NWBInterface.py

import h5py
import numpy as np
import FormatInterface

#These classes inherit from FormatInterface.
class HandelNWBFile(FormatInterface.FormatInterface):
    def __init__(self,inputFile,isGui):
        super().__init__()
        self.isGui = isGui
        self.inputFile = inputFile
        self.listOfRecordings = []
        self.listOfProcessors = []
        self.extractedFile = []

    #GetData- extracts the data (usually done via python packages).
    #it should extract the data according to the selected channels and time window.
    #It should also extract the time step (sampling rate), the total time duration and the number of channels for
    # both GUI and Console applications.
    def GetData(self):
        try:
            self.extractedFile = h5py.File(self.inputFile,"r")
            self.listOfRecordings = self.ShowFileInnerSection(self.extractedFile['/acquisition/timeseries/'])
            for recording in self.listOfRecordings:
                self. listOfProcessors = self.ShowFileInnerSection(self.extractedFile['/acquisition/timeseries/'
                                                                                      +recording+'/continuous/'])
                for processor in self.listOfProcessors:
                    # sampling rate calculation:
                    startTimestamps = np.array(self.extractedFile['/acquisition/timeseries/' + recording +
                                                                  '/continuous/' + processor + '/timestamps'][0])
                    secondTimestamps = np.array(self.extractedFile['/acquisition/timeseries/' + recording +
                                                                   '/continuous/' + processor + '/timestamps'][1])
                    self.timeStepMS = (secondTimestamps-startTimestamps)*1e3
                    self.durationMS=(self.extractedFile['/acquisition/timeseries/' + recording + '/continuous/' +
                                                        processor + '/timestamps']).shape[0]*self.timeStepMS
                    self.nChannels = self.extractedFile['/acquisition/timeseries/'+
                                                        recording+'/continuous/'+processor+'/data'].shape[1]
                    if (self.isGui==False):
                        self.GetRelevantTimestamps()
                        self.GetRelevantChannels()
                        if ((self.startTimeIndex != None) and (self.endTimeIndex != None) and
                                ( self.startChannel != None) and (self.endChannel != None) and
                                ( self.timestamps[0] != None)):
                            # metadata contains all the requested data, arranged by channels as columns and
                            # timestamps as rows
                            self.metaData = np.array((self.extractedFile['/acquisition/timeseries/'
                                                                         + recording+'/continuous/'+processor+'/data']
                                                                        [self.startTimeIndex:self.endTimeIndex,self.startChannel - 1:self.endChannel]))
                            self.PlotData(self.isGui)
                        else:
                            print("Error Loading Data, Please Try Again")
        except Exception as e:
            print("An exception occurred. Please Try Again")
            print(e)
            return
        
    #GetAndPlotMetaData- Extract the data for GUI application and plots it.      
    def GetAndPlotMetaData(self):
            self.metaData = np.array((self.extractedFile[
                                          '/acquisition/timeseries/' + self.listOfRecordings[0] + '/continuous/' + self.listOfProcessors[0] + '/data'][
                                      self.startTimeIndex:self.endTimeIndex, 0:self.nChannels]))
            return self.PlotData(True)