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 (CM21ba7e05)

• New function frites.core.ent_nd_g() to compute entropy on tensors (CM17587a15)

• New function frites.conn.conn_ii() to estimate the interaction information (CM10938b46)

• New function frites.conn.conn_pid() to estimate the partial information decomposition (CMac9798dd)

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

Bug fixes

• Base 2 frites.core.ent_nd_g() (CM686854de)

v0.4.3

New Features

• frites.conn.conn_links() now accepts to use brain region names as source or target seeds (CM8d7e1fb6)

• 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 (CM3a512537)

• New plotting module with two functions for plotting connectivity matrices, frites.plot.plot_conn_heatmap() and frites.plot.plot_conn_circle() (CM7a107d100e, CMa480371a74, CM33930cc33a1, CM24029c4cf6b)

• Add the possibility to control the node’s size in frites.plot.plot_conn_circle() (CM7454376b)

• Add support for signed connectivity and improve node control of frites.plot.plot_conn_circle() (CM78bbb91c)

Bug fixes

• Fix parallel computing of frites.conn.conn_covgc() (CMf2ff5f67)

• Use linearly spaced indices instead of closest time points in frites.conn.define_windows() (CMb5443ac2)

• frites.conn.conn_spec() average over tapers after computing connectivity metric (CM10966a1be3).Thanks to by adam2392 and by ruuskas from the mne-connectivity package.

v0.4.2

New Features

• New function frites.simulations.sim_ground_truth() for simulating spatio-temporal ground-truths (CMba44a424)

• New function frites.conn.conn_spec() for computing the single-trial spectral connectivity (CM8151486) - by ViniciusLima94

• New method frites.workflow.WfMi.confidence_interval method to estimate the confidence interval (CMad0391987, CM8189622b, CMfc584756, CMfc584756)

• New function frites.conn.conn_net() for computing the net connectivity (CMc86b19f0)

• New function frites.set_mpl_style() for example styles

• New function frites.conn.conn_links() for generating connectivity links (CMa0d0182d1)

• New function frites.utils.downsample() for down-sampling DataArray (CM59e15e67)

• frites.estimator.CorrEstimator can no be defined with Pearson or Spearman correlation with both vector or tensor-based implementations (CMf6e80e921)

• 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 (CMaab68e14)

• frites.conn.conn_links() can now be used for selecting intra and / or inter-hemispheric connections (CM87c762c7)

• frites.conn.conn_links() allows selecting links with inter / intra / both roi connections (CM74d2cc1b)

Internal changes

• Do not allow anymore to add new keys to the CONFIG dict (CMabea6675)

v0.4.1

New Features

• New frites.estimator.CustomEstimator for defining custom estimators (CMe473c713, CM5584654c)

• New function frites.conn.conn_fcd_corr() for computing the temporal correlation across networks (CM2001f0c0)

• New function frites.utils.acf() for computing the auto-correlation (CM48ef0a03)

• New function frites.conn.conn_ccf() for computing the cross-correlation (CM43fceb00)

Bug fixes

• Fix attribute conversion in connectivity functions (CMb990c76)

v0.4.0

New Features

• New estimators (frites.estimator.CorrEstimator, frites.estimator.DcorrEstimator) for continuous / continuous relationships (CM73ed8bbb, CMbc370a93, CMcf7a3456f)

• frites.conn.conn_dfc() supports passing other estimators (CMa864a7b05b)

• frites.utils.time_to_sample() and frites.utils.get_closest_sample() conversion functions (CM7c44478e)

• frites.conn.conn_ravel_directed() reshaping function (CMf9b9d272)

• New frites.workflow.WfMi.copy for internal workflow copy (CM0c2228c7, CM860f3d45)

• New frites.workflow.WfMiCombine and example class for combining workflows (CM62072ee52)

• New frites.estimator.ResamplingEstimator trial-resampling estimator (CM13f6271e)

Bug fixes

• Fix frites.workflow.WfMi.get_params when returning a single output (CM3bde82e6)

• Improve attributes conversion for saving netcdf files (bool and dict) (CM8e7dddb1, CMc6f7a4db)

• Fix Numpy np.float and np.int warnings related (CM896a198a, CM7f2a1caef, CM0d1a1223)

v0.3.9

New Features

• frites.conn.conn_dfc() supports multivariate data + improve computing efficiency (CM1aed842, CMc4ac490)

• Reshaping connectivity arrays support elements on the diagonal + internal drop of duplicated elements (CMdaac241f)

• frites.conn.conn_dfc() supports better channel aggregation (CMa66faa77)

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) (CM85884f3a)

• 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 (CMa33d4437)

• Fix attributes of frites.conn.conn_covgc() (CMc120626)

• Fix frites.dataset.DatasetEphy representation without data copy + html representation (CMb3ae7b8ea, IS16)

• Fix passing tail input to the frites.workflow.WfMi (CM6df86d1e)

v0.3.8

New Features

• new frites.io.Attributes class for managing and printing datasets’ and workflow’s attributes (CMbe046b1)

• new frites.dataset.SubjectEphy single-subject container (CMac22cf4)

• new estimators of mutual-information, frites.estimator.GCMIEstimator (CM901b3cbf, CM65d1e08, CM0015bf58, CMbeed6a09), frites.estimator.BinMIEstimator (CMbeed6a09)

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

Internal Changes

• Removed files (CMcdff9b4, CM9e96f8e, CM14961aa0)

