Corrected invalid geometry problems in isisminer. Addresses DOI-USGS#…

…5612.

* GisGeometry was throwing an exception when isValid() was called and the geometry was indeed invalid
* GisGeometry - added buffer() method
* Strategy was updated to better manage geometries
* Strategy - Added RepairInvalidGeometry and InvalidGeometryAction to allow better user control over invalid geometries
* Strategy - Apply buffer(0) algorithm when an invalid geometry is detected
* Strategy - Added more debug output
* isisminer - improved handling of invalid/bad geometries
* isisminer - Documented new parameters RepairInvalidGeometry and InvalidGeometryAction and updated Calculator strategy documentation

isis/src/base/apps/isisminer/isisminer.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- $Id: isisminer.xml 6513 2016-01-14 23:04:44Z [email protected] $ -->
-<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 
@@ -340,6 +341,40 @@
           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 geoemtry 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>
@@ -990,6 +1025,23 @@ EndObject
           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>
@@ -4698,6 +4750,12 @@ End
         Converted isisminer to callable function. Also converted all Makefile
         tests to gtest format. Moved some data from isis data area to
         "isis/tests/data/isisminer".
+    <change name="Ken Edmundson" date="2024-09-12">
+        Originally implemented in UofA OSIRIS-REx code by Kris Becker, 2018-07-31.
+        Corrected problems with invalid geometries aborting isisminer. Added two
+        new parameters, RepairInvalidGeometry and InvalidGeometryAction, to allow user
+        more control over how invalid geometries are managed. Update some of the
+        documentation.
     </change>
   </history>
 

isis/src/base/apps/isisminer/tsts/badgeomfix/Makefile

@@ -0,0 +1,10 @@
+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;
+