Merges BundleXYZ into dev (#495)

* added Debbies changed files to new BundleXYZ Branch

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@7960 41f8697f-d340-4b68-9986-7bafba869bb8

* added addition typedefs for boost matrices and vectors

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8032 41f8697f-d340-4b68-9986-7bafba869bb8

* Corrected various unit problems

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8043 41f8697f-d340-4b68-9986-7bafba869bb8

* Updated truth file - an old one was mistakenly commited

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8045 41f8697f-d340-4b68-9986-7bafba869bb8

* Updated unitTest.cpp and BundleResults.truth to reflect earlier change to BundleSettings::setSolveOptions method

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8092 41f8697f-d340-4b68-9986-7bafba869bb8

* Updated unitTest.cpp and BundleSettings.truth to reflect earlier change to BundleSettings::setSolveOptions method

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8093 41f8697f-d340-4b68-9986-7bafba869bb8

* Added comment to BundleControlPoint.h and updated BundleUtilities.truth to reflect bug fix to SurfacePoint when converting sigmaLon from angle to meters or reverse.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8094 41f8697f-d340-4b68-9986-7bafba869bb8

* Added comment to ControlPoint.h and fixed missed unit changes in ControlPoint.cpp.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8095 41f8697f-d340-4b68-9986-7bafba869bb8

* Removed commented old code in BundleAdjust.cpp

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8096 41f8697f-d340-4b68-9986-7bafba869bb8

* Merged latest changes to trunk (9-8-2017) into branch and updated history entries.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8108 41f8697f-d340-4b68-9986-7bafba869bb8

* Removed calls to obsolete method ControlNet::IsValid

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8112 41f8697f-d340-4b68-9986-7bafba869bb8

* Fixed removed an extra exclusion in the xml that was causing an input to be dropped in the history.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8132 41f8697f-d340-4b68-9986-7bafba869bb8

* merged trunk r8100 through r8147; support move to v007

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8148 41f8697f-d340-4b68-9986-7bafba869bb8

* Updated to trunk r8148 through r8163

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8164 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Updated branch to trunk #8229

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8230 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Updated branch to trunk #r8254

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8255 41f8697f-d340-4b68-9986-7bafba869bb8

* Changed conversion of covar to km**2 by dividing to avoid round-off errors

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8297 41f8697f-d340-4b68-9986-7bafba869bb8

* Precision updates to SurfacePoint & ControlPoint and truth and test to reflect earlier bug fix in SurfacePoint -- #4649.

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8313 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Updated branch to trunk throug r8313

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8314 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Updated branch to trunk r8314 - r8320

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8321 41f8697f-d340-4b68-9986-7bafba869bb8

* Reversed r8321 - merge of trunk into branch due to build errors

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8322 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Updated branch to trunk r8324

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8325 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Removed missing include in Directory.h that came from trunk

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8326 41f8697f-d340-4b68-9986-7bafba869bb8

* Fixed problems with Directory by grabbing the version in the previous revision

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8327 41f8697f-d340-4b68-9986-7bafba869bb8

* Fixed build problem with LinearAlgebra and test problem with ciss2isis.cpp

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8329 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - updated test Makefile for jigsaw tests mestimator and pole-ra-dec-w0-wDot-mean-radius

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8330 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Added new members to copy constructor in BundleControlPoint

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8332 41f8697f-d340-4b68-9986-7bafba869bb8

* Prog - Added history entry to BundleControlPoint.h

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8333 41f8697f-d340-4b68-9986-7bafba869bb8

* Updated history entry in BundleControlPoint.h

git-svn-id: http://subversion.wr.usgs.gov/repos/prog/isis3/branches/BundleXYZ@8336 41f8697f-d340-4b68-9986-7bafba869bb8

* Removed local

* Added .gitignore and README

* Merged dev into branch and fixed compile errors that resulted

* Added new methods to SurfacePoint, corrected handling of control point types in jigsaw.xml, and did basic clean up in BundleAdjust.cpp

* Refined previous commit by fixing errorsin SurfacePoint, BundleAdjust, and unitTest for BundleUtilities

* Updated BundleAdjust

* Corrected a comment in SurfacePoint.cpp and moved updating of adjusted surface point from BundleAdjust to BundleControlPoint

* Fixed a spacing difference in the BundleSettings truth file and modified Spice and Target classes to include the target body radii in the Naif group of Isis cube labels.

