+#!/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.
'''
-from hooke.libhooke import WX_GOOD, ClickedPoint
+import lib.libhooke as lh
import wxversion
-wxversion.select(WX_GOOD)
-from wx import PostEvent
+wxversion.select(lh.WX_GOOD)
+
import numpy as np
import scipy as sp
-import copy
-import os.path
-import time
import warnings
-warnings.simplefilter('ignore',np.RankWarning)
+warnings.simplefilter('ignore', np.RankWarning)
+import lib.curve
+import lib.prettyformat
-class generalvclampCommands(object):
+class generalvclampCommands:
def _plug_init(self):
- self.basecurrent=None
- self.basepoints=None
- self.autofile=''
+ self.basecurrent = ''
+ self.basepoints = []
+ #TODO: what is self.autofile for?
+ #self.autofile = ''
- def do_distance(self,args):
+ def do_distance(self):
'''
DISTANCE
(generalvclamp.py)
-----------------
Syntax: distance
'''
- if self.current.curve.experiment == 'clamp':
- print 'You wanted to use zpiezo perhaps?'
+ 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
- else:
- dx,unitx,dy,unity=self._delta(set=1)
- print str(dx*(10**9))+' nm'
- to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
- self.outlet.push(to_dump)
-
-
- def do_force(self,args):
+ 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)
---------------
Syntax: force
'''
- if self.current.curve.experiment == 'clamp':
- print 'This command makes no sense for a force clamp experiment.'
+ 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
- dx,unitx,dy,unity=self._delta(set=1)
- print str(dy*(10**12))+' pN'
- to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
- self.outlet.push(to_dump)
-
-
- def do_forcebase(self,args):
+ 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
- took as the average between two points.
+ 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
max: Instead of asking for a point to measure, asks for two points and use
the maximum peak in between
'''
- rebase=False #if true=we select rebase
- maxpoint=False #if true=we measure the maximum peak
-
- plot=self._get_displayed_plot()
- whatset=1 #fixme: for all sets
- if 'rebase' in args or (self.basecurrent != self.current.path):
- rebase=True
- if 'max' in args:
- maxpoint=True
-
- if rebase:
- print 'Select baseline'
- self.basepoints=self._measure_N_points(N=2, whatset=whatset)
- self.basecurrent=self.current.path
-
+ 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:
- print 'Select two points'
- points=self._measure_N_points(N=2, whatset=whatset)
- boundpoints=[points[0].index, points[1].index]
+ 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:
- y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
+ 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:
- print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
+ 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:
- print 'Select point to measure'
- points=self._measure_N_points(N=1, whatset=whatset)
- #whatplot=points[0].dest
- y=points[0].graph_coords[1]
+ maximum_point = self._measure_N_points(N=1, message='Click on the point to measure.', whatset=whatset)
+ y = maximum_point[0].graph_coords[1]
- #fixme: code duplication
- boundaries=[self.basepoints[0].index, self.basepoints[1].index]
+ boundaries = [self.basepoints[0].index, self.basepoints[1].index]
boundaries.sort()
- to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
-
- avg=np.mean(to_average)
- forcebase=abs(y-avg)
- print str(forcebase*(10**12))+' pN'
- to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
- self.outlet.push(to_dump)
-\r
- def plotmanip_multiplier(self, plot, current):
+ 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'\r
+ 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.curve.experiment != 'smfs':
+ if current.driver.experiment != 'smfs':
return plot
- #only one set is present...
- if len(self.plots[0].vectors) != 2:
+ force_multiplier = self.GetFloatFromConfig('generalvclamp', 'force_multiplier')
+ if force_multiplier == 1:
return plot
- #multiplier is 1...
- if (self.config['force_multiplier']==1):
- return plot\r
-\r
- for i in range(len(plot.vectors[0][1])):
- plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier'] \r
-\r
- for i in range(len(plot.vectors[1][1])):
- plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']\r
-\r
- return plot \r
+ 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=False):
+ 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=False)
+ customvalue = int (>0) --> starts the function even if config says no (default=0)
'''
#not a smfs curve...
- if current.curve.experiment != 'smfs':
- return plot
-
- #only one set is present...
