/*!
* \ingroup WlzValuesUtils
* \brief Gets a single grey value/pointer for the given point
* from the 3D values and domain in the work space.
*
* \param gVWSp grey-value work space
* \param plane plane coordinate
* \param line line coordinate
* \param kol column coordinate
*/
void WlzGreyValueGetDir(WlzGreyValueWSpace *gVWSp,
int plane, int line, int kol)
{
int pln0,
pln1,
valSet = 0;
WlzDomain *domP;
WlzValues *valP;
pln0 = plane - gVWSp->domain.p->plane1;
pln1 = gVWSp->domain.p->lastpl - gVWSp->domain.p->plane1;
#ifdef WLZ_FAST_CODE
if((unsigned int)(pln0) <= (unsigned int)(pln1))
#else
if((plane >= gVWSp->domain.p->plane1) &&
(plane <= gVWSp->domain.p->lastpl))
#endif
{
if(gVWSp->gTabType == (WlzObjectType )WLZ_GREY_TAB_TILED)
{
WlzGreyValueGet(gVWSp, plane, line, kol);
valSet = 1;
}
else
{
if(gVWSp->plane == plane)
{
WlzGreyValueGet2D1(gVWSp, line, kol);
valSet = 1;
}
else
{
domP = gVWSp->domain.p->domains + pln0;
valP = gVWSp->values.vox->values + pln0;
/* check for non-NULL domain and valuetable
pointers until empty obj consistently implemented */
if((*domP).core && (*valP).core)
{
gVWSp->plane = plane;
gVWSp->iDom2D = (*domP).i;
gVWSp->values2D = (*valP);
gVWSp->gTabType2D = gVWSp->gTabTypes3D[pln0];
WlzGreyValueGet2D1(gVWSp, line, kol);
valSet = 1;
}
}
}
}
if(valSet == 0)
{
WlzGreyValueSetBkdP(gVWSp->gVal, gVWSp->gPtr, gVWSp->gType, gVWSp->gBkd);
}
}
/*!
* \return Woolz error code.
* \ingroup WlzTransform
* \brief Sets the profile value for walk function.
* \param obj Given object from which to set the value.
* \param pos Position of value in given object.
* \param pWSp Profile workspace.
*/
static WlzErrorNum WlzProfileSetPixels(
WlzObject *obj,
WlzIVertex3 pos,
WlzProfileWalkWSp *pWSp)
{
WlzGreyP gP;
WlzGreyV gV;
WlzErrorNum errNum = WLZ_ERR_NONE;
WlzGreyValueGet(pWSp->gVWSp, pos.vtZ, pos.vtY, pos.vtX);
gP = pWSp->values.r->values;
gV = pWSp->gVWSp->gVal[0];
switch(pWSp->gVWSp->gType)
{
case WLZ_GREY_LONG:
*(gP.lnp + pWSp->index) = gV.lnv;
break;
case WLZ_GREY_INT:
*(gP.inp + pWSp->index) = gV.inv;
break;
case WLZ_GREY_SHORT:
*(gP.shp + pWSp->index) = gV.shv;
break;
case WLZ_GREY_UBYTE:
*(gP.ubp + pWSp->index) = gV.ubv;
break;
case WLZ_GREY_FLOAT:
*(gP.flp + pWSp->index) = gV.flv;
break;
case WLZ_GREY_DOUBLE:
*(gP.dbp + pWSp->index) = gV.dbv;
break;
case WLZ_GREY_RGBA:
*(gP.rgbp + pWSp->index) = gV.rgbv;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
return(errNum);
}
/*!
* \return The grey value as a double.
* \ingroup WlzAccess
* \brief Gets a single grey value for the given point from the
* object with which the given work space was initialised.
* \param gVWSp Grey value work space.
* \param plane Plane (z) coordinate of point.
* \param line Line (y) coordinate of point.
* \param kol Column (x) coordinate of point.
*/
double WlzGreyValueGetD(WlzGreyValueWSpace *gVWSp,
double plane, double line, double kol)
{
double val = 0;
if(gVWSp)
{
WlzGreyValueGet(gVWSp, plane, line, kol);
switch(gVWSp->gType)
{
case WLZ_GREY_LONG:
val = gVWSp->gVal[0].lnv;
break;
case WLZ_GREY_INT:
val = gVWSp->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
val = gVWSp->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
val = gVWSp->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
val = gVWSp->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
val = gVWSp->gVal[0].dbv;
break;
case WLZ_GREY_RGBA:
val = gVWSp->gVal[0].rgbv;
break;
default:
break;
}
}
return(val);
}
/*!
* \return New Woolz object without holes or NULL on error.
* \ingroup WlzDomainOps
* \brief Fills the holes in the given object's domain (which are by
* definition not connected to the outside). When the given
* object's domain has more than one component part, the
* object should first be labeled, this function should then be
* called for each of the labeled parts and then the union of
* the filled domains should be formed.
* \param srcObj Given 3D domain object.
* \param dstErr Destination error pointer, may be NULL.
*/
WlzObject *WlzDomainFill3D(
WlzObject *srcObj,
WlzErrorNum *dstErr)
{
int nPln = 0;
WlzObject *bndObj = NULL,
*filObj = NULL,
*gvnObj = NULL,
*sedObj = NULL,
*shlObj = NULL;
WlzPixelV zeroV;
WlzValues nullVal;
WlzErrorNum errNum = WLZ_ERR_NONE;
nullVal.core = NULL;
zeroV.type = WLZ_GREY_UBYTE;
zeroV.v.ubv = 0;
if(srcObj == NULL)
{
errNum = WLZ_ERR_OBJECT_NULL;
}
else if(srcObj->type != WLZ_3D_DOMAINOBJ)
{
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if(srcObj->domain.core == NULL)
{
errNum = WLZ_ERR_DOMAIN_NULL;
}
else
{
gvnObj = WlzMakeMain(srcObj->type, srcObj->domain, nullVal,
NULL, NULL, &errNum);
}
/* Create a then shell 1 voxel thick just inside the given objects's
* domain. */
if(errNum == WLZ_ERR_NONE)
{
WlzObject *difObj = NULL;
difObj = WlzAssignObject(
WlzBoundaryDomain(gvnObj, &errNum), NULL);
if(errNum == WLZ_ERR_NONE)
{
WlzIBox3 clipBox;
/* Clip the dilated shell domain to make sure it stays within the
* bounding box of the given object then all planes will align. */
clipBox.xMin = gvnObj->domain.p->kol1;
clipBox.yMin = gvnObj->domain.p->line1;
clipBox.zMin = gvnObj->domain.p->plane1;
clipBox.xMax = gvnObj->domain.p->lastkl;
clipBox.yMax = gvnObj->domain.p->lastln;
clipBox.zMax = gvnObj->domain.p->lastpl;
shlObj = WlzAssignObject(
WlzClipObjToBox3D(difObj, clipBox, &errNum), NULL);
}
(void )WlzFreeObj(difObj);
}
/* Make sure that the bounding box of the thin shell domain fits it and
* that it's first and last planes have interrvals. */
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzStandardPlaneDomain(shlObj->domain.p, NULL);
}
/* Create a value table for the shell object with values set to zero. */
if(errNum == WLZ_ERR_NONE)
{
WlzValues val;
WlzObjectType tType;
tType = WlzGreyTableType(WLZ_GREY_TAB_INTL, WLZ_GREY_UBYTE, NULL);
val.vox = WlzMakeVoxelValueTb(WLZ_VOXELVALUETABLE_GREY,
shlObj->domain.p->plane1,
shlObj->domain.p->lastpl,
zeroV, NULL, &errNum);
if(errNum == WLZ_ERR_NONE)
{
int p;
nPln = shlObj->domain.p->lastpl - shlObj->domain.p->plane1 + 1;
shlObj->values = WlzAssignValues(val, NULL);
#ifdef _OPENMP
#pragma omp parallel for shared(shlObj)
#endif
for(p = 0; p < nPln; ++p)
{
if(errNum == WLZ_ERR_NONE)
{
WlzDomain dom2;
WlzErrorNum errNum2;
dom2 = shlObj->domain.p->domains[p];
if(dom2.core)
{
WlzValues val2;
WlzObject *shlObj2;
shlObj2 = WlzMakeMain(WLZ_2D_DOMAINOBJ, dom2, nullVal, NULL, NULL,
&errNum2);
if(errNum2 == WLZ_ERR_NONE)
{
val2.i = WlzMakeIntervalValues(tType, shlObj2, zeroV, &errNum2);
/* WlzMakeIntervalValues() sets all values to zero. */
}
if(errNum2 == WLZ_ERR_NONE)
{
shlObj->values.vox->values[p] = WlzAssignValues(val2, NULL);
}
(void )WlzFreeObj(shlObj2);
if(errNum2 == WLZ_ERR_NONE)
{
#ifdef _OPENMP
#pragma omp critical
{
#endif
if((errNum == WLZ_ERR_NONE) && (errNum2 != WLZ_ERR_NONE))
{
errNum = errNum2;
}
#ifdef _OPENMP
}
#endif
}
}
}
}
}
}
/* Compute the (plane-wise) boundary list for the given object. */
if(errNum == WLZ_ERR_NONE)
{
bndObj = WlzObjToBoundary(gvnObj, 0, &errNum);
}
/* Sweep down through the boundary object setting the values of
* those voxels in the shell object to a non zero value when they
* correspond to top level boundaries. */
if(errNum == WLZ_ERR_NONE)
{
int p;
#ifdef _OPENMP
#pragma omp parallel for shared(bndObj,shlObj)
#endif
for(p = 0; p < nPln; ++p)
{
if(errNum == WLZ_ERR_NONE)
{
WlzDomain bDom2;
bDom2 = bndObj->domain.p->domains[p];
if(bDom2.core)
{
WlzDomain iDom2;
WlzValues iVal2;
WlzObject *iObj2 = NULL;
WlzGreyValueWSpace *gVWSp = NULL;
WlzErrorNum errNum2 = WLZ_ERR_NONE;
iDom2 = shlObj->domain.p->domains[p];
iVal2 = shlObj->values.vox->values[p];
iObj2 = WlzMakeMain(WLZ_2D_DOMAINOBJ, iDom2, iVal2, NULL, NULL,
&errNum2);
if(errNum == WLZ_ERR_NONE)
{
gVWSp = WlzGreyValueMakeWSp(iObj2, &errNum2);
}
if(errNum2 == WLZ_ERR_NONE)
{
WlzBoundList *bnd,
*bnd2;
bnd2 = bDom2.b;
for(bnd = bnd2; bnd != NULL; bnd = bnd->next)
{
if(bnd->poly != NULL)
{
WlzPolygonDomain *ply;
ply = bnd->poly;
if(ply)
{
int i;
WlzIVertex2 *vtx;
vtx = ply->vtx;
for(i = 0; i < ply->nvertices; ++i)
{
WlzGreyValueGet(gVWSp, 0, vtx[i].vtY, vtx[i].vtX);
*(gVWSp->gPtr[0].ubp) = 255;
}
}
}
}
}
else
{
#ifdef _OPENMP
#pragma omp critical
{
#endif
if(errNum == WLZ_ERR_NONE)
{
errNum = errNum2;
}
#ifdef _OPENMP
}
#endif
}
(void )WlzFreeObj(iObj2);
WlzGreyValueFreeWSp(gVWSp);
}
}
}
}
/* Threshold the shell object, throwing away all but where the voxels
* are set to create a seed domain. Then remove the value table from
* the shell object and free it as it's no longer needed. */
if(errNum == WLZ_ERR_NONE)
{
WlzObject *tObj = NULL;
WlzPixelV tV;
tV.type = WLZ_GREY_UBYTE;
tV.v.ubv = 1;
tObj = WlzAssignObject(
WlzThreshold(shlObj, tV, WLZ_THRESH_HIGH, &errNum), NULL);
if(errNum == WLZ_ERR_NONE)
{
sedObj = WlzAssignObject(
WlzMakeMain(tObj->type, tObj->domain, nullVal,
NULL, NULL, &errNum), NULL);
}
(void )WlzFreeObj(tObj); tObj = NULL;
if(errNum == WLZ_ERR_NONE)
{
tObj = WlzAssignObject(
WlzMakeMain(shlObj->type, shlObj->domain, nullVal,
NULL, NULL, &errNum), NULL);
}
(void )WlzFreeObj(shlObj); shlObj = NULL;
if(errNum == WLZ_ERR_NONE)
{
shlObj = tObj;
tObj = NULL;
}
(void )WlzFreeObj(tObj);
#ifdef WLZ_DOMOMAINFILL3D_DEBUG
{
FILE *fP;
fP = fopen("debug-shlObj-00.wlz", "w");
(void )WlzWriteObj(fP, shlObj);
(void )fclose(fP);
}
#endif
}
/* Label the shell domain using 26-connectivity in 3D and then
* keep only those component objects which intersect the seed domain.
