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Convert data to nwb

Project description

nwbn-conversion-tools

Shared tools for converting data from various formats to NWB:N 2.0

Installation

To install nwbn_conversion_tools directly in an existing environment:

$ pip install nwbn-conversion-tools

Alternatively, to clone the repository and set up a conda environment, do:

$ git clone https://github.com/NeurodataWithoutBorders/nwbn-conversion-tools
$ conda env create -f nwbn-conversion-tools/make_env.yml
$ source activate nwbn_conversion

GUI

After activating the correct environment, nwbn_conversion_tools GUI can be imported and run from the python interpreter.

from nwbn_conversion_tools.gui.nwbn_conversion_gui import nwbn_conversion_gui

# YAML metafile
metafile = 'metafile.yml'

# Conversion module
conversion_module = 'conversion_module.py'

# Source files path
source_paths = {}
source_paths['source_file_1'] = {'type': 'file', 'path': ''}
source_paths['source_file_2'] = {'type': 'file', 'path': ''}

# Other options
kwargs = {'option_1': True, 'option_2': False}

nwbn_conversion_gui(
    metafile=metafile,
    conversion_module=conversion_module,
    source_paths=source_paths,
    kwargs_fields=kwargs,
)

Here you can find templates for metafile.yml and conversion_module.py.

optical physiology

processing

Project details


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Files for nwbn-conversion-tools, version 0.2.0
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