From 8a5486aa33b7595384fcdae6bff6c4e6aa46928e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 5 Oct 2023 16:13:46 +0200
Subject: [PATCH] Finished implementing point-based projection
---
.../chaeo/examples/batch_run_patches.py | 6 +++---
extensions/chaeo/tests/test_zstack.py | 2 +-
extensions/chaeo/workflows.py | 20 +++++++++----------
3 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index fb96be1a..2900f060 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -14,7 +14,7 @@ if __name__ == '__main__':
)
where_output_root = Path(
- 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009'
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output'
)
yyyymmdd = strftime('%Y%m%d', localtime())
idx = 0
@@ -51,7 +51,7 @@ if __name__ == '__main__':
}
result = export_patches_from_multichannel_zstack(**export_kwargs)
- break
+
# parse and record results
df = result['dataframe']
df['filename'] = ff.name
@@ -65,4 +65,4 @@ if __name__ == '__main__':
write_accessor_data_to_file(
where_output / k / (ff.stem + '.tif'),
InMemoryDataAccessor(result['interm'][k])
- )
\ No newline at end of file
+ )
\ No newline at end of file
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index 2257b90b..c2d0b113 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -100,7 +100,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
from extensions.chaeo.zmask import project_stack_from_focal_points
- dff = df[df['keeper'] == True]
+ dff = df[df['keeper']]
img = project_stack_from_focal_points(
dff['centroid-0'].to_numpy(),
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 14e3fd2d..23eab18f 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -4,7 +4,7 @@ from typing import Dict
from extensions.ilastik.models import IlastikPixelClassifierModel
from extensions.chaeo.annotators import draw_boxes_on_3d_image
from extensions.chaeo.products import export_patches_from_zstack
-from extensions.chaeo.zmask import build_zmask_from_object_mask
+from extensions.chaeo.zmask import build_zmask_from_object_mask, project_stack_from_focal_points
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.workflows import Timer
@@ -83,15 +83,15 @@ def export_patches_from_multichannel_zstack(
)
ti.click('export_annotated_zstack')
- # from extensions.chaeo.zmask import build_image_flattening_zmask_from_points
- #
- # dff = df[df['keeper'] == True]
- # build_image_flattening_zmask_from_points(
- # dff['centroid-0'],
- # dff['centroid-1'],
- # dff['zi'],
- # stack.get_one_channel_data(patches_channel).data,
- # )
+ # generate multichannel projection from label centroids
+ dff = df[df['keeper']]
+ interm['projected'] = project_stack_from_focal_points(
+ dff['centroid-0'].to_numpy(),
+ dff['centroid-1'].to_numpy(),
+ dff['zi'].to_numpy(),
+ stack,
+ degree=4,
+ )
return {
'pixel_model_id': px_model.model_id,
--
GitLab