Config

Each working directory has a single config.yml file which stores dataset specific parameters. The Config class is implemented in syconn.handler.config. The config itself is stored as config.yml in the working directory. It is used for setting the versions and paths of the different dataset, e.g. KnossosDataset of source data like cell segmentation or predictions of sub-cellular structures (synaptic junctions, mitochondria, ..).

A default config is created inside generate_default_conf() function implemented in syconn.handler.config. The default values can be found at syconn.handler.config.yml and are always used as fallback if a value cannot be found in the config file of the current working directory.

Modifying parameters in a config file

Parameters can be adapted while creating the config file for a new run. In the script that starts the whole pipeline, e.g. example_run.py or full_run.py, one has to extend the key_val_pairs_conf list by a tuple (key, value).

Working directory

The working directory stores SegmentationDatasets and SuperSegmentationDatasets of the initial, the glia split RAG, the cell organelles and contact sites / synapses and is specified in syconn.global_params.py. The above config has to be placed within the working directory.