/*!
* Extracts a slice at section number [sno] from the volume in the
* @@Istack structure@ [v], where [axis] is either x or X for a Y/Z slice or
* y or Y for an X/Z slice. Returns NULL for error.
*/
Islice *mrc_slice_getvol(Istack *v, int sno, char axis)
{
Islice *sout;
Ival val;
int i, j, k;
switch (axis){
case 'y': case 'Y':
sout = sliceCreate(v->vol[0]->xsize, v->zsize, v->vol[0]->mode);
if (!sout)
return(NULL);
for (k = 0; k < sout->ysize; k++)
for(i = 0; i < sout->xsize; i++){
sliceGetVal(v->vol[k], i, sno, val);
slicePutVal(sout, i, k, val);
}
break;
case 'x': case 'X':
sout = sliceCreate(v->vol[0]->ysize, v->zsize, v->vol[0]->mode);
if (!sout)
return(NULL);
for (k = 0; k < sout->ysize; k++)
for (j = 0; j < sout->xsize; j++){
sliceGetVal(v->vol[k], sno, j, val);
slicePutVal(sout, j, k, val);
}
break;
default:
return(NULL);
}
return(sout);
}
// Get slices for storage based on needed size of display
void TumblerWindow::setSlice(TumblerStruct *xtum)
{
int xsize, ysize;
if (xtum->slice)
sliceFree(xtum->slice);
if (xtum->stslice)
sliceFree(xtum->stslice);
if (xtum->bwslice)
sliceFree(xtum->bwslice);
if (xtum->count)
sliceFree(xtum->count);
if (xtum->highres){
xsize = ysize = xtum->ms * xtum->zoom;
if (xtum->stereo && xsize > xtum->width / 2)
xsize = xtum->width / 2;
}else{
xsize = ysize = xtum->ms;
}
xtum->slice = sliceCreate(xsize, ysize, SLICE_MODE_SHORT);
xtum->stslice = sliceCreate(xsize, ysize, SLICE_MODE_SHORT);
xtum->bwslice = sliceCreate(xsize, ysize, xtum->vi->rawImageStore);
xtum->count = sliceCreate(xsize, ysize, SLICE_MODE_SHORT);
newData(xtum);
return;
}
/*!
* Creates a new slice of size [nx], [ny] and resizes the input slice [slin]
* into this slice, with the center of the old slice placed in the center of
* the new one. Fills areas with no data from the old slice with
* the slice mean for every channel of multi-channel data. Returns new slice
* or NULL for error.
*/
Islice *mrc_slice_resize(Islice *slin, int nx, int ny)
{
Islice *sout;
int i, j, x, y;
int sx, sy;
Ival pval, val;
pval[0] = slin->mean;
pval[1] = slin->mean;
pval[2] = slin->mean;
sout = sliceCreate(nx, ny, slin->mode);
if (!sout)
return(sout);
sx = (slin->xsize - nx) / 2;
sy = (slin->ysize - ny) / 2;
for(j = 0, y = sy; j < ny; j++, y++)
for(i = 0, x = sx; i < nx; i++, x++){
if ( (x < 0) || (y < 0) ||
(x >= slin->xsize) || (y >= slin->ysize ) )
slicePutVal(sout, i, j, pval);
else{
sliceGetVal(slin, x, y, val);
slicePutVal(sout, i, j, val);
}
}
return(sout);
}
/*!
* Creates a slice of size [xsize], [ysize] and rotates the input slice [slin]
* by the [angle] (in degrees) about the center point [cx], [cy]. Uses
* quadratic interpolation. For areas where there is no image data, all
* channels will be filled with the slice mean. Returns the new slice or NULL
* for error.
*/
Islice *mrc_slice_rotate(Islice *slin, double angle, int xsize, int ysize,
double cx, double cy)
{
Islice *sout;
sout = sliceCreate(xsize, ysize, slin->mode);
if (sout == NULL)
return(NULL);
mrc_slice_rotates(slin, sout, angle, cx, cy);
return(sout);
}
/* UNUSED except by old mrcspectral 2/5/07 */
Islice *mrc_slice_real(Islice *sin)
{
Islice *sout;
int i, xysize;
if (sin->mode != MRC_MODE_COMPLEX_FLOAT)
return(sin);
sout = sliceCreate(sin->xsize, sin->ysize, MRC_MODE_FLOAT);
xysize = sin->xsize * sin->ysize;
for(i = 0; i < xysize; i++){
sout->data.f[i] = sin->data.f[i * 2];
}
return(sout);
}
/*!
* Creates a slice of size [xsize], [ysize] and expands the input slice [sin]
* by the factors [xz] in X and [yz] in Y about the center point [cx], [cy].
