/*! Set the stored map dimension (rows,sections,columns)
Only allowed when file is opened in write mode before any data
is written.
Note: the row dimension will be overridden during writing
\param mfile (CMMFile *)
\param map_dim (const int *) the map dimension */
void ccp4_cmap_set_dim(CMMFile *mfile, const int *map_dim)
{
if (ccp4_file_is_write(mfile->stream) && !mfile->data.number) {
mfile->map_dim[0] = map_dim[0];
mfile->map_dim[1] = map_dim[1];
mfile->map_dim[2] = map_dim[2];
mfile->data.section_size = map_dim[0]*map_dim[1]*
ccp4_file_itemsize(mfile->stream);
mfile->data.block_size = mfile->data.section_size +
mfile->data.header_size;
}
}
/*! Set the datamode.
This is only allowed if the file is opened in write mode, and
no data has been written.
\param mfile (CMMFile *)
\param datamode (unsigned int) major mode of map */
void ccp4_cmap_set_datamode(CMMFile *mfile, unsigned int datamode)
{
if (ccp4_file_is_write(mfile->stream) && !mfile->data.number &&
datamode <= 6 && datamode != 5) {
mfile->data_mode = datamode;
ccp4_file_setmode(mfile->stream, datamode);
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;
}
}
/*! 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;
}
