Added the extracting program.

ifeq ($(ISISROOT), $(BLANK))

.SILENT:

error:

	echo "Please set ISISROOT";

else

	include $(ISISROOT)/make/isismake.apps

endif

 No newline at end of file

#include "Isis.h"

#include "Application.h"

#include "Cube.h"

#include "CubeAttribute.h"

#include "Portal.h"

#include "ProcessByLine.h"

#include "Pvl.h"

#include "UserInterface.h"

#include <QString>

using namespace std;

using namespace Isis;

#define FLOAT_MIN -16777215

void findTrackBand(UserInterface ui, QString &copyBands, QString &trackBand);

void createMosaicCube(UserInterface ui, QString bands);

void createTrackCube(UserInterface ui, QString trackingBand);

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

void IsisMain() {

  UserInterface &ui = Application::GetUserInterface();

  QString copyBands;

  QString trackBand;

  findTrackBand(ui, copyBands, trackBand);

  createMosaicCube(ui, copyBands);

  createTrackCube(ui, trackBand);

}

/**

 * Finds the index of the tracking band in the BandBin group and stores the index

 * in trackBand. The other bands' indices are stored in copyBands.

 * We store the indices in QStrings because we use them as cube attributes when

 * we process the mosaic and tracking cubes.

 *

 * @param ui        The user interface

 * @param copyBands Indices of the bands to copy over to the mosaic cube

 * @param trackBand Index of the tracking band

 */

void findTrackBand(UserInterface ui, QString &copyBands, QString &trackBand) {

  Cube inputCube = Cube(ui.GetFileName("FROM"));

  Pvl *originalLabel = inputCube.label();

  if (originalLabel->hasObject("IsisCube")) {

    PvlObject &cubeObject = originalLabel->findObject("IsisCube");

    if (cubeObject.hasGroup("BandBin")) {

      PvlGroup &bandBinGroup = cubeObject.findGroup("BandBin");

      PvlKeyword &currentKeyword = bandBinGroup[0];

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

        if (currentKeyword[i] != "TRACKING") {

          copyBands += QString::number(i + 1); // Make it 1 based

          copyBands += ",";

        }

        else {

          trackBand = QString::number(i + 1);

        }

      }

    }

  }

}

/**

 * Creates the mosaic cube by copying the input cube without the tracking band.

 * Then, removes the tracking table from the mosaic label and adds a group pointing

 * to the tracking cube.

 *

 * @param ui    The user interface

 * @param bands The indices of the bands that are not the tracking band

 */

void createMosaicCube(UserInterface ui, QString bands) {

  ProcessByLine p;

  CubeAttributeInput inAtt = CubeAttributeInput("+" + bands);

  p.SetInputCube(ui.GetFileName("FROM"), inAtt);

  p.SetOutputCube("TO");

  p.StartProcess(processCube);

  p.EndProcess();

  Cube mosaicCube;

  try {

    mosaicCube.open(ui.GetFileName("TO"),"rw");

  }

  catch (IException &e) {

    throw IException(IException::User,

                     "Unable to open the file [" + ui.GetFileName("TO") + "] as a cube.",

                     _FILEINFO_);

  }

  Pvl *mosaicLabel = mosaicCube.label();

  // Find the Table object and remove it from the mosaic cube

  if (mosaicLabel->hasObject("Table")) {

    PvlObject &tableObject = mosaicLabel->findObject("Table");

    if (tableObject.hasKeyword("Name")) {

      PvlKeyword &tableName = tableObject.findKeyword("Name", Pvl::Traverse);

      if (tableName[0] == "InputImages") {

        mosaicLabel->deleteObject("Table");

      }

    }

  }

  // Add Tracking Group to the mosaic cube

  PvlGroup trackingGroup = PvlGroup("Tracking");

  PvlKeyword trackingName = PvlKeyword("Filename");

  trackingName.setValue(ui.GetFileName("FROM") + ".cub");

  trackingGroup.addKeyword(trackingName);

  mosaicLabel->addGroup(trackingGroup);

  mosaicCube.close();

}

/**

 * Creates the tracking cube by copying the input cube with only the tracking band.

