1 # Copyright (C) 2008-2010 Alberto Gomez-Casado
4 # Massimo Sandal <devicerandom@gmail.com>
5 # W. Trevor King <wking@drexel.edu>
7 # This file is part of Hooke.
9 # Hooke is free software: you can redistribute it and/or
10 # modify it under the terms of the GNU Lesser General Public
11 # License as published by the Free Software Foundation, either
12 # version 3 of the License, or (at your option) any later version.
14 # Hooke is distributed in the hope that it will be useful,
15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 # GNU Lesser General Public License for more details.
19 # You should have received a copy of the GNU Lesser General Public
20 # License along with Hooke. If not, see
21 # <http://www.gnu.org/licenses/>.
23 """Plugin regarding general velocity clamp measurements
26 from hooke.libhooke import WX_GOOD, ClickedPoint
28 wxversion.select(WX_GOOD)
29 from wx import PostEvent
37 warnings.simplefilter('ignore',np.RankWarning)
40 class generalvclampCommands(object):
47 def do_distance(self,args):
51 Measure the distance (in nm) between two points.
52 For a standard experiment this is the delta X distance.
53 For a force clamp experiment this is the delta Y distance (actually becomes
58 if self.current.curve.experiment == 'clamp':
59 print 'You wanted to use zpiezo perhaps?'
62 dx,unitx,dy,unity=self._delta(set=1)
63 print str(dx*(10**9))+' nm'
64 to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
65 self.outlet.push(to_dump)
68 def do_force(self,args):
72 Measure the force difference (in pN) between two points
76 if self.current.curve.experiment == 'clamp':
77 print 'This command makes no sense for a force clamp experiment.'
79 dx,unitx,dy,unity=self._delta(set=1)
80 print str(dy*(10**12))+' pN'
81 to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
82 self.outlet.push(to_dump)
85 def do_forcebase(self,args):
89 Measures the difference in force (in pN) between a point and a baseline
90 took as the average between two points.
92 The baseline is fixed once for a given curve and different force measurements,
93 unless the user wants it to be recalculated
95 Syntax: forcebase [rebase]
96 rebase: Forces forcebase to ask again the baseline
97 max: Instead of asking for a point to measure, asks for two points and use
98 the maximum peak in between
100 rebase=False #if true=we select rebase
101 maxpoint=False #if true=we measure the maximum peak
103 plot=self._get_displayed_plot()
104 whatset=1 #fixme: for all sets
105 if 'rebase' in args or (self.basecurrent != self.current.path):
111 print 'Select baseline'
112 self.basepoints=self._measure_N_points(N=2, whatset=whatset)
113 self.basecurrent=self.current.path
116 print 'Select two points'
117 points=self._measure_N_points(N=2, whatset=whatset)
118 boundpoints=[points[0].index, points[1].index]
121 y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
123 print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
125 print 'Select point to measure'
126 points=self._measure_N_points(N=1, whatset=whatset)
127 #whatplot=points[0].dest
128 y=points[0].graph_coords[1]
130 #fixme: code duplication
131 boundaries=[self.basepoints[0].index, self.basepoints[1].index]
133 to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
135 avg=np.mean(to_average)
137 print str(forcebase*(10**12))+' pN'
138 to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
139 self.outlet.push(to_dump)
141 def plotmanip_multiplier(self, plot, current):
143 Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
144 configuration variable. Useful for calibrations and other stuff.
148 if current.curve.experiment != 'smfs':
151 #only one set is present...
152 if len(self.plots[0].vectors) != 2:
156 if (self.config['force_multiplier']==1):
159 for i in range(len(plot.vectors[0][1])):
160 plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier']
162 for i in range(len(plot.vectors[1][1])):
163 plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']
168 def plotmanip_flatten(self, plot, current, customvalue=False):
170 Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
171 the best polynomial fit is chosen among polynomials of degree 1 to n, where n is
172 given by the configuration file or by the customvalue.
174 customvalue= int (>0) --> starts the function even if config says no (default=False)
178 if current.curve.experiment != 'smfs':
181 #only one set is present...
182 if len(self.plots[0].vectors) != 2:
185 #config is not flatten, and customvalue flag is false too
186 if (not self.config['flatten']) and (not customvalue):
193 max_cycles=customvalue
195 max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
197 contact_index=self.find_contact_point()
199 valn=[[] for item in range(max_exponent)]
200 yrn=[0.0 for item in range(max_exponent)]
201 errn=[0.0 for item in range(max_exponent)]
203 #Check if we have a proper numerical value
207 #Loudly and annoyingly complain if it's not a number, then fallback to zero
208 print '''Warning: flatten value is not a number!
