Have gaussian_filter plugin operate on copy of input so it does not m…

…odify it in-place (#300) * add .idea/ to gitignore * gaussian_filter plugin operates on a copy, so does not modify input * make inplace modification an option in gaussian_filter plugin --------- Co-authored-by: Erik Schomburg <[email protected]>
seung-lab · Feb 24, 2024 · 97ed0b0 · 97ed0b0
1 parent cbd53f2
commit 97ed0b0
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diff --git a/.gitignore b/.gitignore
@@ -15,6 +15,7 @@ jwu
 *.egg-info/
 .ipynb_checkpoints/
 .vscode/
+*.idea/
 docker/inference/build_docker.sh
 docker/inference/pytorch-emvision/
 docker/inference/pytorch-model/

diff --git a/chunkflow/plugins/gaussian_filter.py b/chunkflow/plugins/gaussian_filter.py
@@ -1,9 +1,12 @@
+import numpy as np
 from chunkflow.chunk import Chunk
 
 from scipy.ndimage import gaussian_filter
 
 
-def execute(chunk: Chunk, sigma: float=1.):
+def execute(chunk: Chunk, sigma: float=1., inplace=False):
+    if not inplace:
+        chunk = chunk.clone()
     for z in range(chunk.shape[-3]):
         if chunk.ndim == 4:
             for channel in range(chunk.shape[0]):