Unverified Commit d7f2a991 authored by Kris J. Becker's avatar Kris J. Becker Committed by GitHub
Browse files

NEAR/MSI msi2isis and MsiCamera model improvements (#4887) 



* Rename NEAR/MSI main.cpp to msi2isis.cpp

Rename the NEAR/MSI ingestion app main.cpp to msi2isis.cpp to covert to callable function

* Remove old msi2isis tests in tsts directory

The old tests have been replaced by new FunctionalTests

* Update msi2isis to support new datasets

msi2isis has been modified to accept expanded datasets

* Accept images that have already been expanded to correct aspect (square pixels)
* New TRIM option added to optional turn off trimming of borders
* Modify SCLK start and stop times to be compatible with NAIF SCLK kernel format. This provides compatiblity for the sumspice application
* Save original start/stop SCLK values to new keywords OriginalSpacecraftClockStartCount/
OriginalSpacecraftClockStopCount
* Convert the app to a callable function

* Add msi2isis functional tests and data

msi2isis funtional test and data

* Converted all old app tests to new functional tests
* Added label and data files
* msi2isis has accompanying .lbl files as input but .gitignore excludes these files. Add explicit ignores for these *.lbl files

* Update MsiCamera model to support sumspice

MsiCamera model modified so that sumspice works correcty

* Use SpacecraftClockStartCount rather than StartTime to determine observation times for sumspice compatibility
* Add IAKs to track in repository
* Add light time and observer parameters to IAK version 2
* Bump camera version in plugin file due to new keywords loaded at spiceinit time

* Add MsiCamera gtest to replace old test

MsiCamera Gtest written to replace old version

* Add new MsiCamera tests and Fixtures

* Add optional keyword in serial number generation

NearMsiSerialNumber.trn update to add option keyword ControlSN to support use of simulated image in control processes

* Removed MsiCamera unit test

msiCamera unitTest.cpp in favor of NearMsiCameraCube.NearMsiCameraTest

* Add updates to CHANGELOG.md

* Add NEAR/MSI spiced cube for MsiCamera unit test

The MsiCamera requires a spiceinit cube, but .gitignore excludes .cub files. This commit addresses this issue by explicitly unignoring the Eros cube used for the test.

* Fix issues from review comments

* Removed space between issue number and url in CHANGELOG.md

msi2isis
* Remove commented code
* Simplify trimming. Let user decide uses for this option rather than assume it should not be used under certain conditions

* Cleaned up NearMsiCameraCube Fixture

* Moved NEAR MSI test to use label and ISD

* Address suggested improvements to msi2isis tests

* Updated tests after feedback from PR review

Co-authored-by: default avatarJesse Mapel <jmapel@usgs.gov>
parent 3a6ba5fa

.gitignore

+4 −0
Original line number Diff line number Diff line
@@ -54,6 +54,10 @@ install/ 
!isis/src/docsys/Object/build

!isis/src/docsys/Application/build



# Unignore msi2isis label files in data area as input files require these

!isis/tests/data/near/msi2isis/*.lbl

!isis/tests/data/near/msicamera/*.cub



# Ignore vs code

.vscode

CHANGELOG.md

+1 −0
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@@ -38,6 +38,7 @@ release. 
### Changed



### Added

- Improved functionality of msi2isis and MsiCamera model to support new Eros dataset, including support for Gaskell's SUMSPICE files that adjust timing, pointing and spacecraft position ephemeris. [#4886](https://github.com/USGS-Astrogeology/ISIS3/issues/4886)



### Deprecated

isis/appdata/serialnumbers/NearMsiSerialNumber.trn

+20 −0
Original line number Diff line number Diff line
@@ -26,3 +26,23 @@ Group = Keyword3 
  OutputPosition = ("Group","SerialNumberKeywords")

  Translation = (*,*)

EndGroup



/* This keyword is an optional keyword that is to be used to */

/* create unique serial numbers for images derived from the  */

/* original. This is intended for use such as applying the  */

/* local incidence backplane as a control source. By manually */

/* adding this keyword to the Instrument group with any   */

/* value, it creates a new (unique) serial number for control */

/* processing. It has no effect if the keyword does not   */

/* exist. */

Group = Keyword4

  Auto

  Optional

  InputKey = ControlSN

  InputGroup = "IsisCube,Instrument"

