brainets/frites

✨ 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)

📋 Changes

• `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)
• 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.

📋 Changes

• 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)
• + 4 more

📋 Changes

• 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)
• Fix attribute conversion in connectivity functions (b990c76)

📋 Changes

• 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 class`frites.estimator.ResamplingEstimator` trial-resampling estimator (13f6271e)
• Fix `frites.workflow.WfMi.get_params` when returning a single output (3bde82e6)
• + 2 more

📋 Changes

• :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)
• 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)
• Fix :py:class:`frites.dataset.SubjectEphy` when the data contains a single time point (a33d4437)
• + 3 more

📋 Changes

• 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`
• 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)
• + 3 more