├── .DS_Store ├── Fig ├── .DS_Store ├── gmca.png ├── ngmca.png └── rgmca.png ├── README.md ├── cxxStarlet ├── .DS_Store ├── CMakeLists.txt ├── build │ └── .DS_Store ├── cmake │ ├── .DS_Store │ └── Modules │ │ └── FindPythonLibsNew.cmake ├── module │ ├── .DS_Store │ ├── pyStarlet.py │ ├── pyStarlet.pyc │ └── sparse2d.so └── sparse2d │ ├── .DS_Store │ └── cxx │ ├── .DS_Store │ ├── NumPyArrayData.h │ ├── sparse2d.cpp │ ├── starlet2d.cpp │ └── starlet2d.h ├── pyGMCA ├── .DS_Store ├── LICENSE.CeCILL ├── __init__.py ├── bss │ ├── .DS_Store │ ├── __init__.py │ ├── amca │ │ ├── __init__.py │ │ └── amca.py │ ├── bgmca │ │ ├── .DS_Store │ │ ├── __init__.py │ │ └── bgmca.py │ ├── gmca │ │ ├── __init__.py │ │ └── gmca.py │ ├── hypgmca │ │ ├── .DS_Store │ │ ├── __init__.py │ │ └── hypgmca.py │ ├── ngmca │ │ ├── LICENSE.CeCILL │ │ ├── __init__.py │ │ ├── base │ │ │ ├── __init__.py │ │ │ ├── algos │ │ │ │ ├── __init__.py │ │ │ │ ├── framework.py │ │ │ │ ├── standard.py │ │ │ │ └── updaters.py │ │ │ ├── images │ │ │ │ ├── barbara256.png │ │ │ │ ├── boat256.png │ │ │ │ ├── lena256.png │ │ │ │ └── peppers256.png │ │ │ ├── sample_nmr_spectra.py │ │ │ └── tools.py │ │ ├── core │ │ │ ├── __init__.py │ │ │ ├── algorithm.py │ │ │ ├── benchmark.py │ │ │ └── tools.py │ │ ├── framework.py │ │ ├── munkres │ │ │ ├── CHANGELOG │ │ │ ├── LICENSE │ │ │ ├── PKG-INFO │ │ │ ├── __init__.py │ │ │ ├── munkres.py │ │ │ ├── setup.cfg │ │ │ └── setup.py │ │ ├── proximal │ │ │ ├── __init__.py │ │ │ ├── algorithms.py │ │ │ └── operators.py │ │ ├── standard.py │ │ ├── tools │ │ │ ├── sample_nmr_spectra.py │ │ │ └── tools.py │ │ └── updaters.py │ ├── rgmca │ │ ├── AGMCA.py │ │ ├── BetaD_ICA.py │ │ ├── FunBetaD.py │ │ ├── __init__.py │ │ ├── data.py │ │ ├── errors.py │ │ ├── main.py │ │ ├── munkres │ │ │ ├── CHANGELOG │ │ │ ├── LICENSE │ │ │ ├── PKG-INFO │ │ │ ├── __init__.py │ │ │ ├── __init__.pyc │ │ │ ├── munkres.py │ │ │ ├── munkres.pyc │ │ │ ├── setup.cfg │ │ │ ├── setup.py │ │ │ └── setup.pyc │ │ ├── parameters.py │ │ ├── readMe.txt │ │ └── rpcaAlgo.py │ └── tr_rgmca │ │ ├── XMCA.py │ │ ├── __init__.py │ │ ├── data.py │ │ ├── errors.py │ │ ├── main.py │ │ ├── munkres │ │ ├── CHANGELOG │ │ ├── LICENSE │ │ ├── PKG-INFO │ │ ├── __init__.py │ │ ├── __init__.pyc │ │ ├── munkres.py │ │ ├── munkres.pyc │ │ ├── setup.cfg │ │ └── setup.py │ │ ├── outliersPursuit.py │ │ ├── parameters.py │ │ └── readMe.txt ├── common │ ├── .DS_Store │ ├── munkres │ │ ├── CHANGELOG │ │ ├── LICENSE │ │ ├── PKG-INFO │ │ ├── __init__.py │ │ ├── __init__.pyc │ │ ├── munkres.py │ │ ├── munkres.pyc │ │ ├── setup.cfg │ │ └── setup.py │ ├── prox │ │ ├── .DS_Store │ │ ├── Prox_SparsePositive.py │ │ └── __init__.py │ ├── utils.py │ └── wavelets │ │ ├── .DS_Store │ │ ├── __init__.py │ │ ├── pyStarlet.py │ │ └── sparse2d.so ├── data │ ├── __init__.py │ ├── barbara256.png │ ├── boat256.png │ ├── lena256.png │ └── peppers256.png └── scripts │ ├── .DS_Store │ ├── __init__.py │ ├── bgmca │ ├── .DS_Store │ ├── launch_bGMCA.py │ ├── sample_nmr_spectra.py │ └── script_bgmca.ipynb │ ├── gmca │ ├── .ipynb_checkpoints │ │ ├── script_gmca_amca-checkpoint.ipynb │ │ ├── script_ngmca-checkpoint.ipynb │ │ ├── script_ngmca_wave-checkpoint.ipynb │ │ ├── script_rgmca-checkpoint.ipynb │ │ └── script_tr_rgmca-checkpoint.ipynb │ ├── __init__.py │ └── script_gmca_amca.ipynb │ ├── hypgmca │ ├── .DS_Store │ ├── .ipynb_checkpoints │ │ └── script_hypgmca-checkpoint.ipynb │ ├── __init__.py │ ├── data │ │ ├── Sources.fits │ │ └── Spectra.fits │ └── script_hypgmca.ipynb │ ├── ngmca │ ├── .ipynb_checkpoints │ │ ├── script_ngmca-checkpoint.ipynb │ │ └── script_ngmca_wave-checkpoint.ipynb │ ├── __init__.py │ ├── benchmarks │ │ ├── bench_S_tau_mad_P5MC12_04déc14_1042_820818.bch │ │ ├── bench_db_basic.py │ │ └── bench_lambda.py │ ├── example_bench.py │ ├── example_fb.py │ ├── example_ngmca.py │ ├── example_ngmca_wave.py │ ├── script_ngmca.ipynb │ └── script_ngmca_wave.ipynb │ └── rgmca │ ├── .ipynb_checkpoints │ ├── script_rgmca-checkpoint.ipynb │ └── script_tr_rgmca-checkpoint.ipynb │ ├── __init__.py │ ├── script_rgmca.ipynb │ ├── script_rgmca.py │ ├── script_tr_rgmca.ipynb │ └── script_tr_rgmca.py └── redwave_toolbox ├── LICENSE.CeCILL ├── __init__.py ├── __init__.pyc ├── __pycache__ └── __init__.cpython-34.pyc ├── pyredwave ├── CMakeLists.txt ├── LICENSE.CeCILL ├── __init__.py ├── __init__.pyc ├── __pycache__ │ └── __init__.cpython-34.pyc ├── build │ ├── BoostNumpy-prefix │ │ ├── src │ │ │ ├── BoostNumpy-build │ │ │ │ ├── CMakeCache.txt │ │ │ │ ├── CMakeFiles │ │ │ │ │ ├── 3.2.1 │ │ │ │ │ │ ├── CMakeCCompiler.cmake │ │ │ │ │ │ ├── CMakeCXXCompiler.cmake │ │ │ │ │ │ ├── CMakeDetermineCompilerABI_C.bin │ │ │ │ │ │ ├── CMakeDetermineCompilerABI_CXX.bin │ │ │ │ │ │ ├── CMakeSystem.cmake │ │ │ │ │ │ ├── CompilerIdC │ │ │ │ │ │ │ ├── CMakeCCompilerId.c │ │ │ │ │ │ │ └── a.out │ │ │ │ │ │ └── CompilerIdCXX │ │ │ │ │ │ │ ├── CMakeCXXCompilerId.cpp │ │ │ │ │ │ │ └── a.out │ │ │ │ │ ├── CMakeDirectoryInformation.cmake │ │ │ │ │ ├── CMakeOutput.log │ │ │ │ │ ├── Makefile.cmake │ │ │ │ │ ├── Makefile2 │ │ │ │ │ ├── TargetDirectories.txt │ │ │ │ │ ├── cmake.check_cache │ │ │ │ │ ├── feature_tests.bin │ │ │ │ │ ├── feature_tests.c │ │ │ │ │ ├── feature_tests.cxx │ │ │ │ │ └── progress.marks │ │ │ │ ├── Makefile │ │ │ │ ├── bin │ │ │ │ │ ├── dtype │ │ │ │ │ ├── fromdata │ │ │ │ │ ├── ndarray │ │ │ │ │ ├── simple │ │ │ │ │ ├── ufunc │ │ │ │ │ └── wrap │ │ │ │ ├── cmake_install.cmake │ │ │ │ ├── install_manifest.txt │ │ │ │ ├── lib │ │ │ │ │ ├── gaussian.so │ │ │ │ │ └── libboost_numpy.a │ │ │ │ └── libs │ │ │ │ │ └── numpy │ │ │ │ │ ├── example │ │ │ │ │ ├── CMakeFiles │ │ │ │ │ │ ├── CMakeDirectoryInformation.cmake │ │ │ │ │ │ ├── dtype.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── dtype.cpp.o │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ └── progress.make │ │ │ │ │ │ ├── fromdata.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── fromdata.cpp.o │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ └── progress.make │ │ │ │ │ │ ├── gaussian.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── gaussian.cpp.o │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ └── progress.make │ │ │ │ │ │ ├── ndarray.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ ├── ndarray.cpp.o │ │ │ │ │ │ │ └── progress.make │ │ │ │ │ │ ├── progress.marks │ │ │ │ │ │ ├── simple.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ ├── progress.make │ │ │ │ │ │ │ └── simple.cpp.o │ │ │ │ │ │ ├── ufunc.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ ├── progress.make │ │ │ │ │ │ │ └── ufunc.cpp.o │ │ │ │ │ │ └── wrap.dir │ │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ │ ├── progress.make │ │ │ │ │ │ │ └── wrap.cpp.o │ │ │ │ │ ├── Makefile │ │ │ │ │ └── cmake_install.cmake │ │ │ │ │ └── src │ │ │ │ │ ├── CMakeFiles │ │ │ │ │ ├── CMakeDirectoryInformation.cmake │ │ │ │ │ ├── boost_numpy.dir │ │ │ │ │ │ ├── CXX.includecache │ │ │ │ │ │ ├── DependInfo.cmake │ │ │ │ │ │ ├── build.make │ │ │ │ │ │ ├── cmake_clean.cmake │ │ │ │ │ │ ├── cmake_clean_target.cmake │ │ │ │ │ │ ├── depend.internal │ │ │ │ │ │ ├── depend.make │ │ │ │ │ │ ├── dtype.cpp.o │ │ │ │ │ │ ├── flags.make │ │ │ │ │ │ ├── link.txt │ │ │ │ │ │ ├── matrix.cpp.o │ │ │ │ │ │ ├── ndarray.cpp.o │ │ │ │ │ │ ├── numpy.cpp.o │ │ │ │ │ │ ├── progress.make │ │ │ │ │ │ ├── scalars.cpp.o │ │ │ │ │ │ └── ufunc.cpp.o │ │ │ │ │ └── progress.marks │ │ │ │ │ ├── Makefile │ │ │ │ │ └── cmake_install.cmake │ │ │ └── BoostNumpy-stamp │ │ │ │ ├── BoostNumpy-build │ │ │ │ ├── BoostNumpy-configure │ │ │ │ ├── BoostNumpy-done │ │ │ │ ├── BoostNumpy-download │ │ │ │ ├── BoostNumpy-gitclone-lastrun.txt │ │ │ │ ├── BoostNumpy-gitinfo.txt │ │ │ │ ├── BoostNumpy-install │ │ │ │ ├── BoostNumpy-mkdir │ │ │ │ └── BoostNumpy-patch │ │ └── tmp │ │ │ ├── BoostNumpy-cfgcmd.txt │ │ │ ├── BoostNumpy-cfgcmd.txt.in │ │ │ ├── BoostNumpy-gitclone.cmake │ │ │ └── BoostNumpy-gitupdate.cmake │ ├── CMakeCache.txt │ ├── CMakeFiles │ │ ├── 3.2.1 │ │ │ ├── CMakeCCompiler.cmake │ │ │ ├── CMakeCXXCompiler.cmake │ │ │ ├── CMakeDetermineCompilerABI_C.bin │ │ │ ├── CMakeDetermineCompilerABI_CXX.bin │ │ │ ├── CMakeSystem.cmake │ │ │ ├── CompilerIdC │ │ │ │ ├── CMakeCCompilerId.c │ │ │ │ └── a.out │ │ │ └── CompilerIdCXX │ │ │ │ ├── CMakeCXXCompilerId.cpp │ │ │ │ └── a.out │ │ ├── BoostNumpy-complete │ │ ├── BoostNumpy.dir │ │ │ ├── DependInfo.cmake │ │ │ ├── Labels.json │ │ │ ├── Labels.txt │ │ │ ├── build.make │ │ │ ├── cmake_clean.cmake │ │ │ ├── depend.internal │ │ │ ├── depend.make │ │ │ └── progress.make │ │ ├── CMakeDirectoryInformation.cmake │ │ ├── CMakeOutput.log │ │ ├── CMakeRuleHashes.txt │ │ ├── Makefile.cmake │ │ ├── Makefile2 │ │ ├── TargetDirectories.txt │ │ ├── cmake.check_cache │ │ ├── feature_tests.bin │ │ ├── feature_tests.c │ │ ├── feature_tests.cxx │ │ ├── progress.marks │ │ └── redwavecxx.dir │ │ │ ├── CXX.includecache │ │ │ ├── DependInfo.cmake │ │ │ ├── build.make │ │ │ ├── cmake_clean.cmake │ │ │ ├── depend.internal │ │ │ ├── depend.make │ │ │ ├── flags.make │ │ │ ├── link.txt │ │ │ ├── progress.make │ │ │ └── pyredwave │ │ │ └── cxx │ │ │ ├── redWaveTools.cpp.o │ │ │ └── redwavecxx.cpp.o │ ├── Makefile │ ├── cmake_install.cmake │ ├── extern │ │ ├── include │ │ │ └── boost │ │ │ │ ├── numpy.hpp │ │ │ │ └── numpy │ │ │ │ ├── dtype.hpp │ │ │ │ ├── internal.hpp │ │ │ │ ├── invoke_matching.hpp │ │ │ │ ├── matrix.hpp │ │ │ │ ├── ndarray.hpp │ │ │ │ ├── numpy_object_mgr_traits.hpp │ │ │ │ ├── scalars.hpp │ │ │ │ └── ufunc.hpp │ │ └── lib │ │ │ └── libboost_numpy.a │ ├── install_manifest.txt │ ├── lib │ │ └── pyredwave │ │ │ ├── __init__.py │ │ │ └── redwave.py │ └── redwavecxx.so ├── cmake │ └── Modules │ │ └── FindPythonLibsNew.cmake ├── pyredwave │ ├── __init__.py │ ├── __init__.pyc │ ├── __pycache__ │ │ └── redwave.cpython-34.pyc │ ├── cxx │ │ ├── redWaveTools.cpp │ │ ├── redWaveTools.hpp │ │ └── redwavecxx.cpp │ ├── redwave.py │ ├── redwave.pyc │ └── redwavecxx.so └── setup.py └── test_func └── test_redwave.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/.DS_Store -------------------------------------------------------------------------------- /Fig/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/Fig/.DS_Store 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | 3 | include(ExternalProject) 4 | include(FindPkgConfig) 5 | 6 | # Adding customized cmake module 7 | list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/") 8 | 9 | project(sparse2d) 10 | 11 | # Find required packages 12 | find_package(Boost REQUIRED COMPONENTS python) 13 | find_package(PythonInterp REQUIRED) 14 | find_package(PythonLibsNew REQUIRED) 15 | 16 | pkg_check_modules(GSL REQUIRED gsl) 17 | pkg_check_modules(CFITSIO REQUIRED cfitsio) 18 | 19 | 20 | # Downloads and compiles the Boost.NumPy package 21 | # The library and include files are located in the build/extern directory 22 | ExternalProject_Add(BoostNumpy 23 | GIT_REPOSITORY https://github.com/ndarray/Boost.NumPy 24 | CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/extern 25 | -DLIBRARY_TYPE=STATIC 26 | ) 27 | set(BoostNumpy_INCLUDE_DIRS ${CMAKE_BINARY_DIR}/extern/include) 28 | set(BoostNumpy_LIBRARY_DIRS ${CMAKE_BINARY_DIR}/extern/lib64) 29 | set(BoostNumpy_LIBRARIES -lboost_numpy) 30 | 31 | 32 | # Define include and library directories 33 | include_directories( 34 | ${GSL_INCLUDE_DIRS} 35 | ${PYTHON_INCLUDE_DIRS} 36 | ${Boost_INCLUDE_DIRS} 37 | ${BoostNumpy_INCLUDE_DIRS} 38 | ${CFITSIO_INCLUDE_DIRS} 39 | ) 40 | link_directories(${BoostNumpy_LIBRARY_DIRS} ${GSL_LIBRARY_DIRS} ${CFITSIO_LIBRARY_DIRS}) 41 | 42 | # Compilation flags 43 | #if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") 44 | # using Clang, disabling OpenMP support 45 | # set(CMAKE_CXX_FLAGS "-O3 -fomit-frame-pointer -fno-common -fPIC") 46 | #else() 47 | # set(CMAKE_CXX_FLAGS "-O3 -fomit-frame-pointer -fno-common -fPIC -fopenmp") 48 | #endif() 49 | 50 | set(CMAKE_CXX_FLAGS "-O3 -fomit-frame-pointer -fno-common -fPIC -fopenmp -DRW_PYTHON_INTERFACE -F/Library/Frameworks -arch x86_64") # For MAC 51 | #set(CMAKE_CXX_FLAGS "-O3 -fomit-frame-pointer -fno-common -fPIC -fopenmp -DRW_PYTHON_INTERFACE") # For Linux 52 | 53 | # Build the tools module 54 | add_library(sparse2d SHARED sparse2d/cxx/sparse2d.cpp sparse2d/cxx/starlet2d.cpp) 55 | add_dependencies(sparse2d BoostNumpy) 56 | target_link_libraries(sparse2d ${BoostNumpy_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES} ${PYTHON_LIBRARIES}) 57 | set_target_properties(sparse2d PROPERTIES SUFFIX .so) 58 | set_target_properties(sparse2d PROPERTIES PREFIX "") 59 | -------------------------------------------------------------------------------- /cxxStarlet/build/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/build/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/cmake/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/cmake/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/module/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/module/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/module/pyStarlet.py: -------------------------------------------------------------------------------- 1 | 2 | import sparse2d as sp2 3 | import numpy as np 4 | 5 | # pyStarlet 6 | 7 | def forward(X,h = [0.0625,0.25,0.375,0.25,0.0625],J = 1): 8 | 9 | nX = np.shape(X) 10 | Lh = np.size(h) 11 | 12 | W = sp2.Starlet2D(nX[1],nX[2],nX[0],J,Lh).forward_omp(np.real(X),np.array(h)) 13 | 14 | return W 15 | 16 | 17 | def backward(W,h = [0.0625,0.25,0.375,0.25,0.0625]): 18 | 19 | nX = np.shape(W) 20 | Lh = np.size(h) 21 | 22 | rec = sp2.Starlet2D(nX[1],nX[2],nX[0],nX[3]-1,Lh).backward_omp(np.real(W)) 23 | 24 | return rec 25 | 26 | def forward1d(X,h = [0.0625,0.25,0.375,0.25,0.0625],J = 1): 27 | 28 | nX = np.shape(X) 29 | Lh = np.size(h) 30 | 31 | W = sp2.Starlet2D(nX[1],1,nX[0],J,Lh).forward1d_omp(np.real(X),np.array(h)) 32 | 33 | return W 34 | 35 | def adjoint1d(W,h = [0.0625,0.25,0.375,0.25,0.0625]): 36 | 37 | nX = np.shape(W) 38 | Lh = np.size(h) 39 | 40 | W = sp2.Starlet2D(nX[1],1,nX[0],nX[2]-1,Lh).adjoint1d(np.real(W),np.array(h)) 41 | 42 | return W 43 | 44 | def backward1d(W,h = [0.0625,0.25,0.375,0.25,0.0625]): 45 | 46 | rec = np.sum(W,axis=2) 47 | 48 | return rec -------------------------------------------------------------------------------- /cxxStarlet/module/pyStarlet.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/module/pyStarlet.pyc -------------------------------------------------------------------------------- /cxxStarlet/module/sparse2d.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/module/sparse2d.so -------------------------------------------------------------------------------- /cxxStarlet/sparse2d/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/sparse2d/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/sparse2d/cxx/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/cxxStarlet/sparse2d/cxx/.DS_Store -------------------------------------------------------------------------------- /cxxStarlet/sparse2d/cxx/NumPyArrayData.h: -------------------------------------------------------------------------------- 1 | // Copyright (c) 2014-2015, CosmicPy Developers 2 | // Licensed under CeCILL 2.1 - see LICENSE.rst 3 | #pragma once 4 | 5 | #include 6 | #include 7 | #include 8 | #include 9 | 10 | namespace bp = boost::python; 11 | namespace np = boost::numpy; 12 | 13 | // Helper class for fast access to array elements 14 | template class NumPyArrayData 15 | { 16 | char* m_data; 17 | const Py_intptr_t* m_strides; 18 | 19 | public: 20 | NumPyArrayData(const np::ndarray &arr) 21 | { 22 | np::dtype dtype = arr.get_dtype(); 23 | np::dtype dtype_expected = np::dtype::get_builtin(); 24 | 25 | if (dtype != dtype_expected) 26 | { 27 | std::stringstream ss; 28 | ss << "NumPyArrayData: Unexpected data type (" << bp::extract(dtype.attr("__str__")()) << ") received. "; 29 | ss << "Expected " << bp::extract(dtype_expected.attr("__str__")()); 30 | throw std::runtime_error(ss.str().c_str()); 31 | } 32 | 33 | m_data = arr.get_data(); 34 | m_strides = arr.get_strides(); 35 | } 36 | 37 | T* data() 38 | { 39 | return reinterpret_cast(m_data); 40 | } 41 | 42 | const Py_intptr_t* strides() 43 | { 44 | return m_strides; 45 | } 46 | 47 | // 1D array access 48 | inline T& operator()(int i) 49 | { 50 | return *reinterpret_cast(m_data + i*m_strides[0]); 51 | } 52 | 53 | // 2D array access 54 | inline T& operator()(int i, int j) 55 | { 56 | return *reinterpret_cast(m_data + i*m_strides[0] + j*m_strides[1]); 57 | } 58 | 59 | // 3D array access 60 | inline T& operator()(int i, int j, int k) 61 | { 62 | return *reinterpret_cast(m_data + i*m_strides[0] + j*m_strides[1] + k*m_strides[2]); 63 | } 64 | 65 | // 4D array access 66 | inline T& operator()(int i, int j, int k, int l) 67 | { 68 | return *reinterpret_cast(m_data + i*m_strides[0] + j*m_strides[1] + k*m_strides[2] + l*m_strides[3]); 69 | } 70 | }; -------------------------------------------------------------------------------- /cxxStarlet/sparse2d/cxx/sparse2d.cpp: -------------------------------------------------------------------------------- 1 | #include "starlet2d.h" 2 | 3 | using namespace boost::python; 4 | 5 | BOOST_PYTHON_MODULE(sparse2d) 6 | { 7 | np::initialize(); 8 | 9 | class_< Starlet2D >("Starlet2D", init()) 10 | .def("forward", &Starlet2D::transform_numpy) 11 | .def("forward_omp", &Starlet2D::transform_omp_numpy) 12 | .def("forward1d_omp", &Starlet2D::transform1d_omp_numpy) 13 | .def("backward", &Starlet2D::reconstruct_numpy) 14 | .def("adjoint1d",&Starlet2D:: adjoint1d_omp_numpy) 15 | .def("backward_omp", &Starlet2D::reconstruct_omp_numpy); 16 | } 17 | -------------------------------------------------------------------------------- /pyGMCA/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | # 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | 43 | import common 44 | import bss 45 | -------------------------------------------------------------------------------- /pyGMCA/bss/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/bss/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | 43 | import amca 44 | import gmca 45 | import rgmca 46 | import tr_rgmca 47 | import ngmca 48 | -------------------------------------------------------------------------------- /pyGMCA/bss/amca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/bgmca/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/bgmca/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/bss/bgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/gmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/hypgmca/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/hypgmca/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/bss/hypgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) - Jerome Bobin (jbobin@cea.fr) 8 | # Created on September 30, 2014, last modified on April 30, 2015 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin & Jerome Bobin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2015 CEA" 41 | # __license__ = "CeCill" 42 | # 43 | 44 | import base 45 | import core 46 | import proximal 47 | import munkres 48 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) - Jerome Bobin (jbobin@cea.fr) 8 | # Created on September 30, 2014, last modified on April 30, 2015 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin & Jerome Bobin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2015 CEA" 41 | # __license__ = "CeCill" 42 | 43 | import algos 44 | import tools 45 | import sample_nmr_spectra 46 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/algos/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | # Created on September 30, 2014, last modified on December 14, 2014 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2014 CEA" 41 | # __license__ = "CeCill" 42 | 43 | import standard 44 | import framework 45 | import updaters 46 | from standard import Ngmca 47 | from framework import Framework 48 | from updaters import SparseUpdater, RedWaveUpdater 49 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/images/barbara256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/ngmca/base/images/barbara256.png -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/images/boat256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/ngmca/base/images/boat256.png -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/images/lena256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/ngmca/base/images/lena256.png -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/base/images/peppers256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/ngmca/base/images/peppers256.png -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/core/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) - Jerome Bobin (jbobin@cea.fr) 8 | # Created on September 30, 2014, last modified on April 30, 2015 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin & Jerome Bobin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2015 CEA" 41 | # __license__ = "CeCill" 42 | # 43 | 44 | import algorithm 45 | from algorithm import Algorithm 46 | import tools 47 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/munkres/CHANGELOG: -------------------------------------------------------------------------------- 1 | 2 | --------------------------------------------------------------------------- 3 | 4 | 1.0.5.3 (2 August, 2009) 5 | 6 | - Fixed documentation of print_matrix() in module docs. 7 | 8 | --------------------------------------------------------------------------- 9 | 1.0.5.2 (30 June, 2008): 10 | 11 | - Incorporated some suggestions optimizations from Mark Summerfield 12 | (mark /at/ qtrac.eu) 13 | - Munkres.make_cost_matrix() is now deprecated, in favor of a module-level 14 | function. 15 | - The module now provides a print_matrix() convenience function. 16 | - Fixed some bugs related to the padding of non-square matrics. 17 | 18 | --------------------------------------------------------------------------- 19 | 1.0.5.1 (26 June, 2008): 20 | 21 | - Some minor doc changes. 22 | 23 | --------------------------------------------------------------------------- 24 | 1.0.5 (26 June, 2008): 25 | 26 | - Now handles non-square cost matrices by padding them with zeros. 27 | - Converted Epydocs to use reStructuredText. 28 | 29 | --------------------------------------------------------------------------- 30 | 1.0.4 (13 June, 2008) 31 | 32 | - Minor bug fix in main (tester) program in munkres.py 33 | 34 | --------------------------------------------------------------------------- 35 | 1.0.3 (16 March, 2008) 36 | 37 | - Minor change to prevent shadowing of built-in min() function. Thanks to 38 | Nelson Castillo (nelson /at/ emqbit.com) for pointing it out. 39 | 40 | --------------------------------------------------------------------------- 41 | 1.0.2 (21 February, 2008) 42 | 43 | - Fixed an overindexing bug reported by Chris Willmore (willmc rpi.edu) 44 | 45 | --------------------------------------------------------------------------- 46 | 1.0.1 (16 February, 2008) 47 | 48 | - Documentation now processed by Epydoc. 49 | 50 | --------------------------------------------------------------------------- 51 | 1.0 (January, 2008) 52 | 53 | - Initial release. 54 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/munkres/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/ngmca/munkres/LICENSE -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/munkres/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) - Jerome Bobin (jbobin@cea.fr) 8 | # Created on September 30, 2014, last modified on April 30, 2015 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin & Jerome Bobin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2015 CEA" 41 | # __license__ = "CeCill" 42 | # 43 | # 44 | 45 | import munkres 46 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/munkres/setup.cfg: -------------------------------------------------------------------------------- 1 | # $Id: 79a7f3922991f85a694f4c57567ad52186b5cf9a $ 2 | 3 | [sdist] 4 | formats: gztar, zip 5 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/munkres/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Distutils setup script for Munkres 4 | # 5 | # $Id: 4648a5304b06dbfc6ffc7df8d413fa621a32c5aa $ 6 | # --------------------------------------------------------------------------- 7 | 8 | from distutils.core import setup 9 | import re 10 | import os 11 | import sys 12 | import imp 13 | 14 | # Load the data. 15 | 16 | here = os.path.dirname(os.path.abspath(sys.argv[0])) 17 | sys.path = [here] + sys.path 18 | mf = os.path.join(here, 'munkres.py') 19 | munkres = imp.load_module('munkres', open(mf), mf, 20 | ('__init__.py', 'r', imp.PY_SOURCE)) 21 | long_description = munkres.