+++ /dev/null
-#!/usr/bin/env python
-
-'''
-generalvclamp.py
-
-Plugin regarding general velocity clamp measurements
-
-Copyright 2008 by Massimo Sandal, Fabrizio Benedetti, Marco Brucale, Bruno Samori (University of Bologna, Italy),
-and Alberto Gomez-Casado (University of Twente)
-with modifications by Dr. Rolf Schmidt (Concordia University, Canada)
-
-This program is released under the GNU General Public License version 2.
-'''
-
-import lib.libhooke as lh
-import wxversion
-wxversion.select(lh.WX_GOOD)
-
-import numpy as np
-import scipy as sp
-
-import warnings
-warnings.simplefilter('ignore', np.RankWarning)
-
-import lib.curve
-import lib.prettyformat
-
-class generalvclampCommands:
-
- def _plug_init(self):
- self.basecurrent = ''
- self.basepoints = []
- #TODO: what is self.autofile for?
- #self.autofile = ''
-
- def do_distance(self):
- '''
- DISTANCE
- (generalvclamp.py)
- Measure the distance (in nm) between two points.
- For a standard experiment this is the delta X distance.
- For a force clamp experiment this is the delta Y distance (actually becomes
- an alias of zpiezo)
- -----------------
- Syntax: distance
- '''
- color = self.GetColorFromConfig('generalvclamp', 'distance', 'color')
- decimals = self.GetIntFromConfig('generalvclamp', 'distance', 'decimals')
- prefix = self.GetStringFromConfig('generalvclamp', 'distance', 'prefix')
- multiplier = 10 ** lib.prettyformat.get_exponent(prefix)
- show = self.GetBoolFromConfig('generalvclamp', 'distance', 'show')
- show_in_legend = self.GetBoolFromConfig('generalvclamp', 'distance', 'show_in_legend')
- size = self.GetIntFromConfig('generalvclamp', 'distance', 'size')
- whatset_str = self.GetStringFromConfig('generalvclamp', 'distance', 'whatset')
- whatset = 'retraction'
- if whatset_str == 'extension':
- whatset = lh.EXTENSION
- if whatset_str == 'retraction':
- whatset = lh.RETRACTION
-
- active_file = self.GetActiveFile()
- if active_file.driver.experiment == 'clamp':
- self.AppendToOutput('You wanted to use zpiezo perhaps?')
- return
- plugin = lib.plugin.Plugin()
- plugin.name = 'generalvclamp'
- plugin.section = 'distance'
- delta = self._delta(message='Click 2 points to measure the distance.', whatset=whatset)
-
- plot = self.GetDisplayedPlotCorrected()
- if show:
- #add the points to the plot
- points = lib.curve.Curve()
- points.color = color
- if show_in_legend:
- points.label = 'distance'
- else:
- points.label = '_nolegend_'
- points.size = size
- points.style = 'scatter'
- points.units.x = delta.units.x
- points.units.y = delta.units.y
- points.x = [delta.point1.x, delta.point2.x]
- points.y = [delta.point1.y, delta.point2.y]
- plot.curves.append(points)
-
- self.UpdatePlot(plot)
-
- output_str = lib.prettyformat.pretty_format(abs(delta.get_delta_x()), delta.units.x, decimals, multiplier)
- self.AppendToOutput(''.join(['Distance: ', output_str]))
-
- def do_force(self):
- '''
- FORCE
- (generalvclamp.py)
- Measure the force difference (in pN) between two points
- ---------------
- Syntax: force
- '''
- color = self.GetColorFromConfig('generalvclamp', 'force', 'color')
- decimals = self.GetIntFromConfig('generalvclamp', 'force', 'decimals')
- prefix = self.GetStringFromConfig('generalvclamp', 'force', 'prefix')
- multiplier = 10 ** lib.prettyformat.get_exponent(prefix)
- show = self.GetBoolFromConfig('generalvclamp', 'force', 'show')
- show_in_legend = self.GetBoolFromConfig('generalvclamp', 'force', 'show_in_legend')
- size = self.GetIntFromConfig('generalvclamp', 'force', 'size')
- whatset_str = self.GetStringFromConfig('generalvclamp', 'force', 'whatset')
- whatset = 'retraction'
- if whatset_str == 'extension':
- whatset = lh.EXTENSION
- if whatset_str == 'retraction':
- whatset = lh.RETRACTION
-
- active_file = self.GetActiveFile()
- if active_file.driver.experiment == 'clamp':
- self.AppendToOutput('This command makes no sense for a force clamp experiment.')
