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/*
* mrc.c
*
* Read the MRC tomography format
*
* (c) 2007 Thomas White <taw27@cam.ac.uk>
*
* dtr - Diffraction Tomography Reconstruction
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include "mrc.h"
#include "control.h"
#include "imagedisplay.h"
#include "itrans.h"
#include "reflections.h"
#include "utils.h"
int mrc_read(ControlContext *ctx) {
FILE *fh;
MRCHeader mrc;
MRCExtHeader ext[1024];
unsigned int i;
unsigned int extsize;
double pixel_size;
int16_t *image_total;
unsigned int x, y;
int max_x, max_y;
int16_t max_val;
ImageDisplay *sum_id;
fh = fopen(ctx->filename, "rb");
/* Read primary header */
fread(&mrc, sizeof(MRCHeader), 1, fh);
printf("%i images in series\n", mrc.nz);
if ( mrc.mode != 1 ) {
fprintf(stderr, "MR: Unknown MRC image mode\n");
fclose(fh);
return -1;
}
if ( (mrc.nxstart != 0) || (mrc.nystart != 0) ) {
fclose(fh);
fprintf(stderr, "MR: Image origin must be at zero: found at %i,%i\n", mrc.nxstart, mrc.nystart);
return -1;
}
/* Read all extended headers, one by one */
extsize = 4*mrc.numintegers + 4*mrc.numfloats;
if ( extsize > sizeof(MRCExtHeader) ) {
fclose(fh);
fprintf(stderr, "MR: MRC extended header is too big - tweak mrc.h\n");
return -1;
}
for ( i=0; i<mrc.nz; i++ ) {
fread(&ext[i], extsize, 1, fh);
}
pixel_size = ext[0].pixel_size;
printf("pixel_size = %f m^-1\n", pixel_size);
ctx->reflectionctx = reflection_init();
ctx->fmode = FORMULATION_PIXELSIZE;
ctx->first_image = 1;
ctx->width = mrc.nx;
ctx->height = mrc.ny;
printf("Judging centre...");
image_total = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
for ( y=0; y<mrc.ny; y++ ) {
for ( x=0; x<mrc.nx; x++ ) {
image_total[x + mrc.nx*y] = 0;
}
}
for ( i=0; i<mrc.nz; i++ ) {
int16_t *image = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
fseek(fh, mrc.next + sizeof(MRCHeader) + mrc.nx*mrc.ny*2*i, SEEK_SET);
fread(image, mrc.nx*mrc.ny*2, 1, fh);
for ( y=0; y<mrc.ny; y++ ) {
for ( x=0; x<mrc.nx; x++ ) {
image_total[x + mrc.nx*y] += image[x + mrc.nx*y]/mrc.nz;
}
}
}
sum_id = imagedisplay_open(image_total, mrc.nx, mrc.ny, "Sum of All Images");
/* Locate the highest point */
max_val = 0; max_x = 0; max_y = 0;
for ( y=0; y<ctx->height; y++ ) {
for ( x=0; x<ctx->width; x++ ) {
if ( image_total[x + ctx->width*y] > max_val ) {
max_val = image_total[x + ctx->width*y];
max_x = x; max_y = y;
}
}
}
imagedisplay_mark_point(sum_id, max_x, max_y);
ctx->x_centre = max_x;
ctx->y_centre = max_y;
printf("done\n");
for ( i=0; i<mrc.nz; i++ ) {
int16_t *image = malloc(mrc.ny * mrc.nx * sizeof(int16_t));
printf("Image #%3i: tilt=%f omega=%f L=%f\t", i, ext[i].a_tilt, ext[i].tilt_axis, ext[i].magnification);
ctx->camera_length = ext[i].magnification;
if ( ext[i].voltage == 0 ) {
ctx->lambda = lambda(200000);
} else {
ctx->lambda = lambda(1000*ext[i].voltage);
}
ctx->omega = ext[i].tilt_axis;
ctx->pixel_size = ext[i].pixel_size;
fseek(fh, mrc.next + sizeof(MRCHeader) + mrc.nx*mrc.ny*2*i, SEEK_SET);
fread(image, mrc.nx*mrc.ny*2, 1, fh);
for ( y=0; y<mrc.ny; y++ ) {
for ( x=0; x<mrc.nx; x++ ) {
image_total[x + mrc.nx*y] += image[x + mrc.nx*y]/mrc.nz;
}
}
itrans_process_image(image, ctx, ext[i].a_tilt);
free(image);
}
fclose(fh);
return 0;
}
unsigned int mrc_is_mrcfile(const char *filename) {
if ( strcmp(filename+(strlen(filename)-4), ".mrc") == 0 ) {
return 1;
}
return 0;
}
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