Merge pull request #479 from SgStapleton/cmakeMosaic

        </p>

        <p>

          MATCHDEM = FALSE, the default does not check the SHAPEMODEL keyword of the input cube

          files and does not propogate what DEM Shapemodel that was used when the input files were

          files and does not propagate what DEM Shapemodel that was used when the input files were

          projected.

        </p>

      </p>

        options is explained in the tables and descriptions below.

      </p>

      <p>

        The Track feature creates a band in the output mosaic file containing the index

              values for every pixel in the output mosaic. The Track-band can only be used appropriately through

        the  QVIEW-AdvancedTracking tool. As the user interactively pans across the displayed

        mosaic band (Band1), for every mosaic pixel location QVIEW-AdvancedTracking will report

        the source cube filename that was input to automos. The Track-band cannot be used outside

        the QVIEW-AdvancedTracking tool. <b>The file (byte) size of the mosaic is increased due to

                the track-band.</b>

        The TRACK feature creates a separate tracking cube in addition to the mosaic cube, and

        contains information for the source files of every pixel within the output mosaic.

        This cube will have the same base-name as the mosaic cube but will end in 

        "_tracking.cub". The tracking cube must always reside in the same directory as the

        mosaic cube to be properly accessed; this means that if the mosaic cube is copied or

        moved, then its associated tracking cube must be copied or moved to the same location.

        <b>The tracking cube will always be of type unsigned integer. Depending on the

        bit-type of the mosaic cube and/or the number of bands it contains, the tracking cube

        may be as much as four times the size of the mosaic cube itself.</b>

      </p>

      <p>

        The Track feature works with Priority options ONTOP (with HIGHSATURATION and

        LOWSATURATION parameters) and BENEATH for single band input cubes.  It does NOT support

        multiple band input cubes with these priority options. It does work for multiband cubes

        when PRIORITY=BAND. Furthermore, this feature is NOT supported when PRIORITY=AVERAGE.

        The tracking cube can be used appropriately through the QVIEW-AdvancedTracking

        tool. As the user pans across the displayed mosaic, for every mosaic pixel location,

        QVIEW-AdvancedTracking will interactively report the index, the filename and the

        serial number of the input cube that was input to automos for that specific pixel

        location. Since the tracking cube is of bit-type unsigned integer, the DN values of

        0, 1 and 2 are reserved for NULL, LRS and LIS, respectively, so valid pixel DN values

        will begin at an offset of 3. In other words, a pixel of DN value 3 in the tracking

        cube means that this same pixel within the mosaic was taken from the first input

        image. The tracking cube cannot be used outside of the QVIEW-AdvancedTracking tool

        except as a visual representation of the source cubes for the different pixels. 

      </p>

      <p>

        The TRACK feature works with Priority options ONTOP and BENEATH for single band input

        cubes. It works for multiband cubes for PRIORITY=ONTOP only when the NULL,

        HIGHSATURATION and LOWSATURATION options are set to true. It also works for multiband

        cubes when PRIORITY=BAND. Furthermore, this feature is NOT supported when

        PRIORITY=AVERAGE.

      </p>

      <p>

        <b>Please Note: Prior to ISIS version 3.6.0, tracking for the various mosaicking apllications

          was being handled with an internal tracking band. Tracking is now being handled by an

          external tracking cube that contains the associated tracking information. This application

          can no longer add to mosaics of the old format. In order to continue to use these

          older mosaics with the updated mosaicking applications, you must first use the

          <def>trackextract</def> utility application to extract the tracking band and the associated

          tracking information into an external tracking cube.</b>

      </p>

      <p>

        <b>

              current input image will appear in the output mosaic (it replaces the output mosaic

              pixel).  Invalid input <def>Special Pixels</def>

              (<def>NULL</def>,<def>HRS</def>,<def>HIS</def>,<def>LRS</def>,<def>LIS</def>) will NOT

              replace an existing Valid output mosaic pixel. Refer to parameters HIGHSATURATION,

              LOWSATURATION, and NULL to override replacement of Valid output mosaic pixels.

              replace an existing Valid output mosaic pixel unless the optional flags are set. Refer

              to parameters HIGHSATURATION,LOWSATURATION, and NULL to override replacement of Valid

              output mosaic pixels. 

