Changelog¶

Fixes¶

• Fix syntax problems with the rst files of the documentation
• Fix docstrings of some python methods
• Fix version of the dependencies
• Fix the float index error from the vem_tools.py script
• Fix the cosine drift problem caused by the latest version of numpy
• Fix the error caused by trying to compute the log(0) in the entropy function
• Fix the bug of the free_energy_computation function when the HRF is not estimated.

Enhancements¶

• Requirements file (requirements.txt) for developing and installation
• Improvement of the installation script (setup.py)
  • Auto-install of dependencies using pip and the requirements.txt file.
  • Python version 2.7.x required
  • C extensions are only compiled when PyHRF is built or installed. The same for the installation of the dependencies
  • The outputs of the installation script are colored in order to highlight important information
• Documentation
  • Improvement readability of the README and CHANGELOG files.
  • Improvement of the documentation with detailed VEM formulas
  • Extension of the documentation with the NeuroElf based visualization tool
  • Extension of the documentation with the installation steps for different GNU/Linux distributions
  • Extension of the documentation with a developer section
  • Deprecated sections of the documentation are hidden

New¶

• PyHRF visualization tool based on the NeuroElf tool
• Creation of a Dockerfile
  • Sharing the docker image on Docker Hub (pyrhf/pyhrf)
  • The CI service (travis) runs the tests and the coveralls using the docker image
  • The releases are now generated using and creating a docker image
• Documentation
  • Using a responsive, friendly and beautiful Sphinx theme (sphinx_bootstrap_theme)
  • Using readthedocs to build automatically the documentation

Optimizations¶

• Optimization of some VEM methods
  • pyhrf.vbjde.vem_tools.create_conditions
  • pyhrf.vbjde.vem_tools.create_neighbours
  • pyhrf.vbjde.vem_tools.poly_drifts_basis
  • pyhrf.vbjde.vem_tools.cosine_drifts_basis
  • pyhrf.vbjde.vem_tools.norm1_constraint
  • pyhrf.vbjde.vem_tools.nrls_expectation
  • pyhrf.vbjde.vem_tools.hrf_entropy
  • pyhrf.vbjde.vem_tools.two_gamma_hrf
  • pyhrf.vbjde.vem_tools.ppms_computation
  • pyhrf.vbjde.vem_tools.computeFit
  • pyhrf.vbjde.vem_tools.contrasts_mean_var_classes
  • pyhrf.vbjde.vem_bold.jde_vem_bold

Fixes¶

• Remove non-existing tests in devel mode
• Correct typo in documentation
• Correct list display in documentation
• Fix bug for numpy >= 1.11.1 version
• Fix bug in contrasts computation
• Clean tmp folders after some unitary tests
• Fix VEM script example

Fixes¶

• Fix VEM algorithm
  • Fix convergence criteria computation
  • Fix underflow and overflow in labels expectation (set labels to previous value if necessary)
• Continue to clean setup.py
• Fix some DeprecationWarning that will become Exceptions in the future
• Fix detection of parcellation files
• Fix for scikit-learn version >= 0.17
• Fix bugs with matplotlib versions >1.4
• Fix bug with Pillow latest version (see #146)
• Fix bug with numpy when installing in virtual environment (see commit a971656)
• Fix the zero constraint on HRF borders

Enhancements¶

• Optimize some functions in vem_tools
• Rewrite and optimize all VEM steps
• Remove old calls to verbose module and replaced them by logging standard library module
• Update website documentation

New¶

• Updating documentation
  • Updating theme
  • Fixing some reST and display errors
• Auto-detect CPUs number (mainly to use on cluster and not yet documented)
• Add covariance regularization matrix
• Load contrasts from SPM.mat
• Save contrasts in the same order that the xml configuration file
• Compute and save PPMs
• Add multi-session support for VEM BOLD and ASL
• Add cosine drifts to VEM
• Add command-line for VEM
• Add Stanford Willard Parcellation

Fixes¶

• Missing function (see #135)
• nipy version required for installation (see #134)

Fixes¶

• Logging level not set by command line (see #113)
• Error with VEM algorithm (see #115)

Enhancements¶

• Clean and update setup.py (see #84)
• Update travis configuration file (see #123)

API Changes¶

• Deprecate verbose module and implements logging module instead

Fixes¶

• Clean up setup.py

No changelog for previous versions