void IsisMain() {
// Create a process by line object
ProcessByLine p;
// Get the size of the cube
Cube *icube = p.SetInputCube("FROM");
// Open output text file
UserInterface &ui = Application::GetUserInterface();
QString to = ui.GetFileName("TO", "txt");
fout.open(to.toAscii().data());
// Print header if needed
if(ui.GetBoolean("HEADER")) {
fout << "Input Cube: " << icube->fileName() << endl;
fout << "Samples:Lines:Bands: " << icube->sampleCount() << ":" <<
icube->lineCount() << ":" << icube->bandCount() << endl;
}
// List the cube
p.StartProcess(isis2ascii);
p.EndProcess();
fout.close();
}
/**
* Constructs a UniversalGroundMap object from a cube
*
* @param cube The Cube to create the UniversalGroundMap from
* @param priority Try to make a camera or projection first
*/
UniversalGroundMap::UniversalGroundMap(Cube &cube, CameraPriority priority) {
p_camera = NULL;
p_projection = NULL;
Pvl &pvl = *cube.label();
try {
if(priority == CameraFirst)
p_camera = CameraFactory::Create(cube);
else
p_projection = Isis::ProjectionFactory::CreateFromCube(pvl);
}
catch (IException &firstError) {
p_camera = NULL;
p_projection = NULL;
try {
if(priority == CameraFirst)
p_projection = Isis::ProjectionFactory::CreateFromCube(pvl);
else
p_camera = CameraFactory::Create(cube);
}
catch (IException &secondError) {
p_projection = NULL;
QString msg = "Could not create camera or projection for [" +
cube.fileName() + "]";
IException realError(IException::Unknown, msg, _FILEINFO_);
realError.append(firstError);
realError.append(secondError);
throw realError;
}
}
}
QList<ControlPoint *> getValidPoints(Cube &cube, STRtree &coordTree) {
ImagePolygon poly;
try {
cube.read(poly);
}
catch (IException &e) {
QString msg = "Footprintinit must be run prior to running cnetadd";
msg += " with POLYGON=TRUE for cube [" + cube.fileName() + "]";
throw IException(e, IException::User, msg, _FILEINFO_);
}
std::vector<void *> matches;
MultiPolygon *polys = poly.Polys();
for (unsigned int i = 0; i < polys->getNumGeometries(); i++) {
const Geometry *geometry = polys->getGeometryN(i);
const Envelope *boundingBox = geometry->getEnvelopeInternal();
coordTree.query(boundingBox, matches);
}
QList<ControlPoint *> results;
for (unsigned int i = 0; i < matches.size(); i++) {
results.append((ControlPoint *) matches[i]);
}
return results;
}
/**
* @brief Initializes an ISIS cube converting it into a SPICE segment
*
* This method is called to extract the perinent contents of an ISIS cube file
* and accumulate generic information that is used to create the output SPICE
* kernel segment. Other specific kernel types can use this class as its base
* class and add to it additional elements to complete the needed content for
* the NAIF kernel.
*
* @param cube ISIS cube file to accumulate information from
*/
void SpiceSegment::init(Cube &cube) {
_kernels.UnLoad(); // Unload all active, owned kernels
init(); // Init local variables
_fname = cube.fileName();
// Extract ISIS CK blob and transform to CK 3 content
NaifStatus::CheckErrors();
try {
// Order is somewhat important here. The call to initialize Kernels
// object checks the NAIF pool for existance. It logs their NAIF
// status as loaded which may cause trouble from here on...
Pvl *label = cube.label();
_kernels.Init(*label);
Camera *camera = cube.camera();
// Determine segment ID from product ID if it exists, otherwise basename
if ( _name.isEmpty() ) {
_name = getKeyValue(*label, "ProductId");
if (_name.isEmpty() ) {
_name = FileName(_fname).baseName();
}
}
// Get instrument and target ids
QString value("");
value = getKeyValue(*label, "InstrumentId");
if (!value.isEmpty()) { _instId = value; }
value = getKeyValue(*label, "TargetName");
if (!value.isEmpty()) { _target = value; }
// Get default times for sorting purposes
setStartTime(camera->cacheStartTime().Et());
setEndTime(camera->cacheEndTime().Et());
} catch ( IException &ie ) {
ostringstream mess;
mess << "Failed to construct Spice Segment basics from ISIS file " << _fname;
throw IException(ie, IException::User, mess.str(), _FILEINFO_);
}
return;
}
void IsisMain(){
const QString hical_program = "hicalbeta";
const QString hical_version = "5.0";
const QString hical_revision = "$Revision: 1.15 $";
const QString hical_runtime = Application::DateTime();
UserInterface &ui = Application::GetUserInterface();
QString 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->sampleCount();
int nlines = hifrom->lineCount();
// Initialize the configuration file
QString 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
QString 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);
////////////////////////////////////////////////////////////////////////////
// Drift Correction (Zf) using buffer pixels
// Extracts specified regions of the calibration buffer pixels and runs
// series of lowpass filters. Apply spline fit if any missing data
// remains. Config file contains parameters for this operation.
procStep = "ZeroBufferSmooth module";
hiconf.selectProfile("ZeroBufferSmooth");
hiprof = hiconf.getMatrixProfile();
HiHistory ZbsHist;
ZbsHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
ZeroBufferSmooth zbs(caldata, hiconf);
calVars->add("ZeroBufferSmooth", zbs.ref());
ZbsHist = zbs.History();
if ( hiprof.exists("DumpModuleFile") ) {
zbs.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
// NOT RECOMMENDED! This is required for the next step!
// SURELY must be skipped with ZeroBufferSmooth step as well!
calVars->add("ZeroBufferSmooth", HiVector(nlines, 0.0));
ZbsHist.add("Debug::SkipModule invoked!");
}
/////////////////////////////////////////////////////////////////////
// ZeroBufferFit
// Compute second level of drift correction. The high level noise
// is removed from a modeled non-linear fit.
