Settings

Module to set ClearMap’s internal parameter and paths to external programs.

Note

Edit the setup() routine to point to set paths for specific hosts.

path()

Returns root path to the ClearMap software.

Returns

pathstr

Root path to ClearMap.

atlas_folder = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/Resources/Atlas'

Absolute path to the ClearMap’s atlas folder.

clearmap_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap'

Absolute path to the ClearMap’s root folder.

elastix_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/External/elastix/build'

Absolute path to the elastix installation

Note

Elastix Webpage

external_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/External'

Absolute path to the ClearMap’s external program folder.

ilastik_path = None

Absolute path to the Ilastik installation

Note

Ilastik Webpage Ilastik Download

imagej_path = None

Absolute path to the ImageJ/Fiji installation

Note

ImageJ/Fiji Webpage

resources_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/Resources'

Absolute path to the ClearMap’s resources folder.

tera_stitcher_path = None

Absolute path to the TeraStitcher installation

Note

TeraSticher Webpage

test_data_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/Tests/Data'

Absolute path to the ClearMap’s test data folder.

test_path = '/home/crousseau/code/icm/ClearMap2-lf003/ClearMap/Tests'

Absolute path to the ClearMap’s test folder.