hooke/driver/hemingclamp.py

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