// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSections::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t dims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(dims);
int64_t xspot = 0, yspot = 0;
int64_t newPosition = 0;
int64_t currentPosition = 0;
std::vector<int64_t> xshifts(dims[2], 0);
std::vector<int64_t> yshifts(dims[2], 0);
find_shifts(xshifts, yshifts);
QList<QString> voxelArrayNames = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArrayNames();
size_t progIncrement = dims[2] / 100;
size_t prog = 1;
size_t progressInt = 0;
size_t slice = 0;
for (size_t i = 1; i < dims[2]; i++)
{
if (i > prog)
{
progressInt = ((float)i / dims[2]) * 100.0f;
QString ss = QObject::tr("Transferring Cell Data || %1% Complete").arg(progressInt);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
prog = prog + progIncrement;
}
if (getCancel() == true)
{
return;
}
slice = (dims[2] - 1) - i;
for (size_t l = 0; l < dims[1]; l++)
{
for (size_t n = 0; n < dims[0]; n++)
{
if (yshifts[i] >= 0) { yspot = l; }
else if (yshifts[i] < 0) { yspot = dims[1] - 1 - l; }
if (xshifts[i] >= 0) { xspot = n; }
else if (xshifts[i] < 0) { xspot = dims[0] - 1 - n; }
newPosition = (slice * dims[0] * dims[1]) + (yspot * dims[0]) + xspot;
currentPosition = (slice * dims[0] * dims[1]) + ((yspot + yshifts[i]) * dims[0]) + (xspot + xshifts[i]);
if ((yspot + yshifts[i]) >= 0 && (yspot + yshifts[i]) <= static_cast<int64_t>(dims[1]) - 1 && (xspot + xshifts[i]) >= 0
&& (xspot + xshifts[i]) <= static_cast<int64_t>(dims[0]) - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
p->copyTuple( static_cast<size_t>(currentPosition), static_cast<size_t>(newPosition));
}
}
if ((yspot + yshifts[i]) < 0 || (yspot + yshifts[i]) > static_cast<int64_t>(dims[1] - 1) || (xspot + xshifts[i]) < 0
|| (xspot + xshifts[i]) > static_cast<int64_t>(dims[0]) - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
EXECUTE_FUNCTION_TEMPLATE(this, initializeArrayValues, p, p, newPosition)
}
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSections::execute()
{
setErrorCondition(0);
VoxelDataContainer* m = getVoxelDataContainer();
if (NULL == m)
{
setErrorCondition(-1);
std::stringstream ss;
ss << " DataContainer was NULL";
notifyErrorMessage(ss.str(), -1);
return;
}
int64_t totalPoints = m->getTotalPoints();
size_t numgrains = m->getNumFieldTuples();
size_t numensembles = m->getNumEnsembleTuples();
dataCheck(false, totalPoints, numgrains, numensembles);
if (getErrorCondition() < 0)
{
return;
}
size_t udims[3] = {0,0,0};
m->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] = {
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
int slice;
int xspot, yspot;
DimType newPosition;
DimType currentPosition;
// unsigned int phase2;
std::vector<int> xshifts;
std::vector<int> yshifts;
xshifts.resize(dims[2],0);
yshifts.resize(dims[2],0);
find_shifts(xshifts, yshifts);
std::list<std::string> voxelArrayNames = m->getCellArrayNameList();
DimType progIncrement = dims[2]/100;
DimType prog = 1;
int progressInt = 0;
std::stringstream ss;
for (DimType i = 1; i < dims[2]; i++)
{
if (i > prog)
{
ss.str("");
progressInt = ((float)i/dims[2])*100.0;
ss << "Transferring Cell Data - " << progressInt << "% Complete";
notifyStatusMessage(ss.str());
prog = prog + progIncrement;
}
if (getCancel() == true)
{
return;
}
slice = static_cast<int>( (dims[2] - 1) - i );
for (DimType l = 0; l < dims[1]; l++)
{
for (DimType n = 0; n < dims[0]; n++)
{
if(yshifts[i] >= 0) yspot = static_cast<int>(l);
