3 """Driver for mcs fluorescence files.
13 class mcsDriver(lib.driver.Driver):
15 def __init__(self, filename):
17 Open the RED (A) ones; the BLUE (D) mirror ones will be automatically opened
19 #obtain name of blue files
21 if othername[-8]=='a': #fixme: how to make it general? (maybe should not be in driverspace but in environment...)
24 othername=''.join(oth)
25 self.filename=filename
26 self.othername=othername
28 #print self.filename, self.othername
30 self.filedata=open(filename,'rb')
31 self.reddata=self.filedata.read()
34 self.filebluedata=open(othername,'rb') #open also the blue ones
35 self.bluedata=self.filebluedata.read()
36 self.filebluedata.close()
39 self.experiment = 'smfluo'
43 self.filebluedata.close()
45 def default_plots(self):
46 #TODO: rename blue and red data to something more appropriate if possible
47 red_data=self.read_file(self.reddata)
48 blue_data=self.read_file(self.bluedata)
49 blue_data=[-1*float(item) for item in blue_data] #visualize blue as "mirror" of red
51 extension = lib.curve.Curve()
52 retraction = lib.curve.Curve()
54 extension.color = 'red'
55 extension.label = 'extension'
56 extension.style = 'plot'
57 extension.title = 'Force curve'
58 #FIXME: if there's an header saying something about the time count, should be used
59 #TODO: time is not really a unit
60 extension.units.x = 'time'
61 extension.units.y = 'count'
62 extension.x = range(len(red_data))
63 extension.y = red_data
64 retraction.color = 'blue'
65 retraction.label = 'retraction'
66 retraction.style = 'plot'
67 retraction.title = 'Force curve'
68 #FIXME: if there's an header saying something about the time count, should be used
69 #TODO: time is not really a unit
70 retraction.units.x = 'time'
71 retraction.units.y = 'count'
72 retraction.x = range(len(blue_data))
73 retraction.y = blue_data
75 plot = lib.plot.Plot()
76 plot.title = os.path.basename(self.filename)
77 plot.curves.append(extension)
78 plot.curves.append(retraction)
84 if self.filename[-3:].lower()=='mcs':
89 def read_file(self, raw_data):
91 intervalsperfile=struct.unpack('h', raw_data[10:12])[0] #read in number of intervals in this file
92 #this data is contained in bit offset 10-12 in mcs file
93 #see http://docs.python.org/library/struct.html#module-struct for additional explanation
95 numbytes=len(raw_data) #data is stored in 4-byte chunks, starting with pos 256
96 for j in range(0,intervalsperfile): #read in all intervals in file
97 temp=raw_data[256+j*4:256+j*4+4] #data starts at byte offset 256
98 real_data.append(struct.unpack('i', temp)[0]) #[0] because it returns a 1-element tuple