VImage VSelectDestImage (VStringConst routine, VImage dest,
int nbands, int nrows, int ncolumns,
VRepnKind pixel_repn)
{
/* If no destination image was specified, allocate one: */
if (! dest)
return VCreateImage (nbands, nrows, ncolumns, pixel_repn);
/* Otherwise check that the destination provided has the appropriate
characteristics: */
if (VImageNBands (dest) != nbands) {
VWarning ("%s: Destination image has %d bands; %d expected",
routine, VImageNBands (dest), nbands);
return NULL;
}
if (VImageNRows (dest) != nrows) {
VWarning ("%s: Destination image has %d rows; %d expected",
routine, VImageNRows (dest), nrows);
return NULL;
}
if (VImageNColumns (dest) != ncolumns) {
VWarning ("%s: Destination image has %d columns; %d expected",
routine, VImageNColumns (dest), ncolumns);
return NULL;
}
if (VPixelRepn (dest) != pixel_repn) {
VWarning ("%s: Destination image has %s pixels; %s expected", routine,
VPixelRepnName (dest), VRepnName (pixel_repn));
return NULL;
}
return dest;
}
VImage VCombineBands (int nels, VImage src_images[], VBand src_bands[],
VImage dest)
{
int n, i;
VImage result, src = src_images[0];
/* Count the number of bands needed in the destination image: */
for (i = n = 0; i < nels; i++)
n += (src_bands[i] == VAllBands) ? VImageNBands (src_images[i]) : 1;
/* Check or allocate the destination image: */
result = VSelectDestImage ("VCombineBands", dest, n,
VImageNRows (src), VImageNColumns (src),
VPixelRepn (src));
if (! result)
return NULL;
/* Copy each source band into the destination image: */
for (i = n = 0; i < nels; i++) {
if (! VCopyBand (src_images[i], src_bands[i], result, n)) {
if (result != dest)
VDestroyImage (result);
return NULL;
}
n += (src_bands[i] == VAllBands) ? VImageNBands (src_images[i]) : 1;
}
return result;
}
VBandInterp VImageColorInterp (VImage image)
{
VLong interp;
VGetAttrResult result;
if (VImageNBands (image) !=
(VImageNFrames (image) * VImageNViewpoints (image) *
VImageNColors (image) * VImageNComponents (image)))
VWarning ("VImageColorInterp: No. bands (%d) conflicts with no. "
"of frames, etc. (%d %d %d %d)",
VImageNBands (image), VImageNFrames (image),
VImageNViewpoints (image), VImageNColors (image),
VImageNComponents (image));
if (! VImageAttrList (image) ||
(result =
VGetAttr (VImageAttrList (image), VColorInterpAttr,
VBandInterpDict, VLongRepn, & interp)) == VAttrMissing)
return VImageNColors (image) > 1 ? VBandInterpOther : VBandInterpNone;
if (result == VAttrBadValue)
return VBandInterpOther;
switch (interp) {
case VBandInterpRGB:
if (VImageNColors (image) != 3) {
VWarning ("VBandColorInterp: RGB image has %d color dimension(s)",
VImageNColors (image));
return VBandInterpOther;
}
return VBandInterpRGB;
}
return VBandInterpOther;
}
VBoolean Compatible (VImage Image1, VImage Image2)
{
/* compare image sizes */
if ((VImageNBands (Image1) != VImageNBands (Image2)) ||
(VImageNRows (Image1) != VImageNRows (Image2)) ||
(VImageNColumns (Image1) != VImageNColumns (Image2)))
{
VError ("Images have different sizes");
return FALSE;
}
return TRUE;
} /* Compatible */
/*
** read several rows of data from a file
*/
void
VReadObjectData (FILE *fp,int object_id,VImage *image)
{
static VImageInfo imageInfo;
static VAttrList list=NULL;
fseek(fp,0L,SEEK_SET);
if (! ReadHeader (fp)) VError("error reading header");
if (! (list = ReadAttrList (fp)))
VError("error reading attr list");
if (! VGetImageInfo(fp,list,object_id,&imageInfo))
VError(" error reading image info");
if (imageInfo.nbands != VImageNBands((*image)))
VError("incorrect number of bands");
if (imageInfo.nrows != VImageNRows((*image)))
VError("incorrect number of rows");
if (imageInfo.ncolumns != VImageNColumns((*image)))
VError("incorrect number of columns");
if (imageInfo.repn != VPixelRepn((*image)))
VError("incorrect pixel representation");
if (! VReadBlockData (fp,&imageInfo,0,imageInfo.nrows,image))
VError(" error reading data");
}
/*!
