brainglobe
`kim_dev...` atlases raise an error
Not sure if this is an error with the atlas, my machine or the plugin, but I noticed that loading all the kim_dev atlases cause an error.
Full traceback
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/projects/brainglobe/brainglobe-napari/src/brainglobe_napari/atlas_viewer_widget.py:130, in AtlasViewerWidget.__init__.<locals>._on_selection_changed()
126 self._selected_atlas_name = self._model.data(
127 self._model.index(self._selected_atlas_row, 0)
128 )
129 selected_atlas = BrainGlobeAtlas(self._selected_atlas_name)
--> 130 self.atlas_info.setText(str(selected_atlas))
selected_atlas = kim dev atlas (res. mouse)
self = <brainglobe_napari.atlas_viewer_widget.AtlasViewerWidget object at 0x7f705ba39b40>
self.atlas_info = <PyQt5.QtWidgets.QTextEdit object at 0x7f705b9eb520>
131 else:
132 self.atlas_info.setText("")
File ~/miniconda3/envs/brainglobe/lib/python3.10/site-packages/bg_atlasapi/bg_atlas.py:204, in BrainGlobeAtlas.__str__(self=kim dev atlas (res. mouse))
202 buf = StringIO()
203 _console = Console(file=buf, force_jupyter=False)
--> 204 _console.print(self)
_console = <console width=163 None>
self = kim dev atlas (res. mouse)
206 return buf.getvalue()
File ~/miniconda3/envs/brainglobe/lib/python3.10/site-packages/rich/console.py:1699, in Console.print(self=<console width=163 None>, sep=' ', end='\n', style=None, justify=None, overflow=None, no_wrap=None, emoji=None, markup=None, highlight=None, width=None, height=None, crop=True, soft_wrap=False, new_line_start=False, *objects=(kim dev atlas (res. mouse),))
1697 if style is None:
1698 for renderable in renderables:
-> 1699 extend(render(renderable, render_options))
render_options = ConsoleOptions(size=ConsoleDimensions(width=163, height=12), legacy_windows=False, min_width=1, max_width=163, is_terminal=False, encoding='utf-8', max_height=12, justify=None, overflow=None, no_wrap=None, highlight=None, markup=None, height=None)
renderable = kim dev atlas (res. mouse)
1700 else:
1701 for renderable in renderables:
File ~/miniconda3/envs/brainglobe/lib/python3.10/site-packages/rich/console.py:1331, in Console.render(self=<console width=163 None>, renderable=kim dev atlas (res. mouse), options=ConsoleOptions(size=ConsoleDimensions(width=163,...p=None, highlight=None, markup=None, height=None))
1329 _Segment = Segment
1330 _options = _options.reset_height()
-> 1331 for render_output in iter_render:
iter_render = <generator object BrainGlobeAtlas.__rich_console__ at 0x7f705ba06b20>
1332 if isinstance(render_output, _Segment):
1333 yield render_output
File ~/miniconda3/envs/brainglobe/lib/python3.10/site-packages/bg_atlasapi/bg_atlas.py:213, in BrainGlobeAtlas.__rich_console__(self=kim dev atlas (res. mouse), *args=(<console width=163 None>, ConsoleOptions(size=ConsoleDimensions(width=163,...p=None, highlight=None, markup=None, height=None)))
208 def __rich_console__(self, *args):
209 """
