-#!/usr/bin/env python
+# Copyright (C) 2008-2010 Alberto Gomez-Casado
+# Massimo Sandal <devicerandom@gmail.com>
+# W. Trevor King <wking@drexel.edu>
+#
+# This file is part of Hooke.
+#
+# Hooke is free software: you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation, either
+# version 3 of the License, or (at your option) any later version.
+#
+# Hooke is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with Hooke. If not, see
+# <http://www.gnu.org/licenses/>.
-'''
-PROCPLOTS
-Processed plots plugin for force curves.
+"""Processed plots plugin for force curves.
+"""
-Licensed under the GNU GPL version 2
-'''
-from libhooke import WX_GOOD
+from ..libhooke import WX_GOOD
import wxversion
wxversion.select(WX_GOOD)
import wx
-import libhookecurve as lhc
import numpy as np
import scipy as sp
import scipy.signal
import copy
-class procplotsCommands:
-
+from .. import curve as lhc
+
+
+class procplotsCommands(object):
+
def _plug_init(self):
pass
-
+
def do_derivplot(self,args):
'''
DERIVPLOT
Plots the derivate (actually, the discrete differentiation) of the current force curve
---------
Syntax: derivplot
- '''
- dplot=self.derivplot_curves()
- plot_graph=self.list_of_events['plot_graph']
+ '''
+ dplot=self.derivplot_curves()
+ plot_graph=self.list_of_events['plot_graph']
wx.PostEvent(self.frame,plot_graph(plots=[dplot]))
-
+
def derivplot_curves(self):
'''
do_derivplot helper function
-
+
create derivate plot curves for force curves.
- '''
+ '''
dplot=lhc.PlotObject()
- dplot.vectors=[]
-
+ dplot.vectors=[]
+
for vector in self.plots[0].vectors:
dplot.vectors.append([])
dplot.vectors[-1].append(vector[0][:-1])
dplot.vectors[-1].append(np.diff(vector[1]))
-
+
dplot.destination=1
dplot.units=self.plots[0].units
-
- return dplot
-
- def do_subtplot(self,args):
+
+ return dplot
+
+ def do_subtplot(self, args):
'''
SUBTPLOT
(procplots.py plugin)
Syntax: subtplot
'''
#FIXME: sub_filter and sub_order must be args
-
+
if len(self.plots[0].vectors) != 2:
print 'This command only works on a curve with two different plots.'
pass
-
+
outplot=self.subtract_curves(sub_order=1)
-
- plot_graph=self.list_of_events['plot_graph']
+
+ plot_graph=self.list_of_events['plot_graph']
wx.PostEvent(self.frame,plot_graph(plots=[outplot]))
-
+
def subtract_curves(self, sub_order):
'''
subtracts the extension from the retraction
- '''
+ '''
xext=self.plots[0].vectors[0][0]
yext=self.plots[0].vectors[0][1]
xret=self.plots[0].vectors[1][0]
yret=self.plots[0].vectors[1][1]
-
+
#we want the same number of points
maxpoints_tot=min(len(xext),len(xret))
xext=xext[0:maxpoints_tot]
yext=yext[0:maxpoints_tot]
xret=xret[0:maxpoints_tot]
yret=yret[0:maxpoints_tot]
-
+
if sub_order:
ydiff=[yretval-yextval for yretval,yextval in zip(yret,yext)]
else: #reverse subtraction (not sure it's useful, but...)
- ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]
-
+ ydiff=[yextval-yretval for yextval,yretval in zip(yext,yret)]
+
outplot=copy.deepcopy(self.plots[0])
outplot.vectors[0][0], outplot.vectors[1][0] = xext,xret #FIXME: if I use xret, it is not correct!
outplot.vectors[1][1]=ydiff
outplot.vectors[0][1]=[0 for item in outplot.vectors[1][0]]
-
+
return outplot
median_filter=customvalue
else:
median_filter=self.config['medfilt']
-
+
if median_filter==0:
return plot
-
+
if float(median_filter)/2 == int(median_filter)/2:
median_filter+=1
-
+
nplots=len(plot.vectors)
c=0
while c<nplots:
plot.vectors[c][1]=scipy.signal.medfilt(plot.vectors[c][1],median_filter)
c+=1
-
+
return plot
-
+
def plotmanip_correct(self, plot, current, customvalue=None):
'''
- the deflection() vector is as long as the X of extension + the X of retraction
- plot.vectors[0][0] is the X of extension curve
- plot.vectors[1][0] is the X of retraction curve
-
+
FIXME: both this method and the picoforce driver have to be updated, deflection() must return
a more senseful data structure!
