From 4f53ce0cb420bd026cd5734e2cc543d454b11265 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 5 Oct 2023 17:46:01 +0200
Subject: [PATCH] Prototyping adaptive sobel-based projection within 3d patch
export
---
extensions/chaeo/examples/batch_run_patches.py | 5 +++--
extensions/chaeo/workflows.py | 10 ++++++++++
2 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index 2900f060..52b01490 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -47,7 +47,7 @@ if __name__ == '__main__':
'where_output': where_output.__str__(),
'mask_type': 'boxes',
'zmask_filters': {'area': (1e3, 1e8)},
- 'zmask_expand_box_by': (128, 0),
+ 'zmask_expand_box_by': (128, 3),
}
result = export_patches_from_multichannel_zstack(**export_kwargs)
@@ -65,4 +65,5 @@ if __name__ == '__main__':
write_accessor_data_to_file(
where_output / k / (ff.stem + '.tif'),
InMemoryDataAccessor(result['interm'][k])
- )
\ No newline at end of file
+ )
+ break
\ No newline at end of file
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 23eab18f..85b16d8b 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -60,6 +60,15 @@ def export_patches_from_multichannel_zstack(
ti.click('generate_zmasks')
# export patches
+ import numpy as np
+ from skimage.filters import gaussian, sobel
+
+ def zs_projector(zs):
+ sigma = 1.5
+ blur = gaussian(sobel(zs), sigma)
+ argmax = np.argmax(blur, axis=3, keepdims=True)
+ return np.take_along_axis(zs, argmax, axis=3)
+
files = export_patches_from_zstack(
Path(where_output) / '2d_patches',
stack.get_one_channel_data(patches_channel),
@@ -67,6 +76,7 @@ def export_patches_from_multichannel_zstack(
prefix=fstem,
draw_bounding_box=True,
rescale_clip=0.0,
+ projector=zs_projector,
)
ti.click('export_patches')
--
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