treeconvert

treeconvert converts NML files [1] to SWC [2]. 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 [2] and here (archive.org, last retrieved on April 16th, 2019).

[1]	For more information about NML files, visit https://github.com/scalableminds/nml-spec.

[2]	(1, 2) http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html

Installation

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.

Requirements

Minimum Python version is 3.7.

Usage

$ 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.

License

Other than declxml (released under MIT License), all of treeconvert’s files are released under the zlib license (c.f. LICENSE).