drivers/jpk.py

   1 #!/usr/bin/env python
   2
   3 '''
   4 jpk.py
   5
   6 Driver for jpk files.
   7
   8 Copyright ??? by Massimo Sandal?
   9 with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
  10
  11 This program is released under the GNU General Public License version 2.
  12 '''
  13
  14 import os.path
  15
  16 import lib.curve
  17 import lib.driver
  18 import lib.plot
  19
  20 class DataChunk(list):
  21     #Dummy class to provide ext and ret methods to the data list.
  22
  23     def ext(self):
  24         halflen=(len(self)/2)
  25         return self[0:halflen]
  26
  27     def ret(self):
  28         halflen=(len(self)/2)
  29         return self[halflen:]
  30
  31 class jpkDriver(lib.driver.Driver):
  32
  33     def __init__(self, filename):
  34         self.filename=filename #self.filename can always be useful, and should be defined
  35         self.filedata = open(filename,'r') #We open the file
  36         self.filelines=self.filedata.readlines()
  37         self.filedata.close()
  38         '''
  39         These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
  40         meaning. They have to be somehow defined however - commands often look for those variables.
  41
  42         self.filetype should contain the name of the exact filetype defined by the driver (so that filetype-specific commands can know
  43                       if they're dealing with the correct filetype)
  44         self.experiment should contain instead the type of data involved (for example, various drivers can be used for force-clamp experiments,
  45                       but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other
  46                       kinds of data)
  47
  48         Of course, all other variables you like can be defined in the class.
  49         '''
  50         self.filetype = 'jpk'
  51         self.experiment = 'smfs'
  52
  53
  54
  55     def __del__(self):
  56         self.filedata.close()
  57
  58     def _read_data_segment(self):
  59         #routine that actually reads the data
  60
  61         height_ms=[]
  62         height_m=[]
  63         height=[]
  64         v_deflection=[]
  65         h_deflection=[]
  66
  67         self.springconstant=0 #if we don't meet any spring constant, use deflection...
  68
  69         for line in self.filelines:
  70             #we meet the segment defining the order of data columns
  71
  72             if line[0:9]=='# columns':
  73                 splitline=line.split()[2:]
  74                 height_ms_index=splitline.index('smoothedStrainGaugeHeight')
  75                 height_m_index=splitline.index('strainGaugeHeight')
  76                 height_index=splitline.index('height')
  77                 v_deflection_index=splitline.index('vDeflection')
  78                 #h_deflection=splitline.index('hDeflection')
  79
  80             if line[0:16]=='# springConstant':
  81                 self.springconstant=float(line.split()[2])
  82
  83             if line[0] != '#' and len(line.split())>1:
  84                 dataline=line.split()
  85                 height_ms.append(float(dataline[height_ms_index]))
  86                 height_m.append(float(dataline[height_m_index]))
  87                 height.append(float(dataline[height_index]))
  88                 v_deflection.append(float(dataline[v_deflection_index]))
  89                 #h_deflection.append(float(dataline[h_deflection_index]))
  90
  91         if self.springconstant != 0:
  92             force=[item*self.springconstant for item in v_deflection]
  93         else: #we have measured no spring constant :(
  94             force=v_deflection
  95
  96         height_ms=DataChunk([item*-1 for item in height_ms])
  97         height_m=DataChunk([item*-1 for item in height_m])
  98         height=DataChunk([item*-1 for item in height])
  99         deflection=DataChunk(v_deflection)
 100         force=DataChunk(force)
 101
 102         return height_ms,height_m,height,deflection,force
 103
 104     def close_all(self):
 105         self.filedata.close()
 106
 107     def default_plots(self):
 108
 109         height_ms,height_m,height,deflection,force=self._read_data_segment()
 110
 111         height_ms_ext=height_ms.ext()
 112         height_ms_ret=height_ms.ret()
 113         force_ext=force.ext()
 114         force_ret=force.ret()
 115         #reverse the return data, to make it coherent with hooke standard
 116         height_ms_ret.reverse()
 117         force_ret.reverse()
 118
 119         if self.springconstant != 0:
 120             #TODO: force is not really a unit
 121             y_unit = 'force'
 122         else:
 123             y_unit = 'm'
 124
 125         extension = lib.curve.Curve()
 126         retraction = lib.curve.Curve()
 127
 128         extension.color = 'red'
 129         extension.label = 'extension'
 130         extension.style = 'plot'
 131         extension.title = 'Force curve'
 132         extension.units.x = 'm'
 133         extension.units.y = y_unit
 134         extension.x = height_ms_ext
 135         extension.y = force_ext
 136         retraction.color = 'blue'
 137         retraction.label = 'retraction'
 138         retraction.style = 'plot'
 139         retraction.title = 'Force curve'
 140         retraction.units.x = 'm'
 141         retraction.units.y = y_unit
 142         retraction.x = height_ms_ret
 143         retraction.y = force_ret
 144
 145         plot = lib.plot.Plot()
 146         plot.title = os.path.basename(self.filename)
 147         plot.curves.append(extension)
 148         plot.curves.append(retraction)
 149
 150         plot.normalize()
 151         return plot
 152
 153     def deflection(self):
 154         height_ms,height_m,height,deflection,force=self._read_data_segment()
 155         deflection_ext=deflection.ext()
 156         deflection_ret=deflection.ret()
 157         deflection_ret.reverse()
 158         return deflection_ext,deflection_ret
 159
 160     def is_me(self):
 161         '''
 162         we define our magic heuristic for jpk files
 163         '''
 164         myfile=file(self.filename)
 165         headerlines=myfile.readlines()[0:3]
 166         myfile.close()
 167         if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
 168             return True
 169         else:
 170             return False