From b9945ebc652b73fe5896d2cda7ee510439074dd2 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 30 May 2024 16:23:59 +0100
Subject: [PATCH] feature(pipeline):spatial locations added to tiler
Added function to find spatial location on microscopy stage of each
position from the log file. They are added as attributes to the tiler
instance created in run_one_position.
---
src/aliby/pipeline.py | 32 ++++++++++++++++++++++++++++++--
src/aliby/tile/tiler.py | 9 ++++++---
2 files changed, 36 insertions(+), 5 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 7396633..876a8ed 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -23,7 +23,7 @@ except AttributeError:
import aliby.global_parameters as global_parameters
from agora.abc import ParametersABC, ProcessABC
-from agora.io.metadata import MetaData
+from agora.io.metadata import MetaData, find_file, parse_from_swainlab_grammar
from agora.io.signal import Signal
from agora.io.writer import LinearBabyWriter, StateWriter, TilerWriter
from aliby.io.dataset import dispatch_dataset
@@ -237,7 +237,7 @@ class Pipeline(ProcessABC):
self.log(
f"Fetching data using {dispatcher.__class__.__name__}.", "info"
)
- # get log files, either locally or via OMERO
+ # get positions_ids and save microscopy log files
with dispatcher as conn:
position_ids = conn.get_position_ids()
directory = self.store or root_dir / conn.unique_name
@@ -250,8 +250,34 @@ class Pipeline(ProcessABC):
print("\t" + f"{i}: " + pos.split(".")[0])
# add directory to configuration
self.parameters.general["directory"] = str(directory)
+ # find spatial locations on the microscope stage of the positions
+ self.spatial_locations = self.spatial_location_of_positions(
+ position_ids
+ )
return position_ids
+ def spatial_location_of_positions(self, position_ids):
+ """Find spatial location of each position from the microscopy log file."""
+ dir_path = Path(self.parameters.general["directory"])
+ logpath = find_file(dir_path, "*.log")
+ if logpath:
+ raw_meta = parse_from_swainlab_grammar(logpath)
+ location_df = raw_meta["group_position"]
+ locations = {
+ position: (
+ location_df[location_df.Name == position].X.values.astype(
+ "float"
+ )[0],
+ location_df[location_df.Name == position].Y.values.astype(
+ "float"
+ )[0],
+ )
+ for position in position_ids
+ }
+ else:
+ locations = {}
+ return locations
+
def channels_from_OMERO(self):
"""Get a definitive list of channels from OMERO."""
dispatcher = dispatch_dataset(self.expt_id, **self.server_info)
@@ -369,6 +395,8 @@ class Pipeline(ProcessABC):
TilerParameters.from_dict(config["tiler"]),
OMERO_channels=self.OMERO_channels,
)
+ # add location of position on the microscope stage
+ tiler.spatial_location = self.spatial_locations.get(name, None)
# initialise Baby
babyrunner = BabyRunner.from_tiler(
BabyParameters.from_dict(config["baby"]), tiler=tiler
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index 981b4c7..baa53f0 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -25,6 +25,7 @@ the most tiles.
The experiment is stored as an array with a standard indexing order of
(Time, Channels, Z-stack, X, Y).
"""
+
import logging
import re
import typing as t
@@ -576,9 +577,11 @@ class Tiler(StepABC):
channels = [channels]
# convert to indices
channels = [
- self.channels.index(channel)
- if isinstance(channel, str)
- else channel
+ (
+ self.channels.index(channel)
+ if isinstance(channel, str)
+ else channel
+ )
for channel in channels
]
# get the data as a list of length of the number of channels
--
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