Update FileName test and merge dev into testing (#598)

* Update CMakeLists.txt with version 3.6.0 (patch 1)

* Update cmake/CMakeLists.txt library version

* Updated the Installation instructions based on user feedback.  Also fixed a problem with the isis3VarInit.py script.

* Updates made in accordance with requests made on this PR by other developers.

* Fix tgo cassis unit test correctly

* Fix tgo cassis unit test correctly (#544)

* Fixed two bug with AutoReg. One occurs with one dimensional pattern cubes and the other causes the revious registration sample/line to be returned on sub-pixel registration failure.

* Fix tgo cassis camera truth again (#554)

* Update docsys Makefile to support wwwdoc (#559)

The documentation is installed under `docs`, not `doc`, so this file has been updated.
`setisis isis3.6.0` and running `make wwwdoc` in `$ISISROOT/../isis/src/docsys` will properly sync the documentation to our web server.

* Update isis3VarInit.py

Unnecessary 'touch'ing, the '>' redirect will create the file if it doesn't exist.
Also, the first redirect should be the single '>'.  Otherwise, multiple runs of this program will continue appending to these files.  They still work, its just a lot of setting and unsetting for no good reason.

* Fixed isis3Startup scripts

* Removed unneeded LineEquation include

* Make this program more pythonic (#589)

* Updated documentation, user interaction, and made the file and directory
handling more 'pythonic'.

* Correcting for PR comments.

* Fixed broken links in the Installation instructions due to the hyperlinks to our GitHub wiki changing.

* Removed unused Parabola class

* Removed old license, added new unlicense (#594)

* Tweaked FileName test to use ISISROOT variable

LICENSE.txt

@@ -0,0 +1,24 @@
+This is free and unencumbered software released into the public domain.
+
+Anyone is free to copy, modify, publish, use, compile, sell, or
+distribute this software, either in source code form or as a compiled
+binary, for any purpose, commercial or non-commercial, and by any
+means.
+
+In jurisdictions that recognize copyright laws, the author or authors
+of this software dedicate any and all copyright interest in the
+software to the public domain. We make this dedication for the benefit
+of the public at large and to the detriment of our heirs and
+successors. We intend this dedication to be an overt act of
+relinquishment in perpetuity of all present and future rights to this
+software under copyright law.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+For more information, please refer to <http://unlicense.org/>

isis/CMakeLists.txt

@@ -30,16 +30,15 @@ set(PACKAGE            "ISIS")
 set(PACKAGE_NAME       "USGS ISIS")
 
 # Version number
-set(VERSION            "3.6.00.0")
+set(VERSION            "3.6.0.1")
 set(PACKAGE_VERSION    ${VERSION})
 
 # Full name and version number
 set(PACKAGE_STRING     "${PACKAGE_NAME} ${VERSION}")
 
 # Other release information
-set(VERSION_DATE              "2018-11-09")
-set(THIRD_PARTY_LIBS_VERSION  "v008")
-set(RELEASE_STAGE             "alpha") # (alpha, beta, stable)
+set(VERSION_DATE              "2018-10-26")
+set(RELEASE_STAGE             "beta") # (alpha, beta, stable)
 
 # Define to the address where bug reports for this package should be sent.
 set(PACKAGE_BUGREPORT  "https://isis.astrogeology.usgs.gov/fixit")

isis/cmake/CMakeLists.txt

@@ -4,9 +4,9 @@
 message("Setting up post-install behavior...")
 
 # Set up format version numbers for the main shared library on install
-install(CODE "EXECUTE_PROCESS(COMMAND cp -f ${CMAKE_BINARY_DIR}/lib/libisis3${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3.5.0${SO})")
-install(CODE "EXECUTE_PROCESS(COMMAND ln -sf libisis3.5.0${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3.5${SO})")
-install(CODE "EXECUTE_PROCESS(COMMAND ln -sf libisis3.5${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3${SO})")
+install(CODE "EXECUTE_PROCESS(COMMAND cp -f ${CMAKE_BINARY_DIR}/lib/libisis3${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3.6.0${SO})")
+install(CODE "EXECUTE_PROCESS(COMMAND ln -sf libisis3.6.0${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3.6${SO})")
+install(CODE "EXECUTE_PROCESS(COMMAND ln -sf libisis3.6${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis3${SO})")
 install(CODE "EXECUTE_PROCESS(COMMAND ln -sf libisis3${SO} ${CMAKE_INSTALL_PREFIX}/lib/libisis${SO})")
 
