From f8295af06c6469cce51956ba2ac593ba9666ab00 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 12 Oct 2023 11:10:05 +0200
Subject: [PATCH] Confirmed able to catch failures
---
extensions/chaeo/util.py | 3 ++-
extensions/chaeo/workflows.py | 5 ++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/extensions/chaeo/util.py b/extensions/chaeo/util.py
index 7a8406db..411aafd7 100644
--- a/extensions/chaeo/util.py
+++ b/extensions/chaeo/util.py
@@ -86,4 +86,5 @@ def loop_workflow(files, where_output, workflow_func, params,
InMemoryDataAccessor(result['interm'][k])
)
- pd.DataFrame(failures).to_csv(Path(where_output) / 'failures.csv')
\ No newline at end of file
+ if len(failures) > 0:
+ pd.DataFrame(failures).to_csv(Path(where_output) / 'failures.csv')
\ No newline at end of file
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 332f8f9f..c1508f6c 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -32,7 +32,6 @@ def export_patches_from_multichannel_zstack(
export_patch_masks=True,
export_patch_label_maps=True,
) -> Dict:
-
ti = Timer()
stack = generate_file_accessor(Path(input_zstack_path))
fstem = Path(input_zstack_path).stem
@@ -86,7 +85,7 @@ def export_patches_from_multichannel_zstack(
if export_2d_patches_for_annotation:
files = export_multichannel_patches_from_zstack(
- Path(where_output) / '2d_patches',
+ Path(where_output) / '2d_patches_annotation',
stack,
zmask_meta,
prefix=fstem,
@@ -109,7 +108,7 @@ def export_patches_from_multichannel_zstack(
if export_2d_patches_for_training:
files = export_multichannel_patches_from_zstack(
- Path(where_output) / '2d_patches',
+ Path(where_output) / '2d_patches_training',
stack.get_one_channel_data(4),
zmask_meta,
prefix=fstem,
--
GitLab