 * Then, goes through each pixel and subtracts the input cube's pixel type's min value

 * because ProcesMosaic used to add the min value to each pixel.

 *

 * @param ui           The user interface

 * @param trackingBand The index of the tracking band

 */

void createTrackCube(UserInterface ui, QString trackBand) {

  ProcessByLine p;

  CubeAttributeInput inAtt = CubeAttributeInput("+" + trackBand);

  p.SetInputCube(ui.GetFileName("FROM"), inAtt);

  QString cubeName = ui.GetFileName("TO") + "_tracking";

  // CubeAttributeOutput outAtt = CubeAttributeOutput("+Real");

  Cube inputCube = Cube(ui.GetFileName("FROM"));

  int numSample = inputCube.sampleCount();

  int numLine = inputCube.lineCount();

  CubeAttributeOutput outAtt = CubeAttributeOutput();

  p.SetOutputCube(cubeName, outAtt, numSample, numLine);

  p.StartProcess(processCube);

  p.EndProcess();

  Cube trackCube;

  try {

    trackCube.open(cubeName,"rw");

  }

  catch (IException &e) {

    throw IException(IException::User,

                     "Unable to open the file [" + cubeName + "] as a cube.",

                     _FILEINFO_);

  }

  // Convert the old DN to the new DN by subtracting the minimum value of the pixel type

  int offset = 0;

  int defaultVal = 0;

  switch (SizeOf(inputCube.pixelType())) {

    case 1:

      offset = VALID_MIN1;

      defaultVal = NULL1;

      break;

    case 2:

      offset = VALID_MIN2;

      defaultVal = NULL2;

      break;

    case 4:

      offset = FLOAT_MIN;

      defaultVal = INULL4;

      break;

    default:

    QString msg = "Invalid Pixel Type [" + QString(trackCube.pixelType()) + "]";

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

  }

  Portal trackPortal(trackCube.sampleCount(), 1, trackCube.pixelType());

  for (int lineCount = 1; lineCount <= trackCube.lineCount(); lineCount++) {

    trackPortal.SetPosition(1, lineCount, 1); //Cube has only 1 band

    trackCube.read(trackPortal);

    for (int pixel = 0; pixel < trackPortal.size(); pixel++) {

      if (trackPortal[pixel] == (float) defaultVal) { // Skip if it is not part of the mosaic.

          trackPortal[pixel] = defaultVal;

      }

      else {

        trackPortal[pixel] = (int) trackPortal[pixel] - offset;

      }

    }

    trackCube.write(trackPortal);

  }

  trackCube.close();

}

/**

 * Copies DN's from the input cube to the output cube.

 *

 * @param in  Input cube

 * @param out Output cube

 */

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

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

    out[i] = in[i];

  }

}

<?xml version="1.0" encoding="UTF-8"?>

<application name="trackextract" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Application/application.xsd">

  <brief>

    Removes the tracking band from a mosaic and places it into a new tracking cube.

  </brief>

  <description>

    Updates an older mosaic cube with a tracking band by removing the tracking band and table and

    placing them into a separate tracking cube. A reference to the tracking cube is added to the

    mosaic label.

  </description>

  <category>

    <categoryItem>Mosaicking</categoryItem>

  </category>

  <history>

    <change name="Kaitlyn Lee" date="2018-07-20">

      Original version

    </change>

  </history>

  <groups>

    <group name="Files">

      <parameter name="FROM">

        <type>cube</type>

        <fileMode>input</fileMode>

        <brief>

          Input cube with tracking band

        </brief>

        <description>

          The mosaic that contains the tracking band to be extracted.

        </description>

        <filter>

          *.cub

        </filter>

      </parameter>

      <parameter name="TO">

        <type>cube</type>

        <fileMode>output</fileMode>

        <brief>

          Output mosaic and tracking cube

        </brief>

        <description>

          There will be two output cubes: the mosaic cube and the tracking cube, both named

          by the user, but the tracking cube will have "_tracking" appended onto the name.

        </description>

        <filter>

          *.cub

        </filter>

      </parameter>

    </group>

  </groups>

</application>