VBoolean VSetBandInterp (VImage image,
VBandInterp frame_interp, int nframes,
VBandInterp viewpoint_interp, int nviewpoints,
VBandInterp color_interp, int ncolors,
VBandInterp component_interp, int ncomponents)
{
VBoolean result = TRUE;
VString str;
if (VImageNBands (image) !=
nframes * nviewpoints * ncolors * ncomponents) {
VWarning ("VSetBandInterp: No. bands (%d) conflicts with no. "
"of frames, etc. (%d %d %d %d)", VImageNBands (image),
nframes, nviewpoints, ncolors, ncomponents);
result = FALSE;
}
if (frame_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VFrameInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VFrameInterpAttr,
VBandInterpDict, VLongRepn, (VLong) frame_interp);
VImageNFrames (image) = nframes;
if (viewpoint_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VViewpointInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VViewpointInterpAttr,
VBandInterpDict, VLongRepn, (VLong) viewpoint_interp);
VImageNViewpoints (image) = nviewpoints;
if (color_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VColorInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VColorInterpAttr,
VBandInterpDict, VLongRepn, (VLong) color_interp);
VImageNColors (image) = ncolors;
if (component_interp == VBandInterpNone)
result &= VExtractAttr (VImageAttrList (image), VComponentInterpAttr,
NULL, VStringRepn, & str, FALSE);
else VSetAttr (VImageAttrList (image), VComponentInterpAttr,
VBandInterpDict, VLongRepn, (VLong) component_interp);
VImageNComponents (image) = ncomponents;
return result;
}
VImage VCopyImageAttrs (VImage src, VImage dest)
{
VAttrList list;
if (src == dest)
return dest;
if (! dest) {
dest = VCreateImage (VImageNBands (src), VImageNRows (src),
VImageNColumns (src), VPixelRepn (src));
if (! dest)
return NULL;
}
/* Clone the source image's attribute list if it isn't empty: */
if (! VAttrListEmpty (VImageAttrList (src))) {
list = VImageAttrList (dest);
VImageAttrList (dest) = VCopyAttrList (VImageAttrList (src));
} else if (! VAttrListEmpty (VImageAttrList (dest))) {
list = VImageAttrList (dest);
VImageAttrList (dest) = VCreateAttrList ();
} else list = NULL;
if (list)
VDestroyAttrList (list);
/* Preserve band interpretation attributes only if the source and
destination images have the same number of bands: */
if (VImageNBands (src) > 1 && VImageNBands (dest) == VImageNBands (src)) {
VImageNFrames (dest) = VImageNFrames (src);
VImageNViewpoints (dest) = VImageNViewpoints (src);
VImageNColors (dest) = VImageNColors (src);
VImageNComponents (dest) = VImageNComponents (src);
} else {
VExtractAttr (VImageAttrList (dest), VFrameInterpAttr, NULL,
VBitRepn, NULL, FALSE);
VExtractAttr (VImageAttrList (dest), VViewpointInterpAttr, NULL,
VBitRepn, NULL, FALSE);
VExtractAttr (VImageAttrList (dest), VColorInterpAttr, NULL,
VBitRepn, NULL, FALSE);
VExtractAttr (VImageAttrList (dest), VComponentInterpAttr, NULL,
VBitRepn, NULL, FALSE);
VImageNComponents (dest) = VImageNColors (dest) =
VImageNViewpoints (dest) = 1;
VImageNFrames (dest) = VImageNBands (dest);
}
return dest;
}
/*
** slicetime correction for non-constant TR
*/
void
VSlicetime_NC(VAttrList list, VShort minval, VFloat tdel,
VBoolean slicetime_correction, float *onset_array, VString filename) {
FILE *fp = NULL;
