Unverified Commit 53e3bc01 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez Committed by GitHub
Browse files

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?
parent 3d77a879

Jenkinsfile

+3 −1
Original line number Diff line number Diff line
@@ -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

+2 −0
Original line number Diff line number Diff line
@@ -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

+4 −5
Original line number Diff line number Diff line
@@ -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

+0 −1
Original line number Diff line number Diff line
@@ -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 → 100644
+49 −0
Original line number Diff line number Diff line 
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})")