  InputPosition  = (IsisCube, Instrument)

  OutputName = Keyword4

  OutputPosition = ("Group","SerialNumberKeywords")

  Translation = (*,*)

EndGroup

End

isis/src/near/apps/msi2isis/main.cpp

+12 −254
Original line number Diff line number Diff line
@@ -8,270 +8,28 @@ find files of those names at the top level of this repository. **/ 


#include "Isis.h"



#include <QString>

#include "msi2isis.h"



#include "Cube.h"

#include "CubeAttribute.h"

#include "Enlarge.h"

#include "FileName.h"

#include "IException.h"

#include "IString.h"

#include "ProcessBySample.h"

#include "ProcessByBrick.h"

#include "ProcessImportPds.h"

#include "ProcessRubberSheet.h"

#include "Application.h"

#include "Pvl.h"

#include "PvlKeyword.h"

#include "PvlGroup.h"

#include "PvlToPvlTranslationManager.h"

#include "UserInterface.h"



using namespace Isis;

using namespace std;



void flipAndTrim(Buffer &in, Buffer &out);

void trimOnly(Buffer &in, Buffer &out);

void translateMsiLabels(Pvl inputLabelPvl, Pvl *isisLabelPvl);

int g_trim = 33;

int g_numSamples = 537;

using namespace Isis;



void IsisMain() {

  // Get user interface

  UserInterface &ui = Application::GetUserInterface();



  // get the label for the input image

  FileName from = ui.GetFileName("FROM");

  if (from.extension().toUpper() != "LBL") {

    from = from.setExtension("lbl");

    if (!from.fileExists()) {

      from = from.setExtension("LBL");

    }

    if (!from.fileExists()) {

      throw IException(IException::Io,

                       "Unable to find PDS label file for ["

                       + ui.GetFileName("FROM") + "].",

                       _FILEINFO_);

    }

  }



  // These images are small (537 cols x 244 line) and will be run

  //  through 3 processes.

  //  (1) Import to Isis cube format

  //  (2) Enlarge to 537 cols x 412 lines

  //  (3) Flip over horizontal axis, if LINE_DISPLAY_DIRECTION=UP

  //      and null edges.



  //  The first process will import the image into Cube format as is.

  ProcessImportPds importPds;

  Pvl inputLabelPvl;



  importPds.SetPdsFile(from.expanded(), "", inputLabelPvl);



  // from the pds label, verfify that the image is valid before continuing

  if(inputLabelPvl["INSTRUMENT_ID"][0] != "MSI") {

    throw IException(IException::Io,

                     "The input label [" + from.expanded() + "] has an invalid "

                     "value for INSTRUMENT_ID = ["

                     + inputLabelPvl["INSTRUMENT_ID"][0]

                     + "]. The msi2isis program requires INSTRUMENT_ID = [MSI].",

                     _FILEINFO_);

  }

  int lines = inputLabelPvl.findObject("IMAGE")["LINES"][0].toInt();

  int samples = inputLabelPvl.findObject("IMAGE")["LINE_SAMPLES"][0].toInt();

  if ( lines != 244 || samples != 537) {

    QString msg = "The given file [" + from.expanded() + "] does not contain "

                  "a full MSI image. Full NEAR Shoemaker MSI images have "

                  "dimension 537 samples x 244 lines. The given image is ["

                  + QString(toString(samples)) + "] samples by ["

                  + QString(toString(lines)) + "] lines.";

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

  }

  if (inputLabelPvl["SAMPLE_DISPLAY_DIRECTION"][0] != "RIGHT") {

    QString msg = "The input label [" + from.expanded() + "] has an invalid "

                  "value for SAMPLE_DISPLAY_DIRECTION = ["

                  + inputLabelPvl["SAMPLE_DISPLAY_DIRECTION"][0]

                  + "]. The msi2isis program requires "

                  "SAMPLE_DISPLAY_DIRECTION = [RIGHT].";

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

  }

  if (inputLabelPvl["LINE_DISPLAY_DIRECTION"][0] != "UP") {

    QString msg = "The input label [" + from.expanded() + "] has an invalid "

