help > Entering parametres for AAP2 in command line
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Sep 27, 2019  02:09 PM | esteves5 - University of Toronto
Entering parametres for AAP2 in command line
Hi!
This question was also posted in General Discussion and I had the same question so I'd thought I'd post it here too.

"Parameters of APP2 for Command line of Vaa3d
Hi,
I am using the command line to run app2 to trace neuron with vaa3d. I follow this page: https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
Based on the help, to call app2 in terminal we should write:

>> vaa3d -x plugin_name -f app2 -i -o -p vaa3d -x plugin_name -f app2 -i -o -p [inmarker_file [channel [bkg_thresh [b_256cube [b_RadiusFrom2D [is_gsdt [is_gap [length_thresh [is_resample][is_brightfield][is_high_intensity]]]]]]]]]
where -p is for the parameters. When I run it without parameters, it chooses default values and works well. But when I set the parameters and put inmarker_file=NULL, it does not work.
Would appreciate your help."

I also don't understand the naming for each parametre. Some are self-explanatory, but others like b_256cube, less so.

Cheers,
Sam
Dec 3, 2019  10:12 AM | Hanchuan Peng
RE: Entering parametres for AAP2 in command line
Sam,

Normally for the parameters that are hard to understand, they are for various testing purposes and you do not have to use them. Yet, if you need to have a full understanding of the parameters, you are encouraged to check the argument-parsing session in the plugin's source code. For b_256cube, it just means whether or not downsampling a large image to 256x256xN before tracing.

Best,
-Hanchuan


Originally posted by esteves5:
Hi!
This question was also posted in General Discussion and I had the same question so I'd thought I'd post it here too.

"Parameters of APP2 for Command line of Vaa3d
Hi,
I am using the command line to run app2 to trace neuron with vaa3d. I follow this page: https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
Based on the help, to call app2 in terminal we should write:

>> vaa3d -x plugin_name -f app2 -i -o -p vaa3d -x plugin_name -f app2 -i -o -p [inmarker_file [channel [bkg_thresh [b_256cube [b_RadiusFrom2D [is_gsdt [is_gap [length_thresh [is_resample][is_brightfield][is_high_intensity]]]]]]]]]
where -p is for the parameters. When I run it without parameters, it chooses default values and works well. But when I set the parameters and put inmarker_file=NULL, it does not work.
Would appreciate your help."

I also don't understand the naming for each parametre. Some are self-explanatory, but others like b_256cube, less so.

Cheers,
Sam
Jan 3, 2020  09:01 AM | salam
RE: Entering parametres for AAP2 in command line
Hi,

I am trying to run APP2 headlessly from terminal. The commands runs without any problem but i am having difficulty in passing parameters. I want to set custom parameters for "length_thresh=1". The following command running with default parameters although I am setting length_thresh value

/Vaa3D_CentOS_64bit_v3.447/vaa3d -x vn2 -f app2 -i input.tif -p length_thresh=1

I appreciate suggestion and help

Binary Vaa3d version: Vaa3D_CentOS_64bit_v3.447

Shahinur