//! Compute automatic stretch for a portion of the cube
void ChipViewport::computeStretch(Stretch &stretch, bool force) {
if (p_stretchLocked && !force) {
stretch = *p_stretch;
}
else {
Statistics stats;
for (int line = 1; line < p_chip->Lines(); line++) {
for (int samp = 1; samp < p_chip->Samples(); samp++) {
double value = p_chip->GetValue(samp, line);
stats.AddData(&value, 1);
}
}
Histogram hist(stats.BestMinimum(), stats.BestMaximum());
for (int line = 1; line <= p_chip->Lines(); line++) {
for (int samp = 1; samp <= p_chip->Samples(); samp++) {
double value = p_chip->GetValue(samp, line);
hist.AddData(&value, 1);
}
}
stretch.ClearPairs();
if (hist.Percent(0.5) != hist.Percent(99.5)) {
stretch.AddPair(hist.Percent(0.5), 0.0);
stretch.AddPair(hist.Percent(99.5), 255.0);
}
else {
stretch.AddPair(-DBL_MAX, 0.0);
stretch.AddPair(DBL_MAX, 255.0);
}
*p_stretch = stretch;
}
}
void IsisMain() {
// Setup the input and output cubes
ProcessByLine p; // used for getting histograms from input cubes
Cube *icube = p.SetInputCube("FROM", Isis::OneBand);
p.SetOutputCube ("TO");
// Histogram parameters
UserInterface &ui = Application::GetUserInterface();
double minimum = ui.GetDouble("MINPER");
double maximum = ui.GetDouble("MAXPER");
int increment = ui.GetInteger("INCREMENT");
// Histograms from input cubes
Histogram *from = icube->Histogram();
Histogram *match = icube->Histogram();
double fromMin = from->Percent(minimum);
double fromMax = from->Percent(maximum);
int fromBins = from->Bins();
double data[fromBins];
double slope = (fromMax - fromMin) / (fromBins - 1);
// Set "match" to have the same data range and number of bins as "to"
match->SetBins(fromBins);
match->SetValidRange(fromMin, fromMax);
for (int i = 0; i < fromBins; i++) {
data[i] = fromMin + (slope * i);
}
match->AddData(data, fromBins);
stretch.ClearPairs();
double lastPer = from->Percent(minimum);
stretch.AddPair(lastPer, match->Percent(minimum));
for (double i = increment+minimum; i < maximum; i += increment) {
double curPer = from->Percent(i);
if (lastPer < curPer) {
if(abs(lastPer - curPer) > DBL_EPSILON) {
stretch.AddPair(curPer, match->Percent(i));
lastPer = curPer;
}
}
}
double curPer = from->Percent(maximum);
if (lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
stretch.AddPair(curPer, match->Percent(maximum));
}
// Start the processing
p.StartProcess(remap);
p.EndProcess();
}
void IsisMain() {
// Setup the input and output cubes along with histograms
ProcessByLine p;
Cube *mcube = p.SetInputCube("MATCH", Isis::OneBand);
Histogram *match = mcube->histogram();
p.ClearInputCubes();
Cube *icube = p.SetInputCube("FROM", Isis::OneBand);
Histogram *from = icube->histogram();
p.SetOutputCube("TO");
// Histogram specifications
UserInterface &ui = Application::GetUserInterface();
double minimum = ui.GetDouble("MINPER");
double maximum = ui.GetDouble("MAXPER");
stretch.ClearPairs();
// CDF mode selected
if(ui.GetString("STRETCH") == "CDF") {
int increment = ui.GetInteger("INCREMENT");
double lastPer = from->Percent(minimum);
stretch.AddPair(lastPer, match->Percent(minimum));
for(double i = increment + minimum; i < maximum; i += increment) {
double curPer = from->Percent(i);
if(lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
