autocorrelation.C

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/* Gnome gxsm - Gnome X Scanning Microscopy
 * universal STM/AFM/SARLS/SPALEED/... controlling and
 * data analysis software
 *
 * plugin_helper reports your answers as
author          =Erik Muller
pluginname              =autocorrelation
pluginmenuentry         =Auto Correlation
menupath                =Math/Statistics/
entryplace              =Statistics
shortentryplace =ST
abouttext               =Computes the Auto-Correlation of a scan.
smallhelp               =Calc. Auto Correlation from Scan
longhelp                =The Auto-Correlation of a scan is given by the following Z*Z=IFFT (| FT(Z) |^2).
 * 
 * Gxsm Plugin Name: autocorrelation.C
 * ========================================
 * 
 * Copyright (C) 1999 The Free Software Foundation
 *
 * Authors:Erik Muller
 *
 * This program 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 2 of the License, or
 * (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
 */

/* Please do not change the Begin/End lines of this comment section!
 * this is a LaTeX style section used for auto generation of the PlugIn Manual 
 * Chapter. Add a complete PlugIn documentation inbetween the Begin/End marks!
 * All "% PlugInXXX" commentary tags are mandatory
 * All "% OptPlugInXXX" tags are optional
 * --------------------------------------------------------------------------------
% BeginPlugInDocuSection
% PlugInDocuCaption: Autocorrelation
% PlugInName: autocorrelation
% PlugInAuthor: Erik Muller
% PlugInAuthorEmail: emmuller@users.sourceforge.net
% PlugInMenuPath: Math/Statistic/Auto Correlation

% PlugInDescription
Computes the autocorrelation of an image.

\[ Z' = |\text{IFT} (\text{FT} (Z))| \]

% PlugInUsage
Call \GxsmMenu{Math/Statistic/Auto Correlation} to execute.

% OptPlugInSources
The active channel is used as data source.

% OptPlugInDest
The computation result is placed into an existing math channel, else
into a new created math channel.

% OptPlugInNotes
The quadrants of the resulting invers spectrum are aligned in a way,
that the intensity of by it self correlated pixels (distance zero) is
found at the image center and not at all four edges.


% EndPlugInDocuSection
 * -------------------------------------------------------------------------------- 
 */
#include <complex>
#include <gtk/gtk.h>
#include "config.h"
#include "gxsm/plugin.h"
#include "gxsm/xsmmath.h"

// Plugin Prototypes
static void autocorrelation_init( void );
static void autocorrelation_about( void );
static void autocorrelation_configure( void );
static void autocorrelation_cleanup( void );

// Define Type of math plugin here, only one line should be commented in!!
#define GXSM_ONE_SRC_PLUGIN__DEF
// #define GXSM_TWO_SRC_PLUGIN__DEF

// Math-Run-Function, use only one of (automatically done :=)
#ifdef GXSM_ONE_SRC_PLUGIN__DEF
// "OneSrc" Prototype
 static gboolean autocorrelation_run( Scan *Src, Scan *Dest );
#else
// "TwoSrc" Prototype
 static gboolean autocorrelation_run( Scan *Src1, Scan *Src2, Scan *Dest );
#endif

// Fill in the GxsmPlugin Description here
GxsmPlugin autocorrelation_pi = {
  NULL,                   // filled in and used by Gxsm, don't touch !
  NULL,                   // filled in and used by Gxsm, don't touch !
  0,                      // filled in and used by Gxsm, don't touch !
  NULL,                   // The Gxsm-App Class Ref.pointer (called "gapp" in Gxsm) is 
                          // filled in here by Gxsm on Plugin load, 
                          // just after init() is called !!!
  // ----------------------------------------------------------------------
  // Plugins Name, CodeStly is like: Name-M1S|M2S-BG|F1D|F2D|ST|TR|Misc
  "autocorrelation-"
#ifdef GXSM_ONE_SRC_PLUGIN__DEF
  "M1S"
#else
  "M2S"
#endif
  "-ST",
  // Plugin's Category - used to autodecide on Pluginloading or ignoring
  // NULL: load, else
  // example: "+noHARD +STM +AFM"
  // load only, if "+noHARD: no hardware" and Instrument is STM or AFM
  // +/-xxxHARD und (+/-INST or ...)
  NULL,
  // Description, is shown by PluginViewer (Plugin: listplugin, Tools->Plugin Details)
  "Computes the Auto-Correlation of a Scan.",
  // Author(s)
  "Erik Muller",
  // Menupath to position where it is appendet to
  N_("_Math/_Statistics/"),
  // Menuentry
  N_("Auto Correlation"),
  // help text shown on menu
  N_("Do a Auto-Correlation of the scan"),
  // more info...
  "Calc. Auto Correlation of Scan",
  NULL,          // error msg, plugin may put error status msg here later
  NULL,          // Plugin Status, managed by Gxsm, plugin may manipulate it too
  // init-function pointer, can be "NULL", 
  // called if present at plugin load
  autocorrelation_init,  
  // query-function pointer, can be "NULL", 
  // called if present after plugin init to let plugin manage it install itself
  NULL, // query should be "NULL" for Gxsm-Math-Plugin !!!
  // about-function, can be "NULL"
  // can be called by "Plugin Details"
  autocorrelation_about,
  // configure-function, can be "NULL"
  // can be called by "Plugin Details"
  autocorrelation_configure,
  // run-function, can be "NULL", if non-Zero and no query defined, 
  // it is called on menupath->"plugin"
  NULL, // run should be "NULL" for Gxsm-Math-Plugin !!!
  // cleanup-function, can be "NULL"
  // called if present at plugin removeal
  autocorrelation_cleanup
};

