From de7892aa6a6f3fe1e9a2a5930e523c5f739d8148 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 5 Oct 2023 09:20:06 +0200
Subject: [PATCH] Moved examples to chaeo subpackage
---
extensions/chaeo/examples/__init__.py | 0
extensions/{ilastik => chaeo}/examples/batch_run_patches.py | 6 +++---
2 files changed, 3 insertions(+), 3 deletions(-)
create mode 100644 extensions/chaeo/examples/__init__.py
rename extensions/{ilastik => chaeo}/examples/batch_run_patches.py (92%)
diff --git a/extensions/chaeo/examples/__init__.py b/extensions/chaeo/examples/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/extensions/ilastik/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
similarity index 92%
rename from extensions/ilastik/examples/batch_run_patches.py
rename to extensions/chaeo/examples/batch_run_patches.py
index 5b67bb3d..291b5c52 100644
--- a/extensions/ilastik/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -26,14 +26,14 @@ if __name__ == '__main__':
result = export_patches_from_multichannel_zstack(
input_zstack_path=where_czi/ff,
px_model=px_model,
- pxmap_threshold=0.6,
+ pxmap_threshold=0.25,
pixel_class=0,
zmask_channel=0,
patches_channel=4,
where_output=where_output,
mask_type='boxes',
- zmask_filters={'area': (1e2, 1e5)},
- zmask_expand_box_by=(64, 3),
+ zmask_filters={'area': (1e3, 1e5)},
+ zmask_expand_box_by=(128, 3),
)
# parse and record results
--
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