Frites - Version 0.4.4

v0.4.4

New Features

• Functions frites.conn.conn_reshape_undirected and frites.conn.conn_reshape_directed now supports multidimensional arrays (21ba7e05)
• New function frites.core.ent_nd_g to compute entropy on tensors (17587a15)
• New function frites.conn.conn_ii to estimate the interaction information (10938b46)
• New function frites.conn.conn_pid to estimate the partial information decomposition (ac9798dd)
• New function frites.conn.conn_fit to estimate the feature specific information transfer (#59) - @aopy

Bug fixes

• Base 2 frites.core.ent_nd_g (686854de)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb almost 3 years ago

Frites - Version 0.4.3

New Features

• frites.conn.conn_links now accepts to use brain region names as source or target seeds (8d7e1fb6)
• New function frites.stats.confidence_interval for computing confidence intervals, standard deviation (sd) and standard error on the mean (sem) on numpy arrays and xarray DataArray (3a512537)
• New plotting module with two functions for plotting connectivity matrices, frites.plot.plot_conn_heatmap and frites.plot.plot_conn_circle (7a107d100e, a480371a74, 33930cc33a1, 24029c4cf6b)
• Add the possibility to control the node's size in frites.plot.plot_conn_circle (7454376b)
• Add support for signed connectivity and improve node control of frites.plot.plot_conn_circle (78bbb91c)

Bug fixes

• Fix parallel computing of frites.conn.conn_covgc (f2ff5f67)
• Use linearly spaced indices instead of closest time points in frites.conn.define_windows (b5443ac2)
• frites.conn.conn_spec average over tapers after computing connectivity metric (10966a1be3).Thanks to @adam2392 and @ruuskas from the mne-connectivity package.

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb over 3 years ago

Frites - Version 0.4.2

New Features

• New function :func:frites.simulations.sim_ground_truth for simulating spatio-temporal ground-truths (ba44a424)
• New function :func:frites.conn.conn_spec for computing the single-trial spectral connectivity (8151486) - by @ViniciusLima94
• New method :class:frites.workflow.WfMi.confidence_interval method to estimate the confidence interval (ad0391987, 8189622b, fc584756, fc584756)
• New function :func:frites.conn.conn_net for computing the net connectivity (c86b19f0)
• New function :func:frites.set_mpl_style for example styles
• New function :func:frites.conn.conn_links for generating connectivity links (a0d0182d1)
• New function :func:frites.utils.downsample for down-sampling DataArray (59e15e67)
• :class:frites.estimator.CorrEstimator can no be defined with Pearson or Spearman correlation with both vector or tensor-based implementations (f6e80e921)
• :class:frites.workflow.WfStats now allows to pass rfx_center parameter for controlling whether effect-sizes should be centered and rfx_sigma for the hat correction (aab68e14)
• :func:frites.conn.conn_links can now be used for selecting intra and / or inter-hemispheric connections (87c762c7)
• :func:frites.conn.conn_links allows selecting links with inter / intra / both roi connections (74d2cc1b)

Internal changes

• Do not allow anymore to add new keys to the CONFIG dict (abea6675)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb about 4 years ago

Frites - Version 0.4.1

New Features

• New :class:frites.estimator.CustomEstimator for defining custom estimators (e473c713, 5584654c)
• New function :func:frites.conn.conn_fcd_corr for computing the temporal correlation across networks (2001f0c0)
• New function :func:frites.utils.acf for computing the auto-correlation (48ef0a03)
• New function :func:frites.conn.conn_ccf for computing the cross-correlation (43fceb00)

Bug fixes

• Fix attribute conversion in connectivity functions (b990c76)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb over 4 years ago

Frites - Version 0.4.0

New Features

• New estimators (frites.estimator.CorrEstimator, frites.estimator.DcorrEstimator) for continuous / continuous relationships (73ed8bbb, bc370a93, cf7a3456f)
• frites.conn.conn_dfc supports passing other estimators (a864a7b05b)
• frites.utils.time_to_sample and frites.utils.get_closest_sample conversion functions (7c44478e)
• frites.conn.conn_ravel_directed reshaping function (f9b9d272)
• new frites.workflow.WfMi.copy for internal workflow copy (0c2228c7, 860f3d45)
• new frites.workflow.WfMiCombine and example class for combining workflows (62072ee52)
• new classfrites.estimator.ResamplingEstimator trial-resampling estimator (13f6271e)

Bug fixes

• Fix frites.workflow.WfMi.get_params when returning a single output (3bde82e6)
• Improve attributes conversion for saving netcdf files (bool and dict) (8e7dddb1, c6f7a4db)
• Fix Numpy np.float and np.int warnings related (896a198a, 7f2a1caef, 0d1a1223)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb almost 5 years ago

Frites - Version 0.3.9

New Features

• :py:frites.conn.conn_dfc supports multivariate data + improve computing efficiency (1aed842, c4ac490)
• Reshaping connectivity arrays support elements on the diagonal + internal drop of duplicated elements (daac241f)
• :py:frites.conn.conn_dfc supports better channel aggregation (a66faa77)

Internal Changes

• Connectivity metric now use the :py:class:frites.dataset.SubjectEphy for internal conversion of the input data
• :py:class:frites.workflow.WfMi.get_params returns single-subject MI and permutations with dimension name 'subject' (instead of subjects) (85884f3a)
• All connectivity metrics now use :py:frites.conn.conn_io to convert inputs into a similar format
• Improve CI (#18)

Bug fixes

• Fix :py:class:frites.dataset.SubjectEphy when the data contains a single time point (a33d4437)
• Fix attributes of :py:class:frites.conn.conn_covgc (c120626)
• Fix :py:class:frites.dataset.DatasetEphy representation without data copy + html representation (b3ae7b8ea, #16)
• Fix passing tail input to the :py:class:frites.workflow.WfMi (6df86d1e)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb about 5 years ago

Frites - Version 0.3.8

New Features

• new :py:class:frites.io.Attributes class for managing and printing datasets' and workflow's attributes (be046b1)
• new :py:class:frites.dataset.SubjectEphy single-subject container (ac22cf4)
• new estimators of mutual-information, :py:class:frites.estimator.GCMIEstimator (901b3cbf, 65d1e08, 0015bf58, beed6a09), :py:class:frites.estimator.BinMIEstimator (beed6a09)
• new kernel smoothing function :py:frites.utils.kernel_smoothing

Internal Changes

• Removed files (cdff9b4, 9e96f8e, 14961aa0)
• :py:class:frites.dataset.DatasetEphy don't perform internal data copy when getting the data in a specific ROI (2da73ef)
• Compatibility of MI estimators with workflows (7dc76ee9, e7a9c23f)
• Improve the way to manage pairs of brain regions (8b955a16, bfdf2dba, 57c1e4ba, b1ff8c3d)

Breaking changes

• :py:class:frites.dataset.SubjectEphy and :py:class:frites.dataset.DatasetEphy to specify whether channels should be aggregated (default agg_ch=True) or not (agg=False) when computing MI. The agg_ch replace sub_roi (18d4e24)
• The workflow WfComod has been renamed :py:class:frites.workflow.WfConnComod (b7b58248)

Bug fixes

• Bug fixing according to the new version of :py:class:frites.dataset.DatasetEphy (1a15e05, 7b83a3d, abd1b281, 70bfefb, 5879950, 66acdf2, 4309be9c5, 6dc2fbf8)

Scientific Software - Peer-reviewed - Python
Published by EtienneCmb over 5 years ago