else if(yshifts[i] < 0) yspot = static_cast<int>( dims[1] - 1 - l );
if(xshifts[i] >= 0) xspot = static_cast<int>(n);
else if(xshifts[i] < 0) xspot = static_cast<int>( dims[0] - 1 - n );
newPosition = (slice * dims[0] * dims[1]) + (yspot * dims[0]) + xspot;
currentPosition = (slice * dims[0] * dims[1]) + ((yspot + yshifts[i]) * dims[0]) + (xspot + xshifts[i]);
if((yspot + yshifts[i]) >= 0 && (yspot + yshifts[i]) <= dims[1] - 1 && (xspot + xshifts[i]) >= 0
&& (xspot + xshifts[i]) <= dims[0] - 1)
{
for(std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
std::string name = *iter;
IDataArray::Pointer p = m->getCellData(*iter);
p->CopyTuple(currentPosition, newPosition);
}
}
if((yspot + yshifts[i]) < 0 || (yspot + yshifts[i]) > dims[1] - 1 || (xspot + xshifts[i]) < 0
|| (xspot + xshifts[i]) > dims[0] - 1)
{
for(std::list<std::string>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
std::string name = *iter;
IDataArray::Pointer p = m->getCellData(*iter);
p->InitializeTuple(newPosition, 0.0); }
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage("Complete");
}
int main(int argc, char *argv[])
{
int no_error=1; /* Flag set to 0 on error */
int usefile=0; /* Flag set to 1 to use input setup file */
int ncat1,ncat2; /* Number of catalog objects */
int nshift=0; /* Number of matching objects */
int another_loop=1; /* Flag set to 0 when ending a loop */
char fitsfile1[MAXC]; /* The name of the 1st FITS file to load */
char catfile1[MAXC]; /* The name of the 1st SExtractor catalog file */
char fitsfile2[MAXC]; /* The name of the 2nd FITS file to load */
char catfile2[MAXC]; /* The name of the 2nd SExtractor catalog file */
char setupfile[MAXC]; /* Name of the optional setup file */
char line[MAXC]; /* General string to read input */
Pos initshift; /* Initial shift between two images */
Pos shiftmean; /* Mean shift */
Pos shiftrms; /* RMS on shift */
Pos shiftmed; /* Median shift */
Image *image1; /* The container of the 1st FITS image array */
Image *image2; /* The container of the 2nd FITS image array */
Setup *setup1; /* Container for the 1st image display info */
Setup *setup2; /* Container for the 2nd image display info */
Secat *catdat1=NULL; /* SExtractor data for 1st catalog */
Secat *catdat2=NULL; /* SExtractor data for 2nd catalog */
Secat *shiftcat=NULL; /* Catalog of shifts between 1st and 2nd catalogs */
/*
* Check the command line
*/
if(argc < 5) {
fprintf(stderr,"\nfind_dither fitsfile1 catfile1 fitsfile2 catfile2 ");
fprintf(stderr,"(setupfile)\n\n");
return 1;
}
/*
* Get the names of the files.
*/
strcpy(fitsfile1,argv[1]);
strcpy(catfile1,argv[2]);
strcpy(fitsfile2,argv[3]);
strcpy(catfile2,argv[4]);
if(argc == 6) {
usefile = 1;
strcpy(setupfile,argv[5]);
}
else
sprintf(setupfile,"");
/*
* Read the 1st data array.
*/
if(!(image1 = new_Image(fitsfile1))) {
fprintf(stderr,"ERROR. Exiting program. Could not open %s\n\n",
fitsfile1);
return 1;
}
if(load_image_data(image1) == ERROR)
no_error = 0;
/*
* Create setup structure and fill with information used to set plotting
* parameters.
*/
if(no_error)
if(!(setup1 = fill_setup(image1,setupfile,usefile,PIXEL)))
no_error = 0;
/*
* Loop over displaying image until happy with results
*/
if(no_error) {
open_plot_window();
if(display_image(image1,setup1))
no_error = 0;
else
while(no_error && another_loop) {
switch(another_loop = setup_menu(image1,setup1)) {
case 1:
if(display_image(image1,setup1))
no_error = 0;
break;
case 0:
break;
case -1:
no_error = 0;
break;
default:
break;
}
}
}
another_loop = 1;
/*
* Read the 2nd data array.
