Move stat functions from core to stats

Author: EtienneCmb

docs/source/api/api_statistics.rst

@@ -9,7 +9,17 @@ Statistics
    :no-members:
    :no-inherited-members:
 
-Random effect (rfx)
+Non-parametric statistics
++++++++++++++++++++++++++
+
+.. autosummary::
+   :toctree: generated/
+
+   permute_mi_vector
+   permute_mi_trials
+   bootstrap_partitions
+
+Random-effect (rfx)
 +++++++++++++++++++
 
 .. autosummary::

frites/core/__init__.py

@@ -13,4 +13,3 @@
 from .gcmi_nd import (mi_nd_gg, mi_model_nd_gd, cmi_nd_ggg, gcmi_nd_cc,  # noqa
                       gcmi_model_nd_cd, gccmi_nd_ccnd, gccmi_model_nd_cdnd,
                       gccmi_nd_ccc, cmi_nd_ggd)
-from .mi_stats import (permute_mi_vector, permute_mi_trials) # noqa

frites/stats/__init__.py

@@ -10,6 +10,8 @@
 Most of those stastical functions are using
 `MNE Python <https://mne.tools/stable/index.html>`_
 """
-from .stats_param import (ttest_1samp, rfx_ttest)  # noqa
 from .stats_mcp import (testwise_correction_mcp, cluster_correction_mcp,  # noqa
                         cluster_threshold)
+from .stats_nonparam import (permute_mi_vector, permute_mi_trials,  # noqa
+                             bootstrap_partitions)
+from .stats_param import (ttest_1samp, rfx_ttest, dist_to_ci)  # noqa

frites/core/mi_stats.py frites/stats/stats_nonparam.pyfrites/core/mi_stats.py renamed to frites/stats/stats_nonparam.py

@@ -1,6 +1,9 @@
 """Utility functions for stat evaluation."""
 import numpy as np
 
+from frites.utils import nonsorted_unique
+from frites.dataset.ds_utils import multi_to_uni_conditions
+
 
 def permute_mi_vector(y, suj, mi_type='cc', inference='rfx', n_perm=1000,
                       random_state=None):
@@ -93,3 +96,56 @@ def permute_mi_trials(suj, inference='rfx', n_perm=1000, random_state=None):
     assert len(y_p) == n_perm
 
     return y_p
+
+
+def bootstrap_partitions(n_epochs, *groups, n_partitions=200,
+                         random_state=None):
+    """Generate partitions for bootstrap.
+
+    Parameters
+    ----------
+    n_epochs : int
+        Number of epochs
+    groups : array_like
+        Groups within which permutations are performed. Should be arrays of
+        shape (n_epochs,) and of type int
+    n_partitions : int | 200
+        Number of partitions to get
+    random_state : int | None
+        Fix the random state of the machine (use it for reproducibility). If
+        None, a random state is randomly assigned.
+
+    Returns
+    -------
+    partitions : list
+        List of arrays describing the partitions within groups or not
+    """
+    from sklearn.utils import resample
+
+    # define the random state
+    rnd = np.random.randint(1000) if not isinstance(
+        random_state, int) else random_state
+
+    # manage groups
+    if not len(groups):
+        groups = np.zeros((n_epochs), dtype=int)
+    else:
+        if len(groups) == 1:
+            groups = groups[0]
+        else:
+            groups = multi_to_uni_conditions(
+                [np.stack(groups, axis=1)], var_name='boot', verbose=False)[0]
+    u_groups = nonsorted_unique(groups)
+
+    # generate the partitions
+    partitions = []
+    for n_p in range(n_partitions):
+        _part = np.arange(n_epochs)
+        for n_g in u_groups:
+            is_group = groups == n_g
+            n_group = is_group.sum()
+            _part[is_group] = resample(
+                _part[is_group], n_samples=n_group, random_state=rnd + n_p)
+        partitions.append(_part)
+
+    return partitions

frites/core/tests/test_mi_stats.py frites/stats/tests/test_stats_nonparam.pyfrites/core/tests/test_mi_stats.py renamed to frites/stats/tests/test_stats_nonparam.py

@@ -1,7 +1,7 @@
 """Test high-level mutual information functions."""
 import numpy as np
 
-from frites.core import permute_mi_vector, permute_mi_trials
+from frites.stats import permute_mi_vector, permute_mi_trials
 
 rnd = np.random.RandomState(0)
 
@@ -14,7 +14,7 @@
 suj = np.round(np.linspace(0, n_suj, n_epochs)).astype(int)
 
 
-class TestMiStats(object):  # noqa
+class TestNonParam(object):  # noqa
 
     def test_permute_mi_vector(self):
         """Test function permute_mi_vector."""

frites/workflow/wf_conn_comod.py

@@ -5,7 +5,7 @@
 from mne.utils import ProgressBar
 
 from frites.io import (set_log_level, logger)
-from frites.core import permute_mi_trials
+from frites.stats import permute_mi_trials
 from frites.utils import parallel_func, kernel_smoothing
 from frites.workflow.wf_stats import WfStats
 from frites.workflow.wf_base import WfBase