 # On OSX, need to correct all the paths encoded in each of the distributed library files so

isis/scripts/isis3Startup.csh

@@ -24,6 +24,8 @@
 #                       to "/usgs/cpkgs/isis3/testData"
 #       SEP 08 2017 - Christopher Combs - Removed setting of QT_PLUGIN_PATH as
 #                       an environment variable. Fixes #4617
+#       NOV 15 2018 - Jesse Mapel - Changed default ISISROOT to new install
+#                       directory.
 #_VER   $Id: isis3Startup.csh,v 1.5 2010/03/16 19:40:22 ehyer Exp $
 #_END
 ################################################################################
@@ -34,7 +36,7 @@ set Platform = `uname -s`
 # Initialize the ISISROOT environment variable if it doesn't exist
 # TODO: Test is obsolete, fail if no isisroot is set
 if ($?ISISROOT == 0) then
-  setenv ISISROOT /usgs/pkgs/isis3/isis
+  setenv ISISROOT /usgs/pkgs/isis3/install
 endif
 
 # Initialize the ISIS3DATA environment variable

isis/scripts/isis3Startup.py

@@ -12,7 +12,7 @@ def setisis():
 
   #... and if it's not give it a default value
   if ISISROOT is None:
-    ISISROOT = "/usgs/pkgs/isis3/isis"
+    ISISROOT = "/usgs/pkgs/isis3/install"
     os.environ['ISISROOT'] = ISISROOT
 
   #Check for the ISIS3DATA directory. If it does not exist use a default

isis/scripts/isis3Startup.sh

@@ -12,7 +12,7 @@
 # the Isis distribution
 #
 if [ ! "$ISISROOT" ]; then
-  ISISROOT=/usgs/pkgs/isis3/isis
+  ISISROOT=/usgs/pkgs/isis3/install
   export ISISROOT
 fi
 

isis/scripts/isis3VarInit.py

@@ -1,52 +1,97 @@
 #!/usr/bin/env python
+"""This program builds shell scripts that define ISIS3 environment variables during conda environment activation and deactivation, and creates some directories."""
+
 import argparse
 import os
 import sys
-#Author:  Tyler Wilson
-#Date  :  2018-10-05
-#Description:  This script sets ISISROOT/ISIS3DATA/ISIS3TESTDATA for the user and is executed
-#within the conda environment created for the ISIS3 installation.
-#The data directory and test directory are optional command line arguments.  If the user chooses
-#not to set them, they will both be placed created on the same level as the $ISISROOT directory
-#within the conda environment.
-
-parser = argparse.ArgumentParser(description='Usage:  ./isis3VarInit --data_dir <data dir path> --test_dir <test dir path')
-
-isisroot = '$CONDA_PREFIX'
-data_dir='$CONDA_PREFIX/data'
-testdata_dir='$CONDA_PREFIX/testData'
-
-parser.add_argument("--data-dir",default= data_dir,help="ISIS3 Mission Data Directory")
-parser.add_argument("--test-dir",default=testdata_dir,help="ISIS3 Mission Test Data Directory")
 
