From 8f7dba9b02c13eb823e9a3fb2050ad7678457364 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 26 Oct 2023 10:42:28 +0200
Subject: [PATCH] Restored batch example to a working state, confirmed batch
jobs run
---
extensions/chaeo/examples/batch_run_patches.py | 8 +++-----
extensions/chaeo/workflows.py | 2 +-
2 files changed, 4 insertions(+), 6 deletions(-)
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index 48efac25..dcb35207 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -4,11 +4,9 @@ from model_server.util import autonumber_new_directory, get_matching_files, loop
from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
if __name__ == '__main__':
- # where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
- where_czi = 'c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/TREC_STOP_15_Kristineberg/230805_automic_AI_PA/20230805-122525_AI_PA_successfulrun_recognitiononPLL405cilindionas/Selection'
+ where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
where_output = autonumber_new_directory(
- # 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
- 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
+ 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
'batch-output'
)
@@ -31,7 +29,6 @@ if __name__ == '__main__':
'export_patch_masks': True,
}
- # input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
loop_workflow(
@@ -39,6 +36,7 @@ if __name__ == '__main__':
where_output,
export_patches_from_multichannel_zstack,
params,
+ catch_and_continue=False,
)
print('Finished')
\ No newline at end of file
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 7486395e..21880fed 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -23,8 +23,8 @@ def export_patches_from_multichannel_zstack(
pxmap_threshold: float,
pixel_class: int,
zmask_channel: int,
- zmask_zindex: None, # None for MIP,
patches_channel: int,
+ zmask_zindex: int = None, # None for MIP,
rescale_zmask_clip: int = None,
mask_type: str = 'boxes',
zmask_filters: Dict = None,
--
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