                  "value for LINE_DISPLAY_DIRECTION = ["

                  + inputLabelPvl["LINE_DISPLAY_DIRECTION"][0]

                  + "]. The msi2isis program requires "

                  "LINE_DISPLAY_DIRECTION = [UP].";

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

  }

  // Don't import projected image

  if(inputLabelPvl.hasObject("IMAGE_MAP_PROJECTION")) {

    QString msg = "Unable to import the NEAR Shoemaker MSI image from ["

                  + from.expanded() + "] using msi2isis.This program only "

                  "imports images that have not been projected. Use pds2isis. ";

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

  }





  // the given input file appears to be valid, continue with the import process

  FileName importProcessOutCube("$TEMPORARY/" + from.baseName() + ".import.tmp.cub");

  CubeAttributeOutput outatt = CubeAttributeOutput("+Real");

  importPds.SetOutputCube(importProcessOutCube.expanded(), outatt);

  importPds.StartProcess();

  importPds.Finalize();



  CubeAttributeInput inatt;



  // The second process will enlarge the imported cube from 537x244 to 537x412

  FileName enlargeProcessOutCube("$TEMPORARY/" + from.baseName() + ".enlarge.tmp.cub");

  ProcessRubberSheet enlargeProcess;

  Cube *cube = enlargeProcess.SetInputCube(importProcessOutCube.expanded(), inatt);

  enlargeProcess.SetOutputCube(enlargeProcessOutCube.expanded(), outatt, 537, 412, 1);



  // Set up the interpolator

  Interpolator *interp;

  if(ui.GetString("INTERP") == "NEARESTNEIGHBOR") {

    interp = new Interpolator(Interpolator::NearestNeighborType);

  }

  else if(ui.GetString("INTERP") == "BILINEAR") {

    interp = new Interpolator(Interpolator::BiLinearType);

  }

  else { //if(ui.GetString("INTERP") == "CUBICCONVOLUTION") {

    interp = new Interpolator(Interpolator::CubicConvolutionType);

  }



  double sampleScale = 1.0;

  double lineScale = 412.0/(double)lines;

  Enlarge *enlarge = new Enlarge(cube, sampleScale, lineScale);

  enlargeProcess.StartProcess(*enlarge, *interp);

  enlargeProcess.Finalize();



  // The third (last) process will flip the image lines and set the 33 pixels

  // along each border (top, bottom, left, and right) to null.

  ProcessBySample processSamps;

  processSamps.SetInputCube(enlargeProcessOutCube.expanded(), inatt);

  Cube *outputCube = processSamps.SetOutputCube("TO");



  // translate labels

  Pvl appLog;

  try {

    // translate the band bin and archive groups to this pvl

    Pvl bandBinAndArchivePvl;

    importPds.TranslatePdsLabels(bandBinAndArchivePvl);



    // add translated values from band bin and archive groups to the output cube

    PvlGroup outputBandBinGrp("BandBin");

    PvlGroup outputArchiveGrp("Archive");



    if(bandBinAndArchivePvl.findGroup("BandBin").keywords() > 0) {

      outputBandBinGrp = bandBinAndArchivePvl.findGroup("BandBin");

    }



    // This group will never be empty since we translate INSTRUMENT_ID and this

    // is required for the Instrument group

    outputArchiveGrp = bandBinAndArchivePvl.findGroup("Archive");



    outputCube->putGroup(PvlGroup("Instrument"));

    outputCube->putGroup(outputBandBinGrp);

    outputCube->putGroup(outputArchiveGrp);

    outputCube->putGroup(PvlGroup("Kernels"));



    Pvl *isisLabelPvl = outputCube->label();

    translateMsiLabels(inputLabelPvl, isisLabelPvl);

    msi2isis(ui, &appLog);

  }

  catch(IException &e) {

    delete enlarge;

    delete interp;

    remove(importProcessOutCube.expanded().toLatin1());

    remove(enlargeProcessOutCube.expanded().toLatin1());

    QString msg = "Unable to translate the labels from [" + from.expanded()