+##########################################################################################################
+#
+#  This work is free and unencumbered software released into the public domain.
+#  In jurisdictions that recognize copyright laws, the author or authors
+#  of this software dedicate any and all copyright interest in the
+#  software to the public domain.
+#
+#
+#   Description:  This program builds the shell scripts that define the 
+#       ISISROOT/ISIS3DATA/ISIS3TESTDATA environment variables for the user 
+#       when the ISIS3 conda environment is activated, and clean up when it is
+#       deactivated.
+#
+#       The data directory and test directory are optional command line arguments.  
+#       If the user chooses not to set them, they will both be created in the
+#       $ISISROOT directory.
+#
+#   History:
+#       Author:  Tyler Wilson, USGS
+#       Date:    2018-10-05
+#       Description: Initial commit.
+#
+#       Author:  Tyler Wilson, USGS
+#       Date:    2018-11-01
+#       Description:  Removed a pair of lines which were causing output errors on Mac OS X and were not
+#                     required anyway.
+#
+#       Author:  Ross Beyer
+#       Date:    2018-11-19
+#       Description: Streamlined the program, improved documentation, and made the directory and
+#                    file creation more `pythonic' rather than using system calls.
+#
+#
+##########################################################################################################
+
+# There are still a lot of Python 2 installations out there, and if people don't have
+# their conda environment set up properly, the error message they'll get will be hard
+# to decipher.  This might help:
+assert( sys.version_info >= (3,2) ) # Must be using Python 3.2 or later, is conda set up?
+
+
+# This just wraps and reports on the directory creation:
+def mkdir( p ):
+    if os.path.exists( p ): print( 'Tried to create '+p+', but it already exists.' )
+    else:
+        os.makedirs( p )
+        print( 'Created '+p )
+    return
+
+
+# Set up and then parse the command line:
+parser = argparse.ArgumentParser( description=__doc__ )
+
+parser.add_argument('-d','--data-dir', 
+                    default=os.environ['CONDA_PREFIX']+'/data',
+                    help='ISIS3 Data Directory, default: %(default)s' )
+parser.add_argument('-t','--test-dir',
+                    default=os.environ['CONDA_PREFIX']+'/testData',
+                    help='ISIS3 Test Data Directory, default: %(default)s')
 args=parser.parse_args()
-if (data_dir != args.data_dir):
-    os.system("mkdir -p "+args.data_dir)
-    data_dir = args.data_dir
-else:    
-    os.system("mkdir -p "+data_dir)
-
-if (testdata_dir != args.test_dir):
-    os.system("mkdir -p "+args.test_dir)
-    testdata_dir=args.test_dir
-else:
-    os.system("mkdir -p "+testdata_dir)
-
-os.popen('mkdir -p '+isisroot+'/etc/conda/activate.d')
-os.popen('mkdir -p '+isisroot+'/etc/conda/deactivate.d')
-
-os.system("echo -n '' >"+isisroot+"/etc/conda/activate.d/env_vars.sh")
-os.popen("echo -n '' >"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")
-os.popen('touch '+isisroot+'/etc/conda/activate.d/env_vars.sh')
-os.popen('touch '+isisroot+'/etc/conda/activate.d/env_vars.sh')
-
-os.popen("echo '#!/bin/sh' >> "+isisroot+ "/etc/conda/activate.d/env_vars.sh")
-os.popen("echo 'export ISISROOT="+isisroot+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")
-os.popen("echo 'export ISIS3DATA="+data_dir+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")
-os.popen("echo 'export ISIS3TESTDATA="+testdata_dir+"' >>"+isisroot+"/etc/conda/activate.d/env_vars.sh")
-
-os.popen("echo '#!/bin/sh' >> "+isisroot+ "/etc/conda/deactivate.d/env_vars.sh")
-os.popen("echo 'unset ISISROOT' >>"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")
-os.popen("echo 'unset ISIS3DATA' >>"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")
-os.popen("echo 'unset ISIS3TESTDATA' >>"+isisroot+"/etc/conda/deactivate.d/env_vars.sh")
 
+
+# Create the data directories:
+mkdir( args.data_dir )
+mkdir( args.test_dir )
+
+# Create the conda activation and deactivation directories:
+activate_dir   = os.environ['CONDA_PREFIX']+'/etc/conda/activate.d'
+deactivate_dir = os.environ['CONDA_PREFIX']+'/etc/conda/deactivate.d'
+
+mkdir( activate_dir )
+mkdir( deactivate_dir )
+
+# Write the files that manage the ISIS3 environments:
+activate_vars   =   activate_dir+'/env_vars.sh'
+deactivate_vars = deactivate_dir+'/env_vars.sh'
+
+with open( activate_vars, mode='w' ) as a:
+    a.write('#!/bin/sh\n')
+    a.write('export ISISROOT='+      os.environ['CONDA_PREFIX']+'\n')
+    a.write('export ISIS3DATA='+     args.data_dir +'\n')
+    a.write('export ISIS3TESTDATA='+ args.test_dir +'\n')
+print( 'Wrote '+activate_vars )
+
+with open( deactivate_vars, mode='w' ) as d:
+    d.write('#!/bin/sh\n')
+    d.write('unset ISISROOT\n')
+    d.write('unset ISIS3DATA\n')
+    d.write('unset ISIS3TESTDATA\n')
+print( 'Wrote '+deactivate_vars )

