-# Copyright (C) 2010 Fibrin's Benedetti
-# W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2010 Alberto Gomez-Casado
+# Massimo Sandal <devicerandom@gmail.com>
+# W. Trevor King <wking@drexel.edu>
#
# This file is part of Hooke.
#
# License along with Hooke. If not, see
# <http://www.gnu.org/licenses/>.
-"""The ``curve`` module provides :class:`CurvePlugin` and several
-associated :class:`hooke.command.Command`\s for handling
-:mod:`hooke.curve` classes.
+"""Processed plots plugin for force curves.
"""
-from ..command import Command, Argument, Failure
-from ..plugin import Builtin
-from ..plugin.playlist import current_playlist_callback
-
-
-class CurvePlugin (Builtin):
- def __init__(self):
- super(CurvePlugin, self).__init__(name='curve')
-
- def commands(self):
- return [InfoCommand(), ]
-
-
-# Define common or complicated arguments
-
-def current_curve_callback(hooke, command, argument, value):
- if value != None:
- return value
- playlist = current_playlist_callback(hooke, command, argument, value)
- curve = playlist.current()
- if curve == None:
- raise Failure('No curves in %s' % playlist)
- return curve
-
-CurveArgument = Argument(
- name='curve', type='curve', callback=current_curve_callback,
- help="""
-:class:`hooke.curve.Curve` to act on. Defaults to the current curve
-of the current playlist.
-""".strip())
-
-
-# Define commands
-
-class InfoCommand (Command):
- """Print selected information about a :class:`hooke.curve.Curve`.
- """
- def __init__(self):
- args = [
- CurveArgument,
- Argument(name='all', type='bool', default=False, count=1,
- help='Print all curve information.'),
- ]
- self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
- 'blocks', 'block sizes']
- for field in self.fields:
- args.append(Argument(
- name=field, type='bool', default=False, count=1,
- help='Print curve %s' % field))
- super(InfoCommand, self).__init__(
- name='curve info', arguments=args, help=self.__doc__)
-
- def _run(self, hooke, inqueue, outqueue, params):
- fields = {}
- for key in self.fields:
- fields[key] = params[key]
- if reduce(lambda x,y: x and y, fields.values()) == False:
- params['all'] = True # No specific fields set, default to 'all'
- if params['all'] == True:
- for key in self.fields:
- fields[key] = True
- lines = []
- for key in self.fields:
- if fields[key] == True:
- get = getattr(self, '_get_%s' % key.replace(' ', '_'))
- lines.append('%s: %s' % (key, get(params['curve'])))
- outqueue.put('\n'.join(lines))
-
- def _get_name(self, curve):
- return curve.name
-
- def _get_path(self, curve):
- return curve.path
-
- def _get_experiment(self, curve):
- return curve.info.get('experiment', None)
-
- def _get_driver(self, curve):
- return curve.driver
-
- def _get_filetype(self, curve):
- return curve.info.get('filetype', None)
-
- def _get_note(self, curve):
- return curve.info.get('note', None)
-
- def _get_blocks(self, curve):
- return len(curve.data)
-
- def _get_block_sizes(self, curve):
- return [block.shape for block in curve.data]
-
-
-class ExportCommand (Command):
- """Export a :class:`hooke.curve.Curve` data block as TAB-delimeted
- ASCII text.
- """
- def __init__(self):
- self.fields = ['name', 'path', 'experiment', 'driver', 'filetype', 'note',
- 'blocks', 'block sizes']
- for field in self.fields:
- args.append(Argument(
- name=field, type='bool', default=False, count=1,
- help='Print curve %s' % field))
- super(InfoCommand, self).__init__(
- name='curve info',
- arguments=[
- CurveArgument,
- Argument(name='block', aliases=['set'], type='int', default=0,
- help="""
-Data block to save. For an approach/retract force curve, `0` selects
-the approacing curve and `1` selects the retracting curve.
