void IsisMain() {
//Set up ProcessBySpectra
ProcessBySpectra p;
//Obtain input cube, get bands dimension from input cube and user input number bands
Cube *icube = p.SetInputCube("FROM");
int cubeBands = icube->Bands();
UserInterface &ui = Application::GetUserInterface();
bands = ui.GetInteger("BANDS");
//Check for cases of too many bands
if (bands >= (2 * cubeBands)) {
iString msg = "Parameter bands [" + iString(bands) + "] exceeds maximum allowable size "
+ "of [" + iString((cubeBands * 2) - 1) + "] for cube [" + icube->Filename() + "]";
throw iException::Message(iException::User,msg, _FILEINFO_);
}
//Set the Boxcar Parameters
low = -DBL_MAX;
high = DBL_MAX;
if (ui.WasEntered("LOW")) {
low = ui.GetDouble("LOW");
}
if (ui.WasEntered("HIGH")) {
high = ui.GetDouble("HIGH");
}
//Obtain output cube
p.SetOutputCube("TO");
//Start the filter method
p.StartProcess(Filter);
p.EndProcess();
}
void IsisMain(){
const std::string hical_program = "hicalbeta";
const std::string hical_version = "3.5";
const std::string hical_revision = "$Revision: 1.14 $";
const std::string hical_runtime = Application::DateTime();
UserInterface &ui = Application::GetUserInterface();
string procStep("prepping phase");
try {
// The output from the last processing is the input into subsequent processing
ProcessByLine p;
Cube *hifrom = p.SetInputCube("FROM");
int nsamps = hifrom->Samples();
int nlines = hifrom->Lines();
// Initialize the configuration file
string conf(ui.GetAsString("CONF"));
HiCalConf hiconf(*(hifrom->Label()), conf);
DbProfile hiprof = hiconf.getMatrixProfile();
// Check for label propagation and set the output cube
Cube *ocube = p.SetOutputCube("TO");
if ( !IsTrueValue(hiprof,"PropagateTables", "TRUE") ) {
RemoveHiBlobs(*(ocube->Label()));
}
// Set specified profile if entered by user
if (ui.WasEntered("PROFILE")) {
hiconf.selectProfile(ui.GetAsString("PROFILE"));
}
// Add OPATH parameter to profiles
if (ui.WasEntered("OPATH")) {
hiconf.add("OPATH",ui.GetAsString("OPATH"));
}
else {
// Set default to output directory
hiconf.add("OPATH", Filename(ocube->Filename()).Path());
}
// Do I/F output DN conversions
string units = ui.GetString("UNITS");
// Allocate the calibration list
calVars = new MatrixList;
// Set up access to HiRISE ancillary data (tables, blobs) here. Note it they
// are gone, this will error out. See PropagateTables in conf file.
HiCalData caldata(*hifrom);
////////////////////////////////////////////////////////////////////////////
// FixGaps (Z_f) Get buffer pixels and compute coefficients for equation
// y = a[0] + a[1]*x + a[2] * exp(a[3] * x)
// where y is the average of the buffer pixel region,
// and x is the time at each line in electrons/sec/pixel
procStep = "Zf module";
hiconf.selectProfile("Zf");
hiprof = hiconf.getMatrixProfile();
HiHistory ZfHist;
ZfHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
DriftBuffer driftB(caldata, hiconf);
calVars->add("Zf", driftB.ref());
ZfHist = driftB.History();
if ( hiprof.exists("DumpModuleFile") ) {
driftB.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
// NOT RECOMMENDED! This is required for the next step!
