int main () {
Isis::Preference::Preferences(true);
try {
PvlGroup op("Operator");
op += PvlKeyword("Name","Gradient");
op += PvlKeyword("DeltaLine", 100);
op += PvlKeyword("DeltaSamp", 100);
op += PvlKeyword("Samples", 15);
op += PvlKeyword("Lines", 15);
op += PvlKeyword("MinimumInterest", 1);
PvlObject o("InterestOperator");
o.AddGroup(op);
Pvl pvl;
pvl.AddObject(o);
std::cout << pvl << std::endl;
InterestOperator *iop = InterestOperatorFactory::Create(pvl);
Cube c;
c.Open("$mgs/testData/ab102401.cub");
iop->Operate(c, 100, 350);
std::cout << "Sample: " << iop->CubeSample() << std::endl
<< "Line : " << iop->CubeLine() << std::endl
<< "Interest: " << iop->InterestAmount() << std::endl;
}
catch (iException &e) {
e.Report();
}
return 0;
}
void IsisMain() {
// We will be processing by line
ProcessByBrick p;
p.SetBrickSize(1,1,1);
p.SetOutputBrickSize(1,1,1);
UserInterface &ui = Application::GetUserInterface();
// Basic settings
p.SetInputCube("FROM");
p.SetOutputCube("TO");
Pvl pvl = Pvl(ui.GetFilename("PVL"));
cube.Open(ui.GetFilename("FROM"));
try {
// Get info from the operator group
// Set the pvlkeywords that need to be set to zero
PvlGroup &op = pvl.FindGroup("Operator",Pvl::Traverse);
boxcarSamples = op["Samples"];
boxcarLines = op["Lines"];
op["DeltaLine"]=0;
op["DeltaSamp"]=0;
op["MinimumInterest"]=0.0;
Application::Log(op);
} catch (iException &e) {
std::string msg = "Improper format for InterestOperator PVL ["+pvl.Filename()+"]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
iop = InterestOperatorFactory::Create(pvl);
// Start the processing
p.StartProcess(Operate);
p.EndProcess();
}
/**
* @brief File name based constructor for HiRISE image cleaner
*/
HiImageClean::HiImageClean(const std::string &fname) {
Cube cube;
cube.Open(fname);
_filename = fname;
_lines = _samples = 0;
_totalMaskNulled = _totalDarkNulled = 0;
init(cube);
}
int main () {
Isis::Preference::Preferences(true);
try {
PvlGroup alg("Algorithm");
alg += PvlKeyword("Name","MinimumDifference");
alg += PvlKeyword("Tolerance",5.0);
alg += PvlKeyword("SubpixelAccuracy", "True");
PvlGroup pchip("PatternChip");
pchip += PvlKeyword("Samples",15);
pchip += PvlKeyword("Lines",15);
pchip += PvlKeyword("Sampling",25);
pchip += PvlKeyword("ValidPercent", 10);
PvlGroup schip("SearchChip");
schip += PvlKeyword("Samples",35);
schip += PvlKeyword("Lines",35);
schip += PvlKeyword("Sampling", 50);
PvlObject o("AutoRegistration");
o.AddGroup(alg);
o.AddGroup(pchip);
o.AddGroup(schip);
Pvl pvl;
pvl.AddObject(o);
std::cout << pvl << std::endl;
AutoReg *ar = AutoRegFactory::Create(pvl);
Cube c;
c.Open("$mgs/testData/ab102401.cub");
ar->SearchChip()->TackCube(125.0,50.0);
ar->SearchChip()->Load(c);
ar->PatternChip()->TackCube(120.0,45.0);
ar->PatternChip()->Load(c);
std::cout << "Register = " << ar->Register() << std::endl;
std::cout << "Position = " << ar->CubeSample() << " " <<
ar->CubeLine() << std::endl;
}
catch (iException &e) {
e.Report();
}
return 0;
}
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++;
}
}
/**
* @brief Loads the contents of a BLOB from a cube file
*
* Provides the I/O interface for ISIS cube files.
