/**
* This method performs pass1 on one image. It analyzes each framelet's
* statistics and populates the necessary global variable.
*
* @param progress Progress message
* @param theCube Current cube that needs processing
*
* @return bool True if the file contains a valid framelet
*/
bool CheckFramelets(string progress, Cube &theCube) {
bool foundValidFramelet = false;
LineManager mgr(theCube);
Progress prog;
prog.SetText(progress);
prog.SetMaximumSteps(theCube.Lines());
prog.CheckStatus();
vector<double> frameletAvgs;
// We need to store off the framelet information, because if no good
// framelets were found then no data should be added to the
// global variable for framelets, just files.
vector< pair<int,double> > excludedFrameletsTmp;
Statistics frameletStats;
for(int line = 1; line <= theCube.Lines(); line++) {
if((line-1) % numFrameLines == 0) {
frameletStats.Reset();
}
mgr.SetLine(line);
theCube.Read(mgr);
frameletStats.AddData(mgr.DoubleBuffer(), mgr.size());
if((line-1) % numFrameLines == numFrameLines-1) {
if(IsSpecial(frameletStats.StandardDeviation()) ||
frameletStats.StandardDeviation() > maxStdev) {
excludedFrameletsTmp.push_back(
pair<int,double>((line-1)/numFrameLines, frameletStats.StandardDeviation())
);
}
else {
foundValidFramelet = true;
}
frameletAvgs.push_back(frameletStats.Average());
}
prog.CheckStatus();
}
inputFrameletAverages.push_back(frameletAvgs);
if(foundValidFramelet) {
for(unsigned int i = 0; i < excludedFrameletsTmp.size(); i++) {
excludedFramelets.insert(pair< pair<int,int>, double>(
pair<int,int>(currImage, excludedFrameletsTmp[i].first),
excludedFrameletsTmp[i].second
)
);
}
}
return foundValidFramelet;
}
void IsisMain() {
latLonGrid = NULL;
// We will be processing by line
ProcessByLine p;
Cube *icube = p.SetInputCube("FROM");
UserInterface &ui = Application::GetUserInterface();
string mode = ui.GetString("MODE");
outline = ui.GetBoolean("OUTLINE");
inputSamples = icube->Samples();
inputLines = icube->Lines();
// Line & sample based grid
if(mode == "IMAGE") {
p.SetOutputCube ("TO");
baseLine = ui.GetInteger("BASELINE");
baseSample = ui.GetInteger("BASESAMPLE");
lineInc = ui.GetInteger("LINC");
sampleInc = ui.GetInteger("SINC");
p.StartProcess(imageGrid);
p.EndProcess();
}
// Lat/Lon based grid
else {
CubeAttributeOutput oatt("+32bit");
p.SetOutputCube (ui.GetFilename("TO"), oatt, icube->Samples(),
icube->Lines(), icube->Bands());
baseLat = ui.GetDouble("BASELAT");
baseLon = ui.GetDouble("BASELON");
latInc = ui.GetDouble("LATINC");
lonInc = ui.GetDouble("LONINC");
UniversalGroundMap *gmap = new UniversalGroundMap(*icube);
latLonGrid = new GroundGrid(gmap, icube->Samples(), icube->Lines());
Progress progress;
progress.SetText("Calculating Grid");
latLonGrid->CreateGrid(baseLat, baseLon, latInc, lonInc, &progress);
p.StartProcess(groundGrid);
p.EndProcess();
delete latLonGrid;
latLonGrid = NULL;
delete gmap;
gmap = NULL;
}
}
/**
* @brief Initializes the object by computing all calibration statistics
*
* This method validates the input file, reads labels for needed values
* and computes calibration statistics for data reduction.
*
* @param [in] (CubeInfo &) cube Opened cube where label and ancillary data
* is read from
*/
void HiImageClean::init(Cube &cube) {
_lines = cube.Lines();
_samples = cube.Samples();
_lastGoodLine = _lines - 1;
_totalMaskNulled = _totalDarkNulled = 0;
PvlGroup &instrument = cube.GetGroup("Instrument");
// It may be too late and a non-issue by this time, but should check to ensure
// this is a valid HiRISE image
iString instId = (std::string) instrument["InstrumentId"];
if (instId.UpCase() != "HIRISE") {
string message = "Image must be a HiRISE image (InstrumentId != HIRISE)";
iException::Message(iException::User, message, _FILEINFO_);
}
// Extract what is needed
_binning = instrument["Summing"];
_tdi = instrument["Tdi"];
_cpmm = instrument["CpmmNumber"];
_channelNo = instrument["ChannelNumber"];
// Initialize all HiRISE calibration blobs
_calimg = blobvert(HiCalibrationImage(cube));
_calbuf = blobvert(HiCalibrationBuffer(cube));
_caldark = blobvert(HiCalibrationDark(cube));
_ancbuf = blobvert(HiAncillaryBuffer(cube));
_ancdark = blobvert(HiAncillaryDark(cube));
// Compute statistics from blobs
computeStats();
return;
}
void IsisMain() {
//Get user parameters
UserInterface &ui = Application::GetUserInterface();
Filename inFile = ui.GetFilename("FROM");
int numberOfLines = ui.GetInteger("NL");
int lineOverlap = ui.GetInteger("OVERLAP");
//Throws exception if user is dumb
if ( lineOverlap >= numberOfLines ) {
throw iException::Message( iException::User, "The Line Overlap (OVERLAP) must be less than the Number of Lines (LN).", _FILEINFO_ );
}
//Opens the cube
Cube cube;
cube.Open( inFile.Expanded() );
//Loops through, cropping as desired
int cropNum = 1;
int startLine = 1;
bool hasReachedEndOfCube = false;
while ( startLine <= cube.Lines() && not hasReachedEndOfCube ) {
//! Sets up the proper paramaters for running the crop program
string parameters = "FROM=" + inFile.Expanded() +
" TO=" + inFile.Path() + "/" + inFile.Basename() + ".segment" + iString(cropNum) + ".cub"
+ " LINE=" + iString(startLine) + " NLINES=";
if ( startLine + numberOfLines > cube.Lines() ) {
parameters += iString( cube.Lines() - ( startLine - 1 ) );
hasReachedEndOfCube = true;
}
else {
parameters += iString(numberOfLines);
}
Isis::iApp ->Exec("crop",parameters);
//The starting line for next crop
startLine = 1 + cropNum * ( numberOfLines - lineOverlap );
cropNum++;
}
}
//Helper function to get camera resolution.
void ComputePixRes () {
Process p;
UserInterface &ui = Application::GetUserInterface();
Cube *latCube = p.SetInputCube("LATCUB");
Cube *lonCube = p.SetInputCube("LONCUB");
Brick latBrick(1,1,1,latCube->PixelType());
Brick lonBrick(1,1,1,lonCube->PixelType());
latBrick.SetBasePosition(1,1,1);
latCube->Read(latBrick);
lonBrick.SetBasePosition(1,1,1);
lonCube->Read(lonBrick);
double a = latBrick.at(0) * PI/180.0;
double c = lonBrick.at(0) * PI/180.0;
latBrick.SetBasePosition(latCube->Samples(),latCube->Lines(),1);
latCube->Read(latBrick);
lonBrick.SetBasePosition(lonCube->Samples(),lonCube->Lines(),1);
lonCube->Read(lonBrick);
double b = latBrick.at(0) * PI/180.0;
double d = lonBrick.at(0) * PI/180.0;
double angle = acos(cos(a) * cos(b) * cos(c - d) + sin(a) * sin(b));
angle *= 180/PI;
double pixels = sqrt(pow(latCube->Samples() -1.0, 2.0) + pow(latCube->Lines() -1.0, 2.0));
p.EndProcess();
ui.Clear("RESOLUTION");
ui.PutDouble("RESOLUTION", pixels/angle);
ui.Clear("PIXRES");
ui.PutAsString("PIXRES","PPD");
}
// Gather general statistics on a particular band of a cube
Isis::Statistics GatherStatistics(Cube &icube, const int band,
double sampPercent, std::string maxCubeStr) {
// Create our progress message
iString curCubeStr (g_imageIndex+1);
std::string statMsg = "";
if (icube.Bands() == 1) {
statMsg = "Calculating Statistics for Band 1 in Cube " + curCubeStr +
" of " + maxCubeStr;
}
else {
iString curBandStr (band);
iString maxBandStr (icube.Bands());
statMsg = "Calculating Statistics for Band " + curBandStr + " of " +
maxBandStr + " in Cube " + curCubeStr + " of " + maxCubeStr;
}
int linc = (int) (100.0 / sampPercent + 0.5); // Calculate our line incrementer
// Make sure band is valid
if ((band <= 0) || (band > icube.Bands())) {
string msg = "Invalid band in method [GatherStatistics]";
throw Isis::iException::Message(Isis::iException::Programmer,msg,_FILEINFO_);
}
// Construct a line buffer manager and a statistics object
Isis::LineManager line (icube);
Isis::Progress progress;
progress.SetText(statMsg);
// Calculate the number of steps for the Progress object, and add an extra
// step if the total lines and incrementer do not divide evenly
int maxSteps = icube.Lines() / linc;
if (icube.Lines() % linc != 0) maxSteps += 1;
progress.SetMaximumSteps(maxSteps);
progress.CheckStatus();
// Add data to Statistics object by line
Isis::Statistics stats;
int i=1;
while (i<=icube.Lines()) {
line.SetLine(i,band);
icube.Read(line);
stats.AddData (line.DoubleBuffer(), line.size());
// Make sure we consider the last line
if (i+linc > icube.Lines() && i != icube.Lines()) {
i = icube.Lines();
progress.AddSteps(1);
}
else i += linc; // Increment the current line by our incrementer
progress.CheckStatus();
}
return stats;
}
void IsisMain() {
ProcessRubberSheet p;
// Open the input cube
Cube *icube = p.SetInputCube ("FROM");
// Set up the transform object
UserInterface &ui = Application::GetUserInterface();
Transform *transform = new Rotate(icube->Samples(), icube->Lines(),
ui.GetDouble("DEGREES"));
// Determine the output size
int samples = transform->OutputSamples();
int lines = transform->OutputLines();
// Allocate the output file
p.SetOutputCube ("TO", samples, lines, icube->Bands());
// Set up the interpolator
Interpolator *interp;
if (ui.GetString("INTERP") == "NEARESTNEIGHBOR") {
interp = new Interpolator(Interpolator::NearestNeighborType);
}
else if (ui.GetString("INTERP") == "BILINEAR") {
interp = new Interpolator(Interpolator::BiLinearType);
}
else if (ui.GetString("INTERP") == "CUBICCONVOLUTION") {
interp = new Interpolator(Interpolator::CubicConvolutionType);
}
else {
string msg = "Unknow value for INTERP [" +
ui.GetString("INTERP") + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
p.StartProcess(*transform, *interp);
p.EndProcess();
delete transform;
delete interp;
}
void IsisMain() {
// We will be processing by line
ProcessByLine p;
// Setup the input and output cubes
Cube *icube = p.SetInputCube("FROM");
p.SetOutputCube ("TO");
// Override the defaults if the user entered a value
UserInterface &ui = Application::GetUserInterface();
top = ui.GetInteger ("TOP");
bottom = ui.GetInteger ("BOTTOM");
lleft = ui.GetInteger ("LEFT");
rright = ui.GetInteger ("RIGHT");
// Will anything be trimmed from the cube?
bool notrim = false;
if (top == 0 && bottom == 0 && lleft == 0 && rright == 0) {
notrim = true;
}
// Adjust bottom and right
bottom = icube->Lines() - bottom;
rright = icube->Samples() - rright;
// Start the processing
p.StartProcess(trim);
p.EndProcess();
//The user didn't trim anything
if (notrim == true) {
string message = "No trimming was done-output equals input file";
throw iException::Message(iException::User,message,_FILEINFO_);
}
}
void IsisMain() {
// We will be processing by line
ProcessByLine p;
// Setup the input and output cubes
Cube *icube = p.SetInputCube("FROM");
p.SetOutputCube ("TO");
// Get exposure duration and tranfer time
// Override the lable values if the user entered a value
double expTime,xferTime;
UserInterface &ui = Application::GetUserInterface();
if (ui.WasEntered ("DURATION")) {
expTime = ui.GetDouble ("DURATION");
}
else {
PvlGroup grp = icube->GetGroup("ISIS_INSTRUMENT");
expTime = grp["EXPOSURE_DURATION"];
}
if (ui.WasEntered ("TRANSFER")) {
xferTime = ui.GetDouble ("TRANSFER");
}
else {
PvlGroup grp = icube->GetGroup("ISIS_INSTRUMENT");
xferTime = grp["TRANSFER_TIME"];
}
// Calculate the smear scale
smearScale = xferTime / expTime / icube->Lines();
// Start the processing
p.StartProcess(desmear);
p.EndProcess();
}
// Main program
void IsisMain(){
// Create an object for exporting Isis data
ProcessExport p;
// Open the input cube
Cube *icube = p.SetInputCube("FROM");
// Conform to the Big-Endian format for FITS
if(IsLsb()) p.SetOutputEndian(Isis::Msb);
// Generate the name of the fits file and open it
UserInterface &ui = Application::GetUserInterface();
// specify the bits per pixel
string bitpix;
if (ui.GetString ("BITTYPE") == "8BIT") bitpix = "8";
else if (ui.GetString ("BITTYPE") == "16BIT") bitpix = "16";
else if (ui.GetString ("BITTYPE") == "32BIT") bitpix = "-32";
else {
string msg = "Pixel type of [" + ui.GetString("BITTYPE") + "] is unsupported";
throw iException::Message(iException::User, msg, _FILEINFO_);
}
// Determine bit size and calculate number of bytes to write
// for each line.
