From ac54d2406ec55d14275bf0741eb4500fd7cb314a Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Sun, 8 Oct 2023 07:58:04 +0200
Subject: [PATCH] comments only
---
extensions/chaeo/examples/batch_run_patches.py | 2 ++
extensions/chaeo/workflows.py | 1 +
2 files changed, 3 insertions(+)
diff --git a/extensions/chaeo/examples/batch_run_patches.py b/extensions/chaeo/examples/batch_run_patches.py
index 52b01490..c831c08e 100644
--- a/extensions/chaeo/examples/batch_run_patches.py
+++ b/extensions/chaeo/examples/batch_run_patches.py
@@ -27,6 +27,8 @@ if __name__ == '__main__':
csv_args = {'mode': 'w', 'header': True} # when creating file
px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+ # TODO: try/catch blocks and error handling around workflow calls
+ # TODO: pack JSON-serializable workflow inputs
for ff in where_czi.iterdir():
pattern = 'Selection--W([\d]+)--P([\d]+)-T([\d]+)'
ma = re.match(pattern, ff.stem)
diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py
index 85b16d8b..30c2221b 100644
--- a/extensions/chaeo/workflows.py
+++ b/extensions/chaeo/workflows.py
@@ -8,6 +8,7 @@ from extensions.chaeo.zmask import build_zmask_from_object_mask, project_stack_f
from model_server.accessors import generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.workflows import Timer
+# TODO: unpack and validate inputs
def export_patches_from_multichannel_zstack(
input_zstack_path: str,
ilastik_project_file: str,
--
GitLab