Reading and Writing SWC Files

Reading an SWC File

The most common use case for swick is processing existing SWC files.

In order to accomplish that, of course we’ll need some SWCs! If you don’t have any on hand, you can grab some at NeuroMorpho.org to follow along with this section.

Once you have an SWC file, you can read it into an SWC object as follows:

import swick

# reads swc_file.swc into an object called my_swc
my_swc = swick.read_swc('path/to/swc_file.swc')

Note

The function read_swc() doubles as an SWC validator. If the provided SWC file is invalid, an SWCFormatError will be raised specifying a line number and format issue.

Writing an SWC File

Writing an SWC file is just as simple.

Let’s expand on the above example to read an SWC file again, but this time to also write a copy of the read file to a new location:

import swick

# reads swc_file.swc into an object called my_swc
my_swc = swick.read_swc('path/to/swc_file.swc')

# writes a copy of swc_file.swc to a new file called new_copy.swc
swick.write_swc('path/to/new_copy.swc', my_swc)

Obviously making copies of files is not a problem in need of solving. The real fun of swick is in analyzing or modifying the SWC in between reading and writing: features we’ll begin to explore in the next sections.