diff --git a/brainiak/fcma/preprocessing.py b/brainiak/fcma/preprocessing.py index dd6a31b81..dc80e4f76 100644 --- a/brainiak/fcma/preprocessing.py +++ b/brainiak/fcma/preprocessing.py @@ -30,11 +30,11 @@ logger = logging.getLogger(__name__) __all__ = [ - "RandomType", - "prepare_fcma_data", "generate_epochs_info", + "prepare_fcma_data", "prepare_mvpa_data", "prepare_searchlight_mvpa_data", + "RandomType", ] diff --git a/brainiak/fcma/util.py b/brainiak/fcma/util.py index b513e4fcc..de05e8748 100644 --- a/brainiak/fcma/util.py +++ b/brainiak/fcma/util.py @@ -24,6 +24,10 @@ from scipy.stats.mstats import zscore import math +__all__ = [ + "compute_correlation", +] + def _normalize_for_correlation(data, axis): """normalize the data before computing correlation diff --git a/brainiak/funcalign/srm.py b/brainiak/funcalign/srm.py index 1eef5f79c..023e71872 100644 --- a/brainiak/funcalign/srm.py +++ b/brainiak/funcalign/srm.py @@ -43,7 +43,8 @@ import sys __all__ = [ - "SRM", "DetSRM" + "DetSRM", + "SRM", ] logger = logging.getLogger(__name__) diff --git a/brainiak/funcalign/sssrm.py b/brainiak/funcalign/sssrm.py index 1efc4e9d4..901caa99f 100644 --- a/brainiak/funcalign/sssrm.py +++ b/brainiak/funcalign/sssrm.py @@ -46,7 +46,7 @@ from brainiak.funcalign import srm __all__ = [ - "SSSRM" + "SSSRM", ] logger = logging.getLogger(__name__) diff --git a/brainiak/hyperparamopt/hpo.py b/brainiak/hyperparamopt/hpo.py index fc2be65de..ffa37995e 100644 --- a/brainiak/hyperparamopt/hpo.py +++ b/brainiak/hyperparamopt/hpo.py @@ -38,6 +38,10 @@ logger = logging.getLogger(__name__) +__all__ = [ + "fmin", +] + def get_sigma(x, min_limit=-np.inf, max_limit=np.inf): """Compute the standard deviations around the points for a 1D GMM. diff --git a/brainiak/image.py b/brainiak/image.py index f86261d13..16ef99b74 100644 --- a/brainiak/image.py +++ b/brainiak/image.py @@ -15,10 +15,11 @@ __all__ = [ "ConditionSpec", - "SingleConditionSpec", - "mask_image", "MaskedMultiSubjectData", + "mask_image", + "mask_images", "multimask_images", + "SingleConditionSpec", ] import itertools diff --git a/brainiak/io.py b/brainiak/io.py index 50e32f12a..3b71ec37d 100644 --- a/brainiak/io.py +++ b/brainiak/io.py @@ -15,6 +15,7 @@ __all__ = [ "load_boolean_mask", + "load_images", "load_images_from_dir", "load_labels", "save_as_nifti_file", diff --git a/brainiak/isc.py b/brainiak/isc.py index c1bd3684f..1678d92ea 100644 --- a/brainiak/isc.py +++ b/brainiak/isc.py @@ -58,6 +58,17 @@ logger = logging.getLogger(__name__) +__all__ = [ + "bootstrap_isc", + "compute_summary_statistic", + "isfc", + "isc", + "permutation_isc", + "phaseshift_isc", + "timeshift_isc", +] + + MAX_RANDOM_SEED = 2**32 - 1 @@ -105,7 +116,7 @@ def isc(data, pairwise=False, summary_statistic=None): """ # Check response time series input format - data, n_TRs, n_voxels, n_subjects = check_timeseries_input(data) + data, n_TRs, n_voxels, n_subjects = _check_timeseries_input(data) # No summary statistic if only two subjects if n_subjects == 2: @@ -184,7 +195,7 @@ def isfc(data, pairwise=False, summary_statistic=None): """ # Check response time series input format - data, n_TRs, n_voxels, n_subjects = check_timeseries_input(data) + data, n_TRs, n_voxels, n_subjects = _check_timeseries_input(data) # Handle just two subjects properly if n_subjects == 2: @@ -236,7 +247,7 @@ def isfc(data, pairwise=False, summary_statistic=None): return isfcs -def check_timeseries_input(data): +def _check_timeseries_input(data): """Checks response time series input data for ISC analysis @@ -299,7 +310,7 @@ def check_timeseries_input(data): return data, n_TRs, n_voxels, n_subjects -def check_isc_input(iscs, pairwise=False): +def _check_isc_input(iscs, pairwise=False): """Checks ISC inputs for statistical tests @@ -466,7 +477,7 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median', """ # Standardize structure of input data - iscs, n_subjects, n_voxels = check_isc_input(iscs, pairwise=pairwise) + iscs, n_subjects, n_voxels = _check_isc_input(iscs, pairwise=pairwise) # Check for valid summary statistic if summary_statistic not in ('mean', 'median'): @@ -558,7 +569,7 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median', return observed, ci, p, distribution -def check_group_assignment(group_assignment, n_subjects): +def _check_group_assignment(group_assignment, n_subjects): if type(group_assignment) == list: pass elif type(group_assignment) == np.ndarray: @@ -574,7 +585,7 @@ def check_group_assignment(group_assignment, n_subjects): return group_assignment -def get_group_parameters(group_assignment, n_subjects, pairwise=False): +def _get_group_parameters(group_assignment, n_subjects, pairwise=False): # Set up dictionary to contain group info group_parameters = {'group_assignment': group_assignment, @@ -652,9 +663,9 @@ def get_group_parameters(group_assignment, n_subjects, pairwise=False): return group_parameters -def permute_one_sample_iscs(iscs, group_parameters, i, pairwise=False, - summary_statistic='median', group_matrix=None, - exact_permutations=None, prng=None): +def _permute_one_sample_iscs(iscs, group_parameters, i, pairwise=False, + summary_statistic='median', group_matrix=None, + exact_permutations=None, prng=None): """Applies one-sample permutations to ISC data @@ -720,9 +731,9 @@ def permute_one_sample_iscs(iscs, group_parameters, i, pairwise=False, return isc_sample -def permute_two_sample_iscs(iscs, group_parameters, i, pairwise=False, - summary_statistic='median', - exact_permutations=None, prng=None): +def _permute_two_sample_iscs(iscs, group_parameters, i, pairwise=False, + summary_statistic='median', + exact_permutations=None, prng=None): """Applies two-sample permutations to ISC data @@ -875,19 +886,19 @@ def permutation_isc(iscs, group_assignment=None, pairwise=False, # noqa: C901 """ # Standardize structure of input data - iscs, n_subjects, n_voxels = check_isc_input(iscs, pairwise=pairwise) + iscs, n_subjects, n_voxels = _check_isc_input(iscs, pairwise=pairwise) # Check for valid summary statistic if summary_statistic not in ('mean', 'median'): raise ValueError("Summary statistic must be 'mean' or 'median'") # Check match between group labels and ISCs - group_assignment = check_group_assignment(group_assignment, - n_subjects) + group_assignment = _check_group_assignment(group_assignment, + n_subjects) # Get group parameters - group_parameters = get_group_parameters(group_assignment, n_subjects, - pairwise=pairwise) + group_parameters = _get_group_parameters(group_assignment, n_subjects, + pairwise=pairwise) # Set up permutation type (exact or Monte Carlo) if group_parameters['n_groups'] == 