[#7855] sort neuron swc plugin bug

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State: more information
Open
Date:
2015-05-14 10:00
Priority: more information
3
Submitted By:
sridevi polavaram (spolavar)
Assigned To: more information
Nobody (None)
Hardware: 
PC
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Operating System: 
Linux
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Summary: more information
sort neuron swc plugin bug

Detailed description

reorder the swc tree to get the soma node at the top, it ends up adding extra lines, which are visually also erroneous. This is true for both connected swc and fragmented swc. Attached is an example of connected swc file, which fails to reorder the soma point to the top without adding extraneous nodes.

Response

Message

Date: 2015-05-15 12:22
Sender: Hanbo Chen

Hi, Sridevi

When threshold is 0, click OK will not generate any new connections, click cancel will connect everything to form a complete tree.

Current sorting function only sort based on tree topology. We will consider to include type information when perform sorting in the future and improve its performance.

Hanbo


Date: 2015-05-15 06:04
Sender: sridevi polavaram

After entering the new root number, I was clicking on "ok" as it seems more intuitive to me. This time i tried clicking "cancel", which i am not sure what is the difference. But I do see a difference in the connectivity when i clicked "ok" vs "cancel" at the "0" threshold.

However,  the problem still persists. In the attached file there are two soma nodes located somewhere in the middle of the file, when i reorder, i expect both come to the top. currently, swc_sort is not doing this.


Date: 2015-05-14 10:31
Sender: Zhi Zhou

Can you specify which input parameters you are using when call sort_neuron_swc plugin?

I just tried sort_neuron_swc plugin with input "New root number = 181" followed by "cancel" for connecting all the points. There is no such extra line in the result. Please check the attachment for the sorted swc.

Attached Files:

Name Download
LK06_OLM_1_root.asc.swc_connected.swc_connected.swc Download
LK06_OLM_1_root.asc.swc_connected.swc_connected.swc_sorted.swc Download
2010-01-14-1.asc.swc_connected.swc Download

Changes:

Field Old Value Date By
New Message2015-05-15 12:22cojoc
File Added734: 2010-01-14-1.asc.swc_connected.swc2015-05-15 06:04spolavar
New Message2015-05-15 06:04spolavar
File Added733: LK06_OLM_1_root.asc.swc_connected.swc_connected.swc_sorted.swc2015-05-14 10:31zhizhou
New Message2015-05-14 10:31zhizhou
File Added732: LK06_OLM_1_root.asc.swc_connected.swc_connected.swc2015-05-14 10:00spolavar