From 14b581bd7c13edf6b197d51491eabed73c571a57 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Fri, 2 Aug 2024 10:16:28 +0100
Subject: [PATCH] fix(imageviewer): bug in finding channels in tiler
added get_h5files
---
src/wela/imageviewer.py | 13 +++++++++++--
src/wela/plotting.py | 2 +-
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/src/wela/imageviewer.py b/src/wela/imageviewer.py
index 035b4ee..a2bfd5f 100644
--- a/src/wela/imageviewer.py
+++ b/src/wela/imageviewer.py
@@ -105,7 +105,7 @@ class ImageViewer:
channels = [
ch for ch in self.tiler.channels if ch not in channels_to_skip
]
- channel_indices = [channels.index(ch) for ch in channels]
+ channel_indices = [self.tiler.channels.index(ch) for ch in channels]
for ch_index, ch in zip(channel_indices, channels):
tile_dict_for_ch = self.get_all_tiles(tps, ch_index)
tiles = [x[trap_id] for x in tile_dict_for_ch.values()]
@@ -339,7 +339,7 @@ def colormap(channel):
return colormap
-def get_files(
+def get_files_zarr(
aliby_input: str,
aliby_output: str,
omero_name: str,
@@ -351,3 +351,12 @@ def get_files(
image_file_name = h5file.split("/")[-1].split(".")[0] + ".zarr"
image_file = str(Path(aliby_input) / omero_name / image_file_name)
return {"h5file": h5file, "image_file": image_file}
+
+
+def get_h5files(aliby_output: str, omero_name: str, print=False):
+ """List all positions for a particular experiment."""
+ h5files = [f.name for f in (Path(aliby_output) / omero_name).glob("*.h5")]
+ if print:
+ for file in h5files:
+ print(f"\t{file}")
+ return h5files
diff --git a/src/wela/plotting.py b/src/wela/plotting.py
index 56a412e..d57ec6b 100644
--- a/src/wela/plotting.py
+++ b/src/wela/plotting.py
@@ -82,7 +82,7 @@ def kymograph(
>>> kymograph(dl.df, hue="buddings", group="Msn2")
>>>
>>> from wela.sorting import sort_by_budding
- >>> _, buddings = dl.get_time_series(buddings)
+ >>> _, buddings = dl.get_time_series("buddings")
>>> sort_order = sort_by_budding(buddings)
>>> kymograph(dl.df, hue="flavin", sort_order=sort_order)
"""
--
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