* Uses quadratic interpolation. For areas where
* there is no image data, all channels will be filled with the slice mean
* Returns the new slice or NULL for error.
*/
Islice *mrc_slice_zoom(Islice *sin, double xz, double yz,
int xsize, int ysize, double cx, double cy)
{
Islice *sout;
if ((!xz) || (!yz))
return(NULL);
sout = sliceCreate(xsize, ysize, sin->mode);
if (sout == NULL)
return(NULL);
mrc_slice_zooms(sin, sout, xz, yz, cx, cy);
return (sout);
}
/*!
* Returns a slice with one Z plane of data at Z value [secno] from the file
* described by the @@mrcfiles.html#MrcHeader structure@ [hin].
* The file pointer in [hin] is used. Bytes are swapped if necessary.
* Returns NULL for errors.
*/
Islice *sliceReadFloat(MrcHeader *hin, int secno)
{
Islice *slice;
if (sliceModeIfReal(hin->mode) < 0) {
b3dError(stderr, "ERROR: sliceReadFloat - file mode must be real");
return NULL;
}
slice = sliceCreate(hin->nx, hin->ny, MRC_MODE_FLOAT);
if (!slice)
return NULL;
if (mrcReadFloatSlice(slice->data.f, hin, secno)) {
sliceFree(slice);
return NULL;
}
return slice;
}
/*!
* 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);
}
/* Make a blank slice to write to the output volume, using the pad in opt */
static Islice *clipBlankSlice(MrcHeader *hout, ClipOptions *opt)
{
Ival val;
int i, j;
Islice *ps = sliceCreate(hout->nx, hout->ny, hout->mode);
if (!ps){
fprintf(stderr, "clipBlankSlice: error getting slice\n");
return NULL;
}
val[0] = opt->pad;
val[1] = opt->pad;
val[2] = opt->pad;
for(j = 0; j < hout->ny; j++)
for(i = 0; i < hout->nx; i++)
slicePutVal(ps, i, j, val);
return ps;
}
/*!
* Extracts a subarea of slice [sl] into a new slice and returns the slice
* or NULL for error. The coordinates of the subarea are from [llx] to
* [urx] - 1 in X and [lly] to [ury] -1 in Y, inclusive. For areas where
* there is no image data, the slice mean is used to fill only the first
* channel.
*/
Islice *sliceBox(Islice *sl, int llx, int lly, int urx, int ury)
{
Islice *sout;
int i, j, x, y;
int nx, ny;
Ival val;
nx = urx-llx;
ny = ury-lly;
sout = sliceCreate(nx, ny, sl->mode);
if (!sout)
return(NULL);
for(j = lly, y = 0; y < ny; y++, j++)
for(i = llx, x = 0; x < nx; x++, i++){
sliceGetVal(sl, i, j, val);
slicePutVal(sout, x, y, val);
}
return(sout);
}
/*!
* Creates a slice of size [xsize], [ysize] and translates the input slice
* [sin] by [dx], [dy] using bilinear interpolation, putting the result in
* the new slice. For areas where there is no image data, all channels will
* be filled with the slice mean. Returns the new slice or NULL for error.
*/
Islice *mrc_slice_translate(Islice *sin, double dx, double dy,
int xsize, int ysize)
{
int i, j;
Islice *sout;
Ival val;
double x, y;
sout = sliceCreate(xsize, ysize, sin->mode);
if (sout == NULL)
return(NULL);
for(j = 0; j < ysize; j++){
y = (double)j + dy;
for (i = 0; i < xsize; i++){
x = (double)i + dx;
sliceQuadInterpolate(sin, x, y, val);
slicePutVal(sout, i, j, val);
}
}
return(sout);
}
/*!
* Converts the data in [slice] from modes 0-3 or 6 to complex float. For
* modes 0-2 and 6, the value is placed in the real component and the imaginary
* component is set to 0. This should be slightly more efficient than
* @sliceNewMode is. Returns -1 for error.
*/
int sliceComplexFloat(Islice *slice)
{
Islice *tsl;
Ival val;
int i, j;
if (slice->mode > 3 && slice->mode != MRC_MODE_USHORT)
return(-1);
val[1] = 0;
tsl = sliceCreate(slice->xsize, slice->ysize, MRC_MODE_COMPLEX_FLOAT);
if (!tsl)
return(-1);
for(j = 0; j < slice->ysize; j++)
for(i = 0; i < slice->xsize; i++){
sliceGetVal(slice, i, j, val);
slicePutVal(tsl, i, j, val);
}
free(slice->data.b);
slice->data.f = tsl->data.f;
slice->mode = MRC_MODE_COMPLEX_FLOAT;
free(tsl);
return(0);
}
/*!
