/*! The file is opened.
\param filename (char *) the filename
\param mode (int) the i/o mode , possible values are O_RDONLY, O_WRONLY,
O_RDWR, O_APPEND, O_TMP, O_CREAT, O_TRUNC - see ccp4_sysdep.h
\return (void *) CMMFile structure */
void *ccp4_cmap_open(const char *filename, int mode)
{
CMMFile *mfile;
CCP4File *cfile;
const size_t stamp_offset = 212U;
if ((cfile = ccp4_file_open(filename, mode)) == NULL) {
ccp4_signal( CCP4_ERRLEVEL(3) | CMAP_ERRNO(CMERR_CantOpenFile),
"ccp4_cmap_open",NULL);
return (NULL); }
ccp4_file_raw_setstamp(cfile, stamp_offset);
/* read or write only */
if (cfile->read) {
if (!is_cmap(cfile) || cfile->length < 1025) {
ccp4_signal( CCP4_ERRLEVEL(3) | CMAP_ERRNO(CMERR_NoHeader),
"ccp4_cmap_open",NULL);
ccp4_file_close(cfile);
return NULL; }
ccp4_file_rarch(cfile);
mfile = init_cmap_read();
mfile->stream = cfile;
mfile->file_name = cfile->name;
parse_mapheader(mfile);
parse_maplabels(mfile);
} else if (cfile->write) {
mfile = init_cmap_write();
mfile->stream = cfile;
mfile->file_name = cfile->name;
write_mapheader(mfile);
write_maplabels(mfile);
} else {
ccp4_signal( CCP4_ERRLEVEL(3) | CMAP_ERRNO(CMERR_CantOpenFile),
"ccp4_cmap_open",NULL);
return (NULL); }
return (mfile);
}
/*! 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);
}