From 3dff7010c3bffde82c8a464970f09babbe2644a1 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 2 Nov 2023 14:59:04 +0100
Subject: [PATCH] Updated references to testing fixtures; chaeo tests failing
but suspect this was the case before
---
extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py | 2 +-
extensions/chaeo/conf/testing.py | 6 +++---
extensions/chaeo/examples/batch_obj_cla.py | 4 ++--
extensions/chaeo/examples/export_patch_focus_metrics.py | 2 +-
4 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py b/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py
index 9ad9208e..93a9cf6f 100644
--- a/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py
+++ b/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py
@@ -11,7 +11,7 @@ if __name__ == '__main__':
'batch-output'
)
- px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+ px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
params = {
'pxmap_threshold': 0.25,
diff --git a/extensions/chaeo/conf/testing.py b/extensions/chaeo/conf/testing.py
index 4ca90680..00389e08 100644
--- a/extensions/chaeo/conf/testing.py
+++ b/extensions/chaeo/conf/testing.py
@@ -1,6 +1,6 @@
from pathlib import Path
-root = Path.home() / 'model-server'
+root = Path.home() / 'model_server'
multichannel_zstack = {
'path': root / 'testing' / 'zmask-test-stack-chlorophyl.tif',
@@ -11,12 +11,12 @@ multichannel_zstack = {
}
pixel_classifier = {
- 'path': root / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+ 'path': root / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
}
pipeline_params = {
'threshold': 0.6,
}
-output_path = root / 'testing_output' / 'chaeo'
+output_path = root / 'testing' / 'output' / 'chaeo'
output_path.mkdir(parents=True, exist_ok=True)
\ No newline at end of file
diff --git a/extensions/chaeo/examples/batch_obj_cla.py b/extensions/chaeo/examples/batch_obj_cla.py
index 105f8e46..ec230d79 100644
--- a/extensions/chaeo/examples/batch_obj_cla.py
+++ b/extensions/chaeo/examples/batch_obj_cla.py
@@ -15,8 +15,8 @@ if __name__ == '__main__':
'zmask_to_automic',
)
- px_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
- ob_ilp = Path.home() / 'model-server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
+ px_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'AF405-bodies_boundaries.ilp'
+ ob_ilp = Path.home() / 'model_server' / 'testing' / 'zmask' / 'auto_obj_after.ilp'
params = {
'pxmap_threshold': 0.25,
diff --git a/extensions/chaeo/examples/export_patch_focus_metrics.py b/extensions/chaeo/examples/export_patch_focus_metrics.py
index 93a9fb45..31258117 100644
--- a/extensions/chaeo/examples/export_patch_focus_metrics.py
+++ b/extensions/chaeo/examples/export_patch_focus_metrics.py
@@ -112,7 +112,7 @@ if __name__ == '__main__':
)
csv_args = {'mode': 'w', 'header': True} # when creating file
- px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+ px_ilp = Path.home() / 'model_server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
for ff in where_czi.iterdir():
if ff.stem != 'Selection--W0000--P0009-T0001':
--
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