__doc__ 22 | version = str(munkres.__version__) 23 | (author, email) = re.match('^(.*),\s*(.*)$', munkres.__author__).groups() 24 | url = munkres.__url__ 25 | license = munkres.__license__ 26 | 27 | # Run setup 28 | 29 | setup( 30 | name="munkres", 31 | version=version, 32 | description="munkres algorithm for the Assignment Problem", 33 | long_description=long_description, 34 | url=url, 35 | license=license, 36 | author=author, 37 | author_email=email, 38 | py_modules=["munkres"], 39 | classifiers = [ 40 | 'Intended Audience :: Developers', 41 | 'Intended Audience :: Science/Research', 42 | 'License :: OSI Approved :: BSD License', 43 | 'Operating System :: OS Independent', 44 | 'Programming Language :: Python', 45 | 'Topic :: Scientific/Engineering :: Mathematics', 46 | 'Topic :: Software Development :: Libraries :: Python Modules' 47 | ] 48 | ) 49 | -------------------------------------------------------------------------------- /pyGMCA/bss/ngmca/proximal/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | # Created on September 30, 2014, last modified on December 14, 2014 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "1.0" 38 | # __author__ = "Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2014 CEA" 41 | # __license__ = "CeCill" 42 | 43 | import algorithms 44 | import operators 45 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/CHANGELOG: -------------------------------------------------------------------------------- 1 | 2 | --------------------------------------------------------------------------- 3 | 4 | 1.0.5.3 (2 August, 2009) 5 | 6 | - Fixed documentation of print_matrix() in module docs. 7 | 8 | --------------------------------------------------------------------------- 9 | 1.0.5.2 (30 June, 2008): 10 | 11 | - Incorporated some suggestions optimizations from Mark Summerfield 12 | (mark /at/ qtrac.eu) 13 | - Munkres.make_cost_matrix() is now deprecated, in favor of a module-level 14 | function. 15 | - The module now provides a print_matrix() convenience function. 16 | - Fixed some bugs related to the padding of non-square matrics. 17 | 18 | --------------------------------------------------------------------------- 19 | 1.0.5.1 (26 June, 2008): 20 | 21 | - Some minor doc changes. 22 | 23 | --------------------------------------------------------------------------- 24 | 1.0.5 (26 June, 2008): 25 | 26 | - Now handles non-square cost matrices by padding them with zeros. 27 | - Converted Epydocs to use reStructuredText. 28 | 29 | --------------------------------------------------------------------------- 30 | 1.0.4 (13 June, 2008) 31 | 32 | - Minor bug fix in main (tester) program in munkres.py 33 | 34 | --------------------------------------------------------------------------- 35 | 1.0.3 (16 March, 2008) 36 | 37 | - Minor change to prevent shadowing of built-in min() function. Thanks to 38 | Nelson Castillo (nelson /at/ emqbit.com) for pointing it out. 39 | 40 | --------------------------------------------------------------------------- 41 | 1.0.2 (21 February, 2008) 42 | 43 | - Fixed an overindexing bug reported by Chris Willmore (willmc rpi.edu) 44 | 45 | --------------------------------------------------------------------------- 46 | 1.0.1 (16 February, 2008) 47 | 48 | - Documentation now processed by Epydoc. 49 | 50 | --------------------------------------------------------------------------- 51 | 1.0 (January, 2008) 52 | 53 | - Initial release. 54 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/rgmca/munkres/LICENSE -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/rgmca/munkres/__init__.pyc -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/munkres.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/rgmca/munkres/munkres.pyc -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/setup.cfg: -------------------------------------------------------------------------------- 1 | # $Id: 79a7f3922991f85a694f4c57567ad52186b5cf9a $ 2 | 3 | [sdist] 4 | formats: gztar, zip 5 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Distutils setup script for Munkres 4 | # 5 | # $Id: 4648a5304b06dbfc6ffc7df8d413fa621a32c5aa $ 6 | # --------------------------------------------------------------------------- 7 | 8 | from distutils.core import setup 9 | import re 10 | import os 11 | import sys 12 | import imp 13 | 14 | # Load the data. 15 | 16 | here = os.path.dirname(os.path.abspath(sys.argv[0])) 17 | sys.path = [here] + sys.path 18 | mf = os.path.join(here, 'munkres.py') 19 | munkres = imp.load_module('munkres', open(mf), mf, 20 | ('__init__.py', 'r', imp.PY_SOURCE)) 21 | long_description = munkres.__doc__ 22 | version = str(munkres.__version__) 23 | (author, email) = re.match('^(.*),\s*(.*)$', munkres.__author__).groups() 24 | url = munkres.__url__ 25 | license = munkres.__license__ 26 | 27 | # Run setup 28 | 29 | setup( 30 | name="munkres", 31 | version=version, 32 | description="munkres algorithm for the Assignment Problem", 33 | long_description=long_description, 34 | url=url, 35 | license=license, 36 | author=author, 37 | author_email=email, 38 | py_modules=["munkres"], 39 | classifiers = [ 40 | 'Intended Audience :: Developers', 41 | 'Intended Audience :: Science/Research', 42 | 'License :: OSI Approved :: BSD License', 43 | 'Operating System :: OS Independent', 44 | 'Programming Language :: Python', 45 | 'Topic :: Scientific/Engineering :: Mathematics', 46 | 'Topic :: Software Development :: Libraries :: Python Modules' 47 | ] 48 | ) 49 | -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/munkres/setup.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/rgmca/munkres/setup.pyc -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/parameters.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | Parameters for the data generation and the algorithms. 4 | Dictionaries: 5 | data_setting: data generation 6 | algo_setting: parameters for the algorithms 7 | param_setting: other parameters, such as verbose 8 | 9 | 10 | """ 11 | #Import' 12 | import numpy as np 13 | ################################################################################################################################################################################################################################# 14 | 15 | 16 | #Data generation parameters 17 | data_setting={} 18 | 19 | #Dimensions of the problem 20 | data_setting['m'] =16 #number of observations 21 | data_setting['n'] =8 #number of sources 22 | data_setting['t'] =4096 #number of samples 23 | 24 | #sources 25 | data_setting['alphaS'] =2 #parameter of the Generalized Gaussian law for the amplitude 26 | data_setting['pS'] =0.05 # activation parameter for the Bernoulli law (for the support) 27 | data_setting['ampliS'] = 100 # standard deviation (amplitude) 28 | 29 | #outliers 30 | data_setting['nbCol']=0.1*data_setting['t'] #Number of corrupted columns 31 | data_setting['ampliO'] =100. # standard deviation (amplitude) 32 | data_setting['alphaO'] =2 #parameter of the Generalized Gaussian law for the amplitude 33 | 34 | #Gaussian noise 35 | data_setting['ampliN'] =0.1 #standard deviation (amplitude) 36 | 37 | dS=data_setting 38 | 39 | ################################################################################################################################################################################################################################# 40 | 41 | #Algorithm parameters 42 | algo_setting={}; 43 | 44 | algo_setting['iteMaxGMCA']=300 #Number of iterations for GMCA 45 | algo_setting['iteMaxrAMCA']=100 #Number of outer loops for rAMCA 46 | algo_setting['iteMaxrGMCA']=25 # Number of outer loops for rGMCA 47 | algo_setting['iteMaxAMCA']=1000 #Number of iterations for AMCA 48 | algo_setting['iteMaxBeta']=700 #Number of iterations for the beta-divergence 49 | algo_setting['iteMaxPCP']=5000 #Number of iterations for PCP 50 | 51 | 52 | algo_setting['kSMax']=3.# Final threshold for the sources with 3*mad 53 | algo_setting['kOMax']=3 # Final threshold for the outliers with 3*mad 54 | 55 | aS=algo_setting 56 | 57 | ################################################################################################################################################################################################################################# 58 | 59 | 60 | #Other parameters 61 | param_setting={} 62 | 63 | #Verbose# 64 | param_setting['verbose']=1 # print will be displayed if set to one 65 | param_setting['verboseAMCA']=1 * param_setting['verbose'] #Specific for AMCA 66 | param_setting['verboserAMCA']=1 * param_setting['verbose'] #Specific for rAMCA 67 | param_setting['verboseGMCA']=1 * param_setting['verbose'] #Specific for GMCA 68 | param_setting['verboserGMCA']=1 * param_setting['verbose'] #Specific for rGMCA 69 | param_setting['verbosePCP']=1* param_setting['verbose'] #Specific for PCP 70 | param_setting['verboseBeta']=1 * param_setting['verbose'] #Specific for Beta-div. 71 | 72 | 73 | #ForMonte Carlo simulations and benchmark: 74 | param_setting['nbreParam']=9 #number of varying parameters 75 | param_setting['param']=np.array([1,5,10,15,20,25,30,35,40]) #Values of the varying parameters 76 | 77 | #Number of iterations for each parameters 78 | param_setting['nbreIter']=1 79 | 80 | #Save the results 81 | param_setting['saveFile']=0 #Set to 1 to save the results 82 | param_setting['nameFile']="varyingNbreO" #Name of the file to be save 83 | 84 | #Display the results 85 | param_setting['plot']=1 #set to 1 to display the results 86 | 87 | pS=param_setting -------------------------------------------------------------------------------- /pyGMCA/bss/rgmca/readMe.txt: -------------------------------------------------------------------------------- 1 | This file contains the python implementations of the algorithms used in the numerical experiments section in the report ‘Unsupervised separation of sparse sources in the presence of outliers’, C.Chenot and J.Bobin, namely: GMCA, AMCA, rGMCA, rAMCA, the minimization of the beta-divergence and the combination PCP+GMCA. 2 | 3 | The files are organized as follows: 4 | - the file ‘main.py’ in which the benchmark (data generation, calls of the algorithms, save and plot of the results) is performed. 5 | - ‘parameters.py’: in which the parameters (for the data generation, benchmark, algorithms) are set. 6 | - ‘data.py’: called to generate the data 7 | - ‘AGMCA.py’: algorithms AMCA, GMCA, rAMCA, and rGMCA 8 | - ‘BetaD_ICA.py’: minimization of the beta-divergence (estimation of S updated the 14/06/16). 9 | - ‘FunBetaD.py’: functions called when minimizing the beta-divergence, used by ‘BetaD_ICA.py’ 10 | - ‘rpcaAlgo.py’: combination PCP+GMCA 11 | - ‘errors.py’: to compute the errors made on the estimation of the mixing matrix (the package munkres is needed). 12 | 13 | The references to the corresponding articles or previous implementations of these algorithms are presented directly in the python files. 14 | 15 | 16 | By running the file ‘main.py’ provided, a comparison (for 1run) of these different algorithms is performed, for varying percentage of corrupted samples (9 different percentages), in the presence of 8 sources and 16 measurements of 4096 samples. The results are displayed (but not saved). 17 | 18 | First version: 10/06/16. 19 | Second Version 14/06/16. (Estimation of S for the minimization of the beta-divergence updated). 