\fn VImage VDTDilate(VImage src,VImage dest,VDouble radius)
\brief 3D morphological dilation
\param src input image (bit repn)
\param dest output image (bit repn)
\param radius radius of the spherical structural element
*/
VImage
VDTDilate(VImage src,VImage dest,VDouble radius)
{
VImage float_image;
VBit *bin_pp;
VFloat *float_pp;
int i,nbands,nrows,ncols,npixels;
if (VPixelRepn(src) != VBitRepn)
VError("Input image must be of type VBit");
nbands = VImageNBands(src);
nrows = VImageNRows(src);
ncols = VImageNColumns(src);
npixels = nbands * nrows * ncols;
float_image = VChamferDist3d(src,NULL,VFloatRepn);
if (! float_image)
VError("VDTDilate failed.\n");
dest = VSelectDestImage("VDTDilate",dest,nbands,nrows,ncols,VBitRepn);
if (! dest) return NULL;
float_pp = (VFloat *) VPixelPtr(float_image,0,0,0);
bin_pp = (VBit *) VPixelPtr(dest,0,0,0);
for (i=0; i<npixels; i++)
*bin_pp++ = ((*float_pp++ > radius) ? 0 : 1);
VDestroyImage(float_image);
VCopyImageAttrs (src,dest);
return dest;
}
VImage VImageManager::vtimestep( VAttrList list, VImage dest, int step )
{
VFillImage( dest, VAllBands, 0 );
VPointer src_pp = NULL;
VPointer dest_pp = NULL;
VAttrListPosn posn;
VShort *ptr1 = NULL;
VShort *ptr2 = NULL;
VString str;
VImage src;
int n = 0;
int npixels = 0;
bool revert = false;
for ( VFirstAttr ( list, & posn ); VAttrExists ( & posn ); VNextAttr ( & posn ) ) {
if ( VGetAttrRepn ( & posn ) != VImageRepn )
continue;
VGetAttrValue ( &posn, NULL, VImageRepn, &src );
if ( VPixelRepn( src ) != VShortRepn )
continue;
if ( ( VGetAttr ( VImageAttrList ( src ), "MPIL_vista_0", NULL,
VStringRepn, ( VPointer ) & str ) != VAttrFound ) &&
( VGetAttr ( VImageAttrList ( src ), "repetition_time", NULL,
VStringRepn, ( VPointer ) & str ) != VAttrFound ) )
continue;
/* doch nicht rumdrehen!
if (VGetAttr (VImageAttrList (src), "extent", NULL,
VStringRepn, (VPointer) & str) != VAttrFound)
revert = true;
*/
if ( n == 0 )
VCopyImageAttrs ( src, dest );
if ( VImageNRows( src ) > 1 ) {
if ( VSelectBand ( "vtimestep", src, step, &npixels, &src_pp ) == FALSE )
VError( "err reading data" );
int destBand = ( revert ) ? VImageNBands( dest ) - n - 1 : n;
dest_pp = VPixelPtr( dest, destBand, 0, 0 );
ptr1 = ( VShort * ) src_pp;
ptr2 = ( VShort * ) dest_pp;
memcpy ( ptr2, ptr1, npixels * sizeof( VShort ) );
}
n++;
}
return dest;
}
VImage VImageManager::scaleImage( VImage src, VImage dest, double factor )
{
int nPixel = VImageSize( src ) / VPixelSize( src );
if ( dest == NULL ) {
dest = VCreateImage(
VImageNBands( src ),
VImageNRows( src ),
VImageNColumns( src ),
VUByteRepn );
}
VUByte *destPtr = ( VUByte * ) VImageData( dest );
VShort *srcPtr = ( VShort * ) VImageData( src );
srcPtr = ( VShort * ) VImageData( src );
for ( int i = 0; i < nPixel; i++ ) {
if ( *srcPtr <= m_xmin )
*destPtr = 0;
else if ( *srcPtr >= m_xmax )
*destPtr = 255;
else {
int val = *srcPtr - m_xmin;
*destPtr = ( VUByte ) ( val * factor );
}
srcPtr++;
destPtr++;
}
return dest;
}
/*
* Zero out one hemisphere of a raster image
*/
void
VImageHemi(VImage *src,VLong hemi)
{
int nbands,nrows,ncols;
int b,r,c,c0,c1,half;
ncols = VImageNColumns (*src);
nrows = VImageNRows (*src);
nbands = VImageNBands (*src);
half = ncols/2;
if (hemi == 1) {
c0 = 0;
c1 = half;
}
else {
c0 = half;
c1 = ncols;
}
for (b=0; b<nbands; b++) {
for (r=0; r<nrows; r++) {
for (c=c0; c<c1; c++) {
VSetPixel((*src),b,r,c,(VDouble) 0);
}
}
}
}
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;
}
int main (int argc, char *argv[])
{
static VShort band;
static VOptionDescRec options[] = {
{ "band", VShortRepn, 1, & band, VOptionalOpt, NULL,"Image band to convert" }
};
FILE *infile, *outfile;
