swc data to test with

[zeffii]

Got any .swc files for me to experiment with?

[MartinPyka]

Here are two files, but you can download many other at
http://neuromorpho.org/

Best,
Martin

On 03.06.2015 11:58, Dealga McArdle wrote:

Got any .swc files for me to experiment with?

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Reply to this email directly or view it on GitHub
#1.

[MartinPyka]

ok, sorry, for this post. was not aware, that my attachments would be depicted as plain text. added two example files to the repository.

[zeffii]

cool thank you!

[zeffii]

[MartinPyka]

do you have any issues? the entorhinal neuron has a long ranging projection. therefore it looks a bit wired. the other neurons looks much more like a "classical" neuron.

[zeffii]

no it works fine, I'd use the csv importer with ' ' delimiter though instead of rolling your own file parser..

[MartinPyka]

thanks for your suggestion. I was worried, that the csv-importer can't handle the comments and empty lines which usually precede the data. therefore, I used my own parser. but I will give it a try.

[zeffii]

Yes, that could be a problem. i'm trying now :)

[zeffii]

ok, after trying it is a little messy. never mind me.

[zeffii]

import csv
import os
import bpy

''' read swc file '''
filepath = '/home/zeffii/Downloads/swc/swc_files/entho.CNG.swc'
with open(filepath, 'r', newline='') as csvfile:
    ofile = csv.reader(csvfile, delimiter=' ')

    # this makes a generator of the remaining non-empty lines
    # assumes there's always a lead and trailing space.. [1:-1] , this may be evil
    rows = (r[1:-1] for r in ofile if r and not r[0].startswith('#'))

    # convert string representation of each line to dict of list-floats
    neurons = {float(r[0].strip()): [float(i) for i in r] for r in rows}

but i'm making assumptions here about the formatting of the file, which is probably not cool.

[MartinPyka]

hey, thanks for the code. When I am back at work, I will try to integrate it into the importer

[zeffii]

in any case you have a working importer, if the csv route fails there is no loss :)

[MartinPyka]

jep, the next step will be to integrate the code of https://github.com/ajayramak/BlenderSWCVizualizer into this addon. I am already in contact with ajayramak about that.

[zeffii]

another repo with no images! :/

[MartinPyka]

changed that for my repo ;)

[zeffii]

as it should be. OK. back to work :)

[zeffii]

btw:

rows = ([j for j in r if j] for r in ofile if r and not r[0].startswith('#'))

may be better, it doesn't assume anything, but does add iff the list item is not empty. I don't know if this is faster than your original code... it may not be..