                  + "] to ISIS format using msi2isis.";

    throw IException(e, IException::Unknown, msg, _FILEINFO_);

  catch (...) {

    for (auto grpIt = appLog.beginGroup(); grpIt!= appLog.endGroup(); grpIt++) {

      Application::Log(*grpIt);

    }

  // now, determine the number of samples, then flip and trim the output cube

  g_numSamples = outputCube->sampleCount();

  processSamps.ProcessCube(flipAndTrim);

  processSamps.Finalize();



  // clean up temp files and "new" pointers

  delete enlarge;

  delete interp;

  remove(importProcessOutCube.expanded().toLatin1());

  remove(enlargeProcessOutCube.expanded().toLatin1());

    throw;

  }



/**

 * @brief Flip the lines and trim the edges.

 *

 * This process will flip over the horizontal axis (i.e. flip lines) and trim

 * 33 pixels from the top, bottom, left and right edges of the input buffer.

 *

 * @param in Reference to the input buffer.

 * @param out Reference to the output buffer.

 */

void flipAndTrim(Buffer &in, Buffer &out) {

  // Trim the left and right sides of the image

  if(in.Sample() <= g_trim || in.Sample() > g_numSamples - g_trim) {

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

      out[i] = NULL8;

    }

  }

  // Otherwise, if the current sample is between 33 and 504, trim the

  // first and last 33 lines and flip the rest.

  else {

    int lastLineIndex = in.size() - 1;

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

      if (in.Line(i) <= g_trim || in.Line(i) > in.LineDimension() - g_trim) {

        out[i] = NULL8;

  for (auto grpIt = appLog.beginGroup(); grpIt!= appLog.endGroup(); grpIt++) {

    Application::Log(*grpIt);

  }

      else {

        out[i] = in[lastLineIndex - i];

      }

    }

  }

}



/**

 * Translate the MSI labels into Isis.

 *

 * This method requires the Instrument, BandBin, and Kernels groups to already

 * exist in the labels.

 *

 * @param inputLabelPvl The PDS input file.

 * @param isisLabelPvl The output Isis cube label Pvl.

 */

void translateMsiLabels(Pvl inputLabelPvl, Pvl *isisLabelPvl) {

  PvlGroup &instGrp(isisLabelPvl->findGroup("Instrument", Pvl::Traverse));

  PvlGroup &bandBinGrp(isisLabelPvl->findGroup("BandBin", Pvl::Traverse));

  PvlGroup &kernelsGrp(isisLabelPvl->findGroup("Kernels", Pvl::Traverse));



  kernelsGrp += PvlKeyword("NaifFrameCode", "-93001");



  PvlToPvlTranslationManager labelXlater(inputLabelPvl,

                                    "$ISISROOT/appdata/translations/NearMsiImportPdsLabel.trn");

  labelXlater.Auto(*isisLabelPvl);



  // Add units to center wave length

  bandBinGrp.findKeyword("Center").setUnits("nm");



  // Read DPU deck temperature value from the labels (This value is also given

  // in celcius in the FITS header under the keyword NEAR-049)

  instGrp += PvlKeyword("DpuDeckTemperature",

                     inputLabelPvl["INSTRUMENT_TEMPERATURE"][1],

                     inputLabelPvl["INSTRUMENT_TEMPERATURE"].unit());



  // we might want to read values from the FITS header in the future. For

  // example...

  //

  // importPds.SaveFileHeader();

  // char *fitsHeader = importPds.FileHeader();

  //

  // or

  //

  // importPds.SaveDataHeader();

  // char *fitsHeader = importPds.DataHeader()



  // int startByte = 4251; //if this keyword value was found between 4251:4260

  // int numBytes = 10;

  // string summingMode(numBytes, '\0');

  // for (int byte = 0; byte < numBytes; byte++) {

  //   summingMode[byte] = fitsHeader[startByte + byte];

  // }

}

isis/src/near/apps/msi2isis/msi2isis.cpp

0 → 100644
+317 −0
Original line number Diff line number Diff line 
/** This is free and unencumbered software released into the public domain.



The authors of ISIS do not claim copyright on the contents of this file.