*
* @param [in] filename (string&) Name of ISIS cube file to read
*/
void Blobber::load(const std::string &filename) {
Cube cube;
cube.Open(filename);
load(cube);
return;
}
int main () {
Isis::Preference::Preferences(true);
/**
* @brief Test ImagePolygon object for accuracy and correct behavior.
*
* @author 2005-11-22 Tracie Sucharski
*
* @history 2007-01-19 Tracie Sucharski, Removed ToGround method (for now)
* because of round off problems going back and forth between
* lat/lon,line/samp.
* @history 2007-01-31 Tracie Sucharski, Added WKT method to return polygon
* in string as WKT.
* @history 2007-11-09 Tracie Sucharski, Remove WKT method, geos now has
* a method to return a WKT string.
* @history 2007-11-20 Tracie Sucharski, Added test for sub-polys
*/
// simple MOC image
string inFile = "/usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub";
//string inFile = "/work1/tsucharski/poly/I17621017RDR_lev2.cub";
// same MOC image, but sinusoidal projection
//string inFile = "/farm/prog1/tsucharski/isis3/ab102401.lev2.cub";
// same MOC image, but sinusoidal projection , doctored left edge
//string inFile = "/farm/prog1/tsucharski/isis3/ab102401.lev2.leftTrim.cub";
// MOC north pole image
//string inFile = "/work1/tsucharski/isis3/poly/e0202226.lev1.cub";
// MOC image with 0/360 boundary
// orkin
//string inFile = "/farm/prog1/tsucharski/isis3/cubes/m0101631.lev1.cub";
// blackflag
//string inFile = "/work1/tsucharski/isis3/poly/m0101631.lev1.cub";
// galileo ssi image
//string inFile = "/farm/prog1/tsucharski/isis3/6700r.cub";
// Open the cube
Cube cube;
Cube cube1;
cube.Open(inFile,"r");
ImagePolygon poly;
try {
poly.Create(cube);
}
catch (iException &e) {
std::string msg = "Cannot create polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
// Test sub-poly option
try {
poly.Create(cube,12,1,384,640,385);
}
catch (iException &e) {
std::string msg = "Cannot create sub-polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
// Test lower quality option
try {
poly.Create(cube,10,12,1,384,640,385);
}
catch (iException &e) {
std::string msg = "Cannot create lower quality polygon for [" + cube.Filename() + "]";
throw iException::Message(iException::Programmer,msg,_FILEINFO_);
}
// write poly as WKT
std::cout<< poly.Polys()->toString()<<std::endl;
cube.Close();
}
int main() {
Preference::Preferences(true);
Chip chip(51, 50);
cout << "Test basics" << endl;
cout << chip.Samples() << endl;
cout << chip.Lines() << endl;
chip.TackCube(453.5, 568.5);
cout << chip.TackSample() << endl;
cout << chip.TackLine() << endl;
cout << "Test chip-to-cube and cube-to-chip mapping" << endl;
chip.SetChipPosition(chip.TackSample(), chip.TackLine());
cout << chip.CubeSample() << endl;
cout << chip.CubeLine() << endl;
chip.SetChipPosition(1.0, 1.0);
cout << chip.CubeSample() << endl;
cout << chip.CubeLine() << endl;
chip.SetCubePosition(chip.CubeSample(), chip.CubeLine());
cout << chip.ChipSample() << endl;
cout << chip.ChipLine() << endl;
cout << "Test assignment of chip data to constant" << endl;
chip.SetAllValues(10.0);
for(int i = 1; i <= chip.Lines(); i++) {
for(int j = 1; j <= chip.Samples(); j++) {
double value = chip.GetValue(j, i);
if(value != 10.0) {
cout << "bad constant (!= 10) at " << j << ", " << i << endl;
}
}
}
cout << "Test loading chip data" << endl;
for(int i = 1; i <= chip.Lines(); i++) {
for(int j = 1; j <= chip.Samples(); j++) {
chip.SetValue(j, i, (double)(i * 100 + j));
}
}
for(int i = 1; i <= chip.Lines(); i++) {
for(int j = 1; j <= chip.Samples(); j++) {
double value = chip.GetValue(j, i);
if(value != (double)(i * 100 + j)) {
cout << "bad at " << j << ", " << i << endl;
}
}
}
chip.SetValidRange(0.0, 5050.0);
cout << "Valid tests" << endl;
// is chip valid at 51, 50?
