Merge pull request #331 from rsagroup/unbalanced_movie

added possibility to run calc_unbalanced for rdm movies

src/rsatoolbox/rdm/calc.py

@@ -9,11 +9,13 @@
 from copy import deepcopy
 from typing import TYPE_CHECKING, Optional, Tuple
 import numpy as np
-from rsatoolbox.rdm.rdms import RDMs
 from rsatoolbox.rdm.rdms import concat
+from rsatoolbox.rdm.calc_unbalanced import calc_rdm_unbalanced
 from rsatoolbox.rdm.combine import from_partials
 from rsatoolbox.data import average_dataset_by
 from rsatoolbox.util.rdm_utils import _extract_triu_
+from rsatoolbox.util.build_rdm import _build_rdms
+
 if TYPE_CHECKING:
     from rsatoolbox.data.base import DatasetBase
     from numpy.typing import NDArray
@@ -101,7 +103,7 @@ def calc_rdm(dataset, method='euclidean', descriptor=None, noise=None,
 def calc_rdm_movie(
         dataset, method='euclidean', descriptor=None, noise=None,
         cv_descriptor=None, prior_lambda=1, prior_weight=0.1,
-        time_descriptor='time', bins=None):
+        time_descriptor='time', bins=None, unbalanced=False):
     """
     calculates an RDM movie from an input TemporalDataset
 
@@ -121,6 +123,8 @@ def calc_rdm_movie(
             dimension in dataset.time_descriptors. Defaults to 'time'.
         bins (array-like): list of bins, with bins[i] containing the vector
             of time-points for the i-th bin. Defaults to no binning.
+        unbalanced (bool): if set to True use calc_rdm_unbalanced,
+            else and by default use calc_rdm
 
     Returns:
         rsatoolbox.rdm.rdms.RDMs: RDMs object with RDM movie
@@ -156,11 +160,20 @@ def calc_rdm_movie(
         rdms = []
         for dat in splited_data:
             dat_single = dat.convert_to_dataset(time_descriptor)
-            rdms.append(calc_rdm(dat_single, method=method,
-                                 descriptor=descriptor, noise=noise,
-                                 cv_descriptor=cv_descriptor,
-                                 prior_lambda=prior_lambda,
-                                 prior_weight=prior_weight))
+            if unbalanced:
+                rdms.append(calc_rdm_unbalanced(
+                    dat_single, method=method,
+                    descriptor=descriptor, noise=noise,
+                    cv_descriptor=cv_descriptor,
+                    prior_lambda=prior_lambda,
+                    prior_weight=prior_weight))
+            else:
+                rdms.append(calc_rdm(
+                    dat_single, method=method,
+                    descriptor=descriptor, noise=noise,
+                    cv_descriptor=cv_descriptor,
+                    prior_lambda=prior_lambda,
+                    prior_weight=prior_weight))
 
         rdm = concat(rdms)
         rdm.rdm_descriptors[time_descriptor] = time
@@ -488,54 +501,3 @@ def _check_noise(noise, n_channel):
     else:
         raise ValueError('noise(s) must have shape n_channel x n_channel')
     return noise
-
-
-def _build_rdms(
-            utv: NDArray,
-            ds: DatasetBase,
-            method: str,
-            obs_desc_name: str | None,
-            obs_desc_vals: Optional[NDArray] = None,
-            cv: Optional[NDArray] = None,
-            noise: Optional[NDArray] = None
-        ) -> RDMs:
-    rdms = RDMs(
-        dissimilarities=np.array([utv]),
-        dissimilarity_measure=method,
-        rdm_descriptors=deepcopy(ds.descriptors)
-    )
-    if (obs_desc_vals is None) and (obs_desc_name is not None):
-        # obtain the unique values in the target obs descriptor
-        _, obs_desc_vals, _ = average_dataset_by(ds, obs_desc_name)
-
-    if _averaging_occurred(ds, obs_desc_name, obs_desc_vals):
-        orig_obs_desc_vals = np.asarray(ds.obs_descriptors[obs_desc_name])
-        for dname, dvals in ds.obs_descriptors.items():
-            dvals = np.asarray(dvals)
-            avg_dvals = np.full_like(obs_desc_vals, np.nan, dtype=dvals.dtype)
-            for i, v in enumerate(obs_desc_vals):
-                subset = dvals[orig_obs_desc_vals == v]
-                if len(set(subset)) > 1:
-                    break
-                avg_dvals[i] = subset[0]
-            else:
-                rdms.pattern_descriptors[dname] = avg_dvals
-    else:
-        rdms.pattern_descriptors = deepcopy(ds.obs_descriptors)
-    # Additional rdm_descriptors
-    if noise is not None:
-        rdms.descriptors['noise'] = noise
-    if cv is not None:
-        rdms.descriptors['cv_descriptor'] = cv
-    return rdms
-
-
-def _averaging_occurred(
-            ds: DatasetBase,
-            obs_desc_name: str | None,
-            obs_desc_vals: NDArray | None
-        ) -> bool:
-    if obs_desc_name is None:
-        return False
-    orig_obs_desc_vals = ds.obs_descriptors[obs_desc_name]
-    return len(obs_desc_vals) != len(orig_obs_desc_vals)

