What’s new

v0.4.5.dev

v0.4.4

New Features

• Functions frites.conn.conn_reshape_undirected() and frites.conn.conn_reshape_directed() now supports multidimensional arrays (brainets/frites)

• New function frites.core.ent_nd_g() to compute entropy on tensors (brainets/frites)

• New function frites.conn.conn_ii() to estimate the interaction information (brainets/frites)

• New function frites.conn.conn_pid() to estimate the partial information decomposition (brainets/frites)

• New function frites.conn.conn_fit() to estimate the feature specific information transfer (:PR:`59`) - aopy

Bug fixes

• Base 2 frites.core.ent_nd_g() (brainets/frites)

v0.4.3

New Features

• frites.conn.conn_links() now accepts to use brain region names as source or target seeds (brainets/frites)

• 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 (brainets/frites)

• New plotting module with two functions for plotting connectivity matrices, frites.plot.plot_conn_heatmap() and frites.plot.plot_conn_circle() (brainets/frites, brainets/frites, brainets/frites, brainets/frites)

• Add the possibility to control the node’s size in frites.plot.plot_conn_circle() (brainets/frites)

• Add support for signed connectivity and improve node control of frites.plot.plot_conn_circle() (brainets/frites)

Bug fixes

• Fix parallel computing of frites.conn.conn_covgc() (brainets/frites)

• Use linearly spaced indices instead of closest time points in frites.conn.define_windows() (brainets/frites)

• frites.conn.conn_spec() average over tapers after computing connectivity metric (brainets/frites).Thanks to adam2392 and ruuskas from the mne-connectivity package.

v0.4.2

New Features

• New function frites.simulations.sim_ground_truth() for simulating spatio-temporal ground-truths (brainets/frites)

• New function frites.conn.conn_spec() for computing the single-trial spectral connectivity (brainets/frites) - ViniciusLima94

• New method frites.workflow.WfMi.confidence_interval method to estimate the confidence interval (brainets/frites, brainets/frites, brainets/frites, brainets/frites)

• New function frites.conn.conn_net() for computing the net connectivity (brainets/frites)

• New function frites.set_mpl_style() for example styles

• New function frites.conn.conn_links() for generating connectivity links (brainets/frites)

• New function frites.utils.downsample() for down-sampling DataArray (brainets/frites)

• frites.estimator.CorrEstimator can no be defined with Pearson or Spearman correlation with both vector or tensor-based implementations (brainets/frites)

• 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 (brainets/frites)

• frites.conn.conn_links() can now be used for selecting intra and / or inter-hemispheric connections (brainets/frites)

• frites.conn.conn_links() allows selecting links with inter / intra / both roi connections (brainets/frites)

Internal changes

• Do not allow anymore to add new keys to the CONFIG dict (brainets/frites)

v0.4.1

New Features

• New frites.estimator.CustomEstimator for defining custom estimators (brainets/frites, brainets/frites)

• New function frites.conn.conn_fcd_corr() for computing the temporal correlation across networks (brainets/frites)

• New function frites.utils.acf() for computing the auto-correlation (brainets/frites)

• New function frites.conn.conn_ccf() for computing the cross-correlation (brainets/frites)

Bug fixes

• Fix attribute conversion in connectivity functions (brainets/frites)

v0.4.0

New Features

• New estimators (frites.estimator.CorrEstimator, frites.estimator.DcorrEstimator) for continuous / continuous relationships (brainets/frites, brainets/frites, brainets/frites)

• frites.conn.conn_dfc() supports passing other estimators (brainets/frites)

• frites.utils.time_to_sample() and frites.utils.get_closest_sample() conversion functions (brainets/frites)

• frites.conn.conn_ravel_directed() reshaping function (brainets/frites)

• New frites.workflow.WfMi.copy for internal workflow copy (brainets/frites, brainets/frites)

• New frites.workflow.WfMiCombine and example class for combining workflows (brainets/frites)

• New frites.estimator.ResamplingEstimator trial-resampling estimator (brainets/frites)