- if len(self.plots[0].vectors) != 2:
- return plot
+ if current.driver.experiment != 'smfs':
+ return current
#config is not flatten, and customvalue flag is false too
- if (not self.config['flatten']) and (not customvalue):
- return plot
+ #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
+ max_exponent = 12
+ delta_contact = 0
- if customvalue:
- max_cycles=customvalue
+ if customvalue > 0:
+ max_cycles = customvalue
else:
- max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
+ #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()
+ 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)]
+ 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.vectors[0][0][contact_index+delta_contact:]
- y_ext=plot.vectors[0][1][contact_index+delta_contact:]
- x_ret=plot.vectors[1][0][contact_index+delta_contact:]
- y_ret=plot.vectors[1][1][contact_index+delta_contact:]
+ 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:
+ 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 plot
+ return current
- best_exponent=errn.index(min(errn))
+ best_exponent = errn.index(min(errn))
#extension
- ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
- yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
+ 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.vectors[1][1][0:contact_index+delta_contact]) #contact part
+ 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))
+ ycorr_ext = np.concatenate((yjoin_ext, ycorr_ext))
+ ycorr_ret = np.concatenate((yjoin_ret, ycorr_ret))
- plot.vectors[0][1]=list(ycorr_ext)
- plot.vectors[1][1]=list(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,args):
+ def do_slope(self):
'''
SLOPE
(generalvclamp.py)
The facultative [width] parameter specifies how many
points will be considered for the fit. If [width] is
specified, only one click will be required.
- (c) Marco Brucale, Massimo Sandal 2008
+ Copyright 2008 by Marco Brucale, Massimo Sandal
'''
- # Reads the facultative width argument
- try:
- fitspan=int(args)
- except:
- fitspan=0
-
- # Decides between the two forms of user input, as per (args)
+ 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 current curve vector
- print 'Click twice to delimit chunk'
- clickedpoints=[]
- points=self._measure_N_points(N=2,whatset=1)
- clickedpoints=[points[0].index,points[1].index]
- clickedpoints.sort()
+ # 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:
- print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
- clickedpoints=[]
- points=self._measure_N_points(N=1,whatset=1)
- clickedpoints=[points[0].index-fitspan,points[0].index]
+ 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,[],[]]
+ parameters = [0, 0, [], []]
try:
- parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
+ parameters = self.linefit_between(clicked_points[0], clicked_points[1], whatset=whatset)
except:
- print 'Cannot fit. Did you click twice the same point?'
+ self.AppendToOutput('Cannot fit. Did you click the same point twice?')
return
- # Outputs the relevant slope parameter
- print 'Slope:'
- print str(parameters[0])
- to_dump='slope '+self.current.path+' '+str(parameters[0])
- self.outlet.push(to_dump)
-
+ plot = self.GetDisplayedPlotCorrected()
# Makes a vector with the fitted parameters and sends it to the GUI
xtoplot=parameters[2]
ytoplot=[]
- x=0
+ x = 0
for x in xtoplot:
- ytoplot.append((x*parameters[0])+parameters[1])
+ ytoplot.append((x * parameters[0]) + parameters[1])
- clickvector_x, clickvector_y=[], []
+ clickvector_x = []
+ clickvector_y = []
for item in points:
clickvector_x.append(item.graph_coords[0])
clickvector_y.append(item.graph_coords[1])
- lineplot=self._get_displayed_plot(0) #get topmost displayed plot
-
- lineplot.add_set(xtoplot,ytoplot)
- lineplot.add_set(clickvector_x, clickvector_y)
-
+ 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)
- if lineplot.styles==[]:
- lineplot.styles=[None,None,None,'scatter']
- else:
- lineplot.styles+=[None,'scatter']
- if lineplot.colors==[]:
- lineplot.styles=[None,None,None,None]
- else:
- lineplot.colors+=[None,None]
-
-
- self._send_plot([lineplot])
+ # 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=1):
+ def linefit_between(self, index1, index2, whatset=lh.RETRACTION):
'''
- Creates two vectors (xtofit,ytofit) slicing out from the
- current return trace a portion delimited by the two indexes
+ 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.
- (c) Marco Brucale, Massimo Sandal 2008
+ Copyright 2008 by Marco Brucale, Massimo Sandal
'''
- # Translates the indexes into two vectors containing the x,y data to fit
- xtofit=self.plots[0].vectors[whatset][0][index1:index2]
- ytofit=self.plots[0].vectors[whatset][1][index1:index2]
+ # 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=[]
- linefit=np.polyfit(xtofit,ytofit,1)
+ linefit = np.polyfit(xtofit, ytofit, 1)
+
+ return (linefit[0], linefit[1], xtofit, ytofit)
+
+
- return (linefit[0],linefit[1],xtofit,ytofit)
projects / hooke.git / blobdiff