//
procStep = "ZeroBufferFit module";
HiHistory ZbfHist;
hiconf.selectProfile("ZeroBufferFit");
hiprof = hiconf.getMatrixProfile();
ZbfHist.add("Profile["+ hiprof.Name()+"]");
if (!SkipModule(hiprof) ) {
ZeroBufferFit zbf(hiconf);
calVars->add(hiconf.getProfileName(),
zbf.Normalize(zbf.Solve(calVars->get("ZeroBufferSmooth"))));
ZbfHist = zbf.History();
if ( hiprof.exists("DumpModuleFile") ) {
zbf.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nlines, 0.0));
ZbfHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// ZeroReverse
procStep = "ZeroReverse module";
hiconf.selectProfile("ZeroReverse");
hiprof = hiconf.getMatrixProfile();
HiHistory ZrHist;
ZrHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
ZeroReverse zr(caldata, hiconf);
calVars->add(hiconf.getProfileName(), zr.ref());
ZrHist = zr.History();
if ( hiprof.exists("DumpModuleFile") ) {
zr.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nsamps, 0.0));
ZrHist.add("Debug::SkipModule invoked!");
}
/////////////////////////////////////////////////////////////////
// ZeroDark removes dark current
//
procStep = "ZeroDark module";
hiconf.selectProfile("ZeroDark");
hiprof = hiconf.getMatrixProfile();
HiHistory ZdHist;
ZdHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
ZeroDark zd(hiconf);
calVars->add(hiconf.getProfileName(), zd.ref());
ZdHist = zd.History();
if ( hiprof.exists("DumpModuleFile") ) {
zd.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nsamps, 0.0));
ZdHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainLineDrift correct for gain-based drift
//
procStep = "GainLineDrift module";
hiconf.selectProfile("GainLineDrift");
hiprof = hiconf.getMatrixProfile();
HiHistory GldHist;
GldHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainLineDrift gld(hiconf);
calVars->add(hiconf.getProfileName(), gld.ref());
GldHist = gld.History();
if ( hiprof.exists("DumpModuleFile") ) {
gld.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nlines, 1.0));
GldHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainNonLinearity Correct for non-linear gain
procStep = "GainNonLinearity module";
hiconf.selectProfile("GainNonLinearity");
hiprof = hiconf.getMatrixProfile();
HiHistory GnlHist;
GnlHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainNonLinearity gnl(hiconf);
calVars->add(hiconf.getProfileName(), gnl.ref());
GnlHist = gnl.History();
if ( hiprof.exists("DumpModuleFile") ) {
gnl.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(1, 0.0));
GnlHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainChannelNormalize Correct for sample gain with the G matrix
procStep = "GainChannelNormalize module";
hiconf.selectProfile("GainChannelNormalize");
hiprof = hiconf.getMatrixProfile();
HiHistory GcnHist;
GcnHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainChannelNormalize gcn(hiconf);
calVars->add(hiconf.getProfileName(), gcn.ref());
GcnHist = gcn.History();
if ( hiprof.exists("DumpModuleFile") ) {
gcn.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nsamps, 1.0));
GcnHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainFlatField Flat field correction with A matrix
procStep = "GainFlatField module";
hiconf.selectProfile("GainFlatField");
hiprof = hiconf.getMatrixProfile();
HiHistory GffHist;
GffHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainFlatField gff(hiconf);
calVars->add(hiconf.getProfileName(), gff.ref());
GffHist = gff.History();
if ( hiprof.exists("DumpModuleFile") ) {
gff.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nsamps, 1.0));
GffHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainTemperature - Temperature-dependant gain correction
procStep = "GainTemperature module";
hiconf.selectProfile("GainTemperature");
hiprof = hiconf.getMatrixProfile();
HiHistory GtHist;
GtHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainTemperature gt(hiconf);
calVars->add(hiconf.getProfileName(), gt.ref());
GtHist = gt.History();
if ( hiprof.exists("DumpModuleFile") ) {
gt.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(nsamps, 1.0));
GtHist.add("Debug::SkipModule invoked!");
}
////////////////////////////////////////////////////////////////////
// GainUnitConversion converts to requested units
//
procStep = "GainUnitConversion module";
hiconf.selectProfile("GainUnitConversion");
hiprof = hiconf.getMatrixProfile();
HiHistory GucHist;
GucHist.add("Profile["+ hiprof.Name()+"]");
if ( !SkipModule(hiprof) ) {
GainUnitConversion guc(hiconf, units);
calVars->add(hiconf.getProfileName(), guc.ref());
GucHist = guc.History();
if ( hiprof.exists("DumpModuleFile") ) {
guc.Dump(hiconf.getMatrixSource("DumpModuleFile",hiprof));
}
}
else {
calVars->add(hiconf.getProfileName(), HiVector(1,1.0));
GucHist.add("Debug::SkipModule invoked!");
GucHist.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 QString 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));
QString hdumpFile = hdump.expanded();
ofstream ofile(hdumpFile.toAscii().data(), ios::out);
if (!ofile) {
QString mess = "Unable to open/create history dump file " +
hdump.expanded();
IException(IException::User, mess, _FILEINFO_).print();
}
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 */\n"
<< "/* hdn = (idn - ZeroBufferFit(ZeroBufferSmooth) - ZeroReverse - ZeroDark) */\n"
<< "/* odn = hdn / GainLineDrift * GainNonLinearity * GainChannelNormalize */\n"
<< "/* * GainFlatField * GainTemperature / GainUnitConversion */\n\n";
ofile << "****** PARAMETER GENERATION HISTORY *******" << endl;
ofile << "\nZeroBufferSmooth = " << ZbsHist << endl;
ofile << "\nZeroBufferFit = " << ZbfHist << endl;
ofile << "\nZeroReverse = " << ZrHist << endl;
ofile << "\nZeroDark = " << ZdHist << endl;
ofile << "\nGainLineDrift = " << GldHist << endl;
ofile << "\nGainNonLinearity = " << GnlHist << endl;
ofile << "\nGainChannelNormalize = " << GcnHist << endl;
ofile << "\nGainFlatField = " << GffHist << endl;
ofile << "\nGainTemperature = " << GtHist << endl;
ofile << "\nGainUnitConversion = " << GucHist << endl;
ofile.close();
}
}
// Ensure the RadiometricCalibration group is out there
const QString rcalGroup("RadiometricCalibration");
if (!ocube->hasGroup(rcalGroup)) {
PvlGroup temp(rcalGroup);
ocube->putGroup(temp);
}
PvlGroup &rcal = ocube->group(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 - ZeroBufferFit(ZeroBufferSmooth) */");
key.addComment("/* - ZeroReverse - ZeroDark */");
key.addComment("/* odn = hdn / GainLineDrift * GainNonLinearity */");
key.addComment("/* * GainChannelNormalize * GainFlatField */");
key.addComment("/* * GainTemperature / GainUnitConversion */");
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",QString("TRUE")),"TRUE")) {
rcal += ZbsHist.makekey("ZeroBufferSmooth");
rcal += ZbfHist.makekey("ZeroBufferFit");
rcal += ZrHist.makekey("ZeroReverse");
rcal += ZdHist.makekey("ZeroDark");
rcal += GldHist.makekey("GainLineDrift");
rcal += GnlHist.makekey("GainNonLinearity");
rcal += GcnHist.makekey("GainChannelNormalize");
rcal += GffHist.makekey("GainFlatField");
rcal += GtHist.makekey("GainTemperature");
rcal += GucHist.makekey("GainUnitConversion");
}
p.EndProcess();
}
catch (IException &ie) {
delete calVars;
calVars = 0;
QString mess = "Failed in " + procStep;
throw IException(ie, IException::User, mess, _FILEINFO_);
}
// Clean up parameters
delete calVars;
calVars = 0;
}
void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
Process p;
// Get the histogram
Cube *icube = p.SetInputCube("FROM");
double validMin = Isis::ValidMinimum;
double validMax = Isis::ValidMaximum;
if(ui.WasEntered("VALIDMIN")) {
validMin = ui.GetDouble("VALIDMIN");
}
if(ui.WasEntered("VALIDMAX")) {
validMax = ui.GetDouble("VALIDMAX");
}
// Set a global Pvl for storing results
Pvl mainpvl;
// Get the number of bands to process
int bandcount = icube->bandCount();
for (int i = 1; i <= bandcount; i++) {
Histogram *stats = icube->histogram(i, validMin, validMax);
// Construct a label with the results
PvlGroup results("Results");
results += PvlKeyword("From", icube->fileName());
results += PvlKeyword("Band", toString(icube->physicalBand(i)));
if(stats->ValidPixels() != 0) {
results += PvlKeyword("Average", toString(stats->Average()));
results += PvlKeyword("StandardDeviation", toString(stats->StandardDeviation()));
results += PvlKeyword("Variance", toString(stats->Variance()));
// These statistics only worked on a histogram
results += PvlKeyword("Median", toString(stats->Median()));
results += PvlKeyword("Mode", toString(stats->Mode()));
results += PvlKeyword("Skew", toString(stats->Skew()));
results += PvlKeyword("Minimum", toString(stats->Minimum()));
results += PvlKeyword("Maximum", toString(stats->Maximum()));
results += PvlKeyword("Sum", toString(stats->Sum()));
}
results += PvlKeyword("TotalPixels", toString(stats->TotalPixels()));
results += PvlKeyword("ValidPixels", toString(stats->ValidPixels()));
results += PvlKeyword("OverValidMaximumPixels", toString(stats->OverRangePixels()));
results += PvlKeyword("UnderValidMinimumPixels", toString(stats->UnderRangePixels()));
results += PvlKeyword("NullPixels", toString(stats->NullPixels()));
results += PvlKeyword("LisPixels", toString(stats->LisPixels()));
results += PvlKeyword("LrsPixels", toString(stats->LrsPixels()));
results += PvlKeyword("HisPixels", toString(stats->HisPixels()));
results += PvlKeyword("HrsPixels", toString(stats->HrsPixels()));
mainpvl.addGroup(results);
delete stats;
// Write the results to the log
Application::Log(results);
}
// Write the results to the output file if the user specified one
if(ui.WasEntered("TO")) {
QString outFile = FileName(ui.GetFileName("TO")).expanded();
bool exists = FileName(outFile).fileExists();
bool append = ui.GetBoolean("APPEND");
ofstream os;
bool writeHeader = false;
//write the results in the requested format.
