void IsisMain() {
// Get user interface
UserInterface &ui = Application::GetUserInterface();
// Open the shift definitions file
Pvl shiftdef;
if (ui.WasEntered("SHIFTDEF")) {
shiftdef.Read(ui.GetFilename("SHIFTDEF"));
}
else {
shiftdef.AddObject(PvlObject("Hiccdstitch"));
}
PvlObject &stitch = shiftdef.FindObject("Hiccdstitch", Pvl::Traverse);
// Open the first cube. It will be matched to the second input cube.
HiJitCube trans;
CubeAttributeInput &attTrans = ui.GetInputAttribute("FROM");
vector<string> bandTrans = attTrans.Bands();
trans.SetVirtualBands(bandTrans);
trans.OpenCube(ui.GetFilename("FROM"), stitch);
// Open the second cube, it is held in place. We will be matching the
// first to this one by attempting to compute a sample/line translation
HiJitCube match;
CubeAttributeInput &attMatch = ui.GetInputAttribute("MATCH");
vector<string> bandMatch = attMatch.Bands();
match.SetVirtualBands(bandMatch);
match.OpenCube(ui.GetFilename("MATCH"), stitch);
// Ensure only one band
if ((trans.Bands() != 1) || (match.Bands() != 1)) {
string msg = "Input Cubes must have only one band!";
throw Isis::iException::Message(Isis::iException::User,msg,_FILEINFO_);
}
// Now test compatability (basically summing)
trans.Compatable(match);
// Determine intersection
if (!trans.intersects(match)) {
string msg = "Input Cubes do not overlap!";
throw Isis::iException::Message(Isis::iException::User,msg,_FILEINFO_);
}
// Get overlapping regions of each cube
HiJitCube::Corners fcorns, mcorns;
trans.overlap(match, fcorns);
match.overlap(trans, mcorns);
#if defined(ISIS_DEBUG)
cout << "FROM Poly: " << trans.PolyToString() << std::endl;
cout << "MATCH Poly: " << match.PolyToString() << std::endl;
cout << "From Overlap: (" << fcorns.topLeft.sample << ","
<< fcorns.topLeft.line << "), ("
<< fcorns.lowerRight.sample << ","
<< fcorns.lowerRight.line << ")\n" ;
cout << "Match Overlap: (" << mcorns.topLeft.sample << ","
<< mcorns.topLeft.line << "), ("
<< mcorns.lowerRight.sample << ","
<< mcorns.lowerRight.line << ")\n" ;
#endif
// We need to get a user definition of how to auto correlate around each
// of the grid points.
Pvl regdef;
Filename regFile(ui.GetFilename("REGDEF"));
regdef.Read(regFile.Expanded());
AutoReg *ar = AutoRegFactory::Create(regdef);
double flines(fcorns.lowerRight.line - fcorns.topLeft.line + 1.0);
double fsamps(fcorns.lowerRight.sample - fcorns.topLeft.sample + 1.0);
// We want to create a grid of control points that is N rows by M columns.
// Get row and column variables, if not entered, default to 1% of the input
// image size
int rows(1), cols(1);
if (ui.WasEntered("ROWS")) {
rows = ui.GetInteger("ROWS");
}
else {
rows = (int)(((flines - 1.0) / ar->SearchChip()->Lines()) + 1);
}
cols = ui.GetInteger("COLUMNS");
if (cols == 0) {
cols = (int)(((fsamps - 1.0) / ar->SearchChip()->Samples()) + 1);
}
// Calculate spacing for the grid of points
double lSpacing = floor(flines / rows);
double sSpacing = floor(fsamps / cols);
#if defined(ISIS_DEBUG)
cout << "# Samples in Overlap: " << fsamps << endl;
cout << "# Lines in Overlap : " << flines << endl;
cout << "# Rows: " << rows << endl;
cout << "# Columns: " << cols << endl;
cout << "Line Spacing: " << lSpacing << endl;
cout << "Sample Spacing: " << sSpacing << endl;
#endif
// Display the progress...10% 20% etc.
