Xmipp structure - I2PC/xmipp GitHub Wiki
Introduction
XMIPP software is split in three repositories (XmippCore, XmippViz and Xmipp) plus the repository regarding to the Scipion's plugin (scipion-em-xmipp). All this four repositories are in I2PC gitHub.
- scipion-em-xmipp: It is the Scipion's plugin. Protocol (wrappers), viewers, tests... are there. All Xmipp regarding Scipion is there.
- xmipp: EM-reconstraction methods. Usually wrote in C++.
- xmippCore: Low-level image-processing and EM-images definitions. In addition, metadata_labels, metadata and data are there.
- xmippViz: Basically ShowJ, coordinates viewer and Xmipp Picker. Java code.
We call xmipp-bundle to the folder that contains the four repositories listed above in the following structure.
xmipp-bundle # This is the https://github.com/I2PC/xmipp repository
βββ CHANGELOG.md
βββ LICENSE
βββ README.md
β
βββ xmipp # Main script
βββ xmipp.conf # Config file
β
βββ scripts
βΒ Β βββ (...)
βββ sonar-project.properties
β
βββ src # Sources directory
βΒ Β βββ scipion-em-xmipp # This is the https://github.com/I2PC/scipion-em-xmipp repository
βΒ Β βΒ Β βββ (...)
βΒ Β βββ xmipp
βΒ Β βΒ Β βββ (...)
βΒ Β βββ xmippCore # This is the https://github.com/I2PC/xmippCore repository
βΒ Β βΒ Β βββ (...)
βΒ Β βββ xmippViz # This is the https://github.com/I2PC/xmippViz repository
βΒ Β Β Β βββ (...)
β
βββ build # Self-contained directory with all runnable Xmipp (created during the installation)
Β Β βββ bin # All binaries of Xmipp
Β Β βΒ Β βββ (...)
Β Β βββ bindings # Bindings to other languages
Β Β βΒ Β βββ (...)
Β Β βββ lib # Libraries that some binaries use
Β Β βΒ Β βββ (...)
Β Β βββ pylib # Python modules that some binaries use
Β Β βΒ Β βββ (...)
Β Β βββ v3.20.07 # Installation token containing the version number
Β Β βββ xmipp.bashrc # bash script to set Xmipp env. vars. (run 'source xmipp.basrc')
Β Β βββ xmippEnv.json # Variables to set environ for Xmipp in running time
Β Β βββ xmipp.fish # fish script to set Xmipp env. vars. (run 'fish xmipp.fish')
To get this structure in a certain directory, run
cd certain_directory
git clone https://github.com/I2PC/xmipp xmipp-bundle
cd xmipp-bundle
./xmipp get_devel_sources
Check below a detailed structure of Xmipp. Please, check also the Xmipp API.
xmipp-bundle -> this is the https://github.com/I2PC/xmipp repository <-
β
βββ xmipp # Main script
βββ xmipp.conf # Config file
βββ xmippEnv.json # Temporary compilation environ saving for runtime uses
βββ CHANGELOG.md
βββ LICENSE
βββ README.md
βββ scripts
βΒ Β βββ install_cuda_travis.sh
βΒ Β βββ tar.py
βββ sonar-project.properties
β
βββ src # Main folder containing sources subrepos (scipion-em-xmipp, xmippCore and xmippViz).
β β
βΒ Β βββ scipion-em-xmipp # Repository of the Scipion's plugin -> this is the https://github.com/I2PC/scipion-em-xmipp repository <-
βΒ Β βΒ Β βββ CHANGES.txt
βΒ Β βΒ Β βββ LICENSE
βΒ Β βΒ Β βββ MANIFEST.in
βΒ Β βΒ Β βββ README.md
βΒ Β βΒ Β βββ requirements.txt
βΒ Β βΒ Β βββ scipion_em_xmipp.egg-info
βΒ Β βΒ Β βββ setup.py
βΒ Β βΒ Β βββ sonar-project.properties
βΒ Β βΒ Β βββ xmipp3 # Xmipp plugin for Scipion
βΒ Β βΒ Β βββ base.py
βΒ Β βΒ Β βββ bibtex.py
βΒ Β βΒ Β βββ constants.py
βΒ Β βΒ Β βββ convert
β β β βββ (...)
