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NeuroBox3D / AnaMorph

Framework for creating 3d neuronal morphologies from point/diameter descriptions.
GNU Lesser General Public License v3.0
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am_cellgen: command not found #16

Open FireworkZhao opened 3 months ago

FireworkZhao commented 3 months ago

After cmake .. and make, I got the reslult: 


[100%] Built target am_meshstat```
But, when I try to run ```am_cellgen -i L-glu-8-31-16-b0023-image.CNG.swc```, it says: am_cellgen: command not found.
What's the possible cause of this situation
FireworkZhao commented 3 months ago

I tried to add the newly generated bin file to the path and tried to generated again. The result shows: AnaMorph cell generator (non-linear geometric modelling). swc input file name: "L-glu-8-31-16-b0023-image.CNG.swc" reading network from input swc file "L-glu-8-31-16-b0023-image.CNG.swc"..ERROR: Caught string exception at top level. message: "CellNetwork::readFromNeuroMorphoSWCFile(): unable to open SWC file for reading."

FireworkZhao commented 3 months ago

the error seems to change once I input a different swc file. Some of them can be processed but the output seems to be fault. for example this swc file and its corresponding result: fig1

bsumirak commented 3 months ago

Hi FireworkZhao,

I downloaded the "L-glu-8-31-16-b0023-image.CNG.swc" geometry from neuromorpho.org and also got an error. The (initial) problem is that the file does not specify any soma points. This is unsupported (yet the absenece of any useful hint to this problem is definitely not helping). Apparently, any vertex without parent (predecessor index -1) must be a soma vertex. Changing vertex 1 to soma type (1) circumvents this issue. But then there are geometrical problems in the geometry and the 3d geometry generation still fails.

The problem with the geometry "cell011.CNG" (also obtained from neuromorpho-org) is that it contains "custom" vertices (compartment type 7), which are unsupported in AnaMorph and silently ignored. I replaced 7 by 3 (basal dendrite) and then it worked and the output seems to be in line with what your picture displays.

I do not know why only compartment types 1 through 4 are supported, as the type does not matter to AnaMorph anyway (except soma/non-soma), but that is what the code says.

Hth. :)