Merge branch 'dev' into web_spice_calls

Author: chkim-usgs

.github/workflows/gitlab-lts.yml

@@ -60,12 +60,14 @@ jobs:
           git clone https://isis-codebuild-ci:[email protected]/astrogeology/isis-codebuild-ci.git
           echo $LTS_VERSION
           cd isis-codebuild-ci
-          if [[ "git ls-remote --exit-code origin $LTS_VERSION" == 2 ]]; then
+          if [[ $(git ls-remote --heads origin $LTS_VERSION | wc -l) -eq 0 ]]; then
+            echo "Branch $LTS_VERSION does not exist, will create"
             git checkout -b $LTS_VERSION
           else
+            echo "Branch $LTS_VERSION already exists"
             git checkout $LTS_VERSION
             git reset --hard origin/main
           fi
           echo -e "\nenv: \n  shell: bash \n  variables: \n    LTS_VERSION: $LTS_VERSION \n    BASE_LTS: $BASE_LTS \n    ANACONDA_API_TOKEN: $ANACONDA_TOKEN \n    GITHUB_SHA: $GITHUB_SHA" >> buildspec-lts.yml
           git commit -a -m "$LTS_VERSION"
-          git push origin $LTS_VERSION --force
+          git push origin $LTS_VERSION --force

CHANGELOG.md

@@ -36,14 +36,22 @@ release.
 ## [Unreleased]
 
 ### Added
+- Added adjusted XYZ point coordinate sigmas to the points.csv jigsaw output file. Modified
+ctest FunctionalTestJigsawApollo to validate this output. [#5710](https://github.com/DOI-USGS/ISIS3/issues/5710)
+- Added OFFBODY and OFFBODYTRIM parameters to cam2cam. Added tests and updated documentation. [#3602] (https://github.com/DOI-USGS/ISIS3/issues/3602)
+- Added support for reading, writing, and viewing GeoTIFFs in ISIS. [#5618](https://github.com/DOI-USGS/ISIS3/pull/5618)
+- Added GDAL SRS propagation for systems outside of ISIS to display projected GTiffs. [#5736](https://github.com/DOI-USGS/ISIS3/pull/5736)
 
 ### Changed
+- Enhanced csminit by removing the need to specify model and plugin [#5585](https://github.com/DOI-USGS/ISIS3/issues/5585)
+- Changed file format to propagate from the input image format to the output image format [#5737](https://github.com/DOI-USGS/ISIS3/pull/5737)
 
 ### Fixed
 - Fixed kaguyatc2isis invalid BandBin values [#5629](https://github.com/DOI-USGS/ISIS3/issues/5629)
 - Fixed SpiceClient to handle redirect requests.
 - Fixed jigsaw to default OUTADJUSTMENTH5 option to false and allow this feature to run on read-only images [#5700](https://github.com/DOI-USGS/ISIS3/issues/5700)
 - Fixed Cube::fromIsd to add "LineScanTimes" table from HRSC isds [#5668](https://github.com/DOI-USGS/ISIS3/issues/5668)
+- Fixed segfault in SpiceClient when an authentication error was encountered. [#5735](https://github.com/DOI-USGS/ISIS3/pull/5735)
 
 ## [9.0.0] - 09-25-2024
 

environment.yml

@@ -6,8 +6,8 @@ dependencies:
   - ale =0.10.0,<1
   - aom
   - armadillo
-  - boost >=1.78.0,<1.79
-  - boost-cpp >=1.78.0,<1.79
+  - boost >=1.76.0,<1.82
+  - boost-cpp >=1.76.0,<1.82
   - blas
   - usgs-astrogeology::bullet
   - bz2file
@@ -23,6 +23,7 @@ dependencies:
   - ffmpeg
   - geos >=3.12, <3.13
   - geotiff
+  - gdal >=3.5 ,<3.9.0a0
   - gmp
   - graphviz
   - conda-forge::gsl >=2.6, <2.7
@@ -35,10 +36,10 @@ dependencies:
   - kalasiris
   - krb5
   - libgdal >=3.7,<3.8
-  - libopencv >=4.7,<4.8
+  - libopencv >=4.5,<4.8
   - libpng >=1.6.34,<1.7
   - libprotobuf
-  - libtiff >=4.5,<4.6
+  - libtiff >=4.5,<4.8
   - libxml2
   - make
   - mesalib
@@ -48,17 +49,17 @@ dependencies:
   - nlohmann_json=3.11.2
   - ninja >=1.7.2,<1.8
   - nn
-  - opencv >=4.7,<4.8
+  - opencv >=4.5,<4.8
   - openssl >=3.1.2,<3.2
   - pcl >=1.13,<1.14
   - plio
   - protobuf
-  - python >=3.10
-  - python_abi >=3.10
+  - python >=3.9
+  - python_abi >=3.9
   - pytest
   - rclone
   - qhull
-  - qt-main>=5.15.8, <5.16
+  - qt-main>=5.15, <5.16
   - qwt <6.3.0
   - usgs-astrogeology/label/dev::spiceql
   - sqlite >=3.46.0,<3.47

