Updated SpreadsheetDataReader.py from c302. Updated to read from NeuronConnect.xls (OpenWorm)

SpreadsheetDataReader.py

# -*- coding: utf-8 -*-
from NeuroMLUtilities import ConnectionInfo

from xlrd import open_workbook

############################################################

#    A simple script to read the values in CElegansNeuronTables.xls.

############################################################


def readDataFromSpreadsheet(dir="../../", include_nonconnected_cells=False, neuron_connect=False):

# reading the NeuronConnect.xls file if neuron_connect = True
    if neuron_connect:
        conns = []
        cells = []
        filename = dir+"NeuronConnect.xlsx"
        rb = open_workbook(filename)
        print "Opened Excel file: " + filename

        for row in range(1,rb.sheet_by_index(0).nrows):
            pre = str(rb.sheet_by_index(0).cell(row,0).value)
            post = str(rb.sheet_by_index(0).cell(row,1).value)
            syntype = rb.sheet_by_index(0).cell(row,2).value
            num = int(rb.sheet_by_index(0).cell(row,3).value)
            synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse'

            conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
            if pre not in cells:
                cells.append(pre)
            if post not in cells:
                cells.append(post)

        return cells, conns

    else:
        conns = []
        cells = []
        filename = dir+"CElegansNeuronTables.xls"
        rb = open_workbook(filename)

        print "Opened Excel file: " + filename

        known_nonconnected_cells = ['CANL', 'CANR', 'VC6']


        for row in range(1,rb.sheet_by_index(0).nrows):
            pre = str(rb.sheet_by_index(0).cell(row,0).value)
            post = str(rb.sheet_by_index(0).cell(row,1).value)
            syntype = rb.sheet_by_index(0).cell(row,2).value
            num = int(rb.sheet_by_index(0).cell(row,3).value)
            synclass = rb.sheet_by_index(0).cell(row,4).value

            conns.append(ConnectionInfo(pre, post, num, syntype, synclass))
            if pre not in cells:
                cells.append(pre)
            if post not in cells:
                cells.append(post)

        if include_nonconnected_cells:
            for c in known_nonconnected_cells: cells.append(c)

        return cells, conns


def main():

    cells, conns = readDataFromSpreadsheet()

    print("%i cells in spreadsheet: %s"%(len(cells),sorted(cells)))

    from os import listdir
    from os.path import isfile
    cell_names = [ f[:-9] for f in listdir('../morphologies/') if f.endswith('.java.xml')]

    cell_names.remove('MDL08') # muscle

    print("%i cell morphologies found: %s"%(len(cell_names),sorted(cell_names)))

    for c in cells: cell_names.remove(c)

    print("Difference: %s"%cell_names)


    cells2, conns2 = readDataFromSpreadsheet(include_nonconnected_cells=True)


    assert(len(cells2) == 302)

if __name__ == '__main__':

    main()