20 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/data.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | Building of the components, whose parameters are set in the file paremeters. 4 | """ 5 | #Import files" 6 | from parameters import* 7 | import numpy as np 8 | import scipy as sp 9 | from scipy.fftpack import idct,dct 10 | from scipy import stats 11 | 12 | ################################################################################################################################################################################################################################# 13 | 14 | def sources(): 15 | ''' 16 | Creation of the sources, exactly sparse in DCT. 17 | Output: a n*t matrix, sparse in DCT. 18 | ''' 19 | S=np.zeros((dS['n'],dS['t'])) 20 | S=np.array(sp.stats.bernoulli.rvs(dS['pS'],size=( dS['n'],dS['t']))) 21 | S[S>0]=1 22 | S=S*np.random.randn( dS['n'],dS['t'])*dS['gS'] 23 | S=idct(S, type=2, norm='ortho',axis=1) 24 | return S 25 | 26 | 27 | ################################################################################################################################################################################################################################# 28 | def gaussianNoise(): 29 | ''' 30 | For the Gaussian noise. 31 | Output: a m*t matrix, with i.i.d normal entries 32 | ''' 33 | N=np.random.randn( dS['m'],dS['t'])*dS['gN'] 34 | return N 35 | 36 | 37 | ################################################################################################################################################################################################################################# 38 | def outliers() : 39 | '''Creation of the outliers matrix, O. 40 | A total of dS['nbCol'] columns of O are entirely corrupted, with Gaussian active entries. 41 | Output: a m*t matrix. 42 | ''' 43 | O=np.zeros((dS['m'],dS['t'])) 44 | while np.sum(O[0,:]>0)0]=1 47 | O=O* np.random.randn( dS['m'],dS['t']) 48 | return O 49 | ################################################################################################################################################################################################################################# 50 | def mixingMatrix(): 51 | ''' 52 | Create the mixing matrix. 53 | First a m*n matrix, with i.i.d. entries drawn from the normal law is generated. 54 | Then the columns of A are normalized. 55 | Output: a m by n matrix. 56 | ''' 57 | 58 | A=np.random.randn(dS['m'], dS['n']) 59 | A/=np.linalg.norm(A, axis=0) 60 | 61 | return A 62 | 63 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/CHANGELOG: -------------------------------------------------------------------------------- 1 | 2 | --------------------------------------------------------------------------- 3 | 4 | 1.0.5.3 (2 August, 2009) 5 | 6 | - Fixed documentation of print_matrix() in module docs. 7 | 8 | --------------------------------------------------------------------------- 9 | 1.0.5.2 (30 June, 2008): 10 | 11 | - Incorporated some suggestions optimizations from Mark Summerfield 12 | (mark /at/ qtrac.eu) 13 | - Munkres.make_cost_matrix() is now deprecated, in favor of a module-level 14 | function. 15 | - The module now provides a print_matrix() convenience function. 16 | - Fixed some bugs related to the padding of non-square matrics. 17 | 18 | --------------------------------------------------------------------------- 19 | 1.0.5.1 (26 June, 2008): 20 | 21 | - Some minor doc changes. 22 | 23 | --------------------------------------------------------------------------- 24 | 1.0.5 (26 June, 2008): 25 | 26 | - Now handles non-square cost matrices by padding them with zeros. 27 | - Converted Epydocs to use reStructuredText. 28 | 29 | --------------------------------------------------------------------------- 30 | 1.0.4 (13 June, 2008) 31 | 32 | - Minor bug fix in main (tester) program in munkres.py 33 | 34 | --------------------------------------------------------------------------- 35 | 1.0.3 (16 March, 2008) 36 | 37 | - Minor change to prevent shadowing of built-in min() function. Thanks to 38 | Nelson Castillo (nelson /at/ emqbit.com) for pointing it out. 39 | 40 | --------------------------------------------------------------------------- 41 | 1.0.2 (21 February, 2008) 42 | 43 | - Fixed an overindexing bug reported by Chris Willmore (willmc rpi.edu) 44 | 45 | --------------------------------------------------------------------------- 46 | 1.0.1 (16 February, 2008) 47 | 48 | - Documentation now processed by Epydoc. 49 | 50 | --------------------------------------------------------------------------- 51 | 1.0 (January, 2008) 52 | 53 | - Initial release. 54 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/tr_rgmca/munkres/LICENSE -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/tr_rgmca/munkres/__init__.pyc -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/munkres.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/bss/tr_rgmca/munkres/munkres.pyc -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/setup.cfg: -------------------------------------------------------------------------------- 1 | # $Id: 79a7f3922991f85a694f4c57567ad52186b5cf9a $ 2 | 3 | [sdist] 4 | formats: gztar, zip 5 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/munkres/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Distutils setup script for Munkres 4 | # 5 | # $Id: 4648a5304b06dbfc6ffc7df8d413fa621a32c5aa $ 6 | # --------------------------------------------------------------------------- 7 | 8 | from distutils.core import setup 9 | import re 10 | import os 11 | import sys 12 | import imp 13 | 14 | # Load the data. 15 | 16 | here = os.path.dirname(os.path.abspath(sys.argv[0])) 17 | sys.path = [here] + sys.path 18 | mf = os.path.join(here, 'munkres.py') 19 | munkres = imp.load_module('munkres', open(mf), mf, 20 | ('__init__.py', 'r', imp.PY_SOURCE)) 21 | long_description = munkres.__doc__ 22 | version = str(munkres.__version__) 23 | (author, email) = re.match('^(.*),\s*(.*)$', munkres.__author__).groups() 24 | url = munkres.__url__ 25 | license = munkres.__license__ 26 | 27 | # Run setup 28 | 29 | setup( 30 | name="munkres", 31 | version=version, 32 | description="munkres algorithm for the Assignment Problem", 33 | long_description=long_description, 34 | url=url, 35 | license=license, 36 | author=author, 37 | author_email=email, 38 | py_modules=["munkres"], 39 | classifiers = [ 40 | 'Intended Audience :: Developers', 41 | 'Intended Audience :: Science/Research', 42 | 'License :: OSI Approved :: BSD License', 43 | 'Operating System :: OS Independent', 44 | 'Programming Language :: Python', 45 | 'Topic :: Scientific/Engineering :: Mathematics', 46 | 'Topic :: Software Development :: Libraries :: Python Modules' 47 | ] 48 | ) 49 | -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/parameters.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | """ 3 | File building the dictionaries, containing the parameters 4 | """ 5 | import numpy as np 6 | 7 | """Data parameters""" 8 | data_setting={} 9 | '''dimensions''' 10 | data_setting['m'] =6 #Number of observations 11 | data_setting['n'] =6 #Number of sources 12 | data_setting['t'] =4096 # Number of Samples 13 | '''Sources''' 14 | data_setting['pS'] =0.05 #Activation parameter of the Bernoulli-Gaussian law 15 | data_setting['gS'] = 100. #Standard deviation of the Gaussian law 16 | 17 | '''Gaussian Noise''' 18 | data_setting['gN'] =50. # SNR in dB 19 | 20 | '''Outliers''' 21 | data_setting['nbCol']=0.1*data_setting['t'] #Number of corrupted columns 22 | data_setting['gO']=-10. #Signal to Outliers ratio in dB 23 | 24 | dS=data_setting 25 | 26 | 27 | 28 | 29 | """Algorithms Parameters""" 30 | algo_setting={}; 31 | 32 | algo_setting['iteMaxXMCA']=300 #Number of iterations for GMCA, AMCA or MCA 33 | algo_setting['iteMax']=10000 #(Maximal) Number of Iterations for iterative processes 34 | algo_setting['Rew']=4 #Number of reweighting loops 35 | algo_setting['kSMax']=3. # Thresholding of the sources with kSMax-mad 36 | algo_setting['kOMax']=3. #Thresholding of the outliers with kOMax-mad 37 | 38 | aS=algo_setting 39 | 40 | 41 | """Simulations Parameters""" 42 | param_setting={} 43 | param_setting['nbreParam']= 3# Number of parameters 44 | param_setting['param']=np.array([[6,20,60]]) # Varying parameters 45 | param_setting['nbreIter']=1 #Number of runs 46 | param_setting['nameFile']="mVar" #Prefix of the name of the file to be saved 47 | 48 | pS=param_setting -------------------------------------------------------------------------------- /pyGMCA/bss/tr_rgmca/readMe.txt: -------------------------------------------------------------------------------- 1 | This file contains a python implementation of some algorithms used in the numerical experiments section in the report ‘Blind Source Separation with outliers in transformed domains’, C.Chenot and J.Bobin, namely: GMCA, tr-rGMCA, MCA, and Outlier Pursuit. 2 | 3 | The files are organized as follows: 4 | - the file ‘main.py’ in which the benchmark (data generation, calls of the algorithms, plot of the results) is performed. 5 | - ‘parameters.py’: in which the parameters (for the data generation, benchmark, algorithms) are set. 6 | - ‘data.py’: called to generate the data 7 | - ‘XMCA.py’: algorithms AMCA/GMCA (Sparsity and Adaptivity for the Blind Separation of Partially Correlated Sources;J.Bobin et al), MCA (Simultaneous cartoon and texture image inpainting using morphological component analysis (MCA); M.Elad et al.)and tr-rGMCA 8 | - ‘outliersPursuit.py’: Outliers Pursuit (Robust PCA via Outlier Pursuit; H.Xu et al) 9 | - ‘errors.py’: to compute the errors made on the estimation of the mixing matrix (the package munkres is needed). 10 | 11 | The references to the corresponding articles or previous implementations of these algorithms are presented directly in the python files. 12 | 13 | 14 | By running the file ‘main.py’ provided, a comparison (for 1run) of these different algorithms is performed, for varying number of observations, sources sparsely represented in DCT and outliers in the direct domain. -------------------------------------------------------------------------------- /pyGMCA/common/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/common/munkres/CHANGELOG: -------------------------------------------------------------------------------- 1 | 2 | --------------------------------------------------------------------------- 3 | 4 | 1.0.5.3 (2 August, 2009) 5 | 6 | - Fixed documentation of print_matrix() in module docs. 7 | 8 | --------------------------------------------------------------------------- 9 | 1.0.5.2 (30 June, 2008): 10 | 11 | - Incorporated some suggestions optimizations from Mark Summerfield 12 | (mark /at/ qtrac.eu) 13 | - Munkres.make_cost_matrix() is now deprecated, in favor of a module-level 14 | function. 15 | - The module now provides a print_matrix() convenience function. 16 | - Fixed some bugs related to the padding of non-square matrics. 17 | 18 | --------------------------------------------------------------------------- 19 | 1.0.5.1 (26 June, 2008): 20 | 21 | - Some minor doc changes. 22 | 23 | --------------------------------------------------------------------------- 24 | 1.0.5 (26 June, 2008): 25 | 26 | - Now handles non-square cost matrices by padding them with zeros. 27 | - Converted Epydocs to use reStructuredText. 28 | 29 | --------------------------------------------------------------------------- 30 | 1.0.4 (13 June, 2008) 31 | 32 | - Minor bug fix in main (tester) program in munkres.py 33 | 34 | --------------------------------------------------------------------------- 35 | 1.0.3 (16 March, 2008) 36 | 37 | - Minor change to prevent shadowing of built-in min() function. Thanks to 38 | Nelson Castillo (nelson /at/ emqbit.com) for pointing it out. 39 | 40 | --------------------------------------------------------------------------- 41 | 1.0.2 (21 February, 2008) 42 | 43 | - Fixed an overindexing bug reported by Chris Willmore (willmc rpi.edu) 44 | 45 | --------------------------------------------------------------------------- 46 | 1.0.1 (16 February, 2008) 47 | 48 | - Documentation now processed by Epydoc. 