int iiMRCopenNew(ImodImageFile *inFile, const char *mode)
{
errno = 0;
inFile->fp = fopen(inFile->filename, mode);
if (!inFile->fp) {
b3dError(stderr, "ERROR: iiMRCopenNew - Could not open %s%s%s\n" , inFile->filename,
errno ? " - system message: " : "", errno ? strerror(errno) : "");
return 1;
}
inFile->header = (char *)malloc(sizeof(MrcHeader));
if (!inFile->header) {
b3dError(stderr, "ERROR: iiMRCopenNew - Allocating MRC header\n");
return 1;
}
mrc_head_new((MrcHeader *)inFile->header, 1, 1, 1, 0);
iiMRCsetIOFuncs(inFile, 0);
((MrcHeader *)(inFile->header))->fp = inFile->fp;
inFile->file = IIFILE_MRC;
return 0;
}
/*!
* Writes the data from [slice] into a new MRC file whose name is given in
* [filename]. Returns -1 for error opening the file, -2 for error writing
* header, or an error from ferror if there is an error writing the data.
* Unused as of 2/3/07, but seems usable.
*/
int sliceWriteMRCfile(char *filename, Islice *slice)
{
MrcHeader hout;
FILE *fp = fopen(filename, "wb");
int error;
if (!fp) return -1;
mrc_head_new(&hout, slice->xsize, slice->ysize, 1, slice->mode);
sliceMMM(slice);
hout.amin = slice->min;
hout.amax = slice->max;
hout.amean = slice->mean;
if (mrc_head_write(fp, &hout)) {
fclose(fp);
return -2;
}
b3dFwrite(slice->data.b, slice->dsize,
slice->csize * slice->xsize * slice->ysize, fp);
error = ferror(fp);
fclose(fp);
return(error);
}
/*
* Sets up output size and file header based on output options
* Returns first z section to write, or negative for error.
*/
int set_output_options(ClipOptions *opt, MrcHeader *hout)
{
int z = 0;
/* create a new file */
if (!opt->add2file){
mrc_head_new(hout, opt->ox, opt->oy, opt->oz, opt->mode);
if (mrc_head_write(hout->fp, hout))
return -1;
} else {
if ((opt->ox != hout->nx) || (opt->oy != hout->ny)){
opt->ox = hout->nx;
opt->oy = hout->ny;
show_warning("clip - Appended file can't change size.");
}
if (opt->mode != hout->mode){
opt->mode = hout->mode;
show_warning("clip - Appended file can't change mode.");
}
if (IP_APPEND_ADD == opt->add2file){
/* If appending, scale mean down so complete mean can be computed
by adding slice mean / new nz */
z = hout->nz;
hout->nz += opt->oz;
hout->amean = z * hout->amean / hout->nz;
} else{
z = opt->isec;
hout->nz = opt->oz + opt->isec;
}
if (mrc_head_write(hout->fp, hout))
return -1;
/* DNM 1/15/05: removed the calculation of data size and file seek */
}
return(z);
}
/* Write the data volume with potential padding */
int grap_volume_write(Istack *v, MrcHeader *hout, ClipOptions *opt)
{
FILE *fp = hout->fp;
int zs, ks, z;
int k;
float min, max, mean, zscale;
Islice *s, *ps = NULL;
int labels;
if (opt->mode == IP_DEFAULT)
opt->mode = v->vol[0]->mode;
if (opt->ox == IP_DEFAULT)
opt->ox = v->vol[0]->xsize;
if (opt->oy == IP_DEFAULT)
opt->oy = v->vol[0]->ysize;
if (opt->oz == IP_DEFAULT)
opt->oz = v->zsize;
if (v->vol[0]->mode != opt->mode)
for(k = 0; k < v->zsize; k++){
sliceNewMode(v->vol[k], opt->mode);
}
/* calculate min, max, mean of volume. */
sliceMMM(v->vol[0]);
min = v->vol[0]->min;
max = v->vol[0]->max;
mean = v->vol[0]->mean;
for(k = 1; k < v->zsize; k++){
sliceMMM(v->vol[k]);
min = B3DMIN(min, v->vol[k]->min);
max = B3DMAX(max, v->vol[k]->max);
mean += v->vol[k]->mean;
}
mean /= (float)v->zsize;
/* DNM 6/26/02: do not make a new header if appending or overwriting! */
switch(opt->add2file){
case IP_APPEND_OVERWRITE:
ks = opt->isec;
hout->nz = ks + opt->oz;
opt->ox = hout->nx;
opt->oy = hout->ny;
if (hout->mode != v->vol[0]->mode){
fprintf(stderr,
"overwriting requires data modes to be the same.\n");
return(-1);
}
/* DNM 6/26/02: fix min and max, also fix mz and zlen */
/* DNM 9/13/02: oops, had xlen instead of zlen */
/* todo: recalc mmm. This is a start but not much */
hout->amin = B3DMIN(min, hout->amin);
hout->amax = B3DMAX(max, hout->amax);
zscale = hout->zlen / hout->mz;
hout->mz = hout->nz;
hout->zlen = hout->mz * zscale;
break;
case IP_APPEND_ADD:
ks = hout->nz;
hout->nz = hout->nz + opt->oz;
opt->ox = hout->nx;
opt->oy = hout->ny;
if (hout->mode != v->vol[0]->mode){
fprintf(stderr, "inserting requires data modes to be the same.\n");
return(-1);
}
hout->amin = B3DMIN(min, hout->amin);
hout->amax = B3DMAX(max, hout->amax);
hout->amean = ((hout->amean * ks) + (mean * opt->oz)) / hout->nz;
zscale = hout->zlen / hout->mz;
hout->mz = hout->nz;
hout->zlen = hout->mz * zscale;
break;
case IP_APPEND_FALSE:
/* New file: reinitialize header but preserve the labels, set
min/max/mean */
labels = hout->nlabl;
mrc_head_new(hout, opt->ox, opt->oy, opt->oz, v->vol[0]->mode);
hout->nlabl = labels;
hout->amin = min;
hout->amax = max;
hout->amean = mean;
ks = 0;
}
if (opt->pad == IP_DEFAULT)
opt->pad = hout->amean;
if (mrc_head_write(fp, hout))
return -1;
zs = (v->zsize - opt->oz) / 2;
for (k = ks, z = zs; k < hout->nz; k++, z++) {
/* printf("%d %d\n", k, z);*/
/* Write blank slice outside z range */
if ((z < 0) || (z >= v->zsize)) {
if (!ps) {
ps = clipBlankSlice(hout, opt);
if (!ps)
return -1;
}
if (mrc_write_slice((void *)ps->data.b, fp, hout, k, 'z'))
return (-1);
} else {
/* Resize slice only if necessary */
s = v->vol[z];
if (opt->ox != v->vol[0]->xsize || opt->oy != v->vol[0]->ysize) {
v->vol[z]->mean = opt->pad;
s = mrc_slice_resize(v->vol[z], opt->ox, opt->oy);
if (!s){
fprintf(stderr, "volume_write: error resizing slice.\n");
return(-1);
}
}
if (mrc_write_slice((void *)s->data.b, fp, hout, k, 'z'))
return (-1);
if (opt->ox != v->vol[0]->xsize || opt->oy != v->vol[0]->ysize)
sliceFree(s);
}
}
if (ps)
sliceFree(ps);
return(0);
}