Progress prog;
prog.SetMaximumSteps(rows * cols);
prog.CheckStatus();
// Initialize control point network
ControlNet cn;
cn.SetType(ControlNet::ImageToImage);
cn.SetUserName(Application::UserName());
cn.SetCreatedDate(iTime::CurrentLocalTime());
// Get serial numbers for input cubes
string transSN = SerialNumber::Compose(trans, true);
string matchSN = SerialNumber::Compose(match, true);
cn.SetTarget(transSN);
cn.SetDescription("Records s/c jitter between two adjacent HiRISE images");
// Set up results parameter saves
JitterParms jparms;
jparms.fromCorns = fcorns;
jparms.fromJit = trans.GetInfo();
jparms.matchCorns = mcorns;
jparms.matchJit = match.GetInfo();
jparms.regFile = regFile.Expanded();
jparms.cols = cols;
jparms.rows = rows;
jparms.lSpacing = lSpacing;
jparms.sSpacing = sSpacing;
jparms.nSuspects = 0;
// Loop through grid of points and get statistics to compute
// translation values
RegList reglist;
double fline0(fcorns.topLeft.line-1.0), fsamp0(fcorns.topLeft.sample-1.0);
double mline0(mcorns.topLeft.line-1.0), msamp0(mcorns.topLeft.sample-1.0);
for (int r=0; r<rows; r++) {
int line = (int)(lSpacing / 2.0 + lSpacing * r + 0.5);
for (int c=0; c<cols; c++) {
int samp = (int)(sSpacing / 2.0 + sSpacing * c + 0.5);
ar->PatternChip()->TackCube(msamp0+samp, mline0+line);
ar->PatternChip()->Load(match);
ar->SearchChip()->TackCube(fsamp0+samp, fline0+line);
ar->SearchChip()->Load(trans);
// Set up ControlMeasure for cube to translate
ControlMeasure cmTrans;
cmTrans.SetCubeSerialNumber(transSN);
cmTrans.SetCoordinate(msamp0+samp, mline0+line,
ControlMeasure::Unmeasured);
cmTrans.SetChooserName("hijitreg");
cmTrans.SetReference(false);
// Set up ControlMeasure for the pattern/Match cube
ControlMeasure cmMatch;
cmMatch.SetCubeSerialNumber(matchSN);
cmMatch.SetCoordinate(fsamp0+samp, fline0+line,
ControlMeasure::Automatic);
cmMatch.SetChooserName("hijitreg");
cmMatch.SetReference(true);
// Match found
if (ar->Register()==AutoReg::Success) {
RegData reg;
reg.fLine = fline0 + line;
reg.fSamp = fsamp0 + samp;
reg.fLTime = trans.getLineTime(reg.fLine);
reg.mLine = mline0 + line;
reg.mSamp = msamp0 + samp;
reg.mLTime = match.getLineTime(reg.mLine);
reg.regLine = ar->CubeLine();
reg.regSamp = ar->CubeSample();
reg.regCorr = ar->GoodnessOfFit();
if (fabs(reg.regCorr) > 1.0) jparms.nSuspects++;
double sDiff = reg.fSamp - reg.regSamp;
double lDiff = reg.fLine - reg.regLine;
jparms.sStats.AddData(&sDiff,(unsigned int)1);
jparms.lStats.AddData(&lDiff,(unsigned int)1);
// Record the translation in the control point
cmTrans.SetCoordinate(ar->CubeSample(), ar->CubeLine(),
ControlMeasure::Automatic);
cmTrans.SetError(sDiff, lDiff);
cmTrans.SetGoodnessOfFit(ar->GoodnessOfFit());
// Reread the chip location centering the offset and compute
// linear regression statistics
try {
Chip &pchip(*ar->PatternChip());
Chip fchip(pchip.Samples(), pchip.Lines());
fchip.TackCube(ar->CubeSample(), ar->CubeLine());
fchip.Load(trans);
// Writes correlated chips to files for visual inspection
#if defined(ISIS_DEBUG)
ostringstream tstr;
tstr << "R" << r << "C" << c << "_chip.cub";
string fcname("from" + tstr.str());
string mcname("match" + tstr.str());
pchip.Write(mcname);
fchip.Write(fcname);
#endif
MultivariateStatistics mstats;
for (int line = 1 ; line <= fchip.Lines() ; line++) {
for(int sample = 1; sample < fchip.Samples(); sample++) {
double fchipValue = fchip.GetValue(sample,line);
double pchipValue = pchip.GetValue(sample,line);
mstats.AddData(&fchipValue, &pchipValue, 1);
}
}
// Get regression and correlation values