cout << chip.IsValid(chip.Samples(), chip.Lines()) << endl;
// is chip valid at 50, 50?
cout << chip.IsValid(chip.Samples() - 1, chip.Lines()) << endl;
// is at least 95% of chip values valid?
cout << chip.IsValid(95.0) << endl;
// is at least 99.99% of chip values valid?
cout << chip.IsValid(99.99) << endl;
cout << "Extract test" << endl;
// Extract 4 by 3 subchip at 26, 25
Chip sub = chip.Extract(4, 3, chip.TackSample(), chip.TackLine());
for(int i = 1; i <= sub.Lines(); i++) {
for(int j = 1; j <= sub.Samples(); j++) {
cout << sub.GetValue(j, i) << " ";
}
cout << endl;
}
cout << "Test writing chip" << endl;
chip.Write("junk.cub");
Cube junk;
junk.open("junk.cub");
LineManager line(junk);
for(int i = 1; i <= chip.Lines(); i++) {
line.SetLine(i);
junk.read(line);
for(int j = 1; j <= chip.Samples(); j++) {
double value = chip.GetValue(j, i);
if(value != line[j-1]) {
cout << "bad at " << j << ", " << i << endl;
}
}
}
cout << "Test load chip from cube with rotation" << endl;
chip.TackCube(26.0, 25.0);
chip.Load(junk, 45.0);
for(int i = 1; i <= chip.Lines(); i++) {
for(int j = 1; j <= chip.Samples(); j++) {
cout << std::setw(14) << chip.GetValue(j, i) << " ";
}
cout << endl;
}
cout << "Test load chip from cube with rotation and clipping polygon " << endl;
chip.TackCube(26.0, 25.0);
geos::geom::CoordinateSequence *pts = new geos::geom::CoordinateArraySequence();
pts->add(geos::geom::Coordinate(23.0, 22.0));
pts->add(geos::geom::Coordinate(28.0, 22.0));
pts->add(geos::geom::Coordinate(28.0, 27.0));
pts->add(geos::geom::Coordinate(25.0, 28.0));
pts->add(geos::geom::Coordinate(23.0, 22.0));
vector<geos::geom::Geometry *> polys;
geos::geom::GeometryFactory gf;
polys.push_back(gf.createPolygon(gf.createLinearRing(pts), NULL));
geos::geom::MultiPolygon *mPolygon = gf.createMultiPolygon(polys);
chip.SetClipPolygon(*mPolygon);
chip.Load(junk, 45.0);
for(int i = 1; i <= chip.Lines(); i++) {
for(int j = 1; j <= chip.Samples(); j++) {
cout << std::setw(14) << chip.GetValue(j, i) << " ";
}
cout << endl;
}
// Test affine transformation
cout << "\nTesting Affine transformation extraction (-1, -1)...\n";
Affine affine;
affine.Translate(-1.0, -1.0);
Chip mychip(51, 50); // Needed because chip has poly clipping
mychip.TackCube(26.0, 25.0);
mychip.Load(junk);
mychip.SetChipPosition(mychip.TackSample(), mychip.TackLine());
cout << "Cube Sample, Line = " << mychip.CubeSample() << ", "
<< mychip.CubeLine() << endl;
Chip shift(25, 25);
mychip.Extract(shift, affine);
// shift.SetChipPosition(shift.TackSample(), shift.TackLine());
cout << "Shift Cube Sample, Line = " << shift.CubeSample() << ", "
<< shift.CubeLine() << endl;
Chip io = shift;
io.TackCube(25.0, 24.0);
io.Load(junk);
io.SetChipPosition(io.TackSample(), io.TackLine());