// SURELY must be skipped with Z_d step as well!
calVars->add("Zf", HiVector(nlines, 0.0));
ZfHist.add("Debug::SkipModule invoked!");
}
/////////////////////////////////////////////////////////////////////
// DriftCorrect (Z_d)
// Now compute the equation of fit
//
procStep = "Zd module";
HiHistory ZdHist;
hiconf.selectProfile("Zd");
hiprof = hiconf.getMatrixProfile();
ZdHist.add("Profile["+ hiprof.Name()+"]");
if (!SkipModule(hiconf.getMatrixProfile("Zd")) ) {
DriftCorrect driftC(hiconf);
calVars->add("Zd", driftC.Normalize(driftC.Solve(calVars->get("Zf"))));
ZdHist = driftC.History();
if ( hiprof.exists("DumpModuleFile") ) {
driftC.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zd", HiVector(nlines, 0.0));
ZdHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// ZeroCorrect (Z_z) Get reverse clock
procStep = "Zz module";
hiconf.selectProfile("Zz");
hiprof = hiconf.getMatrixProfile();
HiHistory ZzHist;
ZzHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
OffsetCorrect zoff(caldata, hiconf);
calVars->add("Zz", zoff.ref());
ZzHist = zoff.History();
if ( hiprof.exists("DumpModuleFile") ) {
zoff.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zz", HiVector(nsamps, 0.0));
ZzHist.add("Debug::SkipModule invoked!");
}
/////////////////////////////////////////////////////////////////
// DarkSubtract (Z_b) Remove dark current
//
procStep = "Zb module";
hiconf.selectProfile("Zb");
hiprof = hiconf.getMatrixProfile();
HiHistory ZbHist;
ZbHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
DarkSubtractComp dark(hiconf);
calVars->add("Zb", dark.ref());
ZbHist = dark.History();
if ( hiprof.exists("DumpModuleFile") ) {
dark.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zb", HiVector(nsamps, 0.0));
ZbHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainVLineCorrect (Z_g) Correct for gain-based drift
//
procStep = "Zg module";
hiconf.selectProfile("Zg");
hiprof = hiconf.getMatrixProfile();
HiHistory ZgHist;
ZgHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainVLineComp gainV(hiconf);
calVars->add("Zg", gainV.ref());
ZgHist = gainV.History();
if ( hiprof.exists("DumpModuleFile") ) {
gainV.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zg", HiVector(nlines, 1.0));
ZgHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainCorrect (Z_gg) Correct for gain with the G matrix
procStep = "Zgg module";
hiconf.selectProfile("Zgg");
hiprof = hiconf.getMatrixProfile();
HiHistory ZggHist;
ZggHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
double bin = ToDouble(hiprof("Summing"));
double tdi = ToDouble(hiprof("Tdi"));
double factor = 128.0 / tdi / (bin*bin);
HiVector zgg = hiconf.getMatrix("G", hiprof);
for ( int i = 0 ; i < zgg.dim() ; i++ ) { zgg[i] *= factor; }
calVars->add("Zgg", zgg);;
ZggHist.add("LoadMatrix(G[" + hiconf.getMatrixSource("G",hiprof) +
"],Band[" + ToString(hiconf.getMatrixBand(hiprof)) +
"],Factor[" + ToString(factor) + "])");
if ( hiprof.exists("DumpModuleFile") ) {
Component zg("GMatrix", ZggHist);
zg.Process(zgg);
zg.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zgg", HiVector(nsamps, 1.0));
ZggHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// FlatField (Z_a) Flat field correction with A matrix
procStep = "Za module";
hiconf.selectProfile("Za");
hiprof = hiconf.getMatrixProfile();
HiHistory ZaHist;
ZaHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
FlatFieldComp flat(hiconf);
calVars->add("Za", flat.ref());
ZaHist = flat.History();
if ( hiprof.exists("DumpModuleFile") ) {
flat.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Za", HiVector(nsamps, 1.0));
ZaHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// FlatField (Z_t) Temperature-dependant gain correction
procStep = "Zt module";
hiconf.selectProfile("Zt");