int nimages;
VAttrList attributes;
VImage *images, image;
char prg[50];
sprintf(prg,"vtopgm V%s", getVersion());
fprintf (stderr, "%s\n", prg);
/* Parse command line arguments and identify the input and output files */
VParseFilterCmd (VNumber (options), options, argc, argv,
& infile, & outfile);
/* Read all images from the input file */
if ((nimages = VReadImages (infile, & attributes, & images)) == 0)
exit (EXIT_FAILURE); /* no images found */
fclose (infile);
/* Ensure that the specified band exists: */
if (nimages != 1)
VWarning ("Only the first of %d images will be converted", nimages);
if (band < 0 || band >= VImageNBands (images[0]))
VError ("Image of %d band(s) has no band %d",
VImageNBands (images[0]), band);
/* Convert the image to UByte: */
if (VPixelRepn(images[0]) != VUByteRepn) {
image = VConvertImageRange (images[0], NULL, (VBand) band, VUByteRepn);
if (! image)
exit (EXIT_FAILURE);
band = 0;
} else image = images[0];
/* Output the first image as a pgm file. */
WritePgmFile (outfile, image, (VBand) band);
return EXIT_SUCCESS;
}
VImage
VSelSlices (VImage src,VImage dest,VShort first,VShort last)
{
int nbands,nrows,ncols,nbands_neu,npixels;
int i,b,bn;
VRepnKind repn;
nbands = VImageNBands(src);
nrows = VImageNRows(src);
ncols = VImageNColumns(src);
repn = VPixelRepn(src);
if (first < 0) VError("VSelSlices: parameter <first> must be positive");
if (last < 0) last = nbands-1;
if (last >= nbands) last = nbands-1;
if (first > last)
VError("VSelSlices: <first> must be less than <last>.");
nbands_neu = last - first + 1;
if (dest == NULL)
dest = VCreateImage(nbands_neu,nrows,ncols,repn);
npixels = nrows * ncols;
#define SelSlices(type) \
{ \
type *src_pp, *dest_pp; \
bn = 0; \
for (b=first; b<=last; b++) { \
src_pp = VPixelPtr(src,b,0,0); \
dest_pp = VPixelPtr(dest,bn,0,0); \
for (i=0; i<npixels; i++) *dest_pp++ = *src_pp++; \
bn++; \
} \
}
/* Instantiate the macro once for each source pixel type: */
switch (repn) {
case VBitRepn: SelSlices (VBit); break;
case VUByteRepn: SelSlices (VUByte); break;
case VSByteRepn: SelSlices (VSByte); break;
case VShortRepn: SelSlices (VShort); break;
case VLongRepn: SelSlices (VLong); break;
case VFloatRepn: SelSlices (VFloat); break;
case VDoubleRepn: SelSlices (VDouble); break;
default: ;
}
/* Let the destination inherit any attributes of the source image: */
VCopyImageAttrs (src, dest);
return dest;
}
VBoolean VCopyBand (VImage src, VBand src_band, VImage dest, VBand dest_band)
{
int nbands, src_npixels, dest_npixels;
VPointer src_pixels, dest_pixels;
/* The destination image must exist: */
if (! dest) {
VWarning ("VCopyBand: No destination specified");
return FALSE;
}
/* VAllBands not accepted for destination band: */
if (dest_band < 0 || dest_band >= VImageNBands (dest)) {
VWarning ("VCopyBand: Band %d referenced in image of %d bands",
(int) dest_band, (int) VImageNBands (dest));
return FALSE;
}
/* Ensure that the destination image has the appropriate dimensions
and pixel representation: */
nbands = dest_band;
if (src_band == VAllBands)
nbands += VImageNBands (src) - 1;
if (nbands < VImageNBands (dest))
nbands = VImageNBands (dest);
if (! VSelectDestImage ("VCopyBand", dest, nbands, VImageNRows (src),
VImageNColumns (src), VPixelRepn (src)))
return FALSE;
/* Locate the specified source and destination bands: */
if (! VSelectBand ("VCopyBand", src, src_band,
& src_npixels, & src_pixels))
return FALSE;
if (! VSelectBand ("VCopyBand", dest, dest_band,
& dest_npixels, & dest_pixels))
return FALSE;
/* Copy from the source band to the destination band: */
memcpy (dest_pixels, src_pixels, src_npixels * VPixelSize (src));