49 | 50 | --------------------------------------------------------------------------- 51 | 1.0 (January, 2008) 52 | 53 | - Initial release. 54 | -------------------------------------------------------------------------------- /pyGMCA/common/munkres/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/munkres/LICENSE -------------------------------------------------------------------------------- /pyGMCA/common/munkres/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /pyGMCA/common/munkres/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/munkres/__init__.pyc -------------------------------------------------------------------------------- /pyGMCA/common/munkres/munkres.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/munkres/munkres.pyc -------------------------------------------------------------------------------- /pyGMCA/common/munkres/setup.cfg: -------------------------------------------------------------------------------- 1 | # $Id: 79a7f3922991f85a694f4c57567ad52186b5cf9a $ 2 | 3 | [sdist] 4 | formats: gztar, zip 5 | -------------------------------------------------------------------------------- /pyGMCA/common/munkres/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Distutils setup script for Munkres 4 | # 5 | # $Id: 4648a5304b06dbfc6ffc7df8d413fa621a32c5aa $ 6 | # --------------------------------------------------------------------------- 7 | 8 | from distutils.core import setup 9 | import re 10 | import os 11 | import sys 12 | import imp 13 | 14 | # Load the data. 15 | 16 | here = os.path.dirname(os.path.abspath(sys.argv[0])) 17 | sys.path = [here] + sys.path 18 | mf = os.path.join(here, 'munkres.py') 19 | munkres = imp.load_module('munkres', open(mf), mf, 20 | ('__init__.py', 'r', imp.PY_SOURCE)) 21 | long_description = munkres.__doc__ 22 | version = str(munkres.__version__) 23 | (author, email) = re.match('^(.*),\s*(.*)$', munkres.__author__).groups() 24 | url = munkres.__url__ 25 | license = munkres.__license__ 26 | 27 | # Run setup 28 | 29 | setup( 30 | name="munkres", 31 | version=version, 32 | description="munkres algorithm for the Assignment Problem", 33 | long_description=long_description, 34 | url=url, 35 | license=license, 36 | author=author, 37 | author_email=email, 38 | py_modules=["munkres"], 39 | classifiers = [ 40 | 'Intended Audience :: Developers', 41 | 'Intended Audience :: Science/Research', 42 | 'License :: OSI Approved :: BSD License', 43 | 'Operating System :: OS Independent', 44 | 'Programming Language :: Python', 45 | 'Topic :: Scientific/Engineering :: Mathematics', 46 | 'Topic :: Software Development :: Libraries :: Python Modules' 47 | ] 48 | ) 49 | -------------------------------------------------------------------------------- /pyGMCA/common/prox/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/prox/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/common/prox/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/common/wavelets/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/wavelets/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/common/wavelets/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # r""" 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/common/wavelets/pyStarlet.py: -------------------------------------------------------------------------------- 1 | 2 | import sparse2d as sp2 3 | import numpy as np 4 | 5 | # pyStarlet 6 | 7 | def forward(X,h = [0.0625,0.25,0.375,0.25,0.0625],J = 1): 8 | 9 | nX = np.shape(X) 10 | Lh = np.size(h) 11 | 12 | W = sp2.Starlet2D(nX[1],nX[2],nX[0],J,Lh).forward_omp(np.real(X),np.array(h)) 13 | 14 | return W 15 | 16 | 17 | def backward(W,h = [0.0625,0.25,0.375,0.25,0.0625]): 18 | 19 | nX = np.shape(W) 20 | Lh = np.size(h) 21 | 22 | rec = sp2.Starlet2D(nX[1],nX[2],nX[0],nX[3]-1,Lh).backward_omp(np.real(W)) 23 | 24 | return rec 25 | 26 | def forward1d(X,h = [0.0625,0.25,0.375,0.25,0.0625],J = 1): 27 | 28 | nX = np.shape(X) 29 | Lh = np.size(h) 30 | 31 | W = sp2.Starlet2D(nX[1],1,nX[0],J,Lh).forward1d_omp(np.real(X),np.array(h)) 32 | 33 | normFact = np.array([ 0.72358037, 0.28547571, 0.17796025, 0.12221233, 0.08578265, 34 | 0.06062301, 0.04293804, 0.0302886 , 0.02141538, 0.01511499, 35 | 0.01055062, 0.00739429, 0.00522072, 0.00372874, 0.00252544, 36 | 0.00280893]) 37 | 38 | for ii in range(np.shape(W)[2]-1): # Warning: the coarse scale is not normalized, tested 39 | W[:,:,ii] = W[:,:,ii]/normFact[ii] 40 | 41 | return W 42 | 43 | def backward1d(W,h = [0.0625,0.25,0.375,0.25,0.0625]): 44 | 45 | normFact = np.array([ 0.72358037, 0.28547571, 0.17796025, 0.12221233, 0.08578265, 46 | 0.06062301, 0.04293804, 0.0302886 , 0.02141538, 0.01511499, 47 | 0.01055062, 0.00739429, 0.00522072, 0.00372874, 0.00252544, 48 | 0.00280893]) 49 | 50 | for ii in range(np.shape(W)[2]-1): # Warning: the coarse scale is not denormalized, tested 51 | W[:,:,ii] = W[:,:,ii]*normFact[ii] 52 | 53 | rec = np.sum(W,axis=2) 54 | 55 | return rec -------------------------------------------------------------------------------- /pyGMCA/common/wavelets/sparse2d.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/common/wavelets/sparse2d.so -------------------------------------------------------------------------------- /pyGMCA/data/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/data/barbara256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/data/barbara256.png -------------------------------------------------------------------------------- /pyGMCA/data/boat256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/data/boat256.png -------------------------------------------------------------------------------- /pyGMCA/data/lena256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/data/lena256.png -------------------------------------------------------------------------------- /pyGMCA/data/peppers256.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/data/peppers256.png -------------------------------------------------------------------------------- /pyGMCA/scripts/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/scripts/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/scripts/bgmca/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/scripts/bgmca/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/scripts/gmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/scripts/hypgmca/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/scripts/hypgmca/.DS_Store -------------------------------------------------------------------------------- /pyGMCA/scripts/hypgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /pyGMCA/scripts/hypgmca/data/Sources.fits: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/scripts/hypgmca/data/Sources.fits -------------------------------------------------------------------------------- /pyGMCA/scripts/hypgmca/data/Spectra.fits: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/pyGMCA/scripts/hypgmca/data/Spectra.fits -------------------------------------------------------------------------------- /pyGMCA/scripts/ngmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | 43 | from pyGMCA.bss.ngmca import framework 44 | from pyGMCA.bss.ngmca import standard 45 | from pyGMCA.bss.ngmca import updaters 46 | -------------------------------------------------------------------------------- /pyGMCA/scripts/ngmca/benchmarks/bench_db_basic.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | from pyGMCA.bss.ngmca import base as bss 3 | 4 | # settings which are passed to the data_generator 5 | # exactly one tuple is allowed between variables data_settings and 6 | # algorithm_settings (below). This tuple contains the values on which to 7 | # perform the benchmark (bench variable) 8 | data_settings = {} 9 | data_settings['rows'] = 100 10 | data_settings['rank'] = 10 11 | data_settings['columns'] = 200 12 | data_settings['dB'] = (10, 20) 13 | data_settings['bernoulli_S'] = 0.08 14 | data_settings['alpha_S'] = 1 15 | 16 | 17 | # settings which are passed to all the algorithms 18 | # exactly one tuple is allowed between variables data_settings and 19 | # algorithm_settings (below). This tuple contains the values on which to 20 | # perform the benchmark 21 | algorithm_settings = {"number_of_iterations": 10} 22 | 23 | # dictionary of algorithms to be used for the benchmark 24 | algorithms = {"nGMCA": bss.algos.Ngmca()} 25 | 26 | # settings for the processing of the benchmark, including; 27 | # - the number of repetitions for each point of the bench variable. 28 | # - the criteria to be saved (all the criteria must be computed by 29 | # the bss.tools.evaluatuation function, to add a criterion, modify 30 | # this function) 31 | # - data_generator: the function which creates the data 32 | # - display: if the field is present, results will be displayed during the 33 | # computation. It can take arguments for the display function. 34 | # - additional_inputs: function which returns a dictionary which will be 35 | # appended to the parameters. This can be useful for providing data 36 | # dependant settings, or more complex input parameters. 37 | processing_settings = {"number_of_repetitions": 10, 38 | "criteria": ["SDR_S", "SIR_S", "SNR_S", "SAR_S", 39 | "SDR_A", "SIR_A", "SNR_A", "SAR_A"], 40 | "data_generator": bss.tools.create_sparse_data, 41 | "display": {}} 42 | -------------------------------------------------------------------------------- /pyGMCA/scripts/ngmca/benchmarks/bench_lambda.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | import pyGMCA.bss.ngmca.base as bss 3 | import numpy as np 4 | 5 | 6 | # settings which are passed to the data_generator 7 | # exactly one tuple is allowed between variables data_settings and 8 | # algorithm_settings (below). This tuple contains the values on which to 9 | # perform the benchmark (bench variable) 10 | data_settings = {'rows': 24, 11 | 'rank': 12, 12 | 'dB': 20, 13 | 'S_tau_mad': (0, 0.5, 1, 2, 3)} 14 | 15 | # settings which are passed to all the algorithms 16 | # exactly one tuple is allowed between variables data_settings and 17 | # algorithm_settings (below). This tuple contains the values on which to 18 | # perform the benchmark 19 | algorithm_settings = {"maximum_iteration": 200} 20 | 21 | # dictionary of algorithms to be used for the benchmark 22 | algorithms = {"nGMCA": bss.algos.Ngmca(), 23 | "nGMCA_framework": bss.algos.Framework({ 24 | 'A_updater': bss.algos.SparseUpdater(tau_mad=0)})} 25 | 26 | 27 | def provide_tau_mad(data_settings, reference): 28 | # set up tau_mad for different algoriths 29 | tau_mad = data_settings["S_tau_mad"] 30 | from pyGMCA import bss # not convenient, but works 31 | return {'S_updater': bss.algos.SparseUpdater(tau_mad=tau_mad), 32 | 'S_parameters': {"tau_mad":tau_mad}} 33 | 34 | # settings for the processing of the benchmark, including; 35 | # - the number of repetitions for each point of the bench variable. 36 | # - the criteria to be saved (all the criteria must be computed by 37 | # the bss.tools.evaluatuation function, to add a criterion, modify 38 | # this function) 39 | # - data_generator: the function which creates the data 40 | # - display: if the field is present, results will be displayed during the 41 | # computation. It can take arguments for the display function. 42 | # - additional_inputs: function which returns a dictionary which will be 43 | # appended to the parameters. This can be useful for providing data 44 | # dependant settings, or more complex input parameters. 45 | processing_settings = {"number_of_repetitions": 12, 46 | "criteria": ["SDR_S", "SIR_S", "SNR_S", "SAR_S", 47 | "SDR_A", "SIR_A", "SNR_A", "SAR_A"], 48 | "data_generator": bss.tools.create_realistic_nmr_mixtures, 49 | "additional_inputs": provide_tau_mad, 50 | "display": {}} 51 | -------------------------------------------------------------------------------- /pyGMCA/scripts/ngmca/example_bench.