if (bitpix == "8") p.SetOutputType(Isis::UnsignedByte);
if (bitpix == "16") p.SetOutputType(Isis::SignedWord);
if (bitpix == "-32") p.SetOutputType(Isis::Real);
// determine core base and multiplier, set up the stretch
PvlGroup pix = icube->Label()->FindObject("IsisCube").FindObject("Core").FindGroup("Pixels");
double scale = pix["Multiplier"][0].ToDouble();
double base = pix["Base"][0].ToDouble();
if (ui.GetString("STRETCH") != "NONE" && bitpix != "-32") {
if (ui.GetString("STRETCH") == "LINEAR") {
p.SetInputRange();
}
else if (ui.GetString("STRETCH") == "MANUAL") {
p.SetInputRange(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"));
}
// create a proper scale so pixels look like 32bit data.
scale = ((p.GetInputMaximum() - p.GetInputMinimum()) *
(p.GetOutputMaximum() - p.GetOutputMinimum()));
// round off after 14 decimals to avoid system architecture differences
scale = ((floor(scale * 1e14)) / 1e14);
// create a proper zero point so pixels look like 32bit data.
base = -1.0 * (scale * p.GetOutputMinimum()) + p.GetInputMinimum();
// round off after 14 decimals to avoid system architecture differences
base = ((floor(base * 1e14)) / 1e14);
}
//////////////////////////////////////////
// Write the minimal fits header //
//////////////////////////////////////////
string header;
// specify that this file conforms to simple fits standard
header += FitsKeyword("SIMPLE", true, "T");
// specify the bits per pixel
header += FitsKeyword("BITPIX", true, bitpix);
// specify the number of data axes (2: samples by lines)
int axes = 2;
if (icube->Bands() > 1) {
axes = 3;
}
header += FitsKeyword("NAXIS", true, iString(axes));
// specify the limit on data axis 1 (number of samples)
header += FitsKeyword("NAXIS1", true, iString(icube->Samples()));
// specify the limit on data axis 2 (number of lines)
header += FitsKeyword("NAXIS2", true, iString(icube->Lines()));
if (axes == 3){
header += FitsKeyword("NAXIS3", true, iString(icube->Bands()));
}
header += FitsKeyword("BZERO", true, base);
header += FitsKeyword("BSCALE", true, scale);
// Sky and All cases
if (ui.GetString("INFO") == "SKY" || ui.GetString("INFO") == "ALL") {
iString msg = "cube has not been skymapped";
PvlGroup map;
if (icube->HasGroup("mapping")) {
map = icube->GetGroup("mapping");
msg = (string)map["targetname"];
}
// If we have sky we want it
if (msg == "Sky") {
double midRa = 0, midDec = 0;
midRa = ((double)map["MaximumLongitude"] +
(double)map["MinimumLongitude"])/2;
midDec = ((double)map["MaximumLatitude"] +
(double)map["MinimumLatitude"])/2;
header += FitsKeyword("OBJCTRA", true, iString(midRa));
// Specify the Declination
header += FitsKeyword("OBJCTDEC", true, iString(midDec));
}
if (ui.GetString("INFO") == "ALL") {
header += WritePvl("INSTRUME","Instrument","InstrumentId", icube, true);
header += WritePvl("OBSERVER","Instrument","SpacecraftName", icube, true);
header += WritePvl("OBJECT ","Instrument","TargetName", icube, true);
// StartTime is sometimes middle of the exposure and somtimes beginning,
// so StopTime can't be calculated off of exposure reliably.
header += WritePvl("DATE-OBS","Instrument","StartTime", icube, true);
// Some cameras don't have StopTime
if (icube->HasGroup("Instrument")) {
PvlGroup inst = icube->GetGroup("Instrument");
if (inst.HasKeyword("StopTime")) {
header += WritePvl("TIME_END","Instrument","StopTime", icube, true);
}
if (inst.HasKeyword("ExposureDuration")) {
header += WritePvl("EXPTIME","Instrument","ExposureDuration", icube, false);
}
}
}
// If we were set on SKY and Sky doesn't exist
else if (msg != "Sky") {
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
// signal the end of the header
header += FitsKeyword("END", false, "");
// fill the rest of the fits header with space so to conform with the fits header
// size of 2880 bytes
for (int i = header.length() % 2880 ; i < 2880 ; i++) header += " ";
// open the cube for writing
string to = ui.GetFilename("TO","fits");
ofstream fout;
fout.open (to.c_str (), ios::out|ios::binary);
if (!fout.is_open ()) {
string msg = "Cannot open fits output file";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
fout.seekp(0);
fout.write(header.c_str(),header.length());
// write the raw cube data
p.StartProcess (fout);
// Finish off data area to a number n % 2880 == 0 is true
// 2880 is the size of the data blocks
int count = 2880 - (fout.tellp() % 2880);
for (int i = 0; i < count; i++) {
// Write nul characters as needed. ascii 0, hex 00...
fout.write("\0", 1);
}
fout.close();
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;
}
void IsisMain() {
// Get the list of cubes to process
FileList imageList;
UserInterface &ui = Application::GetUserInterface();
imageList.Read(ui.GetFilename("FROMLIST"));
// Read to list if one was entered
FileList outList;
if (ui.WasEntered("TOLIST")) {
outList.Read(ui.GetFilename("TOLIST"));
}
// Check for user input errors and return the file list sorted by CCD numbers
ErrorCheck(imageList, outList);
// Adds statistics for whole and side regions of every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_s.Reset();
g_sl.Reset();
g_sr.Reset();
iString maxCube ((int)imageList.size());
iString curCube (img+1);
ProcessByLine p;
p.Progress()->SetText("Gathering Statistics for Cube " +
curCube + " of " + maxCube);
CubeAttributeInput att;
const std::string inp = imageList[img];
p.SetInputCube(inp, att);
p.StartProcess(GatherStatistics);
p.EndProcess();
g_allStats.push_back(g_s);
g_leftStats.push_back(g_sl);
g_rightStats.push_back(g_sr);
}
// Initialize the object that will calculate the gains and offsets
g_oNorm = new OverlapNormalization(g_allStats);
// Add the known overlaps between two cubes, and apply a weight to each
// overlap equal the number of pixels in the overlapping area
for (int i=0; i<(int)imageList.size()-1; i++) {
int j = i+1;
g_oNorm->AddOverlap(g_rightStats[i], i, g_leftStats[j], j,
g_rightStats[i].ValidPixels());
}
// Read in and then set the holdlist
FileList holdList;
holdList.Read(ui.GetFilename("HOLD"));
for (unsigned i=0; i<holdList.size(); i++) {
int index = -1;
for (unsigned j=0; j<imageList.size(); j++) {
std::string curName = imageList.at(j);
if (curName.compare(holdList[i]) == 0) {
index = j;
g_oNorm->AddHold(index);
}
}
}
// Attempt to solve the least squares equation
g_oNorm->Solve(OverlapNormalization::Both);
// Apply correction to the cubes if desired
bool applyopt = ui.GetBoolean("APPLY");
if (applyopt) {
// Loop through correcting the gains and offsets by line for every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_imageNum = img;
ProcessByLine p;
iString max_cube ((int)imageList.size());
iString cur_cube (img+1);
p.Progress()->SetText("Equalizing Cube " + cur_cube + " of " + max_cube);
CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
Filename file = imageList[img];
// Establish the output file depending upon whether or not a to list
// was entered
std::string out;
if (ui.WasEntered("TOLIST")) {
out = outList[img];
}
else {
Filename file = imageList[img];
out = file.Path() + "/" + file.Basename() + ".equ." + file.Extension();
}
CubeAttributeOutput outAtt;
p.SetOutputCube(out,outAtt,icube->Samples(),icube->Lines(),icube->Bands());
p.StartProcess(Apply);
p.EndProcess();
}
}
// Setup the output text file if the user requested one
if (ui.WasEntered("OUTSTATS")) {
std::string out = Filename(ui.GetFilename("OUTSTATS")).Expanded();
std::ofstream os;
os.open(out.c_str(),std::ios::app);
// Get statistics for each cube with PVL
Pvl p;
PvlObject equ("EqualizationInformation");
for (int img=0; img<(int)imageList.size(); img++) {
std::string cur = imageList[img];
PvlGroup a("Adjustment");
a += PvlKeyword("FileName", cur);
a += PvlKeyword("Average", g_oNorm->Average(img));
a += PvlKeyword("Base", g_oNorm->Offset(img));
a += PvlKeyword("Multiplier", g_oNorm->Gain(img));
equ.AddGroup(a);
}
p.AddObject(equ);
os << p << std::endl;
}
PvlGroup results ("Results");
for (int img=0; img<(int)imageList.size(); img++) {
results += PvlKeyword("FileName", imageList[img]);
results += PvlKeyword("Average", g_oNorm->Average(img));
results += PvlKeyword("Base", g_oNorm->Offset(img));
results += PvlKeyword("Multiplier", g_oNorm->Gain(img));
}
Application::Log(results);
// Clean-up for batch list runs
delete g_oNorm;
g_oNorm = NULL;
g_allStats.clear();
g_leftStats.clear();
g_rightStats.clear();
}
void IsisMain() {
Process p;
// Get the list of names of input CCD cubes to stitch together
FileList flist;
UserInterface &ui = Application::GetUserInterface();
flist.Read(ui.GetFilename("FROMLIST"));
if (flist.size() < 1) {
string msg = "The list file[" + ui.GetFilename("FROMLIST") +
" does not contain any filenames";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
string projection("Equirectangular");
if(ui.WasEntered("MAP")) {
Pvl mapfile(ui.GetFilename("MAP"));
projection = (string) mapfile.FindGroup("Mapping")["ProjectionName"];
}
if(ui.WasEntered("PROJECTION")) {
projection = ui.GetString("PROJECTION");
}
// Gather other user inputs to projection
string lattype = ui.GetString("LATTYPE");
string londir = ui.GetString("LONDIR");
string londom = ui.GetString("LONDOM");
int digits = ui.GetInteger("PRECISION");
// Fix them for mapping group
lattype = (lattype == "PLANETOCENTRIC") ? "Planetocentric" : "Planetographic";
londir = (londir == "POSITIVEEAST") ? "PositiveEast" : "PositiveWest";
Progress prog;
prog.SetMaximumSteps(flist.size());
prog.CheckStatus();
Statistics scaleStat;
Statistics longitudeStat;
Statistics latitudeStat;
Statistics equiRadStat;
Statistics poleRadStat;
PvlObject fileset("FileSet");
// Save major equitorial and polar radii for last occuring
double eqRad;
double eq2Rad;
double poleRad;
string target("Unknown");
for (unsigned int i = 0 ; i < flist.size() ; i++) {
// Set the input image, get the camera model, and a basic mapping
// group
Cube cube;
cube.Open(flist[i]);
int lines = cube.Lines();
int samples = cube.Samples();
PvlObject fmap("File");
fmap += PvlKeyword("Name",flist[i]);
fmap += PvlKeyword("Lines", lines);
fmap += PvlKeyword("Samples", samples);
Camera *cam = cube.Camera();
Pvl mapping;
cam->BasicMapping(mapping);
PvlGroup &mapgrp = mapping.FindGroup("Mapping");
mapgrp.AddKeyword(PvlKeyword("ProjectionName",projection),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("LatitudeType",lattype),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("LongitudeDirection",londir),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("LongitudeDomain",londom),Pvl::Replace);
// Get the radii
double radii[3];
cam->Radii(radii);
eqRad = radii[0] * 1000.0;
eq2Rad = radii[1] * 1000.0;
poleRad = radii[2] * 1000.0;
target = cam->Target();
equiRadStat.AddData(&eqRad, 1);
poleRadStat.AddData(&poleRad, 1);
// Get resolution
double lowres = cam->LowestImageResolution();
double hires = cam->HighestImageResolution();
scaleStat.AddData(&lowres, 1);
scaleStat.AddData(&hires, 1);
double pixres = (lowres+hires)/2.0;
double scale = Scale(pixres, poleRad, eqRad);
mapgrp.AddKeyword(PvlKeyword("PixelResolution",pixres),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("Scale",scale,"pixels/degree"),Pvl::Replace);
mapgrp += PvlKeyword("MinPixelResolution",lowres,"meters");
mapgrp += PvlKeyword("MaxPixelResolution",hires,"meters");
// Get the universal ground range
double minlat,maxlat,minlon,maxlon;
cam->GroundRange(minlat,maxlat,minlon,maxlon,mapping);
mapgrp.AddKeyword(PvlKeyword("MinimumLatitude",minlat),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("MaximumLatitude",maxlat),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("MinimumLongitude",minlon),Pvl::Replace);
mapgrp.AddKeyword(PvlKeyword("MaximumLongitude",maxlon),Pvl::Replace);
fmap.AddGroup(mapgrp);
fileset.AddObject(fmap);
longitudeStat.AddData(&minlon, 1);
longitudeStat.AddData(&maxlon, 1);
latitudeStat.AddData(&minlat, 1);
latitudeStat.AddData(&maxlat, 1);
p.ClearInputCubes();
prog.CheckStatus();
}
// Construct the output mapping group with statistics
PvlGroup mapping("Mapping");
double avgPixRes((scaleStat.Minimum()+scaleStat.Maximum())/2.0);
double avgLat((latitudeStat.Minimum()+latitudeStat.Maximum())/2.0);
double avgLon((longitudeStat.Minimum()+longitudeStat.Maximum())/2.0);
double avgEqRad((equiRadStat.Minimum()+equiRadStat.Maximum())/2.0);
double avgPoleRad((poleRadStat.Minimum()+poleRadStat.Maximum())/2.0);
double scale = Scale(avgPixRes, avgPoleRad, avgEqRad);
mapping += PvlKeyword("ProjectionName",projection);
mapping += PvlKeyword("TargetName", target);
mapping += PvlKeyword("EquatorialRadius",eqRad,"meters");
mapping += PvlKeyword("PolarRadius",poleRad,"meters");
mapping += PvlKeyword("LatitudeType",lattype);
mapping += PvlKeyword("LongitudeDirection",londir);
mapping += PvlKeyword("LongitudeDomain",londom);
mapping += PvlKeyword("PixelResolution", SetRound(avgPixRes, digits), "meters/pixel");
mapping += PvlKeyword("Scale", SetRound(scale, digits), "pixels/degree");
mapping += PvlKeyword("MinPixelResolution",scaleStat.Minimum(),"meters");
mapping += PvlKeyword("MaxPixelResolution",scaleStat.Maximum(),"meters");
mapping += PvlKeyword("CenterLongitude", SetRound(avgLon,digits));
mapping += PvlKeyword("CenterLatitude", SetRound(avgLat,digits));
mapping += PvlKeyword("MinimumLatitude", MAX(SetFloor(latitudeStat.Minimum(),digits), -90.0));
mapping += PvlKeyword("MaximumLatitude", MIN(SetCeil(latitudeStat.Maximum(),digits), 90.0));
mapping += PvlKeyword("MinimumLongitude",MAX(SetFloor(longitudeStat.Minimum(),digits), -180.0));
mapping += PvlKeyword("MaximumLongitude",MIN(SetCeil(longitudeStat.Maximum(),digits), 360.0));
PvlKeyword clat("PreciseCenterLongitude", avgLon);
clat.AddComment("Actual Parameters without precision applied");
mapping += clat;
mapping += PvlKeyword("PreciseCenterLatitude", avgLat);
mapping += PvlKeyword("PreciseMinimumLatitude", latitudeStat.Minimum());
mapping += PvlKeyword("PreciseMaximumLatitude", latitudeStat.Maximum());
mapping += PvlKeyword("PreciseMinimumLongitude",longitudeStat.Minimum());
mapping += PvlKeyword("PreciseMaximumLongitude",longitudeStat.Maximum());
Application::GuiLog(mapping);
// Write the output file if requested
if (ui.WasEntered("TO")) {
Pvl temp;
temp.AddGroup(mapping);
temp.Write(ui.GetFilename("TO","map"));
}
if (ui.WasEntered("LOG")) {
Pvl temp;
temp.AddObject(fileset);
temp.Write(ui.GetFilename("LOG","log"));
}
p.EndProcess();
}
void IsisMain(){
UserInterface &ui = Application::GetUserInterface();
ProcessByLine proc;
Cube *cube = proc.SetInputCube("FROM");
BigInt npixels(cube->Lines() * cube->Samples());
// Initialize the cleaner routine
try {
delete iclean;
iclean = new HiImageClean(*cube);
}
catch (iException &ie) {
std::string message = "Error attempting to initialize HiRISE cleaner object";
throw (iException::Message(iException::Programmer,message,_FILEINFO_));
}
catch (...) {
std::string message = "Unknown error occured attempting to initialize "
"HiRISE cleaner object";
throw (iException::Message(iException::Programmer,message,_FILEINFO_));
}
// For IR10, channel 1 lets restrict the last 3100 lines of dark current
PvlGroup &instrument = cube->GetGroup("Instrument");
std::string ccd = (std::string) instrument["CcdId"];
int channel = instrument["ChannelNumber"];
if ((ccd == "IR10") && (channel == 1)) {
int bin = instrument["Summing"];
int lastLine = cube->Lines() - ((3100/bin) + iclean->getFilterWidth()/2);
if (lastLine > 1) { iclean->setLastGoodLine(lastLine); }
}
#if defined(DEBUG)
std::cout << "Lines: " << cube->Lines() << " GoodLines: "
<< iclean->getLastGoodLine() << std::endl;
#endif
// Get the output file reference for label update
Cube *ocube = proc.SetOutputCube("TO");
proc.StartProcess(cleanImage);
iclean->propagateBlobs(ocube);
proc.EndProcess();
// Write statistics to file if requested
if (ui.WasEntered("CLEANSTATS")) {
std::string darkfile = ui.GetFilename("CLEANSTATS");
std::ofstream dfile;
dfile.open(darkfile.c_str(), std::ios::out | std::ios::trunc);
dfile << *iclean;
dfile.close();
}
// Dump stats to standard out
Pvl p;
PvlGroup grp;
iclean->PvlImageStats(grp);
p.AddGroup(grp);
Application::Log(grp);
BigInt nNulled = iclean->TotalNulled();
delete iclean;
iclean = 0;
// Check for calibration problems
if (nNulled != 0) {
double tpixels((double) nNulled / (double) npixels);
std::ostringstream mess;
mess << "There were " << nNulled << " of " << npixels << " ("
<< std::setw(6) << std::setprecision(2) << (tpixels * 100.0)
<< "%) due to insufficient calibration data (LUTTED or Gaps)"
<< std::ends;
throw (iException::Message(iException::Math,mess.str(),_FILEINFO_));
}
}
void IsisMain() {
// Get the camera information
Process p1;
Cube *icube = p1.SetInputCube("FROM",OneBand);
cam = icube->Camera();
// We will be processing by brick.
ProcessByBrick p;
// Find out which bands are to be created
UserInterface &ui = Application::GetUserInterface();
nbands = 0;
if ((phase = ui.GetBoolean("PHASE"))) nbands++;
if ((emission = ui.GetBoolean("EMISSION"))) nbands++;
if ((incidence = ui.GetBoolean("INCIDENCE"))) nbands++;
if ((latitude = ui.GetBoolean("LATITUDE"))) nbands++;
if ((longitude = ui.GetBoolean("LONGITUDE"))) nbands++;
if ((pixelResolution = ui.GetBoolean("PIXELRESOLUTION"))) nbands++;
if ((lineResolution = ui.GetBoolean("LINERESOLUTION"))) nbands++;
if ((sampleResolution = ui.GetBoolean("SAMPLERESOLUTION"))) nbands++;
if ((detectorResolution = ui.GetBoolean("DETECTORRESOLUTION"))) nbands++;
if ((northAzimuth = ui.GetBoolean("NORTHAZIMUTH"))) nbands++;
if ((sunAzimuth = ui.GetBoolean("SUNAZIMUTH"))) nbands++;
if ((spacecraftAzimuth = ui.GetBoolean("SPACECRAFTAZIMUTH"))) nbands++;
if ((offnadirAngle = ui.GetBoolean("OFFNADIRANGLE"))) nbands++;
if (nbands < 1) {
string message = "At least one photometry parameter must be entered"
"[PHASE, EMISSION, INCIDENCE, LATITUDE, LONGITUDE]";
throw iException::Message (iException::User, message, _FILEINFO_);
}
// Create a bandbin group for the output label
PvlKeyword name("Name");
if (phase) name += "Phase Angle";
if (emission) name += "Emission Angle";
if (incidence) name += "Incidence Angle";
if (latitude) name += "Latitude";
if (longitude) name += "Longitude";
if (pixelResolution) name += "Pixel Resolution";
if (lineResolution) name += "Line Resolution";
if (sampleResolution) name += "Sample Resolution";
if (detectorResolution) name += "Detector Resolution";
if (northAzimuth) name += "North Azimuth";
if (sunAzimuth) name += "Sun Azimuth";
if (spacecraftAzimuth) name += "Spacecraft Azimuth";
if (offnadirAngle) name += "OffNadir Angle";
PvlGroup bandBin("BandBin");
bandBin += name;
// Create the output cube. Note we add the input cube to expedite propagation
// of input cube elements (label, blobs, etc...). It *must* be cleared
// prior to systematic processing.
(void) p.SetInputCube("FROM", OneBand);
Cube *ocube = p.SetOutputCube("TO",icube->Samples(), icube->Lines(), nbands);
p.SetBrickSize(64,64,nbands);
p.ClearInputCubes(); // Toss the input file as stated above
// Start the processing
p.StartProcess(phocube);
// Add the bandbin group to the output label. If a BandBin group already
// exists, remove all existing keywords and add the keywords for this app.
// Otherwise, just put the group in.
PvlObject &cobj = ocube->Label()->FindObject("IsisCube");
if (cobj.HasGroup("BandBin")) {
PvlGroup &bb = cobj.FindGroup("BandBin");
bb.Clear();
PvlContainer::PvlKeywordIterator k = bandBin.Begin();
while (k != bandBin.End()) {
bb += *k;
++k;
}
}
else {
ocube->PutGroup(bandBin);
}
p.EndProcess();
}
/**
* This is the main method. Makeflat runs in three steps:
*
* 1) Calculate statistics
* - For all cameras, this checks for one band and matching
* sample counts.
* - For framing cameras, this checks the standard deviation of
* the images and records the averages of each image
* - For push frame cameras, this calls CheckFramelets for each
* image.
*
* 2) Create the temporary file, collect more detailed statistics
* - For all cameras, this generates the temporary file and calculates
* the final exclusion list
* - For framing/push frame cameras, the temporary file is
* 2 bands, where the first is a sum of DNs from each image/framelet
* and the second band is a count of valid DNs that went into each sum
*
* 3) Create the final flat field file
* - For all cameras, this processes the temporary file to create the final flat
* field file.
*/
void IsisMain() {
// Initialize variables
ResetGlobals();
UserInterface &ui = Application::GetUserInterface();
maxStdev = ui.GetDouble("STDEVTOL");
if(ui.GetString("IMAGETYPE") == "FRAMING") {
cameraType = Framing;
// framing cameras need to figure this out automatically
// during step 1
numFrameLines = -1;
}
else if(ui.GetString("IMAGETYPE") == "LINESCAN") {
cameraType = LineScan;
numFrameLines = ui.GetInteger("NUMLINES");
}
else {
cameraType = PushFrame;
numFrameLines = ui.GetInteger("FRAMELETHEIGHT");
}
FileList inList(ui.GetFilename("FROMLIST"));
Progress progress;
tempFileLength = 0;
numOutputSamples = 0;
/**
* Line scan progress is based on the input list, whereas
* the other cameras take much longer and are based on the
* images themselves. Prepare the progress if we're doing
* line scan.
*/
if(cameraType == LineScan) {
progress.SetText("Calculating Number of Image Lines");
progress.SetMaximumSteps(inList.size());
progress.CheckStatus();
}
/**
* For a push frame camera, the temp file is one framelet.
* Technically this is the same for the framing, but we
* don't know the height of a framelet yet.
*/
if(cameraType == PushFrame) {
tempFileLength = numFrameLines;
}
/**
* Start pass 1, use global currImage so that methods called
* know the image we're processing.
*/
for(currImage = 0; currImage < inList.size(); currImage++) {
/**
* Read the current cube into memory
*/
Cube tmp;
tmp.Open(Filename(inList[currImage]).Expanded());
/**
* If we haven't determined how many samples the output
* should have, we can do so now
*/
if(numOutputSamples == 0 && tmp.Bands() == 1) {
numOutputSamples = tmp.Samples();
}
/**
* Try and validate the image, quick tests first!
*
* (imageValid &= means imageValid = imageValid && ...)
*/
bool imageValid = true;
// Only single band images are acceptable
imageValid &= (tmp.Bands() == 1);
// Sample sizes must always match
imageValid &= (numOutputSamples == tmp.Samples());
// For push frame cameras, there must be valid all framelets
if(cameraType == PushFrame) {
imageValid &= (tmp.Lines() % numFrameLines == 0);
}
// For framing cameras, we need to figure out the size...
// setTempFileLength is used to revert if the file
// is decided to be invalid
bool setTempFileLength = false;
if(cameraType == Framing) {
if(tempFileLength == 0 && imageValid) {
tempFileLength = tmp.Lines();
numFrameLines = tempFileLength;
setTempFileLength = true;
}
imageValid &= (tempFileLength == tmp.Lines());
}
// Statistics are necessary at this point for push frame and framing cameras
// because the framing camera standard deviation tolerance is based on
// entire images, and push frame framelet exclusion stats can not be collected
// during pass 2 cleanly
if((cameraType == Framing || cameraType == PushFrame) && imageValid) {
string prog = "Calculating Standard Deviation " + iString((int)currImage+1) + "/";
prog += iString((int)inList.size()) + " (" + Filename(inList[currImage]).Name() + ")";
if(cameraType == Framing) {
Statistics *stats = tmp.Statistics(1, prog);
imageValid &= !IsSpecial(stats->StandardDeviation());
imageValid &= !IsSpecial(stats->Average());
imageValid &= stats->StandardDeviation() <= maxStdev;
vector<double> fileStats;
fileStats.push_back(stats->Average());
inputFrameletAverages.push_back(fileStats);
delete stats;
}
else if(cameraType == PushFrame) {
imageValid &= CheckFramelets(prog, tmp);
}
if(setTempFileLength && !imageValid) {
tempFileLength = 0;
}
}
// The line scan camera needs to actually count the number of lines in each image to know
// how many total frames there are before beginning pass 2.
if(imageValid && (cameraType == LineScan)) {
int lines = (tmp.Lines() / numFrameLines);
// partial frame?
if(tmp.Lines() % numFrameLines != 0) {
lines ++;
}
tempFileLength += lines;
}
else if(!imageValid) {
excludedFiles.insert(pair<int, bool>(currImage, true));
}
tmp.Close();
if(cameraType == LineScan) {
progress.CheckStatus();
}
}
/**
* If the number of output samples could not be determined, we never
* found a legitimate cube.
*/
if(numOutputSamples <= 0) {
string msg = "No valid input cubes were found";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
/**
* If theres no temp file length, which is based off of valid data in
* the input cubes, then we havent found any valid data.
*/
if(tempFileLength <= 0) {
string msg = "No valid input data was found";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
/**
* ocube is now the temporary file (for pass 2).
*/
ocube = new Cube();
ocube->SetDimensions(numOutputSamples, tempFileLength, 2);
PvlGroup &prefs = Preference::Preferences().FindGroup("DataDirectory", Pvl::Traverse);
iString outTmpName = (string)prefs["Temporary"][0] + "/";
outTmpName += Filename(ui.GetFilename("TO")).Basename() + ".tmp.cub";
ocube->Create(outTmpName);
oLineMgr = new LineManager(*ocube);
oLineMgr->SetLine(1);
ProcessByBrick p;
int excludedCnt = 0;
if(cameraType == LineScan) {
outputTmpAverages.resize(numOutputSamples);
outputTmpCounts.resize(numOutputSamples);
numInputDns.resize(numOutputSamples);
}
cubeInitialized = false;
for(currImage = 0; currImage < inList.size(); currImage++) {
if(Excluded(currImage)) {
excludedCnt ++;
continue;
}
PvlObject currFile("Exclusions");
currFile += PvlKeyword("Filename", inList[currImage]);
currFile += PvlKeyword("Tolerance", maxStdev);
if(cameraType == LineScan) {
currFile += PvlKeyword("FrameLines", numFrameLines);
}
else if(cameraType == PushFrame) {
currFile += PvlKeyword("FrameletLines", numFrameLines);
}
excludedDetails.push_back(currFile);
CubeAttributeInput inAtt;
// This needs to be set constantly because ClearInputCubes
// seems to be removing the input brick size.
if(cameraType == LineScan) {
p.SetBrickSize(1, numFrameLines, 1);
}
else if(cameraType == Framing || cameraType == PushFrame) {
p.SetBrickSize(numOutputSamples, 1, 1);
}
p.SetInputCube(inList[currImage], inAtt);
iString progText = "Calculating Averages " + iString((int)currImage+1);
progText += "/" + iString((int)inList.size());
progText += " (" + Filename(inList[currImage]).Name() + ")";
p.Progress()->SetText(progText);
p.StartProcess(CreateTemporaryData);
p.EndProcess();
p.ClearInputCubes();
if(excludedDetails[excludedDetails.size()-1].Groups() == 0) {
excludedDetails.resize(excludedDetails.size()-1);
}
}
/**
* Pass 2 completed. The processing methods were responsible for writing
* the entire temporary cube.
*/
if(oLineMgr) {
delete oLineMgr;
oLineMgr = NULL;
}
if(ocube) {
ocube->Close();
delete ocube;
}
/**
* ocube is now the final output
*/
ocube = new Cube();
if(cameraType == LineScan) {
ocube->SetDimensions(numOutputSamples, 1, 1);
}
else if(cameraType == Framing || cameraType == PushFrame) {
ocube->SetDimensions(numOutputSamples, tempFileLength, 1);
}
ocube->Create(Filename(ui.GetFilename("TO")).Expanded());
oLineMgr = new LineManager(*ocube);
oLineMgr->SetLine(1);
// We now have the necessary temp file, let's go ahead and combine it into
// the final output!
p.SetInputBrickSize(numOutputSamples, 1, 2);
p.SetOutputBrickSize(numOutputSamples, 1, 1);
cubeInitialized = false;
CubeAttributeInput inAtt;
p.Progress()->SetText("Calculating Final Flat Field");
p.SetInputCube(outTmpName, inAtt);
p.StartProcess(ProcessTemporaryData);
p.EndProcess();
if(cameraType == LineScan) {
ocube->Write(*oLineMgr);
}
if(oLineMgr) {
delete oLineMgr;
oLineMgr = NULL;
}
if(ocube) {
ocube->Close();
delete ocube;
ocube = NULL;
}
/**
* Build a list of excluded files
*/
PvlGroup excludedFiles("ExcludedFiles");
for(currImage = 0; currImage < inList.size(); currImage++) {
if(Excluded(currImage)) {
excludedFiles += PvlKeyword("File", inList[currImage]);
}
}
// log the results
Application::Log(excludedFiles);
if(ui.WasEntered("EXCLUDE")) {
Pvl excludeFile;
// Find excluded files
excludeFile.AddGroup(excludedFiles);
for(unsigned int i = 0; i < excludedDetails.size(); i++) {
excludeFile.AddObject(excludedDetails[i]);
}
excludeFile.Write(Filename(ui.GetFilename("EXCLUDE")).Expanded());
}
remove(outTmpName.c_str());
// Clean up settings
ResetGlobals();
}
void IsisMain() {
//Create a process to create the input cubes
Process p;
//Create the input cubes, matching sample/lines
Cube *inCube = p.SetInputCube ("FROM");
Cube *latCube = p.SetInputCube("LATCUB", SpatialMatch);
Cube *lonCube = p.SetInputCube("LONCUB", SpatialMatch);
//A 1x1 brick to read in the latitude and longitude DN values from
//the specified cubes
Brick latBrick(1,1,1, latCube->PixelType());
Brick lonBrick(1,1,1, lonCube->PixelType());
UserInterface &ui = Application::GetUserInterface();
//Set the sample and line increments
int sinc = (int)(inCube->Samples() * 0.10);
if(ui.WasEntered("SINC")) {
sinc = ui.GetInteger("SINC");
}
int linc = (int)(inCube->Lines() * 0.10);
if(ui.WasEntered("LINC")) {
linc = ui.GetInteger("LINC");
}
//Set the degree of the polynomial to use in our functions
int degree = ui.GetInteger("DEGREE");
//We are using a polynomial with two variables
PolynomialBivariate sampFunct(degree);
PolynomialBivariate lineFunct(degree);
//We will be solving the function using the least squares method
LeastSquares sampSol(sampFunct);
LeastSquares lineSol(lineFunct);
//Setup the variables for solving the stereographic projection
//x = cos(latitude) * sin(longitude - lon_center)
//y = cos(lat_center) * sin(latitude) - sin(lat_center) * cos(latitude) * cos(longitude - lon_center)
//Get the center lat and long from the input cubes
double lat_center = latCube->Statistics()->Average() * PI/180.0;
double lon_center = lonCube->Statistics()->Average() * PI/180.0;
/**
* Loop through lines and samples projecting the latitude and longitude at those
* points to stereographic x and y and adding these points to the LeastSquares
* matrix.
*/
for(int i = 1; i <= inCube->Lines(); i+= linc) {
for(int j = 1; j <= inCube->Samples(); j+= sinc) {
latBrick.SetBasePosition(j, i, 1);
latCube->Read(latBrick);
if(IsSpecial(latBrick.at(0))) continue;
double lat = latBrick.at(0) * PI/180.0;
lonBrick.SetBasePosition(j, i, 1);
lonCube->Read(lonBrick);
if(IsSpecial(lonBrick.at(0))) continue;
double lon = lonBrick.at(0) * PI/180.0;
//Project lat and lon to x and y using a stereographic projection
double k = 2/(1 + sin(lat_center) * sin(lat) + cos(lat_center)*cos(lat)*cos(lon - lon_center));
double x = k * cos(lat) * sin(lon - lon_center);
double y = k * (cos(lat_center) * sin(lat)) - (sin(lat_center) * cos(lat) * cos(lon - lon_center));
//Add x and y to the least squares matrix
vector<double> data;
data.push_back(x);
data.push_back(y);
sampSol.AddKnown(data, j);
lineSol.AddKnown(data, i);
//If the sample increment goes past the last sample in the line, we want to
//always read the last sample..
if(j != inCube->Samples() && j + sinc > inCube->Samples()) {
j = inCube->Samples() - sinc;
}
}
//If the line increment goes past the last line in the cube, we want to
//always read the last line..
if(i != inCube->Lines() && i + linc > inCube->Lines()) {
i = inCube->Lines() - linc;
}
}
//Solve the least squares functions using QR Decomposition
sampSol.Solve(LeastSquares::QRD);
lineSol.Solve(LeastSquares::QRD);
//If the user wants to save the residuals to a file, create a file and write
//the column titles to it.
TextFile oFile;
if(ui.WasEntered("RESIDUALS")) {
oFile.Open(ui.GetFilename("RESIDUALS"), "overwrite");
oFile.PutLine("Sample,\tLine,\tX,\tY,\tSample Error,\tLine Error\n");
}
//Gather the statistics for the residuals from the least squares solutions
Statistics sampErr;
Statistics lineErr;
vector<double> sampResiduals = sampSol.Residuals();
vector<double> lineResiduals = lineSol.Residuals();
for(int i = 0; i < (int)sampResiduals.size(); i++) {
sampErr.AddData(sampResiduals[i]);
lineErr.AddData(lineResiduals[i]);
}
//If a residuals file was specified, write the previous data, and the errors to the file.
if(ui.WasEntered("RESIDUALS")) {
for(int i = 0; i < sampSol.Rows(); i++) {
vector<double> data = sampSol.GetInput(i);
iString tmp = "";
tmp += iString(sampSol.GetExpected(i));
tmp += ",\t";
tmp += iString(lineSol.GetExpected(i));
tmp += ",\t";
tmp += iString(data[0]);
tmp += ",\t";
tmp += iString(data[1]);
tmp += ",\t";
tmp += iString(sampResiduals[i]);
tmp += ",\t";
tmp += iString(lineResiduals[i]);
oFile.PutLine(tmp + "\n");
}
}
oFile.Close();
//Records the error to the log
PvlGroup error( "Error" );
error += PvlKeyword( "Degree", degree );
error += PvlKeyword( "NumberOfPoints", (int)sampResiduals.size() );
error += PvlKeyword( "SampleMinimumError", sampErr.Minimum() );
error += PvlKeyword( "SampleAverageError", sampErr.Average() );
error += PvlKeyword( "SampleMaximumError", sampErr.Maximum() );
error += PvlKeyword( "SampleStdDeviationError", sampErr.StandardDeviation() );
error += PvlKeyword( "LineMinimumError", lineErr.Minimum() );
error += PvlKeyword( "LineAverageError", lineErr.Average() );
error += PvlKeyword( "LineMaximumError", lineErr.Maximum() );
error += PvlKeyword( "LineStdDeviationError", lineErr.StandardDeviation() );
Application::Log( error );
//Close the input cubes for cleanup
p.EndProcess();
//If we want to warp the image, then continue, otherwise return
if(!ui.GetBoolean("NOWARP")) {
//Creates the mapping group
Pvl mapFile;
mapFile.Read(ui.GetFilename("MAP"));
PvlGroup &mapGrp = mapFile.FindGroup("Mapping",Pvl::Traverse);
//Reopen the lat and long cubes
latCube = new Cube();
latCube->SetVirtualBands(ui.GetInputAttribute("LATCUB").Bands());
latCube->Open(ui.GetFilename("LATCUB"));
lonCube = new Cube();
lonCube->SetVirtualBands(ui.GetInputAttribute("LONCUB").Bands());
lonCube->Open(ui.GetFilename("LONCUB"));
PvlKeyword targetName;
//If the user entered the target name
if(ui.WasEntered("TARGET")) {
targetName = PvlKeyword("TargetName", ui.GetString("TARGET"));
}
//Else read the target name from the input cube
else {
Pvl fromFile;
fromFile.Read(ui.GetFilename("FROM"));
targetName = fromFile.FindKeyword("TargetName", Pvl::Traverse);
}
mapGrp.AddKeyword(targetName, Pvl::Replace);
PvlKeyword equRadius;
PvlKeyword polRadius;
//If the user entered the equatorial and polar radii
if(ui.WasEntered("EQURADIUS") && ui.WasEntered("POLRADIUS")) {
equRadius = PvlKeyword("EquatorialRadius", ui.GetDouble("EQURADIUS"));
polRadius = PvlKeyword("PolarRadius", ui.GetDouble("POLRADIUS"));
}
//Else read them from the pck
else {
Filename pckFile("$base/kernels/pck/pck?????.tpc");
pckFile.HighestVersion();
string pckFilename = pckFile.Expanded();
furnsh_c(pckFilename.c_str());
string target = targetName[0];
SpiceInt code;
SpiceBoolean found;
bodn2c_c (target.c_str(), &code, &found);
if (!found) {
string msg = "Could not convert Target [" + target +
"] to NAIF code";
throw Isis::iException::Message(Isis::iException::Io,msg,_FILEINFO_);
}
SpiceInt n;
SpiceDouble radii[3];
bodvar_c(code,"RADII",&n,radii);
equRadius = PvlKeyword("EquatorialRadius", radii[0] * 1000);
polRadius = PvlKeyword("PolarRadius", radii[2] * 1000);
}
mapGrp.AddKeyword(equRadius, Pvl::Replace);
mapGrp.AddKeyword(polRadius, Pvl::Replace);
//If the latitude type is not in the mapping group, copy it from the input
if(!mapGrp.HasKeyword("LatitudeType")) {
if(ui.GetString("LATTYPE") == "PLANETOCENTRIC") {
mapGrp.AddKeyword(PvlKeyword("LatitudeType","Planetocentric"), Pvl::Replace);
}
else {
mapGrp.AddKeyword(PvlKeyword("LatitudeType","Planetographic"), Pvl::Replace);
}
}
//If the longitude direction is not in the mapping group, copy it from the input
if(!mapGrp.HasKeyword("LongitudeDirection")) {
if(ui.GetString("LONDIR") == "POSITIVEEAST") {
mapGrp.AddKeyword(PvlKeyword("LongitudeDirection","PositiveEast"), Pvl::Replace);
}
else {
mapGrp.AddKeyword(PvlKeyword("LongitudeDirection","PositiveWest"), Pvl::Replace);
}
}
//If the longitude domain is not in the mapping group, assume it is 360
if(!mapGrp.HasKeyword("LongitudeDomain")) {
mapGrp.AddKeyword(PvlKeyword("LongitudeDomain","360"), Pvl::Replace);
}
//If the default range is to be computed, use the input lat/long cubes to determine the range
if(ui.GetString("DEFAULTRANGE") == "COMPUTE") {
//NOTE - When computing the min/max longitude this application does not account for the
//longitude seam if it exists. Since the min/max are calculated from the statistics of
//the input longitude cube and then converted to the mapping group's domain they may be
//invalid for cubes containing the longitude seam.
Statistics *latStats = latCube->Statistics();
Statistics *lonStats = lonCube->Statistics();
double minLat = latStats->Minimum();
double maxLat = latStats->Maximum();
bool isOcentric = ((std::string)mapGrp.FindKeyword("LatitudeType")) == "Planetocentric";
if(isOcentric) {
if(ui.GetString("LATTYPE") != "PLANETOCENTRIC") {
minLat = Projection::ToPlanetocentric(minLat, (double)equRadius, (double)polRadius);
maxLat = Projection::ToPlanetocentric(maxLat, (double)equRadius, (double)polRadius);
}
}
else {
if(ui.GetString("LATTYPE") == "PLANETOCENTRIC") {
minLat = Projection::ToPlanetographic(minLat, (double)equRadius, (double)polRadius);
maxLat = Projection::ToPlanetographic(maxLat, (double)equRadius, (double)polRadius);
}
}
int lonDomain = (int)mapGrp.FindKeyword("LongitudeDomain");
double minLon = lonDomain == 360 ? Projection::To360Domain(lonStats->Minimum()) : Projection::To180Domain(lonStats->Minimum());
double maxLon = lonDomain == 360 ? Projection::To360Domain(lonStats->Maximum()) : Projection::To180Domain(lonStats->Maximum());
bool isPosEast = ((std::string)mapGrp.FindKeyword("LongitudeDirection")) == "PositiveEast";
if(isPosEast) {
if(ui.GetString("LONDIR") != "POSITIVEEAST") {
minLon = Projection::ToPositiveEast(minLon, lonDomain);
maxLon = Projection::ToPositiveEast(maxLon, lonDomain);
}
}
else {
if(ui.GetString("LONDIR") == "POSITIVEEAST") {
minLon = Projection::ToPositiveWest(minLon, lonDomain);
maxLon = Projection::ToPositiveWest(maxLon, lonDomain);
}
}
if(minLon > maxLon) {
double temp = minLon;
minLon = maxLon;
maxLon = temp;
}
mapGrp.AddKeyword(PvlKeyword("MinimumLatitude", minLat),Pvl::Replace);
mapGrp.AddKeyword(PvlKeyword("MaximumLatitude", maxLat),Pvl::Replace);
mapGrp.AddKeyword(PvlKeyword("MinimumLongitude", minLon),Pvl::Replace);
mapGrp.AddKeyword(PvlKeyword("MaximumLongitude", maxLon),Pvl::Replace);
}
//If the user decided to enter a ground range then override
if (ui.WasEntered("MINLAT")) {
mapGrp.AddKeyword(PvlKeyword("MinimumLatitude",
ui.GetDouble("MINLAT")),Pvl::Replace);
}
if (ui.WasEntered("MAXLAT")) {
mapGrp.AddKeyword(PvlKeyword("MaximumLatitude",
ui.GetDouble("MAXLAT")),Pvl::Replace);
}
if (ui.WasEntered("MINLON")) {
mapGrp.AddKeyword(PvlKeyword("MinimumLongitude",
ui.GetDouble("MINLON")),Pvl::Replace);
}
if (ui.WasEntered("MAXLON")) {
mapGrp.AddKeyword(PvlKeyword("MaximumLongitude",
ui.GetDouble("MAXLON")),Pvl::Replace);
}
//If the pixel resolution is to be computed, compute the pixels/degree from the input
if (ui.GetString("PIXRES") == "COMPUTE") {
latBrick.SetBasePosition(1,1,1);
latCube->Read(latBrick);
lonBrick.SetBasePosition(1,1,1);
lonCube->Read(lonBrick);
//Read the lat and long at the upper left corner
double a = latBrick.at(0) * PI/180.0;
double c = lonBrick.at(0) * PI/180.0;
latBrick.SetBasePosition(latCube->Samples(),latCube->Lines(),1);
latCube->Read(latBrick);
lonBrick.SetBasePosition(lonCube->Samples(),lonCube->Lines(),1);
lonCube->Read(lonBrick);
//Read the lat and long at the lower right corner
double b = latBrick.at(0) * PI/180.0;
double d = lonBrick.at(0) * PI/180.0;
//Determine the angle between the two points
double angle = acos(cos(a) * cos(b) * cos(c - d) + sin(a) * sin(b));
//double angle = acos((cos(a1) * cos(b1) * cos(b2)) + (cos(a1) * sin(b1) * cos(a2) * sin(b2)) + (sin(a1) * sin(a2)));
angle *= 180/PI;
//Determine the number of pixels between the two points
double pixels = sqrt(pow(latCube->Samples() -1.0, 2.0) + pow(latCube->Lines() -1.0, 2.0));
//Add the scale in pixels/degree to the mapping group
mapGrp.AddKeyword(PvlKeyword("Scale",
pixels/angle, "pixels/degree"),
Pvl::Replace);
if (mapGrp.HasKeyword("PixelResolution")) {
mapGrp.DeleteKeyword("PixelResolution");
}
}
// If the user decided to enter a resolution then override
if (ui.GetString("PIXRES") == "MPP") {
mapGrp.AddKeyword(PvlKeyword("PixelResolution",
ui.GetDouble("RESOLUTION"), "meters/pixel"),
Pvl::Replace);
if (mapGrp.HasKeyword("Scale")) {
mapGrp.DeleteKeyword("Scale");
}
}
else if (ui.GetString("PIXRES") == "PPD") {
mapGrp.AddKeyword(PvlKeyword("Scale",
ui.GetDouble("RESOLUTION"), "pixels/degree"),
Pvl::Replace);
if (mapGrp.HasKeyword("PixelResolution")) {
mapGrp.DeleteKeyword("PixelResolution");
}
}
//Create a projection using the map file we created
int samples,lines;
Projection *outmap = ProjectionFactory::CreateForCube(mapFile,samples,lines,false);
//Write the map file to the log
Application::GuiLog(mapGrp);
//Create a process rubber sheet
ProcessRubberSheet r;
//Set the input cube
inCube = r.SetInputCube("FROM");
double tolerance = ui.GetDouble("TOLERANCE") * outmap->Resolution();
//Create a new transform object
Transform *transform = new nocam2map (sampSol, lineSol, outmap,
latCube, lonCube,
ui.GetString("LATTYPE") == "PLANETOCENTRIC",
ui.GetString("LONDIR") == "POSITIVEEAST",
tolerance, ui.GetInteger("ITERATIONS"),
inCube->Samples(), inCube->Lines(),
samples, lines);
//Allocate the output cube and add the mapping labels
Cube *oCube = r.SetOutputCube ("TO", transform->OutputSamples(),
transform->OutputLines(),
inCube->Bands());
oCube->PutGroup(mapGrp);
//Determine which interpolation to use
Interpolator *interp = NULL;
if (ui.GetString("INTERP") == "NEARESTNEIGHBOR") {
interp = new Interpolator(Interpolator::NearestNeighborType);
}
else if (ui.GetString("INTERP") == "BILINEAR") {
interp = new Interpolator(Interpolator::BiLinearType);
}
else if (ui.GetString("INTERP") == "CUBICCONVOLUTION") {
interp = new Interpolator(Interpolator::CubicConvolutionType);
}
//Warp the cube
r.StartProcess(*transform, *interp);
r.EndProcess();
// add mapping to print.prt
PvlGroup mapping = outmap->Mapping();
Application::Log(mapping);
//Clean up
delete latCube;
delete lonCube;
delete outmap;
delete transform;
delete interp;
}
}
void IsisMain() {
// We will be warping a cube
ProcessRubberSheet p;
// Get the map projection file provided by the user
UserInterface &ui = Application::GetUserInterface();
Pvl userPvl(ui.GetFilename("MAP"));
PvlGroup &userMappingGrp = userPvl.FindGroup("Mapping",Pvl::Traverse);
// Open the input cube and get the projection
Cube *icube = p.SetInputCube ("FROM");
// Get the mapping group
PvlGroup fromMappingGrp = icube->GetGroup("Mapping");
Projection *inproj = icube->Projection();
PvlGroup outMappingGrp = fromMappingGrp;
// If the default range is FROM, then wipe out any range data in user mapping file
if(ui.GetString("DEFAULTRANGE").compare("FROM") == 0 && !ui.GetBoolean("MATCHMAP")) {
if(userMappingGrp.HasKeyword("MinimumLatitude")) {
userMappingGrp.DeleteKeyword("MinimumLatitude");
}
if(userMappingGrp.HasKeyword("MaximumLatitude")) {
userMappingGrp.DeleteKeyword("MaximumLatitude");
}
if(userMappingGrp.HasKeyword("MinimumLongitude")) {
userMappingGrp.DeleteKeyword("MinimumLongitude");
}
if(userMappingGrp.HasKeyword("MaximumLongitude")) {
userMappingGrp.DeleteKeyword("MaximumLongitude");
}
}
// Deal with user overrides entered in the GUI. Do this by changing the user's mapping group, which
// will then overlay anything in the output mapping group.
if(ui.WasEntered("MINLAT") && !ui.GetBoolean("MATCHMAP")) {
userMappingGrp.AddKeyword( PvlKeyword("MinimumLatitude", ui.GetDouble("MINLAT")), Pvl::Replace );
}
if(ui.WasEntered("MAXLAT") && !ui.GetBoolean("MATCHMAP")) {
userMappingGrp.AddKeyword( PvlKeyword("MaximumLatitude", ui.GetDouble("MAXLAT")), Pvl::Replace );
}
if(ui.WasEntered("MINLON") && !ui.GetBoolean("MATCHMAP")) {
userMappingGrp.AddKeyword( PvlKeyword("MinimumLongitude", ui.GetDouble("MINLON")), Pvl::Replace );
}
if(ui.WasEntered("MAXLON") && !ui.GetBoolean("MATCHMAP")) {
userMappingGrp.AddKeyword( PvlKeyword("MaximumLongitude", ui.GetDouble("MAXLON")), Pvl::Replace );
}
/**
* If the user is changing from positive east to positive west, or vice-versa, the output minimum is really
* the input maximum. However, the user mapping group must be left unaffected (an input minimum must be the
* output minimum). To accomplish this, we swap the minimums/maximums in the output group ahead of time. This
* causes the minimums and maximums to correlate to the output minimums and maximums. That way when we copy
* the user mapping group into the output group a mimimum overrides a minimum and a maximum overrides a maximum.
*/
bool sameDirection = true;
if(userMappingGrp.HasKeyword("LongitudeDirection")) {
if(((string)userMappingGrp["LongitudeDirection"]).compare(fromMappingGrp["LongitudeDirection"]) != 0) {
sameDirection = false;
}
}
// Since the out mapping group came from the from mapping group, which came from a valid cube,
// we can assume both min/max lon exists if min longitude exists.
if(!sameDirection && outMappingGrp.HasKeyword("MinimumLongitude")) {
double minLon = outMappingGrp["MinimumLongitude"];
double maxLon = outMappingGrp["MaximumLongitude"];
outMappingGrp["MaximumLongitude"] = minLon;
outMappingGrp["MinimumLongitude"] = maxLon;
}
if(ui.GetString("PIXRES").compare("FROM") == 0 && !ui.GetBoolean("MATCHMAP")) {
// Resolution will be in fromMappingGrp and outMappingGrp at this time
// delete from user mapping grp
if(userMappingGrp.HasKeyword("Scale")) {
userMappingGrp.DeleteKeyword("Scale");
}
if(userMappingGrp.HasKeyword("PixelResolution")) {
userMappingGrp.DeleteKeyword("PixelResolution");
}
}
else if(ui.GetString("PIXRES").compare("MAP") == 0 || ui.GetBoolean("MATCHMAP")) {
// Resolution will be in userMappingGrp - delete all others
if(outMappingGrp.HasKeyword("Scale")) {
outMappingGrp.DeleteKeyword("Scale");
}
if(outMappingGrp.HasKeyword("PixelResolution")) {
outMappingGrp.DeleteKeyword("PixelResolution");
}
if(fromMappingGrp.HasKeyword("Scale")); {
fromMappingGrp.DeleteKeyword("Scale");
}
if(fromMappingGrp.HasKeyword("PixelResolution")) {
fromMappingGrp.DeleteKeyword("PixelResolution");
}
}
else if(ui.GetString("PIXRES").compare("MPP") == 0) {
// Resolution specified - delete all and add to outMappingGrp
if(outMappingGrp.HasKeyword("Scale")) {
outMappingGrp.DeleteKeyword("Scale");
}
if(outMappingGrp.HasKeyword("PixelResolution")) {
outMappingGrp.DeleteKeyword("PixelResolution");
}
if(fromMappingGrp.HasKeyword("Scale")) {
fromMappingGrp.DeleteKeyword("Scale");
}
if(fromMappingGrp.HasKeyword("PixelResolution")) {
fromMappingGrp.DeleteKeyword("PixelResolution");
}
if(userMappingGrp.HasKeyword("Scale")) {
userMappingGrp.DeleteKeyword("Scale");
}
if(userMappingGrp.HasKeyword("PixelResolution")) {
userMappingGrp.DeleteKeyword("PixelResolution");
}
outMappingGrp.AddKeyword(PvlKeyword("PixelResolution", ui.GetDouble("RESOLUTION"), "meters/pixel"), Pvl::Replace);
}
else if(ui.GetString("PIXRES").compare("PPD") == 0) {
// Resolution specified - delete all and add to outMappingGrp
if(outMappingGrp.HasKeyword("Scale")) {
outMappingGrp.DeleteKeyword("Scale");
}
if(outMappingGrp.HasKeyword("PixelResolution")) {
outMappingGrp.DeleteKeyword("PixelResolution");
}
if(fromMappingGrp.HasKeyword("Scale")) {
fromMappingGrp.DeleteKeyword("Scale");
}
if(fromMappingGrp.HasKeyword("PixelResolution")) {
fromMappingGrp.DeleteKeyword("PixelResolution");
}
if(userMappingGrp.HasKeyword("Scale")) {
userMappingGrp.DeleteKeyword("Scale");
}
if(userMappingGrp.HasKeyword("PixelResolution")) {
userMappingGrp.DeleteKeyword("PixelResolution");
}
outMappingGrp.AddKeyword(PvlKeyword("Scale", ui.GetDouble("RESOLUTION"), "pixels/degree"), Pvl::Replace);
}
// Rotation will NOT Propagate
if(outMappingGrp.HasKeyword("Rotation")) {
outMappingGrp.DeleteKeyword("Rotation");
}
/**
* The user specified map template file overrides what ever is in the
* cube's mapping group.
*/
for(int keyword = 0; keyword < userMappingGrp.Keywords(); keyword ++) {
outMappingGrp.AddKeyword(userMappingGrp[keyword], Pvl::Replace);
}
/**
* Now, we have to deal with unit conversions. We convert only if the following are true:
* 1) We used values from the input cube
* 2) The values are longitudes or latitudes
* 3) The map file or user-specified information uses a different measurement system than
* the input cube for said values.
*
* The data is corrected for:
* 1) Positive east/positive west
* 2) Longitude domain
* 3) planetographic/planetocentric.
*/
// First, the longitude direction
if(!sameDirection) {
PvlGroup longitudes = inproj->MappingLongitudes();
for(int index = 0; index < longitudes.Keywords(); index ++) {
if(!userMappingGrp.HasKeyword(longitudes[index].Name())) {
// use the from domain because that's where our values are coming from
if(((string)userMappingGrp["LongitudeDirection"]).compare("PositiveEast") == 0) {
outMappingGrp[longitudes[index].Name()] =
Projection::ToPositiveEast(outMappingGrp[longitudes[index].Name()], outMappingGrp["LongitudeDomain"]);
}
else {
outMappingGrp[longitudes[index].Name()] =
Projection::ToPositiveWest(outMappingGrp[longitudes[index].Name()], outMappingGrp["LongitudeDomain"]);
}
}
}
}
// The minimum/maximum longitudes should be in order now. However, if the user entered a
// maximum that was lower than the minimum, or a minimum that was higher than the maximum this
// may still fail. Let it throw an error when we instantiate the projection.
// Second, longitude domain
if(userMappingGrp.HasKeyword("LongitudeDomain")) { // user set a new domain?
if((int)userMappingGrp["LongitudeDomain"] != (int)fromMappingGrp["LongitudeDomain"]) { // new domain different?
PvlGroup longitudes = inproj->MappingLongitudes();
for(int index = 0; index < longitudes.Keywords(); index ++) {
if(!userMappingGrp.HasKeyword(longitudes[index].Name())) {
if((int)userMappingGrp["LongitudeDomain"] == 180) {
outMappingGrp[longitudes[index].Name()] = Projection::To180Domain(outMappingGrp[longitudes[index].Name()]);
}
else {
outMappingGrp[longitudes[index].Name()] = Projection::To360Domain(outMappingGrp[longitudes[index].Name()]);
}
}
}
}
}
// Third, planetographic/planetocentric
if(userMappingGrp.HasKeyword("LatitudeType")) { // user set a new domain?
if(((string)userMappingGrp["LatitudeType"]).compare(fromMappingGrp["LatitudeType"]) != 0) { // new lat type different?
PvlGroup latitudes = inproj->MappingLatitudes();
for(int index = 0; index < latitudes.Keywords(); index ++) {
if(!userMappingGrp.HasKeyword(latitudes[index].Name())) {
if(((string)userMappingGrp["LatitudeType"]).compare("Planetographic") == 0) {
outMappingGrp[latitudes[index].Name()] = Projection::ToPlanetographic(
(double)fromMappingGrp[latitudes[index].Name()],
(double)fromMappingGrp["EquatorialRadius"],
(double)fromMappingGrp["PolarRadius"]);
}
else {
outMappingGrp[latitudes[index].Name()] = Projection::ToPlanetocentric(
(double)fromMappingGrp[latitudes[index].Name()],
(double)fromMappingGrp["EquatorialRadius"],
(double)fromMappingGrp["PolarRadius"]);
}
}
}
}
}
// If MinLon/MaxLon out of order, we weren't able to calculate the correct values
if((double)outMappingGrp["MinimumLongitude"] >= (double)outMappingGrp["MaximumLongitude"]) {
if(!ui.WasEntered("MINLON") || !ui.WasEntered("MAXLON")) {
string msg = "Unable to determine the correct [MinimumLongitude,MaximumLongitude].";
msg += " Please specify these values in the [MINLON,MAXLON] parameters";
throw iException::Message(iException::Pvl,msg,_FILEINFO_);
}
}
int samples,lines;
Pvl mapData;
// Copy to preserve cube labels so we can match cube size
if (userPvl.HasObject("IsisCube")) {
mapData = userPvl;
mapData.FindObject("IsisCube").DeleteGroup("Mapping");
mapData.FindObject("IsisCube").AddGroup(outMappingGrp);
}
else {
mapData.AddGroup(outMappingGrp);
}
// *NOTE: The UpperLeftX,UpperLeftY keywords will not be used in the CreateForCube
// method, and they will instead be recalculated. This is correct.
Projection *outproj = ProjectionFactory::CreateForCube(mapData,samples,lines,
ui.GetBoolean("MATCHMAP"));
// Set up the transform object which will simply map
// output line/samps -> output lat/lons -> input line/samps
Transform *transform = new map2map (icube->Samples(),
icube->Lines(),
icube->Projection(),
samples,
lines,
outproj,
ui.GetBoolean("TRIM"));
// Allocate the output cube and add the mapping labels
Cube *ocube = p.SetOutputCube ("TO", transform->OutputSamples(),
transform->OutputLines(),
icube->Bands());
PvlGroup cleanOutGrp = outproj->Mapping();
// ProjectionFactory::CreateForCube updated mapData to have the correct
// upperleftcornerx, upperleftcornery, scale and resolution. Use these
// updated numbers.
cleanOutGrp.AddKeyword(mapData.FindGroup("Mapping",Pvl::Traverse)["UpperLeftCornerX"], Pvl::Replace);
cleanOutGrp.AddKeyword(mapData.FindGroup("Mapping",Pvl::Traverse)["UpperLeftCornerY"], Pvl::Replace);
cleanOutGrp.AddKeyword(mapData.FindGroup("Mapping",Pvl::Traverse)["Scale"], Pvl::Replace);
cleanOutGrp.AddKeyword(mapData.FindGroup("Mapping",Pvl::Traverse)["PixelResolution"], Pvl::Replace);
ocube->PutGroup(cleanOutGrp);
// Set up the interpolator
Interpolator *interp;
if (ui.GetString("INTERP") == "NEARESTNEIGHBOR") {
interp = new Interpolator(Interpolator::NearestNeighborType);
}
else if (ui.GetString("INTERP") == "BILINEAR") {
interp = new Interpolator(Interpolator::BiLinearType);
}
else if (ui.GetString("INTERP") == "CUBICCONVOLUTION") {
interp = new Interpolator(Interpolator::CubicConvolutionType);
}
else {
string msg = "Unknow value for INTERP [" + ui.GetString("INTERP") + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// Warp the cube
p.StartProcess(*transform, *interp);
p.EndProcess();
Application::Log(cleanOutGrp);
// Cleanup
delete transform;
delete interp;
}
void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
/*Processing steps
1. Open and read the jitter table, convert the pixel offsets to angles,
and create the polynomials (solve for the coefficients) to use to do
the high pass filter putting the results into a rotation matrix in the jitter class.
