Propagate chunk sizes from sim to msim and modify gitignore

histopathology · Dec 15, 2023 · c01ce06 · c01ce06
1 parent aa9f510
commit c01ce06
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -91,3 +91,4 @@ site/
 
 notebooks/fused*
 notebooks/Grid*
+notebooks/*.zarr
diff --git a/src/multiview_stitcher/msi_utils.py b/src/multiview_stitcher/msi_utils.py
@@ -175,7 +175,7 @@ def get_sim_from_msim(msim, scale="scale0"):
     return sim
 
 
-def get_msim_from_sim(sim, scale_factors=None):
+def get_msim_from_sim(sim, scale_factors=None, chunks=None):
     """
     highest scale sim from msim with affine transforms
     """
@@ -208,7 +208,8 @@ def get_msim_from_sim(sim, scale_factors=None):
     if scale_factors is None:
         scale_factors = get_optimal_multi_scale_factors_from_sim(sim)
 
-    chunks = {dim: 256 if dim not in ["c", "t"] else 1 for dim in sim.dims}
+    if chunks is not None:
+        chunks = {dim: 256 if dim not in ["c", "t"] else 1 for dim in sim.dims}
 
     msim = msi.to_multiscale(
         sim,
Original file line number	Diff line number	Diff line change
Expand Up		@@ -91,3 +91,4 @@ site/

		notebooks/fused*
		notebooks/Grid*
		notebooks/*.zarr