From a3830b06c8c3089d191e8c494a1143770fae0859 Mon Sep 17 00:00:00 2001 From: Malte Benedikt Kuehl Date: Wed, 26 Nov 2025 14:11:53 +0100 Subject: [PATCH] Do not unnecessarily increase community numbers in assign_communities --- spatiomic/segment/_assign_communities.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/spatiomic/segment/_assign_communities.py b/spatiomic/segment/_assign_communities.py index 727ea78..75ef4e7 100644 --- a/spatiomic/segment/_assign_communities.py +++ b/spatiomic/segment/_assign_communities.py @@ -50,8 +50,9 @@ def assign_communities( # Initialize output with same shape as masks community_image = np.zeros_like(masks) - # Assign community labels (adding 1 to avoid confusion with background) + # Assign community labels (adding 1 to avoid confusion with background, if needed) + pseudocount = 1 if communities_array.min() == 0 else 0 for i, region_id in enumerate(unique_regions): - community_image[masks == region_id] = communities_array[i] + 1 + community_image[masks == region_id] = communities_array[i] + pseudocount return community_image