*/
if(!(image2 = new_Image(fitsfile2))) {
fprintf(stderr,"ERROR. Exiting program. Could not open %s\n\n",
fitsfile1);
return 1;
}
if(load_image_data(image2) == ERROR)
no_error = 0;
/*
* Create setup structure and fill with information used to set plotting
* parameters.
*/
if(no_error)
if(!(setup2 = fill_setup(image2,setupfile,usefile,PIXEL)))
no_error = 0;
/*
* Loop over displaying image until happy with results
*/
if(no_error) {
open_plot_window();
if(display_image(image2,setup2))
no_error = 0;
else
while(no_error && another_loop) {
switch(another_loop = setup_menu(image2,setup2)) {
case 1:
if(display_image(image2,setup2))
no_error = 0;
break;
case 0:
break;
case -1:
no_error = 0;
break;
default:
break;
}
}
}
another_loop = 1;
/*
* Read in the first SExtractor catalog file
*/
printf("---------------------------------------------------------------\n");
if(no_error)
if(!(catdat1 = read_secat(catfile1,'#',&ncat1,6)))
no_error = 0;
/*
* Plot the catalog
*/
if(no_error) {
cpgslct(1);
printf("\nPlotting SExtractor positions for first catalog\n");
if(plot_secat(setup1,catdat1,ncat1,2,3,2.0))
no_error = 0;
}
/*
* Read in second SExtractor catalog file
*/
if(no_error)
if(!(catdat2 = read_secat(catfile2,'#',&ncat2,6)))
no_error = 0;
/*
* Plot the catalog
*/
if(no_error) {
cpgslct(2);
printf("\nPlotting SExtractor positions for second catalog\n");
if(plot_secat(setup2,catdat2,ncat2,2,3,2.0))
no_error = 0;
}
/*
* Get initial shift
*/
if(no_error) {
get_init_shift(catdat1,ncat1,catdat2,ncat2,&initshift);
}
/*
* Calculate shifts between first and second catalogs
*/
if(no_error)
if(!(shiftcat = find_shifts(catdat1,ncat1,catdat2,ncat2,initshift,
setup2,&nshift,0)))
no_error = 0;
else
printf("\nCalculated shifts between %d pairs.\n",nshift);
/*
* Get statistics on the shifts and plot results
*/
if(no_error)
plot_shifts(shiftcat,nshift);
/*
* Clean up and exit
*/
cpgend();
cpgend();
image1 = del_Image(image1);
setup1 = del_setup(setup1);
catdat1 = del_secat(catdat1);
image2 = del_Image(image2);
setup2 = del_setup(setup2);
catdat2 = del_secat(catdat2);
shiftcat = del_secat(shiftcat);
if(no_error) {
printf("\nProgram find_dither.c completed.\n\n");
return 0;
}
else {
fprintf(stderr,"\nERROR. Exiting find_dither.c\n\n");
return 1;
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void AlignSections::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer m = getDataContainerArray()->getDataContainer(getDataContainerName());
size_t udims[3] = { 0, 0, 0 };
m->getGeometryAs<ImageGeom>()->getDimensions(udims);
#if (CMP_SIZEOF_SIZE_T == 4)
typedef int32_t DimType;
#else
typedef int64_t DimType;
#endif
DimType dims[3] =
{
static_cast<DimType>(udims[0]),
static_cast<DimType>(udims[1]),
static_cast<DimType>(udims[2]),
};
DimType slice = 0;
DimType xspot = 0, yspot = 0;
DimType newPosition = 0;
DimType currentPosition = 0;
std::vector<int64_t> xshifts(dims[2], 0);
std::vector<int64_t> yshifts(dims[2], 0);
find_shifts(xshifts, yshifts);
if (getSubtractBackground())
{
/**fit x and y shifts to lines