• frites.dataset.DatasetEphy don’t perform internal data copy when getting the data in a specific ROI (CM2da73ef)

• Compatibility of MI estimators with workflows (CM7dc76ee9, CMe7a9c23f)

• Improve the way to manage pairs of brain regions (CM8b955a16, CMbfdf2dba, CM57c1e4ba, CMb1ff8c3d)

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 (CM18d4e24)

• The workflow WfComod has been renamed frites.workflow.WfConnComod (CMb7b58248)

Bug fixes

• Bug fixing according to the new version of frites.dataset.DatasetEphy (CM1a15e05, CM7b83a3d, CMabd1b281, CM70bfefb, CM5879950, CM66acdf2, CM4309be9c5, CM6dc2fbf8)

v0.3.6

New Features

• frites.dataset.DatasetEphy support multi-level anatomical informations (CM3a9ce540)

Internal Changes

• Connectivity functions have a better support of Xarray inputs (CM60cc16, CMb72d1519, CM3d24c98, CM65bf08)

• Replace every string comparison ‘is’ with ‘==’ to test the content (CM1337aa6e)

v0.3.5

New Features

• New function for reshaping undirected connectivity arrays (like DFC) frites.conn.conn_reshape_undirected() (CMffcae34, CM56515fe)

• New function frites.utils.savgol_filter() that works on DataArray (CM3e0e256)

• New function for reshaping directed connectivity arrays (like COVGC) frites.conn.conn_reshape_directed() (CM8c2bb63)

• New method frites.workflow.WfMi.get_params in order to get the internal arrays formatted as DataArray (CM03dd2f3)

• Integration of MNE’s progress bar (CM74dc66, CM8ec636d, CM2bb7e75)

• 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 (CM2d6a61)

• sigma parameter when performing the t-test can be changed though the CONFIG file (CM5d7ba9f)

Bug fixes

• Fix ttested attribute when saving (CM3d029be)

• Fix computing the sigma across all ROI since it uses the maximum over every axes (CMffaca1e)

• Fix high RAM consumption when computing the pop_mean_surr (CMfe6e4d1)

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v0.3.4

Bug fixes

• Fix frites.workflow.WfMi.conjunction_analysis for seeg data (CM6ca64c5)

Breaking changes

• Xarray is now the default output type as it supports the definition of multi-dimensional containers with label to each coordinates (CM8174e4) + illustrating examples of how to use xarray (CMf5d28e)

• Every connectivity measures have been moved to frites.conn (CMa33d536)

• Deep support for correcting for multiple-comparisons using multi-dimensional data (CM840327, CMe0e1a5b) + support for frites.workflow.WfStatsEphy (CM563910d) + support for frites.dataset.DatasetEphy (CM10a3697) + support for frites.workflow.WfMi (CM9c6165)

New Features

• New class frites.simulations.StimSpecAR for generating Auto-Regressive Models (CM4688539, CM5fd1199)

• Conditional Covariance based Granger Causality + example (CMa148310)

Internal Changes

• Improve testings (CM6644cd)

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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 (CM18e1)

• 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 (CM4e77)

• New function frites.utils.define_windows() and frites.utils.plot_windows() in order to generate and plot slicing windows + tests + example (CM6fcf)

• New function for computing the DFC frites.core.dfc_gc (CM8f6f)

• When using DataArray with frites.core.dfc_gc and frites.core.covgc, temporal attributes are added (CM5df6, CM6266)

• New function for computing the covgc frites.core.covgc (CMea26)

• Step parameter for frites.core.covgc (CM874af)

• frites.core.covgc can no be computed using Gaussian-Copula (CMaea6a8b)

• Add frites.workflow.WfMi.conjunction_analysis for performing conjunction analysis + example (CM7dd0bea)

Bug fixes

• Fix when data contains a single time point (CMc815e40)

• Fix mi model and mixture (1d only) (CM2b119d4)

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v0.3.2

Breaking changes

• Avoid duplicates dataset construction when using MNE / xarray (CMfef9, CM9dde)

• frites.dataset.DatasetEphy supports None for the y input (CMa53a)

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 (CM7cc1)

New Features

• frites.dataset.DatasetEphy supports Xarray inputs + selection though coordinates (CM7418)

• New workflow for computing pairwise connectivity frites.workflow.WfConn (CM65ae)

Documentation

• Adding new examples for creating datasets (CM4df9)

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v0.3.1

Breaking changes

• change frites.workflow.WfFit input directed for net (CM3ec0, IS1)

• The GCRN is automatically defined (per subject when RFX / across subjects when FFX) (CMb8a9)

• Remove the level input parameter + only mcp is used + only maxstat when performing cluster based (CMd8fb)

New Features

• frites.dataset.DatasetEphy support spatio-temporal slicing (CM60d1), resampling (CM3785) and savitzki-golay filter (CM9707)

• Support setting random_state in frites.workflow.WfMi and frites.workflow.WfFit (CM0688)

• DataArray outputs contains attributes that reflect the configuration of the workflow (CM18181)

Bug fixes

• Fix multi-sites concatenation (CM3bcc) in frites.dataset.DatasetEphy

• Fix p-values to zeros in frites.workflow.WfFit (CM2062)

• Fix FIT outputs for 3D arrays and DataArray (CM18181)

Internal Changes

• Remap multiple conditions when integers (CM6092) in frites.dataset.DatasetEphy

• Workflows now have an internal configuration (CM18181)

Documentation

• Reformat examples gallery (CM4d4c)