mstats.LinearRegression(reg.B0, reg.B1);
reg.Bcorr = mstats.Correlation();
if (IsSpecial(reg.B0)) throw 1;
if (IsSpecial(reg.B1)) throw 2;
if (IsSpecial(reg.Bcorr)) throw 3;
}
catch (...) {
// If fails, flag this condition
reg.B0 = 0.0;
reg.B1= 0.0;
reg.Bcorr = 0.0;
}
reglist.push_back(reg);
}
// Add the measures to a control point
string str = "Row " + iString(r) + " Column " + iString(c);
ControlPoint cp(str);
cp.SetType(ControlPoint::Tie);
cp.Add(cmTrans);
cp.Add(cmMatch);
if (!cmTrans.IsMeasured()) cp.SetIgnore(true);
cn.Add(cp);
prog.CheckStatus();
}
}
// If flatfile was entered, create the flatfile
// The flatfile is comma seperated and can be imported into an excel
// spreadsheet
if (ui.WasEntered("FLATFILE")) {
string fFile = ui.GetFilename("FLATFILE");
ofstream os;
string fFileExpanded = Filename(fFile).Expanded();
os.open(fFileExpanded.c_str(),ios::out);
dumpResults(os, reglist, jparms, *ar);
}
// If a cnet file was entered, write the ControlNet pvl to the file
if (ui.WasEntered("CNETFILE")) {
cn.Write(ui.GetFilename("CNETFILE"));
}
// Don't need the cubes opened anymore
trans.Close();
match.Close();
// Write translation to log
PvlGroup results("AverageTranslation");
if (jparms.sStats.ValidPixels() > 0) {
double sTrans = (int)(jparms.sStats.Average() * 100.0) / 100.0;
double lTrans = (int)(jparms.lStats.Average() * 100.0) / 100.0;
results += PvlKeyword ("Sample",sTrans);
results += PvlKeyword ("Line",lTrans);
results += PvlKeyword ("NSuspects",jparms.nSuspects);
}
else {
results += PvlKeyword ("Sample","NULL");
results += PvlKeyword ("Line","NULL");
}
Application::Log(results);
// add the auto registration information to print.prt
PvlGroup autoRegTemplate = ar->RegTemplate();
Application::Log(autoRegTemplate);
return;
}
void IsisMain() {
// Get user interface
UserInterface &ui = Application::GetUserInterface();
bool register_ignored = ui.GetBoolean("REGISTERIGNOREDONLY");
// Open the files list in a SerialNumberList for
// reference by SerialNumber
SerialNumberList files(ui.GetFilename("FILES"));
// Create a ControlNet from the input file
ControlNet inNet(ui.GetFilename("CNET"));
// Create an AutoReg from the template file
Pvl pvl(ui.GetFilename("TEMPLATE"));
AutoReg *ar = AutoRegFactory::Create(pvl);
// Create the output ControlNet
ControlNet outNet;
outNet.SetType(inNet.Type());
outNet.SetUserName(Application::UserName());
outNet.SetDescription(inNet.Description());
outNet.SetCreatedDate(iTime::CurrentLocalTime());
outNet.SetTarget(inNet.Target());
outNet.SetNetworkId(inNet.NetworkId());
Progress progress;
progress.SetMaximumSteps(inNet.Size());
progress.CheckStatus();
int ignored=0, unmeasured=0, registered=0, unregistered=0, validated=0;
CubeManager cubeMgr;
cubeMgr.SetNumOpenCubes(50);
// Register the points and create a new
// ControlNet containing the refined measurements
for (int i=0; i<inNet.Size(); i++) {
ControlPoint &inPoint = inNet[i];
ControlPoint outPoint;
outPoint.SetType(inPoint.Type());
outPoint.SetId(inPoint.Id());
outPoint.SetUniversalGround(inPoint.UniversalLatitude(), inPoint.UniversalLongitude(), inPoint.Radius());
outPoint.SetHeld(inPoint.Held());
outPoint.SetIgnore(inPoint.Ignore());
// CHECK TO SEE IF THE CONTROL POINT SHOULD BE REGISTERED
// "Ignore" point and we are not registering ignored
if (inPoint.Ignore() && !register_ignored){
ignored++;
// add "Ignored" to network only if indicated
if (ui.GetBoolean("OUTPUTIGNORED")) {
// only include appropriate control measures
for (int j = 0; j < inPoint.Size(); j++) {
if (inPoint[j].IsMeasured()){
outPoint.Add(inPoint[j]);
}
else{