hiprof = hiconf.getMatrixProfile();
HiHistory ZtHist;
ZtHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
TempGainCorrect tcorr(hiconf);
calVars->add("Zt", tcorr.ref());
ZtHist = tcorr.History();
if ( hiprof.exists("DumpModuleFile") ) {
tcorr.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add("Zt", HiVector(nsamps, 1.0));
ZtHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// I/FCorrect (Z_iof) Conversion to I/F
//
procStep = "Ziof module";
hiconf.selectProfile("Ziof");
hiprof = hiconf.getMatrixProfile();
HiHistory ZiofHist;
ZiofHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
double sed = ToDouble(hiprof("ScanExposureDuration")); // units = us
if ( IsEqual(units, "IOF") ) {
// Add solar I/F correction parameters
double au = hiconf.sunDistanceAU();
ZiofHist.add("SunDist[" + ToString(au) + " (AU)]");
double suncorr = 1.5 / au;
suncorr *= suncorr;
double zbin = ToDouble(hiprof("ZiofBinFactor"));
ZiofHist.add("ZiofBinFactor[" + ToString(zbin) + "]");
double zgain = ToDouble(hiprof("FilterGainCorrection"));
ZiofHist.add("FilterGainCorrection[" + ToString(zgain) + "]");
ZiofHist.add("ScanExposureDuration[" + ToString(sed) + "]");
double ziof = (zbin * zgain) * (sed * 1.0e-6) * suncorr;
calVars->add("Ziof", HiVector(1, ziof));
ZiofHist.add("I/F_Factor[" + ToString(ziof) + "]");
ZiofHist.add("Units[I/F Reflectance]");
}
else if ( IsEqual(units, "DN/US") ) {
// Ziof is a divisor in calibration equation
double ziof = sed;
calVars->add("Ziof", HiVector(1, ziof));
ZiofHist.add("ScanExposureDuration[" + ToString(sed) + "]");
ZiofHist.add("DN/US_Factor[" + ToString(ziof) + "]");
ZiofHist.add("Units[DNs/microsecond]");
}
else {
// Units are already in DN
double ziof = 1.0;
calVars->add("Ziof", HiVector(1, ziof));
ZiofHist.add("DN_Factor[" + ToString(ziof) + "]");
ZiofHist.add("Units[DN]");
}
}
else {
calVars->add("Ziof", HiVector(1,1.0));
ZiofHist.add("Debug::SkipModule invoked!");
ZiofHist.add("Units[Unknown]");
}
// Reset the profile selection to default
hiconf.selectProfile();
//----------------------------------------------------------------------
//
/////////////////////////////////////////////////////////////////////////
// Call the processing function
procStep = "calibration phase";
p.StartProcess(calibrate);
// Get the default profile for logging purposes
hiprof = hiconf.getMatrixProfile();
const std::string conf_file = hiconf.filepath(conf);
// Quitely dumps parameter history to alternative format file. This
// is completely controlled by the configuration file
if ( hiprof.exists("DumpHistoryFile") ) {
procStep = "logging/reporting phase";
Filename hdump(hiconf.getMatrixSource("DumpHistoryFile",hiprof));
string hdumpFile = hdump.Expanded();
ofstream ofile(hdumpFile.c_str(), ios::out);
if (!ofile) {
string mess = "Unable to open/create history dump file " +
hdump.Expanded();
iException::Message(iException::User, mess, _FILEINFO_).Report();
}
else {
ofile << "Program: " << hical_program << endl;
ofile << "RunTime: " << hical_runtime << endl;
ofile << "Version: " << hical_version << endl;
ofile << "Revision: " << hical_revision << endl << endl;
ofile << "FROM: " << hifrom->Filename() << endl;
ofile << "TO: " << ocube->Filename() << endl;
ofile << "CONF: " << conf_file << endl << endl;
ofile << "/* " << hical_program << " application equation */" << endl
<< "/* hdn = (idn - Zd(Zf) - Zz - Zb) */"
<< endl << "/* odn = hdn / Zg * Zgg * Za * Zt / Ziof */"
<< endl << endl;
ofile << "****** PARAMETER GENERATION HISTORY *******" << endl;
ofile << "\nZf = " << ZfHist << endl;
ofile << "\nZd = " << ZdHist << endl;
ofile << "\nZz = " << ZzHist << endl;
ofile << "\nZb = " << ZbHist << endl;
ofile << "\nZg = " << ZgHist << endl;
ofile << "\nZgg = " << ZggHist << endl;
ofile << "\nZa = " << ZaHist << endl;