if(ui.GetString("FORMAT") == "PVL") {
if(append) {
mainpvl.append(outFile);
}
else {
mainpvl.write(outFile);
}
}
else {
//if the format was not PVL, write out a flat file.
if(append) {
os.open(outFile.toAscii().data(), ios::app);
if(!exists) {
writeHeader = true;
}
}
else {
os.open(outFile.toAscii().data(), ios::out);
writeHeader = true;
}
if(writeHeader) {
for(int i = 0; i < mainpvl.group(0).keywords(); i++) {
os << mainpvl.group(0)[i].name();
if( i < mainpvl.group(0).keywords() - 1 ) {
os << ",";
}
}
os << endl;
}
for(int i = 0; i < mainpvl.groups(); i++) {
for (int j = 0; j < mainpvl.group(i).keywords(); j++) {
os << (QString)mainpvl.group(i)[j];
if(j < mainpvl.group(i).keywords() - 1) {
os << ",";
}
}
os << endl;
}
}
}
}
void IsisMain() {
// We will be processing by line
ProcessByBrick p;
UserInterface &ui = Application::GetUserInterface();
// Use the def file for filter constants
Pvl uvvisDef("$clementine1/calibration/uvvis/uvvis.def");
// Setup the input and output cubes
Cube *icube = p.SetInputCube("FROM");
Cube *dccube;
if(ui.WasEntered("DCFILE")) {
dccube = p.SetInputCube("DCFILE");
}
else {
QString dcfileloc = "$clementine1/calibration/uvvis/";
dcfileloc += "dark_5_15_96.cub";
CubeAttributeInput cubeAtt;
dccube = p.SetInputCube(dcfileloc, cubeAtt);
}
QString filter = (QString)(icube->group("BandBin"))["FilterName"];
filter = filter.toLower();
Cube *ffcube;
if(ui.WasEntered("FFFILE")) {
ffcube = p.SetInputCube("FFFILE");
}
else {
// compute default fffile
double compressRatio = (icube->group("Instrument"))["EncodingCompressionRatio"];
// check to see if cube is compressed or uncompressed
if(compressRatio == 1.0) {
QString fffileLoc = "$clementine1/calibration/uvvis/";
fffileLoc += "lu" + filter + "_uncomp_flat_long.cub";
CubeAttributeInput cubeAtt;
ffcube = p.SetInputCube(fffileLoc, cubeAtt);
}
else {
QString fffileLoc = "$clementine1/calibration/uvvis/";
fffileLoc += "lu" + filter + "_comp_flat_long.cub";
CubeAttributeInput cubeAtt;
ffcube = p.SetInputCube(fffileLoc, cubeAtt);
}
}
Cube *ocube = p.SetOutputCube("TO");
avgFF = uvvisDef.findGroup("Filter" + filter.toUpper())["AVGFF"];
cr = uvvisDef.findGroup("Filter" + filter.toUpper())["CO"];
gain = uvvisDef.findGroup(QString("GainModeID") + QString(icube->group("Instrument")["GainModeID"][0]))["GAIN"];
useDcconst = ui.WasEntered("DCCONST");
if(useDcconst) {
dcconst = ui.GetDouble("DCCONST");
}
else {
dcconst = 0.0;
}
conv = ui.GetBoolean("CONV");
exposureDuration = icube->group("Instrument")["ExposureDuration"];
offsetModeID = icube->group("Instrument")["OffsetModeID"];
if(((QString)icube->group("Instrument")["FocalPlaneTemperature"]).compare("UNK") == 0) {
//if FocalPlaneTemp is unknown set it to zero
focalPlaneTemp = 0.0;
}
else {
focalPlaneTemp = icube->group("Instrument")["FocalPlaneTemperature"];
}
Camera *cam = icube->camera();
bool camSuccess = cam->SetImage(icube->sampleCount() / 2, icube->lineCount() / 2);
if(!camSuccess) {
throw IException(IException::Unknown, "Unable to calculate the Solar Distance for this cube.", _FILEINFO_);
}
dist = cam->SolarDistance();
// If temp. correction set to true, or focal plane temp is zero then use temperature correction
if(ui.GetBoolean("TCOR") || abs(focalPlaneTemp) <= DBL_EPSILON) {
// Temperature correction requires the use of the mission phase
// (PRELAUNCH, EARTH, LUNAR) and the product ID.
QString productID = (QString)(icube->group("Archive")["ProductID"]);
QChar missionPhase = ((QString)((icube->group("Archive"))["MissionPhase"])).at(0);
QString n1subQString(productID.mid(productID.indexOf('.') + 1, productID.length() - 1));
QString n2subQString(productID.mid(4, productID.indexOf('.') - 5));
int n1 = toInt(n1subQString);
int n2 = toInt(n2subQString);
int phase = 0;
if(missionPhase == 'L') {
phase = 0;
}
else if(missionPhase == 'E') {
phase = 1;
}
else if(missionPhase == 'P') {
phase = 2;
}
else {
throw IException(IException::Unknown, "Invalid Mission Phase", _FILEINFO_);
}
// This formula makes the primary search critera the original product ID's extension,
// the secondary search criteria the mission phase and finally the numerical part of the
// original product ID.
int imageID = (100000 * n1) + (10000 * phase) + n2;
FixTemp(imageID);
}
if(focalPlaneTemp <= 0.0) {
focalPlaneTemp = 272.5;
}
// Start the processing
p.SetBrickSize(icube->sampleCount(), icube->lineCount(), 1);
p.StartProcess(UvVisCal);
// Add the radiometry group
PvlGroup calgrp("Radiometry");
calgrp += PvlKeyword("FlatFieldFile", ffcube->fileName());
if(ui.GetString("DARKCURRENT").compare("DCFILE") == 0) {
calgrp += PvlKeyword("DarkCurrentFile", dccube->fileName());
}
else {
calgrp += PvlKeyword("DarkCurrentConstant", toString(dcconst));
}
calgrp += PvlKeyword("CorrectedFocalPlaneTemp", toString(focalPlaneTemp));
calgrp += PvlKeyword("C1", toString(avgFF));
calgrp += PvlKeyword("C2", toString(C2));
calgrp += PvlKeyword("C3", toString(C3));
calgrp += PvlKeyword("C4", toString(C4));
calgrp += PvlKeyword("C5", toString(C5));
calgrp += PvlKeyword("CR", toString(cr));
calgrp += PvlKeyword("FrameTransferTimePerRow", toString(cr));
calgrp += PvlKeyword("Gain", toString(gain));
calgrp += PvlKeyword("CorrectedExposureDuration", toString(correctedExposureDuration));
calgrp += PvlKeyword("ConvertToRadiance", toString(conv));
calgrp += PvlKeyword("ACO", toString(ACO));
calgrp += PvlKeyword("BCO", toString(BCO));
calgrp += PvlKeyword("CCO", toString(CCO));
calgrp += PvlKeyword("DCO", toString(DCO));
ocube->putGroup(calgrp);
p.EndProcess();
}
void IsisMain() {
// We will be processing by line
ProcessByLine p;
// Setup the input and make sure it is a mariner10 file
UserInterface & ui = Application::GetUserInterface();
Isis::Pvl lab(ui.GetFileName("FROM"));
Isis::PvlGroup & inst = lab.findGroup("Instrument", Pvl::Traverse);
QString mission = inst["SpacecraftName"];
if (mission != "Mariner_10") {
string msg = "This is not a Mariner 10 image. Mar10cal requires a Mariner 10 image.";
throw IException(IException::User, msg, _FILEINFO_);
}
Cube * icube = p.SetInputCube("FROM", OneBand);
// If it is already calibrated then complain
if (icube->hasGroup("Radiometry")) {
QString msg = "This Mariner 10 image [" + icube->fileName() + "] has "
"already been radiometrically calibrated";
throw IException(IException::User, msg, _FILEINFO_);
}
// Get label parameters we will need for calibration equation
QString instId = inst["InstrumentId"];
QString camera = instId.mid(instId.size()-1);
QString filter = (QString)(icube->group("BandBin"))["FilterName"];
filter = filter.toUpper().mid(0,3);
QString target = inst["TargetName"];
iTime startTime((QString) inst["StartTime"]);
double exposure = inst["ExposureDuration"];
double exposureOffset = 0.0;
if (ui.WasEntered("EXPOFF")) {
exposureOffset = ui.GetDouble("EXPOFF");
}
else {
if (camera == "A") {
exposureOffset = 0.316;
}
else if (camera == "B") {
exposureOffset = 3.060;
}
else {
QString msg = "Camera [" + camera + "] is not supported.";
throw IException(IException::User, msg, _FILEINFO_);
}
}
correctedExp = exposure + exposureOffset;
Cube * dcCube;
if (ui.WasEntered ("DCCUBE") ) {
dcCube = p.SetInputCube("DCCUBE");
}
else {
// Mercury Dark current
// ??? NOTE: Need to find Mark's dc for venus and moon ????
