variable length header.
*
* Based on the Java-Code from
* http://rsb.info.nih.gov/ij/plugins/open-sif.html
* written by
* L. Stirling Churchman (stirling at stanford.edu)
* Philippe Carl (pcarl at uni-muenster.de)
* Yoshiyuki Arai (arai at phys1.med.osaka-u.ac.jp)
*
* Currently tested SIF versions: 4.16.12005.0
* 4.16.30001.0
* 4. 6. 3.0
*/
#ifndef VIGRA_SIFIMPORT_HXX
#define VIGRA_SIFIMPORT_HXX
#include <fstream>
#include <cstring>
#include <cstddef>
#include <vector>
#include "multi_array.hxx"
#include "array_vector.hxx"
namespace vigra {
/** \addtogroup VigraSIFImport Import of Images from Andor Cameras
Read an Andor SIF file into a MultiArrayView.
*/
//@{
/********************************************************/
/* */
/* SIFImportInfo */
/* */
/********************************************************/
/** \brief Extracts image properties from an Andor SIF file header.
See \ref readSIF() for a usage example. This object must be
used to read the image header of an Andor SIF file
and enquire its properties.
<b>\#include</b> \<vigra/sifImport.hxx\><br>
Namespace: vigra
*/
class SIFImportInfo
{
public:
/** Construct SIFImportInfo object.
The header of the Andor SIF file \a filename is accessed to
read the image properties.
\code
SIFImportInfo info(filename);
\endcode
*/
VIGRA_EXPORT SIFImportInfo(const char* filename);
/** Get the width in pixels.
*/
VIGRA_EXPORT int width() const;
/** Get the height in pixels.
*/
VIGRA_EXPORT int height() const;
/** Get the stacksize, that is the number of
images contained in the dataset.
*/
VIGRA_EXPORT int stacksize() const;
/** Get the number of dimensions of the dataset represented by this info object.
*/
VIGRA_EXPORT MultiArrayIndex numDimensions() const;
/** Get the shape of the dataset represented by this info object.
*/
VIGRA_EXPORT ArrayVector<size_t> const & shape() const;
/** Get the shape (length) of the dataset along dimension \a dim.
*/
VIGRA_EXPORT MultiArrayIndex shapeOfDimension(const int dim) const;
/** Get the offset to the beginning of the actual data.
Everything before this point belongs to the
variable length header.
*/
VIGRA_EXPORT std::ptrdiff_t getOffset() const;
/** Get the filename of this SIF object.
*/
VIGRA_EXPORT const char * getFileName() const;
/** Output all information such as shutter, Temperature etc.
as human readable output.
<b> Usage:</b>
<b>\#include</b> \<vigra/sifImport.hxx\><br>
Namespace: vigra
\code
SIFImportInfo info(filename);
std::cout << info << std::endl; // print infos to the console
\endcode
*/
VIGRA_EXPORT friend std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
private:
const char* m_filename;
ArrayVector<size_t> m_dims;
std::ptrdiff_t m_offset;
int mod;
int left, right, bottom, top;
int xbin, ybin, xres, yres;
int headerlen;
double readout;
double temperature1, temperature2;
long long d;
std::string cycleTime, temperature, exposureTime, EMGain,
verticalShiftSpeed, version, model, originalFilename, preAmpGain;
size_t filesize;
};
/** \brief Read the image data specified by the given \ref vigra::SIFImportInfo object
and write them into the given 'array'.
The array must have the correct number of dimensions and shape for the dataset
represented by 'info'.
<b> Declaration:</b>
\code
namespace vigra {
void
readSIF(const SIFImportInfo &info, MultiArrayView<3, float> array);
}
\endcode
<b> Usage:</b>
<b>\#include</b> \<vigra/sifImport.hxx\><br>
Namespace: vigra
\code
SIFImportInfo info(filename);
// create a 3D array of appropriate size
typedef MultiArray<3, float>::difference_type Shape;
MultiArray<3, float> in(Shape(info.width(), info.height(), info.stacksize()));
readSIF(info, in);
\endcode
*/
VIGRA_EXPORT void readSIF(const SIFImportInfo &info, MultiArrayView<3, float> array);
template <unsigned int N, class T, class S>
void readSIF(const SIFImportInfo &info, MultiArrayView<N, T, S> array)
{
vigra_precondition(false, "readSIF(): Destination array must be MultiArrayView<3, float>.");
}
inline void readSIF(const SIFImportInfo &info, MultiArrayView<3, float, UnstridedArrayTag> array)
{
readSIF(info, MultiArrayView<3, float>(array));
}
/**
\brief Read parts of the image data from an Andor SIF file specified with an SIFImportInfo object
and write them into the MultiArray array.
\code
SIFImportInfo info(filename);
// create a 3D array of appropriate size
MultiArray<3, float> in(Shape3(info.width(), info.height(), 1));
readBlock(info, Shape3(0,0,0), Shape3(w,h,1), im); // read the first frame only
\endcode
*/
VIGRA_EXPORT void readSIFBlock(const SIFImportInfo &info, Shape3 offset, Shape3 shape, MultiArrayView<3, float> array);
template <unsigned int N, class T, class S>
void readSIFBlock(const SIFImportInfo &info, Shape3 offset, Shape3 shape, MultiArrayView<N, T, S> array)
{
vigra_precondition(false, "readSIFBlock(): Destination array must be MultiArrayView<3, float>.");
}
inline void readSIFBlock(const SIFImportInfo &info, Shape3 offset, Shape3 shape, MultiArrayView<3, float, UnstridedArrayTag> array)
{
readSIFBlock(info, offset, shape, MultiArrayView<3, float>(array));
}
VIGRA_EXPORT std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
//@}
} // namespace vigra
#endif // VIGRA_SIFIMPORT_HXX
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