gtest

@@ -267,6 +267,7 @@ find_package(CSM       3.0.3.3 REQUIRED)
 find_package(CSPICE    65      REQUIRED)
 find_package(Eigen             REQUIRED)
 find_package(Embree    3.13.0  REQUIRED)
+find_package(GDAL              REQUIRED CONFIG)
 find_package(GeoTIFF   2       REQUIRED)
 SET(GSL_ROOT_DIR $ENV{CONDA_PREFIX})
 find_package(GSL       2.2.1   REQUIRED)
@@ -354,7 +355,7 @@ foreach (_variableName ${_variableNames})
 endforeach()
 
 # add target based linkages to ALLLIBS variable
-list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree)
+list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree GDAL::GDAL)
 
 # Sometimes we add the same lib more than once (especially with LIBDIRS)
 list(REMOVE_DUPLICATES ALLLIBDIRS)

isis/CMakeLists.txt

@@ -312,7 +312,6 @@ function(build_object_docs)
   file(MAKE_DIRECTORY ${docInstallFolder}/${docVersion}/Object/apps)
   file(MAKE_DIRECTORY ${docInstallFolder}/${docVersion}/Object/Developer)
   file(MAKE_DIRECTORY ${docInstallFolder}/${docVersion}/Object/Programmer)
-  file(MAKE_DIRECTORY ${docInstallFolder}/${docVersion}/documents/DocStyle/assets)
   copy_wildcard("${docBuildFolder}/Object/*.html" ${docInstallFolder}/${docVersion}/Object/)
   #copy_file(${objBuildDir}/isisDoxyDefs.doxydef ${docInstallFolder}/documents/DocStyle/assets/isisDoxyDefs.doxydef)
 

isis/cmake/BuildDocs.cmake

@@ -715,11 +715,11 @@ namespace Isis {
     att.setFileFormat( panC[0]->format() );
     att.setByteOrder(  panC[0]->byteOrder() );
     att.setPixelType(  panC[0]->pixelType() );
-    if (panC[0]->labelsAttached()) {
-      att.setLabelAttachment(AttachedLabel);
+    if (panC[0]->labelsAttached() == Cube::AttachedLabel) {
+      att.setLabelAttachment(Cube::AttachedLabel);
     }
     else {
-      att.setLabelAttachment(DetachedLabel);
+      att.setLabelAttachment(Cube::DetachedLabel);
     }
 
     //define an output cube

isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp

@@ -0,0 +1,5 @@
+Group = ShapeModel
+  RayTraceEngine = Bullet
+  OnError = Continue
+EndGroup
+End

