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/*
* xfm2def.c
*
* Approximates a deformation grid from an input transformation
*
* Copyright Andrew Janke - a.janke@gmail.com
* Permission to use, copy, modify, and distribute this software and its
* documentation for any purpose and without fee is hereby granted,
* provided that the above copyright notice appear in all copies. The
* author makes no representations about the suitability of this software for
* any purpose. It is provided "as is" without express or implied warranty.
*/
#include <math.h>
#include <float.h>
#include <unistd.h>
#include <sys/stat.h>
#include <volume_io.h>
#include <ParseArgv.h>
#include <time_stamp.h>
#define WORLD_NDIMS 3
#define DEF_BOOL -1
static char *std_dimorder_v[] = { MIxspace, MIyspace, MIzspace, MIvector_dimension };
/* argument variables and table */
static int verbose = FALSE;
static int clobber = FALSE;
static nc_type dtype = NC_SHORT;
static int is_signed = FALSE;
static int nelem[WORLD_NDIMS + 1] = { 100, 100, 100, 3 };
static double start[WORLD_NDIMS] = { -50.0, -50.0, -50.0 };
static double step[WORLD_NDIMS] = { 1.0, 1.0, 1.0 };
static double dircos[WORLD_NDIMS][WORLD_NDIMS] = {
{1.0, 0.0, 0.0},
{0.0, 1.0, 0.0},
{0.0, 0.0, 1.0}
};
static ArgvInfo argTable[] = {
{"-verbose", ARGV_CONSTANT, (char *)TRUE, (char *)&verbose,
"Print out extra information."},
{"-clobber", ARGV_CONSTANT, (char *)TRUE, (char *)&clobber,
"Overwrite existing files."},
{NULL, ARGV_HELP, NULL, NULL, "\nOuput grid Options"},
{"-byte", ARGV_CONSTANT, (char *)NC_BYTE, (char *)&dtype,
"Create a byte data."},
{"-short", ARGV_CONSTANT, (char *)NC_SHORT, (char *)&dtype,
"Create a short integer data.(Default)"},
{"-int", ARGV_CONSTANT, (char *)NC_INT, (char *)&dtype,
"Create a 32-bit integer"},
{"-float", ARGV_CONSTANT, (char *)NC_FLOAT, (char *)&dtype,
"Create a single-precision data."},
{"-double", ARGV_CONSTANT, (char *)NC_DOUBLE, (char *)&dtype,
"Create a double-precision data."},
{"-signed", ARGV_CONSTANT, (char *)TRUE, (char *)&is_signed,
"Create a signed integer data."},
{"-unsigned", ARGV_CONSTANT, (char *)FALSE, (char *)&is_signed,
"Create a unsigned integer data. (Default)"},
{"-xnelements", ARGV_INT, (char *)1, (char *)&nelem[0],
"Number of samples in x dimension."},
{"-ynelements", ARGV_INT, (char *)1, (char *)&nelem[1],
"Number of samples in y dimension."},
{"-znelements", ARGV_INT, (char *)1, (char *)&nelem[2],
"Number of samples in z dimension."},
{"-xstart", ARGV_FLOAT, (char *)1, (char *)&start[0],
"Starting coordinate for x dimension."},
{"-ystart", ARGV_FLOAT, (char *)1, (char *)&start[1],
"Starting coordinate for y dimension."},
{"-zstart", ARGV_FLOAT, (char *)1, (char *)&start[2],
"Starting coordinate for z dimension."},
{"-xstep", ARGV_FLOAT, (char *)1, (char *)&step[0],
"Step size for x dimension."},
{"-ystep", ARGV_FLOAT, (char *)1, (char *)&step[1],
"Step size for y dimension."},
{"-zstep", ARGV_FLOAT, (char *)1, (char *)&step[2],
"Step size for z dimension."},
{"-xdircos", ARGV_FLOAT, (char *)3, (char *)dircos[0],