* Then free the shell and seed domains replacing the shell domain
* with the union of the intersecting labeled component objects.
* Finaly free the intersecting component objects, keeping only the
* new shell domain. */
if(errNum == WLZ_ERR_NONE)
{
int i,
j,
nCSObj = 0;
WlzIBox3 bBox;
WlzObject **csObj = NULL;
bBox = WlzBoundingBox3I(shlObj, &errNum);
if(errNum == WLZ_ERR_NONE)
{
int maxCSObj;
maxCSObj = ((bBox.xMax - bBox.xMin + 1) *
(bBox.yMax - bBox.yMin + 1) *
(bBox.zMax - bBox.zMin + 1)) / 8;
if(maxCSObj < 8)
{
maxCSObj = 8;
}
errNum = WlzLabel(shlObj, &nCSObj, &csObj, maxCSObj, 0,
WLZ_26_CONNECTED);
}
if(errNum == WLZ_ERR_NONE)
{
for(i = 0; i < nCSObj; ++i)
{
if(!WlzHasIntersection(csObj[i], sedObj, &errNum))
{
(void )WlzFreeObj(csObj[i]);
csObj[i] = NULL;
}
}
}
if(errNum == WLZ_ERR_NONE)
{
/* Squeeze out any NULL objects reseting their number.*/
for(i = 0, j = 0; i < nCSObj; ++i)
{
if(csObj[i])
{
csObj[j++] = csObj[i];
}
}
nCSObj = j;
}
if(errNum == WLZ_ERR_NONE)
{
WlzObject *iObj = NULL,
*uObj = NULL;
uObj = WlzAssignObject(
WlzUnionN(nCSObj, csObj, 0, &errNum), NULL);
iObj = WlzAssignObject(
WlzIntersect2(uObj, shlObj, &errNum), NULL);
(void )WlzFreeObj(uObj);
(void )WlzFreeObj(shlObj);
shlObj = iObj;
#ifdef WLZ_DOMOMAINFILL3D_DEBUG
{
FILE *fP;
fP = fopen("debug-shlObj-01.wlz", "w");
(void )WlzWriteObj(fP, shlObj);
(void )fclose(fP);
}
#endif
}
if(csObj)
{
for(i = 0; i < nCSObj; ++i)
{
(void )WlzFreeObj(csObj[i]);
}
(void )AlcFree(csObj);
}
}
/* Sweep down through the boundary lists again creating new boundary lists
* which do not have boundaries that do not intersect the new shell domain.
* Then create a new filled object from these boundary lists. */
if(errNum == WLZ_ERR_NONE)
{
int p,
nPlnFil;
WlzDomain filDom;
nPlnFil = shlObj->domain.p->lastpl - shlObj->domain.p->plane1 + 1;
filDom.p = WlzMakePlaneDomain(WLZ_PLANEDOMAIN_DOMAIN,
shlObj->domain.p->plane1, shlObj->domain.p->lastpl,
shlObj->domain.p->line1, shlObj->domain.p->lastln,
shlObj->domain.p->kol1, shlObj->domain.p->lastkl,
&errNum);
#ifdef _OPENMP
#pragma omp parallel for shared(bndObj,shlObj)
#endif
for(p = 0; p < nPlnFil; ++p)
{
if(errNum == WLZ_ERR_NONE)
{
WlzDomain bDom2;
bDom2 = bndObj->domain.p->domains[p];
if(bDom2.core)
{
WlzDomain sDom2;
WlzObject *fObj2 = NULL;
WlzBoundList *newBnd = NULL;
WlzErrorNum errNum2 = WLZ_ERR_NONE;
sDom2 = shlObj->domain.p->domains[p];
if(sDom2.core)
{
newBnd = WlzDomFill3DDoBound2D(bDom2.b, sDom2, &errNum2);
if(newBnd != NULL)
{
fObj2 = WlzBoundToObj(newBnd, WLZ_SIMPLE_FILL, &errNum2);
(void )WlzFreeBoundList(newBnd);
}
if(errNum2 == WLZ_ERR_NONE)
{
if(fObj2)
{
filDom.p->domains[p] = WlzAssignDomain(fObj2->domain, NULL);
}
}
else
{
#ifdef _OPENMP
#pragma omp critical
{
#endif
if(errNum == WLZ_ERR_NONE)
{
errNum = errNum2;
}
#ifdef _OPENMP
}
#endif
}
(void )WlzFreeObj(fObj2);
}
}
}
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzStandardPlaneDomain(filDom.p, NULL);
}
if(errNum == WLZ_ERR_NONE)
{
WlzObject *tObj0 = NULL,
*tObj1 = NULL;
/* Put back any isolated voxels this function has removed. */
tObj0 = WlzAssignObject(
WlzMakeMain(srcObj->type, filDom, nullVal,
NULL, NULL, &errNum), NULL);
if(errNum == WLZ_ERR_NONE)
{
tObj1 = WlzUnion2(gvnObj, tObj0, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
filObj = WlzMakeMain(tObj1->type, tObj1->domain, nullVal,
NULL, NULL, &errNum);
}
(void )WlzFreeObj(tObj0);
(void )WlzFreeObj(tObj1);
}
}
(void )WlzFreeObj(bndObj);
(void )WlzFreeObj(gvnObj);
(void )WlzFreeObj(shlObj);
(void )WlzFreeObj(sedObj);
if((errNum != WLZ_ERR_NONE) && (filObj != NULL))
{
(void )WlzFreeObj(filObj);
filObj = NULL;
}
if(dstErr)
{
*dstErr = errNum;
}
return(filObj);
}
XImage *HGU_XmObjToXImageLut2D(
XWindowAttributes *win_att,
WlzObject *obj,
HGU_XmLut lut,
WlzErrorNum *dstErr)
{
XImage *rtnImage=NULL;
Dimension width, height;
WlzUByte *data, *dst_data;
WlzGreyValueWSpace *gVWSp = NULL;
WlzErrorNum errNum=WLZ_ERR_NONE;
int i, j;
int rIndx=0, gIndx=0, bIndx=0, aIndx=0;
WlzUInt r, g, b, a;
/* allocate space for the data */
width = obj->domain.i->lastkl - obj->domain.i->kol1 + 1;
height = obj->domain.i->lastln - obj->domain.i->line1 + 1;
if( (gVWSp = WlzGreyValueMakeWSp(obj, &errNum)) ) {
if( (data = (WlzUByte *) AlcMalloc(((win_att->depth == 8)?1:4)
*width*height*sizeof(char))) ) {
dst_data = data;
if( (rtnImage = XCreateImage(DisplayOfScreen(win_att->screen),
win_att->visual, win_att->depth,
ZPixmap, 0, (char *) dst_data,
width, height, 8, 0)) ) {
/* establish rgb index values if 24 bit */
if( win_att->depth == 24 ) {
rIndx = HGU_XmGetColorIndexFromMask24(win_att->visual->red_mask,
rtnImage->byte_order);
gIndx = HGU_XmGetColorIndexFromMask24(win_att->visual->green_mask,
rtnImage->byte_order);
bIndx = HGU_XmGetColorIndexFromMask24(win_att->visual->blue_mask,
rtnImage->byte_order);
aIndx = HGU_XmGetColorIndexFromMask24(~(win_att->visual->red_mask|
win_att->visual->green_mask|
win_att->visual->blue_mask),
rtnImage->byte_order);
}
/* fill in the values */
a = 0xff;
for(j=0; j < height; j++) {
for(i=0; i < width; i++, data++) {
WlzGreyValueGet(gVWSp, 0, j + obj->domain.i->line1,
i + obj->domain.i->kol1);
switch( gVWSp->gType ) {
default:
case WLZ_GREY_INT:
r = *(gVWSp->gPtr[0].inp);
g = b = r;
break;
case WLZ_GREY_SHORT:
r = *(gVWSp->gPtr[0].shp);
g = b = r;
break;
case WLZ_GREY_UBYTE:
r = *(gVWSp->gPtr[0].ubp);
g = b = r;
break;
case WLZ_GREY_FLOAT:
r = *(gVWSp->gPtr[0].flp);
g = b = r;
break;
case WLZ_GREY_DOUBLE:
r = *(gVWSp->gPtr[0].dbp);
g = b = r;
break;
case WLZ_GREY_RGBA:
b = *(gVWSp->gPtr[0].rgbp);
r = WLZ_RGBA_RED_GET(b);
g = WLZ_RGBA_GREEN_GET(b);
b = WLZ_RGBA_BLUE_GET(b);
break;
}
switch( lut.core->type ) {
case HGU_XmLUT_GREY:
r = lut.g->lut[r - lut.g->min];
g = lut.g->lut[g - lut.g->min];
b = lut.g->lut[b - lut.g->min];
break;
case HGU_XmLUT_RGB:
r = lut.rgb->lut[0][r - lut.rgb->min[0]];
g = lut.rgb->lut[1][g - lut.rgb->min[1]];
b = lut.rgb->lut[2][b - lut.rgb->min[2]];
break;
case HGU_XmLUT_COMPOUND:
break;
}
switch( win_att->depth ) {
case 24:
data[rIndx] = r;
data[gIndx] = g;
data[bIndx] = b;
data[aIndx] = a;
data += 3;
break;
case 8:
data[0] = r;
break;
}
}
}
}
else {
errNum = WLZ_ERR_UNSPECIFIED;
AlcFree((void *) dst_data);
}
}
else {
errNum = WLZ_ERR_MEM_ALLOC;
}
WlzGreyValueFreeWSp(gVWSp);
}
if( dstErr ) {
*dstErr = errNum;
}
return rtnImage;
}
/*!
* \return Transformed object.
* \ingroup WlzTransform
* \brief Transform an object using the given view-transform.
* Typically this is for mapping section data back into
* the 3D space of the reference image/reconstruction.
* \param srcObj Given source object.
* \param viewStr Given view transform.
* \param dstErr Destination error pointer, may be NULL.
