Bug fixed in isisminer to properly handle self-intersecting polygon geometries. (#5620)

- Updated pixel2map documentation

### Fixed

- Fixed a bug in isisminer in which bad (e.g. self-intersecting) polygon geometries were not treated properly. Added pertinent unit tests to GisGeometry and Strategy classes. Issue: [5612](https://github.com/DOI-USGS/ISIS3/issues/5612)

- Fixed a bug in kaguyasp2isis that doesn't work for data with a detached label.

## [8.3.0] - 2024-09-30

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

<!-- $Id: isisminer.xml 6513 2016-01-14 23:04:44Z kbecker@GS.DOI.NET $ -->

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

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

<application name="isisminer" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="/usgs/pkgs/isis3/isis/doc/Schemas/Application/application.xsd">

  <brief>

       Run a series of algorithms (Strategies) that perform various operations on input 

      in well-known-text (WKT) or well-known-binary (WKB) as conversions are 

      restricted to text representations of geometries (format requirements are 

      the same as functions like 

      <a href="http://www.postgis.org/docs/ST_GeomFromText.html">ST_GeomFromWKT</a> and 

      <a href="http://www.postgis.org/docs/ST_GeomFromWKB.html">ST_GeomFromWKB</a>, 

      <a href="http://postgis.net/docs/ST_GeomFromText.html">ST_GeomFromWKT</a> and 

      <a href="http://postgis.net/docs/ST_GeomFromWKB.html">ST_GeomFromWKB</a>, 

      respectively). Resources may also contain Assets. Assets are typically 

      another list of Resources created from Strategies that are attached to a 

      (parent) Resource. If Assets are represented as Resource lists, they can 

          as these strings can be quite large.

        </TD>

      </TR>

      <TR>

        <TD>RepairInvalidGeometry</TD>

        <TD>Optional</TD>

        <TD>

         There are times when invalid geometries will be passed into <b>isisminer</b>.

         One of the most common invalid geometries encountered is self-intersecting

         geometries. <b>footprintinit</b> will at times create self-intersecting geometries,

         usually when it uses the shape model in projecting/intersecting to ground,

         that are often read by <b>isisminer</b> as output from <b>caminfo</b>.

         These types of invalid geometries can

         be repaired by applying the GIS buffer algorithm with a width of 0. If an

         invalid geometry occurs in isisminer, and RepairInvalidGeometry = True, the

         buffer algorithm will be run to attempt to repair the geometry. The default

         value of this keyword is true so that invalid geometries will be repaired.

         See also InvalidGeometryAction.

        </TD>

      </TR>

      <TR>

        <TD>InvalidGeometryAction</TD>

        <TD>Optional</TD>

        <TD>

          This parameter determines the action taken when an invalid geometry occurs

          and is either not repaired (RepairInvalidGeometry = False) or could not be

          sucessfully repaired (RepairInvalidGeometry = True). The options are:

          continue, disable or error. For InvalidGeometryAction = continue, the state

          of the invalid geometry is retained in the Resource (some GIS operations

          still function) and it is not disabled and no error occurs - the issue is

          ignored. If InvalidGeometryAction = disable, then the geometry is retained

          in the Resource but the status is set to "discard". It can be re-enabled by

          using the ResourceManager strategy. If InvalidGeometryAction = error, then

          an error is thrown and <b>isisminer</b> terminates. The default is to 

          disable the Resource.

        </TD>

      </TR>

      <TR>

        <TD>GisSimplifyTolerance</TD>

        <TD>Optional</TD>

          not already exist in the Resources.

        </TD>

      </TR>

      <TR>

        <TD>InitializersArgs</TD>

        <TD>Optional</TD>

        <TD>

          Using this parameter, users can list existing keywords in a Resource or

          from the global parameter pool in this keyword to create new variables

          in the Initializers group. This works by substituting ordered numerical index

          values specified as %1, %2, etc..., with a keyword value referenced by

          the index in the InitializersArgs array keyword. The InitializersArgs keyword

          should have the same number of keywords as %[index], where index is 

          numbered from 1 to n, specified in the keywords found in the 

          Initializers group. These initialzers should not involve equations as 

          they are not resovled in this step.