              <p>

                <b>NOTE:</b> When using this priority with multi-band mosaics and with the TRACK

                option set, all Special Pixel flags must be set as well. This is because the same

                pixel within different bands of a single input image may hold both Valid and Special

                Pixel values, and since our Tracking capabilities can only track one input image per

                pixel (as it is a single band), it must accept the values for that particular pixel

                from <b>every</b> band in the input image being placed on top.

              </p>

            </td>

          </tr>

          <tr>

              Overlapping Valid pixel values from the current input image and output mosaic will be

              averaged for the new mosaic pixel values. A count-band is created with the output

              mosaic file.  The count-band keeps track of the number of images involved in the

              averaging of the input dn values for each pixel in the mosaic. Invalid input pixel

              averaging of the input DN values for each pixel in the mosaic. Invalid input pixel

              values will not be included in the average.  In the case where only one Valid pixel

              exists between the input image pixels or the current mosaic pixel, the Valid pixel is

              retained in the current output mosaic. Refer to parameters HIGHSATURATION,

      Added parameter checking to XML MAXLON and MAXLAT to check if they are greater than their

      minimum counterpart. Fixes #5148

    </change>

    <change name="Summer Stapleton" date="2018-08-13">

      Updated documentation to reflect new handling of tracking capabilities with an external

      tracking cube as well as clarify why special pixel flags are required when priority=ontop for

      multiband mosaics. References #2092

    </change>

  </history>

  <groups>

          the same ProjectionName, PixelResolution (or MapScale), EquatorialRadius,

          PolarRadius, LatitudeType, LongitudeDirection and specific map projection keywords

          such as CenterLatitude and CenterLongitude.  This includes the output mosaic

          if it already exists.  The latitude and longtiude extents of each input file may

          if it already exists.  The latitude and longitude extents of each input file may

          vary.

        </description>

        <filter>

              pixels. Special pixels in the corresponding bands will not replace the output mosaic

              pixel unless the HIGHSATURATION, LOWSATURATION and NULL flags are set to TRUE.  Refer

              to parameters HIGHSATURATION, LOWSATURATION, and NULL. This means, if the results

              of the priority band comparison says that the input pixel should be on top, but the

              of the priority band comparison shows that the input pixel should be on top, but the

              input pixel on any other band is NULL, without the NULL=TRUE, the output mosaic pixel

              will remain unchanged for that band.

            </description>

          The keyword values can be found on the labels of the input files under

          the "BandBin" Group. For instance, KEYNAME=NAME where the KEYVALUE

          can then be set to "Phase Angle", "Emission Angle", "Incidence Angle",

          "Pixel Resolution".  Refer to the <b>phocube</b> application that will

          "Pixel Resolution".  Refer to the <def>phocube</def> application that will

          create these 'Named' Bands.

          </description>

      </parameter>

          <brief>The lower DN value of the input priority band will replace the mosaic pixel

            </brief>

            <description>

              If the dn value of a pixel in the priority band of the input cube

              If the DN value of a pixel in the priority band of the input cube

              is lesser than the corresponding pixel in the mosaic priority band,

              then the output pixel of the mosaic will be replaced by the input

              cube pixel. This will apply to all bands at this pixel location.

           <brief>The greater DN value of the input priority band will replace the mosaic pixel

            </brief>

            <description>

              If the dn value of a pixel in the priority band of the input cube

              If the DN value of a pixel in the priority band of the input cube

              is greater than the corresponding pixel in the mosaic priority band,

              then the output pixel of the mosaic will be retained on NOT be

              replaced by the input cube pixel. This will apply to all bands at

        <type>double</type>

        <brief>Maximum Longitude</brief>

        <description>

          The maximum longitude value bounary extent for the output mosaic.

          The maximum longitude value boundary extent for the output mosaic.

        </description>

        <greaterThan>

            <item>MINLON</item>

          </brief>

          <description>

            <p>

              The Track feature creates a band in the output mosaic file containing the index

              values for every pixel in the output mosaic. The Track-band can only be used

              appropriately through the  QVIEW-AdvancedTracking tool. As the user interactively

              pans across the displayed mosaic band (Band1), for every mosaic pixel location

              QVIEW-AdvancedTracking will report the source cube filename that was input to

              automos. The Track-band cannot be used outside the QVIEW-AdvancedTracking tool.

