4 Plugin regarding general velocity clamp measurements
7 from libhooke import WX_GOOD, ClickedPoint
9 wxversion.select(WX_GOOD)
10 from wx import PostEvent
18 warnings.simplefilter('ignore',np.RankWarning)
21 class generalvclampCommands(object):
28 def do_distance(self,args):
32 Measure the distance (in nm) between two points.
33 For a standard experiment this is the delta X distance.
34 For a force clamp experiment this is the delta Y distance (actually becomes
39 if self.current.curve.experiment == 'clamp':
40 print 'You wanted to use zpiezo perhaps?'
43 dx,unitx,dy,unity=self._delta(set=1)
44 print str(dx*(10**9))+' nm'
45 to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
46 self.outlet.push(to_dump)
49 def do_force(self,args):
53 Measure the force difference (in pN) between two points
57 if self.current.curve.experiment == 'clamp':
58 print 'This command makes no sense for a force clamp experiment.'
60 dx,unitx,dy,unity=self._delta(set=1)
61 print str(dy*(10**12))+' pN'
62 to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
63 self.outlet.push(to_dump)
66 def do_forcebase(self,args):
70 Measures the difference in force (in pN) between a point and a baseline
71 took as the average between two points.
73 The baseline is fixed once for a given curve and different force measurements,
74 unless the user wants it to be recalculated
76 Syntax: forcebase [rebase]
77 rebase: Forces forcebase to ask again the baseline
78 max: Instead of asking for a point to measure, asks for two points and use
79 the maximum peak in between
81 rebase=False #if true=we select rebase
82 maxpoint=False #if true=we measure the maximum peak
84 plot=self._get_displayed_plot()
85 whatset=1 #fixme: for all sets
86 if 'rebase' in args or (self.basecurrent != self.current.path):
92 print 'Select baseline'
93 self.basepoints=self._measure_N_points(N=2, whatset=whatset)
94 self.basecurrent=self.current.path
97 print 'Select two points'
98 points=self._measure_N_points(N=2, whatset=whatset)
99 boundpoints=[points[0].index, points[1].index]
102 y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
104 print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
106 print 'Select point to measure'
107 points=self._measure_N_points(N=1, whatset=whatset)
108 #whatplot=points[0].dest
109 y=points[0].graph_coords[1]
111 #fixme: code duplication
112 boundaries=[self.basepoints[0].index, self.basepoints[1].index]
114 to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
116 avg=np.mean(to_average)
118 print str(forcebase*(10**12))+' pN'
119 to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
120 self.outlet.push(to_dump)
122 def plotmanip_multiplier(self, plot, current):
124 Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
\r
125 configuration variable. Useful for calibrations and other stuff.
129 if current.curve.experiment != 'smfs':
132 #only one set is present...
133 if len(self.plots[0].vectors) != 2:
137 if (self.config['force_multiplier']==1):
140 for i in range(len(plot.vectors[0][1])):
141 plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier']
\r
143 for i in range(len(plot.vectors[1][1])):
144 plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']
\r
149 def plotmanip_flatten(self, plot, current, customvalue=False):
151 Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
152 the best polynomial fit is chosen among polynomials of degree 1 to n, where n is
153 given by the configuration file or by the customvalue.
155 customvalue= int (>0) --> starts the function even if config says no (default=False)
159 if current.curve.experiment != 'smfs':
162 #only one set is present...
163 if len(self.plots[0].vectors) != 2:
166 #config is not flatten, and customvalue flag is false too
167 if (not self.config['flatten']) and (not customvalue):
174 max_cycles=customvalue
176 max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
178 contact_index=self.find_contact_point()
180 valn=[[] for item in range(max_exponent)]
181 yrn=[0.0 for item in range(max_exponent)]
182 errn=[0.0 for item in range(max_exponent)]
184 for i in range(int(max_cycles)):
186 x_ext=plot.vectors[0][0][contact_index+delta_contact:]
187 y_ext=plot.vectors[0][1][contact_index+delta_contact:]
188 x_ret=plot.vectors[1][0][contact_index+delta_contact:]
189 y_ret=plot.vectors[1][1][contact_index+delta_contact:]
190 for exponent in range(max_exponent):
192 valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
193 yrn[exponent]=sp.polyval(valn[exponent],x_ret)
194 errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
196 print 'Cannot flatten!'
