From 3041f0d8856e0d228a234a3bebc4f74d77a7d464 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Heiko=20Sch=C3=BCtt?= <heiko.schutt@uni.lu>
Date: Mon, 29 Jul 2024 12:09:44 +0200
Subject: [PATCH 1/2] allow passing a target descriptor for ordering in
 concatenation. Also check uniqueness

---
 src/rsatoolbox/rdm/rdms.py | 35 +++++++++++++++++++++++------------
 1 file changed, 23 insertions(+), 12 deletions(-)

diff --git a/src/rsatoolbox/rdm/rdms.py b/src/rsatoolbox/rdm/rdms.py
index 447ed480..5a379e1a 100644
--- a/src/rsatoolbox/rdm/rdms.py
+++ b/src/rsatoolbox/rdm/rdms.py
@@ -542,7 +542,7 @@ def load_rdm(filename, file_type=None):
     return rdms_from_dict(rdm_dict)
 
 
-def concat(*rdms: RDMs) -> RDMs:
+def concat(*rdms: RDMs, target_pdesc: Optional[str] = None) -> RDMs:
     """Merge into single RDMs object
     requires that the rdms have the same shape
     descriptor and pattern descriptors are taken from the first rdms object
@@ -552,6 +552,7 @@ def concat(*rdms: RDMs) -> RDMs:
     Args:
         rdms(iterable of rsatoolbox.rdm.RDMs): RDMs objects to be concatenated
             or multiple RDMs as separate arguments
+        target_pdesc(optional, str): a pattern descriptor to use for sorting
 
     Returns:
         rsatoolbox.rdm.RDMs: concatenated rdms object
@@ -569,14 +570,24 @@ def concat(*rdms: RDMs) -> RDMs:
 
     descriptors, rdm_descriptors = _merged_rdm_descriptors(rdms_list)
 
-    ## see if we can find an authoritative descriptor for pattern order
-    pdescs = rdms_list[0].pattern_descriptors.keys()
-    pdesc_candidates = list(filter(lambda n: n!='index', pdescs))
-    target_pdesc = None
-    if len(pdesc_candidates) > 0:
-        target_pdesc = pdesc_candidates[0]
-    if len(pdesc_candidates) > 1:
-        warnings.warn(f'[concat] Multiple pattern descriptors found, using "{target_pdesc}"')
+    if target_pdesc is None:
+        # see if we can find an authoritative descriptor for pattern order
+        pdescs = rdms_list[0].pattern_descriptors.keys()
+        pdesc_candidates = list(filter(
+            lambda n: n != 'index' and (
+                len(rdms_list[0].pattern_descriptors[n])
+                == len(set(rdms_list[0].pattern_descriptors[n]))),
+                pdescs))
+        target_pdesc = None
+        if len(pdesc_candidates) > 0:
+            target_pdesc = pdesc_candidates[0]
+        if len(pdesc_candidates) > 1:
+            warnings.warn(f'[concat] Multiple pattern descriptors found, using "{target_pdesc}"')
+    else:
+        assert target_pdesc in rdms_list[0].pattern_descriptors.keys(), \
+            'The provided descriptor is not a pattern descriptor'
+        assert len(rdms_list[0].pattern_descriptors[target_pdesc]) == rdms_list[0].n_cond, \
+            'The provided descriptor is not unique'
 
     for rdm_new in rdms_list[1:]:
         assert isinstance(rdm_new, RDMs), 'rdm for concat should be an RDMs'
@@ -584,12 +595,12 @@ def concat(*rdms: RDMs) -> RDMs:
         assert rdm_new.dissimilarity_measure == rdms_list[0].dissimilarity_measure, \
             'appended rdm had wrong dissimilarity measure'
         if target_pdesc:
-            ## if we have a target descriptor, check if the order is the same
+            # if we have a target descriptor, check if the order is the same
             auth_order = rdms_list[0].pattern_descriptors[target_pdesc]
             other_order = rdm_new.pattern_descriptors[target_pdesc]
             if not np.all(other_order == auth_order):
-                ## order varies; reorder this rdms object
-                _, new_order = np.where(auth_order[:,None] == other_order)
+                # order varies; reorder this rdms object
+                _, new_order = np.where(auth_order[:, None] == other_order)
                 rdm_new.reorder(new_order)
 
     dissimilarities = np.concatenate([

From 967be717d004d16304b05d003f22dd64132087cd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Heiko=20Sch=C3=BCtt?= <heiko.schutt@uni.lu>
Date: Thu, 1 Aug 2024 12:45:03 +0200
Subject: [PATCH 2/2] added bures similarities to compare tooltip

---
 src/rsatoolbox/rdm/compare.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/rsatoolbox/rdm/compare.py b/src/rsatoolbox/rdm/compare.py
index c9f057a4..768c65c1 100644
--- a/src/rsatoolbox/rdm/compare.py
+++ b/src/rsatoolbox/rdm/compare.py
@@ -48,6 +48,10 @@ def compare(rdm1, rdm2, method='cosine', sigma_k=None):
 
             'neg_riem_dist' = negative riemannian distance
 
+            'bures' = bures similarity of equivalend cented kernel matrices
+
+            'bures_metric' = distances based on bures similarity, which is a metric
+
         sigma_k (numpy.ndarray):
             covariance matrix of the pattern estimates.
             Used only for methods 'corr_cov' and 'cosine_cov'.