return TRUE;
}
VBoolean VSelectBand (VStringConst routine, VImage image, VBand band,
int *npixels, VPointer *first_pixel)
{
if (band == VAllBands) {
if (npixels)
*npixels = VImageNPixels (image);
if (first_pixel)
*first_pixel = VImageData (image);
} else if (band >= 0 && band < VImageNBands (image)) {
if (npixels)
*npixels = VImageNRows (image) * VImageNColumns (image);
if (first_pixel)
*first_pixel = image->band_index[band][0];
} else {
VWarning ("%s: Band %d referenced in image of %d band(s)",
routine, band, VImageNBands (image));
return FALSE;
}
return TRUE;
}
VImage VCopyImage (VImage src, VImage dest, VBand band)
{
VImage result;
if (src == dest &&
(band == VAllBands || (band == 0 && VImageNBands (src) == 1)))
return src;
if ((result = VCopyImagePixels (src, dest, band)) != 0)
VCopyImageAttrs (src, result);
return result;
}
VBoolean FunctionalZero (VImage Image)
{
int Pixels; /* number of pixels */
VShort* image; /* image data pointer */
int n; /* index */
/* check image size */
if ((VImageNBands (Image) == 1) && (VImageNRows (Image) == 1) && (VImageNColumns (Image) == 1))
return TRUE;
/* check image content */
Pixels = VImageNBands (Image) * VImageNRows (Image) * VImageNColumns (Image);
image = (VShort*) VPixelPtr (Image, 0, 0, 0);
for (n = 0; n < Pixels; ++n)
if (*(image++) != 0)
return FALSE;
return TRUE;
} /* FunctionalZero */
unsigned short CVImage::getSize( Direction dir, VImage image )
{
switch( dir ) {
case read:
return VImageNColumns( image );
break;
case phase:
return VImageNRows( image );
break;
case slice:
return VImageNBands( image );
break;
}
}
VImage VCombineBandsVa (VImage dest, ...)
{
va_list args;
VImage src, result;
int nbands;
VBand src_band, dest_band;
/* Count the number of bands to be combined: */
va_start (args, dest);
for (nbands = 0; (src = va_arg (args, VImage)) != 0; nbands +=
(va_arg (args, VBand) == VAllBands) ? VImageNBands (src) : 1) ;
va_end (args);
/* Check or allocate the destination image: */
va_start (args, dest);
src = va_arg (args, VImage);
va_end (args);
result = VSelectDestImage ("VCombineBandsVa", dest, nbands,
VImageNRows (src), VImageNColumns (src),
VPixelRepn (src));
if (! result)
return NULL;
/* Copy each source band into the destination image: */
va_start (args, dest);
for (dest_band = 0; (src = va_arg (args, VImage)) != 0; ) {
src_band = va_arg (args, VBand);
if (! VCopyBand (src, src_band, result, dest_band)) {
if (result != dest)
VDestroyImage (result);
return NULL;
}
dest_band += (src_band == VAllBands) ? VImageNBands (src) : 1;
}
va_end (args);
return result;
}
/*!
\fn VImage VMedianImage2d (VImage src, VImage dest, int dim, VBoolean ignore)
\param src input image
\param dest output image
\param dim kernel size
\param ignore whether to ignore zero voxels
*/
VImage
VMedianImage2d (VImage src, VImage dest, int dim, VBoolean ignore)
{
int nbands,nrows,ncols;
int i,len,b,r,c,rr,cc,d=0;
gsl_vector *vec=NULL;
double u,tiny=1.0e-10;
if (dim%2 == 0) VError("VMedianImage2d: dim (%d) must be odd",dim);
nrows = VImageNRows (src);
ncols = VImageNColumns (src);
nbands = VImageNBands (src);
d = dim/2;
len = dim * dim;
vec = gsl_vector_calloc(len);
dest = VCopyImage(src,dest,VAllBands);
for (b=0; b<nbands; b++) {
for (r=d; r<nrows-d; r++) {
for (c=d; c<ncols-d; c++) {
gsl_vector_set_zero(vec);
u = VGetPixel(src,b,r,c);
if ( !ignore || ABS(u) > tiny) {
i = 0;
for (rr=r-d; rr<=r+d; rr++) {
for (cc=c-d; cc<=c+d; cc++) {
u = VGetPixel(src,b,rr,cc);
if (ABS(u) > 0) {
gsl_vector_set(vec,i,u);
i++;
}
}
}
gsl_sort_vector(vec);
u = gsl_stats_median_from_sorted_data(vec->data,vec->stride,i);
VSetPixel(dest,b,r,c,u);
}
}
}
}
return dest;
}
/*!
