From 080ea5e79c83de548ca1e0d7f94ee39c4008f7cf Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Thu, 2 Sep 2010 10:06:54 -0400 Subject: [PATCH] Remove hooke/plugin/generalvclamp.py. The only functions without analogs in the current framework are already listed at the OldCruft class at the end of hooke/plugin/curve.py. --- hooke/plugin/generalvclamp.py | 487 ---------------------------------- 1 file changed, 487 deletions(-) delete mode 100644 hooke/plugin/generalvclamp.py diff --git a/hooke/plugin/generalvclamp.py b/hooke/plugin/generalvclamp.py deleted file mode 100644 index ccfb5cc..0000000 --- a/hooke/plugin/generalvclamp.py +++ /dev/null @@ -1,487 +0,0 @@ -#!/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) - - - -- 2.26.2