For more details about the LICENSE terms and the AUTHORS, you will

find files of those names at the top level of this repository. **/



/* SPDX-License-Identifier: CC0-1.0 */



#include "msi2isis.h"



#include <QString>



#include "Cube.h"

#include "CubeAttribute.h"

#include "Enlarge.h"

#include "FileName.h"

#include "IException.h"

#include "IString.h"

#include "ProcessBySample.h"

#include "ProcessByBrick.h"

#include "ProcessImportPds.h"

#include "ProcessRubberSheet.h"

#include "Pvl.h"

#include "PvlKeyword.h"

#include "PvlGroup.h"

#include "PvlToPvlTranslationManager.h"

#include <QScopedPointer>

#include "UserInterface.h"



using namespace std;



namespace Isis {





  static void translateMsiLabels(Pvl inputLabelPvl, Pvl *isisLabelPvl);





  void msi2isis( UserInterface &ui, Pvl *log ) {



    // get the label for the input image

    FileName from = ui.GetFileName("FROM");

    if (from.extension().toUpper() != "LBL") {

      from = from.setExtension("lbl");

      if (!from.fileExists()) {

        from = from.setExtension("LBL");

      }

      if (!from.fileExists()) {

        throw IException(IException::Io,

                        "Unable to find PDS label file for ["

                        + ui.GetFileName("FROM") + "].",

                        _FILEINFO_);

      }

    }



    // These images are small (537 cols x 244 line) and will be run

    //  through 3 processes.

    //  (1) Import to Isis cube format

    //  (2) Enlarge to 537 cols x 412 lines

    //  (3) Flip over horizontal axis, if LINE_DISPLAY_DIRECTION=UP

    //      and null edges.



    //  The first process will import the image into Cube format as is.

    ProcessImportPds importPds;

    Pvl inputLabelPvl;



    importPds.SetPdsFile(from.expanded(), "", inputLabelPvl);





    // from the pds label, verfify that the image is valid before continuing

    if(inputLabelPvl["INSTRUMENT_ID"][0] != "MSI") {

      throw IException(IException::Io,

                      "The input label [" + from.expanded() + "] has an invalid "

                      "value for INSTRUMENT_ID = ["

                      + inputLabelPvl["INSTRUMENT_ID"][0]

                      + "]. The msi2isis program requires INSTRUMENT_ID = [MSI].",

                      _FILEINFO_);

    }

    int lines = inputLabelPvl.findObject("IMAGE")["LINES"][0].toInt();

    int samples = inputLabelPvl.findObject("IMAGE")["LINE_SAMPLES"][0].toInt();

    if ( (  (lines != 244) && (lines != 412) ) || samples != 537) {

      QString msg = "The given file [" + from.expanded() + "] does not contain "

                    "a full MSI image. Full NEAR Shoemaker MSI images have "

                    "dimension 537 samples x 244 (or 412) lines. The given image is ["

                    + QString(toString(samples)) + "] samples by ["

                    + QString(toString(lines)) + "] lines.";

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

    }

    if (inputLabelPvl["SAMPLE_DISPLAY_DIRECTION"][0] != "RIGHT") {

      QString msg = "The input label [" + from.expanded() + "] has an invalid "

                    "value for SAMPLE_DISPLAY_DIRECTION = ["

                    + inputLabelPvl["SAMPLE_DISPLAY_DIRECTION"][0]

                    + "]. The msi2isis program requires "

                    "SAMPLE_DISPLAY_DIRECTION = [RIGHT].";

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

    }

    if (inputLabelPvl["LINE_DISPLAY_DIRECTION"][0] != "UP") {

      QString msg = "The input label [" + from.expanded() + "] has an invalid "

                    "value for LINE_DISPLAY_DIRECTION = ["

                    + inputLabelPvl["LINE_DISPLAY_DIRECTION"][0]

                    + "]. The msi2isis program requires "

                    "LINE_DISPLAY_DIRECTION = [UP].";

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

    }

    // Don't import projected image

    if(inputLabelPvl.hasObject("IMAGE_MAP_PROJECTION")) {

      QString msg = "Unable to import the NEAR Shoemaker MSI image from ["

                    + from.expanded() + "] using msi2isis.This program only "

                    "imports images that have not been projected. Use pds2isis. ";