200 best_exponent=errn.index(min(errn))
203 ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
204 yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
206 ycorr_ret=y_ret-yrn[best_exponent]+y_ext[0] #noncontact part
207 yjoin_ret=np.array(plot.vectors[1][1][0:contact_index+delta_contact]) #contact part
209 ycorr_ext=np.concatenate((yjoin_ext, ycorr_ext))
210 ycorr_ret=np.concatenate((yjoin_ret, ycorr_ret))
212 plot.vectors[0][1]=list(ycorr_ext)
213 plot.vectors[1][1]=list(ycorr_ret)
218 def do_slope(self,args):
222 Measures the slope of a delimited chunk on the return trace.
223 The chunk can be delimited either by two manual clicks, or have
224 a fixed width, given as an argument.
226 Syntax: slope [width]
227 The facultative [width] parameter specifies how many
228 points will be considered for the fit. If [width] is
229 specified, only one click will be required.
230 (c) Marco Brucale, Massimo Sandal 2008
233 # Reads the facultative width argument
239 # Decides between the two forms of user input, as per (args)
241 # Gets the Xs of two clicked points as indexes on the current curve vector
242 print 'Click twice to delimit chunk'
244 points=self._measure_N_points(N=2,whatset=1)
245 clickedpoints=[points[0].index,points[1].index]
248 print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
250 points=self._measure_N_points(N=1,whatset=1)
251 clickedpoints=[points[0].index-fitspan,points[0].index]
253 # Calls the function linefit_between
254 parameters=[0,0,[],[]]
256 parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
258 print 'Cannot fit. Did you click twice the same point?'
261 # Outputs the relevant slope parameter
263 print str(parameters[0])
264 to_dump='slope '+self.current.path+' '+str(parameters[0])
265 self.outlet.push(to_dump)
267 # Makes a vector with the fitted parameters and sends it to the GUI
268 xtoplot=parameters[2]
272 ytoplot.append((x*parameters[0])+parameters[1])
274 clickvector_x, clickvector_y=[], []
276 clickvector_x.append(item.graph_coords[0])
277 clickvector_y.append(item.graph_coords[1])
279 lineplot=self._get_displayed_plot(0) #get topmost displayed plot
281 lineplot.add_set(xtoplot,ytoplot)
282 lineplot.add_set(clickvector_x, clickvector_y)
285 if lineplot.styles==[]:
286 lineplot.styles=[None,None,None,'scatter']
288 lineplot.styles+=[None,'scatter']
289 if lineplot.colors==[]:
290 lineplot.styles=[None,None,None,None]
292 lineplot.colors+=[None,None]
295 self._send_plot([lineplot])
297 def linefit_between(self,index1,index2,whatset=1):
299 Creates two vectors (xtofit,ytofit) slicing out from the
300 current return trace a portion delimited by the two indexes
302 Then does a least squares linear fit on that slice.
303 Finally returns [0]=the slope, [1]=the intercept of the
304 fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
306 (c) Marco Brucale, Massimo Sandal 2008
308 # Translates the indexes into two vectors containing the x,y data to fit
309 xtofit=self.plots[0].vectors[whatset][0][index1:index2]
310 ytofit=self.plots[0].vectors[whatset][1][index1:index2]
312 # Does the actual linear fitting (simple least squares with numpy.polyfit)
314 linefit=np.polyfit(xtofit,ytofit,1)
316 return (linefit[0],linefit[1],xtofit,ytofit)