Updated from trunk.

#include "Isis.h"

#include "SerialNumberList.h"

#include "ImageOverlapSet.h"

#include "FileList.h"

#include "ImageOverlapSet.h"

#include "SerialNumber.h"

#include "SerialNumberList.h"

using namespace std;

using namespace Isis;

  vector< pair<QString, QString> > sortedList;

  if (images.size() == 1) {

    throw IException(IException::User, "The list [" + ui.GetFileName("FROMLIST") +

                     "] only contains one image.", _FILEINFO_);

  }

  // We want to sort the input data by serial number so that the same

  //   results are produced every time this program is run with the same

  //   images. This is a modified insertion sort.

  for (int image = 0; image < images.size(); image++) {

    unsigned int insertPos = 0;

    QString sn = SerialNumber::Compose(images[image].toString());

    for (insertPos = 0; insertPos < sortedList.size(); insertPos++) {

      if (sn.compare(sortedList[insertPos].first) < 0) break;

    }

    pair<QString, QString> newPair = pair<QString, QString>(sn, images[image].toString());

    sortedList.insert(sortedList.begin() + insertPos, newPair);

  }

      Fixed a bug where ImageOverlapSet was not recording overlaps where 

      one image is fully enveloped within another. Fixes #2199.

    </change>

    <change name="Marjorie Hahn" date="2016-10-03">

      Added an exception for giving findimageoverlaps a cube list of only 

      one cube. Fixes #4200.

    </change>

  </history>

  <groups>

  FileList cubes;

  cubes.read(ui.GetFileName("FROMLIST"));

  int hns = ui.GetInteger("HNS");

  int hnl = ui.GetInteger("HNL");

  int lns = ui.GetInteger("LNS");

  int lnl = ui.GetInteger("LNL");

  int samples = ui.GetInteger("SAMPLES");

  int lines = ui.GetInteger("LINES");

  QString match = ui.GetAsString("MATCHBANDBIN");

  //Sets upt the pathName to be used for most application calls

    QString outParam = pathName + inFile.baseName() + "_highpass.cub";

    parameters = "FROM=" + inFile.expanded() +

                 " TO=" + outParam

                 + " SAMPLES=" + toString(hns) + " LINES=" + toString(hnl);

                 + " SAMPLES=" + toString(samples) + " LINES=" + toString(lines);

    ProgramLauncher::RunIsisProgram("highpass", parameters);

    //Reads the just created highpass cube into a list file for automos

    highPassList << outParam << endl;

  //Does a lowpass on the original mosaic

  parameters = "FROM=" + pathName + "OriginalMosaic.cub"

               + " TO=" + pathName + "LowpassMosaic.cub"

               + " SAMPLES=" + toString(lns) + " LINES=" + toString(lnl);

               + " SAMPLES=" + toString(samples) + " LINES=" + toString(lines);

  ProgramLauncher::RunIsisProgram("lowpass", parameters);

  //Finally combines the highpass and lowpass mosaics

    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

    xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Application/application.xsd">

  <brief>Creates a mosaic with little to no seams using a list of map projected

  <brief>Create a mosaic with little to no seams using a list of map projected

      cubes</brief>

  <description>

    This program uses a text-based list of cubes, all in the same map projection

    and equivalent projection parameters (PixelResolution, CenterLongitude,

    LatitudeSystem, etc), to generate a seamless mosaic.   The size of the

    mosaic is determined automatically by examining each listed cube.

    This application uses the automos application in order to generate the mosaic.

    The parameters FROMLIST and MATCHBANDBIN are forwarded into automos and the rest of

    the parameters are left at their default value. To know more about automos parameters,

    This program, noseam, creates a mosaic using an algorithm that minimizes seams.

    The user will enter a text-based list of cubes that must be 1) in the same map projection

    and 2) contain equivalent projection parameters such as PixelResolution, CenterLongitude, and 

    LatitudeSystem. More help is given in the Parameter Groups and with examples at the end of 

    this document. 

