From b7738938be70d87ec02e5874ebc8484eec8c050c Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 12 Oct 2023 09:06:26 +0200
Subject: [PATCH] Exposed export product flags in batch runner
---
extensions/chaeo/examples/batch_run_patches.py | 11 +++++++++--
extensions/chaeo/workflows.py | 6 ++++--
2 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index 948a131a..acc6d8aa 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -9,7 +9,7 @@ from model_server.accessors import InMemoryDataAccessor, write_accessor_data_to_
if __name__ == '__main__':
where_czi = Path(
- 'c:/Users/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
+ 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
)
where_output_root = Path(
@@ -54,6 +54,13 @@ if __name__ == '__main__':
'mask_type': 'boxes',
'zmask_filters': {'area': (1e3, 1e8)},
'zmask_expand_box_by': (128, 3),
+ 'export_pixel_probabilities': False,
+ 'export_2d_patches_for_training': True,
+ 'export_2d_patches_for_annotation': False,
+ 'export_3d_patches': False,
+ 'export_annotated_zstack': False,
+ 'export_patch_masks': False,
+ 'export_patch_label_maps': True,
}
result = export_patches_from_multichannel_zstack(**export_kwargs)
@@ -61,7 +68,7 @@ if __name__ == '__main__':
# parse and record results
df = result['dataframe']
df['source_path'] = ff
- df.to_csv(where_output / 'df_objects.csv', **csv_args)
+ df.to_csv(where_output / 'df_objects.csv', index=False, **csv_args)
pd.DataFrame(result['timer_results'], index=[0]).to_csv(where_output / 'timer_results.csv', **csv_args)
pd.json_normalize(export_kwargs).to_csv(where_output / 'workflow_params.csv', **csv_args)
csv_args = {'mode': 'a', 'header': False} # append to CSV from here on
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 62fe918b..9a290ec5 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -24,10 +24,12 @@ def export_patches_from_multichannel_zstack(
zmask_filters: Dict = None,
zmask_expand_box_by: int = None,
export_pixel_probabilities=True,
- export_2d_patches=True,
+ export_2d_patches_for_training=True,
+ export_2d_patches_for_annotation=True,
export_3d_patches=True,
export_annotated_zstack=True,
export_patch_masks=True,
+ export_patch_label_maps=True,
) -> Dict:
ti = Timer()
@@ -81,7 +83,7 @@ def export_patches_from_multichannel_zstack(
)
ti.click('export_3d_patches')
- if export_2d_patches:
+ if export_2d_patches_for_annotation:
files = export_multichannel_patches_from_zstack(
Path(where_output) / '2d_patches',
stack,
--
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