#!/usr/bin/env python
'''
-libhemingclamp.py
+hemingclamp.py
Library for interpreting Hemingway force spectroscopy files.
-Copyright (C) 2008 Massimo Sandal, Marco Brucale (University of Bologna, Italy)
+Copyright 2008 by Massimo Sandal, Marco Brucale (University of Bologna, Italy)
+with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
This program is released under the GNU General Public License version 2.
'''
+
__version__='2007_02_15_devel'
__changelog__='''
+2010_01_22: initial release for Hooke GUI
2007_02_15: fixed time counter with my counter
-2007_02_07: Initial implementation
+2007_02_07: initial implementation
'''
+
+import copy
+import os.path
import string
-import libhookecurve as lhc
+
+import lib.curve
+import lib.driver
+import lib.plot
class DataChunk(list):
- '''Dummy class to provide ext and ret methods to the data list.
+ #TODO: something similar is also used in jpk.py
+ #potential for OOP/inheritance?
+ '''
+ Dummy class to provide ext and ret methods to the data list.
In this case ext and self can be equal.
'''
-
+
def ext(self):
return self
-
+
def ret(self):
return self
-class hemingclampDriver(lhc.Driver):
-
+class hemingclampDriver(lib.driver.Driver):
+
def __init__(self, filename):
-
+
self.filedata = open(filename,'r')
self.data = self.filedata.readlines()[6:]
self.filedata.close()
-
+
self.filetype = 'hemingclamp'
self.experiment = 'clamp'
-
+
self.filename=filename
-
+
def __del__(self):
- self.filedata.close()
-
- def is_me(self):
- '''
- we define our magic heuristic for HemingClamp files
- '''
- myfile=file(self.filename)
- headerlines=myfile.readlines()[0:3]
- myfile.close()
- if headerlines[0][0:10]=='#Hemingway' and headerlines[1][0:19]=='#Experiment: FClamp':
- return True
- else:
- return False
-
+ self.filedata.close()
+
def _getdata_all(self):
time = []
phase = []
imposed = []
trim_indexes = []
trim_counter = 0.0
-
+
for i in self.data:
temp = string.split(i)
#time.append(float(temp[0])*(1.0e-3)) # This is managed differently now, since each data point = 1ms: see below
if phase[x] != trim_counter:
trim_indexes.append(x)
trim_counter = phase[x]
-
+
#we rebuild the time counter assuming 1 point = 1 millisecond
c=0.0
for z in zpiezo:
time.append(c)
- c+=(1.0e-3)
-
- return time,phase,zpiezo,defl,imposed,trim_indexes
-
- def time(self):
- return DataChunk(self._getdata_all()[0])
+ c+=(1.0e-3)
- def phase(self):
- return DataChunk(self._getdata_all()[1])
-
- def zpiezo(self):
- return DataChunk(self._getdata_all()[2])
-
- def deflection(self):
- return DataChunk(self._getdata_all()[3])
-
- def imposed(self):
- return DataChunk(self._getdata_all()[4])
+ return time,phase,zpiezo,defl,imposed,trim_indexes
- def trimindexes(self):
- return DataChunk(self._getdata_all()[5])
-
def close_all(self):
'''
Explicitly closes all files
'''
self.filedata.close()
-
+
def default_plots(self):
- main_plot=lhc.PlotObject()
- defl_plot=lhc.PlotObject()
-
time=self.time()
phase=self.phase()
zpiezo=self.zpiezo()
deflection=self.deflection()
imposed=self.imposed()
-
- main_plot.vectors=[[time,zpiezo],[time,phase]]
- main_plot.units=['seconds','meters']
- main_plot.destination=0
- main_plot.title=self.filename
-
- defl_plot.vectors=[[time,deflection],[time,imposed]]
- defl_plot.units=['seconds','Newtons']
- defl_plot.destination=1
-
- return [main_plot, defl_plot]
-
\ No newline at end of file
+
+ #return [main_plot, defl_plot]
+ main_extension = lib.curve.Curve()
+ main_retraction = lib.curve.Curve()
+
+ #TODO: check 'title' below
+ main_extension.color = 'red'
+ main_extension.label = 'extension'
+ main_extension.style = 'plot'
+ main_extension.title = 'Force curve'
+ main_extension.units.x = 's'
+ main_extension.units.y = 'm'
+ main_extension.x = time
+ main_extension.y = zpiezo
+ main_retraction.color = 'blue'
+ main_retraction.label = 'retraction'
+ main_retraction.style = 'plot'
+ main_retraction.title = 'Force curve'
+ main_retraction.units.x = 's'
+ #TODO: what is the real unit for y?
+ main_retraction.units.y = 'degree'
+ main_retraction.x = time
+ main_retraction.y = phase
+
+ deflection_extension = copy.deepcopy(main_extension)
+ deflection_retraction = copy.deepcopy(main_retraction)
+ #TODO: check 'title' below
+ deflection_extension.destination.row = 2
+ deflection_extension.units.y = 'N'
+ deflection_extension.y = deflection
+ #TODO: what is the real unit for y?
+ deflection_retraction.destination.row = 2
+ deflection_retraction.units.y = 'N'
+ deflection_retraction.y = imposed
+
+ plot = lib.plot.Plot()
+ plot.title = os.path.basename(self.filename)
+ plot.curves.append(main_extension)
+ plot.curves.append(main_retraction)
+ plot.curves.append(deflection_extension)
+ plot.curves.append(deflection_retraction)
+
+ plot.normalize()
+ return plot
+
+ def deflection(self):
+ return DataChunk(self._getdata_all()[3])
+
+ def imposed(self):
+ return DataChunk(self._getdata_all()[4])
+
+ def is_me(self):
+ '''
+ we define our magic heuristic for HemingClamp files
+ '''
+ myfile=file(self.filename)
+ headerlines=myfile.readlines()[0:3]
+ myfile.close()
+ if headerlines[0][0:10]=='#Hemingway' and headerlines[1][0:19]=='#Experiment: FClamp':
+ return True
+ else:
+ return False
+
+ def phase(self):
+ return DataChunk(self._getdata_all()[1])
+
+ def time(self):
+ return DataChunk(self._getdata_all()[0])
+
+ def trimindexes(self):
+ return DataChunk(self._getdata_all()[5])
+
+ def zpiezo(self):
+ return DataChunk(self._getdata_all()[2])
projects / hooke.git / blobdiff