'''
#use only for force spectroscopy experiments!
if current.curve.experiment != 'smfs':
return plot
-
+
if customvalue != None:
execute_me=customvalue
else:
execute_me=self.config['correct']
if not execute_me:
return plot
-
+
defl_ext,defl_ret=current.curve.deflection()
#halflen=len(deflall)/2
-
+
plot.vectors[0][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[0][0],defl_ext)]
plot.vectors[1][0]=[(zpoint-deflpoint) for zpoint,deflpoint in zip(plot.vectors[1][0],defl_ret)]
return plot
+
+
+ def plotmanip_centerzero(self, plot, current, customvalue=None):
+ '''
+ Centers the force curve so the median (the free level) corresponds to 0 N
+ Assumes that:
+ - plot.vectors[0][1] is the Y of extension curve
+ - plot.vectors[1][1] is the Y of retraction curve
+
+
+ '''
+ #use only for force spectroscopy experiments!
+ if current.curve.experiment != 'smfs':
+ return plot
+
+ if customvalue != None:
+ execute_me=customvalue
+ else:
+ execute_me=self.config['centerzero']
+ if not execute_me:
+ return plot
+
+
+
+ #levelapp=float(np.median(plot.vectors[0][1]))
+ levelret=float(np.median(plot.vectors[1][1][-300:-1]))
+
+ level=levelret
+
+ approach=[i-level for i in plot.vectors[0][1]]
+ retract=[i-level for i in plot.vectors[1][1]]
+
+ plot.vectors[0][1]=approach
+ plot.vectors[1][1]=retract
+ return plot
'''
def plotmanip_detriggerize(self, plot, current, customvalue=None):
#DEPRECATED
if self.config['detrigger']==0:
return plot
-
+
cutindex=2
startvalue=plot.vectors[0][0][0]
-
- for index in range(len(plot.vectors[0][0])-1,2,-2):
+
+ for index in range(len(plot.vectors[0][0])-1,2,-2):
if plot.vectors[0][0][index]>startvalue:
cutindex=index
else:
plot.vectors[0][0]=plot.vectors[0][0][:cutindex]
plot.vectors[0][1]=plot.vectors[0][1][:cutindex]
-
+
return plot
- '''
-
-
-
+ '''
+
+
+
#FFT---------------------------
def fft_plot(self, vector):
'''
'''
fftplot=lhc.PlotObject()
fftplot.vectors=[[]]
-
+
fftlen=len(vector)/2 #need just 1/2 of length
- fftplot.vectors[-1].append(np.arange(1,fftlen).tolist())
-
+ fftplot.vectors[-1].append(np.arange(1,fftlen).tolist())
+
try:
fftplot.vectors[-1].append(abs(np.fft(vector)[1:fftlen]).tolist())
except TypeError: #we take care of newer NumPy (1.0.x)
fftplot.vectors[-1].append(abs(np.fft.fft(vector)[1:fftlen]).tolist())
-
-
+
+
fftplot.destination=1
-
-
+
+
return fftplot
-
-
+
+
def do_fft(self,args):
'''
FFT
Plots the fast Fourier transform of the selected plot
---
Syntax: fft [top,bottom] [select] [0,1...]
-
+
By default, fft performs the Fourier transform on all the 0-th data set on the
top plot.
-
+
[top,bottom]: which plot is the data set to fft (default: top)
[select]: you pick up two points on the plot and fft only the segment between
[0,1,...]: which data set on the selected plot you want to fft (default: 0)
'''
-
+
#args parsing
#whatplot = plot to fft
#whatset = set to fft in the plot
whatset=int(arg)
except ValueError:
pass
-
+
if select:
points=self._measure_N_points(N=2, whatset=whatset)
boundaries=[points[0].index, points[1].index]
y_to_fft=self.plots[whatplot].vectors[whatset][1][boundaries[0]:boundaries[1]] #y
else:
y_to_fft=self.plots[whatplot].vectors[whatset][1] #y
-
- fftplot=self.fft_plot(y_to_fft)
+
+ fftplot=self.fft_plot(y_to_fft)
fftplot.units=['frequency', 'power']
- plot_graph=self.list_of_events['plot_graph']
+ plot_graph=self.list_of_events['plot_graph']
wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))
-
\ No newline at end of file
projects / hooke.git / blobdiff