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/*
* prealign.c
*
* Rough initial alignment of images
*
* (c) 2007 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include "control.h"
#include "imagedisplay.h"
#include "main.h"
#include "image.h"
#include "utils.h"
typedef struct {
int n;
ControlContext *ctx;
ImageDisplay *id;
} PreAlignBlock;
static gint prealign_clicked(GtkWidget *widget, GdkEventButton *event, PreAlignBlock *pb) {
double xoffs, yoffs, scale;
double x, y;
x = event->x; y = event->y;
xoffs = (pb->id->drawingarea_width - pb->id->view_width) / 2;
yoffs = (pb->id->drawingarea_height - pb->id->view_height) / 2;
scale = (double)pb->id->view_width/pb->id->imagerecord.width;
x -= xoffs; y -= yoffs;
x /= scale; y /= scale;
y = pb->id->imagerecord.height - y;
pb->ctx->images->images[pb->n].x_centre = x;
pb->ctx->images->images[pb->n].y_centre = y;
pb->n++;
if ( pb->n >= pb->ctx->images->n_images ) {
/* Finished */
imagedisplay_close(pb->id);
main_do_reconstruction(pb->ctx);
free(pb);
} else {
/* Display the next pattern */
imagedisplay_put_data(pb->id, pb->ctx->images->images[pb->n]);
}
return 0;
}
/* No peak-detection nor 3D mapping has been done yet.
Ask the user to give a rough idea (i.e. as accurately as possible...)
of the centre of each image. */
void prealign_do_series(ControlContext *ctx) {
PreAlignBlock *pb;
ctx->have_centres = 1; /* Inhibit "centre-finding by stacking" */
pb = malloc(sizeof(PreAlignBlock));
pb->n = 0;
pb->ctx = ctx;
pb->id = imagedisplay_open_with_message(ctx->images->images[pb->n], "Image Pre-alignment",
"Click the centre of the zero-order beam as accurately as you can.", IMAGEDISPLAY_QUIT_IF_CLOSED,
G_CALLBACK(prealign_clicked), pb);
}
/* Sum the image stack, taking pre-existing centres into account if available.
* If no centres available, select the brightest pixel from the sum and assign
* that as the centre to all the images. */
void prealign_sum_stack(ImageList *list, int have_centres, int sum_stack) {
int twidth, theight;
int mnorth, msouth, mwest, meast;
int x, y, i;
uint16_t *image_total;
ImageDisplay *sum_id;
ImageRecord total_record;
/* Determine maximum size of image to accommodate, and allocate memory */
mnorth = 0; msouth = 0; mwest = 0; meast = 0;
for ( i=0; i<list->n_images; i++ ) {
if ( list->images[i].width-list->images[i].x_centre > meast ) meast = list->images[i].width-list->images[i].x_centre;
if ( list->images[i].x_centre > mwest ) mwest = list->images[i].x_centre;
if ( list->images[i].height-list->images[i].y_centre > mnorth ) mnorth = list->images[i].height-list->images[i].y_centre;
if ( list->images[i].y_centre > msouth ) msouth = list->images[i].y_centre;
}
twidth = mwest + meast;
theight = mnorth + msouth;
image_total = malloc(twidth * theight * sizeof(uint16_t));
memset(image_total, 0, twidth * theight * sizeof(uint16_t));
/* Add the image stack together */
if ( !have_centres ) {
int max_x, max_y;
uint16_t max_val;
for ( i=0; i<list->n_images; i++ ) {
int xoffs, yoffs;
xoffs = (twidth - list->images[i].width)/2;
yoffs = (theight - list->images[i].height)/2;
for ( y=0; y<list->images[i].height; y++ ) {
for ( x=0; x<list->images[i].width; x++ ) {
assert(x+xoffs < twidth);
assert(y+yoffs < theight);
assert(x+xoffs >= 0);
assert(y+yoffs >= 0);
image_total[(x+xoffs) + twidth*(y+yoffs)] +=
list->images[i].image[x + list->images[i].width*y]/list->n_images;
}
}
}
/* Locate the highest point */
max_val = 0; max_x = 0; max_y = 0;
for ( y=0; y<theight; y++ ) {
for ( x=0; x<twidth; x++ ) {