2. Apply the jitter correction in the LineScanCameraRotation object of the master cube.
3. Loop through FROMLIST correcting the pointing and writing out the
updated camera pointing from the master cube
*/
int degree = ui.GetInteger("DEGREE");
// Get the input file list to make sure it is not empty and the master cube is included
FileList list;
list.Read(ui.GetFilename("FROMLIST"));
if (list.size() < 1) {
string msg = "The input list file [" + ui.GetFilename("FROMLIST") + "is empty";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
int ifile = 0;
// Make sure the master file is included in the input file list
while (ifile < (int) list.size() && Filename(list[ifile]).Expanded() != Filename(ui.GetFilename("MASTER")).Expanded()) {
ifile++;
}
if (ifile >= (int) list.size()) {
string msg = "The master file, [" + Filename(ui.GetFilename("MASTER")).Expanded() + " is not included in " +
"the input list file " + ui.GetFilename("FROMLIST") + "]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
bool step2 = false;
PvlGroup gp("AppjitResults");
//Step 1: Create the jitter rotation
try {
// Open the master cube
Cube cube;
cube.Open(ui.GetFilename("MASTER"),"rw");
//check for existing polygon, if exists delete it
if (cube.Label()->HasObject("Polygon")){
cube.Label()->DeleteObject("Polygon");
}
// Get the camera
Camera *cam = cube.Camera();
if (cam->DetectorMap()->LineRate() == 0.0) {
string msg = "[" + ui.GetFilename("MASTER") + "] is not a line scan camera image";
throw iException::Message(Isis::iException::User,msg,_FILEINFO_);
}
// Create the master rotation to be corrected
int frameCode = cam->InstrumentRotation()->Frame();
cam->SetImage(int(cube.Samples()/2), int(cube.Lines()/2) );
double tol = cam->PixelResolution();
if (tol < 0.) {
// Alternative calculation of .01*ground resolution of a pixel
tol = cam->PixelPitch()*cam->SpacecraftAltitude()*1000./cam->FocalLength()/100.;
}
LineScanCameraRotation crot(frameCode, *(cube.Label()), cam->InstrumentRotation()->GetFullCacheTime(), tol );
crot.SetPolynomialDegree(ui.GetInteger("DEGREE"));
crot.SetAxes(1, 2, 3);
if (ui.WasEntered("PITCHRATE")) crot.ResetPitchRate(ui.GetDouble("PITCHRATE"));
if (ui.WasEntered("YAW")) crot.ResetYaw(ui.GetDouble("YAW"));
crot.SetPolynomial();
double baseTime = crot.GetBaseTime();
double timeScale = crot.GetTimeScale();
double fl = cam->FocalLength();
double pixpitch = cam->PixelPitch();
std::vector<double> cacheTime = cam->InstrumentRotation()->GetFullCacheTime();
// Get the jitter in pixels, compute jitter angles, and fit a polynomial to each angle
PixelOffset jitter(ui.GetFilename("JITTERFILE"), fl, pixpitch, baseTime, timeScale, degree);
jitter.LoadAngles(cacheTime);
jitter.SetPolynomial();
// Set the jitter and apply to the instrument rotation
crot.SetJitter( &jitter );
crot.ReloadCache();
// Pull out the pointing cache as a table and write it
Table cmatrix = crot.Cache("InstrumentPointing");
cmatrix.Label().AddComment("Corrected using appjit and" + ui.GetFilename("JITTERFILE"));
cube.Write(cmatrix);
// Write out the instrument position table
Isis::PvlGroup kernels = cube.Label()->FindGroup("Kernels",Isis::Pvl::Traverse);
// Write out the "Table" label to the tabled kernels in the kernels group
kernels["InstrumentPointing"] = "Table";
// kernels["InstrumentPosition"] = "Table";
cube.PutGroup(kernels);
cube.Close();
gp += PvlKeyword("StatusMaster",ui.GetFilename("MASTER") + ": camera pointing updated");
// Apply the dejittered pointing to the rest of the files
step2 = true;
for (int ifile = 0; ifile < (int) list.size(); ifile++) {
if (list[ifile] != ui.GetFilename("MASTER")) {
// Open the cube
cube.Open(list[ifile],"rw");
//check for existing polygon, if exists delete it
if (cube.Label()->HasObject("Polygon")){
cube.Label()->DeleteObject("Polygon");
}
// Get the camera and make sure it is a line scan camera
Camera *cam = cube.Camera();
if (cam->DetectorMap()->LineRate() == 0.0) {
string msg = "[" + ui.GetFilename("FROM") + "] is not a line scan camera";
throw iException::Message(Isis::iException::User,msg,_FILEINFO_);
}
// Pull out the pointing cache as a table and write it
cube.Write(cmatrix);
cube.PutGroup(kernels);
cube.Close();
gp += PvlKeyword("Status" + iString(ifile), list[ifile] + ": camera pointing updated");
}
}
Application::Log( gp );
}
catch (iException &e) {
string msg;
if (!step2) {
msg = "Unable to fit pointing for [" + ui.GetFilename("MASTER") + "]";
}
else {
msg = "Unable to update pointing for nonMaster file(s)";
}
throw iException::Message(Isis::iException::User,msg,_FILEINFO_);
}
}
void IsisMain() {
// Get the list of cubes to mosaic
FileList imageList;
UserInterface &ui = Application::GetUserInterface();
imageList.Read(ui.GetFilename("FROMLIST"));
if (imageList.size() < 1) {
std::string msg = "The list file [" + ui.GetFilename("FROMLIST") +
"] does not contain any data";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Make sure the user enters a "OUTSTATS" file if the CALCULATE option
// is selected
std::string processOpt = ui.GetString("PROCESS");
if (processOpt == "CALCULATE") {
if (!ui.WasEntered("OUTSTATS")) {
std::string msg = "If the CALCULATE option is selected, you must enter";
msg += " an OUTSTATS file";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
// Make sure number of bands and projection parameters match for all cubes
for (unsigned int i=0; i<imageList.size(); i++) {
Cube cube1;
cube1.Open(imageList[i]);
g_maxBand = cube1.Bands();
for (unsigned int j=(i+1); j<imageList.size(); j++) {
Cube cube2;
cube2.Open(imageList[j]);
// Make sure number of bands match
if (g_maxBand != cube2.Bands()) {
string msg = "Number of bands do not match between cubes [" +
imageList[i] + "] and [" + imageList[j] + "]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
//Create projection from each cube
Projection *proj1 = cube1.Projection();
Projection *proj2 = cube2.Projection();
// Test to make sure projection parameters match
if (*proj1 != *proj2) {
string msg = "Mapping groups do not match between cubes [" +
imageList[i] + "] and [" + imageList[j] + "]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Read hold list if one was entered
std::vector<int> hold;
if (ui.WasEntered("HOLD")) {
FileList holdList;
holdList.Read(ui.GetFilename("HOLD"));
// Make sure each file in the holdlist matches a file in the fromlist
for (int i=0; i<(int)holdList.size(); i++) {
bool matched = false;
for (int j=0; j<(int)imageList.size(); j++) {
if (holdList[i] == imageList[j]) {
matched = true;
hold.push_back(j);
break;
}
}
if (!matched) {
std::string msg = "The hold list file [" + holdList[i] +
"] does not match a file in the from list";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Read to list if one was entered
FileList outList;
if (ui.WasEntered("TOLIST")) {
outList.Read(ui.GetFilename("TOLIST"));
// Make sure each file in the tolist matches a file in the fromlist
if (outList.size() != imageList.size()) {
std::string msg = "Each input file in the FROM LIST must have a ";
msg += "corresponding output file in the TO LIST.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Make sure that all output files do not have the same names as their
// corresponding input files
for (unsigned i = 0; i < outList.size(); i++) {
if (outList[i].compare(imageList[i]) == 0) {
std::string msg = "The to list file [" + outList[i] +
"] has the same name as its corresponding from list file.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Test to ensure sampling percent in bound
double sampPercent = ui.GetDouble("PERCENT");
if (sampPercent <= 0.0 || sampPercent > 100.0) {
string msg = "The sampling percent must be a decimal (0.0, 100.0]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
int mincnt = ui.GetInteger("MINCOUNT");
bool wtopt = ui.GetBoolean("WEIGHT");
if (processOpt != "APPLY") {
// Loop through all the input cubes, calculating statistics for each cube to use later
iString maxCubeStr ((int)imageList.size());
for (int band=1; band<=g_maxBand; band++) {
std::vector<Statistics> statsList;
for (int img=0; img<(int)imageList.size(); img++) {
Process p;
const CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
// Add a Statistics object to the list for every band of every input cube
g_imageIndex = img;
Statistics stats = GatherStatistics(*icube, band, sampPercent, maxCubeStr);
statsList.push_back(stats);
p.EndProcess();
}
// Create a separate OverlapNormalization object for every band
OverlapNormalization *oNorm = new OverlapNormalization (statsList);
for (int h=0; h<(int)hold.size(); h++) oNorm->AddHold(hold[h]);
g_oNormList.push_back(oNorm);
}
// A list for keeping track of which input cubes are known to overlap another
std::vector<bool> doesOverlapList;
for (unsigned int i=0; i<imageList.size(); i++) doesOverlapList.push_back(false);
// Find overlapping areas and add them to the set of known overlaps for each
// band shared amongst cubes
for (unsigned int i=0; i<imageList.size(); i++){
Cube cube1;
cube1.Open(imageList[i]);
for (unsigned int j=(i+1); j<imageList.size(); j++) {
Cube cube2;
cube2.Open(imageList[j]);
iString cubeStr1 ((int)(i+1));
iString cubeStr2 ((int)(j+1));
string statMsg = "Gathering Overlap Statisitcs for Cube " +
cubeStr1 + " vs " + cubeStr2 + " of " + maxCubeStr;
// Get overlap statistics for cubes
OverlapStatistics oStats(cube1, cube2, statMsg, sampPercent);
// Only push the stats onto the oList vector if there is an overlap in at
// least one of the bands
if (oStats.HasOverlap()) {
oStats.SetMincount(mincnt);
g_overlapList.push_back(oStats);
for (int band=1; band<=g_maxBand; band++) {
// Fill wt vector with 1's if the overlaps are not to be weighted, or
// fill the vector with the number of valid pixels in each overlap
int weight = 1;
if (wtopt) weight = oStats.GetMStats(band).ValidPixels();
// Make sure overlap has at least MINCOUNT pixels and add
if (oStats.GetMStats(band).ValidPixels() >= mincnt) {
g_oNormList[band-1]->AddOverlap(oStats.GetMStats(band).X(), i,
oStats.GetMStats(band).Y(), j, weight);
doesOverlapList[i] = true;
doesOverlapList[j] = true;
}
}
}
}
}
// Print an error if one or more of the images does not overlap another
{
std::string badFiles = "";
for (unsigned int img=0; img<imageList.size(); img++) {
// Print the name of each input cube without an overlap
if (!doesOverlapList[img]) {
badFiles += "[" + imageList[img] + "] ";
}
}
if (badFiles != "") {
std::string msg = "File(s) " + badFiles;
msg += " do(es) not overlap any other input images with enough valid pixels";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
// Determine whether to calculate gains or offsets
std::string adjust = ui.GetString("ADJUST");
OverlapNormalization::SolutionType sType = OverlapNormalization::Both;
if (adjust == "CONTRAST") sType = OverlapNormalization::Gains;
if (adjust == "BRIGHTNESS") sType = OverlapNormalization::Offsets;
// Loop through each band making all necessary calculations
for (int band=0; band<g_maxBand; band++) {
g_oNormList[band]->Solve(sType);
}
}
// Print gathered statistics to the gui and the print file
int validCnt = 0;
int invalidCnt = 0;
if (processOpt != "APPLY") {
PvlGroup results("Results");
// Compute the number valid and invalid overlaps
for (unsigned int o=0; o<g_overlapList.size(); o++) {
for (int band=1; band<=g_maxBand; band++) {
if (g_overlapList[o].IsValid(band)) validCnt++;
else invalidCnt++;
}
}
results += PvlKeyword("TotalOverlaps", validCnt+invalidCnt);
results += PvlKeyword("ValidOverlaps", validCnt);
results += PvlKeyword("InvalidOverlaps", invalidCnt);
std::string weightStr = "false";
if (wtopt) weightStr = "true";
results += PvlKeyword("Weighted", weightStr);
results += PvlKeyword("MinCount", mincnt);
// Name and band modifiers for each image
for (unsigned int img=0; img<imageList.size(); img++) {
results += PvlKeyword("FileName", imageList[img]);
// Band by band statistics
for (int band=1; band<=g_maxBand; band++) {
iString mult (g_oNormList[band-1]->Gain(img));
iString base (g_oNormList[band-1]->Offset(img));
iString avg (g_oNormList[band-1]->Average(img));
iString bandNum (band);
std::string bandStr = "Band" + bandNum;
PvlKeyword bandStats(bandStr);
bandStats += mult;
bandStats += base;
bandStats += avg;
results += bandStats;
}
}
// Write the results to the log
Application::Log(results);
}
// Setup the output text file if the user requested one
if (ui.WasEntered("OUTSTATS")) {
PvlObject equ("EqualizationInformation");
PvlGroup gen("General");
gen += PvlKeyword("TotalOverlaps", validCnt+invalidCnt);
gen += PvlKeyword("ValidOverlaps", validCnt);
gen += PvlKeyword("InvalidOverlaps", invalidCnt);
std::string weightStr = "false";
if (wtopt) weightStr = "true";
gen += PvlKeyword("Weighted", weightStr);
gen += PvlKeyword("MinCount", mincnt);
equ.AddGroup(gen);
for (unsigned int img=0; img<imageList.size(); img++) {
// Format and name information
PvlGroup norm("Normalization");
norm.AddComment("Formula: newDN = (oldDN - AVERAGE) * GAIN + AVERAGE + OFFSET");
norm.AddComment("BandN = (GAIN, OFFSET, AVERAGE)");
norm += PvlKeyword("FileName", imageList[img]);
// Band by band statistics
for (int band=1; band<=g_maxBand; band++) {
iString mult (g_oNormList[band-1]->Gain(img));
iString base (g_oNormList[band-1]->Offset(img));
iString avg (g_oNormList[band-1]->Average(img));
iString bandNum (band);
std::string bandStr = "Band" + bandNum;
