sifImport.hxx

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/*                                                          
 *  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 &, MultiArrayView<N, T, S>)
{
    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 &, Shape3, Shape3, MultiArrayView<N, T, S>)
{
    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