// special math Plugin-Strucure, use
// GxsmMathOneSrcPlugin autocorrelation_m1s_pi -> "OneSrcMath"
// GxsmMathTwoSrcPlugin autocorrelation_m2s_pi -> "TwoSrcMath"
#ifdef GXSM_ONE_SRC_PLUGIN__DEF
 GxsmMathOneSrcPlugin autocorrelation_m1s_pi
#else
 GxsmMathTwoSrcPlugin autocorrelation_m2s_pi
#endif
 = {
   // math-function to run, see prototype(s) above!!
   autocorrelation_run
 };

// Text used in Aboutbox, please update!!
static const char *about_text = N_("Gxsm autocorrelation Plugin\n\n"
                                   "Computes the Auto-Correlation of a scan:\n"
                                   "The Auto-Correlation of a scan is computed\n"
                                   "by FT the source Scan, setting the phase\n"
                                   "to zero and doing the IFT.");

// Symbol "get_gxsm_plugin_info" is resolved by dlsym from Gxsm, used to get Plugin's info!! 
// Essential Plugin Function!!
GxsmPlugin *get_gxsm_plugin_info ( void ){ 
  autocorrelation_pi.description = g_strdup_printf(N_("Gxsm MathOneArg autocorrelation plugin %s"), VERSION);
  return &autocorrelation_pi; 
}

// Symbol "get_gxsm_math_one|two_src_plugin_info" is resolved by dlsym from Gxsm, 
// used to find out which Math Type the Plugin is!! 
// Essential Plugin Function!!
#ifdef GXSM_ONE_SRC_PLUGIN__DEF
GxsmMathOneSrcPlugin *get_gxsm_math_one_src_plugin_info( void ) {
  return &autocorrelation_m1s_pi; 
}
#else
GxsmMathTwoSrcPlugin *get_gxsm_math_two_src_plugin_info( void ) { 
  return &autocorrelation_m2s_pi; 
}
#endif


/* Here we go... */
// init-Function
static void autocorrelation_init(void)
{
  PI_DEBUG (DBG_L2, "autocorrelation Plugin Init");
}

// about-Function
static void autocorrelation_about(void)
{
  const gchar *authors[] = { autocorrelation_pi.authors, NULL};
  gtk_widget_show(gnome_about_new ( autocorrelation_pi.name,
                                    VERSION,
                                    N_("(C) 2000 the Free Software Foundation"),
                                    about_text,
                                    authors,
                                    NULL, NULL, NULL
                                    ));
}

int WindowDefault=0;
int WindowLast=0;

int window_callback(GtkComboBox *widget, gpointer data){
        WindowDefault =  gtk_combo_box_get_active (widget);
        return 0;
}

// configure-Function
static void autocorrelation_configure(void)
{


}

// cleanup-Function
static void autocorrelation_cleanup(void)
{
  PI_DEBUG (DBG_L2, "autocorrelation Plugin Cleanup");
}


// run-Function
 static gboolean autocorrelation_run(Scan *Src, Scan *Dest)
{ 

/*-------------------------------------------------*/

        // Selects the data in the rectangle if there is a rectangle
        // else, uses all the data
        int StartX=0,EndX=0,StartY=0,EndY=0;

