added findfeaturesSegment script (#5091)

* added findfeaturesSegment script

* now parrallelized

* updated logging code

* added help string

* added help string

* added envs and fixed progress bar output

* staging things

* added python stuff, fixed segment issues, addressed coments

* addressing comments

* added more doc strings

* made pybindings on by default

* addressing comments

* fixed some things, local testing

* updated install steps

* added basic tests

* reverting ale pin

* changed license

* turn on pybindings in jenkins

* renamed script

* shadow rename?

Jenkinsfile

@@ -48,7 +48,7 @@ pipeline {
                 cd build
                 cmake -GNinja -DJP2KFLAG=ON  \
                       -DKAKADU_INCLUDE_DIR=${KAKADU_HEADERS} \
-                      -Dpybindings=OFF \
+                      -Dpybindings=ON \
                       -DCMAKE_BUILD_TYPE=RELEASE \
                       -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} \
                       ../isis
@@ -117,6 +117,8 @@ pipeline {
                     cd $WORKSPACE/isis/pytests 
                     pytest .
 
+                    cd $WORKSPACE/isis/python_bindings/tests  
+                    pytest .
                     '''
                 }
             }

environment.yml

@@ -3,6 +3,7 @@ channels:
   - defaults
 
 dependencies:
+  - kalasiris 
   - ale=0.9.1
   - armadillo
   - boost=1.72
@@ -48,6 +49,7 @@ dependencies:
   - opencv>=4.5.2
   - openssl>=1.1.1k
   - pcl >= 1.10.0
+  - plio
   - protobuf<3.20
   - python>=3.7.11
   - pytest

isis/CMakeLists.txt

@@ -78,7 +78,7 @@ option(buildMissions   "Build the mission specific modules"             ON  )
 option(buildStaticCore "Build libisis static as well as dynamic"        OFF )
 option(buildTests      "Set up unit, application, and module tests."    ON  )
 option(JP2KFLAG        "Whether or not to build using JPEG2000 support" OFF )
-option(pybindings      "Turn on to build Python bindings"               OFF )
+option(pybindings      "Turn on to build Python bindings"               ON )
 
 # if cmake install prefix is not set, and conda env is activated, use the
 # conda env as the install directory.
@@ -309,10 +309,6 @@ if(APPLE)
   find_package(OpenGL REQUIRED)
 endif(APPLE)
 
-if(pybindings)
- find_package(Python REQUIRED)
-endif()
-
 # Iterate through all variables and extract the libraries and include directories
 get_cmake_property(_variableNames VARIABLES) # Get All VARIABLES
 
@@ -378,6 +374,9 @@ include_directories(${CMAKE_BINARY_DIR}/inc)
 set(CORE_LIB_NAME isis)
 message(STATUS "CORE LIB:  ${CORE_LIB_NAME}")
 
+if(pybindings)
+ add_subdirectory(python_bindings)
+endif()
 
 # Specify relative library include paths which will be set up on
 #  the installed files.

isis/cmake/AddIsisModule.cmake

@@ -6,7 +6,6 @@ include(CodeGeneration)
 
 # Incorporate an application folder
 function(add_isis_app folder libDependencies)
-
   # The internal build name will be different than the output name
   # - This deals with problems compiling same-named targets on case-insensitive machines.
   get_filename_component(appName ${folder}  NAME)