*
* y = mx + b
*
* m = (n*sum(x_i * y_i) - sum(x_i) * sum(y_i)) / (n*sum(x_i^2)-sum(x_i)^2
*
* b = (sum(y_i)-m*sum(x_i))/n
*
*/
// same for both
double sumX = 0.0; // sum(x_i)
double sumX_2 = 0.0; // sum(x_i^2)
// x shift line
double x_sumY = 0.0; // sum(y_i)
double x_sumXY = 0.0; // sum(x_i * y_i)
// y shift line
double y_sumY = 0.0; // sum(y_i)
double y_sumXY = 0.0; // sum(x_i * y_i)
for (DimType iter = 0; iter < dims[2]; iter++)
{
slice = static_cast<DimType>( (dims[2] - 1) - iter );
sumX = static_cast<double>(sumX + iter);
sumX_2 = static_cast<double>(sumX_2 + iter * iter);
x_sumY = static_cast<double>(x_sumY + xshifts[iter]);
x_sumXY = static_cast<double>(x_sumXY + iter * xshifts[iter]);
y_sumY = static_cast<double>(y_sumY + yshifts[iter]);
y_sumXY = static_cast<double>(y_sumXY + iter * yshifts[iter]);
}
double mx = static_cast<double>((dims[2] * x_sumXY - x_sumXY) / (dims[2] * sumX_2 - sumX));
double my = static_cast<double>((dims[2] * y_sumXY - y_sumXY) / (dims[2] * sumX_2 - sumX));
// adjust shifts so that fit line has 0 slope (~ends of the sample are fixed)
for (DimType iter = 1; iter < dims[2]; iter++)
{
slice = (dims[2] - 1) - iter;
xshifts[iter] = static_cast<int64_t>(xshifts[iter] - iter * mx);
yshifts[iter] = static_cast<int64_t>(yshifts[iter] - iter * my);
}
}
QList<QString> voxelArrayNames = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArrayNames();
DimType progIncrement = dims[2] / 100;
DimType prog = 1;
DimType progressInt = 0;
for (DimType i = 1; i < dims[2]; i++)
{
if (i > prog)
{
progressInt = ((float)i / dims[2]) * 100.0f;
QString ss = QObject::tr("Transferring Cell Data || %1% Complete").arg(progressInt);
notifyStatusMessage(getMessagePrefix(), getHumanLabel(), ss);
prog = prog + progIncrement;
}
if (getCancel() == true)
{
return;
}
slice = (dims[2] - 1) - i;
for (DimType l = 0; l < dims[1]; l++)
{
for (DimType n = 0; n < dims[0]; n++)
{
if (yshifts[i] >= 0) { yspot = l; }
else if (yshifts[i] < 0) { yspot = dims[1] - 1 - l; }
if (xshifts[i] >= 0) { xspot = n; }
else if (xshifts[i] < 0) { xspot = dims[0] - 1 - n; }
newPosition = (slice * dims[0] * dims[1]) + (yspot * dims[0]) + xspot;
currentPosition = (slice * dims[0] * dims[1]) + ((yspot + yshifts[i]) * dims[0]) + (xspot + xshifts[i]);
if ((yspot + yshifts[i]) >= 0 && (yspot + yshifts[i]) <= dims[1] - 1 && (xspot + xshifts[i]) >= 0
&& (xspot + xshifts[i]) <= dims[0] - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
p->copyTuple(currentPosition, newPosition);
}
}
if ((yspot + yshifts[i]) < 0 || (yspot + yshifts[i]) > dims[1] - 1 || (xspot + xshifts[i]) < 0
|| (xspot + xshifts[i]) > dims[0] - 1)
{
for (QList<QString>::iterator iter = voxelArrayNames.begin(); iter != voxelArrayNames.end(); ++iter)
{
IDataArray::Pointer p = m->getAttributeMatrix(getCellAttributeMatrixName())->getAttributeArray(*iter);
p->initializeTuple(newPosition, 0);
}
}
}
}
}
// If there is an error set this to something negative and also set a message
notifyStatusMessage(getHumanLabel(), "Complete");
}