isis/src/base/apps/cam2cam/assets/files/BulletEngineSelect.pref

@@ -0,0 +1,26 @@
+#!/bin/sh
+
+# Get example image acquired by OREX OCAMS during "Detailed Survey" phase\
+dtype="map_iofL2b"\
+fbase="20190509T180552S020"\
+
+# Download the OSIRIS-REx image. Note wget can be installed using the command\
+# "conda install wget"\
+wget -P . "https://sbnarchive.psi.edu/pds4/orex/orex.ocams/data_calibrated/detailed_survey/$\{fbase\}_$\{dtype\}.fits"\
+
+# Import into ISIS\
+ocams2isis from="$\{fbase\}_$\{dtype\}.fits" to="$\{fbase\}_pck.cub"\
+ocams2isis from="$\{fbase\}_$\{dtype\}.fits" to="$\{fbase\}_dtm.cub"\
+
+spiceinit from="$\{fbase\}_pck.cub" shape=ellipsoid\
+spiceinit from="$\{fbase\}_dtm.cub" shape=user model='$osirisrex/kernels/dsk/g_00880mm_alt_ptm_0000n00000_v020.bds' -pref=$ISISROOT/BulletEngineSelect.pref\
+
+# Run cam2cam for each set\
+cam2cam from="$\{fbase\}_pck.cub" match="$\{fbase\}_dtm.cub" to="$\{fbase\}_pck_to_dtm_def.cub"\
+cam2cam from="$\{fbase\}_pck.cub" match="$\{fbase\}_dtm.cub" to="$\{fbase\}_pck_to_dtm_off.cub" offbody=true offbodytrim=false\
+cam2cam from="$\{fbase\}_pck.cub" match="$\{fbase\}_dtm.cub" to="$\{fbase\}_pck_to_dtm_offtrim.cub" offbody=true offbodytrim=true\
+
+cam2cam from="$\{fbase\}_dtm.cub" match="$\{fbase\}_pck.cub" to="$\{fbase\}_dtm_to_pck_def.cub"\
+cam2cam from="$\{fbase\}_dtm.cub" match="$\{fbase\}_pck.cub" to="$\{fbase\}_dtm_to_pck_off.cub" offbody=true offbodytrim=false\
+cam2cam from="$\{fbase\}_dtm.cub" match="$\{fbase\}_pck.cub" to="$\{fbase\}_dtm_to_pck_offtrim.cub" offbody=true offbodytrim=true\
+

isis/src/base/apps/cam2cam/assets/files/cam2camExample3.sh

@@ -1,11 +1,17 @@
+/** This is free and unencumbered software released into the public domain.
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
 #include <cmath>
 
 #include "cam2cam.h"
 
 #include "Application.h"
 #include "Camera.h"
 #include "CameraFactory.h"
-#include "Distance.h"
 #include "ProcessRubberSheet.h"
 
 using namespace std;
@@ -56,10 +62,15 @@ namespace Isis {
     referenceBand += (referenceBand % 2);
     referenceBand /= 2;
 
-   // See if the user wants to override the reference band
+    // See if the user wants to override the reference band
     if (ui.WasEntered("REFBAND")) {
       referenceBand = ui.GetInteger("REFBAND");
     }
+ 
+    // Check for propagation of off-body (based upon RA/Dec) pixels as well
+    // but allow for trimming of off target intersections in FROM file.
+    bool offbody = ui.GetBoolean("OFFBODY");
+    bool trim = ui.GetBoolean("OFFBODYTRIM");
 
     // Using the Camera method out of the object opack will not work, because the
     // filename required by the Camera is not passed by the process class in this
@@ -95,7 +106,9 @@ namespace Isis {
                                             cam2camGlobal::incam,
                                             ocube->sampleCount(),
                                             ocube->lineCount(),
-                                            outcam);
+                                            outcam,
+                                            offbody,
+                                            trim);
 
     // Add the reference band to the output if necessary
     ocube->putGroup(instgrp);
@@ -127,56 +140,4 @@ namespace Isis {
   }
 
 
-  // Transform object constructor
-  cam2camXform::cam2camXform(const int inputSamples, const int inputLines,
-                             Camera *incam, const int outputSamples,
-                             const int outputLines, Camera *outcam) {
-    p_inputSamples = inputSamples;
-    p_inputLines = inputLines;
-    p_incam = incam;
-
-    p_outputSamples = outputSamples;
-    p_outputLines = outputLines;
-    p_outcam = outcam;
-  }
-
-  // Transform method mapping output line/samps to lat/lons to input line/samps
-  bool cam2camXform::Xform(double &inSample, double &inLine,
-                           const double outSample, const double outLine) {
-    // See if the output image coordinate converts to lat/lon
-    if (!p_outcam->SetImage(outSample, outLine)) return false;
-
-    // Get the universal lat/lon and see if it can be converted to input line/samp
-    double lat = p_outcam->UniversalLatitude();
-    double lon = p_outcam->UniversalLongitude();
-    Distance rad = p_outcam->LocalRadius();
-    if (rad.isValid()) {
-      if (!p_incam->SetUniversalGround(lat, lon, rad.meters())) return false;
-    }
-    else {
-      if (!p_incam->SetUniversalGround(lat, lon)) return false;
-    }
-
-    // Make sure the point is inside the input image
-    if (p_incam->Sample() < 0.5) return false;
-    if (p_incam->Line() < 0.5) return false;
-    if (p_incam->Sample() > p_inputSamples + 0.5) return false;
-    if (p_incam->Line() > p_inputLines + 0.5) return false;
-
-    // Everything is good
-    inSample = p_incam->Sample();
-    inLine = p_incam->Line();
-    return true;
-  }
-
-
-  int cam2camXform::OutputSamples() const {
-    return p_outputSamples;
-  }
-
-
-  int cam2camXform::OutputLines() const {
-    return p_outputLines;
-  }
-
 }