"Direction cosines along the x dimension"},
{"-ydircos", ARGV_FLOAT, (char *)3, (char *)dircos[1],
"Direction cosines along the y dimension"},
{"-zdircos", ARGV_FLOAT, (char *)3, (char *)dircos[2],
"Direction cosines along the z dimension"},
{NULL, ARGV_HELP, NULL, NULL, ""},
{NULL, ARGV_END, NULL, NULL, NULL}
};
int main(int argc, char *argv[])
{
char *xfm_fn;
char *out_fn;
char *history;
progress_struct progress;
Volume def_grid;
General_transform xfm;
int x, y, z, v;
double vcoord[4], wcoord[3], wcoord_t[3];
double min, max;
double value;
int i;
/* get the history string */
history = time_stamp(argc, argv);
/* get args and file names */
if(ParseArgv(&argc, argv, argTable, 0) || (argc != 3)){
fprintf(stderr, "\nUsage: %s [options] <input.xfm> <def_vol.mnc>\n", argv[0]);
fprintf(stderr, " %s [-help] %d\n\n", argv[0], argc);
exit(EXIT_FAILURE);
}
xfm_fn = argv[1];
out_fn = argv[2];
/* check for infile and outfile */
if(access(xfm_fn, F_OK) != 0){
fprintf(stderr, "%s: Couldn't find input xfm %s.\n\n", argv[0], xfm_fn);
exit(EXIT_FAILURE);
}
if(access(out_fn, F_OK) == 0 && !clobber){
fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0], out_fn);
exit(EXIT_FAILURE);
}
/* read in the input transformation */
if(input_transform_file(xfm_fn, &xfm) != OK){
fprintf(stderr, "%s: Error reading in xfm %s\n\n", argv[0], xfm_fn);
}
/* create the def_grid volume */
def_grid = create_volume(4, std_dimorder_v, dtype, is_signed, 0.0, 0.0);
set_volume_sizes(def_grid, nelem);
set_volume_starts(def_grid, start);
set_volume_separations(def_grid, step);
for(i = 0; i < WORLD_NDIMS; i++){
set_volume_direction_cosine(def_grid, i, dircos[i]);
}
alloc_volume_data(def_grid);
/* generate the grid itself */
min = DBL_MAX;
max = -DBL_MAX;
vcoord[3] = 0;
initialize_progress_report(&progress, FALSE, nelem[0], "Creating grid");
for(x = nelem[0]; x--;){
for(y = nelem[1]; y--;){
for(z = nelem[2]; z--;){
/* figure out where we are in world space */
vcoord[0] = x;
vcoord[1] = y;
vcoord[2] = z;
convert_voxel_to_world(def_grid,
vcoord,
&wcoord[0], &wcoord[1], &wcoord[2]);
/* transform that */
general_transform_point(&xfm,
wcoord[0], wcoord[1], wcoord[2],
&wcoord_t[0], &wcoord_t[1], &wcoord_t[2]);
/* write out dx, dy and dz */
for(v = nelem[3]; v--;){
value = wcoord_t[v] - wcoord[v];
if(value < min){
min = value;
}
if(value > max){
max = value;
}
set_volume_real_value(def_grid, x, y, z, v, 0, value);
}
}
}
update_progress_report(&progress, x + 1);
}
terminate_progress_report(&progress);
/* set the range */
if(verbose){
fprintf(stdout, " + data range: [%g:%g]\n", min, max);
}
set_volume_real_range(def_grid, min, max);
/* output the result */
if(verbose){
fprintf(stdout, "Outputting %s...\n", out_fn);
}
if(output_volume(out_fn, dtype, is_signed, 0.0, 0.0, def_grid, history, NULL) != OK){
fprintf(stderr, "Problems outputing: %s\n\n", out_fn);
exit(EXIT_FAILURE);
}
/* tidy up */
delete_volume(def_grid);
delete_general_transform(&xfm);
return (EXIT_SUCCESS);
}
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