From 871801f41fd045e430e0685514fbe8b756e24cae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 21 Jan 2022 18:22:48 +0000
Subject: [PATCH] add fields and defaults
---
aliby/experiment.py | 8 ++++++--
aliby/pipeline.py | 4 +++-
aliby/tile/tiler.py | 2 +-
3 files changed, 10 insertions(+), 4 deletions(-)
diff --git a/aliby/experiment.py b/aliby/experiment.py
index 451a8d06..6dcc953d 100644
--- a/aliby/experiment.py
+++ b/aliby/experiment.py
@@ -114,11 +114,15 @@ class MetaData:
metadata_dict = self.load_logs()
self.metadata_writer.write(path="/", meta=metadata_dict, overwrite=False)
- def add_omero_id(self, omero_id):
+ def add_field(self, field_name, field_value):
self.metadata_writer.write(
- path="/", meta={"omero_id": omero_id}, overwrite=False
+ path="/", meta={field_name: field_value}, overwrite=False
)
+ def add_fields(self, fields_values: dict):
+ for field, value in field_values.items():
+ self.add_field(field, value)
+
########################### Old Objects ####################################
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index f572dc4e..b6dabd6c 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -196,7 +196,9 @@ class Pipeline(ProcessABC):
# if True: # not Path(filename).exists():
meta = MetaData(directory, filename)
meta.run()
- meta.add_omero_id(config["general"]["id"])
+ meta.add_fields(
+ {"omero_id,": config["general"]["id"], "image_id": image_id}
+ )
tiler = Tiler.from_image(
image, TilerParameters.from_dict(config["tiler"])
)
diff --git a/aliby/tile/tiler.py b/aliby/tile/tiler.py
index a0e795ac..cd5b91a8 100644
--- a/aliby/tile/tiler.py
+++ b/aliby/tile/tiler.py
@@ -142,7 +142,7 @@ class TilerParameters(ParametersABC):
@classmethod
def default(cls):
- return cls(96, "Brightfield", 0)
+ return cls(117, "Brightfield", 0)
class Tiler(ProcessABC):
--
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