\fn VImage VMapImageRange(VImage src,VImage dest,VRepnKind repn)
\brief
The minimum and maximum grey values of the input images are computed,
and a linear mapping is performed mapping the input minimum(maximum)
of the input image to the min(max) value of the output pixel repn.
E.g. if the input image min is -17 and its max is +2376, and the output repn
is VUByteRepn, then the linear mapping function maps -17 to 0 and
+2376 to 255.
\param src input image (any repn)
\param dest output image
\param repn the output pixel repn (e.g. VUByteRepn)
*/
VImage
VMapImageRange(VImage src,VImage dest,VRepnKind repn)
{
int i,nbands,nrows,ncols,npixels;
float u,ymin,ymax,dmin,dmax,slope;
if (repn == VDoubleRepn || repn == VLongRepn || repn == VSByteRepn)
VError(" VMapImageRange: double, long and sbyte are not supported");
nbands = VImageNBands(src);
nrows = VImageNRows(src);
ncols = VImageNColumns(src);
npixels = VImageNPixels(src);
dest = VSelectDestImage("VMapImageRange",dest,nbands,nrows,ncols,repn);
if (! dest) VError(" err creating dest image");
VFillImage(dest,VAllBands,0);
ymin = VPixelMaxValue(src);
ymax = VPixelMinValue(src);
for (i=0; i<npixels; i++) {
u = VGetPixelValue (src,i);
if (u < ymin) ymin = u;
if (u > ymax) ymax = u;
}
dmax = VPixelMaxValue(dest);
dmin = VPixelMinValue(dest);
slope = (dmax - dmin) / (ymax - ymin);
for (i=0; i<npixels; i++) {
u = VGetPixelValue (src,i);
u = slope * (u - ymin);
if (u < dmin) u = dmin;
if (u > dmax) u = dmax;
VSetPixelValue(dest,i,(VFloat) u);
}
VCopyImageAttrs (src, dest);
return dest;
}
template <class T> void OpticalFlow (VImage S, VImage M, VImage G, VImage G2, VImage& V)
{
const float EPSILON = 1; /* threshold for denominator of optical flow */
int Pixels; /* number of pixels */
T *s, *m; /* source and model data pointer */
VFloat *g, *g2; /* gradient data pointer */
VFloat *v; /* optical flow data pointer */
float nom, denom; /* fraction */
int n; /* index */
/* get image size */
Pixels = VImageNPixels (S);
/* create optical flow */
V = VCreateImage (VImageNBands (S), VImageNRows (S), VImageNColumns (S), VFloatRepn);
/* compute optical flow */
s = (T*) VPixelPtr (S, 0, 0, 0);
m = (T*) VPixelPtr (M, 0, 0, 0);
g = (VFloat*) VPixelPtr (G, 0, 0, 0);
g2 = (VFloat*) VPixelPtr (G2, 0, 0, 0);
v = (VFloat*) VPixelPtr (V, 0, 0, 0);
for (n = 0; n < Pixels; ++n)
{
/* compute fraction */
nom = (float) (*(m++) - *(s++));
denom = (float) (*(g2++) + (nom * nom));
/* assign optical flow */
if (denom < EPSILON) *(v++) = 0;
else *(v++) = (VFloat) ((nom / denom) * *g);
++g;
}
} /* OpticalFlow */
VImage VCopyImagePixels (VImage src, VImage dest, VBand band)
{
int npixels;
VPointer src_pixels;
VImage result;
/* Locate the source and destination of the copy: */
