cmutil is a Python script to convert between (Py)KNOSSOS and
CATMAID annotations. CATMAID's export feature creates JSON files of your
annotation. With cmutil, you can convert those JSON files to
KNOSSOS-readable NML files [1], and vice versa.
| [1] | For more information about NML files, visit https://github.com/scalableminds/nml-spec. |
cmutil is not affiliated with CATMAID, but was developed internally at
ariadne-service gmbh by simply parsing the output of CATMAID's export
feature. This is not an official conversion script.
Thanks to Tom Kazimiers for insights into CATMAID's data structure and other helpful hints.
Currently, cmutil only has a single dependency: declxml. For
convenience, declxml is included directly inside cmutil's source tree.
This way, cmutil is easily packaged as an executable Python zip archive,
and should be able to run on any Python 3 environment.
Go to Releases to download the self-contained zip file.
Minimum Python version is 3.
Note: We recommend to set up CATMAID using Python >3 as well, since CATMAID's import/export feature seems to behave differently using Python 2.
Conversion between KNOSSOS and CATMAID files was tested on Python 3.5.2.
$ python3 cmutil.pyz
usage: cmutil.pyz [-h] -convert {nml,catmaid} [-o OUTPUT] [-u USER]
[-pyknossos]
[source]
cmutil.pyz: error: the following arguments are required: -convert
| Argument | Description |
|---|---|
| -convert | Either nml or catmaid. Specifies output format. |
| -o | Path to output file. If not specified, output is printed to stdout. |
| -u | CATMAID user ID. If not specified, user ID will be asked for during conversion. |
| -pyknossos | (Flag) If this flag is set, input file is treated as PyKNOSSOS NML file. |
| [source] | (Positional) Path to input file. If not specified, input is read from stdin. |
There a subtle differences between NML files created from KNOSSOS and those
created from PyKNOSSOS. Because of this, you need to explicitly add the
-pyknossos flag if your source file was created in PyKNOSSOS.
Other than declxml (released under MIT License), all of cmutil's files
are released under the zlib license (c.f. LICENSE).