Source code for cno.io.xmlmidas

"""This is an experimental module to design an XML 
format for MIDAS data sets.

"""
import xml.etree.ElementTree as ET

from cno.io.measurements import Measurements
from cno.io.measurements import Measurement

__all__ = ["XMLMIDAS"]


class XMLMIDAS(object):
    """Class to read MIDAS in XML format. """
    def __init__(self, filename):
        self.tree = ET.parse(filename)
        self.root = self.tree.getroot()
        self._data = None

    def readXML(self):
        """Read XML MIDAS file and build up a Measurements instance"""
        # scan all measurements
        mb = Measurements()
        for this in self.tree.findall("measurements")[0].findall("measurement"):

            tr = this.find('treatments')
            species_parser = this.find('species')
            time_parser = this.find('time')
            cell_parser = this.find('cell')

            # get time 
            time = float(time_parser.find('value').text)
            time_units = time_parser.find('value').attrib['units']

            # get cell name
            cellname = cell_parser.find('name').text

            # get species information
            species_name = species_parser.find('name').text
            value = species_parser.find('value').text

            # get stimuli and inhibitors
            dict_stimuli = {}
            dict_inhibitors = {}
            if tr.find('stimuli') is not None:
                for stimulus in tr.find('stimuli').findall('stimulus'):
                    name = stimulus.find('name').text
                    value = float(stimulus.find('value').text)
                    dict_stimuli[name] = value

            if tr.find('inhibitors') is not None:
                for inhibitor in tr.find('inhibitors').findall('inhibitor'):
                    name = inhibitor.find('name').text
                    value = float(inhibitor.find('value').text)
                    dict_inhibitors[name] = value

            measure = Measurement(species_name, time, dict_stimuli, 
                    dict_inhibitors, value, 
                    cellLine=cellname, units=time_units)
            mb.append(measure)
        return mb
            
    def _get_midas(self):
        from cno.io.measurements import MIDASBuilder

        # create measurements 
        measurements = self.readXML()

        # add them to a MIDASBuilder
        xm = MIDASBuilder()
        xm.add_measurements(measurements)

        # get the MIDAS file itself
        midas = xm.xmidas
        return midas
    xmidas = property(_get_midas, doc='Get XMIDAS instance from the XML')