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/*
cmap_header.c: read and write map file headers
Copyright (C) 2001 CCLRC, Charles Ballard
This library is free software: you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
version 3, modified in accordance with the provisions of the
license to address the requirements of UK law.
You should have received a copy of the modified GNU Lesser General
Public License along with this library. If not, copies may be
downloaded from http://www.ccp4.ac.uk/ccp4license.php
This program 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 Lesser General Public License for more details.
*/
#include <string.h>
#include <math.h>
#include <stdarg.h>
#include "cmaplib.h"
#include "cmap_errno.h"
#include "cmap_skew.h"
/*! Internal: read header from file and fill CMMFile struct.
Called after file is opened for read.
\param mfile (CMMFile *)
\return 1 on success, EOF on failure*/
int parse_mapheader(CMMFile *mfile)
{
const int read_total = 77;
const size_t header_size = 1024U, n_byt_symop = 80U;
unsigned char buffer[224];
int result;
float fmean,frms;
ccp4_file_rewind(mfile->stream);
memset(buffer,'\0',224);
result = ccp4_file_readint(mfile->stream, &buffer[0], 10) ;
result += ccp4_file_readfloat(mfile->stream, &buffer[40], 6);
result += ccp4_file_readint(mfile->stream, &buffer[64], 3);
result += ccp4_file_readfloat(mfile->stream, &buffer[76], 3);
result += ccp4_file_readint(mfile->stream, &buffer[88], 3);
/* skew matrix and translation */
result += ccp4_file_readfloat(mfile->stream, &buffer[100], 12);
/* reserved */
result += ccp4_file_readint(mfile->stream, &buffer[148], 8);
/* user access */
result += ccp4_file_readchar(mfile->stream, &buffer[180], 28);
/* map and machine stamp */
result += ccp4_file_readint(mfile->stream, &buffer[208], 2);
/* ARMS */
result += ccp4_file_readfloat(mfile->stream, &buffer[216], 1);
result += ccp4_file_readint(mfile->stream, &buffer[220], 1);
if (result != read_total) {
ccp4_signal( CCP4_ERRLEVEL(3) | CMAP_ERRNO(CMERR_ReadFail),
"parse_header",
NULL);
return EOF; }
memcpy(&mfile->map_dim[0],&buffer[0],sizeof(mfile->map_dim));
memcpy(&mfile->data_mode,&buffer[12],sizeof(int));
memcpy(&mfile->origin[0],&buffer[16],sizeof(mfile->origin));
memcpy(&mfile->cell_grid[0],&buffer[28],sizeof(mfile->cell_grid));
memcpy(&mfile->cell[0],&buffer[40],sizeof(mfile->cell));
memcpy(&mfile->axes_order[0],&buffer[64],sizeof(mfile->axes_order));
memcpy(&mfile->stats.min,&buffer[76],sizeof(float));
memcpy(&mfile->stats.max,&buffer[80],sizeof(float));
memcpy(&fmean,&buffer[84],sizeof(float));
mfile->stats.mean = (double) fmean;
memcpy(&mfile->spacegroup,&buffer[88],sizeof(int));
/* Additions for EM support.
Define contents as image, image stack, volume or volume stack.
In latter case, allows for 400+ispg convention. */
mfile->EM_spacegroup = mfile->spacegroup;
strncpy(mfile->EM_contents,"VOLU",4);
if (mfile->spacegroup > 400 && mfile->spacegroup < 631) {
mfile->spacegroup = mfile->spacegroup - 400;
strncpy(mfile->EM_contents,"VLST",4);
}
if (mfile->spacegroup == 0) {
if (mfile->map_dim[2] == 1) strncpy(mfile->EM_contents,"IMAG",4);
if (mfile->map_dim[2] > 1) strncpy(mfile->EM_contents,"IMST",4);
}
memcpy(&mfile->symop.size,&buffer[92],sizeof(int));
memcpy(&mfile->user_access,&buffer[180],sizeof(mfile->user_access));
/* memcpy(&mfile->data.header_size,&buffer[204],sizeof(int)); */
memcpy(&frms,&buffer[216],sizeof(float));
mfile->stats.rms = (double) frms;
memcpy(&mfile->labels.number,&buffer[220],sizeof(int));
memcpy(&result,&buffer[96],sizeof(int));
if (result !=0) {
memcpy(&mfile->skew.rotation[0][0],&buffer[100],sizeof(mfile->skew.rotation));
memcpy(&mfile->skew.translation[0],&buffer[136],sizeof(mfile->skew.translation));
}
ccp4_file_setmode(mfile->stream, mfile->data_mode);
/* may go to seperate function */
mfile->symop.offset = header_size;
mfile->data.offset = mfile->symop.offset + mfile->symop.size;
mfile->data.section_size = mfile->map_dim[0]*mfile->map_dim[1]
*ccp4_file_itemsize(mfile->stream);
mfile->data.block_size = mfile->data.section_size + mfile->data.header_size;
mfile->data.number = mfile->map_dim[2];
mfile->symop.number = mfile->symop.size / n_byt_symop;
return 1;
}
/*! Internal: write summary of current CMMFile struct to file.