VImage src;
VAttrListPosn posn;
VString buf, str;
int b, r, c, i, j, nt = 0, mt = 0, val, del = 0;
double xmin, xmax, sum, nx, estim_tr = 0;
double *xx = NULL, *yy = NULL, xi, yi, slicetime = 0, u = 0;
gsl_interp_accel *acc = NULL;
gsl_spline *spline = NULL;
xmin = (VShort) VRepnMinValue(VShortRepn);
xmax = (VShort) VRepnMaxValue(VShortRepn);
buf = VMalloc(LEN);
/*
** read scan times from file, non-constant TR
*/
if(strlen(filename) > 2) {
fp = fopen(filename, "r");
if(!fp)
VError(" error opening file %s", filename);
i = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '%' || buf[0] == '#')
continue;
if(strlen(buf) < 2)
continue;
i++;
}
rewind(fp);
nt = i;
fprintf(stderr, " num timesteps: %d\n", nt);
xx = (double *) VCalloc(nt, sizeof(double));
yy = (double *) VCalloc(nt, sizeof(double));
i = 0;
sum = 0;
while(!feof(fp)) {
for(j = 0; j < LEN; j++)
buf[j] = '\0';
fgets(buf, LEN, fp);
if(buf[0] == '%' || buf[0] == '#')
continue;
if(strlen(buf) < 2)
continue;
if(sscanf(buf, "%lf", &u) != 1)
VError(" line %d: illegal input format", i + 1);
xx[i] = u * 1000.0; /* convert to millisec */
if(i > 1)
sum += xx[i] - xx[i - 1];
i++;
}
fclose(fp);
estim_tr = sum / (double)(nt - 2);
fprintf(stderr, " average scan interval = %.3f sec\n", estim_tr / 1000.0);
}
/*
** process data
*/
b = -1;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VShortRepn)
continue;
VSetAttr(VImageAttrList(src), "repetition_time", NULL, VLongRepn, (VLong)estim_tr);
VExtractAttr(VImageAttrList(src), "MPIL_vista_0", NULL, VStringRepn, &str, FALSE);
b++;
if(VImageNRows(src) < 2)
continue;
/*
** get header info
*/
if(VGetAttr(VImageAttrList(src), "slice_time", NULL,
VDoubleRepn, (VPointer) & slicetime) != VAttrFound && slicetime_correction && onset_array == NULL)
VError(" 'slice_time' info missing");
if(onset_array != NULL)
slicetime = onset_array[b];
if(nt != VImageNBands(src))
VError(" inconsistent number of time steps, %d %d",
nt, VImageNBands(src));
if(acc == NULL && slicetime_correction) {
acc = gsl_interp_accel_alloc();
spline = gsl_spline_alloc(gsl_interp_akima, nt);
for(i = 0; i < 5; i++) {
if(xx[i] / 1000.0 > tdel)
break;
}
del = i;
fprintf(stderr, " The first %.2f secs (%d timesteps) will be replaced.\n", tdel, del);
}
/*
** loop through all voxels in current slice
*/
if(slicetime_correction)
fprintf(stderr, " slice: %3d, %10.3f ms\r", b, slicetime);
for(r = 0; r < VImageNRows(src); r++) {
for(c = 0; c < VImageNColumns(src); c++) {
if(VPixel(src, 0, r, c, VShort) < minval)
continue;
/* replace first few time steps by average */
if(del > 0) {
mt = del + 10;
if(mt > nt)
mt = nt;
sum = nx = 0;
for(i = del; i < mt; i++) {
sum += VPixel(src, i, r, c, VShort);
nx++;
}
if(nx < 1)
continue;
val = sum / nx;
for(i = 0; i < del; i++) {
VPixel(src, i, r, c, VShort) = val;
}
}
if(!slicetime_correction)
continue;
/* correct for slicetime offsets using cubic spline interpolation */
for(i = 0; i < nt; i++) {
yy[i] = VPixel(src, i, r, c, VShort);
}
gsl_spline_init(spline, xx, yy, nt);
for(i = 1; i < nt; i++) {
xi = xx[i] - slicetime;
yi = gsl_spline_eval(spline, xi, acc);
val = (int)(yi + 0.49);
if(val > xmax)
val = xmax;
if(val < xmin)
val = xmin;
VPixel(src, i, r, c, VShort) = val;
}
}
}
}
fprintf(stderr, "\n");
}