    To generate the mosaic, noseam uses the automos application. The FROMLIST and MATCHBANDBIN 

    parameters are taken from noseam and forwarded to automos as well as the remainder of the 

    parameters except with their default values. To learn more about <def link="automos">automos</def> parameters,

    see the automos application documentation.

  </description>

      use the correct temporary folder.

    </change>

    <change name="Kelvin Rodriguez" date="2016-6-29">

      Added a short description of how noseam utlizes automos in the documentation. 

      Added a short description of how noseam utilizes automos in the documentation. 

    </change>

    <change name="Makayla Shepherd" date="2016-8-18">

      The noseam parameters HNS HNL LNS and LNL, which correspond to the size of the 

      boxcar for the highpass and lowpass filters, have been condensed down to two 

      parameters, SAMPLES and LINES as the size of the boxcars must be the same. Fixes #258.

    </change>

  </history>

    </group>

    <group name="Filter Sizes">

      <parameter name="HNS">

      <parameter name="SAMPLES">

        <type>integer</type>

        <brief>

              Number of samples in high frequency data boxcar

              Number of samples for the boxcar filters

        </brief>

        <description>

          This is the total number of samples in the high frequency data boxcar.

          It must be odd and can not exceed twice the number of samples in the

          input cubes.  In general, the size of the boxcar does not cause the

          program to operate significantly slower.

        </description>

        <odd />

        <minimum inclusive="yes">1</minimum>

      </parameter>

      <parameter name="HNL">

        <type>integer</type>

        <brief>

                Number of lines in high frequency data boxcar

        </brief>

        <description> This is the total number of lines in the high frequency

           data boxcar. It must be odd and can not exceed twice the number of

           lines in the input cubes.  In general, the size of the boxcar does

           not cause the program to operate significantly slower.

          This is the total number of samples in the boxcar dimension applied using the highpass 

          and lowpass filters. The number must be odd and cannot exceed twice the number of samples 

          in the input cubes. The smaller the boxcar dimension, the more confined the filtered 

          results are near the image seams, which will remain similar to the original mosaic.

          The larger the boxcar dimension, the greater the extent of the filter effects are beyond 

          the seams. 

        </description>

        <odd />

        <minimum inclusive="yes">1</minimum>

      </parameter>

      <parameter name="LNS">

      <parameter name="LINES">

        <type>integer</type>

        <brief>

                Number of samples in low frequency data boxcar

                Number of lines for the boxcar filters

        </brief>

        <description> 

          This is the total number of samples in the low frequency data boxcar.

          It must be odd and can not exceed twice the number of samples in the

          input cubes.  In general, the size of the boxcar does not cause the

          program to operate significantly slower.

        </description>

        <odd />

        <minimum inclusive="yes">1</minimum>

      </parameter>

      <parameter name="LNL">

        <type>integer</type>

        <brief>

                Number of lines in low frequency data boxcar

        </brief>

        <description>

          This is the total number of lines in the low frequency data boxcar. It

          must be odd and can not exceed twice the number of lines in the input

          cubes.  In general, the size of the boxcar does not cause the program

          to operate significantly slower.

          This is the total number of lines in the boxcar dimension applied using the highpass 

          and lowpass filters. The number must be odd and cannot exceed twice the number of lines 

          in the input cubes. The smaller the boxcar dimension, the more confined the filtered 

          results are near the image seams, which will remain similar to the original mosaic.

          The larger the boxcar dimension, the greater the extent of the filter effects are beyond 

          the seams. 

        </description>

        <odd />

        <minimum inclusive="yes">1</minimum>

        <default><item>TRUE</item></default>

        <brief>Destroy intermediate data</brief>

        <description>

          Multiple cube images as well as lists are created durring the

          Multiple cube images as well as lists are created during the

          production of the final seamless mosaic.  If this parameter is changed

          to false, those temporary cubes and lists will not be destroyed.