          Note: This is the only way to create new keywords specificially in

          <b>isisminer</b>.

        </TD>

      </TR>

      <TR>

        <TD>Equation</TD>

        <TD>Optional</TD>

        tests to gtest format. Moved some data from isis data area to

        "isis/tests/data/isisminer".

    </change>

    <change name="Ken Edmundson" date="2024-09-23">

        Originally implemented in UofA OSIRIS-REx code by Kris Becker, 2018-07-31.

        Corrected problems with invalid geometries causeing isisminer to abort.

        Added two new parameters, RepairInvalidGeometry and InvalidGeometryAction,

        to allow user more control over how invalid geometries are managed. Updated

        documentation. Ken Edmundson added unit tests to GisGeometry and Strategy

        classes to address these changes.

    </change>

  </history>

  <groups>

APPNAME = isisminer

include $(ISISROOT)/make/isismake.tsts

commands:

	$(LS) $(INPUT)/*.pvl >& $(OUTPUT)/badgeomfix_data.lis;

	$(APPNAME) config=$(INPUT)/badgeomfix.conf \

	  parameters="fromlist:$(OUTPUT)/badgeomfix_data.lis@tocsv:$(OUTPUT)/badgeomfix.csv" > /dev/null

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

###############################################################################

#  

# @author 2017-06-24 Kris Becker

#

###############################################################################

Object = IsisMiner

  Name = MakeDatabase

  RequiredParameters = (fromlist, tocsv)

  Object = Strategy

    Name = LoadCaminfoPvls

    Type = PvlReader

    # Debug = true

     RepairInvalidGeometry = true

     InvalidGeometryAction = error

    FromList = "%1"

    FromListArgs = "FromList"

  # Resource targets are for reading multiple rows from the DB.  The fields

  # from each row are created as Resources.

    Identity = "%1"

    IdentityArgs = "SourceProductId"

  # Include/exclude conditions

    Excludes = Mapping

  #  Can specify a GIS keyword that will be converted on input

    GisGeometryRef = GisFootprint

    GisType        = WKT

    # Tolerance of 0.0004 <degrees> ~= 0.005 m/p at equator

    GisSimplifyTolerance = 0.05 <degrees>

    GisGeometryPointsKey = GisPoints

    RemoveGisKeywordAfterImport = True

  EndObject

  Object = Strategy

   Name = SetSerialNumber

   Type = Calculator

   InitializersArgs = (IsisId, CkTableStartTime)

   Group = Initializers

     SerialNumber = %1

     ObservationTime =  %2

   EndGroup

   Group = Equations_DNE

     ObservationTime =  CkTableStartTime

   EndGroup

   EndObject

   Object = Strategy

    # Write result of StereoPair strategy for each Resource that has a

    # StereoPairs asset.

    Name = WritePairs

    Type = CsvWriter

    Description = "Write CSV file of caminfo data"

    SkipEmptyLists = True

    CsvFileArgs = ("ToCSV" )

    CsvFile = "%1"

    Keywords = (From, SourceProductId, SerialNumber, Target,

                MeanValue, MinimumValue, MaximumValue, StandardDeviation,

                Lines, Samples, InstrumentId, FilterName, MissionPhase, 

                StartTime, EndTime, ObservationTime, ExposureDuration,

                FocusPosition, CenterLongitude, CenterLatitude, CenterRadius,

                PixelResolution, MeanGroundResolution,

                HasNorthPole, HasSouthPole, HasLongitudeBoundary,

                RightAscension, Declination, OffNadir, SolarLongitude,

                LocalTime, CentroidLine, CentroidSample,

                CentroidLatitude, CentroidLongitude, 

                CentroidRadius, SurfaceArea, GlobalCoverage,

                IncidenceAngle, EmissionAngle, PhaseAngle, 

                SubSolarGroundAzimuth, SubSpacecraftGroundAzimuth,

                SubSpacecraftLongitude, SubSpacecraftLatitude, 

                SubSolarLongitude, SubSolarLatitude, 

                TargetCenterDistance, SlantDistance, 

                ParallaxX, ParallaxY, ShadowX, ShadowY,

                GisFootprint)

    GisGeometryKey = GisFootprint

    GisType        = WKB

  EndObject

EndObject

End