#!/usr/bin/env python
-import string
-import libhookecurve as lhc
+'''
+jpk.py
+
+Driver for jpk files.
+
+Copyright ??? by Massimo Sandal?
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
+
+This program is released under the GNU General Public License version 2.
+'''
+
+import os.path
+
+import lib.curve
+import lib.driver
+import lib.plot
class DataChunk(list):
#Dummy class to provide ext and ret methods to the data list.
-
+
def ext(self):
halflen=(len(self)/2)
return self[0:halflen]
-
+
def ret(self):
halflen=(len(self)/2)
return self[halflen:]
-class jpkDriver(lhc.Driver):
+class jpkDriver(lib.driver.Driver):
def __init__(self, filename):
self.filename=filename #self.filename can always be useful, and should be defined
self.filedata = open(filename,'r') #We open the file
self.filelines=self.filedata.readlines()
- self.filedata.close()
- '''These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
+ self.filedata.close()
+ '''
+ These are two strings that can be used by Hooke commands/plugins to understand what they are looking at. They have no other
meaning. They have to be somehow defined however - commands often look for those variables.
-
+
self.filetype should contain the name of the exact filetype defined by the driver (so that filetype-specific commands can know
if they're dealing with the correct filetype)
self.experiment should contain instead the type of data involved (for example, various drivers can be used for force-clamp experiments,
- but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other
+ but hooke commands could like to know if we're looking at force clamp data, regardless of their origin, and not other
kinds of data)
-
+
Of course, all other variables you like can be defined in the class.
'''
self.filetype = 'jpk'
self.experiment = 'smfs'
-
-
+
+
def __del__(self):
- self.filedata.close()
-
- def is_me(self):
- '''
- we define our magic heuristic for jpk files
- '''
- myfile=file(self.filename)
- headerlines=myfile.readlines()[0:3]
- myfile.close()
- if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
- return True
- else:
- return False
-
- def close_all(self):
self.filedata.close()
-
+
def _read_data_segment(self):
#routine that actually reads the data
-
+
height_ms=[]
height_m=[]
height=[]
v_deflection=[]
h_deflection=[]
-
+
self.springconstant=0 #if we don't meet any spring constant, use deflection...
-
+
for line in self.filelines:
#we meet the segment defining the order of data columns
-
+
if line[0:9]=='# columns':
splitline=line.split()[2:]
height_ms_index=splitline.index('smoothedStrainGaugeHeight')
height_index=splitline.index('height')
v_deflection_index=splitline.index('vDeflection')
#h_deflection=splitline.index('hDeflection')
-
+
if line[0:16]=='# springConstant':
self.springconstant=float(line.split()[2])
-
+
if line[0] != '#' and len(line.split())>1:
dataline=line.split()
height_ms.append(float(dataline[height_ms_index]))
height.append(float(dataline[height_index]))
v_deflection.append(float(dataline[v_deflection_index]))
#h_deflection.append(float(dataline[h_deflection_index]))
-
+
if self.springconstant != 0:
force=[item*self.springconstant for item in v_deflection]
else: #we have measured no spring constant :(
force=v_deflection
-
+
height_ms=DataChunk([item*-1 for item in height_ms])
height_m=DataChunk([item*-1 for item in height_m])
height=DataChunk([item*-1 for item in height])
deflection=DataChunk(v_deflection)
force=DataChunk(force)
-
+
return height_ms,height_m,height,deflection,force
-
- def deflection(self):
- height_ms,height_m,height,deflection,force=self._read_data_segment()
- deflection_ext=deflection.ext()
- deflection_ret=deflection.ret()
- deflection_ret.reverse()
- return deflection_ext,deflection_ret
-
+
+ def close_all(self):
+ self.filedata.close()
+
def default_plots(self):
-
+
height_ms,height_m,height,deflection,force=self._read_data_segment()
-
+
height_ms_ext=height_ms.ext()
height_ms_ret=height_ms.ret()
force_ext=force.ext()
#reverse the return data, to make it coherent with hooke standard
height_ms_ret.reverse()
force_ret.reverse()
-
- main_plot=lhc.PlotObject()
- main_plot.add_set(height_ms_ext,force_ext)
- main_plot.add_set(height_ms_ret,force_ret)
-
-
-
+
if self.springconstant != 0:
- main_plot.units=['meters','force']
+ #TODO: force is not really a unit
+ y_unit = 'force'
else:
- main_plot.units=['meters','meters']
-
- main_plot.normalize_vectors()
-
- main_plot.destination=0
- main_plot.title=self.filename
-
- return [main_plot]
\ No newline at end of file
+ y_unit = 'm'
+
+ extension = lib.curve.Curve()
+ retraction = lib.curve.Curve()
+
+ extension.color = 'red'
+ extension.label = 'extension'
+ extension.style = 'plot'
+ extension.title = 'Force curve'
+ extension.units.x = 'm'
+ extension.units.y = y_unit
+ extension.x = height_ms_ext
+ extension.y = force_ext
+ retraction.color = 'blue'
+ retraction.label = 'retraction'
+ retraction.style = 'plot'
+ retraction.title = 'Force curve'
+ retraction.units.x = 'm'
+ retraction.units.y = y_unit
+ retraction.x = height_ms_ret
+ retraction.y = force_ret
+
+ plot = lib.plot.Plot()
+ plot.title = os.path.basename(self.filename)
+ plot.curves.append(extension)
+ plot.curves.append(retraction)
+
+ plot.normalize()
+ return plot
+
+ def deflection(self):
+ height_ms,height_m,height,deflection,force=self._read_data_segment()
+ deflection_ext=deflection.ext()
+ deflection_ret=deflection.ret()
+ deflection_ret.reverse()
+ return deflection_ext,deflection_ret
+
+ def is_me(self):
+ '''
+ we define our magic heuristic for jpk files
+ '''
+ myfile=file(self.filename)
+ headerlines=myfile.readlines()[0:3]
+ myfile.close()
+ if headerlines[0][0:11]=='# xPosition' and headerlines[1][0:11]=='# yPosition':
+ return True
+ else:
+ return False
projects / hooke.git / blobdiff