From bae852a448da1792a3c6f727ffcbb3584113a478 Mon Sep 17 00:00:00 2001
From: HU Xuesong <87519979+huxs001@users.noreply.github.com>
Date: Tue, 18 Feb 2025 17:02:16 +0800
Subject: [PATCH] Support anndata.X in Sparse Matrix

anndata.X can either be ndarray or SparseCSCMatrix.
---
 scenvi/utils.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/scenvi/utils.py b/scenvi/utils.py
index 0d1fd93..843f755 100644
--- a/scenvi/utils.py
+++ b/scenvi/utils.py
@@ -181,7 +181,10 @@ def CalcCovMats(spatial_data, kNN, genes, spatial_key="spatial", batch_key=-1):
     :meta private:
     """
 
-    ExpData = np.log(spatial_data[:, genes].X + 1)
+    if isinstance(spatial_data.X, np.ndarray):
+        ExpData = np.log(spatial_data[:, genes].X + 1)
+    else:
+        ExpData = np.log(np.asarray(spatial_data[:, genes].X.todense()) + 1)
 
     if batch_key == -1:
         kNNGraph = sklearn.neighbors.kneighbors_graph(