              TRACK must be set to TRUE at the time of mosaic creation only and cannot be turned

              on after the mosaic is created. When a mosaic is created with TRACK=TRUE, all

              subsequent runs will default to TRACK=TRUE. When a mosaic is created with

              TRACK=FALSE, an error will be encountered if subsequent runs have TRACK=TRUE.

              <b>The file (byte) size of the mosaic is increased due to

                the track-band.</b>

            </p>

            <p>

              A table, called InputImages, containing the names of the images used in the mosaic

              will be added to the cube when TRACK=TRUE.

              The Track feature creates a separate tracking cube containing the index values for

              the source of every pixel in the output mosaic. The tracking cube can only be used

              appropriately through the  QVIEW-AdvancedTracking tool. As the user pans across the

              displayed mosaic, for every mosaic pixel location QVIEW-AdvancedTracking will

              interactively report the filename, the serial number and the index of the input cube

              that was input to automos for that specific pixel location. The tracking cube cannot

              be used outside the QVIEW-AdvancedTracking tool except as a visual representation of

              the source cubes for the different pixels. TRACK must be set to TRUE at the time of

              mosaic creation only and cannot be turned on after the mosaic is created. When a

              mosaic is created with TRACK=TRUE, all subsequent runs will default to TRACK=TRUE.

              When a mosaic is created with TRACK=FALSE, an error will be encountered if subsequent

              runs have TRACK=TRUE. <b>The tracking cube will always be of type unsigned integer.

              Depending on the bit-type of the mosaic cube and/or the number of bands it contains,

              the tracking cube may be as much as four times the size of the mosaic cube itself.</b>

            </p>

            <p>

              WARNING:

              If Tracking is turned on in a mosaic, any subsequent applications that modify "dn"

              values will corrupt the track-band, for instance the application <def>reduce</def>.

              If Tracking is turned on in a mosaic, any subsequent applications that modify DN

              values, such as the application<def>reduce</def>, will corrupt the DN values in the

              tracking cube.

            </p>

          </description>

        </parameter>

          The default is FALSE.  If set to TRUE, this application will create a

          Mosaic Group in the keyword labels of the new output mosaic cube including

          a ShapeModel keyword.  The output mosaic is created with the first input

          cube listed in the FROMLIST file, the ShapeModel keyword and it's value

          will be propogated to the the Mosaic Group of the output mosaic cube file.

          cube listed in the FROMLIST file, the ShapeModel keyword and its value

          will be propagated to the Mosaic Group of the output mosaic cube file.

          Subsequently, the ShapeModel keyword value of the remaining input cubes will

          be checked against the ShapeModel value in the mosaic cube.   This application

          will fail if the ShapeModel keywords don't match.

          clarify what happens during the mosaic process.

        </p>

        <p>

          The output mosaic shows the result of the second input image being mosaiced with the

          The output mosaic shows the result of the second input image being mosaicked with the

          first input image. You can see in band one that none of the special pixels were retained

          because none of the special pixel flags were set. In other words, regardless of whether

          there was a valid comparison at that pixel of the priority band, all other bands will

        <p>

          In band two, you can still see where the special pixels were in the second input image.

          The second image would have been "on top" because in band two, the pixels are less than

          those of the mosaic. However, the valid data in the mosaic was left alone because the

          those of the mosaic. However, the valid data in the mosaic was disregarded because the

          special pixel flags were not set. You cannot see the special pixels from the first image

          because the valid pixels from the second image were kept instead.

        </p>

    nl = ui.GetInteger("NLINES");

    nb = ui.GetInteger("NBANDS");

    // Create the origin band if the Track Flag is set

    if (bTrack) {

      nb += 1;

    }

    else if (overlay == ProcessMosaic::AverageImageWithMosaic) {

    if (overlay == ProcessMosaic::AverageImageWithMosaic) {

      nb *= 2;

    }

    p.SetCreateFlag(true);