Bug fixed in isisminer to properly handle self-intersecting polygon g…

…eometries. (#5620) * Fixed issues with GisGeometry/Strategy classes. Addresses #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 * Corrected invalid geometry problems in isisminer. Addresses #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 * 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. Fixed incorrect links and minor typos in isisminer documentation. Addresses #5612. * Per reviewer comments, corrected additional typos in GisGeometry.cpp. Addresses #5612. --------- Co-authored-by: Kris J. Becker <kbecker@orex.lpl.arizona.edu>
DOI-USGS · Oct 17, 2024 · 7ca57fa · 7ca57fa
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -45,6 +45,7 @@ release.
 - 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

diff --git a/isis/src/base/apps/isisminer/isisminer.xml b/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 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 
@@ -48,8 +49,8 @@
       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 
@@ -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 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>
@@ -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>
@@ -4655,14 +4707,14 @@ End
        feature.
     </change>
     <change name="Kris Becker" date="2015-06-12">
-      Improved GisOverlap and StereoPair strategies. StereoAngle can now be
-      computed from the GIS centroid of the overlapping region, providing a
-      much higher degree of accuracy. Improved global variable pool management
-      whilst traversing through Strategy/Resource depths in the mining process.
-      Ensure Asset is cleared when Mode = Create is used in AssetSideBar strategy.
+       Improved GisOverlap and StereoPair strategies. StereoAngle can now be
+       computed from the GIS centroid of the overlapping region, providing a
+       much higher degree of accuracy. Improved global variable pool management
+       whilst traversing through Strategy/Resource depths in the mining process.
+       Ensure Asset is cleared when Mode = Create is used in AssetSideBar strategy.
     </change>
     <change name="Kris Becker" date="2015-06-17">
-        Fixed bug in creation of GEOS SRTree when only one geometry occurs 
+       Fixed bug in creation of GEOS SRTree when only one geometry occurs 
        (requires two or more).  Changed name of IsisMiner objects within the 
        GisOverlap strategy (since we now have two of them) to CandidateMiner and 
        OverlapMiner. Added feature to simplify geometry whilst preserving 
@@ -4674,21 +4726,21 @@ End
        Add ability to process the set of GisOverlap results for each Resource
        as they are matched. This is handled in the OverlapMiner Strategy object.
     </change>
-   <change name="Kris Becker" date="2015-07-07">
+    <change name="Kris Becker" date="2015-07-07">
        Added more content to documentation and added an example demonstrating a 
        real application of the isisminer application.
-   </change>
-   <change name="Kris Becker" date="2015-09-27">
+    </change>
+    <change name="Kris Becker" date="2015-09-27">
        Refactored the Resource class to contain all but the active status so 
        that copies can be maintained in separate instances. Reworked the 
        AssetSidebar strategy to take advantage of this work.
-   </change>
-   <change name="Kris Becker" date="2015-10-11">
+    </change>
+    <change name="Kris Becker" date="2015-10-11">
        Fixed bug in argument scanning when the number of arguments reached 10 or 
        more as %1 was replacing %10, etc... Scan and replace i reverse order 
        corrected this problem. Enhanced the Calculator strategy to provide 
        argument replacement in the Initializers group.
-   </change> 
+    </change> 
     <change name="Kris Becker" date="2015-11-01">
         Modified CsvReader strategy to have the provided header length determine 
         the number of keywords created/Resource. This allows the jigsaw residual 
@@ -4699,6 +4751,14 @@ End
         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>

diff --git a/isis/src/base/apps/isisminer/tsts/badgeomfix/Makefile b/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;
+