allensdk.internal.morphology.validate_swc module¶
- class allensdk.internal.morphology.validate_swc.TestNode(n, t, x, y, z, r, pn)[source]¶
Bases:
object
- allensdk.internal.morphology.validate_swc.resave_swc(orig_swc, new_file)[source]¶
Reads SWC file into AllenSDK Morphology object and resaves it. This can fix some problems in an SWC file that may disrupt other software tools reading the file (e.g., NEURON)
- Parameters:
- orig_swc: string
- Name of SWC file to read
- new_file: string
- Name of output SWC file
- allensdk.internal.morphology.validate_swc.validate_swc(swc_file)[source]¶
Tests SWC files for compatibility with AllenSDK
- To be compatible with NEURON, SWC files must have the following properties:
a single root node with parent ID ‘-1’
sequentially increasing ID numbers
immediate children of the soma cannot branch
To be compatible with feature analysis, SWC files can only have node types in the range 1-4:
1 = soma 2 = axon 3 = [basal] dendrite 4 = apical dendrite