forked from fristed/BEaST
/
mincio.c
166 lines (132 loc) · 4.46 KB
/
mincio.c
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/* mincio.c
*
* Copyright 2011 Simon Fristed Eskildsen, Vladimir Fonov,
* Pierrick Coupé, Jose V. Manjon
*
* This file is part of mincbeast.
*
* mincbeast 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 3 of the License, or
* (at your option) any later version.
*
* mincbeast 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 mincbeast. If not, see <http://www.gnu.org/licenses/>.
*
* For questions and feedback, please contact:
* Simon Fristed Eskildsen <eskild@gmail.com>
*/
#include <float.h>
#include "mincio.h"
void set_volume(float *data, VIO_Volume vol, int *sizes){
int i,j,k;
for (i=0;i<sizes[0];i++)
for (j=0;j<sizes[1];j++)
for (k=0;k<sizes[2];k++)
data[i*sizes[1]*sizes[2]+j*sizes[2]+k] = get_volume_real_value(vol,i,j,k,0,0);
}
void get_volume(float *data, VIO_Volume vol, int *sizes){
int i,j,k;
for (i=0;i<sizes[0];i++)
for (j=0;j<sizes[1];j++)
for (k=0;k<sizes[2];k++)
set_volume_real_value(vol,i,j,k,0,0,data[i*sizes[1]*sizes[2]+j*sizes[2]+k]);
}
int write_volume(char *name, VIO_Volume vol, float *data){
int i,j,k,index,sizes[5];
float min=FLT_MAX,max=FLT_MIN;
fprintf(stderr,"Writing %s\n",name);
get_volume_sizes(vol,sizes);
for (i=0;i<sizes[0];i++){
for (j=0;j<sizes[1];j++){
for (k=0;k<sizes[2];k++){
index=i*sizes[2]*sizes[1] + j*sizes[2] + k;
min=MIN(min,data[index]);
max=MAX(max,data[index]);
}
}
}
set_volume_real_range(vol,min,max);
get_volume(data, vol, sizes);
output_volume( name, NC_FLOAT,FALSE,min,max,vol,NULL, (minc_output_options *)NULL);
return STATUS_OK;
}
int write_minc(char *filename, float *image, image_metadata *meta,VIO_BOOL binary_mask){
VIO_Volume volume;
int i,j,k,index;
float min=FLT_MAX,max=FLT_MIN;
VIO_Real dummy[3];
if(binary_mask)
{
volume = create_volume(3,NULL,NC_BYTE,FALSE,0.0,1.0);
printf("Writing a binary volume...\n");
}
else
volume = create_volume(3,NULL,NC_FLOAT,FALSE,FLT_MIN,FLT_MAX);
if(!volume)
return STATUS_ERR;
if(!binary_mask)
{
for (i=0;i<meta->length[0];i++){
for (j=0;j<meta->length[1];j++){
for (k=0;k<meta->length[2];k++){
index=i*meta->length[2]*meta->length[1] + j*meta->length[2] + k;
min=MIN(min,image[index]);
max=MAX(max,image[index]);
}
}
}
set_volume_real_range(volume,min,max);
} else {
set_volume_real_range(volume,0.0,1.0);
}
set_volume_sizes(volume,meta->length);
dummy[0]=meta->start[0];
dummy[1]=meta->start[1];
dummy[2]=meta->start[2];
set_volume_starts(volume,dummy);
dummy[0]=meta->step[0];
dummy[1]=meta->step[1];
dummy[2]=meta->step[2];
set_volume_separations(volume,dummy);
alloc_volume_data(volume);
get_volume(image, volume, meta->length);
if(!binary_mask)
output_volume( filename, NC_FLOAT,FALSE,min, max,volume,meta->history,(minc_output_options *)NULL);
else
output_volume( filename, NC_BYTE,FALSE,0, 1.0,volume,meta->history,(minc_output_options *)NULL);
delete_volume(volume);
return STATUS_OK;
}
image_metadata * read_minc(char *filename, float **image, int *sizes){
VIO_Volume volume;
VIO_Real dummy[3];
image_metadata *meta;
if( input_volume(filename, 3, NULL, NC_UNSPECIFIED, FALSE, 0.0, 0.0, TRUE, &volume, (minc_input_options *) NULL ) != VIO_OK )
return( NULL );
meta = (image_metadata *)calloc( 1 , sizeof(image_metadata) ) ;
meta->start = calloc(3,sizeof(float));
meta->step = calloc(3,sizeof(float));
meta->length = calloc(3,sizeof(int));
get_volume_sizes(volume,sizes);
*image=malloc(sizes[0]*sizes[1]*sizes[2]*sizeof(**image));
set_volume(*image, volume, sizes);
meta->length[0]=sizes[0];
meta->length[1]=sizes[1];
meta->length[2]=sizes[2];
get_volume_starts(volume,dummy);
meta->start[0]=dummy[0];
meta->start[1]=dummy[1];
meta->start[2]=dummy[2];
get_volume_separations(volume,dummy);
meta->step[0]=dummy[0];
meta->step[1]=dummy[1];
meta->step[2]=dummy[2];
delete_volume(volume);
return meta;
}