QString dcFile("$mariner10/calibration/mariner_10_" + camera +
"_dc.cub");
CubeAttributeInput cubeAtt;
dcCube = p.SetInputCube(dcFile, cubeAtt);
}
// Open blemish removal file
Cube * blemCube = 0;
useBlem = (ui.GetBoolean("BLEMMASK")) ? true : false;
if (useBlem) {
QString blemFile("$mariner10/calibration/mariner_10_blem_" + camera + ".cub");
CubeAttributeInput cubeAtt;
blemCube = p.SetInputCube(blemFile, cubeAtt);
}
if (filter == "FAB" || filter == "WAF") {
QString msg = "Filter type [" + filter + "] is not supported at this time.";
throw IException(IException::User, msg, _FILEINFO_);
}
if (ui.WasEntered ("COEFCUBE")) {
coCube.open(ui.GetFileName("COEFCUBE"));
}
else {
FileName coFile("$mariner10/calibration/mariner_10_" + filter + "_" +
camera + "_coef.cub");
coCube.open(coFile.expanded());
}
coef = new Brick(icube->sampleCount(), 1, 6, coCube.pixelType());
if (ui.WasEntered("ABSCOEF")) {
absCoef = ui.GetDouble("ABSCOEF");
}
else {
if (camera == "A") {
absCoef = 16.0;
}
else if (camera == "B") {
absCoef = 750.0;
}
else {
QString msg = "Camera [" + camera + "] is not supported.";
throw IException(IException::User, msg, _FILEINFO_);
}
}
mask = ui.GetBoolean("MASK");
xparm = ui.GetDouble("XPARM");
// Get the distance between Mars and the Sun at the given time in
// Astronomical Units (AU)
Camera * cam = icube->camera();
bool camSuccess = cam->SetImage(icube->sampleCount()/2,icube->lineCount()/2);
if (!camSuccess) {
throw IException(IException::Unknown,
"Unable to calculate the Solar Distance on [" +
icube->fileName() + "]", _FILEINFO_);
}
sunDist = cam->SolarDistance();
// Setup the output cube
Cube *ocube = p.SetOutputCube("TO");
// Add the radiometry group
PvlGroup calgrp("Radiometry");
calgrp += PvlKeyword("DarkCurrentCube", dcCube->fileName());
if (useBlem) {
calgrp += PvlKeyword("BlemishRemovalCube", blemCube->fileName());
}
calgrp += PvlKeyword("CoefficientCube", coCube.fileName());
calgrp += PvlKeyword("AbsoluteCoefficient", toString(absCoef));
ocube->putGroup(calgrp);
// Start the line-by-line calibration sequence
p.StartProcess(Mar10Cal);
p.EndProcess();
}
// Main moccal routine
void IsisMain() {
// We will be processing by line
ProcessByLine p;
// Setup the input and make sure it is a ctx file
UserInterface &ui = Application::GetUserInterface();
Isis::Pvl lab(ui.GetFileName("FROM"));
Isis::PvlGroup &inst =
lab.findGroup("Instrument", Pvl::Traverse);
QString instId = inst["InstrumentId"];
if(instId != "CTX") {
QString msg = "This is not a CTX image. Ctxcal requires a CTX image.";
throw IException(IException::User, msg, _FILEINFO_);
}
Cube *icube = p.SetInputCube("FROM", OneBand);
Cube flatFile;
if(ui.WasEntered("FLATFILE")) {
flatFile.open(ui.GetFileName("FLATFILE"));
}
else {
FileName flat = FileName("$mro/calibration/ctxFlat_????.cub").highestVersion();
flatFile.open(flat.expanded());
}
flat = new Brick(5000, 1, 1, flatFile.pixelType());
flat->SetBasePosition(1, 1, 1);
flatFile.read(*flat);
// If it is already calibrated then complain
if(icube->hasGroup("Radiometry")) {
QString msg = "The CTX image [" + icube->fileName() + "] has already "
"been radiometrically calibrated";
throw IException(IException::User, msg, _FILEINFO_);
}
// Get label parameters we will need for calibration equation
iTime startTime((QString) inst["StartTime"]);
double etStart = startTime.Et();
// Read exposure and convert to milliseconds
exposure = inst["LineExposureDuration"];
//exposure *= 1000.;
sum = inst["SpatialSumming"];
// If firstSamp > 0, adjust by 38 to account for prefix pixels.
firstSamp = inst["SampleFirstPixel"];
if(firstSamp > 0) firstSamp -= 38;
// Read dark current info, if no dc exit?
Table dcTable("Ctx Prefix Dark Pixels");
icube->read(dcTable);
// TODO:: make sure dc records match cube nlines.
// If summing mode = 1 , average odd & even dc pixels separately for
// a & b channels.