unmeasured++;
if (ui.GetBoolean("OUTPUTUNMEASURED")){
outPoint.Add(inPoint[j]);
}
}
}
// only add this point if OUTPUTIGNORED
outNet.Add(outPoint);
}
// go to next control point
continue;
}
// Not "Ignore" point (i.e. "valid") and we are only registering "Ignored"
else if (!inPoint.Ignore() && register_ignored) {
// add all "valid" points to network
// only include appropriate control measures
for (int j = 0; j < inPoint.Size(); j++) {
if (inPoint[j].IsMeasured()){
outPoint.Add(inPoint[j]);
}
else{
unmeasured++;
if (ui.GetBoolean("OUTPUTUNMEASURED")) {
outPoint.Add(inPoint[j]);
}
}
}
// add this point since it is not ignored
outNet.Add(outPoint);
// go to next control point
continue;
}
// "Ignore" point or "valid" point to be registered
else { // if ( (inPoint.Ignore() && register_ignored) || (!inPoint.Ignore() && !register_ignored ) ) {
if (inPoint.Ignore()) { outPoint.SetIgnore(false); }
ControlMeasure &patternCM = inPoint[inPoint.ReferenceIndex()];
Cube &patternCube = *cubeMgr.OpenCube(files.Filename(patternCM.CubeSerialNumber()));
ar->PatternChip()->TackCube(patternCM.Sample(), patternCM.Line());
ar->PatternChip()->Load(patternCube);
if (patternCM.IsValidated()) validated++;
if (!patternCM.IsMeasured()) continue;
if(!patternCM.IsReference()) {
patternCM.SetReference(true);
patternCM.SetChooserName("Application pointreg");
patternCM.SetDateTime();
}
outPoint.Add(patternCM);
// reset goodMeasureCount for this point before looping measures
int goodMeasureCount = 0;
// Register all the unvalidated measurements
for (int j = 0; j < inPoint.Size(); j++) {
// don't register the reference, go to next measure
if (j == inPoint.ReferenceIndex()){
if (!inPoint[j].Ignore()) goodMeasureCount++;
continue;
}
// if the measurement is valid, keep it as is and go to next measure
if (inPoint[j].IsValidated()) {
validated++;
outPoint.Add(inPoint[j]);
if (!inPoint[j].Ignore()) goodMeasureCount++;
continue;
}
// if the point is unmeasured, add to output only if necessary and go to next measure
if (!inPoint[j].IsMeasured()) {
unmeasured++;
if (ui.GetBoolean("OUTPUTUNMEASURED")) {
outPoint.Add(inPoint[j]);
}
continue;
}
ControlMeasure searchCM = inPoint[j];
// refresh pattern cube pointer to ensure it stays valid
Cube &patternCube = *cubeMgr.OpenCube(files.Filename(patternCM.CubeSerialNumber()));
Cube &searchCube = *cubeMgr.OpenCube(files.Filename(searchCM.CubeSerialNumber()));
ar->SearchChip()->TackCube(searchCM.Sample(), searchCM.Line());
try {
ar->SearchChip()->Load(searchCube,*(ar->PatternChip()),patternCube);
// If the measurements were correctly registered
// Write them to the new ControlNet
AutoReg::RegisterStatus res = ar->Register();
double score1, score2;
ar->ZScores(score1, score2);
searchCM.SetZScores(score1, score2);
if(res == AutoReg::Success) {
registered++;
searchCM.SetType(ControlMeasure::Automatic);
searchCM.SetError(searchCM.Sample() - ar->CubeSample(), searchCM.Line() - ar->CubeLine());
searchCM.SetCoordinate(ar->CubeSample(),ar->CubeLine());
searchCM.SetGoodnessOfFit(ar->GoodnessOfFit());
searchCM.SetChooserName("Application pointreg");
searchCM.SetDateTime();
searchCM.SetIgnore(false);
outPoint.Add(searchCM);
goodMeasureCount++;
}
// Else use the original marked as "Estimated"
else {
unregistered++;
searchCM.SetType(ControlMeasure::Estimated);
if(res == AutoReg::FitChipToleranceNotMet) {
searchCM.SetError(inPoint[j].Sample() - ar->CubeSample(), inPoint[j].Line() - ar->CubeLine());
searchCM.SetGoodnessOfFit(ar->GoodnessOfFit());
}
searchCM.SetChooserName("Application pointreg");
searchCM.SetDateTime();