stretch.AddPair(curPer, match->Percent(i));
lastPer = curPer;
}
}
double curPer = from->Percent(maximum);
if(lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
stretch.AddPair(curPer, match->Percent(maximum));
}
}
// Modal mode is selected
else {
stretch.AddPair(from->Percent(minimum), match->Percent(minimum));
stretch.AddPair(from->Mode(), match->Mode());
stretch.AddPair(from->Percent(maximum), match->Percent(maximum));
}
// Start the processing
p.StartProcess(remap);
p.EndProcess();
}
void IsisMain ()
{
stretch.ClearPairs();
for (int i=0; i<6; i++) {
gapCount[i] = 0;
suspectGapCount[i] = 0;
invalidCount[i] = 0;
lisCount[i] = 0;
hisCount[i] = 0;
validCount[i] = 0;
}
void TranslateHiriseEdrLabels (Filename &labelFile, Cube *);
void SaveHiriseCalibrationData (ProcessImportPds &process, Cube *,
Pvl &pdsLabel);
void SaveHiriseAncillaryData (ProcessImportPds &process, Cube *);
void FixDns8 (Buffer &buf);
void FixDns16 (Buffer &buf);
ProcessImportPds p;
Pvl pdsLabel;
UserInterface &ui = Application::GetUserInterface();
// Get the input filename and make sure it is a HiRISE EDR
Filename inFile = ui.GetFilename("FROM");
iString id;
bool projected;
try {
Pvl lab(inFile.Expanded());
id = (string) lab.FindKeyword ("DATA_SET_ID");
projected = lab.HasObject("IMAGE_MAP_PROJECTION");
}
catch (iException &e) {
string msg = "Unable to read [DATA_SET_ID] from input file [" +
inFile.Expanded() + "]";
throw iException::Message(iException::Io,msg, _FILEINFO_);
}
//Checks if in file is rdr
if( projected ) {
string msg = "[" + inFile.Name() + "] appears to be an rdr file.";
msg += " Use pds2isis.";
throw iException::Message(iException::User,msg, _FILEINFO_);
}
id.ConvertWhiteSpace();
id.Compress();
id.Trim(" ");
if (id != "MRO-M-HIRISE-2-EDR-V1.0") {
string msg = "Input file [" + inFile.Expanded() + "] does not appear to be " +
"in HiRISE EDR format. DATA_SET_ID is [" + id + "]";
throw iException::Message(iException::Io,msg, _FILEINFO_);
}
p.SetPdsFile (inFile.Expanded(), "", pdsLabel);
// Make sure the data we need for the BLOBs is saved by the Process
p.SaveFileHeader();
p.SaveDataPrefix();
p.SaveDataSuffix();
// Let the Process create the output file but override any commandline
// output bit type and min/max. It has to be 16bit for the rest of hi2isis
// to run.
// Setting the min/max to the 16 bit min/max keeps all the dns (including
// the 8 bit special pixels from changing their value when they are mapped
// to the 16 bit output.
CubeAttributeOutput &outAtt = ui.GetOutputAttribute("TO");
outAtt.PixelType (Isis::SignedWord);
outAtt.Minimum((double)VALID_MIN2);
outAtt.Maximum((double)VALID_MAX2);
Cube *ocube = p.SetOutputCube(ui.GetFilename("TO"), outAtt);
p.StartProcess ();
TranslateHiriseEdrLabels (inFile, ocube);
// Pull out the lookup table so we can apply it in the second pass
// and remove it from the labels.
// Add the UNLUTTED keyword to the instrument group so we know
// if the lut has been used to convert back to 14 bit data
PvlGroup &instgrp = ocube->GetGroup("Instrument");
PvlKeyword lutKey = instgrp["LookupTable"];
PvlSequence lutSeq;
lutSeq = lutKey;
// Set up the Stretch object with the info from the lookup table
// If the first entry is (0,0) then no lut was applied.