* Cleaned up documentation

* Removed meters to radians and radians to meters except in SurfacePoint

* Added ticket numbers to history entries for BundleXYZ branch

* Fixed missed initialization in SurfacePoint, removed cam2map targCodeFromNaifKeywordsObj test and added jigsaw bundleXYZ test suite

* Removed un-needed OS truth data for ImportPdsTable

* Modified bundleXYZ test to reduce number of decimal places

* Added tolerance to equalizer nonOverlapRetryBoth

* Bundle xyz clean up (#521)

* General cleanup

* Added CASSIS test makefiles back

isis/src/base/apps/equalizer/tsts/nonOverlapRetryBoth/Makefile

@@ -1,12 +1,14 @@
 # This tests calculating statistics for input with non-overlapping files,
-# correcting the input list by REMOVING non-overlaps and recalculating to 
-# determine normalization gains and offsets for equalization, 
+# correcting the input list by REMOVING non-overlaps and recalculating to
+# determine normalization gains and offsets for equalization,
 # and then applying corrections.
 #
 # NOTE: An exception occurs when there are non-overlaps during calculation,
 # it is handled and the output is sent to nonOverlapError.txt
 APPNAME = equalizer
 
+I10047011EDR.proj.reduced.cub.TOLERANCE = .00001
+
 include $(ISISROOT)/make/isismake.tsts
 
 commands:

isis/src/base/objs/Spice/Spice.cpp

@@ -258,7 +258,12 @@ namespace Isis {
     *m_ckCode   = *m_ikCode;
 
     if (!m_target->isSky()) {
+      // Get target body code and radii and store them in the Naif group
+      // DAC modified to look for and store body code so that the radii keyword name
+      // will be able to be constructed even for new bodies not in the standard PCK yet.
       QString radiiKey = "BODY" + Isis::toString(m_target->naifBodyCode()) + "_RADII";
+      QVariant result = m_target->naifBodyCode();
+      storeValue("BODY_CODE", 0, SpiceIntType, result);
       std::vector<Distance> radii(3,Distance());
       radii[0] = Distance(getDouble(radiiKey, 0), Distance::Kilometers);
       radii[1] = Distance(getDouble(radiiKey, 1), Distance::Kilometers);

isis/src/base/objs/Spice/Spice.h

@@ -269,7 +269,7 @@ namespace Isis {
    *   @history 2015-07-21 Kristin Berry - Added additional NaifStatus::CheckErrors() to see if any
    *                           NAIF errors were signaled. References #2248.
    *   @history 2016-05-18 Jeannie Backer and Stuart Sides - Moved the construction of the Target
-   *                           after the NAIF kenels have been loaded or the NAIF keywords
+   *                           after the NAIF kernels have been loaded or the NAIF keywords
    *                           have been pulled from the cube labels, so we can find target
    *                           body codes that are defined in kernels and not just body codes
    *                           build into spicelib. References #3934
@@ -278,6 +278,13 @@ namespace Isis {
    *                           m_et is set. References #4476. 
    *   @history 2016-10-21 Jeannie Backer - Reorder method signatures and member variable
    *                           declarations to fit ISIS coding standards. References #4476.
+   *   @history 2018-06-07 Debbie A Cook - Added BODY_CODE to Naif keywords.  This code
+   *                           is used in the target body radii keyword name.  Isis retrieves this code
+   *                           from the standard PCK.  Because target bodies new to Naif are not 
+   *                           included in the standard PCK, missions create a special body-specific
+   *                           PCK to define the new body, including its body code.  This PCK is only
+   *                           loaded in spiceinit so the code needs to be saved so that the radii 
+   *                           keyword can be created to retrieve the target radii.
    */
   class Spice {
     public:

isis/src/base/objs/Spice/Spice.truth

@@ -2,7 +2,7 @@ Unit test for Isis::Spice
 Testing unknown target ...
 **ERROR** Unable to look up NAIF body code for this Target.
 **I/O ERROR** Could not convert Target [Mard] to NAIF body code.
-**I/O ERROR** Can not find [BODY_FRAME_CODE] in text kernels.
+**I/O ERROR** Can not find [BODY_CODE] in text kernels.
 
 Creating Spice object ...
 BodyCode        = 499
@@ -592,6 +592,7 @@ Target Name = Mars
 
 Get Stored Naif Keywords...
 Object = NaifKeywords
+  BODY_CODE = 499
   BODY499_RADII = (3397.0, 3397.0, 3375.0)
   BODY_FRAME_CODE = 10014
   FRAME_MGS_MOC = -94031