* Filters a slice [sin] by convolving with the square matrix [mat] of
* dimension [dim] and returns a float slice, or NULL for error. Pixels outside
* the image bounds are obtained by replicated pixels on the edge, so there is
* no need to set the {mean} value of the slice.
*/
Islice *slice_mat_filter(Islice *sin, float *mat, int dim)
{
Islice *sout;
float *imat;
Ival val;
int i,j;
imat = (float *)malloc(dim * dim * sizeof(float));
if (!imat)
return(NULL);
sout = sliceCreate(sin->xsize, sin->ysize, MRC_MODE_FLOAT);
if (!sout)
return NULL;
for(j = 0; j < sin->ysize; j++){
for(i = 0; i < sin->xsize; i++){
mrc_slice_mat_getimat(sin, i, j, dim, imat);
val[0] = mrc_slice_mat_mult(mat, imat, dim);
slicePutVal(sout, i, j, val);
}
}
free(imat);
return(sout);
}
/*!
* Converts the data in slice [s] from its current mode to [mode], allocating
* a new data array as needed. Complex values are converted to others by
* taking the magnitude. Values are converted to complex modes by setting the
* real component to the value, and the imaginary component to 0. RGB values
* are converted by taking a weighted sum of components. When converting to a
* mode with integer or byte values, the data are truncated to fit within the
* range of the new mode. Returns the new mode or -1 for error.
*/
int sliceNewMode(Islice *s, int mode)
{
Islice *ns;
Ival val;
int i, j;
int default_copy = 0;
int limit_val = 0;
float minval, maxval;
if (!s)
return(-1);
if (s->mode == mode)
return(mode);
ns = sliceCreate(s->xsize, s->ysize, mode);
/* Set up limiting values */
if (mode == MRC_MODE_BYTE || mode == MRC_MODE_RGB) {
limit_val = 1;
minval = 0.;
maxval = 255;
} else if (mode == MRC_MODE_SHORT) {
limit_val = 1;
minval = -32768.;
maxval = 32767.;
} else if (mode == MRC_MODE_USHORT) {
limit_val = 1;
minval = 0.;
maxval = 65535.;
}
if (!ns)
return(-1);
switch(s->mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
default_copy = 1;
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
val[1] = 0;
default_copy = 1;
break;
case MRC_MODE_RGB:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
val[2] = val[1] = val[0];
slicePutVal(ns, i, j, val);
}
break;
default:
default_copy = 1;
break;
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (float)sqrt(val[0] * val[0] + val[1] * val[1]);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
default_copy = 1;
break;
case MRC_MODE_RGB:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (float)sqrt(val[0] * val[0] + val[1] * val[1]);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
val[2] = val[1] = val[0];
slicePutVal(ns, i, j, val);
}
break;
}
break;
case MRC_MODE_RGB:
switch(mode){
case MRC_MODE_BYTE:
case MRC_MODE_SHORT:
case MRC_MODE_USHORT:
case MRC_MODE_FLOAT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (val[0] * 0.3f) +
(val[1] * 0.59f) + (val[2] * 0.11f);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
break;
case MRC_MODE_COMPLEX_FLOAT:
case MRC_MODE_COMPLEX_SHORT:
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
val[0] = (val[0] * 0.3f) +
(val[1] * 0.59f) + (val[2] * 0.11f);
val[1] = 0;
slicePutVal(ns, i, j, val);
}
break;
default:
default_copy = 1;
break;
}
break;
default:
default_copy = 1;
break;
}
if (default_copy){
for(j = 0; j < s->ysize; j++)
for(i = 0; i < s->xsize; i++){
sliceGetVal(s, i, j, val);
if (limit_val)
val[0] = B3DMIN(maxval, B3DMAX(minval, val[0]));
slicePutVal(ns, i, j, val);
}
}
free(s->data.b);
/* 2/3/07: switch from copying ns to s to just setting data and mode */
s->data.b = ns->data.b;
s->mode = mode;
free(ns);
return(mode);
}
/*!
* Converts the data in [slice] to float mode. For complex data, the magnitude
* is taken; for RGB data, a weighed sum of the components is taken. This
* should be slightly more efficient than @sliceNewMode is. Returns -1 for
* error.