isis/python_bindings/CMakeLists.txt

@@ -0,0 +1,49 @@
+cmake_minimum_required(VERSION 3.14)
+
+# Setup for SWIG
+set(CMAKE_SWIG_FLAGS)
+find_package(SWIG REQUIRED)
+include(UseSWIG)
+list(APPEND CMAKE_SWIG_FLAGS "-py3;-DPY3")
+
+message(STATUS "SWIG flags: " ${CMAKE_SWIG_FLAGS} )
+
+# Setup for Python linking
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
+
+# Setup for wrapper library
+set(ASTROSET_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/astroset")
+set(ASTROSET_SOURCES astroset.i
+                   UserInterface.i 
+                   )
+
+set(ASTROSET_APPS apps/)
+
+set_source_files_properties(${ASTROSET_SOURCES} PROPERTIES CPLUSPLUS ON)
+swig_add_library(astroset
+                 LANGUAGE python
+                 SOURCES ${ASTROSET_SOURCES}
+                 OUTPUT_DIR ${ASTROSET_OUTPUT_DIR})
+swig_link_libraries(astroset isis Python3::Module)
+set_target_properties(astroset PROPERTIES SWIG_USE_TARGET_INCLUDE_DIRECTORIES TRUE)
+set_target_properties(astroset PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${ASTROSET_OUTPUT_DIR})
+
+# Create the files to install the Python wrapper
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in
+               ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/__init__.py
+               ${ASTROSET_OUTPUT_DIR}/__init__.py
+               COPYONLY)
+
+file(COPY ${ASTROSET_APPS}
+          DESTINATION
+          ${ASTROSET_OUTPUT_DIR}/apps/)
+
+set(ASTROSET_APP_XML_FILES "apps/findFeaturesSegment/findFeaturesSegment.xml")
+file(COPY ${ASTROSET_APP_XML_FILES} DESTINATION ${CMAKE_BINARY_DIR}/bin/xml/ )
+install(FILES ${ASTROSET_APP_XML_FILES} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin/xml/)
+
+# Setup to run setup tools on install 
+install(CODE "execute_process(COMMAND $ENV{CONDA_PREFIX}/bin/pip install ${CMAKE_CURRENT_BINARY_DIR}/ --prefix=${CMAKE_INSTALL_PREFIX}
+                              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})")
+

isis/python_bindings/UserInterface.i

@@ -0,0 +1,42 @@
+%module(package="astroset") UserInterface
+
+
+%{
+  #include "Gui.h"
+  #include "Pvl.h"
+  #include "UserInterface.h"
+%}
+
+%include <QVector>
+%include <QString>
+
+// Rename the constructors to Python-friendly names
+%rename(UserInterfaceFromArgsv) UserInterface(const QString &xmlfile, int &argc, char *argv[]);
+%rename(UserInterfaceFromList) UserInterface(const QString &xmlfile, QVector<QString> &args);
+
+%rename(GetFileName) IsisAml::GetFileName(QString const &) const;
+%rename(GetFileNameWithExt) IsisAml::GetFileName(QString const &, QString) const;
+%rename(GetFileNames) IsisAml::GetFileName(QString const &, std::vector<QString> &) const;
+
+%rename(GetAsString) IsisAml::GetAsString(QString const &) const;
+%rename(GetAsStrings) IsisAml::GetAsString(QString const &, std::vector<QString> &) const;
+
+%rename(GetString) IsisAml::GetString(QString const &) const;
+%rename(GetStrings) IsisAml::GetString(QString const &, std::vector<QString> &) const;
+
+%rename(GetCubeNameWithExt) IsisAml::GetCubeName(QString const &,QString) const;
+%rename(GetCubeName) IsisAml::GetCubeName(QString const &) const;
+
+%rename(GetInteger) IsisAml::GetInteger(const QString &) const;
+%rename(GetIntegers) IsisAml::GetInteger(const QString &, std::vector<int> &) const;
+
+%rename(GetDouble) IsisAml::GetDouble(const QString &) const;
+%rename(GetDoubles) IsisAml::GetDouble(const QString &, std::vector<int> &) const;
+
+%rename(GetBoolean) IsisAml::GetBoolean(const QString &) const;
+%rename(GetBooleans) IsisAml::GetBoolean(const QString &, std::vector<bool> &) const;
+
+%include "Pvl.h"
+%include "IsisAml.h"
+%include "UserInterface.h"
+

isis/python_bindings/__init__.py

@@ -0,0 +1,22 @@
+from .astroset import *
+
+from pathlib import Path 
+import os
+
+try: 
+    ISISROOT = Path(os.environ["ISISROOT"])
+except KeyError: 
+    raise EnvironmentError("Please set ISISROOT before importing anything")
+
+def init_application(args): 
+    appname = os.path.basename(args[0])
+    args = args[1:]
+
+    xmlpath = Path(appname).with_suffix(".xml")
+    if not xmlpath.exists() or not xmlpath.is_file():
+        xmlpath = ISISROOT / "bin" / "xml" / xmlpath
+        print(xmlpath)
+        if not xmlpath.exists(): 
+            raise FileExistsError(f"{appname} does not have an XML file")
+
+    return UserInterfaceFromList(str(xmlpath), args)

isis/python_bindings/apps/__init__.py

@@ -0,0 +1 @@
+from . import findFeaturesSegment