- return
- plugin = lib.plugin.Plugin()
- plugin.name = 'generalvclamp'
- plugin.section = 'force'
- delta = self._delta(message='Click 2 points to measure the force.', whatset=whatset)
-
- plot = self.GetDisplayedPlotCorrected()
- if show:
- #add the points to the plot
- points = lib.curve.Curve()
- points.color = color
- if show_in_legend:
- points.label = 'force'
- else:
- points.label = '_nolegend_'
- points.size = size
- points.style = 'scatter'
- points.units.x = delta.units.x
- points.units.y = delta.units.y
- points.x = [delta.point1.x, delta.point2.x]
- points.y = [delta.point1.y, delta.point2.y]
- plot.curves.append(points)
-
- self.UpdatePlot(plot)
-
- output_str = lib.prettyformat.pretty_format(abs(delta.get_delta_y()), delta.units.y, decimals, multiplier)
- self.AppendToOutput(''.join(['Force: ', output_str]))
-
- def do_forcebase(self):
- '''
- FORCEBASE
- (generalvclamp.py)
- Measures the difference in force (in pN) between a point and a baseline
- taken as the average between two points.
-
- The baseline is fixed once for a given curve and different force measurements,
- unless the user wants it to be recalculated
- ------------
- Syntax: forcebase [rebase]
- rebase: Forces forcebase to ask again the baseline
- max: Instead of asking for a point to measure, asks for two points and use
- the maximum peak in between
- '''
- baseline_color = self.GetColorFromConfig('generalvclamp', 'forcebase', 'baseline_color')
- baseline_show = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'baseline_show')
- baseline_show_in_legend = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'baseline_show_in_legend')
- baseline_size = self.GetIntFromConfig('generalvclamp', 'forcebase', 'baseline_size')
- decimals = self.GetIntFromConfig('generalvclamp', 'forcebase', 'decimals')
- maximum_color = self.GetColorFromConfig('generalvclamp', 'forcebase', 'maximum_color')
- maximum_show = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'maximum_show')
- maximum_show_in_legend = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'maximum_show_in_legend')
- maximum_size = self.GetIntFromConfig('generalvclamp', 'forcebase', 'maximum_size')
- maximumrange_color = self.GetColorFromConfig('generalvclamp', 'forcebase', 'maximumrange_color')
- maximumrange_show = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'maximumrange_show')
- maximumrange_show_in_legend = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'maximumrange_show_in_legend')
- maximumrange_size = self.GetIntFromConfig('generalvclamp', 'forcebase', 'maximumrange_size')
- maxpoint = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'max')
- prefix = self.GetStringFromConfig('generalvclamp', 'forcebase', 'prefix')
- multiplier = 10 ** lib.prettyformat.get_exponent(prefix)
- rebase = self.GetBoolFromConfig('generalvclamp', 'forcebase', 'rebase')
- whatset_str = self.GetStringFromConfig('generalvclamp', 'forcebase', 'whatset')
- whatset = 'retraction'
- if whatset_str == 'extension':
- whatset = lh.EXTENSION
- if whatset_str == 'retraction':
- whatset = lh.RETRACTION
-
- plot = self.GetDisplayedPlotCorrected()
-
- filename = self.GetActiveFile().name
- if rebase or (self.basecurrent != filename):
- self.basepoints = self._measure_N_points(N=2, message='Click on 2 points to select the baseline.', whatset=whatset)
- self.basecurrent = filename
-
- #TODO: maxpoint does not seem to be picking up the 'real' maximum (at least not with test.hkp/default.000)
- maximumrange_points = []
- maximum_point = []
- if maxpoint:
- maximumrange_points = self._measure_N_points(N=2, message='Click 2 points to select the range for maximum detection.', whatset=whatset)
- boundpoints = [maximumrange_points[0].index, maximumrange_points[1].index]
- boundpoints.sort()
- try:
- vector_x = plot.curves[whatset].x[boundpoints[0]:boundpoints[1]]
- vector_y = plot.curves[whatset].y[boundpoints[0]:boundpoints[1]]
- y = min(vector_y)
- index = vector_y.index(y)
- maximum_point = [self._clickize(vector_x, vector_y, index)]
- except ValueError:
- self.AppendToOutput('Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of the interval?')