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | from pyGMCA.bss.ngmca.core.benchmark import Benchmark 4 | 5 | 6 | # load the provided configuration file 7 | #bench = Benchmark("benchmarks/bench_lambda.py") 8 | bench = Benchmark("pyGMCA/scripts/ngmca/benchmarks/bench_db_basic.py") 9 | 10 | # compute the benchmark and save it in the "benchmarks" (relative) folder 11 | bench.run("benchmarks") 12 | 13 | 14 | 15 | 16 | # if the benchmark is already computed and saved, 17 | # it is possible to reload it by providing the relative path to the 18 | # file. 19 | from pyGMCA.bss.ngmca.core.benchmark import Benchmark 20 | #bench = Benchmark("benchmarks/bench_dB_P2MC10_10nov.14_2200_172631.bch") 21 | bench = Benchmark("pyGMCA/scripts/ngmca/benchmarks/bench_S_tau_mad_P5MC12_04déc14_1042_820818.bch") 22 | 23 | # one can then display it with any display settings 24 | bench.display(plottype="mean-std") 25 | -------------------------------------------------------------------------------- /pyGMCA/scripts/ngmca/example_fb.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | import numpy as np 4 | import matplotlib.pyplot as plt 5 | from pyGMCA.bss.ngmca import proximal 6 | 7 | 8 | # this script shows how to use the Forward backward algorithm 9 | # this algorithms solves argmin f + lambda g 10 | # with f differentiable and g proximable 11 | 12 | # create data 13 | A = np.array([[1, 2, 3], [5, 4, 3]]) 14 | Y = np.array([[0.5, 0.3, 0.3, 0.4], 15 | [0.07, 0.8, 0.5, 0.6]]) 16 | x0 = np.zeros([3, 4]) 17 | H = A.T.dot(A) 18 | mu = 0.2 19 | AtY = A.T.dot(Y) 20 | 21 | # set up the gradient function of f 22 | def grad(x): 23 | return H.dot(x) - AtY 24 | 25 | # set up the cost function (so as to record its value at each iteration) 26 | def cost(data): 27 | return 0.5 * np.linalg.norm(Y - A.dot(data['x']), 'fro')**2 +\ 28 | mu * np.linalg.norm(data['x'].flatten(), 1) 29 | 30 | # set up the display function, used to display the results during the iterations 31 | def display(data): 32 | plt.plot(data['recording']['cost']) 33 | 34 | 35 | parameters = {} 36 | # set the arguments for the algorithm a list of the necessary and optional 37 | # arguments is available in the docstrings 38 | # gradient function of f 39 | parameters['gradient'] = grad 40 | # proximal operator of g 41 | parameters['proximal'] = proximal.operators.nonnegative_soft_thresholding 42 | parameters['lambda'] = mu 43 | parameters['lipschitz_constant'] = np.linalg.norm(H, 2) 44 | parameters['maximum_iteration'] = 50 45 | parameters['initialization'] = x0 46 | # register the cost function to be recorded 47 | parameters['recording_functions'] = {'cost': cost} 48 | # register the cost function to be recorded 49 | parameters['display_function'] = display 50 | 51 | # create the algorithm instance one can provide the parameters 52 | # at this moment or when calling the run function. 53 | FB = proximal.algorithms.ForwardBackward() 54 | # Launch the algorithm with the parameters. Other parameters can be passed 55 | # independently 56 | res = FB.run(parameters, initialization=x0, verbose=1) 57 | -------------------------------------------------------------------------------- /pyGMCA/scripts/rgmca/__init__.py: -------------------------------------------------------------------------------- 1 | # # -\*- coding: utf-8 -\*- 2 | # 3 | # """ 4 | # __init__.py - This file is part of pygmca. 5 | # The pygmca package aims at performing non-negative matrix factorization. 6 | # Copyright 2014 CEA 7 | # Contributor : J.Bobin, C.Chenot, J.Rapin 8 | # Created on September 30, 2014, last modified on November 28, 2017 9 | # 10 | # This software is governed by the CeCILL license under French law and 11 | # abiding by the rules of distribution of free software. You can use, 12 | # modify and/ or redistribute the software under the terms of the CeCILL 13 | # license as circulated by CEA, CNRS and INRIA at the following URL 14 | # "http://www.cecill.info". 15 | # 16 | # As a counterpart to the access to the source code and rights to copy, 17 | # modify and redistribute granted by the license, users are provided only 18 | # with a limited warranty and the software's author, the holder of the 19 | # economic rights, and the successive licensors have only limited 20 | # liability. 21 | # 22 | # In this respect, the user's attention is drawn to the risks associated 23 | # with loading, using, modifying and/or developing or reproducing the 24 | # software by the user in light of its specific status of free software, 25 | # that may mean that it is complicated to manipulate, and that also 26 | # therefore means that it is reserved for developers and experienced 27 | # professionals having in-depth computer knowledge. Users are therefore 28 | # encouraged to load and test the software's suitability as regards their 29 | # requirements in conditions enabling the security of their systems and/or 30 | # data to be ensured and, more generally, to use and operate it in the 31 | # same conditions as regards security. 32 | # 33 | # The fact that you are presently reading this means that you have had 34 | # knowledge of the CeCILL license and that you accept its terms. 35 | # """ 36 | # 37 | # __version__ = "2.0" 38 | # __author__ = "Jerome Bobin, Cecile Chenot, Jeremy Rapin" 39 | # __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | # __copyright__ = "(c) 2017 CEA" 41 | # __license__ = "CeCill" 42 | -------------------------------------------------------------------------------- /redwave_toolbox/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | r""" 4 | __init__.py - This file is part of pygmca. 5 | The pygmca package aims at performing non-negative matrix factorization. 6 | Copyright 2014 CEA 7 | Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | Created on September 30, 2014, last modified on December 14, 2014 9 | 10 | This software is governed by the CeCILL license under French law and 11 | abiding by the rules of distribution of free software. You can use, 12 | modify and/ or redistribute the software under the terms of the CeCILL 13 | license as circulated by CEA, CNRS and INRIA at the following URL 14 | "http://www.cecill.info". 15 | 16 | As a counterpart to the access to the source code and rights to copy, 17 | modify and redistribute granted by the license, users are provided only 18 | with a limited warranty and the software's author, the holder of the 19 | economic rights, and the successive licensors have only limited 20 | liability. 21 | 22 | In this respect, the user's attention is drawn to the risks associated 23 | with loading, using, modifying and/or developing or reproducing the 24 | software by the user in light of its specific status of free software, 25 | that may mean that it is complicated to manipulate, and that also 26 | therefore means that it is reserved for developers and experienced 27 | professionals having in-depth computer knowledge. Users are therefore 28 | encouraged to load and test the software's suitability as regards their 29 | requirements in conditions enabling the security of their systems and/or 30 | data to be ensured and, more generally, to use and operate it in the 31 | same conditions as regards security. 32 | 33 | The fact that you are presently reading this means that you have had 34 | knowledge of the CeCILL license and that you accept its terms. 35 | """ 36 | 37 | __version__ = "1.0" 38 | __author__ = "Jeremy Rapin" 39 | __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | __copyright__ = "(c) 2014 CEA" 41 | __license__ = "CeCill" 42 | 43 | 44 | -------------------------------------------------------------------------------- /redwave_toolbox/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/__init__.pyc -------------------------------------------------------------------------------- /redwave_toolbox/__pycache__/__init__.cpython-34.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/__pycache__/__init__.cpython-34.pyc -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | cmake_minimum_required(VERSION 2.8) 2 | 3 | include(ExternalProject) 4 | include(FindPkgConfig) 5 | 6 | # Adding customized cmake module 7 | list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules/") 8 | 9 | project(pyredwave) 10 | 11 | # Find required packages 12 | find_package(Boost REQUIRED COMPONENTS python) 13 | find_package(PythonInterp REQUIRED) 14 | find_package(PythonLibsNew REQUIRED) 15 | 16 | #set(BOOST_ROOT /Users/jbobin/Downloads/boost_1_57_0) 17 | set(Boost_INCLUDE_DIR ${BOOST_ROOT}/boost) 18 | set(Boost_LIBRARY_DIR ${BOOST_ROOT}/stage/lib) 19 | 20 | # Downloads and compiles the Boost.NumPy package 21 | # The library and include files are located in the build/extern directory 22 | ExternalProject_Add(BoostNumpy 23 | GIT_REPOSITORY https://github.com/ndarray/Boost.NumPy 24 | CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/extern 25 | -DLIBRARY_TYPE=STATIC 26 | ) 27 | set(BoostNumpy_INCLUDE_DIRS ${CMAKE_BINARY_DIR}/extern/include) 28 | set(BoostNumpy_LIBRARY_DIRS ${CMAKE_BINARY_DIR}/extern/lib) 29 | set(BoostNumpy_LIBRARIES -lboost_numpy) 30 | 31 | 32 | # Define include and library directories 33 | include_directories( 34 | ${PYTHON_INCLUDE_DIRS} 35 | ${Boost_INCLUDE_DIRS} 36 | ${BoostNumpy_INCLUDE_DIRS} 37 | ) 38 | link_directories(${BoostNumpy_LIBRARY_DIRS}) 39 | 40 | 41 | # Compilation flags 42 | set(CMAKE_CXX_FLAGS "-O3 -fomit-frame-pointer -fno-common -fPIC -fopenmp -DRW_PYTHON_INTERFACE -F/Library/Frameworks -arch x86_64") 43 | 44 | 45 | add_library(redwavecxx SHARED pyredwave/cxx/redWaveTools.cpp pyredwave/cxx/redwavecxx.cpp) 46 | add_dependencies(redwavecxx BoostNumpy) 47 | target_link_libraries(redwavecxx ${BoostNumpy_LIBRARIES} ${Boost_LIBRARIES} ${GSL_LIBRARIES} ${PYTHON_LIBRARIES}) 48 | set_target_properties(redwavecxx PROPERTIES PREFIX "") 49 | set_target_properties(redwavecxx PROPERTIES SUFFIX .so) 50 | if(CYGWIN OR MSYS OR MINGW) 51 | # Ensure the output binary is called redwavecxx.pyd on Windows (not redwavecxx.dll) 52 | set_target_properties(redwavecxx PROPERTIES SUFFIX ".pyd") 53 | endif(CYGWIN OR MSYS OR MINGW) 54 | 55 | # Installs the module inside the python package 56 | set(CMAKE_INSTALL_PREFIX ${PROJECT_SOURCE_DIR}) 57 | 58 | install(TARGETS redwavecxx DESTINATION pyredwave) 59 | 60 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | r""" 4 | __init__.py - This file is part of pygmca. 5 | The pygmca package aims at performing non-negative matrix factorization. 6 | Copyright 2014 CEA 7 | Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | Created on December 13, 2014, last modified on December 14, 2014 9 | 10 | This software is governed by the CeCILL license under French law and 11 | abiding by the rules of distribution of free software. You can use, 12 | modify and/ or redistribute the software under the terms of the CeCILL 13 | license as circulated by CEA, CNRS and INRIA at the following URL 14 | "http://www.cecill.info". 15 | 16 | As a counterpart to the access to the source code and rights to copy, 17 | modify and redistribute granted by the license, users are provided only 18 | with a limited warranty and the software's author, the holder of the 19 | economic rights, and the successive licensors have only limited 20 | liability. 21 | 22 | In this respect, the user's attention is drawn to the risks associated 23 | with loading, using, modifying and/or developing or reproducing the 24 | software by the user in light of its specific status of free software, 25 | that may mean that it is complicated to manipulate, and that also 26 | therefore means that it is reserved for developers and experienced 27 | professionals having in-depth computer knowledge. Users are therefore 28 | encouraged to load and test the software's suitability as regards their 29 | requirements in conditions enabling the security of their systems and/or 30 | data to be ensured and, more generally, to use and operate it in the 31 | same conditions as regards security. 