Export ID numbers for ClearMap2.1?

[cardinger]

Hello,

Is there any easy way to export a full list of all of the possible ClearMap2.1 ID numbers? Basically looking for an excel file of the tools > structure selector screen. Is this available?

Thanks!

[crousseau]

How about this ?

"""This assumes you are using the latest version (not default) of the atlas.
This is strongly advised but is not the default in the current version to keep the same behaviour as 2.0."""

import os

import ClearMap.Alignment.Annotation as annotation
import ClearMap.Settings as settings

annotation_file_path = os.path.join(settings.atlas_folder, 'ABA_25um_2017_annotation.tif')
label_file_path = os.path.join(settings.atlas_folder, 'ABA_annotation_last.json') 
annotation.initialize(annotation_file=annotation_file_path, label_file=label_file_path)


desination_file_path = os.path.expanduser('~/labels.csv')  # Replace destination here to your liking
annotation.annotation.df.to_csv(desination_file_path)