6 Plugin regarding general velocity clamp measurements
9 from libhooke import WX_GOOD, ClickedPoint
11 wxversion.select(WX_GOOD)
12 from wx import PostEvent
20 warnings.simplefilter('ignore',np.RankWarning)
23 class generalvclampCommands:
30 def do_distance(self,args):
34 Measure the distance (in nm) between two points.
35 For a standard experiment this is the delta X distance.
36 For a force clamp experiment this is the delta Y distance (actually becomes
41 if self.current.curve.experiment == 'clamp':
42 print 'You wanted to use zpiezo perhaps?'
45 dx,unitx,dy,unity=self._delta(set=1)
46 print str(dx*(10**9))+' nm'
47 to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
48 self.outlet.push(to_dump)
51 def do_force(self,args):
55 Measure the force difference (in pN) between two points
59 if self.current.curve.experiment == 'clamp':
60 print 'This command makes no sense for a force clamp experiment.'
62 dx,unitx,dy,unity=self._delta(set=1)
63 print str(dy*(10**12))+' pN'
64 to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
65 self.outlet.push(to_dump)
68 def do_forcebase(self,args):
72 Measures the difference in force (in pN) between a point and a baseline
73 took as the average between two points.
75 The baseline is fixed once for a given curve and different force measurements,
76 unless the user wants it to be recalculated
78 Syntax: forcebase [rebase]
79 rebase: Forces forcebase to ask again the baseline
80 max: Instead of asking for a point to measure, asks for two points and use
81 the maximum peak in between
83 rebase=False #if true=we select rebase
84 maxpoint=False #if true=we measure the maximum peak
86 plot=self._get_displayed_plot()
87 whatset=1 #fixme: for all sets
88 if 'rebase' in args or (self.basecurrent != self.current.path):
94 print 'Select baseline'
95 self.basepoints=self._measure_N_points(N=2, whatset=whatset)
96 self.basecurrent=self.current.path
99 print 'Select two points'
100 points=self._measure_N_points(N=2, whatset=whatset)
101 boundpoints=[points[0].index, points[1].index]
104 y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
106 print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
108 print 'Select point to measure'
109 points=self._measure_N_points(N=1, whatset=whatset)
110 #whatplot=points[0].dest
111 y=points[0].graph_coords[1]
113 #fixme: code duplication
114 boundaries=[self.basepoints[0].index, self.basepoints[1].index]
116 to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
118 avg=np.mean(to_average)
120 print str(forcebase*(10**12))+' pN'
121 to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
122 self.outlet.push(to_dump)
124 def plotmanip_multiplier(self, plot, current):
126 Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
\r
127 configuration variable. Useful for calibrations and other stuff.
131 if current.curve.experiment != 'smfs':
134 #only one set is present...
135 if len(self.plots[0].vectors) != 2:
139 if (self.config['force_multiplier']==1):
142 for i in range(len(plot.vectors[0][1])):
143 plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier']
\r
145 for i in range(len(plot.vectors[1][1])):
146 plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']
\r
151 def plotmanip_flatten(self, plot, current, customvalue=False):
153 Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
154 the best polynomial fit is chosen among polynomials of degree 1 to n, where n is
155 given by the configuration file or by the customvalue.
157 customvalue= int (>0) --> starts the function even if config says no (default=False)
161 if current.curve.experiment != 'smfs':
164 #only one set is present...
165 if len(self.plots[0].vectors) != 2:
168 #config is not flatten, and customvalue flag is false too
169 if (not self.config['flatten']) and (not customvalue):
176 max_cycles=customvalue
178 max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
180 contact_index=self.find_contact_point()
182 valn=[[] for item in range(max_exponent)]
183 yrn=[0.0 for item in range(max_exponent)]
184 errn=[0.0 for item in range(max_exponent)]
186 for i in range(int(max_cycles)):
188 x_ext=plot.vectors[0][0][contact_index+delta_contact:]
189 y_ext=plot.vectors[0][1][contact_index+delta_contact:]
190 x_ret=plot.vectors[1][0][contact_index+delta_contact:]
191 y_ret=plot.vectors[1][1][contact_index+delta_contact:]
192 for exponent in range(max_exponent):
194 valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
195 yrn[exponent]=sp.polyval(valn[exponent],x_ret)
196 errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
198 print 'Cannot flatten!'