if ((lutKey.IsNull()) ||
(lutSeq.Size()==1 && lutSeq[0][0]=="0" && lutSeq[0][1]=="0")) {
stretch.AddPair(0.0, 0.0);
stretch.AddPair(65536.0, 65536.0);
instgrp.AddKeyword(PvlKeyword("Unlutted","TRUE"));
instgrp.DeleteKeyword ("LookupTable");
}
// The user wants it unlutted
else if (ui.GetBoolean("UNLUT")) {
for (int i=0; i<lutSeq.Size(); i++) {
stretch.AddPair(i, (((double)lutSeq[i][0] + (double)lutSeq[i][1]) / 2.0));
}
instgrp.AddKeyword(PvlKeyword("Unlutted","TRUE"));
instgrp.DeleteKeyword ("LookupTable");
}
// The user does not want the data unlutted
else {
stretch.AddPair(0.0, 0.0);
stretch.AddPair(65536.0, 65536.0);
instgrp.AddKeyword(PvlKeyword("Unlutted","FALSE"));
}
ocube->PutGroup(instgrp);
// Save the calibration and ancillary data as BLOBs. Both get run thru the
// lookup table just like the image data.
SaveHiriseCalibrationData (p, ocube, pdsLabel);
SaveHiriseAncillaryData (p, ocube);
// Save off the input bit type so we know how to process it on the
// second pass below.
Isis::PixelType inType = p.PixelType();
// All finished with the ImportPds object
p.EndProcess ();
// Make another pass thru the data using the output file in read/write mode
// This allows us to correct gaps, remap special pixels and accumulate some
// counts
lsbGap = ui.GetBoolean("LSBGAP");
ProcessByLine p2;
string ioFile = ui.GetFilename("TO");
CubeAttributeInput att;
p2.SetInputCube(ioFile, att, ReadWrite);
p2.Progress()->SetText("Converting special pixels");
section = 4;
p2.StartProcess((inType == Isis::UnsignedByte) ? FixDns8 : FixDns16);
p2.EndProcess();
// Log the results of the image conversion
PvlGroup results("Results");
results += PvlKeyword ("From", inFile.Expanded());
results += PvlKeyword ("CalibrationBufferGaps", gapCount[0]);
results += PvlKeyword ("CalibrationBufferLIS", lisCount[0]);
results += PvlKeyword ("CalibrationBufferHIS", hisCount[0]);
results += PvlKeyword ("CalibrationBufferPossibleGaps", suspectGapCount[0]);
results += PvlKeyword ("CalibrationBufferInvalid", invalidCount[0]);
results += PvlKeyword ("CalibrationBufferValid", validCount[0]);
results += PvlKeyword ("CalibrationImageGaps", gapCount[1]);
results += PvlKeyword ("CalibrationImageLIS", lisCount[1]);
results += PvlKeyword ("CalibrationImageHIS", hisCount[1]);
results += PvlKeyword ("CalibrationImagePossibleGaps", suspectGapCount[1]);
results += PvlKeyword ("CalibrationImageInvalid", invalidCount[1]);
results += PvlKeyword ("CalibrationImageValid", validCount[1]);
results += PvlKeyword ("CalibrationDarkGaps", gapCount[2]);
results += PvlKeyword ("CalibrationDarkLIS", lisCount[2]);
results += PvlKeyword ("CalibrationDarkHIS", hisCount[2]);
results += PvlKeyword ("CalibrationDarkPossibleGaps", suspectGapCount[2]);
results += PvlKeyword ("CalibrationDarkInvalid", invalidCount[2]);
results += PvlKeyword ("CalibrationDarkValid", validCount[2]);
results += PvlKeyword ("ObservationBufferGaps", gapCount[3]);
results += PvlKeyword ("ObservationBufferLIS", lisCount[3]);
results += PvlKeyword ("ObservationBufferHIS", hisCount[3]);
results += PvlKeyword ("ObservationBufferPossibleGaps", suspectGapCount[3]);
results += PvlKeyword ("ObservationBufferInvalid", invalidCount[3]);
results += PvlKeyword ("ObservationBufferValid", validCount[3]);
