when running brainglobe-heatmap through a jupyter notebook instantiation through code ocean, i am running into this error:
`f = bgh.Heatmap(
values,
position=1000,
orientation="sagittal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
thickness=1000,
atlas_name="allen_cord_20um",
format='2D'
).show()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
File /opt/conda/lib/python3.10/site-packages/brainrender/atlas.py:26, in Atlas.__init__(self, atlas_name)
25 try:
---> 26 super().__init__(atlas_name=atlas_name, print_authors=False)
27 except TypeError:
28 # The latest version of BGatlas has no print_authors argument
TypeError: BrainGlobeAtlas.__init__() got an unexpected keyword argument 'print_authors'
During handling of the above exception, another exception occurred:
OSError Traceback (most recent call last)
Cell In[23], line 1
----> 1 f = bgh.Heatmap(
2 values,
3 position=1000,
4 orientation="sagittal", # 'frontal' or 'sagittal', or 'horizontal' or a tuple (x,y,z)
5 thickness=1000,
6 atlas_name="allen_cord_20um",
7 format='2D'
8 ).show()
File /opt/conda/lib/python3.10/site-packages/brainglobe_heatmap/heatmaps.py:82, in Heatmap.__init__(self, values, position, orientation, hemisphere, title, cmap, vmin, vmax, format, thickness, interactive, zoom, atlas_name, label_regions, **kwargs)
79 self.label_regions = label_regions
81 # create a scene
---> 82 self.scene = Scene(
83 atlas_name=atlas_name,
84 title=title,
85 title_color=grey_darker,
86 **kwargs,
87 )
89 # prep colors range
90 self.prepare_colors(values, cmap, vmin, vmax)
File /opt/conda/lib/python3.10/site-packages/brainrender/scene.py:57, in Scene.__init__(self, root, atlas_name, inset, title, screenshots_folder, plotter, title_color)
54 self.actors = [] # stores all actors in the scene
55 self.labels = [] # stores all `labels` actors in scene
---> 57 self.atlas = Atlas(atlas_name=atlas_name)
59 self.screenshots_folder = (
60 Path(screenshots_folder)
61 if screenshots_folder is not None
62 else Path().cwd()
63 )
64 self.screenshots_folder.mkdir(exist_ok=True)
File /opt/conda/lib/python3.10/site-packages/brainrender/atlas.py:29, in Atlas.__init__(self, atlas_name)
26 super().__init__(atlas_name=atlas_name, print_authors=False)
27 except TypeError:
28 # The latest version of BGatlas has no print_authors argument
---> 29 super().__init__(atlas_name=atlas_name)
File /opt/conda/lib/python3.10/site-packages/brainglobe_atlasapi/bg_atlas.py:86, in BrainGlobeAtlas.__init__(self, atlas_name, brainglobe_dir, interm_download_dir, check_latest, config_dir, fn_update)
84 # Look for this atlas in local brainglobe folder:
85 if self.local_full_name is None:
---> 86 if self.remote_version is None:
87 check_internet_connection(raise_error=True)
88 check_gin_status(raise_error=True)
File /opt/conda/lib/python3.10/site-packages/brainglobe_atlasapi/bg_atlas.py:122, in BrainGlobeAtlas.remote_version(self)
118 remote_url = self._remote_url_base.format("last_versions.conf")
120 try:
121 # Grasp remote version
--> 122 versions_conf = utils.conf_from_url(remote_url)
123 except requests.ConnectionError:
124 return None
File /opt/conda/lib/python3.10/site-packages/brainglobe_atlasapi/utils.py:314, in conf_from_url(url)
311 cache_path.parent.mkdir(parents=True, exist_ok=True)
313 # Cache the available atlases
--> 314 with open(cache_path, "w") as f_out:
315 config_obj.write(f_out)
317 return config_obj
OSError: [Errno 30] Read-only file system: '/data/.brainglobe/last_versions.conf'
i ran into a similar issue when running brainglobe_atlasapi alone. this is due to this recent (commit) in latest_version.conf cache which now writes a file to a directory. in my setup, the directory is read-only so i simply add the check_latest = False parameter here:
BrainGlobeAtlas('allen_mouse_10um', check_latest=False). could you add a check_latest variable to the bgh.Heatmap function to bypass writing a file to the directory?
when running brainglobe-heatmap through a jupyter notebook instantiation through code ocean, i am running into this error:
i ran into a similar issue when running brainglobe_atlasapi alone. this is due to this recent (commit) in latest_version.conf cache which now writes a file to a directory. in my setup, the directory is read-only so i simply add the check_latest = False parameter here: BrainGlobeAtlas('allen_mouse_10um', check_latest=False). could you add a check_latest variable to the bgh.Heatmap function to bypass writing a file to the directory?