*/
WlzObject *Wlz3DViewTransformObj(
WlzObject *srcObj,
WlzThreeDViewStruct *viewStr,
WlzErrorNum *dstErr)
{
WlzErrorNum errNum=WLZ_ERR_NONE;
AlcErrno alcErr = ALC_ER_NONE;
WlzObject *dstObj=NULL;
int area;
int i, k, p, xp, yp, line;
int plane1, lastpl, line1, lastln, kol1, lastkl;
WlzIVertex3 *vertices;
int numVtxs, vtxIdx;
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzDomain domain, tmpDomain;
WlzValues values;
int numInts, itvlFlg;
WlzInterval *itvl;
/* check the object */
if( srcObj == NULL ) {
errNum = WLZ_ERR_OBJECT_NULL;
}
else {
switch( srcObj->type ) {
case WLZ_2D_DOMAINOBJ:
if( srcObj->domain.core == NULL ) {
errNum = WLZ_ERR_DOMAIN_NULL;
}
area = WlzArea(srcObj, &errNum);
if( area == 0 ) {
dstObj = WlzMakeEmpty(&errNum);
}
break;
case WLZ_2D_POLYGON: /* to be done at some time to 3D polyline */
case WLZ_BOUNDLIST: /* convert to 3D polylines */
case WLZ_TRANS_OBJ:
errNum = WLZ_ERR_OBJECT_TYPE;
break;
default:
errNum = WLZ_ERR_OBJECT_TYPE;
break;
}
}
/* create the voxel list */
if( (errNum == WLZ_ERR_NONE) && (dstObj == NULL) ) {
numVtxs = sizeof(WlzIVertex3) * (area+4);
vertices = AlcMalloc(sizeof(WlzIVertex3) * (area+4));
numVtxs = 0;
if( vertices ) {
errNum = WlzInitRasterScan(srcObj, &iwsp, WLZ_RASTERDIR_ILIC);
}
else {
errNum = WLZ_ERR_MEM_ALLOC;
}
if( errNum == WLZ_ERR_NONE ) {
while( (errNum = WlzNextInterval(&iwsp)) == WLZ_ERR_NONE ) {
float x, y, z;
if((iwsp.linpos < (int) viewStr->minvals.vtY) ||
(iwsp.linpos > (int) viewStr->maxvals.vtY)) {
continue;
}
yp = iwsp.linpos - (int) viewStr->minvals.vtY;
for(k=iwsp.lftpos; k <= iwsp.rgtpos; k++) {
if((k < (int) viewStr->minvals.vtX) ||
(k > (int) viewStr->maxvals.vtX)) {
continue;
}
xp = k - (int) viewStr->minvals.vtX;
x = (float )(viewStr->xp_to_x[xp] + viewStr->yp_to_x[yp]);
y = (float )(viewStr->xp_to_y[xp] + viewStr->yp_to_y[yp]);
z = (float )(viewStr->xp_to_z[xp] + viewStr->yp_to_z[yp]);
vertices[numVtxs].vtX = WLZ_NINT(x);
vertices[numVtxs].vtY = WLZ_NINT(y);
vertices[numVtxs].vtZ = WLZ_NINT(z);
numVtxs++;
}
}
if(errNum == WLZ_ERR_EOO) /* Reset error from end of object */
{
errNum = WLZ_ERR_NONE;
}
}
}
/* sort wrt planes, lines, kols */
if( (errNum == WLZ_ERR_NONE) && (dstObj == NULL) ) {
qsort((void *) vertices, (size_t) numVtxs, sizeof(WlzIVertex3),
compareVtxVal);
/* create planedomain */
plane1 = vertices[0].vtZ;
lastpl = vertices[numVtxs - 1].vtZ;
line1 = vertices[0].vtY;
lastln = line1;
kol1 = vertices[0].vtX;
lastkl = kol1;
for(i=1; i < numVtxs; i++) {
if( kol1 > vertices[i].vtX ) {
kol1 = vertices[i].vtX;
}
if( lastkl < vertices[i].vtX ) {
lastkl = vertices[i].vtX;
}
if( line1 > vertices[i].vtY ) {
line1 = vertices[i].vtY;
}
if( lastln < vertices[i].vtY ) {
lastln = vertices[i].vtY;
}
}
if( (domain.p = WlzMakePlaneDomain(WLZ_PLANEDOMAIN_DOMAIN,
plane1, lastpl,
line1, lastln,
kol1, lastkl,
&errNum)) == NULL ) {
AlcFree((void *) vertices);
}
}
/* for each plane count intervals and make domain */
if( (errNum == WLZ_ERR_NONE) && (dstObj == NULL) ) {
vtxIdx = 0;
for(p=plane1; p <= lastpl; p++) {
/* increment vertex index to current plane */
while( vertices[vtxIdx].vtZ < p ) {
vtxIdx++;
}
/* check for empty domain */
if( vertices[vtxIdx].vtZ > p ) {
domain.p->domains[p - plane1].i = NULL;
continue;
}
/* estimate intervals - foreach pixel add one,
foreach adjacent pixel on the same line subtract one */
numInts = 1;
kol1 = vertices[vtxIdx].vtX;
lastkl = kol1;
for(i=vtxIdx+1; i < numVtxs; i++) {
if( vertices[i].vtZ > p ) {
break;
}
numInts++;
if((vertices[i].vtY == vertices[i-1].vtY) &&
((vertices[i].vtX == (vertices[i-1].vtX)) ||
(vertices[i].vtX == (vertices[i-1].vtX + 1))
)) {
numInts--;
}
if(kol1 > vertices[i].vtX) {
kol1 = vertices[i].vtX;
}
if(lastkl < vertices[i].vtX) {
lastkl = vertices[i].vtX;
}
}
line1 = vertices[vtxIdx].vtY;
lastln = vertices[i-1].vtY;
/* make the domain and add the intervals pointer */
tmpDomain.i = WlzMakeIntervalDomain(WLZ_INTERVALDOMAIN_INTVL,
line1, lastln,
kol1, lastkl,
&errNum);
itvl = (WlzInterval *) AlcMalloc(sizeof(WlzInterval)*numInts);
tmpDomain.i->freeptr = AlcFreeStackPush(tmpDomain.i->freeptr,
(void *) itvl,
&alcErr);
if(alcErr != ALC_ER_NONE) {
errNum = WLZ_ERR_MEM_ALLOC;
}
/* one more loop to add the intervals */
itvl->ileft = vertices[vtxIdx].vtX - kol1;
line = vertices[vtxIdx].vtY;
itvlFlg = 1; /* interval started */
numInts = 1;
for(i=vtxIdx+1; i < numVtxs; i++) {
/* new plane -> interval finished if started */
if( vertices[i].vtZ > p ) {
if( itvlFlg ) {
itvl[numInts-1].iright = vertices[i-1].vtX - kol1;
WlzMakeInterval(line, tmpDomain.i, numInts, itvl);
itvl += numInts;
itvlFlg = 0; /* interval finished */
numInts = 0;
}
break;
}
/* check if new interval */
if( !itvlFlg ) {
itvl->ileft = vertices[i].vtX - kol1;
line = vertices[i].vtY;
itvlFlg = 1;
numInts = 1;
continue; /* no further tests */
}
/* check for gap - increment interval count */
if((vertices[i].vtY == line) &&
((vertices[i].vtX - vertices[i-1].vtX) > 1)) {
itvl[numInts-1].iright = vertices[i-1].vtX - kol1;
numInts++;
itvl[numInts-1].ileft = vertices[i].vtX - kol1;
itvlFlg = 1;
}
/* check for new-line */
if( line < vertices[i].vtY ) {
itvl[numInts-1].iright = vertices[i-1].vtX - kol1;
WlzMakeInterval(line, tmpDomain.i, numInts, itvl);
itvl += numInts;
itvl->ileft = vertices[i].vtX - kol1;
line = vertices[i].vtY;
itvlFlg = 1;
numInts = 1;
}
}
/* complete the last interval */
if( itvlFlg ) {
itvl[numInts-1].iright = vertices[i-1].vtX - kol1;
WlzMakeInterval(line, tmpDomain.i, numInts, itvl);
itvl += numInts;
}
/* add the domain to the planedomain */
domain.p->domains[p - plane1] =
WlzAssignDomain(tmpDomain, &errNum);
(void) WlzIntervalCount(tmpDomain.i, 0);
}
}
/* create the new object */
if( (errNum == WLZ_ERR_NONE) && (dstObj == NULL) ) {
values.core = NULL;
dstObj = WlzMakeMain(WLZ_3D_DOMAINOBJ, domain, values,
NULL, NULL, &errNum);
}
/* check for grey-level data */
if((errNum == WLZ_ERR_NONE) && dstObj &&
(dstObj->type != WLZ_EMPTY_OBJ) && srcObj->values.core ) {
WlzPixelV bckgrnd;
WlzObject *tmpObj;
WlzValues tmpValues;
WlzDVertex3 vtx;
WlzGreyValueWSpace *gVWSp = NULL;
WlzObjectType valueTbType;
/* explicit intialisation to satisfy strict ANSI on SGI */
bckgrnd = WlzGetBackground(srcObj, &errNum);
valueTbType = WlzGreyTableType(WLZ_GREY_TAB_RAGR,
bckgrnd.type, NULL);
/* make a voxel table */
values.vox = WlzMakeVoxelValueTb(WLZ_VOXELVALUETABLE_GREY,
plane1, lastpl, bckgrnd,
NULL, &errNum);
dstObj->values = WlzAssignValues(values, &errNum);
/* set up grey-value random access to original
and loop through planes setting values */
gVWSp = WlzGreyValueMakeWSp(srcObj, NULL);
for(p=plane1; p <= lastpl; p++) {
/* check for empty domain */
if( domain.p->domains[p-plane1].core == NULL ) {
continue;
}
/* make a value table */
tmpObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domain.p->domains[p-plane1],
values.vox->values[p-plane1], NULL, NULL, &errNum);
tmpValues.v = WlzNewValueTb(tmpObj, valueTbType, bckgrnd, &errNum);
values.vox->values[p-plane1] = WlzAssignValues(tmpValues, &errNum);
tmpObj->values = WlzAssignValues(tmpValues, &errNum);
/* transfer values */
errNum = WlzInitGreyScan(tmpObj, &iwsp, &gwsp);
while((errNum == WLZ_ERR_NONE) &&
((errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE)) {
for(i=0; i<iwsp.colrmn; i++) {
vtx.vtX = iwsp.colpos + i;
vtx.vtY = iwsp.linpos;
vtx.vtZ = p;
Wlz3DSectionTransformVtx(&vtx, viewStr);
WlzGreyValueGet(gVWSp, 0.0,
WLZ_NINT(vtx.vtY), WLZ_NINT(vtx.vtX));
switch( gwsp.pixeltype ) {
case WLZ_GREY_LONG:
*(gwsp.u_grintptr.lnp+i) = gVWSp->gVal[0].lnv;
break;
case WLZ_GREY_INT:
*(gwsp.u_grintptr.inp+i) = gVWSp->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
*(gwsp.u_grintptr.shp+i) = gVWSp->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
*(gwsp.u_grintptr.ubp+i) = gVWSp->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
*(gwsp.u_grintptr.flp+i) = gVWSp->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
*(gwsp.u_grintptr.dbp+i) = gVWSp->gVal[0].dbv;
break;
case WLZ_GREY_RGBA:
*(gwsp.u_grintptr.rgbp+i) = gVWSp->gVal[0].rgbv;
break;
case WLZ_GREY_BIT: /* not sure what to do with these */
default:
break;
}
}
}
if(errNum == WLZ_ERR_EOO) /* Reset error from end of object */
{
errNum = WLZ_ERR_NONE;
}
WlzFreeObj(tmpObj);
}
WlzGreyValueFreeWSp(gVWSp);
}
/* clean temp allocation */
if( vertices ) {
AlcFree((void *) vertices);
}
if( dstErr ) {
*dstErr = errNum;
}
return dstObj;
}
/*!
* \return Rescaled object.
* \ingroup WlzTransform
* \brief Rescales the given 2D domain object using an integer scale.
* \param obj Given object.
* \param scale Integer scale factor.
* \param expand If zero use \f$\frac{1}{scale}\f$.
* \param dstErr Destination error pointer, may be NULL.