isis/src/base/apps/cam2cam/assets/images/example1/cam2cam_example1_FROM_AS15-M-1537.jpeg

@@ -1,11 +1,21 @@
+/** This is free and unencumbered software released into the public domain.
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
 #ifndef cam2cam_h
 #define cam2cam_h
 
+#include <memory>
+
 #include "Transform.h"
 
 #include "Application.h"
 #include "Camera.h"
 #include "Cube.h"
+#include "Distance.h"
 #include "UserInterface.h"
 
 namespace Isis {
@@ -26,21 +36,86 @@ namespace Isis {
       int p_inputLines;
       int p_outputSamples;
       int p_outputLines;
+      bool p_offbody;
+      bool p_trim;
 
     public:
       // constructor
       cam2camXform(const int inputSamples, const int inputLines, Isis::Camera *incam,
-                   const int outputSamples, const int outputLines, Isis::Camera *outcam);
+                   const int outputSamples, const int outputLines, Isis::Camera *outcam,
+                   const bool offbody = false, const bool trim = true) {
 
+        p_inputSamples = inputSamples;
+        p_inputLines = inputLines;
+        p_incam = incam;
+    
+        p_outputSamples = outputSamples;
+        p_outputLines = outputLines;
+        p_outcam = outcam;
+        p_offbody = offbody;
+        p_trim = trim;
+      }
+      
       // destructor
-      ~cam2camXform() {};
+      virtual ~cam2camXform() {};
 
-      // Override parent's pure virtual members
-      bool Xform(double &inSample, double &inLine,
-                 const double outSample, const double outLine);
-      int OutputSamples() const;
-      int OutputLines() const;
+      /** Transform method mapping output line/samps to lat/lons to input line/samps */
+      inline bool Xform(double &inSample, double &inLine,
+                        const double outSample, const double outLine) {
+                
+       // See if the output image coordinate converts to lat/lon
+       if ( p_outcam->SetImage(outSample, outLine) )  {
+         // Get the universal lat/lon and see if it can be converted to input line/samp
+         double lat = p_outcam->UniversalLatitude();
+         double lon = p_outcam->UniversalLongitude();
+         Distance rad = p_outcam->LocalRadius();
+         if (rad.isValid()) {
+           if(!p_incam->SetUniversalGround(lat, lon, rad.meters())) return false;
+         }
+         else {
+           if(!p_incam->SetUniversalGround(lat, lon)) return false;
+         }
+       }
+       else if ( p_offbody ) {
+         double ra = p_outcam->RightAscension();
+         double dec = p_outcam->Declination();
+         if ( !p_incam->SetRightAscensionDeclination(ra,dec) ) return false;
+         if ( p_trim ) {
+           if ( p_incam->SetImage(p_incam->Sample(), p_incam->Line()) ) return (false);
+         }
+       }
+       else {
+         return false;
+       }
+      
+       // Make sure the point is inside the input image
+       if (p_incam->Sample() < 0.5) return false;
+       if (p_incam->Line() < 0.5) return false;
+       if (p_incam->Sample() > p_inputSamples + 0.5) return false;
+       if (p_incam->Line() > p_inputLines + 0.5) return false;
+      
+       // Everything is good
+       inSample = p_incam->Sample();
+       inLine = p_incam->Line();
+       return true;
+       }
+      
+      
+       inline int OutputSamples() const {
+         return p_outputSamples;
+       }
+      
+      
+       inline int OutputLines() const {
+         return p_outputLines;
+       }
+    
   };
+
+
+ 
+  
+
 }
 
 #endif