cout << "New Cube Sample, Line = " << io.CubeSample() << ", "
<< io.CubeLine() << endl;
int ioNull(0), shiftNull(0);
double sumDiff(0.0);
for(int il = 1 ; il <= io.Lines() ; il++) {
for(int is = 1 ; is <= io.Samples() ; is++) {
if(IsSpecial(io.GetValue(is, il))) {
ioNull++;
}
else if(IsSpecial(shift.GetValue(is, il))) {
shiftNull++;
}
else {
sumDiff += io.GetValue(is, il) - shift.GetValue(is, il);
}
}
}
cout << "I/O Nulls: " << ioNull << endl;
cout << "Shift Nulls: " << shiftNull << endl;
cout << "Sum Diff: " << sumDiff << endl;
cout << "\nTesting direct Affine Application...\n";
Chip affchip(25, 25);
affchip.TackCube(25.0, 24.0);
affchip.SetTransform(io.GetTransform());
affchip.SetChipPosition(affchip.TackSample(), affchip.TackLine());
cout << "Affine Cube Sample, Line = " << affchip.CubeSample() << ", "
<< affchip.CubeLine() << endl;
cout << "\nTest reading with new Affine transform...\n";
affchip.Load(junk, io.GetTransform());
ioNull = shiftNull = 0;
sumDiff = 0.0;
for(int il = 1 ; il <= io.Lines() ; il++) {
for(int is = 1 ; is <= io.Samples() ; is++) {
if(IsSpecial(io.GetValue(is, il))) {
ioNull++;
}
else if(IsSpecial(affchip.GetValue(is, il))) {
shiftNull++;
}
else {
sumDiff += io.GetValue(is, il) - affchip.GetValue(is, il);
}
}
}
cout << "I/O Nulls: " << ioNull << endl;
cout << "Shift Nulls: " << shiftNull << endl;
cout << "Sum Diff: " << sumDiff << endl;
affchip.SetChipPosition(affchip.TackSample(), affchip.TackLine());
cout << "Affine Cube loaded at Sample, Line = " << affchip.CubeSample() << ", "
<< affchip.CubeLine() << endl;
// Test Load using match chip method
cout << "\nTest reading with match chip and cube...\n";
Cube junkCube;
junkCube.open("$base/testData/ab102401_ideal.cub");
// 4 by 4 chip at samle 1000 line 500
Chip matchChip(4, 4);
matchChip.TackCube(1000, 500);
matchChip.Load(junkCube);
cout << "\nMatch chip values..." << endl;
for(int i = 1; i <= matchChip.Lines(); i++) {
for(int j = 1; j <= matchChip.Samples(); j++) {
cout << std::setw(14) << matchChip.GetValue(j, i) << " ";
}
cout << endl;
}
// make sure that if we create a new chip from the same cube that is matched
// to the match chip, the chips should be almost identical
Chip newChip(4, 4);
newChip.TackCube(1000, 500);
newChip.Load(junkCube, matchChip, junkCube);
cout << "\nLoading new chip values from match chip..." << endl;
cout << "Passes if difference is less than EPSILON = " << 2E-6 << endl;
for(int i = 1; i <= newChip.Lines(); i++) {
for(int j = 1; j <= newChip.Samples(); j++) {
double difference = newChip.GetValue(j, i) - matchChip.GetValue(j, i);
if(fabs(difference) > 2E-6) {
cout << "bad at " << j << ", " << i << endl;
cout << "difference at " << j << ", " << i << " is " << difference << endl;
}
else{
cout << "\tPASS\t\t";
// the following comment prints actual difference.