isis/src/base/apps/appjit/LineScanCameraRotation.cpp

@@ -8,7 +8,6 @@
 #include "Cube.h"
 #include "LineScanCameraRotation.h"
 #include "Quaternion.h"
-#include "LineEquation.h"
 #include "BasisFunction.h"
 #include "LeastSquares.h"
 #include "BasisFunction.h"

isis/src/base/apps/appjit/PixelOffset.cpp

@@ -8,7 +8,6 @@
 
 #include "PixelOffset.h"
 #include "TextFile.h"
-#include "LineEquation.h"
 #include "LeastSquares.h"
 #include "BasisFunction.h"
 #include "PolynomialUnivariate.h"

isis/src/base/objs/AutoReg/AutoReg.cpp

@@ -671,9 +671,11 @@ namespace Isis {
     // Before we attempt to apply the reduction factor, we need to make sure
     // we won't produce a chip of a bad size.
     // ----------------------------------------------------------------------
-    if(gradientPatternChip.Samples() / p_reduceFactor < 2 || gradientPatternChip.Lines() / p_reduceFactor < 2) {
-      string msg = "Reduction factor is too large";
-      throw IException(IException::User, msg, _FILEINFO_);
+    if (p_reduceFactor != 1) {
+      if(gradientPatternChip.Samples() / p_reduceFactor < 2 || gradientPatternChip.Lines() / p_reduceFactor < 2) {
+        string msg = "Reduction factor is too large";
+        throw IException(IException::User, msg, _FILEINFO_);
+      }
     }
 
     // Establish the center search tack point as best pixel to start for the
@@ -852,15 +854,21 @@ namespace Isis {
       if (!window.IsValid(100.0 * 2.1 / 3.0)) {
         p_surfaceModelNotEnoughValidDataCount++;
         p_registrationStatus = SurfaceModelNotEnoughValidData;
+        p_chipSample = p_bestSamp;
+        p_chipLine = p_bestLine;
         return SurfaceModelNotEnoughValidData;
       }
 
       // Now that we know we have enough data to model the surface we call
       // SetSubpixelPosition() to get the sub-pixel accuracy we are looking for.
       bool computedSubPixel = SetSubpixelPosition(window);
-      if (!computedSubPixel)
-        return p_registrationStatus;
-
+      if (!computedSubPixel) {
+        p_chipSample = p_bestSamp;
+        p_chipLine = p_bestLine;
+        p_registrationStatus = SurfaceModelSolutionInvalid;
+        return SurfaceModelSolutionInvalid;
+      }
+
       // See if the surface model solution moved too far from our whole pixel
       // solution
       p_sampMovement = fabs(p_bestSamp - p_chipSample);
@@ -870,18 +878,20 @@ namespace Isis {
 
         p_surfaceModelDistanceInvalidCount++;
         p_registrationStatus = SurfaceModelDistanceInvalid;
+        p_chipSample = p_bestSamp;
+        p_chipLine = p_bestLine;
         return SurfaceModelDistanceInvalid;
       }
 
       p_registrationStatus = SuccessSubPixel;
+      return SuccessSubPixel;
     }
     else {
       p_chipSample = p_bestSamp;
       p_chipLine = p_bestLine;
       p_registrationStatus = SuccessPixel;
+      return SuccessPixel;
     }
-
-    return p_registrationStatus;
   }
 
 
@@ -1320,3 +1330,4 @@ namespace Isis {
     return reg;
   }
 }
+

isis/src/base/objs/AutoReg/AutoReg.h

@@ -173,6 +173,12 @@ namespace Isis {
    *             give useful results due to the 2x2 matrix it uses.
    *    @history 2012-01-05 Travis Addair - Added separate variables for Whole
    *             Pixel Correlation and Subpixel Correlation.
+   *    @history 2018-07-27 Makayla Shepherd - Fixed a bug that made registration fail for
+   *                            one dimensional pattern chips. Fixes #5247.
+   *    @history 2018-07-27 Makayla Shepherd - Fixed a bug that upon sub-pixel registration failure
+   *                            caused the previous registration to be returned. If sub-pixel 
+   *                            registration fails now it will return to the whole pixel 
+   *                            registration values. Fixes #5248.
    */
   class AutoReg {
     public: