int main(int argc, char **argv)
{
int idx,
option,
deriv = 0,
asciiFlag = 0,
rsvFlag = 0,
ok = 1,
usage = 0;
double sigma = 1.0;
WlzErrorNum errNum = WLZ_ERR_NONE;
FILE *fP = NULL;
WlzHistogramDomain *histDom;
WlzObject *inObj = NULL,
*outObj = NULL;
char *outObjFileStr,
*inObjFileStr;
const char *errMsg;
static char optList[] = "aro:d:s:h",
outObjFileStrDef[] = "-",
inObjFileStrDef[] = "-";
opterr = 0;
outObjFileStr = outObjFileStrDef;
inObjFileStr = inObjFileStrDef;
while(ok && ((option = getopt(argc, argv, optList)) != -1))
{
switch(option)
{
case 'a':
asciiFlag = 1;
break;
case 'r':
rsvFlag = 1;
break;
case 'o':
outObjFileStr = optarg;
break;
case 'd':
if((sscanf(optarg, "%d", &deriv) != 1) ||
(deriv < 0) || (deriv > 2))
{
usage = 1;
ok = 0;
}
break;
case 's':
if(sscanf(optarg, "%lg", &sigma) != 1)
{
usage = 1;
ok = 0;
}
break;
case 'h':
default:
usage = 1;
ok = 0;
break;
}
}
if((inObjFileStr == NULL) || (*inObjFileStr == '\0') ||
(outObjFileStr == NULL) || (*outObjFileStr == '\0'))
{
ok = 0;
usage = 1;
}
if(ok && (optind < argc))
{
if((optind + 1) != argc)
{
usage = 1;
ok = 0;
}
else
{
inObjFileStr = *(argv + optind);
}
}
if(ok)
{
errNum = WLZ_ERR_READ_EOF;
if((inObjFileStr == NULL) ||
(*inObjFileStr == '\0') ||
((fP = (strcmp(inObjFileStr, "-")?
fopen(inObjFileStr, "r"): stdin)) == NULL) ||
((inObj= WlzAssignObject(WlzReadObj(fP, &errNum), NULL)) == NULL))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to read object from file %s (%s).\n",
*argv, inObjFileStr, errMsg);
}
if(fP && strcmp(inObjFileStr, "-"))
{
fclose(fP);
}
}
if(ok)
{
if(inObj->type != WLZ_HISTOGRAM)
{
ok = 0;
(void )fprintf(stderr,
"%s: input object read from file %s not a histogram\n",
*argv, inObjFileStr);
}
}
if(ok)
{
outObj = WlzAssignObject(inObj, NULL);
if(rsvFlag)
{
errNum = WlzHistogramRsvGauss(outObj, sigma, deriv);
}
else
{
errNum = WlzHistogramCnvGauss(outObj, sigma, deriv);
}
if(errNum != WLZ_ERR_NONE)
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to filter histogram (%s).\n",
*argv, errMsg);
}
}
if(ok)
{
if(asciiFlag)
{
if((fP = (strcmp(outObjFileStr, "-")?
fopen(outObjFileStr, "w"): stdout)) == NULL)
{
ok = 0;
(void )fprintf(stderr,
"%s: failed to write output data\n",
*argv);
}
else
{
histDom = outObj->domain.hist;
switch(histDom->type)
{
case WLZ_HISTOGRAMDOMAIN_INT:
for(idx = 0; idx < histDom->nBins; ++idx)
{
fprintf(fP, "%8g %8d\n",
histDom->origin + (idx * histDom->binSize),
*(histDom->binValues.inp + idx));
}
break;
case WLZ_HISTOGRAMDOMAIN_FLOAT:
for(idx = 0; idx < histDom->nBins; ++idx)
{
fprintf(fP, "%8g %8g\n",
histDom->origin + (idx * histDom->binSize),
*(histDom->binValues.dbp + idx));
}
break;
default:
break;
}
}
}
else
{
errNum = WLZ_ERR_WRITE_EOF;
if(((fP = (strcmp(outObjFileStr, "-")?
fopen(outObjFileStr, "w"):
stdout)) == NULL) ||
((errNum = WlzWriteObj(fP, outObj)) != WLZ_ERR_NONE))
{
ok = 0;
(void )WlzStringFromErrorNum(errNum, &errMsg);
(void )fprintf(stderr,
"%s: failed to write output object (%s).\n",
*argv, errMsg);
}
}
if(fP && strcmp(outObjFileStr, "-"))
{
fclose(fP);
}
}
if(inObj)
{
WlzFreeObj(inObj);
}
if(outObj)
{
WlzFreeObj(outObj);
}
if(usage)
{
(void )fprintf(stderr,
"Usage: %s%s%s%sExample: %s%s",
*argv,
" [-h] [-a] [-r] [-o<out file>] [-d#] [-s#] [<in object>]\n"
"Version: ",
WlzVersion(),
"\n"
"Options:\n"
" -a Output the histogram as ascii data not a Woolz histogram object.\n"
" -r Use a recursive IIR filter.\n"
" -o Output object/data file name.\n"
" -d Derivative, range [0-2].\n"
" -s Gaussian sigma (standard deviation).\n"
" -h Help, prints this usage message.\n"
"Convolves the bin values of a Woolz histogram object with a Gaussian\n"
"or it's 1st or 2nd derivtive.\n"
"Objects/data are read from stdin and written to stdout unless the\n"
"filenames are given.\n",
*argv,
" -s3 -a myhist.wlz | xgraph\n"
"The input Woolz histogram object is read from myhist.wlz, filtered\n"
"by convolving the histogram bins with a Gaussian (sigma = 3.0) and\n"
"written as ascii to the program xgraph for display.\n");
}
return(!ok);
}
/*!
* \return Woolz error code.
* \ingroup WlzBinaryOps
* \brief Splits the reference object into component objects cliped
* from the reference object, with the bounding box of each
* of the component objects determined using the pre-processed
* object. The component objects are returned in size order.
* \param refObj Reference object.
* \param ppObj Pre-processed object which is
* normalised to values in the range
* 0 - 255 as WlzUByte greys.
* \param bWidth Border width.
* \param bgdFrac Minimum fraction of values which are
* background values, with range
* [0.0+ - 1.0-].
* \param sigma Histogram smoothing parameter used
* by WlzHistogramCnvGauss().
* \param compThrMethod Method for computing threshold, used
* in call to WlzCompThresholdVT().
* \param nReqComp Number of required components.
* \param dstNComp Destination pointer for the number of
* components extracted, must not be NULL.
* \param dstComp Destination pointer for the extracted
* components, must not be NULL.
*/
WlzErrorNum WlzSplitObj(WlzObject *refObj, WlzObject *ppObj,
int bWidth, double bgdFrac, double sigma,
WlzCompThreshType compThrMethod,
int nReqComp, int *dstNComp,
WlzObject ***dstComp)
{
int dim,
idC;
WlzObject *hObj = NULL,
*tObj = NULL;
WlzObject **comp = NULL;
WlzBox box;
WlzPixelV tV;
WlzSplitObjData split;
WlzThresholdType tType;
WlzConnectType lCon;
WlzErrorNum errNum = WLZ_ERR_NONE;
const int maxComp = 1024;
split.nLComp = 0;
split.compI = NULL;
split.lCompSz = NULL;
split.lComp = NULL;
if((refObj == NULL) || (ppObj == NULL))
{
errNum = WLZ_ERR_OBJECT_NULL;
}
else if((refObj->domain.core == NULL) || (ppObj->domain.core == NULL))
{
errNum = WLZ_ERR_DOMAIN_NULL;
}
else if((refObj->values.core == NULL) || (ppObj->values.core == NULL))
{
errNum = WLZ_ERR_VALUES_NULL;
}