if (! VSelectBand ("VCopyImagePixels", src, band, & npixels, & src_pixels))
return NULL;
result = VSelectDestImage ("VCopyImagePixels", dest,
band == VAllBands ? VImageNBands (src) : 1,
VImageNRows (src), VImageNColumns (src),
VPixelRepn (src));
if (! result)
return NULL;
/* Copy pixel values from src to dest: */
memcpy (VImageData (result), src_pixels, npixels * VPixelSize (src));
return result;
}
VImage
VSConvolveRow (VImage src,VImage dest,VImage kernel)
{
int b,r,c,nbands,nrows,ncols;
int r0,r1,rr;
float sum,x;
VFloat *float_pp;
int d,dim;
dim = VImageNColumns(kernel);
d = dim/2;
nrows = VImageNRows (src);
ncols = VImageNColumns (src);
nbands = VImageNBands (src);
dest = VSelectDestImage("VConvolveRow",dest,nbands,nrows,ncols,VFloatRepn);
for (b=0; b<nbands; b++) {
for (r=d; r<nrows-d; r++) {
for (c=0; c<ncols; c++) {
float_pp = (VFloat *) VImageData(kernel);
sum = 0;
r0 = r-d;
r1 = r+d;
if (r0 < 0) r0 = 0;
if (r1 >= nrows) r1 = nrows-1;
for (rr=r0; rr<=r1; rr++) {
x = VPixel(src,b,rr,c,VFloat);
sum += x * (*float_pp++);
}
VPixel(dest,b,r,c,VFloat) = sum;
}
}
}
return dest;
}
VImage
VSConvolveCol (VImage src,VImage dest,VImage kernel)
{
int b,r,c,nbands,nrows,ncols;
int c0,c1,cc;
float sum,x;
VFloat *float_pp;
int dim,d;
nrows = VImageNRows (src);
ncols = VImageNColumns (src);
nbands = VImageNBands (src);
dest = VSelectDestImage("VConvolveCol",dest,nbands,nrows,ncols,VFloatRepn);
VFillImage(dest,VAllBands,0);
dim = VImageNColumns(kernel);
d = dim/2;
for (b=0; b<nbands; b++) {
for (r=0; r<nrows; r++) {
for (c=d; c<ncols-d; c++) {
float_pp = (VFloat *) VImageData(kernel);
sum = 0;
c0 = c-d;
c1 = c+d;
if (c0 < 0) c0 = 0;
if (c1 >= ncols) c1 = ncols-1;
for (cc=c0; cc<=c1; cc++) {
x = VPixel(src,b,r,cc,VFloat);
sum += x * (*float_pp++);
}
VPixel(dest,b,r,c,VFloat) = sum;
}
}
}
return dest;
}
VImage
VSConvolveBand (VImage src,VImage dest,VImage kernel)
{
int b,r,c,nbands,nrows,ncols;
int b0,b1,bb;
float sum,x;
VFloat *float_pp;
int d,dim;
dim = VImageNColumns(kernel);
d = dim/2;
nrows = VImageNRows (src);
ncols = VImageNColumns (src);
nbands = VImageNBands (src);
dest = VSelectDestImage("VConvolveBand",dest,nbands,nrows,ncols,VFloatRepn);
for (b=d; b<nbands-d; b++) {
for (r=0; r<nrows; r++) {
for (c=0; c<ncols; c++) {
float_pp = (VFloat *) VImageData(kernel);
sum = 0;
b0 = b-d;
b1 = b+d;
if (b0 < 0) b0 = 0;
if (b1 >= nbands) b1 = nbands-1;
for (bb=b0; bb<=b1; bb++) {
x = VPixel(src,bb,r,c,VFloat);
sum += x * (*float_pp++);
}
VPixel(dest,b,r,c,VFloat) = sum;
}
}
}
return dest;
}
/*
* Flip3dImage
*
*/
VImage Flip3dImage(VImage src, VImage dest, VBand band, VBoolean x_axis, VBoolean y_axis, VBoolean z_axis) {
int nx, ny, nz;
int i, j, k;
nx = VImageNColumns(src);
ny = VImageNRows(src);
nz = VImageNBands(src);
/* Check the destination image.