- return
- else:
- maximum_point = self._measure_N_points(N=1, message='Click on the point to measure.', whatset=whatset)
- y = maximum_point[0].graph_coords[1]
-
- boundaries = [self.basepoints[0].index, self.basepoints[1].index]
- boundaries.sort()
- to_average = plot.curves[whatset].y[boundaries[0]:boundaries[1]] #y points to average
-
- avg = np.mean(to_average)
- forcebase = abs(y - avg)
-
- curve = plot.curves[whatset]
- if self.basepoints and baseline_show:
- #add the baseline points to the plot
- baseline = lib.curve.Curve()
- baseline.color = baseline_color
- if baseline_show_in_legend:
- baseline.label = 'baseline'
- else:
- baseline.label = '_nolegend_'
- baseline.size = baseline_size
- baseline.style = 'scatter'
- baseline.units.x = curve.units.x
- baseline.units.y = curve.units.y
- for point in self.basepoints:
- baseline.x += [point.graph_coords[0]]
- baseline.y += [point.graph_coords[1]]
- plot.curves.append(baseline)
-
- if maximumrange_points and maximumrange_show:
- #add the range points to the plot
- maximumrange = lib.curve.Curve()
- maximumrange.color = maximumrange_color
- if maximumrange_show_in_legend:
- maximumrange.label = 'maximumrange'
- else:
- maximumrange.label = '_nolegend_'
- maximumrange.size = maximumrange_size
- maximumrange.style = 'scatter'
- maximumrange.units.x = curve.units.x
- maximumrange.units.y = curve.units.y
- for point in maximumrange_points:
- maximumrange.x += [point.graph_coords[0]]
- maximumrange.y += [point.graph_coords[1]]
- plot.curves.append(maximumrange)
-
- if maximum_show:
- #add the maximum to the plot
- maximum = lib.curve.Curve()
- maximum.color = maximum_color
- if maximum_show_in_legend:
- maximum.label = 'maximum'
- else:
- maximum.label = '_nolegend_'
- maximum.size = maximum_size
- maximum.style = 'scatter'
- maximum.units.x = curve.units.x
- maximum.units.y = curve.units.y
- maximum.x = [maximum_point[0].graph_coords[0]]
- maximum.y = [maximum_point[0].graph_coords[1]]
- plot.curves.append(maximum)
-
- self.UpdatePlot(plot)
-
- unit_str = plot.curves[whatset].units.y
- output_str = lib.prettyformat.pretty_format(forcebase, unit_str, decimals, multiplier)
- self.AppendToOutput(''.join(['Force: ', output_str]))
-
- def plotmanip_multiplier(self, plot, current, customvalue=False):
- '''
- Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
- configuration variable. Useful for calibrations and other stuff.
- '''
-
- #not a smfs curve...
- if current.driver.experiment != 'smfs':
- return plot
-
- force_multiplier = self.GetFloatFromConfig('generalvclamp', 'force_multiplier')
- if force_multiplier == 1:
- return plot
-
- plot.curves[lh.EXTENSION].y = [element * force_multiplier for element in plot.curves[lh.EXTENSION].y]
- plot.curves[lh.RETRACTION].y = [element * force_multiplier for element in plot.curves[lh.RETRACTION].y]
-
- return plot
-
- def plotmanip_flatten(self, plot, current, customvalue=0):
- '''
- Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
- the best polynomial fit is chosen among polynomials of degree 1 to n, where n is
- given by the configuration file or by the customvalue.