// cout << std::setw(14) << difference << "\t";
}
}
cout << endl;
}
cout << endl;
cout << endl;
cout << "Test interpolator set/get methods" << endl;
cout << "default: " << chip.GetReadInterpolator() << endl;
chip.SetReadInterpolator(Isis::Interpolator::NearestNeighborType);
cout << "nearest neighbor: " << chip.GetReadInterpolator() << endl;
chip.SetReadInterpolator(Isis::Interpolator::BiLinearType);
cout << "bilinear: " << chip.GetReadInterpolator() << endl;
chip.SetReadInterpolator(Isis::Interpolator::CubicConvolutionType);
cout << "cubic convolution: " << chip.GetReadInterpolator() << endl;
cout << endl;
cout << endl;
cout << "Generate Errors:" << endl;
Cube junkCube2;
junkCube2.open("$base/testData/f319b18_ideal.cub");
// 4 by 4 chip at samle 1000 line 500
matchChip.TackCube(1, 1);
matchChip.Load(junkCube2);
cout << "Try to set interpolator to type 0 (Interpolator::None):" << endl;
try {
chip.SetReadInterpolator(Isis::Interpolator::None);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to set interpolator to type 3 (enum value not assigned):" << endl;
try {
chip.SetReadInterpolator((Isis::Interpolator::interpType) 3);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to set chip size with input parameter equal to 0:" << endl;
try {
newChip.SetSize(0, 1);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to load a cube that is not camera or map projection:" << endl;
try {
newChip.Load(junk, matchChip, junkCube);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to load a cube with a match cube that is not camera or map projection:" << endl;
try {
newChip.Load(junkCube, matchChip, junk);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to load a cube with match chip and cube that can not find at least 3 points for Affine Transformation:" << endl;
try {
newChip.Load(junkCube, matchChip, junkCube2);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to set valid range with larger number passed in as first parameter:" << endl;
try {
newChip.SetValidRange(4, 3);
}
catch(IException &e) {
ReportError(e.toString());
}
cout << "Try to extract a sub-chip with samples or lines greater than original chip:" << endl;
try {
newChip.Extract(2, 5, 1, 1);
}
catch(IException &e) {
ReportError(e.toString());
}
junk.close(true);// the "true" flag removes junk.cub from the /tmp/ directory
junkCube.close(); // these cubes are kept in test data area, do not delete
junkCube2.close();
#if 0
try {
junk.Open("/work2/janderso/moc/ab102401.lev1.cub");
chip.TackCube(453.0, 567.0);
chip.Load(junk);
Cube junk2;
junk2.Open("/work2/janderso/moc/ab102402.lev0.cub");
Chip chip2(75, 70);
chip2.TackCube(166.0, 567.0);
chip2.Load(junk2, chip);
chip.Write("junk3.cub");
chip2.Write("junk4.cub");
}
catch(IException &e) {
e.print();
}
#endif
return 0;
}
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();
}
/**
* 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() {
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
UserInterface &ui = Application::GetUserInterface();
FileList flist(ui.GetFilename("FROMLIST"));
vector<Cube *> clist;
try {
if (flist.size() < 1) {
string msg = "the list file [" +ui.GetFilename("FROMLIST") +
"does not contain any data";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// open all the cube and place in vector clist
for (int i=0; i<(int)flist.size(); i++) {
Cube *c = new Cube();
clist.push_back(c);
c->Open(flist[i]);
}
// run the compair function here. This will conpair the
// labels of the first cube to the labels of each following cube.
PvlKeyword sourceProductId("SourceProductId");
string ProdId;
for (int i=0; i<(int)clist.size(); i++) {
