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vigra/sifImport.hxx VIGRA

00001 /************************************************************************/
00002 /*                                                                      */
00003 /*       Copyright 2010 by Joachim Schleicher and Ullrich Koethe        */
00004 /*                                                                      */
00005 /*    This file is part of the VIGRA computer vision library.           */
00006 /*    The VIGRA Website is                                              */
00007 /*        http://hci.iwr.uni-heidelberg.de/vigra/                       */
00008 /*    Please direct questions, bug reports, and contributions to        */
00009 /*        ullrich.koethe@iwr.uni-heidelberg.de    or                    */
00010 /*        vigra@informatik.uni-hamburg.de                               */
00011 /*                                                                      */
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00019 /*    conditions:                                                       */
00020 /*                                                                      */
00021 /*    The above copyright notice and this permission notice shall be    */
00022 /*    included in all copies or substantial portions of the             */
00023 /*    Software.                                                         */
00024 /*                                                                      */
00025 /*    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND    */
00026 /*    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES   */
00027 /*    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND          */
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00032 /*    OTHER DEALINGS IN THE SOFTWARE.                                   */
00033 /*                                                                      */
00034 /************************************************************************/
00035 
00036 
00037 /*                                                          
00038  *  Opens an Andor .sif file as MultiImageView.             
00039  *  The width, height and number of images are extracted    
00040  *  from the ASCII encoded variable length header.          
00041  *                                                          
00042  *  Based on the Java-Code from                             
00043  *  http://rsb.info.nih.gov/ij/plugins/open-sif.html        
00044  *  written by                                              
00045  *  L. Stirling Churchman (stirling at stanford.edu)        
00046  *  Philippe Carl (pcarl at uni-muenster.de)                
00047  *  Yoshiyuki Arai (arai at phys1.med.osaka-u.ac.jp)        
00048  *                                                          
00049  *  Currently tested SIF versions: 4.16.12005.0             
00050  *                                 4.16.30001.0             
00051  *                                 4. 6.    3.0             
00052 */
00053 
00054 #ifndef VIGRA_SIFIMPORT_HXX
00055 #define VIGRA_SIFIMPORT_HXX
00056 
00057 #include <fstream>
00058 #include <cstring>
00059 #include <vector> 
00060 #include "vigra/multi_array.hxx"
00061 
00062 namespace vigra {
00063  
00064  
00065  /** \addtogroup VigraSIFImport Import of Images from Andor Cameras
00066 
00067     Read an Andor SIF file into a MultiArrayView.
00068 **/
00069 //@{
00070 
00071 /********************************************************/
00072 /*                                                      */
00073 /*                   SIFImportInfo                      */
00074 /*                                                      */
00075 /********************************************************/
00076 /** \brief Extracts image properties from an Andor SIF file header.
00077 
00078 See \ref readSIF() for a usage example. This object must be
00079 used to read the image header of an Andor SIF file
00080 and enquire its properties.
00081 
00082 <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/hdf5impex.hxx</a>><br>
00083 Namespace: vigra
00084 **/
00085 class SIFImportInfo
00086 {
00087     public:
00088         /** Construct SIFImportInfo object.
00089 
00090             The header of the Andor SIF file \a filename is accessed to 
00091             read the image properties. 
00092             
00093             \code
00094             SIFImportInfo info(filename);
00095             \endcode
00096          **/
00097         VIGRA_EXPORT SIFImportInfo(const char* filename);
00098 
00099         /** Get the width in pixels.
00100          **/
00101         VIGRA_EXPORT const int width() const;
00102 
00103         /** Get the height in pixels.
00104          **/
00105         VIGRA_EXPORT const int height() const;
00106 
00107         /** Get the stacksize, that is the number of 
00108          *  images contained in the dataset.
00109          **/
00110         VIGRA_EXPORT const int stacksize() const;
00111 
00112         /** Get the offset to the beginning of the actual data.
00113          *  Everything before this point belongs to the 
00114          *  variable lenght header.
00115          **/
00116         VIGRA_EXPORT const ptrdiff_t getOffset() const;
00117 
00118         /** Get the filename of this SIF object.
00119          **/
00120         VIGRA_EXPORT const char * getFileName() const;
00121 
00122         /** Output all information such as shutter, Temperature etc. 
00123            as human readable output.
00124           
00125         <b> Usage:</b>
00126         
00127         <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/sifImport.hxx</a>><br>
00128         Namespace: vigra
00129         
00130         \code
00131         SIFImportInfo info(filename);
00132         std::cout << info << std::endl; // print infos to the console
00133 
00134         \endcode
00135          **/
00136         VIGRA_EXPORT friend std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
00137 
00138     private:
00139         const char* m_filename;
00140         int m_width;
00141         int m_height;
00142         int m_stacksize;
00143         ptrdiff_t m_offset;
00144         int mod;
00145         int left, right, bottom, top;
00146         int xbin, ybin, xres, yres;
00147         int headerlen;
00148         double readout;
00149         double temperature1, temperature2;
00150         long long d;
00151         std::string cycleTime, temperature, exposureTime, EMGain,
00152         verticalShiftSpeed, version, model, originalFilename, preAmpGain;   
00153         size_t filesize;
00154     
00155 };
00156 
00157 
00158 
00159 
00160     /** \brief Read the image data specified by the given \ref vigra::SIFImportInfo object
00161                 and write them into the given 'array'.
00162                 
00163     The array must have the correct number of dimensions and shape for the dataset 
00164     represented by 'info'. 
00165     
00166     <b> Declaration:</b>
00167     
00168     \code
00169     namespace vigra {
00170         void 
00171         readSIF(const SIFImportInfo &info, MultiArrayView<3, float, UnstridedArrayTag> array);
00172     }
00173     \endcode
00174     
00175     <b> Usage:</b>
00176     
00177     <b>\#include</b> <<a href="sifImport_8hxx_source.html">vigra/sifImport.hxx</a>><br>
00178     Namespace: vigra
00179     
00180     \code
00181     SIFImportInfo info(filename);
00182 
00183     // create a 3D array of appropriate size
00184     typedef MultiArray<3, float>::difference_type Shape;
00185     MultiArray<3, float> in(Shape(info.width(), info.height(), info.stacksize()));
00186 
00187     readSIF(info, in); 
00188     \endcode
00189 */
00190 VIGRA_EXPORT void readSIF(const SIFImportInfo &info, MultiArrayView<3, float, UnstridedArrayTag> array);
00191 
00192 VIGRA_EXPORT std::ostream& operator<<(std::ostream& os, const SIFImportInfo& info);
00193 
00194 //@}
00195 
00196 } // namespace vigra
00197 
00198 #endif // VIGRA_SIFIMPORT_HXX

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de)
Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany

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