Metadata-Version: 2.1
Name: axel-lab-to-nwb
Version: 0.1.0
Summary: NWB conversion scripts and tutorials.
Home-page: UNKNOWN
Author: Luiz Tauffer and Ben Dichter
License: UNKNOWN
Description: # axel-lab-to-nwb
        NWB conversion scripts and tutorials.
        A collaboration with [Axel Lab](https://www.axellab.columbia.edu/).
        
        # Install
        To clone the repository and set up a conda environment, do:
        ```
        $ git clone https://github.com/ben-dichter-consulting/axel-lab-to-nwb.git
        $ conda env create -f axel-lab-to-nwb/make_env.yml
        $ source activate convert_to_nwb
        ```
        
        Alternatively, to install directly in an existing environment:
        ```
        $ pip install axel-lab-to-nwb
        ```
        
        # Use
        After activating the correct environment, the conversion function can be used in different forms:
        
        **1. Imported and run from a python script:** <br/>
        Here's an example: we'll grab the data from the same experiment but stored in different `.npz` files and save it to a single `.nwb` file.
        ```python
        from axel_lab_to_nwb import conversion_function
        
        source_paths = {}
        source_paths['processed data'] = {'type': 'file', 'path': PATH_TO_FILE}
        source_paths['sparse matrix'] = {'type': 'file', 'path': PATH_TO_FILE}
        source_paths['ref image'] = {'type': 'file', 'path': PATH_TO_FILE}
        
        f_nwb = 'fly2.nwb'
        
        metafile = 'metafile.yml'
        
        conversion_function(source_paths=source_paths,
                            f_nwb=f_nwb,
                            metafile=metafile,
                            plot_rois=False)
        ```
        <br/>
        
        **2. Command line:** <br/>
        Similarly, the conversion function can be called from the command line in terminal:
        ```
        $ python conversion_module.py [processed_data_file] [sparse_matrix_file] [ref_image_file] 
          [output_file] [metadata_file]
        ```
        <br/>
        
        **3. Graphical User Interface:** <br/>
        To use the GUI, just run the auxiliary function `nwb_gui.py` from terminal:
        ```
        $ python nwb_gui.py
        ```
        ![](/media/gui.PNG)
        <br/>
        
        **4. Tutorial:** <br/>
        At [tutorials](https://github.com/ben-dichter-consulting/axel-lab-to-nwb/tree/master/tutorials) you can also find Jupyter notebooks with the step-by-step process of conversion.
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