Bug fixes

• Fix frites.workflow.WfMi.get_params when returning a single output (brainets/frites)

• Improve attributes conversion for saving netcdf files (bool and dict) (brainets/frites, brainets/frites)

• Fix Numpy np.float and np.int warnings related (brainets/frites, brainets/frites, brainets/frites)

v0.3.9

New Features

• frites.conn.conn_dfc() supports multivariate data + improve computing efficiency (brainets/frites, brainets/frites)

• Reshaping connectivity arrays support elements on the diagonal + internal drop of duplicated elements (brainets/frites)

• frites.conn.conn_dfc() supports better channel aggregation (brainets/frites)

Internal Changes

• Connectivity metric now use the frites.dataset.SubjectEphy for internal conversion of the input data

• frites.workflow.WfMi.get_params returns single-subject MI and permutations with dimension name ‘subject’ (instead of subjects) (brainets/frites)

• All connectivity metrics now use frites.conn.conn_io() to convert inputs into a similar format

• Improve CI

Bug fixes

• Fix frites.dataset.SubjectEphy when the data contains a single time point (brainets/frites)

• Fix attributes of frites.conn.conn_covgc() (brainets/frites)

• Fix frites.dataset.DatasetEphy representation without data copy + html representation (brainets/frites, brainets/frites#16)

• Fix passing tail input to the frites.workflow.WfMi (brainets/frites)

v0.3.8

New Features

• new frites.io.Attributes class for managing and printing datasets’ and workflow’s attributes (brainets/frites)

• new frites.dataset.SubjectEphy single-subject container (brainets/frites)

• new estimators of mutual-information, frites.estimator.GCMIEstimator (brainets/frites, brainets/frites, brainets/frites, brainets/frites), frites.estimator.BinMIEstimator (brainets/frites)

• new kernel smoothing function frites.utils.kernel_smoothing()

Internal Changes

• Removed files (brainets/frites, brainets/frites, brainets/frites)

• frites.dataset.DatasetEphy don’t perform internal data copy when getting the data in a specific ROI (brainets/frites)

• Compatibility of MI estimators with workflows (brainets/frites, brainets/frites)

• Improve the way to manage pairs of brain regions (brainets/frites, brainets/frites, brainets/frites, brainets/frites)

Breaking changes

• frites.dataset.SubjectEphy and 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 (brainets/frites)

• The workflow WfComod has been renamed frites.workflow.WfConnComod (brainets/frites)

Bug fixes

• Bug fixing according to the new version of frites.dataset.DatasetEphy (brainets/frites, brainets/frites, brainets/frites, brainets/frites, brainets/frites, brainets/frites, brainets/frites, brainets/frites)

v0.3.6

New Features

• frites.dataset.DatasetEphy support multi-level anatomical informations (brainets/frites)

Internal Changes

• Connectivity functions have a better support of Xarray inputs (brainets/frites, brainets/frites, brainets/frites, brainets/frites)

• Replace every string comparison ‘is’ with ‘==’ to test the content (brainets/frites)

v0.3.5

New Features

• New function for reshaping undirected connectivity arrays (like DFC) frites.conn.conn_reshape_undirected() (brainets/frites, brainets/frites)

• New function frites.utils.savgol_filter() that works on DataArray (brainets/frites)

• New function for reshaping directed connectivity arrays (like COVGC) frites.conn.conn_reshape_directed() (brainets/frites)

• New method frites.workflow.WfMi.get_params in order to get the internal arrays formatted as DataArray (brainets/frites)

• Integration of MNE’s progress bar (brainets/frites, brainets/frites, brainets/frites)

• Possibility to cache computations in the parallel function

Internal Changes

• DataArray now contain a name such as a type to make it clear what is it (brainets/frites)

• sigma parameter when performing the t-test can be changed though the CONFIG file (brainets/frites)

Bug fixes

• Fix ttested attribute when saving (brainets/frites)

• Fix computing the sigma across all ROI since it uses the maximum over every axes (brainets/frites)

