hooke/driver/hemingclamp.py

   1 #!/usr/bin/env python
   2
   3 '''
   4 libhemingclamp.py
   5
   6 Library for interpreting Hemingway force spectroscopy files.
   7
   8 Copyright (C) 2008 Massimo Sandal, Marco Brucale (University of Bologna, Italy)
   9
  10 This program is released under the GNU General Public License version 2.
  11 '''
  12 __version__='2007_02_15_devel'
  13
  14 __changelog__='''
  15 2007_02_15: fixed time counter with my counter
  16 2007_02_07: Initial implementation
  17 '''
  18 import string
  19 import libhookecurve as lhc
  20
  21 class DataChunk(list):
  22     '''Dummy class to provide ext and ret methods to the data list.
  23     In this case ext and self can be equal.
  24     '''
  25
  26     def ext(self):
  27         return self
  28
  29     def ret(self):
  30         return self
  31
  32 class hemingclampDriver(lhc.Driver):
  33
  34     def __init__(self, filename):
  35
  36         self.filedata = open(filename,'r')
  37         self.data = self.filedata.readlines()[6:]
  38         self.filedata.close()
  39
  40         self.filetype = 'hemingclamp'
  41         self.experiment = 'clamp'
  42
  43         self.filename=filename
  44
  45     def __del__(self):
  46         self.filedata.close()
  47
  48     def is_me(self):
  49         '''
  50         we define our magic heuristic for HemingClamp files
  51         '''
  52         myfile=file(self.filename)
  53         headerlines=myfile.readlines()[0:3]
  54         myfile.close()
  55         if headerlines[0][0:10]=='#Hemingway' and headerlines[1][0:19]=='#Experiment: FClamp':
  56             return True
  57         else:
  58             return False
  59
  60     def _getdata_all(self):
  61         time = []
  62         phase = []
  63         zpiezo = []
  64         defl = []
  65         imposed = []
  66         trim_indexes = []
  67         trim_counter = 0.0
  68
  69         for i in self.data:
  70             temp = string.split(i)
  71             #time.append(float(temp[0])*(1.0e-3)) # This is managed differently now, since each data point = 1ms: see below
  72             phase.append(float(temp[1])*(1.0e-7)) # The nonsensical (e-7) multiplier is just there to make phase data nicely plottable along other data
  73             zpiezo.append(float(temp[2])*(1.0e-9))
  74             defl.append(float(temp[3])*(1.0e-9))
  75             imposed.append(float(temp[4])*(1.0e-9))
  76
  77         for x in range (0,len(phase)):
  78             if phase[x] != trim_counter:
  79                 trim_indexes.append(x)
  80                 trim_counter = phase[x]
  81
  82         #we rebuild the time counter assuming 1 point = 1 millisecond
  83         c=0.0
  84         for z in zpiezo:
  85             time.append(c)
  86             c+=(1.0e-3)
  87
  88         return time,phase,zpiezo,defl,imposed,trim_indexes
  89
  90     def time(self):
  91         return DataChunk(self._getdata_all()[0])
  92
  93     def phase(self):
  94         return DataChunk(self._getdata_all()[1])
  95
  96     def zpiezo(self):
  97         return DataChunk(self._getdata_all()[2])
  98
  99     def deflection(self):
 100         return DataChunk(self._getdata_all()[3])
 101
 102     def imposed(self):
 103         return DataChunk(self._getdata_all()[4])
 104
 105     def trimindexes(self):
 106         return DataChunk(self._getdata_all()[5])
 107
 108     def close_all(self):
 109         '''
 110         Explicitly closes all files
 111         '''
 112         self.filedata.close()
 113
 114     def default_plots(self):
 115         main_plot=lhc.PlotObject()
 116         defl_plot=lhc.PlotObject()
 117
 118         time=self.time()
 119         phase=self.phase()
 120         zpiezo=self.zpiezo()
 121         deflection=self.deflection()
 122         imposed=self.imposed()
 123
 124         main_plot.vectors=[[time,zpiezo],[time,phase]]
 125         main_plot.units=['seconds','meters']
 126         main_plot.destination=0
 127         main_plot.title=self.filename
 128
 129         defl_plot.vectors=[[time,deflection],[time,imposed]]
 130         defl_plot.units=['seconds','Newtons']
 131         defl_plot.destination=1
 132
 133         return [main_plot, defl_plot]
 134