PvlKeyword bandStats(bandStr);
bandStats += mult;
bandStats += base;
bandStats += avg;
norm += bandStats;
}
equ.AddGroup(norm);
}
// Write the equalization and overlap statistics to the file
std::string out = Filename(ui.GetFilename("OUTSTATS")).Expanded();
std::ofstream os;
os.open(out.c_str(),std::ios::app);
Pvl p;
p.SetTerminator("");
p.AddObject(equ);
os << p << std::endl;
for (unsigned int i=0; i<g_overlapList.size(); i++) {
os << g_overlapList[i];
if (i != g_overlapList.size()-1) os << std::endl;
}
os << "End";
}
// Check for errors with the input statistics
if (processOpt == "APPLY") {
Pvl inStats (ui.GetFilename("INSTATS"));
PvlObject &equalInfo = inStats.FindObject("EqualizationInformation");
// Make sure each file in the instats matches a file in the fromlist
if (imageList.size() > (unsigned)equalInfo.Groups()-1) {
std::string msg = "Each input file in the FROM LIST must have a ";
msg += "corresponding input file in the INPUT STATISTICS.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Check that each file in the FROM LIST is present in the INPUT STATISTICS
for (unsigned i = 0; i < imageList.size(); i++) {
std::string fromFile = imageList[i];
bool foundFile = false;
for (int j = 1; j < equalInfo.Groups(); j++) {
PvlGroup &normalization = equalInfo.Group(j);
std::string normFile = normalization["Filename"][0];
if (fromFile == normFile) {
// Store the index in INPUT STATISTICS file corresponding to the
// current FROM LIST file
normIndices.push_back(j);
foundFile = true;
}
}
if (!foundFile) {
std::string msg = "The from list file [" + fromFile +
"] does not have any corresponding file in the stats list.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Apply the correction to the images if the user wants this done
if (processOpt != "CALCULATE") {
iString maxCubeStr ((int)imageList.size());
for (int img=0; img<(int)imageList.size(); img++) {
// Set up for progress bar
ProcessByLine p;
iString curCubeStr (img+1);
p.Progress()->SetText("Equalizing Cube " + curCubeStr + " of " + maxCubeStr);
// Open input cube
CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
// Establish the output file depending upon whether or not a to list
// was entered
std::string out;
if (ui.WasEntered("TOLIST")) {
out = outList[img];
}
else {
Filename file = imageList[img];
out = file.Path() + "/" + file.Basename() + ".equ." + file.Extension();
}
// Allocate output cube
CubeAttributeOutput outAtt;
p.SetOutputCube(out,outAtt,icube->Samples(),icube->Lines(),icube->Bands());
// Apply gain/offset to the image
g_imageIndex = img;
if (processOpt == "APPLY") {
// Apply correction based on pre-determined statistics information
Pvl inStats (ui.GetFilename("INSTATS"));
PvlObject &equalInfo = inStats.FindObject("EqualizationInformation");
PvlGroup &normalization = equalInfo.Group(normIndices[g_imageIndex]);
gains.clear();
offsets.clear();
avgs.clear();
// Get and store the modifiers for each band
for (int band = 1; band < normalization.Keywords(); band++) {
gains.push_back(normalization[band][0]);
offsets.push_back(normalization[band][1]);
avgs.push_back(normalization[band][2]);
}
p.StartProcess(ApplyViaFile);
}
else {
// Apply correction based on the statistics gathered in this run
p.StartProcess(ApplyViaObject);
}
p.EndProcess();
}
}
// Clean-up for batch list runs
for (unsigned int o=0; o<g_oNormList.size(); o++) delete g_oNormList[o];
g_oNormList.clear();
g_overlapList.clear();
normIndices.clear();
gains.clear();
offsets.clear();
avgs.clear();
}
void Histogram::InitializeFromCube(Cube &cube, const int band, Progress *progress) {
// Make sure band is valid
if ((band < 0) || (band > cube.Bands())) {
string msg = "Invalid band in [Histogram constructor]";
throw Isis::iException::Message(Isis::iException::Programmer,msg,_FILEINFO_);
}
double min,max;
int nbins;
if (cube.PixelType() == Isis::UnsignedByte) {
min = 0.0 * cube.Multiplier() + cube.Base();
max = 255.0 * cube.Multiplier() + cube.Base();
nbins = 256;
}
else if (cube.PixelType() == Isis::SignedWord) {
min = -32768.0 * cube.Multiplier() + cube.Base();
max = 32767.0 * cube.Multiplier() + cube.Base();
nbins = 65536;
}
else if (cube.PixelType() == Isis::Real) {
// Determine the band for statistics
int bandStart = band;
int bandStop = band;
int maxSteps = cube.Lines();
if (band == 0){
bandStart = 1;
bandStop = cube.Bands();
maxSteps = cube.Lines() * cube.Bands();
}
// Construct a line buffer manager and a statistics object
LineManager line(cube);
Statistics stats = Statistics();
// Prep for reporting progress if necessary
if (progress != NULL) {
string save = progress->Text ();
progress->SetText("Computing min/max for histogram");
progress->SetMaximumSteps(maxSteps);
progress->CheckStatus();
}
for (int useBand = bandStart ; useBand <= bandStop ; useBand++){
// Loop and get the statistics for a good minimum/maximum
for (int i=1; i<=cube.Lines(); i++) {
line.SetLine(i,useBand);
cube.Read(line);
stats.AddData (line.DoubleBuffer(),line.size());
if (progress != NULL) progress->CheckStatus();
}
}
// Get the min/max for constructing a histogram object
if (stats.ValidPixels() == 0) {
min = 0.0;
max = 1.0;
}
else {
min = stats.BestMinimum ();
max = stats.BestMaximum ();
}
nbins = 65536;
}
else {
std::string msg = "Unsupported pixel type";
throw iException::Message(Isis::iException::Programmer,msg,_FILEINFO_);
}
// Set the bins and range
SetBinRange(min,max);
SetBins(nbins);
}
void IsisMain() {
Process p;
Cube *icube = p.SetInputCube("FROM");
// Setup the histogram
UserInterface &ui = Application::GetUserInterface();
Histogram hist(*icube,1,p.Progress());
if (ui.WasEntered("MINIMUM")) {
hist.SetValidRange(ui.GetDouble("MINIMUM"),ui.GetDouble("MAXIMUM"));
}
if (ui.WasEntered("NBINS")) {
hist.SetBins(ui.GetInteger("NBINS"));
}
// Loop and accumulate histogram
p.Progress()->SetText("Gathering Histogram");
p.Progress()->SetMaximumSteps(icube->Lines());
p.Progress()->CheckStatus();
LineManager line(*icube);
for (int i=1; i<=icube->Lines(); i++) {
line.SetLine(i);
icube->Read(line);
hist.AddData(line.DoubleBuffer(),line.size());
p.Progress()->CheckStatus();
}
if(!ui.IsInteractive() || ui.WasEntered("TO")) {
// Write the results
if (!ui.WasEntered("TO")) {
string msg = "The [TO] parameter must be entered";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
string outfile = ui.GetFilename("TO");
ofstream fout;
fout.open (outfile.c_str());
fout << "Cube: " << ui.GetFilename("FROM") << endl;
fout << "Band: " << icube->Bands() << endl;
fout << "Average: " << hist.Average() << endl;
fout << "Std Deviation: " << hist.StandardDeviation() << endl;
fout << "Variance: " << hist.Variance() << endl;
fout << "Median: " << hist.Median() << endl;
fout << "Mode: " << hist.Mode() << endl;
fout << "Skew: " << hist.Skew() << endl;
fout << "Minimum: " << hist.Minimum() << endl;
fout << "Maximum: " << hist.Maximum() << endl;
fout << endl;
fout << "Total Pixels: " << hist.TotalPixels() << endl;
fout << "Valid Pixels: " << hist.ValidPixels() << endl;
fout << "Null Pixels: " << hist.NullPixels() << endl;
fout << "Lis Pixels: " << hist.LisPixels() << endl;
fout << "Lrs Pixels: " << hist.LrsPixels() << endl;
fout << "His Pixels: " << hist.HisPixels() << endl;
fout << "Hrs Pixels: " << hist.HrsPixels() << endl;
// Write histogram in tabular format
fout << endl;
fout << endl;
fout << "DN,Pixels,CumulativePixels,Percent,CumulativePercent" << endl;
Isis::BigInt total = 0;
double cumpct = 0.0;
for (int i=0; i<hist.Bins(); i++) {
if (hist.BinCount(i) > 0) {
total += hist.BinCount(i);
double pct = (double)hist.BinCount(i) / hist.ValidPixels() * 100.;
cumpct += pct;
fout << hist.BinMiddle(i) << ",";
fout << hist.BinCount(i) << ",";
fout << total << ",";
fout << pct << ",";
fout << cumpct << endl;
}
}
fout.close();
}
// If we are in gui mode, create a histogram plot
if (ui.IsInteractive()) {
// Set the title for the dialog
string title;
if (ui.WasEntered("TITLE")) {
title = ui.GetString("TITLE");
}
else {
title = "Histogram Plot for " + Filename(ui.GetAsString("FROM")).Name();
}
// Create the QHistogram, set the title & load the Isis::Histogram into it
Qisis::HistogramToolWindow *plot = new Qisis::HistogramToolWindow(title.c_str(), ui.TheGui());
// Set the xaxis title if they entered one
if (ui.WasEntered("XAXIS")) {
string xaxis(ui.GetString("XAXIS"));
plot->setAxisLabel(QwtPlot::xBottom,xaxis.c_str());
}
// Set the yLeft axis title if they entered one
if (ui.WasEntered("Y1AXIS")) {
string yaxis(ui.GetString("Y1AXIS"));
plot->setAxisLabel(QwtPlot::yLeft,yaxis.c_str());
}
// Set the yRight axis title if they entered one
if (ui.WasEntered("Y2AXIS")) {
string y2axis(ui.GetString("Y2AXIS"));
plot->setAxisLabel(QwtPlot::yRight,y2axis.c_str());
}
//Transfer data from histogram to the plotcurve
std::vector<double> xarray,yarray,y2array;
double cumpct = 0.0;
for (int i=0; i<hist.Bins(); i++) {
if (hist.BinCount(i) > 0) {
xarray.push_back(hist.BinMiddle(i));
yarray.push_back(hist.BinCount(i));
double pct = (double)hist.BinCount(i) / hist.ValidPixels() * 100.;
cumpct += pct;
y2array.push_back(cumpct);
}
}
Qisis::HistogramItem *histCurve = new Qisis::HistogramItem();
histCurve->setColor(Qt::darkCyan);
histCurve->setTitle("Frequency");
Qisis::PlotToolCurve *cdfCurve = new Qisis::PlotToolCurve();
cdfCurve->setStyle(QwtPlotCurve::Lines);
cdfCurve->setTitle("Percentage");
QPen *pen = new QPen(Qt::red);
pen->setWidth(2);
histCurve->setYAxis(QwtPlot::yLeft);
cdfCurve->setYAxis(QwtPlot::yRight);
cdfCurve->setPen(*pen);
//These are all variables needed in the following for loop.
//----------------------------------------------
QwtArray<QwtDoubleInterval> intervals(xarray.size());
QwtArray<double> values(yarray.size());
double maxYValue = DBL_MIN;
double minYValue = DBL_MAX;
// ---------------------------------------------
for(unsigned int y = 0; y < yarray.size(); y++) {
intervals[y] = QwtDoubleInterval(xarray[y], xarray[y] + hist.BinSize());
values[y] = yarray[y];
if(values[y] > maxYValue) maxYValue = values[y];
if(values[y] < minYValue) minYValue = values[y];
}
histCurve->setData(QwtIntervalData(intervals, values));
cdfCurve->setData(&xarray[0],&y2array[0],xarray.size());
plot->add(histCurve);
plot->add(cdfCurve);
plot->fillTable();
plot->setScale(QwtPlot::yLeft,0,maxYValue);
plot->setScale(QwtPlot::xBottom,hist.Minimum(),hist.Maximum());
QLabel *label = new QLabel(" Average = " + QString::number(hist.Average()) + '\n' +
"\n Minimum = " + QString::number(hist.Minimum()) + '\n' +
"\n Maximum = " + QString::number(hist.Maximum()) + '\n' +
"\n Stand. Dev.= " + QString::number(hist.StandardDeviation()) + '\n' +
"\n Variance = " + QString::number(hist.Variance()) + '\n' +
"\n Median = " + QString::number(hist.Median()) + '\n' +
"\n Mode = " + QString::number(hist.Mode()) +'\n' +
"\n Skew = " + QString::number(hist.Skew()), plot);
plot->getDockWidget()->setWidget(label);
plot->showWindow();
}
p.EndProcess();
}
void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
ProcessByLine p;
Cube *icube = p.SetInputCube("FROM");
numIgnoredLines = 0;
cubeAverage.resize(icube->Bands());
lineAverages.resize(icube->Bands());
for(int i = 0; i < icube->Bands(); i++) {
cubeAverage[i] = 0;
lineAverages[i] = NULL;
}
int boxcarSize;
if(ui.GetString("BOXTYPE").compare("NONE") == 0) {
boxcarSize = (int)(icube->Lines() * 0.10);
}
else if(ui.GetString("BOXTYPE").compare("ABSOLUTE") == 0) {
boxcarSize = ui.GetInteger("BOXSIZE");
}
else if(ui.GetString("BOXTYPE").compare("PERCENTAGE") == 0) {
boxcarSize = (int)(((double)ui.GetInteger("BOXSIZE") / 100.0) * icube->Lines());
}
// Boxcar must be odd size
if(boxcarSize % 2 != 1) {
boxcarSize ++;
}
PvlGroup data("lineeq");
data += PvlKeyword("BoxcarSize", boxcarSize, "lines");
data += PvlKeyword("OutputCsv", ui.GetBoolean("AVERAGES"));
TextFile *csvOutput = NULL;
if(ui.GetBoolean("AVERAGES")) {
csvOutput = new TextFile(ui.GetFilename("CSV"), "overwrite", "");
csvOutput->PutLine("Average,SmoothedAvg");
data += PvlKeyword("CsvFile", ui.GetFilename("CSV"));
}
Application::Log(data);
for(int band = 0; band < icube->Bands(); band ++) {
lineAverages[band] = new double[icube->Lines()];
}
p.Progress()->SetText("Gathering line averages");
p.StartProcess(gatherAverages);
// Now filter the bands
p.Progress()->SetText("Smoothing line averages");
p.Progress()->SetMaximumSteps((icube->Bands() + 1) * icube->Lines());
p.Progress()->CheckStatus();
QuickFilter filter(icube->Lines(), boxcarSize, 1);
if(icube->Lines() <= numIgnoredLines) {
throw iException::Message(iException::User, "Image does not contain any valid data.", _FILEINFO_);
}
for(int band = 0; band < icube->Bands(); band ++) {
cubeAverage[band] /= (icube->Lines() - numIgnoredLines);
filter.AddLine(lineAverages[band]);
for(int line = 0; line < icube->Lines(); line ++) {
p.Progress()->CheckStatus();
double filteredLine = filter.Average(line);
if(csvOutput != NULL) {
csvOutput->PutLine((iString)lineAverages[band][line] + (iString)"," + (iString)filteredLine);
}
lineAverages[band][line] = filteredLine;
}
filter.RemoveLine(lineAverages[band]);
}
if(csvOutput != NULL) {
delete csvOutput; // This closes the file automatically
csvOutput = NULL;
}
p.SetOutputCube("TO");
p.Progress()->SetText("Applying Equalization");
p.StartProcess(apply);
for(int band = 0; band < icube->Bands(); band ++) {
delete [] lineAverages[band];
lineAverages[band] = NULL;
}
p.EndProcess();
}