From 09b24fa8946f112e892462591d6e1bba0a373f45 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sun, 22 Oct 2023 08:22:07 +0200
Subject: [PATCH] Elevate patch annotations to workflow params
---
.../chaeo/actual_runs/20230805_kristineberg_PA.py | 1 +
extensions/chaeo/workflows.py | 11 +++++++----
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py b/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
index bca4017f..e359ccc9 100644
--- a/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
+++ b/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
@@ -39,6 +39,7 @@ if __name__ == '__main__':
'zmask_expand_box_by': (128, 3),
'export_pixel_probabilities': True,
'export_2d_patches_for_training': True,
+ 'draw_bounding_box_on_2d_patch': True,
'export_2d_patches_for_annotation': True,
'export_3d_patches': False,
'export_annotated_zstack': True,
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 0a441bf6..bf1503e4 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -31,6 +31,9 @@ def export_patches_from_multichannel_zstack(
export_pixel_probabilities=True,
export_2d_patches_for_training=True,
export_2d_patches_for_annotation=True,
+ draw_bounding_box_on_2d_patch=True,
+ draw_contour_on_2d_patch=False,
+ draw_mask_on_2d_patch=False,
export_3d_patches=True,
export_annotated_zstack=True,
export_patch_masks=True,
@@ -85,7 +88,7 @@ def export_patches_from_multichannel_zstack(
zmask_meta,
prefix=fstem,
draw_bounding_box=False,
- rescale_clip=0.0,
+ rescale_clip=0.001,
make_3d=True,
)
ti.click('export_3d_patches')
@@ -101,11 +104,11 @@ def export_patches_from_multichannel_zstack(
focus_metric='max_sobel',
ch_white=patches_channel,
ch_rgb_overlay=rgb_overlay_channels,
- draw_bounding_box=False,
+ draw_bounding_box=draw_bounding_box_on_2d_patch,
bounding_box_channel=1,
bounding_box_linewidth=2,
- # draw_contour=True,
- draw_mask=True,
+ draw_contour=draw_contour_on_2d_patch,
+ draw_mask=draw_mask_on_2d_patch,
overlay_gain=rgb_overlay_weights,
)
df_patches = pd.DataFrame(files)
--
GitLab