        EndX=Src->mem2d->GetNx();
        EndY=Src->mem2d->GetNy();

        double hi, lo, z;
        int success = FALSE;
        int n_obj = Src->number_of_object ();
        Point2D p[2];

        while (n_obj--){
                scan_object_data *obj_data = Src->get_object_data (n_obj);
                
                if (strncmp (obj_data->get_name (), "Rectangle", 9) )
                        continue; // only points are used!
                
                if (obj_data->get_num_points () != 2) 
                        continue; // sth. is weired!
                
                double x,y;
                obj_data->get_xy_pixel (0, x, y);
                p[0].x = (int)x; p[0].y = (int)y;
                obj_data->get_xy_pixel (1, x, y);
                p[1].x = (int)x; p[1].y = (int)y;
                
                StartX=p[0].x; EndX=p[1].x;
                StartY=p[0].y; EndY=p[1].y;

                success = TRUE;
                break;
        }
        
        // If the box is outside the scan area...return an error
        if (StartX < 0 | StartY < 0 | EndX > Src->mem2d->GetNx() | EndY > Src->mem2d->GetNy() )
                return MATH_SELECTIONERR;

/* ---------------------------------------------------------------- */

        GtkWidget *dialog, *label, *wmenu;
//      GtkWidget *image;
//      image = gtk_image_new_from_file ("/home/emuller/Gxsm-2.0/plug-ins/math/statistik/test.png");

        dialog = gtk_dialog_new_with_buttons ("Message",
                                              NULL,
                                              //(GtkDialogFlags)(GTK_DIALOG_MODAL | GTK_DIALOG_DESTROY_WITH_PARENT),
                                              GTK_DIALOG_MODAL,
                                              GTK_STOCK_OK,
                                              GTK_RESPONSE_NONE,                                           
                                              NULL);
        
        wmenu = gtk_combo_box_new_text ();
        
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"No Window");
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"Hanning");
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"Hamming");
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"Bartlett");
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"Blackman");
        gtk_combo_box_append_text (GTK_COMBO_BOX (wmenu),"Connes");

        gtk_signal_connect (GTK_OBJECT(wmenu),"changed", GTK_SIGNAL_FUNC (window_callback), (gpointer) 1 );

        gchar *message="Please chose a window function";

        /* Create the widgets */
        label = gtk_label_new (message);
        
        /* Ensure that the dialog box is destroyed when the user responds. */
        g_signal_connect_swapped (dialog,
                                  "response",                       
                                  G_CALLBACK (gtk_widget_destroy),
                                  dialog);
        

        /* Add the label, and show everything we've added to the dialog. */

//      gtk_container_add (GTK_CONTAINER (GTK_DIALOG(dialog)->vbox),
//                         image);
        gtk_container_add (GTK_CONTAINER (GTK_DIALOG(dialog)->vbox),
                           label);

        gtk_container_add (GTK_CONTAINER (GTK_DIALOG(dialog)->vbox),
                           wmenu);
        gtk_widget_show_all (dialog);
        gtk_dialog_run (GTK_DIALOG (dialog));
        
/*-------------------------------------------------*/
        
        int window = WindowDefault;
        int Nx, Ny;
        Nx=(EndX-StartX);
        Ny=(EndY-StartY);


        // Set Dest to Float, Range: +/-100% =^= One Pixel
        Dest->mem2d->Resize(Nx, Ny, ZD_FLOAT);

        // allocate memory for the complex data and one line buffer
        fftw_complex *in1  = new fftw_complex [Nx*Ny];
        fftw_complex *in2  = new fftw_complex [Nx*Ny];
  
        fftw_complex *out1 = new fftw_complex [Nx*Ny];
        fftw_complex *out2 = new fftw_complex [Nx*Ny];


/*-------------------------------------------------*/

        // Applies the window function
        double xfactor=1,yfactor=1;

        // Fill array with data and apply image window to the image
        for (int pos=0, line=StartY; line < EndY; ++line)
                for (int col=StartX; col < EndX; ++col, ++pos){           
                       