Pvl *pmatch = clist[0]->Label();
Pvl *pcomp = clist[i]->Label();
CompareLabels(*pmatch, *pcomp);
PvlGroup g = pcomp->FindGroup("Instrument",Pvl::Traverse);
if (g.HasKeyword("StitchedProductIds")) {
PvlKeyword k = g["StitchedProductIds"];
for (int j=0; j<(int)k.Size(); j++) {
sourceProductId += g["stitchedProductIds"][j];
}
}
ProdId = (string)pmatch->FindGroup("Archive",Pvl::Traverse)["ObservationId"];
iString bandname = (string)pmatch->FindGroup("BandBin",Pvl::Traverse)["Name"];
bandname = bandname.UpCase();
ProdId = ProdId + "_" + bandname;
}
bool runXY=true;
//calculate the min and max lon
double minLat = DBL_MAX;
double maxLat = -DBL_MAX;
double minLon = DBL_MAX;
double maxLon = -DBL_MAX;
double avgLat;
double avgLon;
for (int i=0; i<(int)clist.size(); i++) {
Projection *proj = clist[i]->Projection();
if (proj->MinimumLatitude() < minLat) minLat = proj->MinimumLatitude();
if (proj->MaximumLatitude() > maxLat) maxLat = proj->MaximumLatitude();
if (proj->MinimumLongitude() < minLon) minLon = proj->MinimumLongitude();
if (proj->MaximumLongitude() > maxLon) maxLon = proj->MaximumLongitude();
}
avgLat = (minLat + maxLat) / 2;
avgLon = (minLon + maxLon) / 2;
Projection *proj = clist[0]->Projection();
proj->SetGround(avgLat,avgLon);
avgLat = proj->UniversalLatitude();
avgLon = proj->UniversalLongitude();
// Use camera class to get Inc., emi., phase, and other values
double Cemiss;
double Cphase;
double Cincid;
double ClocalSolTime;
double CsolarLong;
double CsunAzimuth;
double CnorthAzimuth;
for (int i=0; i<(int)clist.size(); i++) {
Camera *cam = clist[i]->Camera();
if (cam->SetUniversalGround(avgLat,avgLon)) {
Cemiss = cam->EmissionAngle();
Cphase = cam->PhaseAngle();
Cincid = cam->IncidenceAngle();
ClocalSolTime = cam->LocalSolarTime();
CsolarLong = cam->SolarLongitude();
CsunAzimuth = cam->SunAzimuth();
CnorthAzimuth = cam->NorthAzimuth();
runXY = false;
break;
}
}
//The code within the if runXY was added in 10/07 to find an intersect with
//pole images that would fail when using projection set universal ground.
// This is run if no intersect is found when using lat and lon in
// projection space.
if (runXY) {
double startX = DBL_MAX;
double endX = DBL_MIN;
double startY = DBL_MAX;
double endY = DBL_MIN;
for (int i=0; i<(int)clist.size(); i++) {
Projection *proj = clist[i]->Projection();
proj->SetWorld(0.5,0.5);
if (i==0) {
startX = proj->XCoord();
endY = proj->YCoord();
}
else {
if (proj->XCoord() < startX) startX = proj->XCoord();
if (proj->YCoord() > endY) endY = proj->YCoord();
}
Pvl *p = clist[i]->Label();
double nlines = p->FindGroup("Dimensions",Pvl::Traverse)["Lines"];
double nsamps = p->FindGroup("Dimensions",Pvl::Traverse)["Samples"];
proj->SetWorld((nsamps+0.5),(nlines+0.5));
if (i==0) {
endX = proj->XCoord();
startY = proj->YCoord();
}
else {
if (proj->XCoord() > endX) endX = proj->XCoord();
if (proj->YCoord() < startY) startY = proj->YCoord();
}
}
double avgX = (startX + endX) / 2;
double avgY = (startY + endY) / 2;
double sample = proj->ToWorldX(avgX);
double line = proj->ToWorldY(avgY);
for (int i=0; i<(int)clist.size(); i++) {
Camera *cam = clist[i]->Camera();
if (cam->SetImage(sample,line)) {
Cemiss = cam->EmissionAngle();
Cphase = cam->PhaseAngle();
Cincid = cam->IncidenceAngle();
ClocalSolTime = cam->LocalSolarTime();
CsolarLong = cam->SolarLongitude();
CsunAzimuth = cam->SunAzimuth();
CnorthAzimuth = cam->NorthAzimuth();
runXY = false;
break;
}
}
}
if (runXY) {
string msg = "Camera did not intersect images to gather stats";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// get the min and max SCLK values ( do this with string comp.)