results += PvlKeyword ("ObservationImageGaps", gapCount[4]);
results += PvlKeyword ("ObservationImageLIS", lisCount[4]);
results += PvlKeyword ("ObservationImageHIS", hisCount[4]);
results += PvlKeyword ("ObservationImagePossibleGaps", suspectGapCount[4]);
results += PvlKeyword ("ObservationImageInvalid", invalidCount[4]);
results += PvlKeyword ("ObservationImageValid", validCount[4]);
results += PvlKeyword ("ObservationDarkGaps", gapCount[5]);
results += PvlKeyword ("ObservationDarkLIS", lisCount[5]);
results += PvlKeyword ("ObservationDarkHIS", hisCount[5]);
results += PvlKeyword ("ObservationDarkPossibleGaps", suspectGapCount[5]);
results += PvlKeyword ("ObservationDarkInvalid", invalidCount[5]);
results += PvlKeyword ("ObservationDarkValid", validCount[5]);
// Write the results to the log
Application::Log(results);
return;
}
void IsisMain() {
colorOffset = 0;
frameletLines.clear();
outputCubes.clear();
uveven = NULL;
uvodd = NULL;
viseven = NULL;
visodd = NULL;
ProcessImportPds p;
Pvl pdsLab;
UserInterface &ui = Application::GetUserInterface();
QString fromFile = ui.GetFileName("FROM");
flip = false;//ui.GetBoolean("FLIP");
p.SetPdsFile(fromFile, "", pdsLab);
ValidateInputLabels(pdsLab);
inputCubeLines = p.Lines();
lookupTable = Stretch();
// read the lut if the option is on
if(ui.GetBoolean("UNLUT") && pdsLab["LRO:LOOKUP_TABLE_TYPE"][0] == "STORED") {
PvlKeyword lutKeyword = pdsLab["LRO:LOOKUP_CONVERSION_TABLE"];
for(int i = 0; i < lutKeyword.size(); i ++) {
IString lutPair = lutKeyword[i];
lutPair.ConvertWhiteSpace();
lutPair.Remove("() ");
QString outValueMin = lutPair.Token(" ,").ToQt();
QString outValueMax = lutPair.Token(" ,").ToQt();
lookupTable.AddPair(i, (toDouble(outValueMin) + toDouble(outValueMax)) / 2.0);
}
}
QString instModeId = pdsLab["INSTRUMENT_MODE_ID"];
// this will be used to convert num input lines to num output lines,
// only changed for when both uv and vis exist (varying summing)
double visOutputLineRatio = 1.0;
double uvOutputLineRatio = 1.0;
int numFilters = 0;
if(ui.GetBoolean("COLOROFFSET")) {
colorOffset = ui.GetInteger("COLOROFFSETSIZE");
}
// Determine our band information based on
// INSTRUMENT_MODE_ID - FILTER_NUMBER is
// only going to be used for BW images
if(instModeId == "COLOR") {
numFilters = 7;
frameletLines.push_back(4);
frameletLines.push_back(4);
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
uveven = new Cube();
uvodd = new Cube();
viseven = new Cube();
visodd = new Cube();
// 14 output lines (1 framelet) from 5vis/2uv lines
visOutputLineRatio = 14.0 / (14.0 * 5.0 + 4.0 * 2.0);
// 4 output lines (1 framelet) from 5vis/2uv lines
uvOutputLineRatio = 4.0 / (14.0 * 5.0 + 4.0 * 2.0);
}
else if(instModeId == "VIS") {
numFilters = 5;
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
frameletLines.push_back(14);
viseven = new Cube();
visodd = new Cube();
// 14 output lines (1 framelet) from 5vis/2uv lines
visOutputLineRatio = 14.0 / (14.0 * 5.0);
}
else if(instModeId == "UV") {
numFilters = 2;
frameletLines.push_back(4);
frameletLines.push_back(4);
uveven = new Cube();
uvodd = new Cube();
// 4 output lines (1 framelet) from 2uv lines
uvOutputLineRatio = 4.0 / (4.0 * 2.0);
}
else if(instModeId == "BW") {
numFilters = 1;