βΒ Β βΒ Β βββ __init__.py
βΒ Β βΒ Β βββ programs.py
βΒ Β βΒ Β βββ protocols
β β β βββ (...)
βΒ Β βΒ Β βββ protocols.conf
βΒ Β βΒ Β βββ tests
β β β βββ (...)
βΒ Β βΒ Β βββ utils.py
βΒ Β βΒ Β βββ viewers
β β β βββ (...)
βΒ Β βΒ Β βββ wizards.py
βΒ Β βΒ Β βββ xmipp_logo.png
β β
βΒ Β βββ xmipp # Main sources for Xmipp
βΒ Β βΒ Β β
βΒ Β βΒ Β βββ applications
βΒ Β βΒ Β βΒ Β βββ programs # This contains the main fuctions for the Xmipp progrmas
βΒ Β βΒ Β βΒ Β βΒ Β βββ angular_accuracy_pca
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xray_psf_create
βΒ Β βΒ Β βΒ Β βββ scripts # This contains programs coded in non-compiling lenguage (e.g. python)
βΒ Β βΒ Β βΒ Β βΒ Β βββ apropos
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ volume_align
βΒ Β βΒ Β βΒ Β βββ tests # This contains some tests
βΒ Β βΒ Β βΒ Β βββ function_tests
βΒ Β βΒ Β βΒ Β βββ aft_tests.h
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ test_funcs_main.cpp
βΒ Β βΒ Β βββ bin # This is created in compilation time
βΒ Β βΒ Β βΒ Β βββ xmipp_angular_accuracy_pca
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ xmipp_xray_psf_create
βΒ Β βΒ Β βββ bindings # This contains binding for other lenguages
βΒ Β βΒ Β βΒ Β βββ matlab
βΒ Β βΒ Β βΒ Β βΒ Β βββ mirt3D_mexinterp.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xmipp_write.m
βΒ Β βΒ Β βΒ Β βββ python
βΒ Β βΒ Β βΒ Β βββ python_constants.cpp
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ xmipp_base.py
βΒ Β βΒ Β βΒ Β βββ xmipp_conda_envs.py
βΒ Β βΒ Β βΒ Β βββ xmippmodule.cpp
βΒ Β βΒ Β βΒ Β βββ xmippmodule.h
βΒ Β βΒ Β βΒ Β βββ xmippmodule.os
βΒ Β βΒ Β βΒ Β βββ xmipp.py
βΒ Β βΒ Β βββ external
βΒ Β βΒ Β βΒ Β βββ condor
βΒ Β βΒ Β βΒ Β βΒ Β βββ CNLSolver.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ Vector.cpp
βΒ Β βΒ Β βΒ Β βββ delaunay
βΒ Β βΒ Β βΒ Β βΒ Β βββ dcel.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ voronoi.cpp
βΒ Β βΒ Β βΒ Β βββ gtest
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ sh_alignment
βΒ Β βΒ Β βΒ Β βββ frm.cpp
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ swig_frm.py
βΒ Β βΒ Β βββ install # This is created in compilation time
βΒ Β βΒ Β βΒ Β βββ scons-tools
βΒ Β βΒ Β βΒ Β βΒ Β βββ AutoConfig.py
βΒ Β βΒ Β βΒ Β βΒ Β βββ Make.py
βΒ Β βΒ Β βΒ Β βΒ Β βββ __pycache__
βΒ Β βΒ Β βΒ Β βββ xmipp.conf
βΒ Β βΒ Β βΒ Β βββ xmipp.template
βΒ Β βΒ Β βββ lib # This contains the compiled final libraries
βΒ Β βΒ Β βΒ Β βββ libcuFFTAdvisor.so
βΒ Β βΒ Β βΒ Β βββ libXmippCuda.a
βΒ Β βΒ Β βΒ Β βββ libXmippInterfaceCuda.so