-""".strip()),
- Argument(name='output', type='file', default='curve.dat',
- help="""
-File name for the output data. Defaults to 'curve.dat'
-""".strip()),
- ],
- help=self.__doc__)
-
- def _run(self, hooke, inqueue, outqueue, params):
- data = params['curve'].data[params['index']]
- f = open(params['output'], 'w')
- data.tofile(f, sep='\t')
- f.close()
+from ..libhooke import WX_GOOD
+import wxversion
+wxversion.select(WX_GOOD)
+
+import wx
+import numpy as np
+import scipy as sp
+import scipy.signal
+import copy
+
+from .. import curve as lhc
+
+
+class procplotsCommands(object):
+
+ def _plug_init(self):
+ pass
+
+ def do_derivplot(self,args):
+ '''
+ DERIVPLOT
+ (procplots.py plugin)
+ 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']
+ 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=[]
+
+ 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):
+ '''
+ SUBTPLOT
+ (procplots.py plugin)
+ Plots the difference between ret and ext current curve
+ -------
+ 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']
+ 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)]
+
+ 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
+
+
+#-----PLOT MANIPULATORS
+ def plotmanip_median(self, plot, current, customvalue=None):
+ '''
+ does the median of the y values of a plot
+ '''
+ if customvalue:
+ 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):
+ '''
+ does the correction for the deflection for a force spectroscopy curve.
+ Assumes that:
+ - the current plot has a deflection() method that returns a vector of values
+ - 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):
+ if plot.vectors[0][0][index]>startvalue:
+ cutindex=index
+ else:
+ break
+
+ 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):
+ '''
+ calculates the fast Fourier transform for the selected vector in the plot
+ '''
+ fftplot=lhc.PlotObject()
+ fftplot.vectors=[[]]
+
+ fftlen=len(vector)/2 #need just 1/2 of length
+ 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
+ (procplots.py plugin)
+ 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
+ select=('select' in args)
+ if 'top' in args:
+ whatplot=0
+ elif 'bottom' in args:
+ whatplot=1
+ else:
+ whatplot=0
+ whatset=0
+ for arg in args:
+ try:
+ whatset=int(arg)
+ except ValueError:
+ pass
+
+ if select:
+ points=self._measure_N_points(N=2, whatset=whatset)
+ boundaries=[points[0].index, points[1].index]
+ boundaries.sort()
+ 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.units=['frequency', 'power']
+ plot_graph=self.list_of_events['plot_graph']
+ wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))
+++ /dev/null
-# 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/>.
-
-"""Processed plots plugin for force curves.
-"""
-
-from ..libhooke import WX_GOOD
-import wxversion
-wxversion.select(WX_GOOD)
-
-import wx
-import numpy as np
-import scipy as sp
-import scipy.signal
-import copy
-
-from .. import curve as lhc
-
-
-class procplotsCommands(object):
-
- def _plug_init(self):
- pass
-
- def do_derivplot(self,args):
- '''
- DERIVPLOT
- (procplots.py plugin)
- 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']
- 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=[]
-
- 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):
- '''
- SUBTPLOT
- (procplots.py plugin)
- Plots the difference between ret and ext current curve
- -------
- 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']
- 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)]
-
- 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
-
-
-#-----PLOT MANIPULATORS
- def plotmanip_median(self, plot, current, customvalue=None):
- '''
- does the median of the y values of a plot
- '''
- if customvalue:
- 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):
- '''
- does the correction for the deflection for a force spectroscopy curve.
- Assumes that:
- - the current plot has a deflection() method that returns a vector of values
- - 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):
- if plot.vectors[0][0][index]>startvalue:
- cutindex=index
- else:
- break
-
- 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):
- '''
- calculates the fast Fourier transform for the selected vector in the plot
- '''
- fftplot=lhc.PlotObject()
- fftplot.vectors=[[]]
-
- fftlen=len(vector)/2 #need just 1/2 of length
- 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
- (procplots.py plugin)
- 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
- select=('select' in args)
- if 'top' in args:
- whatplot=0
- elif 'bottom' in args:
- whatplot=1
- else:
- whatplot=0
- whatset=0
- for arg in args:
- try:
- whatset=int(arg)
- except ValueError:
- pass
-
- if select:
- points=self._measure_N_points(N=2, whatset=whatset)
- boundaries=[points[0].index, points[1].index]
- boundaries.sort()
- 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.units=['frequency', 'power']
- plot_graph=self.list_of_events['plot_graph']
- wx.PostEvent(self.frame,plot_graph(plots=[fftplot]))
projects / hooke.git / commitdiff