2 import libhookecurve as lhc
5 #Dummy class to provide ext and ret methods to the data list.
15 class jpkDriver(lhc.Driver):
17 def __init__(self, filename):
18 self.filename=filename #self.filename can always be useful, and should be defined
19 self.filedata = open(filename,'r') #We open the file
20 self.filelines=self.filedata.readlines()
22 '''These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
23 meaning. They have to be somehow defined however - commands often look for those variables.
25 self.filetype should contain the name of the exact filetype defined by the driver (so that filetype-specific commands can know
26 if they're dealing with the correct filetype)
27 self.experiment should contain instead the type of data involved (for example, various drivers can be used for force-clamp experiments,
28 but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other
31 Of course, all other variables you like can be defined in the class.
34 self.experiment = 'smfs'
43 we define our magic heuristic for jpk files
45 myfile=file(self.filename)
46 headerlines=myfile.readlines()[0:3]
48 if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
56 def _read_data_segment(self):
57 #routine that actually reads the data
65 self.springconstant=0 #if we don't meet any spring constant, use deflection...
67 for line in self.filelines:
68 #we meet the segment defining the order of data columns
70 if line[0:9]=='# columns':
71 splitline=line.split()[2:]
72 height_ms_index=splitline.index('smoothedStrainGaugeHeight')
73 height_m_index=splitline.index('strainGaugeHeight')
74 height_index=splitline.index('height')
75 v_deflection_index=splitline.index('vDeflection')
76 #h_deflection=splitline.index('hDeflection')
78 if line[0:16]=='# springConstant':
79 self.springconstant=float(line.split()[2])
81 if line[0] != '#' and len(line.split())>1:
83 height_ms.append(float(dataline[height_ms_index]))
84 height_m.append(float(dataline[height_m_index]))
85 height.append(float(dataline[height_index]))
86 v_deflection.append(float(dataline[v_deflection_index]))
87 #h_deflection.append(float(dataline[h_deflection_index]))
89 if self.springconstant != 0:
90 force=[item*self.springconstant for item in v_deflection]
91 else: #we have measured no spring constant :(
94 height_ms=DataChunk([item*-1 for item in height_ms])
95 height_m=DataChunk([item*-1 for item in height_m])
96 height=DataChunk([item*-1 for item in height])
97 deflection=DataChunk(v_deflection)
98 force=DataChunk(force)
100 return height_ms,height_m,height,deflection,force
102 def deflection(self):
103 height_ms,height_m,height,deflection,force=self._read_data_segment()
104 deflection_ext=deflection.ext()
105 deflection_ret=deflection.ret()
106 deflection_ret.reverse()
107 return deflection_ext,deflection_ret
109 def default_plots(self):
111 height_ms,height_m,height,deflection,force=self._read_data_segment()
113 height_ms_ext=height_ms.ext()
114 height_ms_ret=height_ms.ret()
115 force_ext=force.ext()
116 force_ret=force.ret()
117 #reverse the return data, to make it coherent with hooke standard
118 height_ms_ret.reverse()
121 main_plot=lhc.PlotObject()
122 main_plot.add_set(height_ms_ext,force_ext)
123 main_plot.add_set(height_ms_ret,force_ret)
127 if self.springconstant != 0:
128 main_plot.units=['meters','force']
130 main_plot.units=['meters','meters']
132 main_plot.normalize_vectors()
134 main_plot.destination=0
135 main_plot.title=self.filename