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;
}
/**
* This program imports Mars Express HRSC files
*
* This works by first determining whether or not the input file
* has prefix data.
*
* If there is prefix data, a StartProcess is called with the
* IgnoreData() function callback in order to get the import class to
* collect prefix data. Once the prefix data is populated, we go ahead
* and look for "gaps" - HRSC files can give us a time and exposure duration
* for each line, we look for where the time + exposure duration != next line's time.
* We populate a table (LineScanTimes) with the prefix data and lineInFile with whether or not
* a gap should be inserted.
*
* For all files, we now process the data using the WriteOutput callback. If there were gaps,
* WriteOutput will put them in their proper places. Finally, we translate the labels and put
* the LineScanTimes (if necessary) in the output cube.
*
* This is a two-pass system for files with prefix data, one-pass for files without.
*
* The Isis2 equivalent to this program is mex2isis.pl. It is worth noting that regardless of the
* input file's byte order, the prefix data byte order is always LSB.
*/
void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
try {
Pvl temp(ui.GetFileName("FROM"));
// Check for HRSC file
if(temp["INSTRUMENT_ID"][0] != "HRSC") throw IException();
}
catch(IException &e) {
IString msg = "File [" + ui.GetFileName("FROM") +
"] does not appear to be a Mars Express HRSC image.";
throw IException(IException::User, msg, _FILEINFO_);
}
ProcessImportPds p;
Pvl label;
lineInFile.clear();
numLinesSkipped = 0;
p.SetPdsFile(ui.GetFileName("FROM"), "", label);
CubeAttributeOutput outAtt(ui.GetFileName("TO"));
outCube = new Cube();
outCube->setByteOrder(outAtt.byteOrder());
outCube->setFormat(outAtt.fileFormat());
outCube->setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
/**
* Isis2 mex2isis.pl:
* if (index($detector_id,"MEX_HRSC_SRC") < 0 &&
* $processing_level_id < 3)
*/
bool hasPrefix = (label["DETECTOR_ID"][0] != "MEX_HRSC_SRC" && (int)label["PROCESSING_LEVEL_ID"] < 3);
TableField ephTimeField("EphemerisTime", TableField::Double);
TableField expTimeField("ExposureTime", TableField::Double);
TableField lineStartField("LineStart", TableField::Integer);
TableRecord timesRecord;
timesRecord += ephTimeField;
timesRecord += expTimeField;
timesRecord += lineStartField;
Table timesTable("LineScanTimes", timesRecord);
if(hasPrefix) {
p.SetDataPrefixBytes((int)label.findObject("IMAGE")["LINE_PREFIX_BYTES"]);
p.SaveDataPrefix();
p.Progress()->SetText("Reading Prefix Data");
p.StartProcess(IgnoreData);
// The prefix data is always in LSB format, regardless of the overall file format
EndianSwapper swapper("LSB");
std::vector<double> ephemerisTimes;
std::vector<double> exposureTimes;
std::vector< std::vector<char *> > prefix = p.DataPrefix();
for(int line = 0; line < p.Lines(); line++) {
double ephTime = swapper.Double((double *)prefix[0][line]);
double expTime = swapper.Float((float *)(prefix[0][line] + 8)) / 1000.0;
if(line > 0) {
/**
* We know how many skipped lines with this equation. We take the
* difference in the current line and the last line's time, which will
* ideally be equal to the last line's exposure duration. We divide this by
* the last line's exposure duration, and the result is the 1-based count of
* how many exposures there were between the last line and the current line.
* We subtract one in order to remove the known exposure, and the remaining should
* be the 1-based count of how many lines were skipped. Add 0.5 to round up.
*/
int skippedLines = (int)((ephTime - ephemerisTimes.back()) / exposureTimes.back() - 1.0 + 0.5);
for(int i = 0; i < skippedLines; i++) {
ephemerisTimes.push_back(ephemerisTimes.back() + exposureTimes.back());
exposureTimes.push_back(exposureTimes.back());
lineInFile.push_back(false);
}
}
ephemerisTimes.push_back(ephTime);
exposureTimes.push_back(expTime);
lineInFile.push_back(true);
}
double lastExp = 0.0;
for(unsigned int i = 0; i < ephemerisTimes.size(); i++) {
if(lastExp != exposureTimes[i]) {
lastExp = exposureTimes[i];
timesRecord[0] = ephemerisTimes[i];
timesRecord[1] = exposureTimes[i];
timesRecord[2] = (int)i + 1;
timesTable += timesRecord;
}
}
outCube->setDimensions(p.Samples(), lineInFile.size(), p.Bands());
}
else {
//Checks if in file is rdr
FileName inFile = ui.GetFileName("FROM");
QString msg = "[" + inFile.name() + "] appears to be an rdr file.";
msg += " Use pds2isis.";
throw IException(IException::User, msg, _FILEINFO_);
}
p.Progress()->SetText("Importing");
outCube->create(ui.GetFileName("TO"));
p.StartProcess(WriteOutput);
if(hasPrefix) {
outCube->write(timesTable);
}
// Get as many of the other labels as we can
Pvl otherLabels;
//p.TranslatePdsLabels (otherLabels);
TranslateHrscLabels(label, otherLabels);
if(otherLabels.hasGroup("Mapping") &&
(otherLabels.findGroup("Mapping").keywords() > 0)) {
outCube->putGroup(otherLabels.findGroup("Mapping"));
}
if(otherLabels.hasGroup("Instrument") &&
(otherLabels.findGroup("Instrument").keywords() > 0)) {
outCube->putGroup(otherLabels.findGroup("Instrument"));
}
if(otherLabels.hasGroup("BandBin") &&
(otherLabels.findGroup("BandBin").keywords() > 0)) {
outCube->putGroup(otherLabels.findGroup("BandBin"));
}
if(otherLabels.hasGroup("Archive") &&
(otherLabels.findGroup("Archive").keywords() > 0)) {
outCube->putGroup(otherLabels.findGroup("Archive"));
}
if(otherLabels.hasGroup("Kernels") &&
(otherLabels.findGroup("Kernels").keywords() > 0)) {
outCube->putGroup(otherLabels.findGroup("Kernels"));
}
p.EndProcess();
outCube->close();
delete outCube;
outCube = NULL;
lineInFile.clear();
}