From 3495066f3cc9216323afe704a6b5d7ecaff51024 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 26 Oct 2023 10:42:50 +0200
Subject: [PATCH] Restored batch example to a working state, confirmed batch
jobs run
---
.../20230805_kristineberg_PA.py | 0
.../20230807_kristineberg_spiked.py | 0
.../20231008_Bilbao_PA.py | 0
.../{actual_runs => batch_jobs}/__init__.py | 0
.../proj0004-exp0038-fixed.py | 0
.../chaeo/examples/batch_run_patches.py | 42 -------------------
6 files changed, 42 deletions(-)
rename extensions/chaeo/{actual_runs => batch_jobs}/20230805_kristineberg_PA.py (100%)
rename extensions/chaeo/{actual_runs => batch_jobs}/20230807_kristineberg_spiked.py (100%)
rename extensions/chaeo/{actual_runs => batch_jobs}/20231008_Bilbao_PA.py (100%)
rename extensions/chaeo/{actual_runs => batch_jobs}/__init__.py (100%)
rename extensions/chaeo/{actual_runs => batch_jobs}/proj0004-exp0038-fixed.py (100%)
delete mode 100644 extensions/chaeo/examples/batch_run_patches.py
diff --git a/extensions/chaeo/actual_runs/20230805_kristineberg_PA.py b/extensions/chaeo/batch_jobs/20230805_kristineberg_PA.py
similarity index 100%
rename from extensions/chaeo/actual_runs/20230805_kristineberg_PA.py
rename to extensions/chaeo/batch_jobs/20230805_kristineberg_PA.py
diff --git a/extensions/chaeo/actual_runs/20230807_kristineberg_spiked.py b/extensions/chaeo/batch_jobs/20230807_kristineberg_spiked.py
similarity index 100%
rename from extensions/chaeo/actual_runs/20230807_kristineberg_spiked.py
rename to extensions/chaeo/batch_jobs/20230807_kristineberg_spiked.py
diff --git a/extensions/chaeo/actual_runs/20231008_Bilbao_PA.py b/extensions/chaeo/batch_jobs/20231008_Bilbao_PA.py
similarity index 100%
rename from extensions/chaeo/actual_runs/20231008_Bilbao_PA.py
rename to extensions/chaeo/batch_jobs/20231008_Bilbao_PA.py
diff --git a/extensions/chaeo/actual_runs/__init__.py b/extensions/chaeo/batch_jobs/__init__.py
similarity index 100%
rename from extensions/chaeo/actual_runs/__init__.py
rename to extensions/chaeo/batch_jobs/__init__.py
diff --git a/extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py b/extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py
similarity index 100%
rename from extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py
rename to extensions/chaeo/batch_jobs/proj0004-exp0038-fixed.py
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
deleted file mode 100644
index dcb35207..00000000
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ /dev/null
@@ -1,42 +0,0 @@
-from pathlib import Path
-
-from model_server.util import autonumber_new_directory, get_matching_files, loop_workflow
-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_output = autonumber_new_directory(
- 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
- 'batch-output'
- )
-
- px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
-
- params = {
- 'ilastik_project_file': px_ilp.__str__(),
- 'pxmap_threshold': 0.25,
- 'pixel_class': 0,
- 'zmask_channel': 0,
- 'patches_channel': 4,
- 'mask_type': 'boxes',
- 'zmask_filters': {'area': (1e3, 1e8)},
- 'zmask_expand_box_by': (128, 3),
- 'export_pixel_probabilities': True,
- 'export_2d_patches_for_training': True,
- 'export_2d_patches_for_annotation': True,
- 'export_3d_patches': False,
- 'export_annotated_zstack': False,
- 'export_patch_masks': True,
- }
-
- input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
-
- loop_workflow(
- input_files,
- where_output,
- export_patches_from_multichannel_zstack,
- params,
- catch_and_continue=False,
- )
-
- print('Finished')
\ No newline at end of file
--
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