// If summing mode != 1, average all dc pixels and use for both
for(int rec = 0; rec < dcTable.Records(); rec++) {
vector<int> darks = dcTable[rec]["DarkPixels"];
bool aChannel = true;
double dcASum = 0.;
double dcBSum = 0.;
int dcACount = 0;
int dcBCount = 0;
double dcSum = 0;
int dcCount = 0;
for(int i = 0; i < (int)darks.size(); i++) {
if(sum == 1) {
if(aChannel == true) {
dcASum += (double)darks.at(i);
dcACount++;
}
else {
dcBSum += (double)darks.at(i);
dcBCount++;
}
aChannel = !aChannel;
}
else if(sum > 1) {
dcSum += (double)darks.at(i);
dcCount ++;
}
}
if(sum == 1) {
dcA.push_back(dcASum / (double)dcACount);
dcB.push_back(dcBSum / (double)dcBCount);
}
else {
dc.push_back(dcSum / (double)dcCount);
}
}
// See if the user wants counts/ms or i/f
// iof = conversion factor from counts/ms to i/f
bool convertIOF = ui.GetBoolean("IOF");
if(convertIOF) {
// Get the distance between Mars and the Sun at the given time in
// Astronomical Units (AU)
QString bspKernel = p.MissionData("base", "/kernels/spk/de???.bsp", true);
furnsh_c(bspKernel.toAscii().data());
QString pckKernel = p.MissionData("base", "/kernels/pck/pck?????.tpc", true);
furnsh_c(pckKernel.toAscii().data());
double sunpos[6], lt;
spkezr_c("sun", etStart, "iau_mars", "LT+S", "mars", sunpos, <);
double dist1 = vnorm_c(sunpos);
unload_c(bspKernel.toAscii().data());
unload_c(pckKernel.toAscii().data());
double dist = 2.07E8;
double w0 = 3660.5;
double w1 = w0 * ((dist * dist) / (dist1 * dist1));
if(exposure *w1 == 0.0) {
QString msg = icube->fileName() + ": exposure or w1 has value of 0.0 ";
throw IException(IException::User, msg, _FILEINFO_);
}
iof = 1.0 / (exposure * w1);
}
else {
iof = 1.0;
}
// Setup the output cube
Cube *ocube = p.SetOutputCube("TO");
// Add the radiometry group
PvlGroup calgrp("Radiometry");
calgrp += PvlKeyword("FlatFile", flatFile.fileName());
calgrp += PvlKeyword("iof", toString(iof));
ocube->putGroup(calgrp);
// Start the line-by-line calibration sequence
p.StartProcess(Calibrate);
p.EndProcess();
}
void IsisMain () {
ResetGlobals();
UserInterface &ui = Application::GetUserInterface();
ProcessByBrick p;
Cube *icube = p.SetInputCube("FROM");
// Make sure it is a WAC cube
Isis::PvlGroup &inst = icube->label()->findGroup("Instrument", Pvl::Traverse);
QString instId = (QString) inst["InstrumentId"];
instId = instId.toUpper();
if (instId != "WAC-VIS" && instId != "WAC-UV") {
QString msg = "This program is intended for use on LROC WAC images only. [";
msg += icube->fileName() + "] does not appear to be a WAC image.";
throw IException(IException::User, msg, _FILEINFO_);
}
// And check if it has already run through calibration
if (icube->label()->findObject("IsisCube").hasGroup("Radiometry")) {
QString msg = "This image has already been calibrated";
throw IException(IException::User, msg, _FILEINFO_);
}
if (icube->label()->findObject("IsisCube").hasGroup("AlphaCube")) {
QString msg = "This application can not be run on any image that has been geometrically transformed (i.e. scaled, rotated, sheared, or reflected) or cropped.";
throw IException(IException::User, msg, _FILEINFO_);
}
g_dark = ui.GetBoolean("DARK");
g_flatfield = ui.GetBoolean("FLATFIELD");
g_radiometric = ui.GetBoolean("RADIOMETRIC");
g_iof = (ui.GetString("RADIOMETRICTYPE") == "IOF");
g_specpix = ui.GetBoolean("SPECIALPIXELS");
g_temprature = ui.GetBoolean("TEMPERATURE");
// Determine the dark/flat files to use
QString offset = (QString) inst["BackgroundOffset"];
QString mode = (QString) inst["Mode"];
QString instModeId = (QString) inst["InstrumentModeId"];
instModeId = instModeId.toUpper();
if (instModeId == "COLOR" && (QString) inst["InstrumentId"] == "WAC-UV")
instModeId = "UV";
else if (instModeId == "VIS")
instModeId = "COLOR";
g_startTemperature = (double) inst["BeginTemperatureFpa"];
g_endTemperature = (double) inst["EndTemperatureFpa"];
g_numFrames = (int) inst["NumFramelets"];
vector<QString> darkFiles;
ui.GetAsString("DARKFILE", darkFiles);
QString flatFile = ui.GetAsString("FLATFIELDFILE");
QString radFile = ui.GetAsString("RADIOMETRICFILE");
QString specpixFile = ui.GetAsString("SPECIALPIXELSFILE");
QString tempFile = ui.GetAsString("TEMPERATUREFILE");
// Figure out which bands are input
for (int i = 1; i <= icube->bandCount(); i++) {
g_bands.push_back(icube->physicalBand(i));
}
Isis::PvlGroup &bandBin = icube->label()->findGroup("BandBin", Pvl::Traverse);
QString filter = (QString) bandBin["Center"][0];
QString filterNum = (QString) bandBin["FilterNumber"][0];
//We have to pay special attention incase we are passed a
//single band image that has been "exploded" from a multiband wac
if (instModeId == "COLOR" && g_bands.size() == 1)
g_bands[0] = (toInt(filterNum) -2);
else if (instModeId == "UV" && g_bands.size() == 1)
g_bands[0] = (toInt(filterNum));
if (g_dark) {
if (darkFiles.size() == 0 || darkFiles[0] =="Default" || darkFiles[0].length() == 0) {
darkFiles.resize(2);
double temp = (double) inst["MiddleTemperatureFpa"];
double time = iTime(inst["StartTime"][0]).Et();
QString darkFile = "$lro/calibration/wac_darks/WAC_" + instModeId;
if (instModeId == "BW")
darkFile += "_" + filter + "_Mode" + mode;
darkFile += "_Offset" + offset + "_*C_*T_Dark.????.cub";
GetDark (darkFile, temp, time, g_darkCube1, g_darkCube2, g_temp1, g_temp2, darkFiles[0], darkFiles[1]);
}
else if (darkFiles.size() == 1) {
CopyCubeIntoBuffer(darkFiles[0], g_darkCube1);
g_temp1 = 0.0;
g_darkCube2 = new Buffer(*g_darkCube1);
g_temp2 = g_temp1;
}
else {
CopyCubeIntoBuffer(darkFiles[0], g_darkCube1);
int index = darkFiles[0].lastIndexOf("_");
g_temp1 = IString(darkFiles[0].mid( darkFiles[0].lastIndexOf("_", index-1), index)).ToDouble();
CopyCubeIntoBuffer(darkFiles[1], g_darkCube2);
index = darkFiles[1].lastIndexOf("_");
g_temp2 = IString(darkFiles[1].mid( darkFiles[1].lastIndexOf("_", index-1), index)).ToDouble();
}
}
if (g_flatfield) {
if (flatFile.toLower() == "default" || flatFile.length() == 0) {
flatFile = "$lro/calibration/wac_flats/WAC_" + instModeId;
if (instModeId == "BW")
flatFile += "_" + filter + "_Mode" + mode;
flatFile += "_Flatfield.????.cub";
}
CopyCubeIntoBuffer(flatFile, g_flatCube);
// invert the flat-field data here so we don't have to divide for every pixel of the wac
for (int i = 0; i < g_flatCube->size(); i++) {
(*g_flatCube)[i] = 1.0 / (*g_flatCube)[i];
}
}
PvlKeyword responsivity;
if (g_radiometric) {
Isis::PvlKeyword &bands = icube->label()->findGroup("BandBin", Pvl::Traverse).findKeyword("FilterNumber");
if (radFile.toLower() == "default" || radFile.length() == 0)
radFile = "$lro/calibration/WAC_RadiometricResponsivity.????.pvl";
FileName radFileName(radFile);
if (radFileName.isVersioned())
radFileName = radFileName.highestVersion();
if (!radFileName.fileExists()) {
QString msg = radFile + " does not exist.";
throw IException(IException::User, msg, _FILEINFO_);
}
Pvl radPvl(radFileName.expanded());
if (g_iof) {
responsivity = radPvl["IOF"];
for (int i = 0; i < bands.size(); i++)
g_iofResponsivity.push_back(toDouble(responsivity[toInt(bands[i]) - 1]));
try {
iTime startTime((QString) inst["StartTime"]);
double etStart = startTime.Et();
// Get the distance between the Moon and the Sun at the given time in
// Astronomical Units (AU)
QString bspKernel1 = p.MissionData("lro", "/kernels/tspk/moon_pa_de421_1900-2050.bpc", false);
QString bspKernel2 = p.MissionData("lro", "/kernels/tspk/de421.bsp", false);
furnsh_c(bspKernel1.toAscii().data());
furnsh_c(bspKernel2.toAscii().data());
QString pckKernel1 = p.MissionData("base", "/kernels/pck/pck?????.tpc", true);
QString pckKernel2 = p.MissionData("lro", "/kernels/pck/moon_080317.tf", false);
QString pckKernel3 = p.MissionData("lro", "/kernels/pck/moon_assoc_me.tf", false);
furnsh_c(pckKernel1.toAscii().data());
furnsh_c(pckKernel2.toAscii().data());
furnsh_c(pckKernel3.toAscii().data());