-
- customvalue = int (>0) --> starts the function even if config says no (default=0)
- '''
-
- #not a smfs curve...
- if current.driver.experiment != 'smfs':
- return current
-
- #config is not flatten, and customvalue flag is false too
- #if (not self.config['generalvclamp']['flatten'].as_bool('value')) and (customvalue == 0):
- ##TODO: do we need this?
- #if (not self.GetBoolFromConfig('generalvclamp', 'flatten')) and (customvalue == 0):
- #return plot
-
- max_exponent = 12
- delta_contact = 0
-
- if customvalue > 0:
- max_cycles = customvalue
- else:
- #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
- max_cycles = self.GetIntFromConfig('generalvclamp', 'max_cycles')
-
- contact_index = self.find_contact_point(plot)
-
- valn = [[] for item in range(max_exponent)]
- yrn = [0.0 for item in range(max_exponent)]
- errn = [0.0 for item in range(max_exponent)]
-
- for i in range(int(max_cycles)):
- x_ext = plot.curves[lh.EXTENSION].x[contact_index + delta_contact:]
- y_ext = plot.curves[lh.EXTENSION].y[contact_index + delta_contact:]
- x_ret = plot.curves[lh.RETRACTION].x[contact_index + delta_contact:]
- y_ret = plot.curves[lh.RETRACTION].y[contact_index + delta_contact:]
- for exponent in range(max_exponent):
- try:
- valn[exponent] = sp.polyfit(x_ext, y_ext, exponent)
- yrn[exponent] = sp.polyval(valn[exponent], x_ret)
- errn[exponent] = sp.sqrt(sum((yrn[exponent] - y_ext) ** 2) / float(len(y_ext)))
- except Exception, e:
- print 'Cannot flatten!'
- print e
- return current
-
- best_exponent = errn.index(min(errn))
-
- #extension
- ycorr_ext = y_ext - yrn[best_exponent] + y_ext[0] #noncontact part
- yjoin_ext = np.array(plot.curves[lh.EXTENSION].y[0:contact_index + delta_contact]) #contact part
- #retraction
- ycorr_ret = y_ret - yrn[best_exponent] + y_ext[0] #noncontact part
- yjoin_ret = np.array(plot.curves[lh.RETRACTION].y[0:contact_index + delta_contact]) #contact part
-
- ycorr_ext = np.concatenate((yjoin_ext, ycorr_ext))
- ycorr_ret = np.concatenate((yjoin_ret, ycorr_ret))
-
- plot.curves[lh.EXTENSION].y = list(ycorr_ext)
- plot.curves[lh.RETRACTION].y = list(ycorr_ret)
-
- return plot
-
- #---SLOPE---
- def do_slope(self):
- '''
- SLOPE
- (generalvclamp.py)
- Measures the slope of a delimited chunk on the return trace.
- The chunk can be delimited either by two manual clicks, or have
- a fixed width, given as an argument.
- ---------------
- Syntax: slope [width]
- The facultative [width] parameter specifies how many
- points will be considered for the fit. If [width] is
- specified, only one click will be required.