1: @@ -956,7 +967,7 @@ def permutation_isc(iscs, group_assignment=None, pairwise=False, # noqa: C901 # If one group, apply sign-flipping procedure if group_parameters['n_groups'] == 1: - isc_sample = permute_one_sample_iscs( + isc_sample = _permute_one_sample_iscs( iscs, group_parameters, i, pairwise=pairwise, summary_statistic=summary_statistic, @@ -965,7 +976,7 @@ def permutation_isc(iscs, group_assignment=None, pairwise=False, # noqa: C901 # If two groups, set up group matrix get the observed difference else: - isc_sample = permute_two_sample_iscs( + isc_sample = _permute_two_sample_iscs( iscs, group_parameters, i, pairwise=pairwise, summary_statistic=summary_statistic, @@ -1057,7 +1068,7 @@ def timeshift_isc(data, pairwise=False, summary_statistic='median', """ # Check response time series input format - data, n_TRs, n_voxels, n_subjects = check_timeseries_input(data) + data, n_TRs, n_voxels, n_subjects = _check_timeseries_input(data) # Get actual observed ISC observed = isc(data, pairwise=pairwise, @@ -1191,7 +1202,7 @@ def phaseshift_isc(data, pairwise=False, summary_statistic='median', """ # Check response time series input format - data, n_TRs, n_voxels, n_subjects = check_timeseries_input(data) + data, n_TRs, n_voxels, n_subjects = _check_timeseries_input(data) # Get actual observed ISC observed = isc(data, pairwise=pairwise, diff --git a/brainiak/reprsimil/brsa.py b/brainiak/reprsimil/brsa.py index 5069c321a..3c912309d 100755 --- a/brainiak/reprsimil/brsa.py +++ b/brainiak/reprsimil/brsa.py @@ -62,8 +62,11 @@ logger = logging.getLogger(__name__) __all__ = [ - "BRSA", "GBRSA", "prior_GP_var_inv_gamma", "prior_GP_var_half_cauchy", - "Ncomp_SVHT_MG_DLD_approx" + "BRSA", + "GBRSA", + "Ncomp_SVHT_MG_DLD_approx", + "prior_GP_var_inv_gamma", + "prior_GP_var_half_cauchy", ] diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py index 1b05f507e..db017782b 100644 --- a/brainiak/searchlight/searchlight.py +++ b/brainiak/searchlight/searchlight.py @@ -23,7 +23,11 @@ """ __all__ = [ - "Searchlight", "Shape", "Cube", "Diamond", "Ball" + "Ball", + "Cube", + "Diamond", + "Searchlight", + "Shape", ] diff --git a/brainiak/utils/fmrisim.py b/brainiak/utils/fmrisim.py index cf047f0f5..5261f484c 100644 --- a/brainiak/utils/fmrisim.py +++ b/brainiak/utils/fmrisim.py @@ -92,16 +92,16 @@ import copy __all__ = [ - "generate_signal", - "generate_stimfunction", - "export_3_column", - "export_epoch_file", - "convolve_hrf", "apply_signal", "calc_noise", + "compute_signal_change", + "convolve_hrf", + "export_3_column", + "export_epoch_file", + "generate_signal", + "generate_stimfunction", "generate_noise", "mask_brain", - "compute_signal_change", ] logger = logging.getLogger(__name__) diff --git a/brainiak/utils/utils.py b/brainiak/utils/utils.py index 74b625a4b..c44ac5488 100644 --- a/brainiak/utils/utils.py +++ b/brainiak/utils/utils.py @@ -30,18 +30,19 @@ """ __all__ = [ - "from_tri_2_sym", - "from_sym_2_tri", - "sumexp_stable", + "center_mass_exp", + "compute_p_from_null_distribution", "concatenate_not_none", "cov2corr", - "ReadDesign", + "ecdf", + "from_tri_2_sym", + "from_sym_2_tri", "gen_design", - "usable_cpu_count", - "center_mass_exp", "phase_randomize", - "ecdf", - "p_from_null" + "p_from_null", + "ReadDesign", + "sumexp_stable", + "usable_cpu_count", ]