Test SubjectEphy + DatasetEphy (small fixes and improvements)

Author: EtienneCmb

frites/config.py

@@ -29,24 +29,30 @@
 
 # mi types table
 CONFIG['MI_TABLE'] = {
-  'int' : {
-    'none': 'cc',
-    'int': 'cd',
-    'float': 'none'
-  },
-  'float': {
-    'none': 'cd',
-    'int': 'ccd',
-    'float': 'ccc'
-  }
+    'int': {
+        'none': 'cc',
+        'int': 'cd',
+        'float': 'none'
+    },
+    'float': {
+        'none': 'cd',
+        'int': 'ccd',
+        'float': 'ccc'
+    },
+    'none': {
+        'none': 'none',
+        'int': 'none',
+        'float': 'none',
+    }
 }
 
 # mi type full description
 CONFIG['MI_REPR'] = {
-  'cc': 'I(x; y (continuous))',
-  'cd': 'I(x; y (discret))',
-  'ccd': 'I(x; y (continuous)) | z (discret)',
-  'ccc': 'I(x; y (continuous)) | z (continuous)',
+    'none': 'none',
+    'cc': 'I(x; y (continuous))',
+    'cd': 'I(x; y (discret))',
+    'ccd': 'I(x; y (continuous)) | z (discret)',
+    'ccc': 'I(x; y (continuous)) | z (continuous)',
 }
 
 # general joblib config

frites/dataset/ds_ephy.py

@@ -59,7 +59,7 @@ class DatasetEphy(object):
     """
 
     def __init__(self, x, y=None, z=None, roi=None, agg_ch=True, times=None,
-                 multivariate=None, nb_min_suj=False, attrs=None,
+                 multivariate=False, nb_min_suj=False, attrs=None,
                  verbose=None):
         """Init."""
         set_log_level(verbose)
@@ -95,7 +95,7 @@ def __init__(self, x, y=None, z=None, roi=None, agg_ch=True, times=None,
             for k in range(n_subjects):
                 x[k] = SubjectEphy(
                     x[k], y=y[k], z=z[k], roi=roi[k], agg_ch=True, times=times,
-                    multivariate=multivariate)
+                    multivariate=multivariate, verbose=verbose)
         self._x = x
 
         # minimum number of subject / roi
@@ -127,7 +127,7 @@ def __init__(self, x, y=None, z=None, roi=None, agg_ch=True, times=None,
             # add additional dimension
             for k in range(len(self._x)):
                 self._x[k] = self._x[k].assign_coords(
-                    agg_ch=('space', agg_split[k]))
+                    agg_ch=('roi', agg_split[k]))
 
         # ============================= Attributes ============================
 
@@ -230,10 +230,10 @@ def get_roi_data(self, roi, groupby='subjects', mi_type='cc', copnorm=True,
             x_r_ms = []
             for s in suj_list:
                 # roi (possibly multi-sites) selection
-                x_roi = self._x[s].sel(space=self._x[s]['roi'].data == roi)
+                x_roi = self._x[s].sel(roi=self._x[s]['roi'].data == roi)
                 # stack roi and trials
-                x_roi = x_roi.stack(rtr=('space', 'trials'))
-                x_r_ms.append(x_roi.astype(np.float32, copy=False))
+                x_roi = x_roi.stack(rtr=('roi', 'trials'))
+                x_r_ms.append(x_roi)
             x_r_ms = xr.concat(x_r_ms, 'rtr')
             # 4d or multivariate
             if self._multivariate:
@@ -242,7 +242,7 @@ def get_roi_data(self, roi, groupby='subjects', mi_type='cc', copnorm=True,
                 x_r_ms = x_r_ms.expand_dims('mv', axis=-2)
 
             # channels aggregation
-            if not self._agg_ch:
+            if not self._agg_ch and ('y' in x_r_ms.dims):
                 # shortcuts
                 ch_id = x_r_ms['agg_ch'].data
                 y = x_r_ms['y'].data

frites/dataset/ds_utils.py

@@ -33,6 +33,10 @@ def multi_to_uni_conditions(x, var_name=None, verbose=None):
 
     if not isinstance(x, (list, tuple)):
         return [x]
+    assert all([type(x[0]) == type(k) for k in x])
+    x_types = type(x[0])
+    if not x_types == np.ndarray:
+        return x
     # get if all variables are integers and multicolumns else skip it
     is_int = all([k.dtype in CONFIG['INT_DTYPE'] for k in x])
     is_ndim = all([k.ndim > 1 for k in x])
@@ -70,5 +74,6 @@ def multi_to_uni_conditions(x, var_name=None, verbose=None):
     z = [0, 1, 0, 0, 1, 2]
     # result = [0, 1, 1, 1, 2, 2]
     x = np.c_[y, z]
+    x = None
     x_new = multi_to_uni_conditions([x], 'x', verbose='debug')
     print(x_new)

frites/dataset/suj_ephy.py

@@ -1,5 +1,4 @@
 """Single-subject container of neurophysiological."""
-import logging
 from collections import OrderedDict
 
 import numpy as np
@@ -8,11 +7,9 @@
 
 import frites
 from frites.config import CONFIG
-from frites.io import Attributes, set_log_level
+from frites.io import Attributes, logger, set_log_level
 from frites.dataset.ds_utils import multi_to_uni_conditions
 
-logger = logging.getLogger("frites")
-
 
 class SubjectEphy(Attributes):
     """Single-subject electrophysiological data container.
@@ -205,12 +202,12 @@ def __new__(self, x, y=None, z=None, roi=None, times=None, agg_ch=True,
             coords['subject'] = ('trials', [name] * n_trials)
         dims += ['trials']
         # build space (potentially) multi-coordinates
-        coords['space'] = ('space', np.arange(n_roi))
-        if (roi is not None) and (len(roi) == n_roi):
-            coords['roi'] = ('space', roi)
-        if not agg_ch:
-            coords['agg_roi'] = ('space', np.arange(n_roi))
-        dims += ['space']
+        coords['roi'] = ('roi', roi)
+        if agg_ch:
+            coords['agg_ch'] = ('roi', [0] * n_roi)
+        else:
+            coords['agg_ch'] = ('roi', np.arange(n_roi))
+        dims += ['roi']
         if _supp_dim:
             coords[_supp_dim[0]] = _supp_dim[1]
             dims += [_supp_dim[0]]