StructureAnalysis

This package provides tools for statistical analysis of the structure of a plant.

warning:: This package in under development, even the master branch is broken

Install

Dependencies

We recommand to use python virtual environments to install the package (conda is a good choice, especialy since conda-only packages are required as dependencies).

Required dependencies available from conda-forge channel are :

• boost
• scons
• openalea.deploy
• openalea.sconsx
• nose (for tests, only via pip install)

Doing the development install

To install the package for developments, you can use the multisetup.py script. It will use the Multisetup from openalea.deploy to compile stat_tool and sequence_analysis packages.

python multisetup.py develop

However, compilation can be a bit long and you may want to install using parallel compilation. To do so, you can use the following sequence (compilation with 4 cores, but you can adapt to your ressources):

cd stat_tool
scons -j4
pip install -e .
cd ../sequence_analysis
scons -j4
pip install -e .
cd ..

After-install issues

Observed only on OSX (so far), you may need to extend your LD_LIBRARY_PATH environment variable to include the path of your newly built libraries:

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/path/to/your/conda/env/lib:/path/to/StructureAnalysis/stat_tool/build-scons/lib/:/path/to/StructureAnalysis/sequence_analysis/build-scons/lib/

Wrapping C++ code

The C++ code is wrapped using boost::python. The wrapping is done using Scons and openalea.sconsx (thin additional layer on top of Scons for OpenAlea projects).

warning:: We still need to make sure that all the C++ code is properly wrapped, and no requirements are missing. Is running all the tests enough ?

Code layout

As a first step, we focus on two packages: stat_tool and sequence_analysis. The other packages are either becoming irrelevant (based on original AML code) or are not yet implemented.

stat_tool

You can find below the structure of the stat_tool package. The Scosntruct file is used to compile the C++ code. The src/cpp directory contains the C++ code, and the src/wrapper directory contains the code to wrap the C++ code into Python. src/openalea/stat_tool contains the Python code that uses the wrapped C++ code.

.
├── AUTHORS.txt
├── ChangeLog.txt
├── LICENSE.txt
├── README.txt
├── SConstruct
├── conda
│   └── meta.yaml
├── debian
│   ├── changelog
│   ├── compat
│   ├── control
│   ├── copyright
│   ├── rules
│   └── source
│       └── format
├── doc
│   ├── Doxyfile
│   ├── Makefile
│   ├── README
│   ├── _static
│   │   ├── fig7_1.png
│   │   └── fig7_2.png
│   ├── conf.py
│   ├── contents.rst
│   ├── cpp
│   │   └── doxygen.conf
│   ├── make.bat
│   ├── pyplots
│   │   └── example1.py
│   └── user
│       ├── admin.rst
│       ├── ...
│       └── visualea_oak_demo.rst
├── examples
│   ├── Model
│   │   ├── Markov
│   │   │   ├── belren1.hsc
│   │   │   ├── ...
│   │   │   └── wij1.hsc
│   │   └── align1.a
│   ├── Sample
│   │   ├── Histogram
│   │   │   ├── meri1.his
│   │   │   ├── ...
│   │   │   └── peup6.his
│   │   └── Sequences
│   │       ├── belren1.seq
│   │       ├── ...
│   │       └── wij1.seq
│   ├── exploratory.aml
│   └── exploratory.py
├── install_stool.sh
├── merge_info.txt
├── methodo.txt
├── setup.py
├── share
│   └── data
│       ├── chene_sessile.vec
│       ├── ...
│       └── peup6.his
├── src
│   ├── cpp
│   │   ├── SConscript
│   │   ├── SConscriptWIG
│   │   ├── categorical_process.cpp
│   │   ├── chain.cpp
│   │   ├── chain_algorithms.cpp
|   |   ├── ...
│   │   ├── chain_reestimation.h
│   │   ├── chain_reestimation.hpp
│   │   ├── vectors.cpp
│   │   └── vectors.h
│   ├── openalea
│   │   └── stat_tool
│   │       ├── __init__.py
│   │       ├── cluster.py
│   │       ├── ...
│   │       └── vectors.py
│   └── wrapper
│       ├── SConscript
│       ├── boost_python_aliases.h
│       ├── export_base.cpp
│       ├── export_base.h
|       ├── ...
│       ├── export_vectors.cpp
│       ├── export_vectors.h
│       ├── stat_tool_wrap.cpp
│       └── wrapper_util.h
└── test
    ├── README.md
    ├── aml
    │   ├── stat_tool_test.aml
    │   ├── stat_tool_test.ipynb
    │   └── stat_tool_test.py
    ├── cpp
    │   ├── SConscript
    │   ├── np_model.mix
    │   └── test_multivariate_mixture.cpp
    ├── data
    │   ├── angles_ahp6_10.seq
    |   ├── ...
    │   └── vectors2.vec
    ├── stat_tool_examples.py
    ├── stat_tool_sequence_analysis_class.txt
    ├── test_cluster.py
    ├── ...
    ├── test_vectors_functional.py
    └── tools.py