*/
static WlzObject *WlzIntRescaleObj2D(
WlzObject *obj,
int scale,
int expand,
WlzErrorNum *dstErr)
{
WlzObject *rtnObj=NULL;
WlzDomain domain;
WlzValues values;
WlzInterval *intvls;
int k1, kl, l1, ll, l, num_intvls;
WlzErrorNum errNum=WLZ_ERR_NONE;
/* check expand or contract */
if( expand )
{
k1 = obj->domain.i->kol1 * scale;
kl = obj->domain.i->lastkl * scale + scale - 1;
l1 = obj->domain.i->line1 * scale;
ll = obj->domain.i->lastln * scale + scale - 1;
}
else {
k1 = obj->domain.i->kol1 / scale;
kl = obj->domain.i->lastkl / scale;
l1 = obj->domain.i->line1 / scale;
ll = obj->domain.i->lastln / scale;
}
/* create a new object */
if((domain.i = WlzMakeIntervalDomain(obj->domain.i->type,
l1, ll, k1, kl, &errNum)) != NULL){
values.core = NULL;
rtnObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domain, values,
NULL, NULL, NULL);
}
/* fill in the intervals */
if( errNum == WLZ_ERR_NONE){
if( domain.i->type == WLZ_INTERVALDOMAIN_INTVL )
{
int intvline_offset, max_offset;
WlzIntervalLine *intvline;
num_intvls = WlzIntervalCount(obj->domain.i, NULL);
num_intvls = expand ? num_intvls * scale : num_intvls;
intvls = (WlzInterval *)AlcMalloc(sizeof(WlzInterval) * num_intvls);
domain.i->freeptr = AlcFreeStackPush(domain.i->freeptr, (void *)intvls,
NULL);
max_offset = obj->domain.i->lastln - obj->domain.i->line1;
for(l=l1; l <= ll; l++)
{
int i;
intvline_offset = (expand?l/scale:l*scale) - obj->domain.i->line1;
intvline_offset = WLZ_MAX(intvline_offset, 0);
intvline_offset = WLZ_MIN(intvline_offset, max_offset);
intvline = obj->domain.i->intvlines + intvline_offset;
for(i=0; i < intvline->nintvs; i++)
{
intvls[i].ileft = (intvline->intvs + i)->ileft;
intvls[i].iright = (intvline->intvs + i)->iright;
if( expand )
{
intvls[i].ileft *= scale;
intvls[i].iright *= scale;
intvls[i].iright += scale - 1;
}
else
{
intvls[i].ileft /= scale;
intvls[i].iright /= scale;
}
}
i = check_intvs(intvls, i);
WlzMakeInterval(l, domain.i, i, intvls);
intvls += i;
}
(void) WlzStandardIntervalDomain( domain.i );
}
}
/* create the valuetable */
if( (errNum == WLZ_ERR_NONE) && obj->values.core )
{
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzPixelV backgrnd;
WlzGreyValueWSpace *gVWSp = NULL;
WlzGreyType gtype;
backgrnd = WlzGetBackground(obj, NULL);
if((values.v = WlzNewValueTb(rtnObj, obj->values.v->type,
backgrnd, &errNum)) != NULL){
rtnObj->values = WlzAssignValues(values, NULL);
/* fill in the grey-values */
errNum = WlzInitGreyScan(rtnObj, &iwsp, &gwsp);
if(errNum == WLZ_ERR_NONE) {
gVWSp = WlzGreyValueMakeWSp(obj, &errNum);
if(errNum == WLZ_ERR_NONE) {
gtype = WlzGreyTableTypeToGreyType(obj->values.v->type, NULL);
}
while((errNum == WLZ_ERR_NONE) &&
(errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE)
{
int k;
int lp = expand ? iwsp.linpos/scale : iwsp.linpos*scale;
for( k=0; k <= (iwsp.rgtpos - iwsp.lftpos); k++ )
{
int kp = expand ? (k+iwsp.lftpos)/scale : (k+iwsp.lftpos)*scale;
WlzGreyValueGet(gVWSp, 0, (double) lp, (double) kp);
switch(gtype)
{
case WLZ_GREY_INT:
gwsp.u_grintptr.inp[k] = (*(gVWSp->gVal)).inv;
break;
case WLZ_GREY_SHORT:
gwsp.u_grintptr.shp[k] = (*(gVWSp->gVal)).shv;
break;
case WLZ_GREY_UBYTE:
gwsp.u_grintptr.ubp[k] = (*(gVWSp->gVal)).ubv;
break;
case WLZ_GREY_FLOAT:
gwsp.u_grintptr.flp[k] = (*(gVWSp->gVal)).flv;
break;
case WLZ_GREY_DOUBLE:
gwsp.u_grintptr.dbp[k] = (*(gVWSp->gVal)).dbv;
break;
case WLZ_GREY_RGBA:
gwsp.u_grintptr.rgbp[k] = (*(gVWSp->gVal)).rgbv;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
}
}
if( errNum == WLZ_ERR_EOO ){
errNum = WLZ_ERR_NONE;
}
WlzGreyValueFreeWSp(gVWSp);
(void )WlzEndGreyScan(&iwsp, &gwsp);
}
}
}
if( dstErr ){
*dstErr = errNum;
}
return rtnObj;
}
double WlzMixtureValue(
WlzObject *obj1,
WlzObject *obj2,
int numCatRows,
int numCatCols,
double **mixing,
double **contrib,
WlzErrorNum *dstErr)
{
double val, con;
WlzObject *tmpObj, *tmpObj1, *tmpObj2;
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzGreyP gptr;
WlzGreyValueWSpace *gVWSp;
WlzPixelV minP, maxP;
int i;
WlzErrorNum errNum=WLZ_ERR_NONE;
/* objects must be same type with grey-values */
if( (obj1 == NULL) || (obj2 == NULL) ){
errNum = WLZ_ERR_OBJECT_NULL;
}
else {
switch( obj1->type ){
case WLZ_2D_DOMAINOBJ:
if( obj2->type != obj1->type ){
errNum = WLZ_ERR_OBJECT_TYPE;
}
else {
if((obj1->values.core == NULL) || (obj2->values.core == NULL)){
errNum = WLZ_ERR_VALUES_NULL;
}
else {
/* convert to int and check range */
if((tmpObj1 = WlzConvertPix(obj1, WLZ_GREY_INT, &errNum)) != NULL){
errNum = WlzGreyRange(tmpObj1, &minP, &maxP);
if( errNum == WLZ_ERR_NONE ){
if((minP.v.inv < 1) || (minP.v.inv > numCatRows) ||
(maxP.v.inv < 1) || (maxP.v.inv > numCatRows)){
errNum = WLZ_ERR_OBJECT_DATA;
WlzFreeObj(tmpObj1);
}
}
else {
WlzFreeObj(tmpObj1);
}
}
if((errNum == WLZ_ERR_NONE) &&
(tmpObj2 = WlzConvertPix(obj2, WLZ_GREY_INT, &errNum)) ){
errNum = WlzGreyRange(tmpObj2, &minP, &maxP);
if( errNum == WLZ_ERR_NONE ){
if((minP.v.inv < 1) || (minP.v.inv > numCatCols) ||
(maxP.v.inv < 1) || (maxP.v.inv > numCatCols)){
errNum = WLZ_ERR_OBJECT_DATA;
WlzFreeObj(tmpObj1);
WlzFreeObj(tmpObj2);
}
}
else {
WlzFreeObj(tmpObj1);
WlzFreeObj(tmpObj2);
}
}
}
}
break;
case WLZ_3D_DOMAINOBJ:
default:
errNum = WLZ_ERR_OBJECT_TYPE;
break;
}
}
/* get the intersection region */
if( errNum == WLZ_ERR_NONE ){
if((tmpObj = WlzIntersect2(tmpObj1, tmpObj2, &errNum)) != NULL){
tmpObj->values = WlzAssignValues(tmpObj1->values, &errNum);
}
else {
WlzFreeObj(tmpObj1);
WlzFreeObj(tmpObj2);
}
}
/* now calculate the mixture value */
if( errNum == WLZ_ERR_NONE ){
errNum = WlzInitGreyScan(tmpObj, &iwsp, &gwsp);
gVWSp = WlzGreyValueMakeWSp(tmpObj2, &errNum);
val = 0.0;
con = 0.0;
while((errNum == WLZ_ERR_NONE) &&
(errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE ){
gptr = gwsp.u_grintptr;
for (i=0; i<iwsp.colrmn; i++, gptr.inp++){
WlzGreyValueGet(gVWSp, 0, iwsp.linpos, iwsp.colpos+i);
val += mixing[(*gptr.inp)-1][gVWSp->gVal[0].inv-1];
con += contrib[(*gptr.inp)-1][gVWSp->gVal[0].inv-1];
}
}
if( errNum == WLZ_ERR_EOO ){
errNum = WLZ_ERR_NONE;
}
WlzGreyValueFreeWSp(gVWSp);
WlzFreeObj(tmpObj);
WlzFreeObj(tmpObj1);
WlzFreeObj(tmpObj2);
}
if( dstErr ){
*dstErr = errNum;
}
if( con > 0.0 ){
return val/con;
}
else {
return 0.0;
}
}
/*!
* \return New filtered object with new values or NULL on error.
* \ingroup WlzValuesFilters
* \brief Applies a seperable filter along the z axis (planes)
* to the given object using the given convolution kernel.
* \param inObj Input 3D spatial domain object to be
* filtered which must have scalar values.
* \param bBox Object's bounding box.
* \param maxThr Maximum number of threads to use.
* \param iBuf Working buffers large enough for any
* column in the image with one for each
* thread.
* \param rBuf Buffers as for iBuf.
* \param cBufSz Convolution kernel size.
* \param cBuf Convolution kernel buffer.
* \param pad Type of padding.
* \param padVal Padding value.
* \param dstErr Destination error pointer may be NULL.
