Metadata-Version: 2.1
Name: x-to-nwb
Version: 0.2.1
Summary: Convert various patch-clamp data formats to NWBv2
Home-page: https://github.com/byte-physics/x-to-nwb
Author: Thomas Braun
Author-email: packages@byte-physics.de
License: UNKNOWN
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        ## Converting ABF/DAT files to NWB
        
        The script `x-to-nwb` allows to convert ABF/DAT files to NeurodataWithoutBorders v2 files.
        
        For programmatic use the function `convert` is designed as public interface.
        
        ```python
        from x_to_nwb import convert
        help(convert)
        ```
        
        ### ABF specialities
        
        As of 9/2018 PClamp/Clampex does not record all required amplifier settings.
        For gathering these please see the `mcc_get_settings.py` script in the ipfx
        repository which gathers all amplifier settings from all active amplifiers and
        writes them to a file in JSON output.
        
        In case you don't have a JSON settings file pass `--no-searchSettingsFile` to avoid warnings.
        
        By default all AD and DA channels are outputted into the NWB file. You can
        select to only export some AD channels with
        
        ```sh
        x-to-nwb --includeChannel ABCD 2018_03_20_0000.abf
        ```
        
        Or to discard some AD channels use
        
        ```sh
        x-to-nwb --discardChannel ABCD 2018_03_20_0000.abf
        ```
        
        #### Required input files
        
        - ABF files acquired with Clampex/pCLAMP.
        - If custom waveforms are used for the stimulus protocol, the source ATF files are required as well.
        
        #### Examples
        
        ##### Convert a single file
        
        ```sh
        x-to-nwb 2018_03_20_0000.abf
        ```
        
        ##### Convert a single file with overwrite and use a directory for finding custom waveforms
        
        Some acquired data might use custom wave forms for defining the stimulus
        protocols. These custom waveforms are stored in external files and don't reside
        in the ABF files. We therefore allow the user to pass a directory where
        these files should be searched. Currently only custom waveforms in ATF (Axon
        Text format) are supported.
        
        ```sh
        x-to-nwb --overwrite --protocolDir protocols 2018_03_20_0000.abf
        ```
        
        ##### Convert a folder with ABF files
        
        The following command converts all ABF files which reside in `someFolder` to a single NWB file.
        
        ```sh
        x-to-nwb --fileType ".abf" --overwrite someFolder
        ```
        
        #### Disabling compression
        
        The following command disables compression of the HDF5 datasets (intended for debugging purposes).
        
        ```sh
        x-to-nwb --no-compression 2018_03_20_0000.abf
        ```
        
        ### DAT specialities
        
        #### Required input files
        
        DAT files acquired with Patchmaster version 2x90.
        
        #### Examples
        
        ##### Convert a single file creating one NWB file per Group
        
        ```sh
        x-to-nwb H18.28.015.11.12.dat
        ```
        
        ##### Convert a single file creating one NWB file with all Groups
        
        ```sh
        x-to-nwb --multipleGroupsPerFile H18.28.015.11.12.dat
        ```
        
        ## Outputting DAT/ABF metadata files for debugging purposes
        
        ```sh
        x-to-nwb --outputMetadata *.dat *.abf
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: Free To Use But Restricted
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
Description-Content-Type: text/markdown; charset=UTF-8
