/*!
* Returns a slice with the gradient of the input slice [sin], or NULL for
* error. The gradient is the absolute value of the difference
* between the current and next pixel, averaged over the X and Y direction.
*/
Islice *sliceGradient(Islice *sin)
{
Islice *s;
int i, j;
Ival val, nval, gval;
s = sliceCreate(sin->xsize, sin->ysize, sin->mode);
if (!s)
return(NULL);
/* Store gradient in X */
for(j = 0; j < sin->ysize; j++){
for(i = 0; i < sin->xsize - 1; i++){
sliceGetVal(sin, i, j, val);
sliceGetVal(sin, i+1, j, nval);
val[0] = nval[0] - val[0];
if (val[0] < 0)
val[0] *= -1;
slicePutVal(s, i, j, val);
}
}
/* Get gradient in Y and average with the one in X, copy last line */
for(i = 0; i < sin->xsize; i++){
for(j = 0; j < sin->ysize - 1; j++){
sliceGetVal(sin, i, j, val);
sliceGetVal(sin, i, j + 1, nval);
sliceGetVal(s, i, j, gval);
val[0] = nval[0] - val[0];
if (val[0] < 0)
val[0] *= -1;
gval[0] = (val[0] + gval[0]) / 2;
slicePutVal(s, i, j, gval);
}
sliceGetVal(s, i, j - 1, val);
slicePutVal(s, i, j, val);
}
/* Copy last column over too */
for(j = 0; j < sin->ysize; j++){
sliceGetVal(s, sin->xsize - 2, j, val);
slicePutVal(s, sin->xsize - 1, j, val);
}
sliceMMM(s);
return(s);
}
/*!
* 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);
}
/* 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);
}
/*
* Write one slice to output file
* kSec is the index of the sections being processed,
* zWrite is address of z value at which to write, maintained here
* freeSlice 1 indicates to free the slice when done
*/
int clipWriteSlice(Islice *slice, MrcHeader *hout, ClipOptions *opt, int kSec,
int *zWrite, int freeSlice)
{
Islice *ps = NULL;
Islice *s;
int z;
int blankBefore = 0;
int blankAfter = 0;
/* Ignore if output size is smaller than # being processed */
if (kSec < (opt->nofsecs - opt->oz) / 2 ||
kSec >= (opt->nofsecs - opt->oz) / 2 + opt->oz) {
if (freeSlice)
sliceFree(slice);
return 0;
}
/* determine if blank slices need to be written before or after this slice */
if (opt->oz > opt->nofsecs) {
if (!kSec) {
if (opt->outBefore == IP_DEFAULT)
blankBefore = (opt->oz - opt->nofsecs) / 2;
else
blankBefore = opt->outBefore;
}
if (kSec == opt->nofsecs - 1) {
if (opt->outAfter == IP_DEFAULT)
blankAfter = opt->oz - opt->nofsecs - (opt->oz - opt->nofsecs) / 2;
else
blankAfter = opt->outAfter;
}
if (blankBefore || blankAfter) {
ps = clipBlankSlice(hout, opt);
if (!ps)
return -1;
}
}
/* Write blank slices before */
for (z = 0; z < blankBefore; z++)
if (mrc_write_slice((void *)ps->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
/* convert slice to output mode if needed */
if (slice->mode != opt->mode && sliceNewMode(slice, opt->mode) < 0)
return -1;
/* Resize slice if necessary */
s = slice;
if (opt->ox != slice->xsize || opt->oy != slice->ysize) {
slice->mean = opt->pad;
s = mrc_slice_resize(slice, opt->ox, opt->oy);
if (!s) {
fprintf(stderr, "clipWriteSlice: error resizing slice.\n");
return(-1);
}
}
/* maintain min & max, add to mean unless overwriting */
sliceMMM(s);
hout->amin = B3DMIN(hout->amin, s->min);
hout->amax = B3DMAX(hout->amax, s->max);
if (opt->add2file != IP_APPEND_OVERWRITE)
hout->amean += (s->mean + (blankBefore + blankAfter) * opt->pad) /
hout->nz;
/* Write slice, free slices as needed */
if (mrc_write_slice((void *)s->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
if (opt->ox != slice->xsize || opt->oy != slice->ysize)
sliceFree(s);
if (freeSlice)
sliceFree(slice);
/* Write blank slices after */
for (z = 0; z < blankAfter; z++)
if (mrc_write_slice((void *)ps->data.b, hout->fp, hout, (*zWrite)++, 'z'))
return -1;
if (ps)
sliceFree(ps);
return 0;
}
