General Question: How to use simple merge to merge skel_ids spread across different folders?

[Mohinta2892]

Hello!

I have written a tiny snippet as below to merge skels of the same label id that are spread across many folders. However, after merge when I visualise it, no skeleton gets plotted. The final file contains data as attached.

I wanted to know what I am doing incorrectly and get your feedback if this is how simple_merge is to be used?

output_skels = “/path/to/out_skels"
## read skel files for the same label id
skels_to_merge = [('27049069.swc',
                   ‘/path1/27049069.swc|/path2/27049069.swc|/path3/27049069.swc|/path4/27049069.swc')]

for i, files in enumerate(skels_to_merge):
    filename = files[0]
    filepaths = files[1].split('|')
    basename, ext = os.path.splitext(filename)
    skels_list = []
    for fp in filepaths:
        if ext == ".swc":
            with open(fp, "rt") as swc:
                skel = Skeleton.from_swc(swc.read())
                skels_list.append(skel)
                # skel.viewer()

    skel = Skeleton.simple_merge(skels_list).consolidate()
    skel = kimimaro.postprocess(
        skel,
        dust_threshold=1000,  # physical units
        tick_threshold=3500  # physical units
    )
    # print(skel)
    fname = f"{output_skels}/{filename}"
    with open(fname, "wt") as f:
        f.write(skel.to_swc())

27049069.swc.zip

Thank you,
Samia

[william-silversmith]

Hi Samia!

When I open your file, I get the following result. I see something similar in SharkViewer. Is this not what you were expecting? Can you show how you are visualizing the data?

[Mohinta2892]

Many thanks William.

I can visualise it in SharkViewer. However, when I do kimimaro view /path/to/skeleton.swc, nothing gets plotted.

Kimimaro version: 4.1.2

Also, I was hoping the skeletons to be connected as one object. This is something that simple_merge should achieve right?

[william-silversmith]

Huh, this is pretty strange. I tried using the CLI and I got the same image I got above. Try updating pip install cloud-volume matplotlib -U? I think there was a breaking change at some point.

Yes, simple_merge should combine them all into one object. All it does is staple them together. So if they are not showing up as a single object, either the input is wrong or the postprocessing is too aggressive. For example, if there is a broken link, then the dust threshold could remove segments.