mcs.py

#!/usr/bin/env python

'''
mcs.py

driver for mcs fluorescence files

Massimo Sandal, Allen Chen (c) 2009
'''

import libhookecurve as lhc
import libhooke as lh
import struct

class mcsDriver(lhc.Driver):
    
    def __init__(self, filename):
        '''
        Open the RED (A) ones; the BLUE (D) mirror ones will be automatically opened
        '''
        #obtain name of blue files
        othername=filename
        if othername[-8]=='a': #fixme: how to make it general? (maybe should not be in driverspace but in environment...)
            oth=list(othername)
            oth[-8]='d'
            othername=''.join(oth)
        self.filename=filename
        self.othername=othername    
        
        #print self.filename, self.othername
        
        self.filedata=open(filename,'rb')
        self.reddata=self.filedata.read()
        self.filedata.close()
        
        self.filebluedata=open(othername,'rb') #open also the blue ones
        self.bluedata=self.filebluedata.read()
        self.filebluedata.close()
        
        self.filetype = 'mcs'
        self.experiment = 'smfluo'
        
    def is_me(self):
        if self.filename[-3:].lower()=='mcs':
            return True
        else:
            return False
        
    def close_all(self):
        self.filedata.close()
        self.filebluedata.close()
        
        
    def default_plots(self):
        red_data=self.read_file(self.reddata)
        blue_data=self.read_file(self.bluedata)
        blue_data=[-1*float(item) for item in blue_data] #visualize blue as "mirror" of red
        
        main_plot=lhc.PlotObject()
        main_plot.add_set(range(len(red_data)),red_data)
        main_plot.add_set(range(len(blue_data)),blue_data)
        main_plot.normalize_vectors()
        main_plot.units=['time','count']  #FIXME: if there's an header saying something about the time count, should be used
        main_plot.destination=0
        main_plot.title=self.filename
        main_plot.colors=['red','blue']
        
        return [main_plot]
    
    def read_file(self, raw_data):    
        real_data=[]
        intervalsperfile=struct.unpack('h', raw_data[10:12])[0] #read in number of intervals in this file
                                                                #this data is contained in bit offset 10-12 in mcs file
        #see http://docs.python.org/library/struct.html#module-struct for additional explanation
        
        numbytes=len(raw_data) #data is stored in 4-byte chunks, starting with pos 256
        for j in range(0,intervalsperfile): #read in all intervals in file
            temp=raw_data[256+j*4:256+j*4+4]    #data starts at byte offset 256
            real_data.append(struct.unpack('i', temp)[0]) #[0] because it returns a 1-element tuple
        return real_data