sequence_analysis

You can find below the structure of the sequence_analysis package, which is similar to stat_tool. The Scosntruct file is used to compile the C++ code. The src/cpp directory contains the C++ code, and the src/wrapper directory contains the code to wrap the C++ code into Python. src/openalea/sequintand src/openalea/sequence_analysis contains the Python code that uses the wrapped C++ code.

.
├── AUTHORS.txt
├── ChangeLog.txt
├── LICENSE.txt
├── README.txt
├── SConstruct
├── conda
│   └── meta.yaml
├── debian
│   ├── changelog
│   ├── compat
│   ├── control
│   ├── copyright
│   ├── rules
│   └── source
│       └── format
├── doc
│   ├── Doxyfile
│   ├── Makefile
│   ├── conf.py
│   ├── contents.rst
│   ├── cpp
│   │   └── doxygen.conf
│   ├── make.bat
│   ├── pyplots
│   │   ├── example_oak_1.py
│   │   ├── ...
│   │   └── sequence_plot_values.py
│   └── user
│       ├── admin.rst
│       ├── autosum.rst
│       ├── index.rst
│       ├── overview.txt
│       ├── scripts
│       │   ├── example_oak.py
│       │   └── example_oak.rst
│       └── tutorial.rst
├── sequence_analysis.py
├── setup.py
├── share
│   ├── README.txt
│   └── data
│       ├── abri13.ren
│       ├── abricotier_suivi_11.seq
│       ├── belren1.hsc
│       ├── belren1.seq
│       ├── ...
│       ├── wij1.hsc
│       └── wij1.seq
├── src
│   ├── cpp
│   │   ├── SConscript
│   │   ├── alignment.cpp
│   │   ├── ...
│   │   └── vomc_distributions2.cpp
│   ├── openalea
│   │   ├── seqint
│   │   │   ├── README.txt
│   │   │   ├── __init__.py
│   │   │   ├── config.py
│   │   │   ├── ...
│   │   │   └── xl_io.py
│   │   └── sequence_analysis
│   │       ├── __init__.py
│   │       ├── _sequence_analysis.so
│   │       ├── compare.py
│   │       ├── ...
│   │       └── variable_order_markov.py
│   ├── sequence_analysis_wralea
│   │   ├── __init__.py
│   │   ├── __wralea__.py
│   │   ├── demo
│   │   │   ├── __init__.py
│   │   │   ├── change_point
│   │   │   │   ├── Demo_ChangePoint_stat_tool_wralea.py
│   │   │   │   ├── __init__.py
│   │   │   │   ├── angelique_internode_length.seq
│   │   │   │   ├── change_point_demo.aml
│   │   │   │   ├── icon.png
│   │   │   │   ├── pin_laricio_7x.seq
│   │   │   │   └── reinet1.hsc
│   │   │   └── stat_tool_tutorial
│   │   │       ├── __init__.py
│   │   │       ├── __wralea__.py
│   │   │       ├── angelique_internode_length.seq
│   │   │       ├── icon.png
│   │   │       ├── pin_laricio_7x.seq
│   │   │       └── reinet1.hsc
│   │   ├── icon.png
│   │   └── stat.py
│   └── wrapper
│       ├── SConscript
│       ├── boost_python_aliases.h
│       ├── csequence.cpp
│       ├── export_base.cpp
│       ├── export_base.h
│       ├── ...
│       ├── sequence_analysis_wrap.cpp
│       └── wrapper_util.h
├── test
│   ├── _test_variable_order_markov.py
│   ├── functional1.py
│   ├── functional2.py
│   ├── functional3.py
│   ├── test_add_absorbing_run.py
│   ├── ...
│   ├── test_transcode.py
│   └── tools.py
└── tutorials
    ├── Code
    │   ├── __init__.py
    │   ├── amlseq2R.py
    │   ├── matrix_plot.py
    │   └── python_dics2R.py
    ├── Utils
    │   ├── __init__.py
    │   ├── __pycache__
    │   │   └── __init__.cpython-310.pyc
    │   ├── dos2unix.py
    │   └── unix2dos.py
    ├── scratch
    ├── seq1v_5s_LR_init.hsmc
    ├── sequences.ipynb
    └── sim_v_5s_LR.hsmc