From 9161ccbfc5779ffa65b8950d74a67765e220c51e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 9 Oct 2023 11:15:11 +0200
Subject: [PATCH] Corrected bounding box annotation
---
extensions/chaeo/examples/export_patch_focus_metrics.py | 2 +-
extensions/chaeo/products.py | 5 +++--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/extensions/chaeo/examples/export_patch_focus_metrics.py b/extensions/chaeo/examples/export_patch_focus_metrics.py
index 36e2ab76..6c963e8b 100644
--- a/extensions/chaeo/examples/export_patch_focus_metrics.py
+++ b/extensions/chaeo/examples/export_patch_focus_metrics.py
@@ -121,7 +121,7 @@ if __name__ == '__main__':
'mask_type': 'boxes',
'zmask_filters': {'area': (1e3, 1e8)},
'zmask_expand_box_by': (128, 3),
- 'annotate_focus_metric': 'rms_sobel'
+ 'annotate_focus_metric': 'max_sobel'
}
result = export_patch_focus_metrics_from_multichannel_zstack(**export_kwargs)
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index df2ac7dc..d0ec388a 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -98,7 +98,7 @@ def export_3d_patches_with_focus_metrics(
Export 3D patches as multi-level z-stacks, along with CSV of various focus methods for each z-position
:param kwargs:
- annotate_focus_metric: name focus metric to use when drawing bounding box at optimal focus z-position
+ annotate_focus_metric: name focus metric to use when drawing bounding box at optimal focus z-position
:return:
list of exported files
"""
@@ -150,7 +150,8 @@ def export_3d_patches_with_focus_metrics(
me_df = pd.DataFrame(me_dict).T
# drawing bounding box only on focused slice
- if ak := kwargs.get('annotate_focus_metric') in me_dict.keys():
+ ak = kwargs.get('annotate_focus_metric')
+ if ak and ak in me_df.columns:
zi_foc = me_df.idxmax().to_dict()[ak]
patch[:, :, 0, zi_foc] = draw_box_on_patch(
patch[:, :, 0, zi_foc],
--
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