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/*
* intensities.c
*
* Extract integrated intensities by relrod estimation
*
* (c) 2007-2009 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "control.h"
#include "reflections.h"
#include "image.h"
#include "reproject.h"
#include "displaywindow.h"
#include "utils.h"
#include "basis.h"
/* Add a Friedel equivalent if missing, otherwise set the
* intensities of both equivalents to the larger intensity */
static void intensity_friedelise(Reflection *ref, ReflectionList *list,
int *n_fried)
{
Reflection *equiv;
equiv = reflectionlist_find(list, -ref->h, -ref->k, -ref->l);
/* Friedel equivalent exists? */
if ( equiv == NULL ) {
/* No, add it */
equiv = reflection_add(list, -ref->x, -ref->y, -ref->z,
ref->intensity, REFLECTION_GENERATED);
equiv->h = -ref->h;
equiv->k = -ref->k;
equiv->l = -ref->l;
(*n_fried)++;
} else {
/* Yes, use largest intensity */
if ( equiv->intensity > ref->intensity )
ref->intensity = equiv->intensity;
else
equiv->intensity = ref->intensity;
}
}
static void intensity_measure(signed int h, signed int k, signed int l,
ImageFeature *feature, ReflectionList *list,
double *max,
int *n_meas, int *n_dupl, int *n_fried)
{
if ( (h!=0) || (k!=0) || (l!=0) ) {
double intensity;
Reflection *ref;
intensity = feature->partner->intensity;
ref = reflectionlist_find(list, h, k, l);
/* Do we already have a value for this reflection? */
if ( ref == NULL ) {
/* No, add it */
ref = reflection_add(list,
feature->reflection->x,
feature->reflection->y,
feature->reflection->z,
intensity, REFLECTION_GENERATED);
ref->h = h;
ref->k = k;
ref->l = l;
if ( intensity > *max ) *max = intensity;
(*n_meas)++;
} else {
/* Yes, record only if the new value is larger */
if ( intensity > ref->intensity ) {
ref->x = feature->reflection->x;
ref->y = feature->reflection->y;
ref->z = feature->reflection->z;
ref->intensity = intensity;
}
(*n_dupl)++;
}
intensity_friedelise(ref, list, n_fried);
}
}
/* Extract integrated reflection intensities by estimating the spike function
* based on the observed intensity and the calculated excitation error from
* the lattice refinement. Easy. */
void intensities_extract(ControlContext *ctx)
{
int i, j;
int n_meas, n_dupl, n_notf, n_fried;
double max;
Reflection *reflection;
/* Free previous analysis if required */
if ( ctx->integrated != NULL ) {
reflectionlist_free(ctx->integrated);
}
ctx->integrated = reflectionlist_new();
n_meas = 0;
n_dupl = 0;
n_notf = 0;
n_fried = 0;
max = 0;
for ( i=0; i<ctx->images->n_images; i++ ) {
ImageRecord *image;
/* Reproject this pattern, if necessary */
image = &ctx->images->images[i];
if ( image->rflist == NULL )
image->rflist = reproject_get_reflections(image,
ctx->cell_lattice, ctx);
/* For each reprojected feature */
for ( j=0; j<image->rflist->n_features; j++ ) {
ImageFeature *feature;
signed int h, k, l;
feature = &image->rflist->features[j];
h = feature->reflection->h;
k = feature->reflection->k;
l = feature->reflection->l;
/* Corresponds to a measured reflection? */
if ( feature->partner != NULL )
intensity_measure(h, k, l, feature,
ctx->integrated, &max,
&n_meas, &n_dupl, &n_fried);
else
n_notf++;
}
}
/* Normalise all reflections to the most intense reflection */
reflection = ctx->integrated->reflections;
while ( reflection ) {
reflection->intensity /= max;
reflection = reflection->next;
}
printf("IN: %5i intensities measured\n", n_meas);
printf("IN: %5i duplicated measurements\n", n_dupl);
printf("IN: %5i reflections generated by Friedel's law\n", n_fried);
printf("IN: %5i predicted reflections not found\n", n_notf);
}
static int intensities_do_save(ReflectionList *integrated, Basis *cell,
const char *filename)
{
FILE *fh;
Reflection *reflection;
UnitCell rcell;
fh = fopen(filename, "w");
rcell = basis_get_cell(cell);
fprintf(fh, "#INT This file contains reflection intensities\n");
fprintf(fh, "a %12.8f\n", rcell.a*1e9);
fprintf(fh, "b %12.8f\n", rcell.b*1e9);
fprintf(fh, "c %12.8f\n", rcell.c*1e9);
fprintf(fh, "alpha %12.8f\n", rad2deg(rcell.alpha));
fprintf(fh, "beta %12.8f\n", rad2deg(rcell.beta));
fprintf(fh, "gamma %12.8f\n", rad2deg(rcell.gamma));
reflection = integrated->reflections;
while ( reflection ) {
fprintf(fh, "%3i %3i %3i %12.8f\n",
reflection->h, reflection->k, reflection->l,
reflection->intensity);
reflection = reflection->next;
}
fclose(fh);
return 0;
}
static gint intensities_save_response(GtkWidget *widget, gint response,
ControlContext *ctx)
{
if ( response == GTK_RESPONSE_ACCEPT ) {
char *filename;
filename = gtk_file_chooser_get_filename(
GTK_FILE_CHOOSER(widget));
if ( intensities_do_save(ctx->integrated,
ctx->cell, filename) ) {
displaywindow_error("Failed to save cache file.",
ctx->dw);
}
g_free(filename);
}
gtk_widget_destroy(widget);
return 0;
}
void intensities_save(ControlContext *ctx)
{
GtkWidget *save;
save = gtk_file_chooser_dialog_new("Save Reflections to File",
GTK_WINDOW(ctx->dw->window),
GTK_FILE_CHOOSER_ACTION_SAVE,
GTK_STOCK_CANCEL, GTK_RESPONSE_CANCEL,
GTK_STOCK_SAVE, GTK_RESPONSE_ACCEPT,
NULL);
g_signal_connect(G_OBJECT(save), "response",
G_CALLBACK(intensities_save_response), ctx);
gtk_widget_show_all(save);
}
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