frameletLines.push_back(14);
viseven = new Cube();
visodd = new Cube();
}
padding.resize(numFilters);
for(int filter = 0; filter < numFilters; filter++) {
padding[filter] = (colorOffset * frameletLines[filter]) * filter;
// dont count UV for VIS offsetting
if(instModeId == "COLOR" && filter > 1) {
padding[filter] -= 2 * colorOffset * frameletLines[filter];
}
}
FileName baseFileName(ui.GetFileName("TO"));
if(uveven && uvodd) {
// padding[1] is max padding for UV
int numSamples = ((viseven) ? p.Samples() / 4 : p.Samples());
numSamples = 128; // UV is alway sum 4 so it is 128 samples
int numLines = (int)(uvOutputLineRatio * inputCubeLines + 0.5) + padding[1];
int numBands = 2;
uveven->setDimensions(numSamples, numLines, numBands);
uveven->setPixelType(Isis::Real);
QString filename = baseFileName.path() + "/" + baseFileName.baseName() + ".uv.even.cub";
uveven->create(filename);
uvodd->setDimensions(numSamples, numLines, numBands);
uvodd->setPixelType(Isis::Real);
filename = baseFileName.path() + "/" + baseFileName.baseName() + ".uv.odd.cub";
uvodd->create(filename);
}
if(viseven && visodd) {
// padding[size-1] is max padding for vis (padding[0] or padding[4] or padding[6])
int numSamples = p.Samples();
int numLines = (int)(visOutputLineRatio * inputCubeLines + 0.5) + padding[padding.size()-1];
int numBands = ((uveven) ? padding.size() - 2 : padding.size());
viseven->setDimensions(numSamples, numLines, numBands);
viseven->setPixelType(Isis::Real);
QString filename = baseFileName.path() + "/" + baseFileName.baseName() + ".vis.even.cub";
viseven->create(filename);
visodd->setDimensions(numSamples, numLines, numBands);
visodd->setPixelType(Isis::Real);
filename = baseFileName.path() + "/" + baseFileName.baseName() + ".vis.odd.cub";
visodd->create(filename);
}
Pvl isis3VisEvenLab, isis3VisOddLab, isis3UvEvenLab, isis3UvOddLab;
TranslateLabels(pdsLab, isis3VisEvenLab, isis3VisOddLab, isis3UvEvenLab, isis3UvOddLab);
writeNullsToFile();
p.StartProcess(separateFramelets);
p.EndProcess();
// Add original labels
OriginalLabel origLabel(pdsLab);
int numFramelets = padding.size();
PvlKeyword numFrameletsKeyword("NumFramelets", toString(numFramelets));
if(uveven) {
for(int grp = 0; grp < isis3UvEvenLab.groups(); grp++) {
uveven->putGroup(isis3UvEvenLab.group(grp));
}
History history("IsisCube");
history.AddEntry();
uveven->write(history);
uveven->write(origLabel);
uveven->close();
delete uveven;
uveven = NULL;
}
if(uvodd) {
for(int grp = 0; grp < isis3UvOddLab.groups(); grp++) {
uvodd->putGroup(isis3UvOddLab.group(grp));
}
History history("IsisCube");
history.AddEntry();
uvodd->write(history);
uvodd->write(origLabel);
uvodd->close();
delete uvodd;
uvodd = NULL;
}
if(viseven) {
for(int grp = 0; grp < isis3VisEvenLab.groups(); grp++) {
viseven->putGroup(isis3VisEvenLab.group(grp));
}
History history("IsisCube");
history.AddEntry();
viseven->write(history);
viseven->write(origLabel);
viseven->close();
delete viseven;
viseven = NULL;
}
if(visodd) {
for(int grp = 0; grp < isis3VisOddLab.groups(); grp++) {
visodd->putGroup(isis3VisOddLab.group(grp));
}
History history("IsisCube");
history.AddEntry();
visodd->write(history);
visodd->write(origLabel);
visodd->close();
delete visodd;
visodd = NULL;
}
}