                        if(window == 0){
                                xfactor=1.0;
                                yfactor=1.0;
                        }
                        else if(window == 1){
                                xfactor = 0.5*(1.0+cos(2.0*M_PI*((line-StartY)-Ny/2.0)/Ny));
                                yfactor = 0.5*(1.0+cos(2.0*M_PI*((col-StartX)-Nx/2.0)/Nx));
                        }
                        else if(window == 2){
                                xfactor = 0.54+0.46*cos(2.0*M_PI*((line-StartY)-Ny/2.0)/Ny);
                                yfactor = 0.54+0.46*cos(2.0*M_PI*((col-StartX)-Nx/2.0)/Nx);
                        }
                        else if(window == 3){
                                xfactor=(1.0-2.0*sqrt(((line-StartY)-Ny/2.0)*(line-StartY-Ny/2.0))/Ny);
                                yfactor=(1.0-2.0*sqrt(((col-StartX)-Nx/2.0)*((col-StartX)-Nx/2.0))/Nx);
                        }
                        else if(window == 4){
                                xfactor = 0.42+0.5*cos(2.0*M_PI*((line-StartY)-Ny/2.0)/Ny)+0.08*cos(4.0*M_PI*((line-StartY)-Ny/2.0)/Ny);
                                yfactor = 0.42+0.5*cos(2.0*M_PI*((col-StartX)-Nx/2.0)/Nx)+0.08*cos(4.0*M_PI*((col-StartX)-Nx/2.0)/Nx);
                        }
                        else if(window == 5){
                                xfactor = (1.0-4.0*((line-StartY)-Ny/2.0)*((line-StartY)-Ny/2.0)/Ny/Ny)*(1.0-4.0*((line-StartY)-Ny/2.0)*((line-StartY)-Ny/2.0)/Ny/Ny);
                                yfactor = (1.0-4.0*((col-StartX)-Nx/2.0)*((col-StartX)-Nx/2.0)/Nx/Nx)*(1.0-4.0*((col-StartX)-Nx/2.0)*((col-StartX)-Nx/2.0)/Nx/Nx);
                        }
                        
                        c_re(in1[pos]) =(Src->mem2d->GetDataPkt(col, line))*xfactor*yfactor;
                        c_im(in1[pos]) = 0.;                    
          }


/*-------------------------------------------------*/

        // do the fourier transform
        // create plan for fft
        fftw_plan plan1 = fftw_plan_dft_2d (Ny, Nx, in1, out1, FFTW_FORWARD, FFTW_ESTIMATE);
        
        // compute fft
        fftw_execute (plan1);

        for(int i=0; i < Ny; ++i)
                for(int j=0; j < Nx; ++j){
                        c_re(in2[j+Nx*i])=0.0;
                        c_im(in2[j+Nx*i])=0.0;                        
                        c_re(in2[j+Nx*i])=c_re(out1[j+Nx*i])*c_re(out1[j+Nx*i])+c_im(out1[j+Nx*i])*c_im(out1[j+Nx*i]);
                        c_im(in2[j+Nx*i])=c_im(out1[j+Nx*i])*c_re(out1[j+Nx*i])-c_re(out1[j+Nx*i])*c_im(out1[j+Nx*i]);
                }


        fftw_plan plan2 = fftw_plan_dft_2d (Ny, Nx, in2, out2, FFTW_BACKWARD, FFTW_ESTIMATE);
        // compute fft
        fftw_execute (plan2);



        //Find Normalization factor
        double SumNorm=0;
        for(int i=0; i < Nx*Ny; i++){
                SumNorm += c_re(in1[i])*c_re(in1[i]);
            }



        //WRITE DATA TO DEST
        for (int pos=0, i=0; i < Ny; ++i)
                for (int j=0; j < Nx; ++j, ++pos){
                        Dest->mem2d->PutDataPkt(c_re(out2[pos])/SumNorm/Nx/Ny,//j, i) ;
                                     QSWP (j,Nx), 
                                     QSWP (i, Ny));
                }

                                             
        // destroy plan
        fftw_destroy_plan (plan1);
        fftw_destroy_plan (plan2);

        
        // free memory
        delete in1;
        delete in2;
                                     
        delete out1;
        delete out2;


        Dest->mem2d->data->MkXLookup(0., Src->data.s.rx*Nx/Src->mem2d->GetNx());
        Dest->mem2d->data->MkYLookup(0., Src->data.s.ry*Ny/Src->mem2d->GetNy());
        UnitObj *u;
//      Dest->data.SetZUnit(u=new LinUnit(" "," ",0.02328,0));
        Dest->data.SetZUnit(u=new LinUnit(" "," ",1.,0));
        Dest->data.SetXUnit(u=new LinUnit(" "," ",1.,0));
        Dest->data.SetYUnit(u=new LinUnit(" "," ",1.,0));


        Dest->data.s.dz=1.0;
        Dest->data.s.dx=1.0;
        Dest->data.s.dy=1.0;
        delete u;



   return MATH_OK;
        
}

---