double sunpos[6], lt;
spkezr_c("sun", etStart, "MOON_ME", "LT+S", "MOON", sunpos, <);
g_solarDistance = vnorm_c(sunpos) / KM_PER_AU;
unload_c(bspKernel1.toAscii().data());
unload_c(bspKernel2.toAscii().data());
unload_c(pckKernel1.toAscii().data());
unload_c(pckKernel2.toAscii().data());
unload_c(pckKernel3.toAscii().data());
}
catch (IException &e) {
QString msg = "Can not find necessary SPICE kernels for converting to IOF";
throw IException(e, IException::User, msg, _FILEINFO_);
}
}
else {
responsivity = radPvl["Radiance"];
for (int i = 0; i < bands.size(); i++)
g_radianceResponsivity.push_back(toDouble(responsivity[toInt(bands[i]) - 1]));
}
}
if (g_specpix) {
if (specpixFile.toLower() == "default" || specpixFile.length() == 0) {
specpixFile = "$lro/calibration/wac_masks/WAC_" + instModeId;
double temp = (double) inst["MiddleTemperatureFpa"];
if (instModeId == "BW")
specpixFile += "_" + filter + "_Mode" + mode;
specpixFile += "_*C_SpecialPixels.????.cub";
GetMask(specpixFile, temp, g_specpixCube);
}
else
CopyCubeIntoBuffer(specpixFile, g_specpixCube);
}
if (g_temprature) {
if (tempFile.toLower() == "default" || tempFile.length() == 0)
tempFile = "$lro/calibration/WAC_TempratureConstants.????.pvl";
FileName tempFileName(tempFile);
if (tempFileName.isVersioned())
tempFileName = tempFileName.highestVersion();
if (!tempFileName.fileExists()) {
QString msg = tempFile + " does not exist.";
throw IException(IException::User, msg, _FILEINFO_);
}
Isis::PvlKeyword &bands = icube->label()->findGroup("BandBin", Pvl::Traverse).findKeyword("FilterNumber");
Pvl tempPvl(tempFileName.expanded());
for (int b = 0; b < bands.size(); b++){
g_TempratureConstants[g_bands[b]][0]=toDouble(tempPvl[bands[b]][0]);
g_TempratureConstants[g_bands[b]][1]=toDouble(tempPvl[bands[b]][1]);
}
}
if (instModeId == "BW") {
if (mode == "1" || mode == "0")
p.SetBrickSize(NO_POLAR_MODE_SAMPLES, VIS_LINES, (int)min(BW_BANDS, g_bands.size()));
else
p.SetBrickSize(POLAR_MODE_SAMPLES, VIS_LINES, (int)min(BW_BANDS, g_bands.size()));
}
else if (instModeId == "COLOR") {
p.SetBrickSize(NO_POLAR_MODE_SAMPLES, VIS_LINES, (int)min(COLOR_BANDS, g_bands.size()));
}
else if (instModeId == "UV") {
p.SetBrickSize(UV_SAMPLES, UV_LINES, (int)min(UV_BANDS, g_bands.size()));
}
g_exposure = inst["ExposureDuration"];
Cube *ocube = p.SetOutputCube("TO");
p.ProcessCube(Calibrate, false);
// Add an output group with the appropriate information
PvlGroup calgrp("Radiometry");
if (g_dark) {
PvlKeyword darks("DarkFiles");
darks.addValue(darkFiles[0]);
if (darkFiles.size() > 1)
darks.addValue(darkFiles[1]);
calgrp += darks;
}
if (g_flatfield)
calgrp += PvlKeyword("FlatFile", flatFile);
if (g_radiometric) {
PvlKeyword vals("ResponsivityValues");
if (g_iof) {
calgrp += PvlKeyword("RadiometricType", "IOF");
for (unsigned int i=0; i< g_iofResponsivity.size(); i++)
vals.addValue(toString(g_iofResponsivity[i]));
}
else {
calgrp += PvlKeyword("RadiometricType", "AbsoluteRadiance");
for (unsigned int i=0; i< g_radianceResponsivity.size(); i++)
vals.addValue(toString(g_radianceResponsivity[i]));
}
calgrp += vals;
calgrp += PvlKeyword("SolarDistance", toString(g_solarDistance));
}
if (g_specpix)
calgrp += PvlKeyword("SpecialPixelsFile", specpixFile);
ocube->putGroup(calgrp);
}
// Main moccal routine
void IsisMain() {
// We will be processing by line
ProcessByLine p;
// Setup the input and make sure it is a moc file
UserInterface &ui = Application::GetUserInterface();
Cube *icube = p.SetInputCube("FROM", OneBand);
gbl::moc = new MocLabels(ui.GetFileName("FROM"));
// If it is already calibrated then complain
if(icube->hasGroup("Radiometry")) {
QString msg = "The MOC image [" + icube->fileName() + "] has already "
"been radiometrically calibrated";
throw IException(IException::User, msg, _FILEINFO_);
}
// Get label parameters we will need for calibration equation
gbl::a = gbl::moc->Gain();
gbl::off = gbl::moc->Offset();
gbl::ex = gbl::moc->ExposureDuration();
// Get the starting, ending, and activation et's. For now, the
// activation et is set to the largest double precision value. If
// The narrow angle B detectors ever get activated then the value
// will need to be changed to the appropriate et
iTime startTime(gbl::moc->StartTime());
double etStart = startTime.Et();
double etNABActivation = DBL_MAX;
// Open the calibration kernel that contains constants for each camera
// and internalize it in a pvl object
QString calKernelFile;
if(ui.WasEntered("CALKERNEL")) {
calKernelFile = ui.GetFileName("CALKERNEL");
}
else {
calKernelFile = p.MissionData("mgs", "/calibration/moccal.ker.???", true);
}
Pvl calKernel(calKernelFile);
// Point to the right group of camera parameters
QString camera;
if(gbl::moc->WideAngleRed()) {
camera = "WideAngleRed";
}
else if(gbl::moc->WideAngleBlue()) {
camera = "WideAngleBlue";
}
else if(etStart > etNABActivation) {
camera = "NarrowAngleB";
}
else {
camera = "NarrowAngleA";
}
PvlGroup &calCamera = calKernel.findGroup(camera);
// Get the camera specific calibration parameters from the kernel file
// and load detector coefficients (gain/offsets at each pixel)
gbl::z = calCamera["Z"];
gbl::dc = calCamera["DC"];
gbl::g = calCamera["G"];
gbl::w0 = calCamera["W0"];
QString coefFile = calCamera["CoefFile"];
gbl::LoadCoefficients(coefFile, icube->sampleCount());
#if 0
// Override with these with any user selected parameters
if(ui.WasEntered("Z")) gbl::z = ui.GetDouble("Z");
if(ui.WasEntered("DC")) gbl::dc = ui.GetDouble("DC");
if(ui.WasEntered("G")) gbl::g = ui.GetDouble("G");
if(ui.WasEntered("W0")) gbl::w0 = ui.GetDouble("W0");
#endif
gbl::nullWago = ui.GetBoolean("NULLWAGO");
// Get the distance between Mars and the Sun at the given time in
// Astronomical Units (AU)
QString bspKernel = p.MissionData("base", "/kernels/spk/de???.bsp", true);
furnsh_c(bspKernel.toAscii().data());
QString pckKernel = p.MissionData("base", "/kernels/pck/pck?????.tpc", true);
furnsh_c(pckKernel.toAscii().data());
double sunpos[6], lt;
spkezr_c("sun", etStart, "iau_mars", "LT+S", "mars", sunpos, <);
double dist = vnorm_c(sunpos);
double kmPerAU = 1.4959787066E8;
double sunAU = dist / kmPerAU;
unload_c(bspKernel.toAscii().data());
unload_c(pckKernel.toAscii().data());
// See if the user wants counts/ms or i/f but if w0 is 0 then
// we must go to counts/ms
// iof = conversion factor from counts/ms to i/f
bool convertIOF = ui.GetBoolean("IOF") && (gbl::w0 > 0.0);
if(convertIOF) {
gbl::iof = sunAU * sunAU / gbl::w0;
}
else {
gbl::iof = 1.0;
}
// Setup the output cube
Cube *ocube = p.SetOutputCube("TO");
// Add the radiometry group
PvlGroup calgrp("Radiometry");
calgrp += PvlKeyword("CalibrationKernel", calKernelFile);
calgrp += PvlKeyword("CoefficientFile", coefFile);
calgrp += PvlKeyword("a", toString(gbl::a));
calgrp["a"].addComment("Radiometric equation in moccal");
calgrp["a"].addComment("r = (pixel - z + off) / a - g / ex - dc");
calgrp += PvlKeyword("off", toString(gbl::off));
calgrp += PvlKeyword("ex", toString(gbl::ex));
calgrp += PvlKeyword("z", toString(gbl::z));
calgrp += PvlKeyword("dc", toString(gbl::dc));
calgrp += PvlKeyword("g", toString(gbl::g));
calgrp += PvlKeyword("w0", toString(gbl::w0));
calgrp["w0"].addComment("Reflectance = r * iof, where iof = (s * s) / w0");
calgrp += PvlKeyword("s", toString(sunAU));
calgrp += PvlKeyword("iof", toString(gbl::iof));
ocube->putGroup(calgrp);
// Start the line-by-line calibration sequence
p.StartProcess(gbl::Calibrate);
p.EndProcess();
// Now go fix errors around the wago changes
gbl::FixWagoLines(ui.GetFileName("TO"));
// Cleanup
gbl::pixelGain.clear();
gbl::pixelOffset.clear();
gbl::inLineAvg.clear();
gbl::outLineAvg.clear();
}
/** The ISIS smtk main application */
void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
// Open the first cube. It is the left hand image.