src/rsatoolbox/rdm/calc_unbalanced.py

@@ -14,9 +14,9 @@
 import numpy as np
 from rsatoolbox.rdm.rdms import RDMs
 from rsatoolbox.rdm.rdms import concat
-from rsatoolbox.rdm.calc import _build_rdms
 from rsatoolbox.util.data_utils import get_unique_inverse
 from rsatoolbox.util.matrix import row_col_indicator_rdm
+from rsatoolbox.util.build_rdm import _build_rdms
 from rsatoolbox.cengine.similarity import calc_one, calc
 if TYPE_CHECKING:
     from rsatoolbox.data.base import DatasetBase

src/rsatoolbox/util/build_rdm.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""helper methods to create RDMs at the end of calculations"""
+
+from __future__ import annotations
+from typing import TYPE_CHECKING, Optional
+from copy import deepcopy
+import numpy as np
+from rsatoolbox.rdm.rdms import RDMs
+from rsatoolbox.data import average_dataset_by
+
+if TYPE_CHECKING:
+    from rsatoolbox.data.base import DatasetBase
+    from numpy.typing import NDArray
+
+
+def _build_rdms(
+            utv: NDArray,
+            ds: DatasetBase,
+            method: str,
+            obs_desc_name: str | None,
+            obs_desc_vals: Optional[NDArray] = None,
+            cv: Optional[NDArray] = None,
+            noise: Optional[NDArray] = None
+        ) -> RDMs:
+    rdms = RDMs(
+        dissimilarities=np.array([utv]),
+        dissimilarity_measure=method,
+        rdm_descriptors=deepcopy(ds.descriptors)
+    )
+    if (obs_desc_vals is None) and (obs_desc_name is not None):
+        # obtain the unique values in the target obs descriptor
+        _, obs_desc_vals, _ = average_dataset_by(ds, obs_desc_name)
+
+    if _averaging_occurred(ds, obs_desc_name, obs_desc_vals):
+        orig_obs_desc_vals = np.asarray(ds.obs_descriptors[obs_desc_name])
+        for dname, dvals in ds.obs_descriptors.items():
+            dvals = np.asarray(dvals)
+            avg_dvals = np.full_like(obs_desc_vals, np.nan, dtype=dvals.dtype)
+            for i, v in enumerate(obs_desc_vals):
+                subset = dvals[orig_obs_desc_vals == v]
+                if len(set(subset)) > 1:
+                    break
+                avg_dvals[i] = subset[0]
+            else:
+                rdms.pattern_descriptors[dname] = avg_dvals
+    else:
+        rdms.pattern_descriptors = deepcopy(ds.obs_descriptors)
+    # Additional rdm_descriptors
+    if noise is not None:
+        rdms.descriptors['noise'] = noise
+    if cv is not None:
+        rdms.descriptors['cv_descriptor'] = cv
+    return rdms
+
+
+def _averaging_occurred(
+            ds: DatasetBase,
+            obs_desc_name: str | None,
+            obs_desc_vals: NDArray | None
+        ) -> bool:
+    if obs_desc_name is None:
+        return False
+    orig_obs_desc_vals = ds.obs_descriptors[obs_desc_name]
+    return len(obs_desc_vals) != len(orig_obs_desc_vals)