βΒ Β βΒ Β βΒ Β βββ libXmippParallelCuda.so
βΒ Β βΒ Β βΒ Β βββ libXmippParallel.so
βΒ Β βΒ Β βΒ Β βββ libXmipp.so
βΒ Β βΒ Β βΒ Β βββ _swig_frm.so
βΒ Β βΒ Β βΒ Β βββ xmippLib.so
βΒ Β βΒ Β βββ libraries # This contains the hard code of Xmipp (xmipp is made of C++ libraries)
βΒ Β βΒ Β βΒ Β βββ classification
βΒ Β βΒ Β βΒ Β βΒ Β βββ ahc_classifier.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ vector_ops.h
βΒ Β βΒ Β βΒ Β βββ data
βΒ Β βΒ Β βΒ Β βΒ Β βββ aft.h
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xmipp_polynomials.cpp
βΒ Β βΒ Β βΒ Β βββ dimred
βΒ Β βΒ Β βΒ Β βΒ Β βββ diffusionMaps.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ transform_dimred.cpp
βΒ Β βΒ Β βΒ Β βββ interface
βΒ Β βΒ Β βΒ Β βΒ Β βββ docfile.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ virus.h
βΒ Β βΒ Β βΒ Β βββ parallel
βΒ Β βΒ Β βΒ Β βΒ Β βββ mpi_angular_accuracy_pca.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xmipp_mpi.cpp
βΒ Β βΒ Β βΒ Β βββ parallel_adapt_cuda
βΒ Β βΒ Β βΒ Β βΒ Β βββ mpi_reconstruct_fourier_gpu.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ mpi_reconstruct_fourier_gpu.h
βΒ Β βΒ Β βΒ Β βΒ Β βββ mpi_reconstruct_fourier_gpu.os
βΒ Β βΒ Β βΒ Β βββ py_xmipp
βΒ Β βΒ Β βΒ Β βΒ Β βββ coordinatesTools
βΒ Β βΒ Β βΒ Β βΒ Β βββ deepConsensusWorkers
βΒ Β βΒ Β βΒ Β βΒ Β βββ deepDenoising
βΒ Β βΒ Β βΒ Β βΒ Β βββ deepLearningToolkitUtils
βΒ Β βΒ Β βΒ Β βΒ Β βββ deepResLearner
βΒ Β βΒ Β βΒ Β βΒ Β βββ example_module2
βΒ Β βΒ Β βΒ Β βΒ Β βββ example_module.py
βΒ Β βΒ Β βΒ Β βββ reconstruction
βΒ Β βΒ Β βΒ Β βΒ Β βββ aalign_significant.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xray_psf_create.cpp
βΒ Β βΒ Β βΒ Β βββ reconstruction_adapt_cuda
βΒ Β βΒ Β βΒ Β βΒ Β βββ align_significant_gpu.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ xmipp_gpu_utils.cpp
βΒ Β βΒ Β βΒ Β βββ reconstruction_cuda
βΒ Β βΒ Β βΒ Β βββ cuda_all.cpp
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ gpu.cpp
βΒ Β βΒ Β βββ resources
βΒ Β βΒ Β βΒ Β βββ test
βΒ Β βΒ Β βΒ Β βββ dimred
βΒ Β βΒ Β βΒ Β βββ EMX
βΒ Β βΒ Β βΒ Β βββ filters
βΒ Β βΒ Β βΒ Β βββ funcs
βΒ Β βΒ Β βΒ Β βββ image
βΒ Β βΒ Β βΒ Β βββ metadata
βΒ Β βΒ Β βΒ Β βββ polynomials
βΒ Β βΒ Β βΒ Β βββ pythoninterface
βΒ Β βΒ Β βΒ Β βββ sampling
βΒ Β βΒ Β βββ SConscript # This contains the instructions to compile Xmipp (SConscript)
βΒ Β βΒ Β βββ SConstruct # This contains the instructions to compile Xmipp (SConstruct)
βΒ Β βΒ Β βββ tests # This is created in testing time
βΒ Β βΒ Β βββ data
βΒ Β βΒ Β βΒ Β βββ gold
βΒ Β βΒ β β Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ input