If it is NULL, then create one of the appropriate size and type. */
dest = VSelectDestImage("Flip3dImage", dest,
nz, ny, nx, VPixelRepn(src));
if(! dest)
return NULL;
for(i = 0; i < nx; i++)
for(j = 0; j < ny; j++)
for(k = 0; k < nz; k++) {
if(! x_axis && ! y_axis && ! z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, k, j, i));
if(x_axis && ! y_axis && ! z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, k, j, nx - i - 1));
if(! x_axis && y_axis && ! z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, k, ny - j - 1, i));
if(! x_axis && ! y_axis && z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, nz - k - 1, j, i));
if(x_axis && y_axis && ! z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, k, ny - j - 1, nx - i - 1));
if(x_axis && ! y_axis && z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, nz - k - 1, j, nx - i - 1));
if(! x_axis && y_axis && z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, nz - k - 1, ny - j - 1, i));
if(x_axis && y_axis && z_axis)
VSetPixel(dest, k, j, i, VGetPixel(src, nz - k - 1, ny - j - 1, nx - i - 1));
};
/* Let the destination inherit any attributes of the source image: */
VCopyImageAttrs(src, dest);
return dest;
};
static VAttrList VImageEncodeAttrMethod (VPointer value, size_t *lengthp)
{
VImage image = value;
VAttrList list;
size_t length;
#define OptionallyPrepend(value, name) \
if (value != 1) \
VPrependAttr (list, name, NULL, VLongRepn, (VLong) value)
/* Temporarily prepend several attributes to the image's attribute list: */
if ((list = VImageAttrList (image)) == NULL)
list = VImageAttrList (image) = VCreateAttrList ();
VPrependAttr (list, VRepnAttr, VNumericRepnDict,
VLongRepn, (VLong) VPixelRepn (image));
VPrependAttr (list, VNColumnsAttr, NULL,
VLongRepn, (VLong) VImageNColumns (image));
VPrependAttr (list, VNRowsAttr, NULL,
VLongRepn, (VLong) VImageNRows (image));
OptionallyPrepend (VImageNComponents (image), VNComponentsAttr);
OptionallyPrepend (VImageNColors (image), VNColorsAttr);
OptionallyPrepend (VImageNViewpoints (image), VNViewpointsAttr);
OptionallyPrepend (VImageNFrames (image), VNFramesAttr);
OptionallyPrepend (VImageNBands (image), VNBandsAttr);
/* Compute the file space needed for the image's binary data: */
length = VImageNPixels (image);
if (VPixelRepn (image) == VBitRepn)
length = (length + 7) / 8;
else length *= VPixelPrecision (image) / 8;
*lengthp = length;
return list;
#undef OptionallyPrepend
}
int
main (int argc,char *argv[])
{
static VString filename = "";
static VString filename1 = "";
static VString filename2 = "";
static VShort first = 2;
static VShort length = 0;
static VShort type = 0;
static VShort minval = 0;
static VShort nproc = 4;
static VOptionDescRec options[] = {
{"in1",VStringRepn,1,(VPointer) &filename1,VRequiredOpt,NULL,"first input file"},
{"in2",VStringRepn,1,(VPointer) &filename2,VRequiredOpt,NULL,"second input file"},
{"mask",VStringRepn,1,(VPointer) &filename,VRequiredOpt,NULL,"mask"},
{"type",VShortRepn,1,(VPointer) &type,VOptionalOpt,TYPDict,"type of concordance measure"},
{"minval",VShortRepn,1,(VPointer) &minval,VOptionalOpt,NULL,"signal threshold"},
{"first",VShortRepn,1,(VPointer) &first,VOptionalOpt,NULL,"first timestep to use"},
{"length",VShortRepn,1,(VPointer) &length,VOptionalOpt,NULL,
"length of time series to use, '0' to use full length"},
{"j",VShortRepn,1,(VPointer) &nproc,VOptionalOpt,NULL,"number of processors to use, '0' to use all"}
};
FILE *out_file,*fp;
VAttrList list=NULL,list1=NULL,list2=NULL,out_list=NULL;
VAttrListPosn posn;
VImage mask=NULL,map=NULL,dest=NULL,disc=NULL;
float *A1=NULL,*A2=NULL,u=0,tiny=1.0e-6;
int b,r,c;
char *prg = "vccm2";
VParseFilterCmd (VNumber (options),options,argc,argv,NULL,&out_file);
if (type > 3) VError("illegal type");
/*
** read mask
*/
fp = VOpenInputFile (filename, TRUE);
list = VReadFile (fp, NULL);
if (! list) VError("Error reading mask file");
fclose(fp);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & mask);