32 | 33 | The fact that you are presently reading this means that you have had 34 | knowledge of the CeCILL license and that you accept its terms. 35 | """ 36 | 37 | __version__ = "1.0" 38 | __author__ = "Jeremy Rapin" 39 | __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | __copyright__ = "(c) 2014 CEA" 41 | __license__ = "CeCill" 42 | 43 | # -*- coding: utf-8 -*- 44 | 45 | from pyredwave.redwave import RedWave 46 | from pyredwave.redwave import mad_std 47 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/__init__.pyc: -------------------------------------------------------------------------------- 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| set(CMAKE_INSTALL_PREFIX "/Users/jbobin/Downloads/GMCAlab-python/pygmca/pyredwave") 6 | endif() 7 | string(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") 8 | 9 | # Set the install configuration name. 10 | if(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) 11 | if(BUILD_TYPE) 12 | string(REGEX REPLACE "^[^A-Za-z0-9_]+" "" 13 | CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") 14 | else() 15 | set(CMAKE_INSTALL_CONFIG_NAME "") 16 | endif() 17 | message(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") 18 | endif() 19 | 20 | # Set the component getting installed. 21 | if(NOT CMAKE_INSTALL_COMPONENT) 22 | if(COMPONENT) 23 | message(STATUS "Install component: \"${COMPONENT}\"") 24 | set(CMAKE_INSTALL_COMPONENT "${COMPONENT}") 25 | else() 26 | set(CMAKE_INSTALL_COMPONENT) 27 | endif() 28 | endif() 29 | 30 | if(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified") 31 | file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/pyredwave" TYPE SHARED_LIBRARY FILES "/Users/jbobin/Downloads/GMCAlab-python/pygmca/pyredwave/build/redwavecxx.so") 32 | if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/pyredwave/redwavecxx.so" AND 33 | NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/pyredwave/redwavecxx.so") 34 | execute_process(COMMAND "/opt/local/bin/install_name_tool" 35 | -id "redwavecxx.so" 36 | "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/pyredwave/redwavecxx.so") 37 | execute_process(COMMAND /opt/local/bin/install_name_tool 38 | -delete_rpath "/Users/jbobin/Downloads/GMCAlab-python/pygmca/pyredwave/build/extern/lib" 39 | "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/pyredwave/redwavecxx.so") 40 | if(CMAKE_INSTALL_DO_STRIP) 41 | execute_process(COMMAND "/opt/local/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/pyredwave/redwavecxx.so") 42 | endif() 43 | endif() 44 | endif() 45 | 46 | if(CMAKE_INSTALL_COMPONENT) 47 | set(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt") 48 | else() 49 | set(CMAKE_INSTALL_MANIFEST "install_manifest.txt") 50 | endif() 51 | 52 | string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT 53 | "${CMAKE_INSTALL_MANIFEST_FILES}") 54 | file(WRITE "/Users/jbobin/Downloads/GMCAlab-python/pygmca/pyredwave/build/${CMAKE_INSTALL_MANIFEST}" 55 | "${CMAKE_INSTALL_MANIFEST_CONTENT}") 56 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/include/boost/numpy.hpp: -------------------------------------------------------------------------------- 1 | // Copyright Jim Bosch 2010-2012. 2 | // Distributed under the Boost Software License, Version 1.0. 3 | // (See accompanying file LICENSE_1_0.txt or copy at 4 | // http://www.boost.org/LICENSE_1_0.txt) 5 | #ifndef BOOST_NUMPY_HPP_INCLUDED 6 | #define BOOST_NUMPY_HPP_INCLUDED 7 | 8 | /** 9 | * @file boost/numpy.hpp 10 | * @brief Main public header file for boost.numpy. 11 | */ 12 | 13 | #include 14 | #include 15 | #include 16 | #include 17 | #include 18 | #include 19 | 20 | namespace boost { 21 | namespace numpy { 22 | 23 | /** 24 | * @brief Initialize the Numpy C-API 25 | * 26 | * This must be called before using anything in boost.numpy; 27 | * It should probably be the first line inside BOOST_PYTHON_MODULE. 28 | * 29 | * @internal This just calls the Numpy C-API functions "import_array()" 30 | * and "import_ufunc()", and then calls 31 | * dtype::register_scalar_converters(). 32 | */ 33 | void initialize(bool register_scalar_converters=true); 34 | 35 | } // namespace boost::numpy 36 | } // namespace boost 37 | 38 | #endif // !BOOST_NUMPY_HPP_INCLUDED 39 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/include/boost/numpy/internal.hpp: -------------------------------------------------------------------------------- 1 | // Copyright Jim Bosch 2010-2012. 2 | // Distributed under the Boost Software License, Version 1.0. 3 | // (See accompanying file LICENSE_1_0.txt or copy at 4 | // http://www.boost.org/LICENSE_1_0.txt) 5 | #ifndef BOOST_NUMPY_INTERNAL_HPP_INCLUDED 6 | #define BOOST_NUMPY_INTERNAL_HPP_INCLUDED 7 | 8 | /** 9 | * @file boost/numpy/internal.hpp 10 | * @brief Internal header file to include the Numpy C-API headers. 11 | * 12 | * This should only be included by source files in the boost.numpy library itself. 13 | */ 14 | 15 | #include 16 | #ifdef BOOST_NUMPY_INTERNAL 17 | #define NO_IMPORT_ARRAY 18 | #define NO_IMPORT_UFUNC 19 | #else 20 | #ifndef BOOST_NUMPY_INTERNAL_MAIN 21 | ERROR_internal_hpp_is_for_internal_use_only 22 | #endif 23 | #endif 24 | #define PY_ARRAY_UNIQUE_SYMBOL BOOST_NUMPY_ARRAY_API 25 | #define PY_UFUNC_UNIQUE_SYMBOL BOOST_UFUNC_ARRAY_API 26 | #include 27 | #include 28 | #include 29 | 30 | #define NUMPY_OBJECT_MANAGER_TRAITS_IMPL(pytype,manager) \ 31 | PyTypeObject const * object_manager_traits::get_pytype() { return &pytype; } 32 | 33 | #endif // !BOOST_NUMPY_INTERNAL_HPP_INCLUDED 34 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/include/boost/numpy/matrix.hpp: -------------------------------------------------------------------------------- 1 | // Copyright Jim Bosch 2010-2012. 2 | // Distributed under the Boost Software License, Version 1.0. 3 | // (See accompanying file LICENSE_1_0.txt or copy at 4 | // http://www.boost.org/LICENSE_1_0.txt) 5 | #ifndef BOOST_NUMPY_MATRIX_HPP_INCLUDED 6 | #define BOOST_NUMPY_MATRIX_HPP_INCLUDED 7 | 8 | /** 9 | * @file boost/numpy/matrix.hpp 10 | * @brief Object manager for numpy.matrix. 11 | */ 12 | 13 | #include 14 | #include 15 | #include 16 | 17 | namespace boost 18 | { 19 | namespace numpy 20 | { 21 | 22 | /** 23 | * @brief A boost.python "object manager" (subclass of object) for numpy.matrix. 24 | * 25 | * @internal numpy.matrix is defined in Python, so object_manager_traits::get_pytype() 26 | * is implemented by importing numpy and getting the "matrix" attribute of the module. 27 | * We then just hope that doesn't get destroyed while we need it, because if we put 28 | * a dynamic python object in a static-allocated boost::python::object or handle<>, 29 | * bad things happen when Python shuts down. I think this solution is safe, but I'd 30 | * love to get that confirmed. 31 | */ 32 | class matrix : public ndarray 33 | { 34 | static python::object construct(object_cref obj, dtype const & dt, bool copy); 35 | static python::object construct(object_cref obj, bool copy); 36 | public: 37 | 38 | BOOST_PYTHON_FORWARD_OBJECT_CONSTRUCTORS(matrix, ndarray); 39 | 40 | /// @brief Equivalent to "numpy.matrix(obj,dt,copy)" in Python. 41 | explicit matrix(python::object const & obj, dtype const & dt, bool copy=true) 42 | : ndarray(python::extract(construct(obj, dt, copy))) {} 43 | 44 | /// @brief Equivalent to "numpy.matrix(obj,copy=copy)" in Python. 45 | explicit matrix(python::object const & obj, bool copy=true) 46 | : ndarray(python::extract(construct(obj, copy))) {} 47 | 48 | /// \brief Return a view of the matrix with the given dtype. 49 | matrix view(dtype const & dt) const; 50 | 51 | /// \brief Copy the scalar (deep for all non-object fields). 52 | matrix copy() const; 53 | 54 | /// \brief Transpose the matrix. 55 | matrix transpose() const; 56 | 57 | }; 58 | 59 | /** 60 | * @brief CallPolicies that causes a function that returns a numpy.ndarray to 61 | * return a numpy.matrix instead. 62 | */ 63 | template 64 | struct as_matrix : Base { 65 | static PyObject * postcall(PyObject *, PyObject * result) { 66 | python::object a = python::object(python::handle<>(result)); 67 | numpy::matrix m(a, false); 68 | Py_INCREF(m.ptr()); 69 | return m.ptr(); 70 | } 71 | }; 72 | 73 | } // namespace boost::numpy 74 | namespace python 75 | { 76 | namespace converter 77 | { 78 | 79 | NUMPY_OBJECT_MANAGER_TRAITS(numpy::matrix); 80 | 81 | } // namespace boost::python::converter 82 | } // namespace boost::python 83 | } // namespace boost 84 | 85 | #endif // !BOOST_NUMPY_MATRIX_HPP_INCLUDED 86 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/include/boost/numpy/numpy_object_mgr_traits.hpp: -------------------------------------------------------------------------------- 1 | // Copyright Jim Bosch 2010-2012. 2 | // Distributed under the Boost Software License, Version 1.0. 3 | // (See accompanying file LICENSE_1_0.txt or copy at 4 | // http://www.boost.org/LICENSE_1_0.txt) 5 | #ifndef BOOST_NUMPY_NUMPY_OBJECT_MGR_TRAITS_HPP_INCLUDED 6 | #define BOOST_NUMPY_NUMPY_OBJECT_MGR_TRAITS_HPP_INCLUDED 7 | 8 | /** 9 | * @file boost/numpy/numpy_object_mgr_traits.hpp 10 | * @brief Macro that specializes object_manager_traits by requiring a 11 | * source-file implementation of get_pytype(). 12 | */ 13 | 14 | #define NUMPY_OBJECT_MANAGER_TRAITS(manager) \ 15 | template <> \ 16 | struct object_manager_traits \ 17 | { \ 18 | BOOST_STATIC_CONSTANT(bool, is_specialized = true); \ 19 | static inline python::detail::new_reference adopt(PyObject* x) \ 20 | { \ 21 | return python::detail::new_reference(python::pytype_check((PyTypeObject*)get_pytype(), x)); \ 22 | } \ 23 | static bool check(PyObject* x) \ 24 | { \ 25 | return ::PyObject_IsInstance(x, (PyObject*)get_pytype()); \ 26 | } \ 27 | static manager* checked_downcast(PyObject* x) \ 28 | { \ 29 | return python::downcast((checked_downcast_impl)(x, (PyTypeObject*)get_pytype())); \ 30 | } \ 31 | static PyTypeObject const * get_pytype(); \ 32 | } 33 | 34 | #endif // !BOOST_NUMPY_NUMPY_OBJECT_MGR_TRAITS_HPP_INCLUDED 35 | 36 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/include/boost/numpy/scalars.hpp: -------------------------------------------------------------------------------- 1 | // Copyright Jim Bosch 2010-2012. 2 | // Distributed under the Boost Software License, Version 1.0. 3 | // (See accompanying file LICENSE_1_0.txt or copy at 4 | // http://www.boost.org/LICENSE_1_0.txt) 5 | #ifndef BOOST_NUMPY_SCALARS_HPP_INCLUDED 6 | #define BOOST_NUMPY_SCALARS_HPP_INCLUDED 7 | 8 | /** 9 | * @file boost/numpy/scalars.hpp 10 | * @brief Object managers for array scalars (currently only numpy.void is implemented). 11 | */ 12 | 13 | #include 14 | #include 15 | #include 16 | 17 | namespace boost 18 | { 19 | namespace numpy 20 | { 21 | 22 | /** 23 | * @brief A boost.python "object manager" (subclass of object) for numpy.void. 24 | * 25 | * @todo This could have a lot more functionality. 26 | */ 27 | class void_ : public python::object 28 | { 29 | static python::detail::new_reference convert(object_cref arg, bool align); 30 | public: 31 | 32 | /** 33 | * @brief Construct a new array scalar with the given size and void dtype. 34 | * 35 | * Data is initialized to zero. One can create a standalone scalar object 36 | * with a certain dtype "dt" with: 37 | * @code 38 | * void_ scalar = void_(dt.get_itemsize()).view(dt); 39 | * @endcode 40 | */ 41 | explicit void_(Py_ssize_t size); 42 | 43 | BOOST_PYTHON_FORWARD_OBJECT_CONSTRUCTORS(void_, object); 44 | 45 | /// @brief Return a view of the scalar with the given dtype. 46 | void_ view(dtype const & dt) const; 47 | 48 | /// @brief Copy the scalar (deep for all non-object fields). 