*/
int sliceFloat(Islice *slice)
{
Islice *tsl;
Ival val;
int i, j;
switch(slice->mode){
case SLICE_MODE_BYTE:
case SLICE_MODE_SHORT:
tsl = sliceCreate(slice->xsize, slice->ysize, SLICE_MODE_FLOAT);
if (!tsl)
return(-1);
for(j = 0; j < slice->ysize; j++)
for(i = 0; i < slice->xsize; i++){
sliceGetVal(slice, i, j, val);
slicePutVal(tsl, i, j, val);
}
free(slice->data.b);
slice->data.f = tsl->data.f;
slice->mode = SLICE_MODE_FLOAT;
free(tsl);
break;
case SLICE_MODE_FLOAT:
break;
case SLICE_MODE_COMPLEX_SHORT:
case SLICE_MODE_COMPLEX_FLOAT:
tsl = sliceCreate(slice->xsize, slice->ysize, SLICE_MODE_FLOAT);
if (!tsl)
return(-1);
for(j = 0; j < slice->ysize; j++)
for(i = 0; i < slice->xsize; i++){
sliceGetVal(slice, i, j, val);
val[0] = (val[0] * val[0]) + (val[1] * val[1]);
val[0] = sqrt(val[0]);
slicePutVal(tsl, i, j, val);
}
free(slice->data.b);
slice->data.f = tsl->data.f;
slice->mode = SLICE_MODE_FLOAT;
free(tsl);
break;
case SLICE_MODE_RGB:
tsl = sliceCreate(slice->xsize, slice->ysize, SLICE_MODE_FLOAT);
if (!tsl)
return(-1);
for(j = 0; j < slice->ysize; j++)
for(i = 0; i < slice->xsize; i++){
sliceGetVal(slice, i, j, val);
val[0] = val[0] * 0.3f + val[1] * 0.59f + val[2] * 0.11f;
slicePutVal(tsl, i, j, val);
}
free(slice->data.b);
slice->data.f = tsl->data.f;
slice->mode = SLICE_MODE_FLOAT;
free(tsl);
break;
default:
return(-1);
}
return(0);
}
/* Read the required data volume */
Istack *grap_volume_read(MrcHeader *hin, ClipOptions *opt)
{
Istack *v;
Islice *s;
Ival val;
int i, j, k, x, y, z;
if (opt->dim == 2){
if (opt->iz == IP_DEFAULT) opt->iz = 0;
if (opt->iz2 == IP_DEFAULT) opt->iz2 = hin->nz - 1;
if (opt->iz2 == 0) opt->iz2 = opt->iz;
if (opt->iz2 < opt->iz) opt->iz2 = opt->iz;
opt->cz = ( opt->iz2 + opt->iz) / 2.;
opt->iz = opt->iz2 - opt->iz + 1;
}
if (opt->ix == IP_DEFAULT) opt->ix = hin->nx;
if (opt->iy == IP_DEFAULT) opt->iy = hin->ny;
if (opt->iz == IP_DEFAULT) opt->iz = hin->nz;
if (opt->cx == IP_DEFAULT) opt->cx = hin->nx / 2.;
if (opt->cy == IP_DEFAULT) opt->cy = hin->ny / 2.;
if (opt->cz == IP_DEFAULT) opt->cz = hin->nz / 2.;
/* Do not set opt->pad yet, just pad with current mean */
val[0] = opt->pad;
if (opt->pad == IP_DEFAULT)
val[0] = hin->amean;
val[1] = val[0];
val[2] = val[0];
/* Create volume and initialize to pad value. */
v = (Istack *)malloc(sizeof(Istack));
v->vol = (Islice **)malloc( opt->iz * sizeof(Islice *));
v->zsize = opt->iz;
for (k = 0; k < opt->iz; k++) {
v->vol[k] = sliceCreate(opt->ix, opt->iy, hin->mode);
if (!v->vol[k])
return(NULL);
for( j = 0; j < opt->iy; j++)
for(i = 0; i < opt->ix; i++)
slicePutVal(v->vol[k], i, j, val);
v->vol[k]->mean = hin->amean;
v->vol[k]->max = hin->amax;
v->vol[k]->min = hin->amin;
}
s = sliceCreate(hin->nx, hin->ny, hin->mode);
if (!s)
return(NULL);
/* Read slices in, copying just the part that is needed */
k = (int)floor(opt->cz - ((float)opt->iz * 0.5f));
/* printf("k = %d\n", k); */
for (z = 0; (k < hin->nz) && (z < opt->iz); k++, z++) {
if (k >= 0) {
if (mrc_read_slice((void *)s->data.b, hin->fp, hin, k, 'z'))
return (NULL);
j = (int)floor(opt->cy - opt->iy / 2.);
for (y = 0; (j < hin->ny) && (y < opt->iy); j++, y++) {
if (j >= 0) {
i = (int)floor(opt->cx - opt->ix / 2.);
x = 0;
if (i < 0) {
x = -i;
i = 0;
}
for (; (i < hin->nx) && (x < opt->ix); i++, x++) {
sliceGetVal(s, i, j, val);
slicePutVal(v->vol[z], x, y, val);
}
}
}
}
}
sliceFree(s);
return(v);
}