Called when file is opened write, and closed write.
\param mfile (CMMFile *)
\return 1 on success, EOF on failure */
int write_mapheader(CMMFile *mfile)
{
const int write_total = 77;
unsigned char buffer[224];
int result;
float fmean,frms;
memset(buffer,'\0',224);
memcpy(&buffer[0],&mfile->map_dim[0],sizeof(mfile->map_dim));
memcpy(&buffer[12],&mfile->data_mode,sizeof(int));
memcpy(&buffer[16],&mfile->origin[0],sizeof(mfile->origin));
memcpy(&buffer[28],&mfile->cell_grid[0],sizeof(mfile->cell_grid));
memcpy(&buffer[40],&mfile->cell[0],sizeof(mfile->cell));
memcpy(&buffer[64],&mfile->axes_order[0],sizeof(mfile->axes_order));
memcpy(&buffer[76],&mfile->stats.min,sizeof(float));
memcpy(&buffer[80],&mfile->stats.max,sizeof(float));
fmean = (float) mfile->stats.mean;
memcpy(&buffer[84],&fmean,sizeof(float));
/* additions for EM support */
if (!strncmp(mfile->EM_contents,"VLST",4)) {
memcpy(&buffer[88],&mfile->EM_spacegroup,sizeof(int));
} else {
memcpy(&buffer[88],&mfile->spacegroup,sizeof(int));
}
memcpy(&buffer[92],&mfile->symop.size,sizeof(int));
memcpy(&buffer[180],&mfile->user_access,sizeof(mfile->user_access));
/* memcpy(&buffer[204],&mfile->data.header_size,sizeof(int)); */
memcpy(&buffer[208],"MAP ",4U);
frms = (float) mfile->stats.rms;
memcpy(&buffer[216],&frms,sizeof(float));
memcpy(&buffer[220],&mfile->labels.number,sizeof(int));
if (skew_set(&mfile->skew) == TRUE) {
result = 1;
memcpy(&buffer[96],&result, sizeof(int));
memcpy(&buffer[100],&mfile->skew.rotation[0][0],sizeof(mfile->skew.rotation));
memcpy(&buffer[148],&mfile->skew.translation[0],sizeof(mfile->skew.translation));
}
ccp4_file_seek(mfile->stream, 0L, SEEK_SET);
result = ccp4_file_writeint(mfile->stream, &buffer[0], 10);
result += ccp4_file_writefloat(mfile->stream, &buffer[40], 6);
result += ccp4_file_writeint(mfile->stream, &buffer[64], 3);
result += ccp4_file_writefloat(mfile->stream, &buffer[76], 3);
result += ccp4_file_writeint(mfile->stream, &buffer[88], 3);
result += ccp4_file_writefloat(mfile->stream, &buffer[100], 12);
result += ccp4_file_writeint(mfile->stream, &buffer[148], 8);
result += ccp4_file_writechar(mfile->stream, &buffer[180], 28);
result += ccp4_file_writeint(mfile->stream, &buffer[208], 2);
result += ccp4_file_writefloat(mfile->stream, &buffer[216], 1);
result += ccp4_file_writeint(mfile->stream, &buffer[220], 1);
if (result != write_total)
ccp4_signal( CCP4_ERRLEVEL(3) | CMAP_ERRNO(CMERR_WriteFail),
"write_header",
NULL);
return ( (result == write_total) ? 1 : EOF);
}
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