*/
static WlzObject *WlzSepFilterZ(WlzObject *inObj,
WlzIBox3 bBox,
int maxThr,
double **iBuf,
double **rBuf,
int cBufSz,
double *cBuf,
AlgPadType pad,
double padVal,
WlzErrorNum *dstErr)
{
WlzObjectType rGTT;
WlzPixelV zV;
WlzObject *rnObj = NULL;
WlzGreyValueWSpace **iVWSp = NULL,
**rVWSp = NULL;
WlzErrorNum errNum = WLZ_ERR_NONE;
zV.v.dbv = 0.0;
zV.type = WLZ_GREY_DOUBLE;
rGTT = WlzGreyTableType(WLZ_GREY_TAB_RAGR, WLZ_GREY_DOUBLE, NULL);
rnObj = WlzNewObjectValues(inObj, rGTT, zV, 1, zV, &errNum);
if(errNum == WLZ_ERR_NONE)
{
if(((iVWSp = (WlzGreyValueWSpace **)
AlcCalloc(maxThr, sizeof(WlzGreyValueWSpace *))) == NULL) ||
((rVWSp = (WlzGreyValueWSpace **)
AlcCalloc(maxThr, sizeof(WlzGreyValueWSpace *))) == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
}
if(errNum == WLZ_ERR_NONE)
{
int idt;
for(idt = 0; (idt < maxThr) && (errNum == WLZ_ERR_NONE); ++idt)
{
iVWSp[idt] = WlzGreyValueMakeWSp(inObj, &errNum);
if(errNum == WLZ_ERR_NONE)
{
rVWSp[idt] = WlzGreyValueMakeWSp(rnObj, &errNum);
}
}
}
if(errNum == WLZ_ERR_NONE)
{
int idy;
#ifdef _OPENMP
#pragma omp parallel for num_threads(maxThr)
#endif
for(idy = bBox.yMin; idy <= bBox.yMax; ++idy)
{
int idx,
thrId = 0;
WlzGreyValueWSpace *iVWSpT,
*rVWSpT;
#ifdef _OPENMP
thrId = omp_get_thread_num();
#endif
iVWSpT = iVWSp[thrId];
rVWSpT = rVWSp[thrId];
for(idx = bBox.xMin; idx <= bBox.xMax; ++idx)
{
int z0,
z1,
idz;
WlzUByte in = 0;
for(idz = bBox.zMin; idz <= bBox.zMax + 1; ++idz)
{
WlzGreyValueGet(iVWSpT, idz, idy, idx);
if(iVWSpT->bkdFlag == 0)
{
double *ibp;
if(in == 0)
{
z0 = idz;
in = 1;
}
z1 = idz;
ibp = iBuf[thrId] + (z1 - z0);
switch(iVWSpT->gType)
{
case WLZ_GREY_INT:
*ibp = iVWSpT->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
*ibp = iVWSpT->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
*ibp = iVWSpT->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
*ibp = iVWSpT->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
*ibp = iVWSpT->gVal[0].dbv;
break;
default:
break;
}
}
else if(in)
{
int idr,
len;
len = z1 - z0 + 1;
AlgConvolveD(len, rBuf[thrId], cBufSz * 2 + 1, cBuf,
len, iBuf[thrId], pad, padVal);
for(idr = z0; idr <= z1; ++idr)
{
WlzGreyValueGet(rVWSpT, idr, idy, idx);
*(rVWSpT->gPtr[0].dbp) = rBuf[thrId][idr - z0];
}
}
}
}
}
}
if(iVWSp)
{
int idt;
for(idt = 0; idt < maxThr; ++idt)
{
WlzGreyValueFreeWSp(iVWSp[idt]);
}
AlcFree(iVWSp);
}
if(rVWSp)
{
int idt;
for(idt = 0; idt < maxThr; ++idt)
{
WlzGreyValueFreeWSp(rVWSp[idt]);
}
AlcFree(rVWSp);
}
if(errNum != WLZ_ERR_NONE)
{
(void )WlzFreeObj(rnObj);
rnObj = NULL;
}
if(dstErr)
{
*dstErr = errNum;
}
return(rnObj);
}
/*!
* \return New filtered object with new values or NULL on error.
* \ingroup WlzValuesFilters
* \brief Applies a seperable filter along the y axis (lines)
* to the given object using the given convolution kernel.
* \param inObj Input 2 or 3D spatial domain object
* to be filtered which must have scalar
* values.
* \param dim Object's dimension.
* \param maxThr Maximum number of threads to use.
* \param iBuf Working buffers large enough for any
* column in the image with one for each
* thread.
* \param rBuf Buffers as for iBuf.
* \param cBufSz Convolution kernel size.
* \param cBuf Convolution kernel buffer.
* \param pad Type of padding.
* \param padVal Padding value.
* \param dstErr Destination error pointer may be NULL.
*/
static WlzObject *WlzSepFilterY(WlzObject *inObj,
int dim,
int maxThr,
double **iBuf,
double **rBuf,
int cBufSz,
double *cBuf,
AlgPadType pad,
double padVal,
WlzErrorNum *dstErr)
{
int idp,
poff,
nPln;
WlzObjectType rGTT;
WlzDomain *domains;
WlzValues *iVal,
*rVal;
WlzPixelV zV;
WlzObject *rnObj = NULL;
WlzErrorNum errNum = WLZ_ERR_NONE;
zV.v.dbv = 0.0;
zV.type = WLZ_GREY_DOUBLE;
rGTT = WlzGreyTableType(WLZ_GREY_TAB_RAGR, WLZ_GREY_DOUBLE, NULL);
if(dim == 3)
{
WlzPlaneDomain *pDom;
WlzVoxelValues *vVal;
pDom = inObj->domain.p;
vVal = inObj->values.vox;
nPln = pDom->lastpl - pDom->plane1 + 1;
domains = pDom->domains;
iVal = vVal->values;
poff = pDom->plane1 - vVal->plane1;
rnObj = WlzNewObjectValues(inObj, rGTT, zV, 1, zV, &errNum);
if(errNum == WLZ_ERR_NONE)
{
rVal = rnObj->values.vox->values;
}
}
else
{
nPln = 1;
poff = 0;
domains = &(inObj->domain);
iVal = &(inObj->values);
rnObj = WlzNewObjectValues(inObj, rGTT, zV, 1, zV, &errNum);
if(errNum == WLZ_ERR_NONE)
{
rVal = &(rnObj->values);
}
}
if(errNum == WLZ_ERR_NONE)
{
#ifdef _OPENMP
#pragma omp parallel for num_threads(maxThr)
#endif
for(idp = 0; idp < nPln; ++idp)
{
if(errNum == WLZ_ERR_NONE)
{
if(domains[idp].core != NULL)
{
int thrId = 0;
WlzIBox2 bBox;
WlzObject *iObj = NULL,
*rObj = NULL;
WlzGreyValueWSpace *iVWSp = NULL,
*rVWSp = NULL;
WlzErrorNum errNum2 = WLZ_ERR_NONE;
#ifdef _OPENMP
thrId = omp_get_thread_num();
#endif
iObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domains[idp], iVal[idp + poff],
NULL, NULL, &errNum);
if(errNum == WLZ_ERR_NONE)
{
rObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domains[idp], rVal[idp],
NULL, NULL, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
bBox = WlzBoundingBox2I(iObj, &errNum);
}
if((errNum == WLZ_ERR_NONE) &&
((iVWSp = WlzGreyValueMakeWSp(iObj, &errNum)) != NULL) &&
((rVWSp = WlzGreyValueMakeWSp(rObj, &errNum)) != NULL))
{
int idx;
for(idx = bBox.xMin; idx <= bBox.xMax; ++idx)
{
int y0,
y1,
idy;
WlzUByte in = 0;
for(idy = bBox.yMin; idy <= bBox.yMax + 1; ++idy)
{
WlzGreyValueGet(iVWSp, 0, idy, idx);
if(iVWSp->bkdFlag == 0)
{
double *ibp;
if(in == 0)
{
y0 = idy;
in = 1;
}
y1 = idy;
ibp = iBuf[thrId] + (y1 - y0);
switch(iVWSp->gType)
{
case WLZ_GREY_INT:
*ibp = iVWSp->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
*ibp = iVWSp->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
*ibp = iVWSp->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
*ibp = iVWSp->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
*ibp = iVWSp->gVal[0].dbv;
break;
default:
break;
}
}
else if(in)
{
int idr,
len;
len = y1 - y0 + 1;
AlgConvolveD(len, rBuf[thrId], cBufSz * 2 + 1, cBuf,
len, iBuf[thrId], pad, padVal);
for(idr = y0; idr <= y1; ++idr)
{
WlzGreyValueGet(rVWSp, 0, idr, idx);
*(rVWSp->gPtr[0].dbp) = rBuf[thrId][idr - y0];
}
}
}
}
}
WlzGreyValueFreeWSp(iVWSp);
WlzGreyValueFreeWSp(rVWSp);
(void )WlzFreeObj(iObj);
(void )WlzFreeObj(rObj);
if(errNum2 != WLZ_ERR_NONE)
{
#ifdef _OPENMP
#pragma omp critical
{
#endif
if(errNum == WLZ_ERR_NONE)
{
errNum = errNum2;
}
#ifdef _OPENMP
}
#endif
}
}
}
}
}
if(errNum != WLZ_ERR_NONE)
{
(void )WlzFreeObj(rnObj);
rnObj = NULL;
}
if(dstErr)
{
*dstErr = errNum;
}
return(rnObj);
}
int main(int argc, char *argv[])
{
int option,
nReg = 0,
tNReg = 0,
ok = 1,
usage = 0,
verbose = 0,
threshSet = 0,
centreSet = 0;
double minArea = 2;
char *inExt,
*dbgExt,
*inDir,
*dbgDir,
*inFile,
*dbgFile,
*inPath = NULL,
*dbgPath = NULL,
*outFile = NULL;
WlzRadDistVal distSort = WLZ_RADDISTVAL_AREA;
WlzRadDistRec *distData = NULL;
WlzPixelV thrVal;
WlzDVertex2 centre;
WlzCompThreshType thrMtd = WLZ_COMPTHRESH_OTSU;
WlzThresholdType thrMod = WLZ_THRESH_HIGH;
WlzEffFormat inFmt = WLZEFF_FORMAT_NONE,
dbgFmt = WLZEFF_FORMAT_NONE;
WlzObject *inObj = NULL,
*disObj = NULL,
*segObj = NULL;
WlzGreyValueWSpace *disGVWSp = NULL;
WlzObject **regObjs = NULL;
FILE *fP = NULL;
WlzErrorNum errNum = WLZ_ERR_NONE;
const int maxObj = 1000000;
char pathBuf[FILENAME_MAX];
const double eps = 1.0e-06;
const char *errMsg;
static char optList[] = "hvAGDHELR:c:d:n:o:t:",
defFile[] = "-";
thrVal.type = WLZ_GREY_DOUBLE;
thrVal.v.dbv = 0.0;
outFile = defFile;
while((usage == 0) && ok &&
((option = getopt(argc, argv, optList)) != -1))
{
switch(option)
{
case 'A':
distSort = WLZ_RADDISTVAL_AREA;
break;
case 'D':
distSort = WLZ_RADDISTVAL_DIST;
break;
case 'G':
distSort = WLZ_RADDISTVAL_ANGLE;
break;
case 'H':
thrMod = WLZ_THRESH_HIGH;
break;
case 'E':
thrMod = WLZ_THRESH_EQUAL;
break;
case 'L':
thrMod = WLZ_THRESH_LOW;
break;
case 'R':
distSort = WLZ_RADDISTVAL_RADIUS;
break;
case 'h':
usage = 1;
break;
case 'v':
verbose = 1;
break;
case 'c':
centreSet = 1;
if(sscanf(optarg, "%lg,%lg", &(centre.vtX), &(centre.vtY)) != 2)
{
usage = 1;
}
break;
case 'd':
dbgPath = optarg;
break;
case 'o':
outFile = optarg;
break;
case 'n':
if(sscanf(optarg, "%lg", &minArea) != 1)
{
usage = 1;
}
break;
case 't':
threshSet = 1;
if(sscanf(optarg, "%lg", &(thrVal.v.dbv)) != 1)
{
usage = 1;
}
break;
default:
usage = 1;
break;
}
}
ok = !usage;
if(ok)
{
if((optind + 1) != argc)
{
usage = 1;
ok = 0;
}
else
{
inPath = *(argv + optind);
}
}
if(ok && verbose)
{
(void )fprintf(stderr, "inPath = %s\n", inPath);
}
/* Parse input file path into path + name + ext. */
if(ok)
{
ok = (usage = WlzRadDistParsePath(inPath, &inDir, &inFile, &inExt,
&inFmt)) == 0;
}
if(ok && verbose)
{
(void )fprintf(stderr, "inDir = %s\n", inDir);
(void )fprintf(stderr, "inFile = %s\n", inFile);
(void )fprintf(stderr, "inExt = %s\n", (inExt)? inExt: "(null)");
(void )fprintf(stderr, "inFmt = %s\n",
WlzEffStringFromFormat(inFmt, NULL));
}
/* Read image. */
if(ok)
{
errNum = WLZ_ERR_READ_EOF;
if(inExt)
{
(void )sprintf(pathBuf, "%s/%s.%s", inDir, inFile, inExt);
}
else
{