if (VPixelRepn(mask) == VFloatRepn || VPixelRepn(mask) == VDoubleRepn) {
mask = NULL;
continue;
}
}
if (mask == NULL) VError(" no mask found");
/* read files */
fp = VOpenInputFile (filename1, TRUE);
list1 = VReadFile (fp, NULL);
if (! list1) VError("Error reading 1st input file");
fclose(fp);
fp = VOpenInputFile (filename2, TRUE);
list2 = VReadFile (fp, NULL);
if (! list2) VError("Error reading 2nd input file");
fclose(fp);
/* get voxel map */
map = GetMap(list1,list2,mask,minval);
/* omp-stuff */
#ifdef _OPENMP
int num_procs=omp_get_num_procs();
if (nproc > 0 && nproc < num_procs) num_procs = nproc;
printf("using %d cores\n",(int)num_procs);
omp_set_num_threads(num_procs);
#endif /* _OPENMP */
/* compute corr matrices */
A1 = VCorrMatrix(list1,map,first,length);
A2 = VCorrMatrix(list2,map,first,length);
/* get concordance between two corr matrices */
dest = VCCM2(A1,A2,map,(int)type);
/* invert to get discordant map */
disc = VCreateImageLike(dest);
VFillImage(disc,VAllBands,0);
if (type < 2) {
for (b=0; b<VImageNBands(dest); b++) {
for (r=0; r<VImageNRows(dest); r++) {
for (c=0; c<VImageNColumns(dest); c++) {
if (VGetPixel(mask,b,r,c) < 1) continue;
u = VPixel(dest,b,r,c,VFloat);
if (u < tiny) continue;
VPixel(disc,b,r,c,VFloat) = 1-u;
}
}
}
}
/* output */
out_list = VCreateAttrList();
VHistory(VNumber(options),options,prg,&list,&out_list);
VAppendAttr(out_list,"concordant",NULL,VImageRepn,dest);
if (type < 2) VAppendAttr(out_list,"discordant",NULL,VImageRepn,disc);
if (! VWriteFile (out_file, out_list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
float *
VCorrMatrix(VAttrList list,VImage map,VShort first,VShort length)
{
VAttrListPosn posn;
VImage src[NSLICES];
size_t b,r,c,i,j,i1,n,m,nt,last,ntimesteps,nrows,ncols,nslices;
gsl_matrix_float *mat=NULL;
float *A=NULL;
/*
** get image dimensions
*/
i = ntimesteps = nrows = ncols = 0;
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & src[i]);
if (VPixelRepn(src[i]) != VShortRepn) continue;
if (VImageNBands(src[i]) > ntimesteps) ntimesteps = VImageNBands(src[i]);
if (VImageNRows(src[i]) > nrows) nrows = VImageNRows(src[i]);
if (VImageNColumns(src[i]) > ncols) ncols = VImageNColumns(src[i]);
i++;
if (i >= NSLICES) VError(" too many slices");
}
nslices = i;
/* get time steps to include */
if (length < 1) length = ntimesteps-2;
last = first + length -1;
if (last >= ntimesteps) last = ntimesteps-1;
if (first < 0) first = 1;
nt = last - first + 1;
i1 = first+1;
if (nt < 2) VError(" not enough timesteps, nt= %d",nt);
/* number of voxels */
n = VImageNColumns(map);
fprintf(stderr," ntimesteps: %d, first= %d, last= %d, nt= %d, nvoxels: %ld\n",
(int)ntimesteps,(int)first,(int)last,(int)nt,(long)n);
/*
** avoid casting to float, copy data to matrix
*/
mat = gsl_matrix_float_calloc(n,nt);
if (!mat) VError(" err allocating mat");
for (i=0; i<n; i++) {
b = VPixel(map,0,0,i,VShort);
r = VPixel(map,0,1,i,VShort);
c = VPixel(map,0,2,i,VShort);
float *ptr = gsl_matrix_float_ptr(mat,i,0);
int k;
j = 0;
for (k=first; k<=last; k++) {
if (j >= mat->size2) VError(" j= %d %d",j,mat->size2);
if (k >= VImageNBands(src[b])) VError(" k= %d %d",k, VImageNBands(src[b]));
*ptr++ = (float) VPixel(src[b],k,r,c,VShort);
j++;
}
}
/*
** compute similarity matrix
*/
m = (n*(n+1))/2;
fprintf(stderr," compute correlation matrix...\n");
A = (float *) VCalloc(m,sizeof(float));
if (!A) VError(" err allocating correlation matrix");
memset(A,0,m*sizeof(float));
size_t progress=0;
#pragma omp parallel for shared(progress) private(j) schedule(guided) firstprivate(mat,A)
for (i=0; i<n; i++) {
if (i%100 == 0) fprintf(stderr," %d00\r",(int)(++progress));
const float *arr1 = gsl_matrix_float_const_ptr(mat,i,0);
for (j=0; j<i; j++) {
const float *arr2 = gsl_matrix_float_const_ptr(mat,j,0);
const double v = Correlation(arr1,arr2,nt);
const size_t k=j+i*(i+1)/2;
if (k >= m) VError(" illegal addr k= %d, m= %d",k,m);
A[k] = v;
}
}
fprintf(stderr," matrix done.\n");
gsl_matrix_float_free(mat);
return A;
}