• Fix high RAM consumption when computing the pop_mean_surr (brainets/frites)

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v0.3.4

Bug fixes

• Fix frites.workflow.WfMi.conjunction_analysis for seeg data (brainets/frites)

Breaking changes

• Xarray is now the default output type as it supports the definition of multi-dimensional containers with label to each coordinates (brainets/frites) + illustrating examples of how to use xarray (brainets/frites)

• Every connectivity measures have been moved to frites.conn (brainets/frites)

• Deep support for correcting for multiple-comparisons using multi-dimensional data (brainets/frites, brainets/frites) + support for frites.workflow.WfStatsEphy (brainets/frites) + support for frites.dataset.DatasetEphy (brainets/frites) + support for frites.workflow.WfMi (brainets/frites)

New Features

• New class frites.simulations.StimSpecAR for generating Auto-Regressive Models (brainets/frites, brainets/frites)

• Conditional Covariance based Granger Causality + example (brainets/frites)

Internal Changes

• Improve testings (brainets/frites)

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v0.3.3

Internal Changes

• frites.workflow.WfFit and frites.workflow.WfConn are now using frites.dataset.DatasetEphy.get_connectivity_pairs (brainets/frites)

• Improve warning messages + assert error for negative determinant for frites.core.covgc

New Features

• New method frites.dataset.DatasetEphy.get_connectivity_pairs in order to get possible connectivity pairs (brainets/frites)

• New function frites.utils.define_windows() and frites.utils.plot_windows() in order to generate and plot slicing windows + tests + example (brainets/frites)

• New function for computing the DFC frites.core.dfc_gc (brainets/frites)

• When using DataArray with frites.core.dfc_gc and frites.core.covgc, temporal attributes are added (brainets/frites, brainets/frites)

• New function for computing the covgc frites.core.covgc (brainets/frites)

• Step parameter for frites.core.covgc (brainets/frites)

• frites.core.covgc can no be computed using Gaussian-Copula (brainets/frites)

• Add frites.workflow.WfMi.conjunction_analysis for performing conjunction analysis + example (brainets/frites)

Bug fixes

• Fix when data contains a single time point (brainets/frites)

• Fix mi model and mixture (1d only) (brainets/frites)

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v0.3.2

Breaking changes

• Avoid duplicates dataset construction when using MNE / xarray (brainets/frites, brainets/frites)

• frites.dataset.DatasetEphy supports None for the y input (brainets/frites)

Internal Changes

• Dtypes of y and z inputs are systematically check in frites.dataset.DatasetEphy in order to define which MI can then be computed (brainets/frites)

New Features

• frites.dataset.DatasetEphy supports Xarray inputs + selection though coordinates (brainets/frites)

• New workflow for computing pairwise connectivity frites.workflow.WfConn (brainets/frites)

Documentation

• Adding new examples for creating datasets (brainets/frites)

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v0.3.1

Breaking changes

• change frites.workflow.WfFit input directed for net (brainets/frites, brainets/frites#1)

• The GCRN is automatically defined (per subject when RFX / across subjects when FFX) (brainets/frites)

• Remove the level input parameter + only mcp is used + only maxstat when performing cluster based (brainets/frites)

New Features

• frites.dataset.DatasetEphy support spatio-temporal slicing (brainets/frites), resampling (brainets/frites) and savitzki-golay filter (brainets/frites)

• Support setting random_state in frites.workflow.WfMi and frites.workflow.WfFit (brainets/frites)

• DataArray outputs contains attributes that reflect the configuration of the workflow (brainets/frites)

Bug fixes

• Fix multi-sites concatenation (brainets/frites) in frites.dataset.DatasetEphy

• Fix p-values to zeros in frites.workflow.WfFit (brainets/frites)

• Fix FIT outputs for 3D arrays and DataArray (brainets/frites)

Internal Changes

• Remap multiple conditions when integers (brainets/frites) in frites.dataset.DatasetEphy

• Workflows now have an internal configuration (brainets/frites)

Documentation

• Reformat examples gallery (brainets/frites)