treeconvert converts NML files1 to SWC2. This allows you to view (Py)KNOSSOS skeletal reconstructions in SWC viewers, e.g. Amira.
If the NML file consists of multiple trees, a separate SWC file will get created for each one.
treeconvert will automatically assign the numeric value of an SWC structure identifier if there is a corresponding comment in the NML node. There exist different conventions on which numeric value to use for an identifier, so treeconvert will use those of “CNIC data” described here 3 and here (archive.org, last retrieved on April 16th, 2019).
treeconvert only has a single dependency: declxml. For convenience, declxml is included directly inside treeconvert's source tree.
The setup.py installs a treeconvert binary that you can use from your PATH.
Alternatively, go to Releases to download a self-contained zip file.
To execute the .pyz file, execute it with python: python3 treeconvert.pyz -h.
Minimum Python version is 3.7.
$ python3 cmutil.pyz -h
usage: treeconvert.pyz [-h] --from {NML,PYKNOSSOS_NML} --to {SWC} [--force]
input_file
Convert annotation files between various formats.
positional arguments:
input_file Input file. Output file will be created automatically
with extension `.[--to]'.
optional arguments:
-h, --help show this help message and exit
--from {NML,PYKNOSSOS_NML}
input format
--to {SWC} output format
--force overwrite existing output files.
If the output format is SWC, and if there are multiple trees in the input
file, treeconvert will create a file for each tree, and append the filename
with its index.There a subtle differences between NML files created from KNOSSOS and those created from PyKNOSSOS. Because of this, the input format must explicitly be nml or pyknossos_nml.
Other than declxml (released under MIT License), all of treeconvert’s files are released under the zlib license (c.f. LICENSE).