210 Method for rich API's console protocol.
211 Prints the atlas metadata as a table nested in a panel
212 """
--> 213 panel = _rich_atlas_metadata(self.atlas_name, self.metadata)
self.atlas_name = 'kim_dev_mouse_mri_dwi_10um'
self.metadata = {'name': 'kim_dev_mouse_mri_dwi', 'citation': 'Kim, Yongsoo (2022), “KimLabDevCCFv001”, Mendeley Data, V1, doi: 10.17632/2svx788ddf.1', 'atlas_link': 'https://data.mendeley.com/datasets/2svx788ddf/1', 'species': 'Mus musculus', 'symmetric': True, 'resolution': [10.0, 10.0, 10.0], 'orientation': 'asr', 'version': '1.1', 'shape': [1320, 800, 1140], 'trasform_to_bg': [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 11400.0], [0.0, 0.0, 0.0, 1.0]], 'additional_references': [], 'atlas_packager': None}
self = kim dev atlas (res. mouse)
214 yield panel
File ~/miniconda3/envs/brainglobe/lib/python3.10/site-packages/bg_atlasapi/utils.py:27, in _rich_atlas_metadata(atlas_name='kim_dev_mouse_mri_dwi_10um', metadata={'additional_references': [], 'atlas_link': 'https://data.mendeley.com/datasets/2svx788ddf/1', 'atlas_packager': None, 'citation': 'Kim, Yongsoo (2022), “KimLabDevCCFv001”, Mendeley Data, V1, doi: 10.17632/2svx788ddf.1', 'name': 'kim_dev_mouse_mri_dwi', 'orientation': 'asr', 'resolution': [10.0, 10.0, 10.0], 'shape': [1320, 800, 1140], 'species': 'Mus musculus', 'symmetric': True, ...})
25 gray = "#A9A9A9"
26 mocassin = "#FFE4B5"
---> 27 cit_name, cit_link = metadata["citation"].split(", ")
metadata["citation"] = 'Kim, Yongsoo (2022), “KimLabDevCCFv001”, Mendeley Data, V1, doi: 10.17632/2svx788ddf.1'
metadata = {'name': 'kim_dev_mouse_mri_dwi', 'citation': 'Kim, Yongsoo (2022), “KimLabDevCCFv001”, Mendeley Data, V1, doi: 10.17632/2svx788ddf.1', 'atlas_link': 'https://data.mendeley.com/datasets/2svx788ddf/1', 'species': 'Mus musculus', 'symmetric': True, 'resolution': [10.0, 10.0, 10.0], 'orientation': 'asr', 'version': '1.1', 'shape': [1320, 800, 1140], 'trasform_to_bg': [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 11400.0], [0.0, 0.0, 0.0, 1.0]], 'additional_references': [], 'atlas_packager': None}
29 # Create a rich table
30 tb = Table(
31 box=None,
32 show_lines=False,
33 title=atlas_name.replace("_", " ").capitalize(),
34 title_style=f"bold {orange}",
35 )
ValueError: too many values to unpack (expected 2)
Interesting! I can't reproduce this on either my Macbook or my Ubuntu desktop, in a clean conda environmen with a pip install git+ from current main branch 🤔
Could it be that you have a dev install of the BG atlas API in your env @adamltyson ?
I can reproduce on macOS with:
- Delete relevant atlases, create env and run napari:
rm -rfv ~/.brainglobe/kim_dev*
micromamba create --name bg-atlastest -c conda-forge python=3.10 napari -y
micromamba activate bg-atlastest
pip install git+https://github.com/brainglobe/brainglobe-napari
napari
-
Plugins->BrainGlobe Atlas Viewer - Click on
kim_dev_mouse_idisco_10um - In the terminal I get the usual
Bgatlas_api: kim_dev_mouse_idisco_10um not found locally. Downloading...which takes a while. - Once download is complete I get the above error.
I'm guessing it's something wrong/different with these atlases, but I don't know why I can reproduce and you can't.
why is it called kim_mouse_idisco_10um for you and kim_mouse_10um for me?
Do we have different versions of the bg-atlasapi? I have 1.0.2 from pypi
FWIW I can type the commands above into a terminal (with mamba instead of micromamba but that shouldn't matter?), click on the first kim atlas and get:
Ah, mystery solved, these are different atlases. I should have been more specific with my original message. kim_mouse_10um works, but any atlas starting with kim_dev doesn't. The Kim lab have made a lot of atlases!
Locally, I don't get any kim_dev atlases - is that because they are not included in the bg-atlasapi version I have?
Huh. The version shouldn't make any difference. What's the output of brainglobe list?
Never mind... I was silly :joy: didn't scroll down far enough :flushed: I can reproduce! :tada:
This can be reproduced without napari or the widget by
from bg_atlasapi import BrainGlobeAtlas
atlas = BrainGlobeAtlas("kim_dev_mouse_stp_10um")
print(atlas)
The problem is that metadata["citation"].split(", ") for this atlas returns a list with 6 elements:
['Kim', 'Yongsoo (2022)', '“KimLabDevCCFv001”', 'Mendeley Data', 'V1', 'doi: 10.17632/2svx788ddf.1']
, but L27 of bg_atlasapi.utils expects just 2 elements.
For reference, the same line metadata["citation"].split(", ") for the allen_mouse_100um atlas at the same point in the code looks like:
['Wang et al 2020', 'https://doi.org/10.1016/j.cell.2020.04.007']
Ultimately, I think this is a problem with the kim_dev_... atlas itself, specifically, the metadata.json file