else if(refObj->type != ppObj->type)
{
errNum = WLZ_ERR_OBJECT_TYPE;
}
else if((dstNComp == NULL) || (dstComp == NULL))
{
errNum = WLZ_ERR_PARAM_NULL;
}
else if((bgdFrac < DBL_EPSILON) || (bgdFrac > (1.0 - DBL_EPSILON)))
{
errNum = WLZ_ERR_PARAM_DATA;
}
else
{
switch(refObj->type)
{
case WLZ_2D_DOMAINOBJ:
dim = 2;
lCon = WLZ_8_CONNECTED;
break;
case WLZ_3D_DOMAINOBJ:
dim = 3;
lCon = WLZ_26_CONNECTED;
break;
default:
errNum = WLZ_ERR_OBJECT_TYPE;
break;
}
}
/* Compute threshold value and type from histogram. */
if(errNum == WLZ_ERR_NONE)
{
hObj = WlzAssignObject(
WlzHistogramObj(ppObj, 256, 0.0, 1.0, &errNum), NULL);
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzHistogramCnvGauss(hObj, sigma, 0);
}
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzCompThresholdVT(hObj, compThrMethod, bgdFrac, 0.0,
0.0, &tV, &tType);
}
(void )WlzFreeObj(hObj); hObj = NULL;
/* Threshold object. */
if(errNum == WLZ_ERR_NONE)
{
tObj = WlzAssignObject(
WlzThreshold(ppObj, tV, tType, &errNum), NULL);
}
/* Label to get connected components. */
if(errNum == WLZ_ERR_NONE)
{
errNum = WlzLabel(tObj, &(split.nLComp), &(split.lComp), maxComp, 0, lCon);
}
/* Sort connected components by size. */
if(errNum == WLZ_ERR_NONE)
{
if(split.nLComp < nReqComp)
{
nReqComp = split.nLComp;
}
if(((split.compI = (int *)AlcMalloc(sizeof(int) *
split.nLComp)) == NULL) ||
((split.lCompSz = (int *)AlcMalloc(sizeof(int) *
split.nLComp)) == NULL))
{
errNum = WLZ_ERR_MEM_ALLOC;
}
}
if(errNum == WLZ_ERR_NONE)
{
idC = 0;
while((errNum == WLZ_ERR_NONE) && (idC < split.nLComp))
{
split.compI[idC] = idC;
split.lCompSz[idC] = (dim == 2)? WlzArea(split.lComp[idC], &errNum):
WlzVolume(split.lComp[idC], &errNum);
++idC;
}
}
if(errNum == WLZ_ERR_NONE)
{
/* Sort component indices by component size. */
AlgQSort(split.compI, split.nLComp, sizeof(int), &split,
WlzSplitObjSortSzFn);
/* Allocate array for cliped component objects. */
if((comp = (WlzObject **)AlcCalloc(sizeof(WlzObject *),
split.nLComp)) == NULL)
{
errNum = WLZ_ERR_MEM_ALLOC;
}
}
/* Compute bounding box and clip objects from the reference object. */
if(errNum == WLZ_ERR_NONE)
{
idC = 0;
while((errNum == WLZ_ERR_NONE) && (idC < nReqComp))
{
if(dim == 2)
{
box.i2 = WlzBoundingBox2I(split.lComp[split.compI[idC]], &errNum);
if(errNum == WLZ_ERR_NONE)
{
box.i2.xMin -= bWidth;
box.i2.yMin -= bWidth;
box.i2.xMax += bWidth;
box.i2.yMax += bWidth;
comp[idC] = WlzClipObjToBox2D(refObj, box.i2, &errNum);
}
}
else /* dim == 3 */
{
box.i3 = WlzBoundingBox3I(split.lComp[split.compI[idC]], &errNum);
if(errNum == WLZ_ERR_NONE)
{
box.i3.xMin -= bWidth;
box.i3.yMin -= bWidth;
box.i3.zMin -= bWidth;
box.i3.xMax += bWidth;
box.i3.yMax += bWidth;
box.i3.zMax += bWidth;
comp[idC] = WlzClipObjToBox3D(refObj, box.i3, &errNum);
}
}
++idC;
}
}
if(errNum == WLZ_ERR_NONE)
{
*dstNComp = nReqComp;
*dstComp = comp;
}
/* Free temporary storage. */
if(split.lComp)
{
for(idC = 0; idC < split.nLComp; ++idC)
{
(void )WlzFreeObj(split.lComp[idC]);
}
AlcFree(split.lComp);
}
AlcFree(split.compI);
AlcFree(split.lCompSz);
(void )WlzFreeObj(tObj);
return(errNum);
}