- Copyright 2008 by Marco Brucale, Massimo Sandal
- '''
-
- decimals = self.GetIntFromConfig('generalvclamp', 'slope', 'decimals')
- fitspan = self.GetIntFromConfig('generalvclamp', 'slope', 'fitspan')
- point_color = self.GetColorFromConfig('generalvclamp', 'slope', 'point_color')
- point_show = self.GetBoolFromConfig('generalvclamp', 'slope', 'point_show')
- point_show_in_legend = self.GetBoolFromConfig('generalvclamp', 'slope', 'point_show_in_legend')
- point_size = self.GetIntFromConfig('generalvclamp', 'slope', 'point_size')
- slope_color = self.GetColorFromConfig('generalvclamp', 'slope', 'slope_color')
- slope_linewidth = self.GetIntFromConfig('generalvclamp', 'slope', 'slope_linewidth')
- slope_show = self.GetBoolFromConfig('generalvclamp', 'slope', 'slope_show')
- slope_show_in_legend = self.GetBoolFromConfig('generalvclamp', 'slope', 'slope_show_in_legend')
- whatset_str = self.GetStringFromConfig('generalvclamp', 'slope', 'whatset')
- whatset = 'retraction'
- if whatset_str == 'extension':
- whatset = lh.EXTENSION
- if whatset_str == 'retraction':
- whatset = lh.RETRACTION
-
- # Decides between the two forms of user input
- #TODO: add an option 'mode' with options 'chunk' and 'point'
- if fitspan == 0:
- # Gets the Xs of two clicked points as indexes on the curve curve vector
- clicked_points = []
- points = self._measure_N_points(N=2, message='Click 2 points to select the chunk.', whatset=whatset)
- clicked_points = [points[0].index, points[1].index]
- clicked_points.sort()
- else:
- clicked_points = []
- points = self._measure_N_points(N=1, message='Click on the leftmost point of the chunk (i.e.usually the peak).', whatset=whatset)
- clicked_points = [points[0].index - fitspan, points[0].index]
-
- # Calls the function linefit_between
- parameters = [0, 0, [], []]
- try:
- parameters = self.linefit_between(clicked_points[0], clicked_points[1], whatset=whatset)
- except:
- self.AppendToOutput('Cannot fit. Did you click the same point twice?')
- return
-
- plot = self.GetDisplayedPlotCorrected()
- # Makes a vector with the fitted parameters and sends it to the GUI
- xtoplot=parameters[2]
- ytoplot=[]
- x = 0
- for x in xtoplot:
- ytoplot.append((x * parameters[0]) + parameters[1])
-
- clickvector_x = []
- clickvector_y = []
- for item in points:
- clickvector_x.append(item.graph_coords[0])
- clickvector_y.append(item.graph_coords[1])
-
- if point_show:
- #add the clicked point to the plot
- point = lib.curve.Curve()
- point.color = point_color
- if point_show_in_legend:
- point.label = 'clicked point'
- else:
- point.label = '_nolegend_'
- point.size = point_size
- point.style = 'scatter'
- point.x = clickvector_x
- point.y = clickvector_y
- plot.curves.append(point)
-
- if slope_show:
- #add the slope to the plot
- slope = lib.curve.Curve()
- slope.color = slope_color
- if slope_show_in_legend:
- slope.label = 'slope'
- else:
- slope.label = '_nolegend_'
- slope.linewidth = slope_linewidth
- slope.style = 'plot'
- slope.units.x = plot.curves[whatset].units.x
- slope.units.y = plot.curves[whatset].units.y
- slope.x = xtoplot
- slope.y = ytoplot
- plot.curves.append(slope)
-
- self.UpdatePlot(plot)
-
- # Outputs the relevant slope parameter
- unit_str = plot.curves[whatset].units.x + '/' + plot.curves[whatset].units.y
- output_str = lib.prettyformat.pretty_format(parameters[0], unit_str, decimals, 1)
- self.AppendToOutput(''.join(['Slope: ', output_str]))
-
- def linefit_between(self, index1, index2, whatset=lh.RETRACTION):
- '''
- Creates two vectors (xtofit, ytofit) slicing out from the
- curve return trace a portion delimited by the two indeces
- given as arguments.
- Then does a least squares linear fit on that slice.
- Finally returns [0]=the slope, [1]=the intercept of the
- fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
- used for the fit.
- Copyright 2008 by Marco Brucale, Massimo Sandal
- '''
- # Translates the indeces into two vectors containing the x, y data to fit
- plot = self.displayed_plot
- xtofit = plot.corrected_curves[whatset].x[index1:index2]
- ytofit = plot.corrected_curves[whatset].y[index1:index2]
-
- # Does the actual linear fitting (simple least squares with numpy.polyfit)
- linefit = np.polyfit(xtofit, ytofit, 1)
-
- return (linefit[0], linefit[1], xtofit, ytofit)
-
-
-
projects / hooke.git / commitdiff