// get the value from the original label blob
string startClock;
string stopClock;
string startTime;
string stopTime;
for (int i=0; i<(int)clist.size(); i++) {
OriginalLabel origLab;
clist[i]->Read(origLab);
PvlGroup timegrp = origLab.ReturnLabels().FindGroup("TIME_PARAMETERS",Pvl::Traverse);
if (i==0) {
startClock = (string)timegrp["SpacecraftClockStartCount"];
stopClock = (string)timegrp["SpacecraftClockStopCount"];
startTime = (string)timegrp["StartTime"];
stopTime = (string)timegrp["StopTime"];
}
else {
string testStartTime = (string)timegrp["StartTime"];
string testStopTime = (string)timegrp["StopTime"];
if (testStartTime < startTime) {
startTime = testStartTime;
startClock = (string)timegrp["SpacecraftClockStartCount"];
}
if (testStopTime > stopTime) {
stopTime = testStopTime;
stopClock = (string)timegrp["spacecraftClockStopCount"];
}
}
}
// Concatenate all TDI's and summing and specialProcessingFlat into one keyword
PvlKeyword cpmmTdiFlag("cpmmTdiFlag");
PvlKeyword cpmmSummingFlag("cpmmSummingFlag");
PvlKeyword specialProcessingFlag("SpecialProcessingFlag");
for (int i=0; i<14; i++) {
cpmmTdiFlag +=(string)"";
cpmmSummingFlag +=(string)"";
specialProcessingFlag +=(string)"";
}
for (int i=0; i<(int)clist.size(); i++) {
Pvl *clab = clist[i]->Label();
PvlGroup cInst = clab->FindGroup("Instrument",Pvl::Traverse);
OriginalLabel cOrgLab;
clist[i]->Read(cOrgLab);
PvlGroup cGrp = cOrgLab.ReturnLabels().FindGroup("INSTRUMENT_SETTING_PARAMETERS",Pvl::Traverse);
cpmmTdiFlag[(int)cInst["CpmmNumber"]] = (string) cGrp["MRO:TDI"];
cpmmSummingFlag[(int)cInst["CpmmNumber"]] = (string) cGrp["MRO:BINNING"];
if (cInst.HasKeyword("Special_Processing_Flag")) {
specialProcessingFlag[cInst["CpmmNumber"]] = (string) cInst["Special_Processing_Flag"];
}
else {
// there may not be the keyword Special_Processing_Flag if no
//keyword then set the output to NOMINAL
specialProcessingFlag[cInst["CpmmNumber"]] = "NOMINAL";
}
}
// Get the blob of original labels from first image in list
OriginalLabel org;
clist[0]->Read(org);
//close all cubes
for (int i=0; i<(int)clist.size(); i++) {
clist[i]->Close();
delete clist[i];
}
clist.clear();
// automos step
string list = ui.GetFilename("FROMLIST");
string toMosaic = ui.GetFilename("TO");
string MosaicPriority = ui.GetString("PRIORITY");
string parameters = "FROMLIST=" + list + " MOSAIC=" + toMosaic + " PRIORITY=" + MosaicPriority;
Isis::iApp ->Exec("automos",parameters);
// write out new information to new group mosaic
PvlGroup mos("Mosaic");
mos += PvlKeyword("ProductId ", ProdId);
mos += PvlKeyword(sourceProductId);
mos += PvlKeyword("StartTime ", startTime);
mos += PvlKeyword("SpacecraftClockStartCount ", startClock);
mos += PvlKeyword("StopTime ", stopTime);
mos += PvlKeyword("SpacecraftClockStopCount ", stopClock);
mos += PvlKeyword("IncidenceAngle ", Cincid, "DEG");
mos += PvlKeyword("EmissionAngle ", Cemiss, "DEG");
mos += PvlKeyword("PhaseAngle ", Cphase, "DEG");
mos += PvlKeyword("LocalTime ", ClocalSolTime, "LOCALDAY/24");
mos += PvlKeyword("SolarLongitude ", CsolarLong, "DEG");
mos += PvlKeyword("SubSolarAzimuth ", CsunAzimuth, "DEG");
mos += PvlKeyword("NorthAzimuth ", CnorthAzimuth, "DEG");
mos += cpmmTdiFlag;
mos += cpmmSummingFlag;
mos += specialProcessingFlag;
Cube mosCube;
mosCube.Open(ui.GetFilename("TO"), "rw");
PvlObject &lab=mosCube.Label()->FindObject("IsisCube");
lab.AddGroup(mos);
//add orginal label blob to the output cube
mosCube.Write(org);
mosCube.Close();
}
catch (iException &e) {
for (int i=0; i<(int)clist.size(); i++) {
clist[i]->Close();
delete clist[i];
}
string msg = "The mosaic [" + ui.GetFilename("TO") + "] was NOT created";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
} // end of isis main