202 best_exponent=errn.index(min(errn))
205 ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
206 yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
208 ycorr_ret=y_ret-yrn[best_exponent]+y_ext[0] #noncontact part
209 yjoin_ret=np.array(plot.vectors[1][1][0:contact_index+delta_contact]) #contact part
211 ycorr_ext=np.concatenate((yjoin_ext, ycorr_ext))
212 ycorr_ret=np.concatenate((yjoin_ret, ycorr_ret))
214 plot.vectors[0][1]=list(ycorr_ext)
215 plot.vectors[1][1]=list(ycorr_ret)
220 def do_slope(self,args):
224 Measures the slope of a delimited chunk on the return trace.
225 The chunk can be delimited either by two manual clicks, or have
226 a fixed width, given as an argument.
228 Syntax: slope [width]
229 The facultative [width] parameter specifies how many
230 points will be considered for the fit. If [width] is
231 specified, only one click will be required.
232 (c) Marco Brucale, Massimo Sandal 2008
235 # Reads the facultative width argument
241 # Decides between the two forms of user input, as per (args)
243 # Gets the Xs of two clicked points as indexes on the current curve vector
244 print 'Click twice to delimit chunk'
246 points=self._measure_N_points(N=2,whatset=1)
247 clickedpoints=[points[0].index,points[1].index]
250 print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
252 points=self._measure_N_points(N=1,whatset=1)
253 clickedpoints=[points[0].index-fitspan,points[0].index]
255 # Calls the function linefit_between
256 parameters=[0,0,[],[]]
258 parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
260 print 'Cannot fit. Did you click twice the same point?'
263 # Outputs the relevant slope parameter
265 print str(parameters[0])
266 to_dump='slope '+self.current.path+' '+str(parameters[0])
267 self.outlet.push(to_dump)
269 # Makes a vector with the fitted parameters and sends it to the GUI
270 xtoplot=parameters[2]
274 ytoplot.append((x*parameters[0])+parameters[1])
276 clickvector_x, clickvector_y=[], []
278 clickvector_x.append(item.graph_coords[0])
279 clickvector_y.append(item.graph_coords[1])
281 lineplot=self._get_displayed_plot(0) #get topmost displayed plot
283 lineplot.add_set(xtoplot,ytoplot)
284 lineplot.add_set(clickvector_x, clickvector_y)
287 if lineplot.styles==[]:
288 lineplot.styles=[None,None,None,'scatter']
290 lineplot.styles+=[None,'scatter']
291 if lineplot.colors==[]:
292 lineplot.styles=[None,None,None,None]
294 lineplot.colors+=[None,None]
297 self._send_plot([lineplot])
299 def linefit_between(self,index1,index2,whatset=1):
301 Creates two vectors (xtofit,ytofit) slicing out from the
302 current return trace a portion delimited by the two indexes
304 Then does a least squares linear fit on that slice.
305 Finally returns [0]=the slope, [1]=the intercept of the
306 fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
308 (c) Marco Brucale, Massimo Sandal 2008
310 # Translates the indexes into two vectors containing the x,y data to fit
311 xtofit=self.plots[0].vectors[whatset][0][index1:index2]
312 ytofit=self.plots[0].vectors[whatset][1][index1:index2]
314 # Does the actual linear fitting (simple least squares with numpy.polyfit)
316 linefit=np.polyfit(xtofit,ytofit,1)
318 return (linefit[0],linefit[1],xtofit,ytofit)