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

    }





    // the given input file appears to be valid, continue with the import process

    FileName importProcessOutCube("$TEMPORARY/" + from.baseName() + ".import.tmp.cub");

    CubeAttributeOutput outatt = CubeAttributeOutput("+Real");

    importPds.SetOutputCube(importProcessOutCube.expanded(), outatt);

    importPds.StartProcess();

    importPds.Finalize();

    importPds.ClearCubes();





    CubeAttributeInput inatt;

    FileName enlargeProcessOutCube("$TEMPORARY/" + from.baseName() + ".enlarge.tmp.cub");

    if ( 412 != lines ) {

      // The second process will enlarge the imported cube from 537x244 to 537x412

      ProcessRubberSheet enlargeProcess;

      Cube *cube = enlargeProcess.SetInputCube(importProcessOutCube.expanded(), inatt);

      enlargeProcess.SetOutputCube(enlargeProcessOutCube.expanded(), outatt, 537, 412, 1);



      // Set up the interpolator

      QScopedPointer<Interpolator>  interp;

      if(ui.GetString("INTERP") == "NEARESTNEIGHBOR") {

              interp.reset( new Interpolator(Interpolator::NearestNeighborType) );

      }

      else if(ui.GetString("INTERP") == "BILINEAR") {

              interp.reset( new Interpolator(Interpolator::BiLinearType) );

      }

      else { //if(ui.GetString("INTERP") == "CUBICCONVOLUTION") {

              interp.reset( new Interpolator(Interpolator::CubicConvolutionType) );

      }



      double sampleScale = 1.0;

      double lineScale = 412.0/(double)lines;

      QScopedPointer<Enlarge> enlarge( new Enlarge(cube, sampleScale, lineScale));

      enlargeProcess.StartProcess(*enlarge, *interp);

      enlargeProcess.Finalize();

      enlargeProcess.ClearCubes();



    }

    else {

        // Image has the proper expanded size

        enlargeProcessOutCube = importProcessOutCube;

    }



    // The third (last) process will flip the image lines and set the 33 pixels

    // along each border (top, bottom, left, and right) to null.

    ProcessBySample processSamps;

    processSamps.SetInputCube(enlargeProcessOutCube.expanded(), inatt);



    QString fname = ui.GetCubeName("TO");

    CubeAttributeOutput &atts = ui.GetOutputAttribute("TO");

    Cube *outputCube = processSamps.SetOutputCube(fname, atts);





    // translate labels

    try {

      // translate the band bin and archive groups to this pvl

      Pvl bandBinAndArchivePvl;

      importPds.TranslatePdsLabels(bandBinAndArchivePvl);



      // add translated values from band bin and archive groups to the output cube

      PvlGroup outputBandBinGrp("BandBin");

      PvlGroup outputArchiveGrp("Archive");



      if(bandBinAndArchivePvl.findGroup("BandBin").keywords() > 0) {

        outputBandBinGrp = bandBinAndArchivePvl.findGroup("BandBin");

      }



      // This group will never be empty since we translate INSTRUMENT_ID and this

      // is required for the Instrument group

      outputArchiveGrp = bandBinAndArchivePvl.findGroup("Archive");



      outputCube->putGroup(PvlGroup("Instrument"));

      outputCube->putGroup(outputBandBinGrp);

      outputCube->putGroup(outputArchiveGrp);

      outputCube->putGroup(PvlGroup("Kernels"));



      Pvl *isisLabelPvl = outputCube->label();

      translateMsiLabels(inputLabelPvl, isisLabelPvl);

    }

    catch ( IException &e) {

      remove(importProcessOutCube.expanded().toLatin1());

      remove(enlargeProcessOutCube.expanded().toLatin1());

      QString msg = "Unable to translate the labels from [" + from.expanded()

                    + "] to ISIS format using msi2isis.";

      throw IException(e, IException::Unknown, msg, _FILEINFO_);

    }



    // Determine trim conditions for this image

    int trim = 33;         // Default trim buffer size

    int numSamples = outputCube->sampleCount();



    if ( !ui.GetBoolean("TRIM") ) { // TRIM=false

      trim = 0;                     // No trimming of lines/samples

    }



//************************************************************************

// Lambda to flip and trim the image data on ingest

//************************************************************************



 /**

   * @brief Flip the lines and trim the edges.