49 | void_ copy() const; 50 | 51 | }; 52 | 53 | } // namespace boost::numpy 54 | 55 | namespace python 56 | { 57 | namespace converter 58 | { 59 | NUMPY_OBJECT_MANAGER_TRAITS(numpy::void_); 60 | } // namespace boost::python::converter 61 | } // namespace boost::python 62 | } // namespace boost 63 | 64 | #endif // !BOOST_NUMPY_SCALARS_HPP_INCLUDED 65 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/extern/lib/libboost_numpy.a: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/build/extern/lib/libboost_numpy.a -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/install_manifest.txt: -------------------------------------------------------------------------------- 1 | /Users/jbobin/Downloads/GMCAlab-python/pygmca/pyredwave/pyredwave/redwavecxx.so -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/lib/pyredwave/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | r""" 4 | __init__.py - This file is part of pygmca. 5 | The pygmca package aims at performing non-negative matrix factorization. 6 | Copyright 2014 CEA 7 | Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | Created on December 13, 2014, last modified on December 14, 2014 9 | 10 | This software is governed by the CeCILL license under French law and 11 | abiding by the rules of distribution of free software. You can use, 12 | modify and/ or redistribute the software under the terms of the CeCILL 13 | license as circulated by CEA, CNRS and INRIA at the following URL 14 | "http://www.cecill.info". 15 | 16 | As a counterpart to the access to the source code and rights to copy, 17 | modify and redistribute granted by the license, users are provided only 18 | with a limited warranty and the software's author, the holder of the 19 | economic rights, and the successive licensors have only limited 20 | liability. 21 | 22 | In this respect, the user's attention is drawn to the risks associated 23 | with loading, using, modifying and/or developing or reproducing the 24 | software by the user in light of its specific status of free software, 25 | that may mean that it is complicated to manipulate, and that also 26 | therefore means that it is reserved for developers and experienced 27 | professionals having in-depth computer knowledge. Users are therefore 28 | encouraged to load and test the software's suitability as regards their 29 | requirements in conditions enabling the security of their systems and/or 30 | data to be ensured and, more generally, to use and operate it in the 31 | same conditions as regards security. 32 | 33 | The fact that you are presently reading this means that you have had 34 | knowledge of the CeCILL license and that you accept its terms. 35 | """ 36 | 37 | __version__ = "1.0" 38 | __author__ = "Jeremy Rapin" 39 | __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | __copyright__ = "(c) 2014 CEA" 41 | __license__ = "CeCill" 42 | 43 | # -*- coding: utf-8 -*- 44 | 45 | from redwave import RedWave, mad_std 46 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/build/redwavecxx.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/build/redwavecxx.so -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/pyredwave/__init__.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | r""" 4 | __init__.py - This file is part of pygmca. 5 | The pygmca package aims at performing non-negative matrix factorization. 6 | Copyright 2014 CEA 7 | Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | Created on December 13, 2014, last modified on December 14, 2014 9 | 10 | This software is governed by the CeCILL license under French law and 11 | abiding by the rules of distribution of free software. You can use, 12 | modify and/ or redistribute the software under the terms of the CeCILL 13 | license as circulated by CEA, CNRS and INRIA at the following URL 14 | "http://www.cecill.info". 15 | 16 | As a counterpart to the access to the source code and rights to copy, 17 | modify and redistribute granted by the license, users are provided only 18 | with a limited warranty and the software's author, the holder of the 19 | economic rights, and the successive licensors have only limited 20 | liability. 21 | 22 | In this respect, the user's attention is drawn to the risks associated 23 | with loading, using, modifying and/or developing or reproducing the 24 | software by the user in light of its specific status of free software, 25 | that may mean that it is complicated to manipulate, and that also 26 | therefore means that it is reserved for developers and experienced 27 | professionals having in-depth computer knowledge. Users are therefore 28 | encouraged to load and test the software's suitability as regards their 29 | requirements in conditions enabling the security of their systems and/or 30 | data to be ensured and, more generally, to use and operate it in the 31 | same conditions as regards security. 32 | 33 | The fact that you are presently reading this means that you have had 34 | knowledge of the CeCILL license and that you accept its terms. 35 | """ 36 | 37 | __version__ = "1.0" 38 | __author__ = "Jeremy Rapin" 39 | __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | __copyright__ = "(c) 2014 CEA" 41 | __license__ = "CeCill" 42 | 43 | # -*- coding: utf-8 -*- 44 | 45 | from redwave import RedWave, mad_std 46 | -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/pyredwave/__init__.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/pyredwave/__init__.pyc -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/pyredwave/__pycache__/redwave.cpython-34.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/pyredwave/__pycache__/redwave.cpython-34.pyc -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/pyredwave/redwave.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/pyredwave/redwave.pyc -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/pyredwave/redwavecxx.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbobin/pyGMCALab/ae44b37b399074abc9a9977231d2e8ef66f7ce8b/redwave_toolbox/pyredwave/pyredwave/redwavecxx.so -------------------------------------------------------------------------------- /redwave_toolbox/pyredwave/setup.py: -------------------------------------------------------------------------------- 1 | # -\*- coding: utf-8 -\*- 2 | 3 | r""" 4 | setup.py - This file is part of pygmca. 5 | The pygmca package aims at performing non-negative matrix factorization. 6 | Copyright 2014 CEA 7 | Contributor : Jérémy Rapin (jeremy.rapin.math@gmail.com) 8 | Created on December 13, 2014, last modified on December 14, 2014 9 | 10 | This software is governed by the CeCILL license under French law and 11 | abiding by the rules of distribution of free software. You can use, 12 | modify and/ or redistribute the software under the terms of the CeCILL 13 | license as circulated by CEA, CNRS and INRIA at the following URL 14 | "http://www.cecill.info". 15 | 16 | As a counterpart to the access to the source code and rights to copy, 17 | modify and redistribute granted by the license, users are provided only 18 | with a limited warranty and the software's author, the holder of the 19 | economic rights, and the successive licensors have only limited 20 | liability. 21 | 22 | In this respect, the user's attention is drawn to the risks associated 23 | with loading, using, modifying and/or developing or reproducing the 24 | software by the user in light of its specific status of free software, 25 | that may mean that it is complicated to manipulate, and that also 26 | therefore means that it is reserved for developers and experienced 27 | professionals having in-depth computer knowledge. Users are therefore 28 | encouraged to load and test the software's suitability as regards their 29 | requirements in conditions enabling the security of their systems and/or 30 | data to be ensured and, more generally, to use and operate it in the 31 | same conditions as regards security. 32 | 33 | The fact that you are presently reading this means that you have had 34 | knowledge of the CeCILL license and that you accept its terms. 35 | """ 36 | 37 | __version__ = "1.0" 38 | __author__ = "Jeremy Rapin" 39 | __url__ = "http://www.cosmostat.org/GMCALab.html" 40 | __copyright__ = "(c) 2014 CEA" 41 | __license__ = "CeCill" 42 | 43 | from distutils.command.build_py import build_py as _build_py 44 | from distutils.core import setup 45 | from subprocess import call 46 | import os 47 | 48 | 49 | class build_py(_build_py): 50 | """Specialized Python source builder.""" 51 | def run(self): 52 | os.environ['CC'] = 'gcc' 53 | os.environ['CXX'] = 'g++' 54 | call(["mkdir", "-p", "build"]) 55 | call(["cmake", "-H.", "-Bbuild"]) 56 | call(["make", "-Cbuild", "install"]) 57 | _build_py.run(self) 58 | 59 | setup(name='pyredwave', 60 | version='1.0', 61 | description='lol', 62 | packages=['pyredwave'], 63 | package_data={'pyredwave': ['pyredwave.so']}, 64 | cmdclass={'build_py': build_py} 65 | ) 66 | -------------------------------------------------------------------------------- /redwave_toolbox/test_func/test_redwave.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | 3 | # so as to build the pyredwave toolbox, 4 | # you need to execute "python setup.py build" 5 | # in the pyredwave folder. 6 | # The compilation requires Boost.Python 7 | # (tested on Mac and Ubuntu, with Python 2.7). 8 | from redwave import RedWave, mad_std 9 | import numpy as np 10 | from scipy import misc 11 | import matplotlib.pyplot as plt 12 | import time 13 | from PyQt4.QtGui import QApplication 14 | from gc import collect 15 | 16 | 17 | # process several slices in parallel (each line of x) 18 | x = np.array([[1.0, 2.0, 3, 4], [3, 4, 3, 4]]) 19 | print("Input matrix:") 20 | print(x) 21 | # parametrize wavelets 22 | wave_filter = "Haar" 23 | number_of_scales = 2 24 | isometric = True 25 | wave_dimensions = 1 26 | wave = RedWave(x, wave_dimensions, wave_filter,number_of_scales, isometric) 27 | wx = wave.forward(x) 28 | print("Output matrix (wavelet performed on dimension 1, on 2 slices):") 29 | print(wx) 30 | x2 = wave.backward(wx) 31 | # in place transformation 32 | wave.transform(x, wx, 1) 33 | # create a wavelet object for inputs of size Lena 34 | print("Wavelet can be performed on any 1 or 2 dimensions.") 35 | # load an image 36 | lena = misc.lena() 37 | # convert it to double 38 | lena = lena.astype("float64") 39 | wave_dimensions = (1, 0) 40 | wave_filter = "Daubechies-4" 41 | wave = RedWave(lena, wave_dimensions, wave_filter, 42 | number_of_scales, isometric) 43 | # convert Lena into wavelets 44 | wlena = wave.forward(lena) 45 | # show Lena in the wavelet domain 46 | plt.imshow(wlena, cmap=plt.cm.gray) 47 | plt.get_current_fig_manager().window.raise_() 48 | QApplication.processEvents() 49 | # Only the first coarse scale is actually used for backward computation 50 | print("Only the first coarse scale is actually used for backward computation.") 51 | wlena = wave.remove_coarse_scales(wlena, inplace=True, 52 | keep_actual_coarse_scale=True) 53 | time.sleep(3) 54 | plt.clf() 55 | collect() 56 | plt.imshow(wlena, cmap=plt.cm.gray) 57 | QApplication.processEvents() 58 | time.sleep(1) 59 | print("In isometric mode, norms are kept (after removing redundant coarse scales):") 60 | print("- norm of Lena: %s." % np.linalg.norm(lena)) 61 | print("- norm of Lena wavelet coefficients: %s." % np.linalg.norm(wlena)) 62 | time.sleep(2) 63 | print("One can also easily get estimate the noise on each scale using ") 64 | print("extract_scale_vals with the mad estimator (or any other).") 65 | scale_mad = wave.extract_scale_vals(wlena, mad_std) 66 | print("Mad estimate on each scale:") 67 | print(scale_mad) 68 | print("From there, one can make a full matrix using make_full_vals.") 69 | # wavelet thresholding 70 | lambdas = 50 * np.ones(wlena.shape) 71 | # do not penalize coarse scales 72 | lambdas = wave.remove_coarse_scales(lambdas, inplace=True, 73 | keep_actual_coarse_scale=False) 74 | smooth_lena = wave.sparse_proximal(lena, lambdas, number_of_iterations=6) 75 | print("This toolbox can also compute the wavelet sparse analysis proximal") 76 | print("operator using the Generalized Forward-Backward algorithm (displayed") 77 | print("results), and the sparse analysis inversion using Chambolle-Pock\nalgorithm.") 78 | plt.clf() 79 | collect() 80 | plt.imshow(smooth_lena, cmap=plt.cm.gray) 81 | QApplication.processEvents() 82 | time.sleep(1) 83 | 84 | --------------------------------------------------------------------------------