(void )sprintf(pathBuf, "%s/%s", inDir, inFile);
}
if(((inObj = WlzAssignObject(WlzEffReadObj(NULL, pathBuf, inFmt,
0, 0, 0,
&errNum), NULL)) == NULL) ||
(inObj->type != WLZ_2D_DOMAINOBJ))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: Failed to read 2D image object from file %s (%s)\n",
*argv, pathBuf, errMsg);
}
}
if(ok && verbose)
{
(void )fprintf(stderr, "read input image ok.\n");
}
/* Convert to grey if needed, normalise 0 - 255 if needed and compute
* threshold value unless already known. */
if(ok)
{
if(WlzGreyTypeFromObj(inObj, NULL) == WLZ_GREY_RGBA)
{
WlzObject *ppObj;
ppObj = WlzAssignObject(
WlzRGBAToModulus(inObj, &errNum), NULL);
if(errNum == WLZ_ERR_NONE)
{
(void )WlzFreeObj(inObj);
inObj = ppObj;
}
}
if(threshSet == 0)
{
WlzObject *hObj = NULL;
errNum = WlzGreyNormalise(inObj, 1);
if(errNum == WLZ_ERR_NONE)
{
hObj = WlzHistogramObj(inObj, 256, 0.0, 1.0, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
threshSet = 1;
errNum = WlzCompThreshold(&thrVal.v.dbv, hObj, thrMtd, 0);
}
(void )WlzFreeObj(hObj);
}
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to normalise object (%s)\n",
*argv, errMsg);
}
}
/* Segment the object. */
if(ok)
{
if(inObj->values.core == NULL)
{
segObj = WlzAssignObject(inObj, NULL);
}
else
{
segObj = WlzAssignObject(
WlzThreshold(inObj, thrVal, thrMod, &errNum), NULL);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to segment image (%s)\n",
*argv, errMsg);
}
}
}
/* Compute object with the same domain as the input object but in which
* the values are the minimum distance from an edge. */
if(ok)
{
WlzObject *bObj = NULL;
bObj = WlzBoundaryDomain(inObj, &errNum);
if(errNum == WLZ_ERR_NONE)
{
disObj = WlzAssignObject(
WlzDistanceTransform(inObj, bObj, WLZ_OCTAGONAL_DISTANCE,
0.0, 0.0, &errNum), NULL);
}
if(errNum == WLZ_ERR_NONE)
{
disGVWSp = WlzGreyValueMakeWSp(disObj, &errNum);
}
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to compute distance object (%s)\n",
*argv, errMsg);
}
(void )WlzFreeObj(bObj);
}
/* Output the debug image if required. */
if(ok && dbgPath)
{
WlzObject *dbgObj;
dbgObj = WlzAssignObject(WlzCopyObject(inObj, &errNum), NULL);
if(errNum == WLZ_ERR_NONE)
{
WlzPixelV iMin,
iMax,
oMin,
oMax;
if(dbgObj->values.core == NULL)
{
WlzValues tmpVal;
oMax.type = WLZ_GREY_UBYTE;
oMax.v.ubv = 255;
tmpVal.v = WlzNewValueTb(dbgObj,
WlzGreyTableType(WLZ_GREY_TAB_RAGR,
WLZ_GREY_UBYTE, NULL),
oMax, &errNum);
if(errNum == WLZ_ERR_NONE)
{
dbgObj->values = WlzAssignValues(tmpVal, NULL);
}
}
else
{
WlzObject *tmpObj = NULL;
oMin.type = WLZ_GREY_UBYTE;
oMin.v.ubv = 0;
oMax.type = WLZ_GREY_UBYTE;
oMax.v.ubv = 200;
errNum = WlzGreyRange(dbgObj, &iMin, &iMax);
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzGreySetRange(dbgObj, iMin, iMax, oMin, oMax, 0);
}
if(errNum == WLZ_ERR_NONE)
{
tmpObj = WlzMakeMain(inObj->type, segObj->domain, dbgObj->values,
NULL, NULL, &errNum);
}
if(errNum == WLZ_ERR_NONE)
{
oMax.v.ubv = 255;
errNum = WlzGreySetValue(tmpObj, oMax);
}
(void )WlzFreeObj(tmpObj);
if(errNum == WLZ_ERR_NONE)
{
tmpObj = WlzConvertPix(dbgObj, WLZ_GREY_UBYTE, &errNum);
(void )WlzFreeObj(dbgObj);
dbgObj = WlzAssignObject(tmpObj, NULL);
}
}
}
if(errNum == WLZ_ERR_NONE)
{
(void )WlzRadDistParsePath(dbgPath, &dbgDir, &dbgFile, &dbgExt,
&dbgFmt);
if(dbgExt)
{
(void )sprintf(pathBuf, "%s/%s.%s", dbgDir, dbgFile, dbgExt);
}
else
{
(void )sprintf(pathBuf, "%s/%s", dbgDir, dbgFile);
}
errNum = WlzEffWriteObj(NULL, pathBuf, dbgObj, dbgFmt);
}
(void )WlzFreeObj(dbgObj);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to output the debug image (%s)\n",
*argv, errMsg);
}
}
/* Label the segmented object. */
if(ok)
{
errNum = WlzLabel(segObj, &nReg, ®Objs, maxObj, 0, WLZ_8_CONNECTED);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
errNum = WLZ_ERR_MEM_ALLOC;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to split into components (%s)\n",
*argv, errMsg);
}
if(ok && verbose)
{
(void )fprintf(stderr, "nReg = %d\n", nReg);
}
}
/* Compute centre of mass if not known. */
if(ok)
{
if(centreSet == 0)
{
centre = WlzCentreOfMass2D(inObj, 1, NULL, &errNum);
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to compute centre of mass (%s)\n",
*argv, errMsg);
}
}
if(ok && verbose)
{
(void )fprintf(stderr, "centre = %lg,%lg\n", centre.vtX, centre.vtY);
}
}
/* Allocate a radial distribution table. */
if(ok)
{
if((distData = (WlzRadDistRec *)
AlcCalloc(nReg, sizeof(WlzRadDistRec))) == NULL)
{
ok = 0;
errNum = WLZ_ERR_MEM_ALLOC;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr, "%s: failed to allocate result lable (%s)\n",
*argv, errMsg);
}
}
/* Compute the redial distribution data. */
if(ok)
{
int idR = 0,
idS = 0;
while((errNum == WLZ_ERR_NONE) && (idR < nReg))
{
double mass;
WlzDVertex2 com;
com = WlzCentreOfMass2D(regObjs[idR], 1, &mass, NULL);
if(mass > minArea - eps)
{
WlzGreyValueGet(disGVWSp, 0.0, com.vtY, com.vtX);
distData[idS].pos = com;
distData[idS].area = mass;
WLZ_VTX_2_SUB(com, centre, com);
distData[idS].radius = WLZ_VTX_2_LENGTH(com);
distData[idS].angle = ALG_M_PI + atan2(com.vtY, com.vtX);
switch(disGVWSp->gType)
{
case WLZ_GREY_LONG:
distData[idS].dist = *(disGVWSp->gPtr[0].lnp);
break;
case WLZ_GREY_INT:
distData[idS].dist = *(disGVWSp->gPtr[0].inp);
break;
case WLZ_GREY_SHORT:
distData[idS].dist = *(disGVWSp->gPtr[0].shp);
break;
case WLZ_GREY_UBYTE:
distData[idS].dist = *(disGVWSp->gPtr[0].ubp);
break;
case WLZ_GREY_FLOAT:
distData[idS].dist = *(disGVWSp->gPtr[0].flp);
break;
case WLZ_GREY_DOUBLE:
distData[idS].dist = *(disGVWSp->gPtr[0].dbp);
break;
default:
distData[idS].dist = 0.0;
break;
}
++idS;
}
++idR;
}
tNReg = idS;
switch(distSort)
{
case WLZ_RADDISTVAL_AREA:
(void )qsort(distData, tNReg, sizeof(WlzRadDistRec),
WlzRadDistRecSortArea);
break;
case WLZ_RADDISTVAL_ANGLE:
(void )qsort(distData, tNReg, sizeof(WlzRadDistRec),
WlzRadDistRecSortAngle);
break;
case WLZ_RADDISTVAL_RADIUS:
(void )qsort(distData, tNReg, sizeof(WlzRadDistRec),
WlzRadDistRecSortRadius);
break;
case WLZ_RADDISTVAL_DIST:
(void )qsort(distData, tNReg, sizeof(WlzRadDistRec),
WlzRadDistRecSortDist);
break;
}
}
/* Output the sorted radial distribution table. */
if(ok)
{
if(((fP = strcmp(outFile, "-")?
fopen(outFile, "w"): stdout)) == NULL)
{
ok = 0;
(void )fprintf(stderr, "%s: failed to open output file %s\n",
*argv, outFile);
}
}
if(ok)
{
int idR;
for(idR = 0; idR < tNReg; ++idR)
{
double a;
a = (distData[idR].angle > 0.0)?
0 + (180 * distData[idR].angle / ALG_M_PI):
360 + (180 * distData[idR].angle / ALG_M_PI);
(void )fprintf(fP, "%g %g %g %g,%g %g\n",
a,
distData[idR].radius,
distData[idR].area,
distData[idR].pos.vtX,
distData[idR].pos.vtY,
distData[idR].dist);
}
}
if(strcmp(outFile, "-"))
{
(void )fclose(fP);
}
/* Tidy up. */
AlcFree(distData);
WlzGreyValueFreeWSp(disGVWSp);
(void )WlzFreeObj(inObj);
(void )WlzFreeObj(disObj);
(void )WlzFreeObj(segObj);
if(regObjs)
{
int idR;
for(idR = 0; idR < nReg; ++idR)
{
(void )WlzFreeObj(regObjs[idR]);
}
AlcFree(regObjs);
}
if(usage)
{
(void )fprintf(stderr,
"Usage: %s [-h] [-v] [-A] [-D] [-G] [-H] [-E] [-L] [-R]\n"
"\t\t[-c #,#] [-d <debug image>] [-n #] [-o <out file>]\n"
"\t\t[-t #] [<input image>]\n"
"Segments the given object using a threshold value and outputs the \n"
"radial distribution of the thresholded components.\n"
"Version: %s\n"
"Options:\n"
" -h Help - prints this usage masseage.\n"
" -v Verbose output.\n"
" -A Sort output by area (default).\n"
" -D Sort output by distance from boundary.\n"
" -G Sort output by angle.\n"
" -H Threshold high, use pixels at or above threshold (default).\n"
" -E Threshold equal, use pixels at threshold.\n"
" -L Threshold low, use pixels below threshold.\n"
" -R Sort output by radial distance from centre.\n"
" -c Centre (default is image centre).\n"
" -d Debug image.\n"
" -n Minimum area (default %g).\n"
" -t Threshold value (default is to compute using Otsu's method).\n"
"By default the input image object is read from the standard input and\n"
"the radial distribution is written to the standard output.\n"
"The image formats understood include wlz, jpg and tif.\n"
"The output format is:\n"
" <angle> <dist from centre> <area> <x pos>,<y pos> <dist form boundary>\n"
"Example:\n"
" %s -o out.txt -d debug.jpg in.tif\n"
"The input image is read from in.tif, a debug image showing the\n"
"segmented regions is written to debug.jpg and the radial distribution\n"
"statistics are written to the file out.txt. With the output in\n"
"out.txt, the following R code would plot the data as a set of circles\n"
"with radius proportional to the square root of the component area:\n"
" data <- read.table(\"out.txt\")\n"
" attach(data)\n"
" symbols(x=data$V1, y=data$V2, circles=sqrt(data$V3))\n",
argv[0],
WlzVersion(),
minArea,
argv[0]);
}
return(!ok);
}
/*!
* \return New 3D domain object with corresponding WLZ_GREY_RGBA values.
* \ingroup WlzValuesUtils
* \brief Creates a WLZ_GREY_RGBA valued object from the given compound
* array. This is a static function which will always be called
* with valid parameters so they aren't checked.
* \param cObj Compound array object.
* \param cSpc The colour space.