   *

   * This process will flip over the horizontal axis (i.e. flip lines) and trim

   * 33 pixels from the top, bottom, left and right edges of the input buffer.

   *

   * @param in Reference to the input buffer.

   * @param out Reference to the output buffer.

   */

    auto flipAndTrim = [&trim, &numSamples](Buffer &in, Buffer &out)->void {

      if ((in.Sample() <= trim) || (in.Sample() > (numSamples - trim)) ) {

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

          out[i] = NULL8;

        }

      }

      // Otherwise, if the current sample is between 33 and 504, trim the

      // first and last 33 lines and flip the rest.

      else {

        int lastLineIndex = in.size() - 1;

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

          if ( (in.Line(i) <= trim) || (in.Line(i) > (in.LineDimension() - trim)) ) {

            out[i] = NULL8;

          }

          else {

            out[i] = in[lastLineIndex - i];

          }

        }

      }

    };





    processSamps.ProcessCube(flipAndTrim);

    processSamps.Finalize();

    processSamps.ClearCubes();





    // clean up temp files and "new" pointers

    remove(importProcessOutCube.expanded().toLatin1());

    remove(enlargeProcessOutCube.expanded().toLatin1());

  }





  /**

   * Translate the MSI labels into Isis.

   *

   * This method requires the Instrument, BandBin, and Kernels groups to already

   * exist in the labels.

   *

   * @param inputLabelPvl The PDS input file.

   * @param isisLabelPvl The output Isis cube label Pvl.

   */

  void translateMsiLabels(Pvl inputLabelPvl, Pvl *isisLabelPvl) {

    PvlGroup &instGrp(isisLabelPvl->findGroup("Instrument", Pvl::Traverse));

    PvlGroup &bandBinGrp(isisLabelPvl->findGroup("BandBin", Pvl::Traverse));

    PvlGroup &kernelsGrp(isisLabelPvl->findGroup("Kernels", Pvl::Traverse));



    kernelsGrp += PvlKeyword("NaifFrameCode", "-93001");



    PvlToPvlTranslationManager labelXlater(inputLabelPvl,

                                      "$ISISROOT/appdata/translations/NearMsiImportPdsLabel.trn");

    labelXlater.Auto(*isisLabelPvl);





    // Add units to center wave length

    bandBinGrp.findKeyword("Center").setUnits("nm");



    // Correct SCLK times for use in camera model and sumspice!

    PvlKeyword &sclkStart = instGrp["SpacecraftClockStartCount"];

    PvlKeyword &sclkStop  = instGrp["SpacecraftClockStopCount"];



    // Record the orignal SCLKS

    instGrp += PvlKeyword("OriginalSpacecraftClockStartCount", sclkStart[0]);

    instGrp += PvlKeyword("OriginalSpacecraftClockStopCount",  sclkStop[0]);



    // Correct format of SCLK by remove the .

    // Test if the correction has been made - it should be an integer

    if ( sclkStart[0].contains(".") ) {

      sclkStart = sclkStart[0].remove(".");

      sclkStop  = sclkStop[0].remove(".");

    }



    // Read DPU deck temperature value from the labels (This value is also given

    // in celcius in the FITS header under the keyword NEAR-049)

    instGrp += PvlKeyword("DpuDeckTemperature",

                      inputLabelPvl["INSTRUMENT_TEMPERATURE"][1],

                      inputLabelPvl["INSTRUMENT_TEMPERATURE"].unit());



    // we might want to read values from the FITS header in the future. For

    // example...

    //

    // importPds.SaveFileHeader();

    // char *fitsHeader = importPds.FileHeader();

    //

    // or

    //

    // importPds.SaveDataHeader();

    // char *fitsHeader = importPds.DataHeader()



    // int startByte = 4251; //if this keyword value was found between 4251:4260

    // int numBytes = 10;

    // string summingMode(numBytes, '\0');

    // for (int byte = 0; byte < numBytes; byte++) {

    //   summingMode[byte] = fitsHeader[startByte + byte];

    // }

  }



} // namespace Isis