From 97219b15f0e935f907f6e1e71ca016c5a266df9e Mon Sep 17 00:00:00 2001
From: polarbean <harry.carey95@gmail.com>
Date: Wed, 21 Aug 2024 17:31:46 +0200
Subject: [PATCH] custom atlasing functions
---
PyNutil/main.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/PyNutil/main.py b/PyNutil/main.py
index 320776e..4a024ec 100644
--- a/PyNutil/main.py
+++ b/PyNutil/main.py
@@ -79,6 +79,8 @@ class PyNutil:
alignment_json=None,
colour=None,
atlas_name=None,
+ atlas_path=None,
+ label_path=None,
atlas_resolution_micron=None,
settings_file=None,
) -> None:
@@ -109,7 +111,12 @@ class PyNutil:
self.alignment_json = alignment_json
self.colour = colour
self.atlas_name = atlas_name
- self.atlas_volume, self.atlas_labels = self.load_atlas_data(atlas_name=atlas_name)
+ if (atlas_path or label_path) and atlas_name:
+ raise ValueError("Please only specify an atlas_path and a label_path or an atlas_name, atlas and label paths are only used for loading custom atlases")
+ if atlas_path and label_path:
+ self.atlas_volume, self.atlas_labels = self.load_custom_atlas(atlas_path, label_path)
+ else:
+ self.atlas_volume, self.atlas_labels = self.load_atlas_data(atlas_name=atlas_name)
###This is just because of the migration to BrainGlobe
def load_atlas_data(self, atlas_name):
--
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