Cube lhImage;
CubeAttributeInput &attLeft = ui.GetInputAttribute("FROM");
vector<QString> bandLeft = attLeft.bands();
lhImage.setVirtualBands(bandLeft);
lhImage.open(ui.GetFileName("FROM"),"r");
// Open the second cube, it is geomertricallty altered. We will be matching the
// first to this one by attempting to compute a sample/line offsets
Cube rhImage;
CubeAttributeInput &attRight = ui.GetInputAttribute("MATCH");
vector<QString> bandRight = attRight.bands();
rhImage.setVirtualBands(bandRight);
rhImage.open(ui.GetFileName("MATCH"),"r");
// Ensure only single bands
if (lhImage.bandCount() != 1 || rhImage.bandCount() != 1) {
QString msg = "Input Cubes must have only one band!";
throw IException(IException::User,msg,_FILEINFO_);
}
// Both images must have a Camera and can also have a Projection. We will
// only deal with a Camera, however as a projected, non-mosaicked image
// uses a Projection internal to the Camera object.
Camera *lhCamera = NULL;
Camera *rhCamera = NULL;
try {
lhCamera = lhImage.camera();
rhCamera = rhImage.camera();
}
catch (IException &ie) {
QString msg = "Both input images must have a camera";
throw IException(ie, IException::User, msg, _FILEINFO_);
}
// Since we are generating a DEM, we must turn off any existing
// DEM that may have been initialized with spiceinit.
lhCamera->IgnoreElevationModel(true);
rhCamera->IgnoreElevationModel(true);
// Get serial number
QString serialLeft = SerialNumber::Compose(lhImage, true);
QString serialRight = SerialNumber::Compose(rhImage, true);
// This still precludes band to band registrations.
if (serialLeft == serialRight) {
QString sLeft = FileName(lhImage.fileName()).name();
QString sRight = FileName(rhImage.fileName()).name();
if (sLeft == sRight) {
QString msg = "Cube Serial Numbers must be unique - FROM=" + serialLeft +
", MATCH=" + serialRight;
throw IException(IException::User,msg,_FILEINFO_);
}
serialLeft = sLeft;
serialRight = sRight;
}
Progress prog;
prog.SetText("Finding Initial Seeds");
int nl = lhImage.lineCount();
int ns = lhImage.sampleCount();
BigInt numAttemptedInitialPoints = 0;
// Declare Gruen matcher
SmtkMatcher matcher(ui.GetFileName("REGDEF"), &lhImage, &rhImage);
// Get line/sample linc/sinc parameters
int space = ui.GetInteger("SPACE");
int linc (space), sinc(space);
// Do we have a seed points from a control net file?
bool useseed = ui.WasEntered("CNET");
// Base points on an input cnet
SmtkQStack gstack;
double lastEigen(0.0);
if (useseed) {
ControlNet cnet(ui.GetFileName("CNET"));
prog.SetMaximumSteps(cnet.GetNumPoints());
prog.CheckStatus();
gstack.reserve(cnet.GetNumPoints());
for (int cpIndex = 0; cpIndex < cnet.GetNumPoints(); cpIndex ++) {
ControlPoint *cp = cnet.GetPoint(cpIndex);
if (!cp->IsIgnored()) {
ControlMeasure *cmLeft(0), *cmRight(0);
for(int cmIndex = 0; cmIndex < cp->GetNumMeasures(); cmIndex ++) {
ControlMeasure *cm = cp->GetMeasure(cmIndex);
if (!cm->IsIgnored()) {
if (cm->GetCubeSerialNumber() == serialLeft)
cmLeft = cp->GetMeasure(cmIndex);
if (cm->GetCubeSerialNumber() == serialRight)
cmRight = cp->GetMeasure(cmIndex);
}
}
// If we have both left and right images in the control point, save it
if ( (cmLeft != 0) && (cmRight != 0) ) {
Coordinate left = Coordinate(cmLeft->GetLine(), cmLeft->GetSample());
Coordinate right = Coordinate(cmRight->GetLine(), cmRight->GetSample());
SmtkPoint spnt = matcher.Create(left, right);
// Insert the point (unregistered)
if ( spnt.isValid() ) {
int line = (int) cmLeft->GetLine();
int samp = (int) cmLeft->GetSample();
matcher.isValid(spnt);
gstack.insert(qMakePair(line, samp), spnt);
lastEigen = spnt.GoodnessOfFit();
}
}
}
prog.CheckStatus();
}
}
else {
// We want to create a grid of control points that is N rows by M columns.
int rows = (lhImage.lineCount() + linc - 1)/linc;
int cols = (lhImage.sampleCount() + sinc - 1)/sinc;
prog.SetMaximumSteps(rows * cols);
prog.CheckStatus();
// First pass stack and eigen value statistics
SmtkQStack fpass;
fpass.reserve(rows * cols);
Statistics temp_mev;
// Loop through grid of points and get statistics to compute
// initial set of points
for (int line = linc / 2 + 1; line < nl; line += linc) {
for (int samp = sinc / 2 + 1 ; samp < ns; samp += sinc) {
numAttemptedInitialPoints ++;
SmtkPoint spnt = matcher.Register(Coordinate(line,samp));
if ( spnt.isValid() ) {
matcher.isValid(spnt);
fpass.insert(qMakePair(line, samp), spnt);
temp_mev.AddData(spnt.GoodnessOfFit());
}
prog.CheckStatus();
}
}
// Now select a subset of fpass points as the seed points
cout << "Number of Potential Seed Points: " << fpass.size() << "\n";
cout << "Min / Max Eigenvalues Matched: " << temp_mev.Minimum() << ", "
<< temp_mev.Maximum() << "\n";
// How many seed points are requested
double nseed = ui.GetDouble("NSEED");
int inseed;
if (nseed >= 1.0) inseed = (int) nseed;
else if (nseed > 0.0) inseed = (int) (nseed * (double) (fpass.size()));
else inseed = (int) ((double) (fpass.size()) * 0.05);
double seedsample = ui.GetDouble("SEEDSAMPLE");
// Generate a new stack
gstack.reserve(inseed);
while ((gstack.size() < inseed) && (!fpass.isEmpty() )) {
SmtkQStack::iterator bestm;
if (seedsample <= 0.0) {
bestm = matcher.FindSmallestEV(fpass);
}
else {
bestm = matcher.FindExpDistEV(fpass, seedsample, temp_mev.Minimum(),
temp_mev.Maximum());
}
// Add point to stack
if (bestm != fpass.end()) {
Coordinate right = bestm.value().getRight();
matcher.isValid(bestm.value());
gstack.insert(bestm.key(), bestm.value());
lastEigen = bestm.value().GoodnessOfFit();
fpass.erase(bestm);
}
}
// If a user wants to see the seed network, write it out here
if (ui.WasEntered("OSEEDNET")) {
WriteCnet(ui.GetFileName("OSEEDNET"), gstack,
lhCamera->target()->name(), serialLeft, serialRight);
}
}
///////////////////////////////////////////////////////////////////////
// All done with seed points. Sanity check ensures we actually found
// some.