ofile << "\nZt = " << ZtHist << endl;
ofile << "\nZiof = " << ZiofHist << endl;
ofile.close();
}
}
// Ensure the RadiometricCalibration group is out there
const std::string rcalGroup("RadiometricCalibration");
if (!ocube->HasGroup(rcalGroup)) {
PvlGroup temp(rcalGroup);
ocube->PutGroup(temp);
}
PvlGroup &rcal = ocube->GetGroup(rcalGroup);
rcal += PvlKeyword("Program", hical_program);
rcal += PvlKeyword("RunTime", hical_runtime);
rcal += PvlKeyword("Version",hical_version);
rcal += PvlKeyword("Revision",hical_revision);
PvlKeyword key("Conf", conf_file);
key.AddCommentWrapped("/* " + hical_program + " application equation */");
key.AddComment("/* hdn = (idn - Zd(Zf) - Zz - Zb) */");
key.AddComment("/* odn = hdn / Zg * Zgg * Za * Zt / Ziof */");
rcal += key;
// Record parameter generation history. Controllable in configuration
// file. Note this is optional because of a BUG!! in the ISIS label
// writer as this application was initially developed
if ( IsEqual(ConfKey(hiprof,"LogParameterHistory",string("TRUE")),"TRUE")) {
rcal += ZfHist.makekey("Zf");
rcal += ZdHist.makekey("Zd");
rcal += ZzHist.makekey("Zz");
rcal += ZbHist.makekey("Zb");
rcal += ZgHist.makekey("Zg");
rcal += ZggHist.makekey("Zgg");
rcal += ZaHist.makekey("Za");
rcal += ZiofHist.makekey("Ziof");
}
p.EndProcess();
}
catch (iException &ie) {
delete calVars;
calVars = 0;
string mess = "Failed in " + procStep;
ie.Message(iException::User, mess.c_str(), _FILEINFO_);
throw;
}
// Clean up parameters
delete calVars;
calVars = 0;
}
int main () {
Isis::Preference::Preferences(true);
/**
* @brief Test ImagePolygon object for accuracy and correct behavior.
*
* @author 2005-11-22 Tracie Sucharski
*
* @history 2007-01-19 Tracie Sucharski, Removed ToGround method (for now)
* because of round off problems going back and forth between
* lat/lon,line/samp.
* @history 2007-01-31 Tracie Sucharski, Added WKT method to return polygon
* in string as WKT.
* @history 2007-11-09 Tracie Sucharski, Remove WKT method, geos now has
* a method to return a WKT string.
* @history 2007-11-20 Tracie Sucharski, Added test for sub-polys
*/
// simple MOC image
string inFile = "/usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub";
//string inFile = "/work1/tsucharski/poly/I17621017RDR_lev2.cub";
// same MOC image, but sinusoidal projection
//string inFile = "/farm/prog1/tsucharski/isis3/ab102401.lev2.cub";
// same MOC image, but sinusoidal projection , doctored left edge
//string inFile = "/farm/prog1/tsucharski/isis3/ab102401.lev2.leftTrim.cub";
// MOC north pole image
//string inFile = "/work1/tsucharski/isis3/poly/e0202226.lev1.cub";
// MOC image with 0/360 boundary
// orkin
//string inFile = "/farm/prog1/tsucharski/isis3/cubes/m0101631.lev1.cub";
// blackflag
//string inFile = "/work1/tsucharski/isis3/poly/m0101631.lev1.cub";
// galileo ssi image
//string inFile = "/farm/prog1/tsucharski/isis3/6700r.cub";
// Open the cube
Cube cube;
Cube cube1;
cube.Open(inFile,"r");
ImagePolygon poly;
try {
poly.Create(cube);
}
catch (iException &e) {
std::string msg = "Cannot create polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
// Test sub-poly option
try {
poly.Create(cube,12,1,384,640,385);
}
catch (iException &e) {
std::string msg = "Cannot create sub-polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
// Test lower quality option
try {
poly.Create(cube,10,12,1,384,640,385);
}
catch (iException &e) {
std::string msg = "Cannot create lower quality polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
cube.Close();
}
/**
* @brief Cube based constructor for HiRISE image cleaner
*/
HiImageClean::HiImageClean(Cube &cube) {
_filename = cube.Filename();
_lines = _samples = 0;
_totalMaskNulled = _totalDarkNulled = 0;
init(cube);
}