βΒ Β βΒ β β Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ MANIFEST
βΒ Β βΒ Β βΒ Β βββ temp.txt
βΒ Β βΒ Β βΒ Β βββ tmpLink
βΒ Β βΒ Β βββ __init__.py
βΒ Β βΒ Β βββ _test_internal.py
βΒ Β βΒ Β βββ test_programs_xmipp.py
βΒ Β βΒ Β βββ test.py
βΒ Β βΒ Β βββ _test_pythoninferface_xmipp.py
β β
βΒ Β βββ xmippCore # Repository of the Core -> this is the https://github.com/I2PC/xmippCore repository <-
βΒ Β βΒ Β β
βΒ Β βΒ Β βββ bindings # This contains bindings to other lenguages
βΒ Β βΒ Β βΒ Β βββ python
βΒ Β βΒ Β βΒ Β βββ python_image.h
βΒ Β βΒ Β βΒ Β βββ xmippmoduleCore.h
βΒ Β βΒ Β βββ CHANGELOG.md
βΒ Β βΒ Β βββ core # This contains the Xmipp CORE code
βΒ Β βΒ Β βΒ Β βββ alglib
βΒ Β βΒ Β βΒ Β βΒ Β βββ alglibinternal.cpp
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ stdafx.h
βΒ Β βΒ Β βΒ Β βββ args.cpp
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ bilib
βΒ Β βΒ Β βΒ Β βΒ Β βββ changebasis.cc
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βΒ Β βββ window.CC
βΒ Β βΒ Β βΒ Β βββ gcc_version.h
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ utils
βΒ Β βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ xmipp_color.cpp
βΒ Β βΒ Β βΒ Β βββ (...)
βΒ Β βΒ Β βΒ Β βββ xvsmooth.os
βΒ Β βΒ Β βββ install # This is created in compilation time
βΒ Β βΒ Β βΒ Β βββ scons-tools
βΒ Β βΒ Β βΒ Β βΒ Β βββ AutoConfig.py
βΒ Β βΒ Β βΒ Β βΒ Β βββ Make.py
βΒ Β βΒ Β βΒ Β βΒ Β βββ __pycache__
βΒ Β βΒ Β βΒ Β βββ xmipp.conf
βΒ Β βΒ Β βΒ Β βββ xmipp.template
βΒ Β βΒ Β βββ lib # Where the final libraries ends up
βΒ Β βΒ Β βΒ Β βββ libXmippCore.so
βΒ Β βΒ Β βΒ Β βββ xmippCore.so
βΒ Β βΒ Β βββ LICENSE
βΒ Β βΒ Β βββ README.md
βΒ Β βΒ Β βββ SConscript # This contains the instructions to compile XmippCore (SConscript)
βΒ Β βΒ Β βββ SConstruct # This contains the instructions to compile XmippCore (SConstruct)
β β
βΒ Β βββ xmippViz # Repository of the Core -> this is the https://github.com/I2PC/xmippViz repository <-
βΒ Β Β Β β
βΒ Β Β Β βββ applications
βΒ Β Β Β βΒ Β βββ scripts
βΒ Β Β Β βΒ Β βββ metadata_plot
βΒ Β Β Β βΒ Β βββ showj
βΒ Β Β Β βββ bin
βΒ Β Β Β βΒ Β βββ xmipp_metadata_plot
βΒ Β Β Β βΒ Β βββ xmipp_showj
βΒ Β Β Β βββ bindings
βΒ Β Β Β βΒ Β βββ java
βΒ Β Β Β βΒ Β βΒ Β βββ src
βΒ Β Β Β βΒ Β βΒ Β β βββ (...)
βΒ Β Β Β βΒ Β βΒ Β βββ xmipp_Aux.cpp
βΒ Β Β Β βΒ Β βΒ Β βββ (...)
βΒ Β Β Β βΒ Β βΒ Β βββ xmipp_TiltPairAligner.cpp
βΒ Β Β Β βΒ Β βββ python
βΒ Β Β Β βΒ Β βββ xmippViz.py
βΒ Β Β Β βββ CHANGELOG.md
βΒ Β Β Β βββ external
βΒ Β Β Β βΒ Β βββ imagej
βΒ Β Β Β βΒ Β βΒ Β βββ (...)