* \param dstErr Destination error pointer may be NULL.
*/
static WlzObject *WlzCompoundToRGBA2D(WlzCompoundArray *cObj,
WlzRGBAColorSpace cSpc, WlzErrorNum *dstErr)
{
int i,
j;
WlzObject *rtnObj=NULL;
WlzPixelV bckgrnd;
WlzObject *objs[4];
WlzObjectType vType;
WlzUInt b[4];
WlzErrorNum errNum=WLZ_ERR_NONE;
/* Make a copy of the object pointers because WlzUnionN() modifies the
* array if it contains empty objects. */
for(i = 0; i < 3; ++i)
{
objs[i] = cObj->o[i];
}
rtnObj = WlzUnionN(3, objs, 0, &errNum);
if(errNum == WLZ_ERR_NONE)
{
/* Add an RGBA valuetable, extract background for each channel */
vType = WlzGreyTableType(WLZ_GREY_TAB_RAGR, WLZ_GREY_RGBA, &errNum);
for(i=0; (errNum == WLZ_ERR_NONE) && (i < 3); i++)
{
bckgrnd = WlzGetBackground(cObj->o[i], &errNum);
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzValueConvertPixel(&bckgrnd, bckgrnd, WLZ_GREY_UBYTE);
b[i] = bckgrnd.v.ubv;
}
}
}
if(errNum == WLZ_ERR_NONE)
{
WlzValues values;
bckgrnd.type = WLZ_GREY_RGBA;
WLZ_RGBA_RGBA_SET(bckgrnd.v.rgbv, b[0], b[1], b[2], 255);
values.v = WlzNewValueTb(rtnObj, vType, bckgrnd, &errNum);
if(values.v != NULL)
{
rtnObj->values = WlzAssignValues(values, &errNum);
}
else
{
(void )WlzFreeObj(rtnObj);
rtnObj = NULL;
}
}
/* Transfer values */
if( errNum == WLZ_ERR_NONE)
{
WlzGreyValueWSpace *gValWSpc[4];
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzGreyV gval;
/* do it dumb fashion for now, rgb only */
gValWSpc[0] = gValWSpc[1] = gValWSpc[2] = gValWSpc[3] = NULL;
for(i=0; i < 3; i++)
{
if((cObj->o[i] != NULL) && (cObj->o[i]->type != WLZ_EMPTY_OBJ))
{
gValWSpc[i] = WlzGreyValueMakeWSp(cObj->o[i], &errNum);
if(errNum != WLZ_ERR_NONE)
{
break;
}
}
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzInitGreyScan(rtnObj, &iwsp, &gwsp);
}
while((errNum == WLZ_ERR_NONE) &&
((errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE))
{
WlzPixelV pix;
for(j = iwsp.lftpos; j <= iwsp.rgtpos; j++)
{
for(i = 0; i < 3; i++)
{
if(gValWSpc[i] == NULL)
{
pix.v.ubv = (i < 2)? 0: 255;
}
else
{
WlzGreyValueGet(gValWSpc[i], 0, iwsp.linpos, j);
pix.type = gValWSpc[i]->gType;
pix.v = gValWSpc[i]->gVal[0];
WlzValueConvertPixel(&pix, pix, WLZ_GREY_UBYTE);
}
b[i] = pix.v.ubv;
}
WLZ_RGBA_RGBA_SET(gval.rgbv, b[0], b[1], b[2], b[3]);
*gwsp.u_grintptr.rgbp = gval.rgbv;
gwsp.u_grintptr.rgbp++;
}
}
if(errNum == WLZ_ERR_EOO)
{
errNum = WLZ_ERR_NONE;
}
for(i=0; i < 3; i++)
{
WlzGreyValueFreeWSp(gValWSpc[i]);
}
}
if(dstErr != NULL)
{
*dstErr = errNum;
}
return(rtnObj);
}
void installViewDomains(
ThreeDViewStruct *view_struct)
{
WlzThreeDViewStruct *wlzViewStr= view_struct->wlzViewStr;
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzGreyValueWSpace *gVWSp = NULL;
float x, y, z;
int xp, yp;
int i;
ViewListEntry *vl = global_view_list;
WlzErrorNum errNum=WLZ_ERR_NONE;
/* all domains on this plane will already have been
checked for consistency, dominance etc. therefore
simply set the corresponding domains in the painted
object */
/* this is the set version of get section and should be in the
woolz library. This is probably faster because many assumptions
are made, mainly the grey-type */
gVWSp = WlzGreyValueMakeWSp(globals.obj, &errNum);
if( errNum == WLZ_ERR_NONE ){
errNum = WlzInitGreyScan( view_struct->painted_object, &iwsp, &gwsp );
while((errNum == WLZ_ERR_NONE) &&
((errNum = WlzNextGreyInterval( &iwsp )) == WLZ_ERR_NONE) )
{
yp = iwsp.linpos - WLZ_NINT(wlzViewStr->minvals.vtY);
for(i=iwsp.lftpos; i <= iwsp.rgtpos; i++){
xp = i - WLZ_NINT(wlzViewStr->minvals.vtX);
x = wlzViewStr->xp_to_x[xp] + wlzViewStr->yp_to_x[yp];
y = wlzViewStr->xp_to_y[xp] + wlzViewStr->yp_to_y[yp];
z = wlzViewStr->xp_to_z[xp] + wlzViewStr->yp_to_z[yp];
WlzGreyValueGet(gVWSp, WLZ_NINT(z), WLZ_NINT(y), WLZ_NINT(x));
*(gVWSp->gPtr[0].ubp) = *(gwsp.u_grintptr.ubp);
gwsp.u_grintptr.ubp++;
}
}
if( errNum == WLZ_ERR_EOO ){
errNum = WLZ_ERR_NONE;
}
WlzGreyValueFreeWSp(gVWSp);
}
/* copy the new domains to the previous domains */
if( errNum == WLZ_ERR_NONE ){
for(i=0; i < 33; i++){
if( view_struct->prev_domain[i] ){
WlzFreeObj(view_struct->prev_domain[i]);
view_struct->prev_domain[i] = NULL;
}
if( view_struct->curr_domain[i] ){
view_struct->prev_domain[i] =
WlzAssignObject(view_struct->curr_domain[i], NULL);
}
}
}
/* set the previous distance and view object - calculate when needed */
if( errNum == WLZ_ERR_NONE ){
view_struct->prev_dist = wlzViewStr->dist;
if( view_struct->prev_view_obj ){
WlzFreeObj(view_struct->prev_view_obj);
view_struct->prev_view_obj = NULL;
}
if( view_struct->view_object ){
view_struct->prev_view_obj = WlzAssignObject(view_struct->view_object,
NULL);
}
else {
view_struct->prev_view_obj = NULL;
}
}
/* display all views to update the new domains */
if( errNum == WLZ_ERR_NONE ){
while( vl != NULL ){
if( vl->view_struct != paint_key ){
if( vl->view_struct == view_struct ){
redisplay_view_cb(view_struct->canvas,
(XtPointer) vl->view_struct, NULL);
}
else {
display_view_cb(view_struct->canvas,
(XtPointer) vl->view_struct, NULL);
}
}
vl = vl->next;
}
}
if( errNum != WLZ_ERR_NONE ){
MAPaintReportWlzError(globals.topl, "installViewDomains", errNum);
}
return;
}
/*!
* \return projection object
* \ingroup WlzTransform
* \brief Use the view transform to define a projection from
* 3D to 2D. Currently only the domain is projected as
* an opaque shadow.
* This is old code temporarily kept for compatibility.
* \param obj source 3D object
* \param viewStr view structure defining the projection
* \param intFunc grey-value summation function
* \param intFuncData data to be passed to the integration function
* \param dstErr error return
*/
WlzObject *WlzGetProjectionFromObject(
WlzObject *obj,
WlzThreeDViewStruct *viewStr,
Wlz3DProjectionIntFn intFunc,
void *intFuncData,
WlzErrorNum *dstErr)
{
WlzObject *rtnObj=NULL,
*obj1;
WlzThreeDViewStruct *viewStr1=NULL;
WlzDomain domain;
WlzValues values;
WlzGreyType srcGType = WLZ_GREY_UBYTE,
dstGType = WLZ_GREY_UBYTE;
WlzPixelV pixval;
WlzPixelP pixptr;
WlzIntervalWSpace iwsp;
WlzGreyWSpace gwsp;
WlzGreyValueWSpace *gVWSp = NULL;
WlzDVertex3 vtx, vtx1;
double x, y, z;
double *s_to_x=NULL;
double *s_to_y=NULL;
double *s_to_z=NULL;
int k, xp, yp, s, sp;
int length = 0, size = 0, occupiedFlg;
WlzErrorNum errNum=WLZ_ERR_NONE;
/* check inputs */
if( obj == NULL ){
errNum = WLZ_ERR_OBJECT_NULL;
}
else if( obj->type != WLZ_3D_DOMAINOBJ ){
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if( obj->domain.core == NULL ){
errNum = WLZ_ERR_DOMAIN_NULL;
}
else if( obj->domain.core->type != WLZ_PLANEDOMAIN_DOMAIN ){
errNum = WLZ_ERR_DOMAIN_TYPE;
}
if( (errNum == WLZ_ERR_NONE) && (viewStr == NULL) ){
errNum = WLZ_ERR_OBJECT_NULL;
}
/* create new view transform */
if( errNum == WLZ_ERR_NONE ){
if((viewStr1 = WlzMake3DViewStruct(WLZ_3D_VIEW_STRUCT, &errNum)) != NULL){
/* need to worry about fixed line mode here sometime */
viewStr1->fixed = viewStr->fixed;
viewStr1->theta = viewStr->theta;
viewStr1->phi = viewStr->phi;
viewStr1->zeta = viewStr->zeta;
viewStr1->dist = viewStr->dist;
viewStr1->scale = viewStr->scale;
viewStr1->voxelSize[0] = viewStr->voxelSize[0];
viewStr1->voxelSize[1] = viewStr->voxelSize[1];
viewStr1->voxelSize[2] = viewStr->voxelSize[2];
viewStr1->voxelRescaleFlg = viewStr->voxelRescaleFlg;
viewStr1->interp = viewStr->interp;
viewStr1->view_mode = viewStr->view_mode;
viewStr1->up = viewStr->up;
/* now intialize it */
/* could optimise by setting fixed point to object centre */
if( (errNum = WlzInit3DViewStruct(viewStr1, obj)) != WLZ_ERR_NONE ){
WlzFree3DViewStruct(viewStr1);
viewStr1 = NULL;
}
}
}
/* set up orthogonal line parameters & luts */
if( errNum == WLZ_ERR_NONE ){
length = WLZ_NINT(viewStr1->maxvals.vtZ) -
WLZ_NINT(viewStr1->minvals.vtZ) + 1;
s_to_x = (double *) AlcMalloc(sizeof(double) * length );
s_to_y = (double *) AlcMalloc(sizeof(double) * length );
s_to_z = (double *) AlcMalloc(sizeof(double) * length );
/* transform a perpendicular vector */
vtx.vtX = 0.0;
vtx.vtY = 0.0;
vtx.vtZ = 1.0;
Wlz3DSectionTransformInvVtx(&vtx, viewStr1);
vtx1.vtX = 0.0;
vtx1.vtY = 0.0;
vtx1.vtZ = 0.0;
Wlz3DSectionTransformInvVtx(&vtx1, viewStr1);
vtx.vtX -= vtx1.vtX;
vtx.vtY -= vtx1.vtY;
vtx.vtZ -= vtx1.vtZ;
