Merged Rolf Schmidt's illysam branch

[hooke.git] / hooke / driver / mcs.py

diff --git a/hooke/driver/mcs.py b/hooke/driver/mcs.py
index 711e8c359625e646ca8225b8476634695810fc35..f8208c04aea545dbfe482eeec35ff48e68feada7 100644 (file)
--- a/hooke/driver/mcs.py
+++ b/hooke/driver/mcs.py
@@ -1,19 +1,17 @@
-#!/usr/bin/env python
+# Copyright
 
-'''
-mcs.py
+"""Driver for mcs fluorescence files.
+"""
 
-driver for mcs fluorescence files
+import os.path
 
-Massimo Sandal, Allen Chen (c) 2009
-'''
-
-import libhookecurve as lhc
-import libhooke as lh
+import lib.curve
+import lib.driver
+import lib.plot
 import struct
 
-class mcsDriver(lhc.Driver):
-    
+class mcsDriver(lib.driver.Driver):
+
     def __init__(self, filename):
         '''
         Open the RED (A) ones; the BLUE (D) mirror ones will be automatically opened
@@ -25,56 +23,77 @@ class mcsDriver(lhc.Driver):
             oth[-8]='d'
             othername=''.join(oth)
         self.filename=filename
-        self.othername=othername    
-        
+        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):
+        #TODO: rename blue and red data to something more appropriate if possible
         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):    
+
+        extension = lib.curve.Curve()
+        retraction = lib.curve.Curve()
+
+        extension.color = 'red'
+        extension.label = 'extension'
+        extension.style = 'plot'
+        extension.title = 'Force curve'
+        #FIXME: if there's an header saying something about the time count, should be used
+        #TODO: time is not really a unit
+        extension.units.x = 'time'
+        extension.units.y = 'count'
+        extension.x = range(len(red_data))
+        extension.y = red_data
+        retraction.color = 'blue'
+        retraction.label = 'retraction'
+        retraction.style = 'plot'
+        retraction.title = 'Force curve'
+        #FIXME: if there's an header saying something about the time count, should be used
+        #TODO: time is not really a unit
+        retraction.units.x = 'time'
+        retraction.units.y = 'count'
+        retraction.x = range(len(blue_data))
+        retraction.y = blue_data
+
+        plot = lib.plot.Plot()
+        plot.title = os.path.basename(self.filename)
+        plot.curves.append(extension)
+        plot.curves.append(retraction)
+
+        plot.normalize()
+        return plot
+
+    def is_me(self):
+        if self.filename[-3:].lower()=='mcs':
+            return True
+        else:
+            return False
+
+    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
\ No newline at end of file
+        return real_data