if ( image_total[x + twidth*y] > max_val ) {
max_val = image_total[x + twidth*y];
max_x = x; max_y = y;
}
}
}
/* Record this measurement on all images */
for ( i=0; i<list->n_images; i++ ) {
list->images[i].x_centre = max_x;
list->images[i].y_centre = max_y;
}
total_record.x_centre = max_x;
total_record.y_centre = max_y;
total_record.omega = list->images[0].omega;
} else {
/* Just sum the stack */
for ( i=0; i<list->n_images; i++ ) {
int xoffs, yoffs;
xoffs = mwest - list->images[i].x_centre;
yoffs = msouth - list->images[i].y_centre;
for ( y=0; y<list->images[i].height; y++ ) {
for ( x=0; x<list->images[i].width; x++ ) {
assert(x+xoffs < twidth);
assert(y+yoffs < theight);
assert(x+xoffs >= 0);
assert(y+yoffs >= 0);
image_total[(x+xoffs) + twidth*(y+yoffs)] +=
list->images[i].image[x + list->images[i].width*y]/list->n_images;
}
}
}
total_record.omega = list->images[0].omega;
total_record.x_centre = mwest;
total_record.y_centre = msouth;
}
/* Display */
if ( sum_stack ) {
total_record.image = image_total;
total_record.width = twidth;
total_record.height = theight;
sum_id = imagedisplay_open(total_record, "Sum of All Images", IMAGEDISPLAY_SHOW_CENTRE | IMAGEDISPLAY_SHOW_TILT_AXIS | IMAGEDISPLAY_FREE);
}
}
#define CENTERING_WINDOW_SIZE 50
void prealign_fine_centering(ImageList *list, int sum_stack) {
int i;
for ( i=0; i<list->n_images; i++ ) {
int sx, sy;
double max;
unsigned int did_something = 1;
int mask_x, mask_y;
int width, height;
width = list->images[i].width;
height = list->images[i].height;
mask_x = list->images[i].x_centre;
mask_y = list->images[i].y_centre;
while ( (did_something) && (distance(mask_x, mask_y, list->images[i].x_centre, list->images[i].y_centre)<100) ) {
double nmax, nmask_x, nmask_y;
nmax = 0.0;
nmask_x = 0;
nmask_y = 0;
max = list->images[i].image[mask_x+width*mask_y];
did_something = 0;
for ( sy=biggest(mask_y-CENTERING_WINDOW_SIZE/2, 0); sy<smallest(mask_y+CENTERING_WINDOW_SIZE/2, height); sy++ ) {
for ( sx=biggest(mask_x-CENTERING_WINDOW_SIZE/2, 0); sx<smallest(mask_x+CENTERING_WINDOW_SIZE/2, width); sx++ ) {
if ( list->images[i].image[sx+width*sy] > nmax ) {
nmax = list->images[i].image[sx+width*sy];
nmask_x = sx;
nmask_y = sy;
}
}
}
if ( nmax > max ) {
max = nmax;
mask_x = nmask_x;
mask_y = nmask_y;
did_something = 1;
}
}
if ( !did_something ) {
assert(mask_x<width);
assert(mask_y<height);
assert(mask_x>=0);
assert(mask_y>=0);
printf("AL: Image %3i: centre offset by %f,%f\n", i, mask_x-list->images[i].x_centre, mask_y-list->images[i].y_centre);
list->images[i].x_centre = mask_x;
list->images[i].y_centre = mask_y;
}
}
prealign_sum_stack(list, TRUE, sum_stack);
}
void prealign_feature_centering(ImageList *list) {
int i;
for ( i=0; i<list->n_images; i++ ) {
double d1, d2;
ImageFeature *feature1;
ImageFeature *feature2;
int idx;
feature1 = image_feature_closest(list->images[i].features, list->images[i].x_centre, list->images[i].y_centre, &d1, &idx);
feature2 = image_feature_second_closest(list->images[i].features, list->images[i].x_centre, list->images[i].y_centre, &d2, &idx);
printf("AL: Image %i, d1=%f, d2=%f\n", i, d1, d2);
if ( (fabs(d2-d1) <= 19.0) && feature1 && feature2 ) {
list->images[i].x_centre = (feature1->x + feature2->x)/2;
list->images[i].y_centre = (feature1->y + feature2->y)/2;
} else {
if ( feature1 ) {
list->images[i].x_centre = feature1->x;
list->images[i].y_centre = feature1->y;
} else {
printf("AL: Couldn't find centre feature for image %i\n", i);
}
}
}
}
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