searchCM.SetIgnore(true);
outPoint.Add(searchCM);
}
} catch (iException &e) {
e.Clear();
unregistered++;
searchCM.SetType(ControlMeasure::Estimated);
searchCM.SetChooserName("Application pointreg");
searchCM.SetDateTime();
searchCM.SetIgnore(true);
outPoint.Add(searchCM);
}
}
// Jeff Anderson put in this test (Dec 2, 2008) to allow for control
// points to be good so long as at least two measure could be
// registered. When a measure can't be registered to the reference then
// that measure is set to be ignored where in the past the whole point
// was ignored
if (goodMeasureCount < 2) {
if (!outPoint.Held() && outPoint.Type() != ControlPoint::Ground) {
outPoint.SetIgnore(true);
}
}
// Otherwise, ignore=false. This is already set at the beginning of the registration process
// Check to see if the control point has now been assigned
// to "ignore". If not, add it to the network. If so, only
// add it to the output if the OUTPUTIGNORED parameter is selected
// 2008-11-14 Jeannie Walldren
if (!outPoint.Ignore()) {
outNet.Add(outPoint);
}
else{
ignored++;
if (ui.GetBoolean("OUTPUTIGNORED")) outNet.Add(outPoint);
}
}
progress.CheckStatus();
}
// If flatfile was entered, create the flatfile
// The flatfile is comma seperated and can be imported into an excel
// spreadsheet
if (ui.WasEntered("FLATFILE")) {
string fFile = Filename(ui.GetFilename("FLATFILE")).Expanded();
ofstream os;
os.open(fFile.c_str(),ios::out);
os << "PointId,OriginalMeasurementSample,OriginalMeasurementLine," <<
"RegisteredMeasurementSample,RegisteredMeasurementLine,SampleDifference," <<
"LineDifference,ZScoreMin,ZScoreMax,GoodnessOfFit" << endl;
os << NULL8 << endl;
for (int i=0; i<outNet.Size(); i++) {
// get point from output control net and its
// corresponding point from input control net
ControlPoint outPoint = outNet[i];
ControlPoint *inPoint = inNet.Find(outPoint.Id());
if (outPoint.Ignore()) continue;
for (int i = 0; i<outPoint.Size();i++) {
// get measure and find its corresponding measure from input net
ControlMeasure cmTrans = outPoint[i];
ControlMeasure cmOrig = (*inPoint)[cmTrans.CubeSerialNumber()];
double inSamp = cmOrig.Sample();
double inLine = cmOrig.Line();
double outSamp = cmTrans.Sample();
double outLine = cmTrans.Line();
double sampErr = cmTrans.SampleError();
double lineErr = cmTrans.LineError();
double zScoreMin = cmTrans.GetZScoreMin();
if (fabs(zScoreMin) <= DBL_EPSILON || zScoreMin == NULL8) zScoreMin = 0;
double zScoreMax = cmTrans.GetZScoreMax();
if (fabs(zScoreMax) <= DBL_EPSILON || zScoreMax == NULL8) zScoreMax = 0;
double goodnessOfFit = cmTrans.GoodnessOfFit();
if (fabs(goodnessOfFit) <= DBL_EPSILON || goodnessOfFit == NULL8) goodnessOfFit = 0;
string pointId = outPoint.Id();
os << pointId << "," << inSamp << ","
<< inLine << "," << outSamp << ","
<< outLine << "," << sampErr << ","
<< lineErr << "," << zScoreMin << ","
<< zScoreMax << "," << goodnessOfFit << endl;
}
}
}
PvlGroup pLog("Points");
pLog+=PvlKeyword("Ignored", ignored);
Application::Log(pLog);
PvlGroup mLog("Measures");
mLog+=PvlKeyword("Validated", validated);
mLog+=PvlKeyword("Registered", registered);
mLog+=PvlKeyword("Unregistered", unregistered);
mLog+=PvlKeyword("Unmeasured", unmeasured);
Application::Log(mLog);
// Log Registration Statistics
Pvl arPvl = ar->RegistrationStatistics();
for(int i = 0; i < arPvl.Groups(); i++) {
Application::Log(arPvl.Group(i));
}
// add the auto registration information to print.prt
PvlGroup autoRegTemplate = ar->RegTemplate();
Application::Log(autoRegTemplate);
outNet.Write(ui.GetFilename("TO"));
delete ar;
}