[BUG] Structures don't load for atlases in user configured brainglobe_dir path

[pderdeyn]

Describe the bug
I have set a different path for my brainglobe_dir variable in the config file for brainglobe_atlasapi than the default. When I load the brainrender widget in napari, I can see the atlases I have in this folder. However, when I click an atlas once to view the structures, I get a stack or errors (shown in screenshots)

To Reproduce
Step 1: Change brainglobe_dir in config file (~/.config/brainglobe/bg_config.conf)
Step 2: Add an atlas to installation
Step 3: Open brainrender widget in napari and click atlas from the list

Expected behaviour
List of structures should appear and I should be able to load in meshes

Screenshots

Computer used (please complete the following information):

• OS: Ubuntu
• Version 18.j04

Additional context
Interestingly, double clicking does work to show the annotation and reference images

[pderdeyn]

I fixed this on my computer with a couple of small changes in https://github.com/brainglobe/brainrender-napari/blob/main/brainrender_napari/utils/load_user_data.py

import json
from pathlib import Path

from brainglobe_atlasapi.list_atlases import get_local_atlas_version
+ from brainglobe_atlasapi import config

def read_atlas_metadata_from_file(atlas_name: str):
    """Reads atlas metadata stored in a `.json` in the BrainGlobe directory."""
-    brainglobe_dir = Path.home() / ".brainglobe"
+    brainglobe_dir = config.get_brainglobe_dir()
    with open(
        brainglobe_dir
        / f"{atlas_name}_v{get_local_atlas_version(atlas_name)}"
        / "metadata.json",
    ) as metadata_file:
        return json.loads(metadata_file.read())


def read_atlas_structures_from_file(atlas_name: str):
    """Reads structure info from a '.json' in the BrainGlobe directory."""
-    brainglobe_dir = Path.home() / ".brainglobe"
+    brainglobe_dir = config.get_brainglobe_dir()
    with open(
        brainglobe_dir
        / f"{atlas_name}_v{get_local_atlas_version(atlas_name)}"
        / "structures.json",
    ) as metadata_file:
        return json.loads(metadata_file.read())

Technically the error I encountered came from just the second function there, I didn't see references to read_atlas_metadata_from_file, but included the change there anyways, too

[alessandrofelder]

Thanks a lot for reporting @pderdeyn - would you want to make a Pull Request with your fixes by any chance? (Happy either way)

[pderdeyn]

Sure, can do, @alessandrofelder! I should be able to do that later in the week