Commit 24b0627e authored by Kristin's avatar Kristin Committed by Jesse Mapel
Browse files

Updates marci2isis to add variable exposure times and associated frame sequences (#3501) 

* Update date and other metadata

* ckwriter_test_fix

* Fix unintentional cmakelists change

* Updated voy2isis to add instrument parameter which can be used to specify the instrument name wac or nac if it is not provided in the image label

* Added simple test

* Updates test and documentation for voy2isis adds instrument_name update

* Updated history documentation to add ticket number for voy2isis changes

* Updated to reverse frameseq number appropriately with flip

* Remove commented-out code

* Added documentation for change and test

* Updated no exposure duration in varexp file condition

* Re-remove iTime.h

* Update warning message for assuming a single exposure time
parent 6a9c0f77

isis/src/mro/apps/marci2isis/main.cpp

+83 −1
Original line number Diff line number Diff line
@@ -5,6 +5,7 @@ 
#include "MultivariateStatistics.h"

#include "OriginalLabel.h"

#include "IException.h"

#include "CSVReader.h"



using namespace std;

using namespace Isis;
@@ -153,6 +154,87 @@ void IsisMain() { 
    isisCube.findGroup("Instrument").addKeyword(PvlKeyword("Framelets", framelets[i]));



    outputCubes[i]->write(origLabel);

  }



  QString prodId = outputCubes[0]->label()->findGroup("Archive", Pvl::Traverse)["ProductId"][0]; 

  prodId = prodId.toUpper();

  vector<int> frameseq;

  vector<double> exptime;

  // Populate with first values

  Pvl *isisLabelInitial = outputCubes[0]->label();

  PvlGroup &instInitial = isisLabelInitial->findGroup("Instrument", Pvl::Traverse);

  double exposure = instInitial["ExposureDuration"][0].toDouble() * 1000.0;



  frameseq.push_back(0);

  exptime.push_back(exposure); 



  QString varExpFile = "$mro/calibration/marci/varexp.tab";

  

  // Load the MARCI exposure duration calibration tables.

  bool header=false;

  int skip=0;

  FileName csvfile(varExpFile);

    

  CSVReader csv(csvfile.expanded(), header, skip);

    // There may be multiple entries in the file for this productID,

    // so we *must* loop through the entire file.

  for(int i = 0 ; i < csv.rows() ; i++) {

      CSVReader::CSVAxis row = csv.getRow(i);

      // The productId in the file is encapsulated by double quotes.

      QString fileProdId = row[0];

      // This is garbage code, but my compiler isn't allowing me to escape the double quotes

      int prodIdLastIndex = fileProdId.size() - 1 ;

      fileProdId.remove(prodIdLastIndex,1);

      fileProdId.remove(0,1);

      // Now, compare product ids from the input image and from the calibration table.

      if(fileProdId == prodId ) {

        if((row.dim1() - 1) != 2) {

          QString msg = "This appears to be a malformed calibration file."; 

                  msg += " There are not enough columns in the CSV";

                  msg += " file to perform the exposure time correction.";

          throw IException(IException::User, msg, _FILEINFO_);

        }

        // Build the two vectors, exptime and frame. We'll relate those to each other

        // back in main(). Remember that a productID may have multiple entries in the table.

        frameseq.push_back(toInt(row[1]));

        exptime.push_back(toDouble(row[2]));

      }

  }



  if (flip && exptime.size() > 0) {

    reverse(frameseq.begin(),frameseq.end());

    reverse(exptime.begin(),exptime.end());

  }



  // If exptime < 2, no additional exposure durations were found in the varexp file, so

  // assume a single exposure duration and warn the user. 

  // Using single exposure duration is correct in many cases, but there is no way to check 

  // using only the information in the label. 

  if (exptime.size() < 2) {

    PvlGroup missing("NoExposureTimeDataFound");

    PvlKeyword message("Message", "No variable exposure information found in the varexp file."

                                  " Assuming exposure time is fixed for [" + inFile.toString() +  "]" );

    missing.addKeyword(message); 

    missing.addKeyword(PvlKeyword("FileNotFoundInVarexpFile", prodId), Pvl::Replace);

    Application::Log(missing);

  }

        

  // Translate labels to every image and close output cubes before calling EndProcess



    // Add these values to the label

    for(unsigned int i = 0; i < outputCubes.size(); i++) {

        Pvl *isisLabel = outputCubes[i]->label();

        PvlGroup &inst = isisLabel->findGroup("Instrument", Pvl::Traverse);



        PvlKeyword varExposure("VariableExposureDuration");

        PvlKeyword frameNumber("FrameNumber");



        for (int i=0; i < exptime.size(); i++) {

          varExposure.addValue( QString::number(exptime[i]), "ms" );

          frameNumber.addValue( QString::number(frameseq[i]) );

        }

      inst.addKeyword(frameNumber);

      inst.addKeyword(varExposure);

      delete outputCubes[i];

    }

isis/src/mro/apps/marci2isis/marci2isis.xml

+4 −0
Original line number Diff line number Diff line
@@ -25,6 +25,10 @@ 
      <change name="Tracie Sucharski" date="2013-06-05">

        Added keywords to the Archive group in labels.

      </change>

      <change name="Kristin Berry" date="2019-11-09">

        Added keywords to the labels for variable exposure duration and the frame sequence. 

	References #2034

      </change>

    </history>



    <category>

isis/src/mro/apps/marci2isis/tsts/varexp/Makefile

0 → 100644
+10 −0
Original line number Diff line number Diff line 
APPNAME = marci2isis



include $(ISISROOT)/make/isismake.tsts



commands:

	$(APPNAME) FROM=$(INPUT)/P07_003640_2331_MA_00N288W.IMG TO=$(OUTPUT)/out.cub > /dev/null;

	catlab FROM=$(OUTPUT)/out.even.cub to=$(OUTPUT)/even.pvl > /dev/null;

	catlab FROM=$(OUTPUT)/out.odd.cub to=$(OUTPUT)/odd.pvl > /dev/null;

	$(APPNAME) FROM=$(INPUT)/P07_003640_2331_MA_00N288W.IMG flip=NO TO=$(OUTPUT)/unflipped.cub > /dev/null;

	catlab FROM=$(OUTPUT)/unflipped.even.cub to=$(OUTPUT)/unflipped.pvl > /dev/null;