///////////////////////////////////////////////////////////////////////
if (gstack.size() <= 0) {
QString msg = "No seed points found - may need to check Gruen parameters.";
throw IException(IException::User, msg, _FILEINFO_);
}
// Report seed point status
if (!useseed) {
cout << "Number of Seed Points used: " << gstack.size() << "\n";
cout << "EV of last Seed Point: " << lastEigen << "\n";
}
else {
cout << "Number of Manual Seed Points: " << gstack.size() << "\n";
}
// Use seed points (in stack) to grow
SmtkQStack bmf;
bmf.reserve(gstack.size()); // Probably need much more but for starters...
BigInt numOrigPoints = gstack.size();
BigInt passpix2 = 0;
int subcbox = ui.GetInteger("SUBCBOX");
int halfBox((subcbox-1)/2);
while (!gstack.isEmpty()) {
SmtkQStackIter cstack = matcher.FindSmallestEV(gstack);
// Print number on stack
if ((gstack.size() % 1000) == 0) {
cout << "Number on Stack: " << gstack.size()
<< ". " << cstack.value().GoodnessOfFit() << "\n";
}
// Test to see if already determined
SmtkQStackIter bmfPt = bmf.find(cstack.key());
if (bmfPt == bmf.end()) {
// Its not in the final stack, process it
// Retrieve the point
SmtkPoint spnt = cstack.value();
// Register if its not already registered
if (!spnt.isRegistered()) {
spnt = matcher.Register(spnt, spnt.getAffine());
}
// Still must check for validity if the point was just registered,
// otherwise should be good
if ( spnt.isValid() ) {
passpix2++;
bmf.insert(cstack.key(), spnt); // inserts (0,0) offset excluded below
int line = cstack.key().first;
int sample = cstack.key().second;
// Determine match points
double eigen(spnt.GoodnessOfFit());
for (int sampBox = -halfBox ; sampBox <= halfBox ; sampBox++ ) {
int csamp = sample + sampBox;
for (int lineBox = -halfBox ; lineBox <= halfBox ; lineBox++) {
int cline = line + lineBox;
if ( !( (sampBox == 0) && (lineBox == 0)) ) {// Already added above
SmtkQPair dupPair(cline, csamp);
SmtkQStackIter temp = bmf.find(dupPair);
SmtkPoint bmfpnt;
if (temp != bmf.end()) {
if (temp.value().GoodnessOfFit() > eigen) {
// Create cloned point with better fit
bmfpnt = matcher.Clone(spnt, Coordinate(cline,csamp));
}
}
else { // ISIS2 is BMF(SAMP,LINE,7) .EQ VALID_MAX4)
// Clone new point for insert
bmfpnt = matcher.Clone(spnt, Coordinate(cline,csamp));
}
// Add if good point
if (bmfpnt.isValid()) {
bmf.insert(dupPair, bmfpnt);
}
}
}
}
// Grow stack with spacing adding info to stack
for (int i = -1 ; i <= 1 ; i ++) { // Sample
for (int j = -1 ; j <= 1 ; j ++) { // Line
// Don't re-add the original sample, line
if ( !((i == 0) && (j == 0)) ) {
// Grow based upon spacing
double ssamp = sample + (i * space);
double sline = line + (j * space);
Coordinate pnt = Coordinate(sline, ssamp);
SmtkPoint gpnt = matcher.Clone(spnt, pnt);
if ( gpnt.isValid() ) {
SmtkQPair growpt((int) sline, (int) ssamp);
// double check we don't have a finalized result at this position
SmtkQStackIter temp = bmf.find(growpt);
if(temp == bmf.end()) {
gstack.insert(growpt, gpnt);
}
}
}
}
}
}
}
// Remove the current point from the grow stack (hole)
gstack.erase(cstack);
}
/////////////////////////////////////////////////////////////////////////
// All done with creating points. Perform output options.
/////////////////////////////////////////////////////////////////////////
// If a TO parameter was specified, create DEM with errors
if (ui.WasEntered("TO")) {
// Create the output DEM
cout << "\nCreating output DEM from " << bmf.size() << " points.\n";
Process p;
Cube *icube = p.SetInputCube("FROM");
Cube *ocube = p.SetOutputCube("TO", icube->sampleCount(),
icube->lineCount(), 3);
p.ClearInputCubes();
int boxsize = ui.GetInteger("BOXSIZE");
double plotdist = ui.GetDouble("PLOTDIST");
TileManager dem(*ocube), eigen(*ocube), stErr(*ocube);
dem.SetTile(1, 1); // DEM Data/elevation
stErr.SetTile(1, 2); // Error in stereo computation
eigen.SetTile(1, 3); // Eigenvalue of the solution
int nBTiles(eigen.Tiles()/3); // Total tiles / 3 bands
prog.SetText("Creating DEM");
prog.SetMaximumSteps(nBTiles);
prog.CheckStatus();
Statistics stAng;
while ( !eigen.end() ) { // Must use the last band for this!!
PointPlot tm = for_each(bmf.begin(), bmf.end(), PointPlot(dem, plotdist));
tm.FillPoints(*lhCamera, *rhCamera, boxsize, dem, stErr, eigen, &stAng);
ocube->write(dem);
ocube->write(stErr);
ocube->write(eigen);
dem.next();
stErr.next();
eigen.next();
prog.CheckStatus();
}
// Report Stereo separation angles
PvlGroup stresultsPvl("StereoSeparationAngle");
stresultsPvl += PvlKeyword("Minimum", toString(stAng.Minimum()), "deg");
stresultsPvl += PvlKeyword("Average", toString(stAng.Average()), "deg");
stresultsPvl += PvlKeyword("Maximum", toString(stAng.Maximum()), "deg");
stresultsPvl += PvlKeyword("StandardDeviation", toString(stAng.StandardDeviation()), "deg");
Application::Log(stresultsPvl);
// Update the label with BandBin keywords
PvlKeyword filter("FilterName", "Elevation", "meters");
filter.addValue("ElevationError", "meters");
filter.addValue("GoodnessOfFit", "unitless");
PvlKeyword center("Center", "1.0");
center.addValue("1.0");
center.addValue("1.0");
PvlGroup &bandbin = ocube->label()->findGroup("BandBin", PvlObject::Traverse);
bandbin.addKeyword(filter, PvlContainer::Replace);
bandbin.addKeyword(center, PvlContainer::Replace);
center.setName("Width");
bandbin.addKeyword(center, PvlContainer::Replace);
p.EndProcess();
}
// If a cnet file was entered, write the ControlNet pvl to the file
if (ui.WasEntered("ONET")) {
WriteCnet(ui.GetFileName("ONET"), bmf, lhCamera->target()->name(), serialLeft,
serialRight);
}
// Create output data
PvlGroup totalPointsPvl("Totals");
totalPointsPvl += PvlKeyword("AttemptedPoints", toString(numAttemptedInitialPoints));
totalPointsPvl += PvlKeyword("InitialSuccesses", toString(numOrigPoints));
totalPointsPvl += PvlKeyword("GrowSuccesses", toString(passpix2));
totalPointsPvl += PvlKeyword("ResultingPoints", toString(bmf.size()));
Application::Log(totalPointsPvl);
Pvl arPvl = matcher.RegistrationStatistics();
PvlGroup smtkresultsPvl("SmtkResults");
smtkresultsPvl += PvlKeyword("SpiceOffImage", toString(matcher.OffImageErrorCount()));
smtkresultsPvl += PvlKeyword("SpiceDistanceError", toString(matcher.SpiceErrorCount()));
arPvl.addGroup(smtkresultsPvl);
for(int i = 0; i < arPvl.groups(); i++) {
Application::Log(arPvl.group(i));
}
// add the auto registration information to print.prt
PvlGroup autoRegTemplate = matcher.RegTemplate();
Application::Log(autoRegTemplate);
// Don't need the cubes opened anymore
lhImage.close();
rhImage.close();
}