          <p>

          If REMOVETEMP=NO:

          <ul>

            <li>OriginalMosaic.cub - This file is the mosaic result (automos) of the input cubes listed 

              in FROMLIST. </li>

            <li>LowpassMosaic.cub  - This file is the low pass filter (samples x lines) applied to the 

              OriginalMosaic.cub. </li>

            <li>HighpassMosaic.cub - This file is the mosaic result (automos) of the high pass filtered 

              input cubes listed in FROMLIST. </li>

            <li>HighPassList.lis - This single column list contains the individual highpass filter image 

              results and filenames. </li>

            <li>_highpass.cub - Every image in the fromlist will have a high pass filter 

              (samples x lines) output result. This is the suffix filename appended the original input 

              filenames. </li>

            <li>LowpassMosaic.cub + HighpassMosaic.cub = TO (noseam output filename) </li>

          </ul>

        </p>

        </description>

      </parameter>

    </group>

        <terminalInterface>

            <commandLine>FROMLIST=cubes.lis

                  TO=final.cub HNS=73 HNL=73 LNS=73 LNL=73</commandLine>

              TO=final.cub SAMPLES=73 LINES=73</commandLine>

            <description>

                Runs noseam with a 73x73 highpass filter and a 73x73 lowpass 

                    filter.  Choosing the same dimensions will preserve the

                    original image and only reduce the presence of seams in the

                    final mosaic.

                filter.

            </description>

        </terminalInterface>

          <dataFile path="assets/cubes.lis">

            <brief>cubes.lis</brief>

            <description>

                 This is a simple file that lists all of the cubes to mosaic.

                 This list as well as the cubes to be mosaiced must

              This is a text-based file that lists all of the cubes to mosaic.

              This list as well as the cubes to be mosaicked must

              be within the current directory when noseam is executed.

            </description>

            <parameterName>FROMLIST</parameterName>

            <image src="assets/images/cube1.jpg" width="204" height="550">

                <brief>First listed cube</brief>

                <description>

                        This is the first cube listed in cubes.lis

                    This is the first cube listed in cubes.lis.

                </description>

                <thumbnail caption="cube1.cub" src="assets/images/cube1.jpg" width="74" height="200"/>

            </image>

            <image src="assets/images/cube2.jpg" width="223" height="550">

                <brief>Second listed cube</brief>

                <description>

                        This is the second cube listed in cubes.lis

                    This is the second cube listed in cubes.lis.

                </description>

                <thumbnail caption="cube2.cub" src="assets/images/cube2.jpg" width="81" height="200"/>

            </image>

            <image src="assets/images/cube3.jpg" width="241" height="550">

                <brief>Third listed cube</brief>

                <description>

                        This is the third cube listed in cubes.lis

                    This is the third cube listed in cubes.lis.

                </description>

                <thumbnail caption="cube3.cub" src="assets/images/cube3.jpg" width="87" height="200"/>

            </image>

            <image src="assets/images/original.jpg" width="404" height="550">

                <brief>Automos result (NOT AN OUTPUT OF NOSEAM)</brief>

                <description>

                        This is the same mosaic created from automos.  Notice

                        the difference between this image and final.cub.  The

                        seams that exist between the original images are nearly

                        invisible in final.cub.  However, those same seams are

                        ugly in this image, automos.cub.

                    This is the same mosaic created using automos.  Notice

                    the difference between automos.cub and final.cub.  The

                    seams that existed between the original images in automos

                    are nearly invisible in final.cub.

                </description>

                <thumbnail caption="automos.cub" src="assets/images/original.jpg" width="147" height="200"/>

            </image>

	$(LS) $(INPUT)/* > $(OUTPUT)/cubes.lis;

	$(APPNAME) FROMLIST=$(OUTPUT)/cubes.lis \

	TO=$(OUTPUT)/result.cub \

	HNS=73 HNL=73 LNS=73 LNL=73 > /dev/null;

	SAMPLES=73 LINES=73 > /dev/null;

	$(RM) $(OUTPUT)/cubes.lis;