βΒ Β Β Β βΒ Β βββ imagej.tgz
βΒ Β Β Β βββ install
βΒ Β Β Β βΒ Β βββ scons-tools
βΒ Β Β Β βΒ Β βΒ Β βββ AutoConfig.py
βΒ Β Β Β βΒ Β βΒ Β βββ Make.py
βΒ Β Β Β βΒ Β βββ xmipp.conf
βΒ Β Β Β βΒ Β βββ xmipp.template
βΒ Β Β Β βββ java
βΒ Β Β Β βΒ Β βββ build
βΒ Β Β Β βΒ Β βΒ Β βββ HandleExtraFileTypes.class
βΒ Β Β Β βΒ Β βΒ Β βββ (...)
βΒ Β Β Β βΒ Β βΒ Β βββ XmippViewer.jar_source.txt
βΒ Β Β Β βΒ Β βββ lib
βΒ Β Β Β βΒ Β βΒ Β βββ commons-cli-1.1.jar
βΒ Β Β Β βΒ Β βΒ Β βββ (...)
βΒ Β Β Β βΒ Β βΒ Β βββ XmippViewer.jar
βΒ Β Β Β βΒ Β βββ src #Β This contains the hard code of xmippViz (coded in Java)
βΒ Β Β Β βΒ Β βββ HandleExtraFileTypes.java
βΒ Β Β Β βΒ Β βββ xmipp
βΒ Β Β Β βΒ Β βββ (...)
βΒ Β Β Β βββ lib
βΒ Β Β Β βΒ Β βββ libXmippJNI.so
βΒ Β Β Β βββ LICENSE
βΒ Β Β Β βββ README.md
βΒ Β Β Β βββ resources
βΒ Β Β Β βΒ Β βββ add.gif
βΒ Β Β Β βΒ Β βββ (...)
βΒ Β Β Β βΒ Β βββ zoom.png
βΒ Β Β Β βββ SConscript # This contains the instructions to compile XmippViz (SConscript)
βΒ Β Β Β βββ SConstruct # This contains the instructions to compile XmippViz (SConstruct)
βΒ Β Β Β βββ xmipp_MetaData.cpp
β
βββ build # After compilation, all binaries ends up to the self-contained build folder
Β Β βββ bin # This contains the binaries to be launched
Β Β βΒ Β βββ xmipp_angular_accuracy_pca
Β Β βΒ Β βββ (...)
Β Β βΒ Β βββ xmipp_xray_psf_create
Β Β βββ bindings # This contains the compiled bindings to other lenguages
Β Β βΒ Β βββ java
Β Β βΒ Β βββ matlab
Β Β βΒ Β βββ python
Β Β βββ lib # This contains the compiled libraries (needed to launch binaries in the bin folder)
Β Β βΒ Β βββ libcuFFTAdvisor.so
Β Β βΒ Β βββ libXmippCore.so
Β Β βΒ Β βββ libXmippCuda.a
Β Β βΒ Β βββ libXmippInterfaceCuda.so
Β Β βΒ Β βββ libXmippJNI.so
Β Β βΒ Β βββ libXmippParallelCuda.so
Β Β βΒ Β βββ libXmippParallel.so
Β Β βΒ Β βββ libXmipp.so
Β Β βββ pylib # Python modules to use in running time
Β Β βΒ Β βββ xmippPyModules
Β Β βΒ Β βββ xmippPyModules
Β Β βΒ Β βββ coordinatesTools
Β Β βΒ Β βββ deepConsensusWorkers
Β Β βΒ Β βββ deepDenoising
Β Β βΒ Β βββ deepLearningToolkitUtils
Β Β βΒ Β βββ deepResLearner
Β Β βΒ Β βββ example_module2
Β Β βΒ Β βββ example_module.py
Β Β βΒ Β βββ __init__.py
Β Β βββ resources
Β Β βΒ Β βββ add.gif
Β Β βΒ Β βββ binocular.png
Β Β βΒ Β βββ brush.png
Β Β βΒ Β βββ (...)
Β Β βΒ Β βββ zoom.png
Β Β βββ v3.20.07 # Installation token containing the version number
Β Β βββ xmipp.bashrc # bash script to set Xmipp env. vars. (run 'source xmipp.basrc')
Β Β βββ xmippEnv.json # Variables to set environ for Xmipp in running time
Β Β βββ xmipp.fish # fish script to set Xmipp env. vars. (run 'fish xmipp.basrc')