/* assign lut values */
s = (int )(WLZ_NINT(viewStr1->minvals.vtZ) - viewStr1->dist);
for(sp=0; sp < length; sp++, s++){
s_to_x[sp] = s * vtx.vtX;
s_to_y[sp] = s * vtx.vtY;
s_to_z[sp] = s * vtx.vtZ;
}
}
/* if there is an integration function then allocate space for
the grey-level array */
if( (errNum == WLZ_ERR_NONE) && (intFunc) ){
srcGType = WlzGreyTypeFromObj(obj, &errNum);
switch( srcGType ){
case WLZ_GREY_LONG:
size = sizeof(WlzLong)*length;
break;
case WLZ_GREY_INT:
size = sizeof(int)*length;
break;
case WLZ_GREY_SHORT:
size = sizeof(short)*length;
break;
case WLZ_GREY_UBYTE:
size = sizeof(WlzUByte)*length;
break;
case WLZ_GREY_FLOAT:
size = sizeof(float)*length;
break;
case WLZ_GREY_DOUBLE:
size = sizeof(double)*length;
break;
case WLZ_GREY_RGBA:
size = sizeof(int)*length;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
if( (pixptr.p.inp = (int *) AlcMalloc(size)) == NULL ){
errNum = WLZ_ERR_MEM_ALLOC;
}
pixptr.type = srcGType;
/* set up the grey-value workspace for random access */
gVWSp = WlzGreyValueMakeWSp(obj, &errNum);
}
/* create rectangular projection image */
if( errNum == WLZ_ERR_NONE ){
if((domain.i = WlzMakeIntervalDomain(WLZ_INTERVALDOMAIN_RECT,
WLZ_NINT(viewStr1->minvals.vtY),
WLZ_NINT(viewStr1->maxvals.vtY),
WLZ_NINT(viewStr1->minvals.vtX),
WLZ_NINT(viewStr1->maxvals.vtX),
&errNum)) != NULL){
values.core = NULL;
if((rtnObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, domain, values, NULL, NULL,
&errNum)) != NULL){
/* note the grey-values required are determined by the integration
function. Here we use WlzUByte and reset later if needed */
dstGType = WLZ_GREY_UBYTE;
pixval.type = WLZ_GREY_UBYTE;
pixval.v.ubv = (WlzUByte )0;
if((values.v = WlzNewValueTb(rtnObj,
WlzGreyTableType(WLZ_GREY_TAB_RECT,
dstGType, NULL),
pixval, &errNum)) != NULL){
rtnObj->values = WlzAssignValues(values, &errNum);
}
else {
WlzFreeObj(rtnObj);
rtnObj = NULL;
}
}
else {
WlzFreeDomain(domain);
domain.core = NULL;
}
}
}
/* scan image setting values */
if( errNum == WLZ_ERR_NONE ){
errNum = WlzInitGreyScan(rtnObj, &iwsp, &gwsp);
}
if( errNum == WLZ_ERR_NONE ){
while( (errNum = WlzNextGreyInterval(&iwsp)) == WLZ_ERR_NONE ){
yp = iwsp.linpos - WLZ_NINT(viewStr1->minvals.vtY);
for(k=iwsp.lftpos; k <= iwsp.rgtpos; k++){
xp = k - WLZ_NINT(viewStr1->minvals.vtX);
vtx.vtX = viewStr1->xp_to_x[xp] + viewStr1->yp_to_x[yp];
vtx.vtY = viewStr1->xp_to_y[xp] + viewStr1->yp_to_y[yp];
vtx.vtZ = viewStr1->xp_to_z[xp] + viewStr1->yp_to_z[yp];
/* get the projection values */
/* if no function then just check for occupancy */
if( intFunc == NULL ){
occupiedFlg = 0;
sp = (int )(viewStr1->dist - WLZ_NINT(viewStr1->minvals.vtZ));
for(; !occupiedFlg && (sp < length); sp++){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
if( WlzInsideDomain(obj, z, y, x, &errNum) ){
occupiedFlg = 1;
}
}
sp = (int )(viewStr1->dist - WLZ_NINT(viewStr1->minvals.vtZ) - 1);
for(; !occupiedFlg && (sp >= 0); sp--){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
if( WlzInsideDomain(obj, z, y, x, &errNum) ){
occupiedFlg = 1;
}
}
/* set the integrated value - only WlzUByte at the moment */
*(gwsp.u_grintptr.ubp) = (WlzUByte )occupiedFlg;
gwsp.u_grintptr.ubp++;
}
/* use integration function */
else {
/* set array of pixel values */
for(sp=0; sp < length; sp++){
x = vtx.vtX + s_to_x[sp];
y = vtx.vtY + s_to_y[sp];
z = vtx.vtZ + s_to_z[sp];
WlzGreyValueGet(gVWSp, WLZ_NINT(z), WLZ_NINT(y),
WLZ_NINT(x));
switch( srcGType ){
case WLZ_GREY_LONG:
pixptr.p.lnp[sp] = gVWSp->gVal[0].lnv;
break;
case WLZ_GREY_INT:
pixptr.p.inp[sp] = gVWSp->gVal[0].inv;
break;
case WLZ_GREY_SHORT:
pixptr.p.shp[sp] = gVWSp->gVal[0].shv;
break;
case WLZ_GREY_UBYTE:
pixptr.p.ubp[sp] = gVWSp->gVal[0].ubv;
break;
case WLZ_GREY_FLOAT:
pixptr.p.flp[sp] = gVWSp->gVal[0].flv;
break;
case WLZ_GREY_DOUBLE:
pixptr.p.dbp[sp] = gVWSp->gVal[0].dbv;
break;
case WLZ_GREY_RGBA:
pixptr.p.rgbp[sp] = gVWSp->gVal[0].rgbv;
break;
default:
errNum = WLZ_ERR_GREY_TYPE;
break;
}
}
/* call integration function and seet value */
intFunc(pixptr, length, (int )(viewStr1->dist -
WLZ_NINT(viewStr1->minvals.vtZ)),
intFuncData, &errNum);
}
}
}
(void )WlzEndGreyScan(&iwsp, &gwsp);
if(errNum == WLZ_ERR_EOO) /* Reset error from end of intervals */
{
errNum = WLZ_ERR_NONE;
}
/* if no integration function then threshold - binary only */
if( intFunc == NULL ){
pixval.v.ubv = 1;
rtnObj = WlzAssignObject(rtnObj, NULL);
if((obj1 = WlzThreshold(rtnObj, pixval, WLZ_THRESH_HIGH,
&errNum)) != NULL){
WlzFreeObj(rtnObj);
values.core = NULL;
rtnObj = WlzMakeMain(WLZ_2D_DOMAINOBJ, obj1->domain, values, NULL, NULL,
&errNum);
WlzFreeObj(obj1);
}
else {
WlzFreeObj(rtnObj);
rtnObj = NULL;
}
}
}
/* clear space */
if( viewStr1 ){
errNum = WlzFree3DViewStruct(viewStr1);
}
if( s_to_x ){
AlcFree( s_to_x );
}
if( s_to_y ){
AlcFree( s_to_y );
}
if( s_to_z ){
AlcFree( s_to_z );
}
/* check error and return */
if( dstErr ){
*dstErr = errNum;
}
return rtnObj;
}
/*!
* \ingroup WlzTransform
* \brief Increments values in the array on the straight line segment
* between (x0, y0) and (x1, y1) using the given look up table
* and the corresponding grey value as an index into this look
* up table.
* \param ary Rectangular array of ints to set
* projected line values in.
* \param lut Value density look up table with
* 256 entries.
* \param gP Grey pointer for access to the
* object's grey values.
* \param gVWSp Grey value workspace for access to
* the object grey values, not used if
* the grey pointer is non null.
* \param vMat View transform matrix.
* \param vMZX Precomputed matrix z -> x.
* \param vMZY Precomputed matrix z -> y.
* \param p0 Line segment start.
* \param p1 Line segment end.
*/
static void WlzProjectObjLineVal(int **ary, WlzUByte lut[256],
WlzUByte *gP,
WlzGreyValueWSpace *gVWSp,
double **vMat, double vMZX, double vMZY,
WlzIVertex3 p0, WlzIVertex3 p1)
{
#ifdef WLZ_FAST_CODE
int v00,
v01,
vMZXI,
vMZYI;
#else
WlzDVertex2 q;
#endif
WlzIVertex2 u;
vMZX += vMat[0][1] * p0.vtY;
vMZY += vMat[1][1] * p0.vtY;
#ifdef WLZ_FAST_CODE
/*
* Use integer arithmetic for evaluating the transform instead of floating
* point and then rounding to the nearest integer, which saves about 20% of
* the execution time for the grey pointer code (mainly be avoiding nint()).
* Integer multiplication and division are used with a factor of 2^10 which
* the compiller should recognise and be able to do an arithmetic shift
* right for division, we can't use >> as it's behaviour for signed ints
* is platfrom dependant.
*/
vMZXI = WLZ_NINT(vMZX);
vMZYI = WLZ_NINT(vMZY);
v00 = WLZ_NINT(vMat[0][0] * 1024.0);
v01 = WLZ_NINT(vMat[1][0] * 1024.0);
#endif
if(gP)
{
/* Use the interval of values given by the grey pointer. */
if(lut)
{
while(1)
{
#ifdef WLZ_FAST_CODE
u.vtX = ((v00 * p0.vtX) / 1024) + vMZXI;
u.vtY = ((v01 * p0.vtX) / 1024) + vMZYI;
#else
q.vtX = (vMat[0][0] * p0.vtX) + vMZX;
q.vtY = (vMat[1][0] * p0.vtY) + vMZY;
WLZ_VTX_2_NINT(u, q);
#endif
*(*(ary + u.vtY) + u.vtX) += lut[*gP++];
if(++(p0.vtX) > p1.vtX)
{
break;
}
}
}
else
{
while(1)
{
#ifdef WLZ_FAST_CODE
u.vtX = ((v00 * p0.vtX) / 1024) + vMZXI;
u.vtY = ((v01 * p0.vtX) / 1024) + vMZYI;
#else
q.vtX = (vMat[0][0] * p0.vtX) + vMZX;
q.vtY = (vMat[1][0] * p0.vtY) + vMZY;
WLZ_VTX_2_NINT(u, q);
#endif
*(*(ary + u.vtY) + u.vtX) += 255 - *gP++;
if(++(p0.vtX) > p1.vtX)
{
break;
}
}
}
}
else
{
/* Need to use random access to the grey values since no grey pointer. */
if(lut)
{
while(1)
{
WlzGreyValueGet(gVWSp, p0.vtZ, p0.vtY, p0.vtX);
#ifdef WLZ_FAST_CODE
u.vtX = ((v00 * p0.vtX) / 1024) + vMZXI;
u.vtY = ((v01 * p0.vtX) / 1024) + vMZYI;
#else
q.vtX = (vMat[0][0] * p0.vtX) + vMZX;
q.vtY = (vMat[1][0] * p0.vtY) + vMZY;
WLZ_VTX_2_NINT(u, q);
#endif
*(*(ary + u.vtY) + u.vtX) += lut[gVWSp->gVal[0].ubv];
if(++(p0.vtX) > p1.vtX)
{
break;
}
}
}
else
{
while(1)
{
WlzGreyValueGet(gVWSp, p0.vtZ, p0.vtY, p0.vtX);
#ifdef WLZ_FAST_CODE
u.vtX = ((v00 * p0.vtX) / 1024) + vMZXI;
u.vtY = ((v01 * p0.vtX) / 1024) + vMZYI;
#else
q.vtX = (vMat[0][0] * p0.vtX) + vMZX;
q.vtY = (vMat[1][0] * p0.vtY) + vMZY;
WLZ_VTX_2_NINT(u, q);
#endif
*(*(ary + u.vtY) + u.vtX) += 255 - gVWSp->gVal[0].ubv;
if(++(p0.vtX) > p1.vtX)
{
break;
}
}
}
}
}
