nathantspencer/webknossos_toolkit

A set of tools for manipulation of the .nml, .swc, .zip, and .hoc files generated from webKnossos and related software. Used for processing of segmentation and skeletonization data.

webknossos_toolkit's Issues

nml2swc Indentation Error

There was an Tab Error in the else statement of line 94 of nml2swc.py which caused it to run incorrectly. I believe I have fixed the error, since after making the spacing adjustments, the code ran fine. Here is the corrected version:

nml2swc2.py.zip

swc_smoother needs documentation

See title. Short and sweet.

nml_merger: knossos compatability

nml_merger, as it stands, can only merge WebKnossos files. The old Knossos format is slightly different and won't merge, instead triggering a warning and skipping the file.

The same information is (maybe?) found in the old Knossos files, it just needs to be parsed differently before it can be merged.

swc2hoc needs guaranteed completion, documentation

As it stands, swc2hoc.py sometimes doesn't terminate. Obviously this needs to be fixed. Documentation is also necessary and should be added to the readme.

reinstate & refactor swc_corrector

swc_corrector.py was removed but should be reinstated and refactored to meet the level of polish that other scripts in this toolkit deliver. My thinking at the time was that integrating it into nml2swc.py would make it unneccessary, but it would still be useful to have as a standalone.

add help dialogue to scripts

There's no help dialogue to help steer a user in the right direction if they misunderstand the intended arguments of a script.

That being said, there probably should be!

swc2hoc soma should be corrected, actually traversed

The soma is currently handled in a very naive way. The swc should be reordered and then traversed to write its nodes, not just copied as is from the file.

swc2hoc comment function should support branching from soma

If multiple branches descend directly from the soma, chaos ensues. The soma is currently treated as a special case but should be treated in the same way as the other branchpoints, except that its branch numbers should have a "d" prepended to them.

incorporate knoss2obj and knoss2nrrd into toolkit

These two scripts really belong in the zip_tools directory of this toolkit, but need to be generalized for use by others. Too much hardcoding etc. exists in those scripts at the moment.

Parse comments in nml to determine swc node types

Comments such as "input", "lost", and "myelin" should trigger swc nodes of a different type

Comment fails when child section comes before parent in hoc code

In swc2hoc.py, sometimes the hoc code will be generated in such a way that a child section is written before its parent. Attempting to use the comment prefix from the parent leads to issues. Perhaps the best solution is to "sort" the sections in a way that this is forbidden before calling comment.

restructuring of toolkit

A few things that should be done here to clean things up a bit:

• standardize the input/output format of python scripts
• separate nml and swc tools
• add swc_corrector to the end of nml2swc to combine the two
• reformat documentation

Reorganize + redocument

Desperately needs better folder structure and new README.

swc2hoc should take axon skeleton

Given the importance of the axon sections in HOC, it seems like that portion of the code should be generated similarly to the soma and dendrite sections.

How to use nml2swc correctly?

I can't get the swc file when using the nml2swc script. I ran it from Spyder (Python version 3.8.5), replacing the first argument of the first function with the path where my .nml file is located. No errors are thrown, yet nothing happens with the nml file.

a few tiny helper scripts needed for hoc processing

• swc_offset.py - should add or subtract an offset from each x, y, and z coordinate in specified file
• swc2pt3dadd.py - converts every line in an swc file to a pt3dadd() for adding a point to a .hoc file

swc2hoc should support directory as argument

Passing a directory to hoc_commenter.py should search the directory for .hoc files and comment each of them as a batch. This is already done by some other tools and should be very easy to implement.

documentation

• swc_components
• swc_corrector

swc2hoc sometimes results in jumpy .hoc

Sometime the HocCode produced by swc2hoc.py has giant jumps in it. It looks to me like this is caused by a failure of the TREES Toolbox to find a branchpoint, but more investigation is needed. Debug comment has been added to help remedy this problem manually.

swc_center needs documentation

Should be added to the readme.

swc_corrector needs to take files as arguments

Right now, it uses an unacceptable method of gathering files, looking in a hard-coded folder for them.