209 Use "set flatten" or edit hooke.conf to set it properly
213 for i in range(int(max_cycles)):
215 x_ext=plot.vectors[0][0][contact_index+delta_contact:]
216 y_ext=plot.vectors[0][1][contact_index+delta_contact:]
217 x_ret=plot.vectors[1][0][contact_index+delta_contact:]
218 y_ret=plot.vectors[1][1][contact_index+delta_contact:]
219 for exponent in range(max_exponent):
221 valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
222 yrn[exponent]=sp.polyval(valn[exponent],x_ret)
223 errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
225 print 'Cannot flatten!'
229 best_exponent=errn.index(min(errn))
232 ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
233 yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
235 ycorr_ret=y_ret-yrn[best_exponent]+y_ext[0] #noncontact part
236 yjoin_ret=np.array(plot.vectors[1][1][0:contact_index+delta_contact]) #contact part
238 ycorr_ext=np.concatenate((yjoin_ext, ycorr_ext))
239 ycorr_ret=np.concatenate((yjoin_ret, ycorr_ret))
241 plot.vectors[0][1]=list(ycorr_ext)
242 plot.vectors[1][1]=list(ycorr_ret)
247 def do_slope(self,args):
251 Measures the slope of a delimited chunk on the return trace.
252 The chunk can be delimited either by two manual clicks, or have
253 a fixed width, given as an argument.
255 Syntax: slope [width]
256 The facultative [width] parameter specifies how many
257 points will be considered for the fit. If [width] is
258 specified, only one click will be required.
259 (c) Marco Brucale, Massimo Sandal 2008
262 # Reads the facultative width argument
268 # Decides between the two forms of user input, as per (args)
270 # Gets the Xs of two clicked points as indexes on the current curve vector
271 print 'Click twice to delimit chunk'
272 points=self._measure_N_points(N=2,whatset=1)
274 print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
275 points=self._measure_N_points(N=1,whatset=1)
277 slope=self._slope(points,fitspan)
279 # Outputs the relevant slope parameter
282 to_dump='slope '+self.current.path+' '+str(slope)
283 self.outlet.push(to_dump)
285 def _slope(self,points,fitspan):
286 # Calls the function linefit_between
287 parameters=[0,0,[],[]]
289 clickedpoints=[points[0].index,points[1].index]
292 clickedpoints=[points[0].index-fitspan,points[0].index]
295 parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
297 print 'Cannot fit. Did you click twice the same point?'
300 # Outputs the relevant slope parameter
302 print str(parameters[0])
303 to_dump='slope '+self.curve.path+' '+str(parameters[0])
304 self.outlet.push(to_dump)
306 # Makes a vector with the fitted parameters and sends it to the GUI
307 xtoplot=parameters[2]
311 ytoplot.append((x*parameters[0])+parameters[1])
313 clickvector_x, clickvector_y=[], []
315 clickvector_x.append(item.graph_coords[0])
316 clickvector_y.append(item.graph_coords[1])
318 lineplot=self._get_displayed_plot(0) #get topmost displayed plot
320 lineplot.add_set(xtoplot,ytoplot)
321 lineplot.add_set(clickvector_x, clickvector_y)
324 if lineplot.styles==[]:
325 lineplot.styles=[None,None,None,'scatter']
327 lineplot.styles+=[None,'scatter']
328 if lineplot.colors==[]:
329 lineplot.colors=[None,None,'black',None]
331 lineplot.colors+=['black',None]
334 self._send_plot([lineplot])
339 def linefit_between(self,index1,index2,whatset=1):
341 Creates two vectors (xtofit,ytofit) slicing out from the
342 current return trace a portion delimited by the two indexes
344 Then does a least squares linear fit on that slice.
345 Finally returns [0]=the slope, [1]=the intercept of the
346 fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
348 (c) Marco Brucale, Massimo Sandal 2008
350 # Translates the indexes into two vectors containing the x,y data to fit
351 xtofit=self.plots[0].vectors[whatset][0][index1:index2]
352 ytofit=self.plots[0].vectors[whatset][1][index1:index2]
354 # Does the actual linear fitting (simple least squares with numpy.polyfit)
356 linefit=np.polyfit(xtofit,ytofit,1)
358 return (linefit[0],linefit[1],xtofit,ytofit)
361 def fit_interval_nm(self,start_index,plot,nm,backwards):
363 Calculates the number of points to fit, given a fit interval in nm
364 start_index: index of point
366 backwards: if true, finds a point backwards.
368 whatset=1 #FIXME: should be decidable
369 x_vect=plot.vectors[1][0]
373 start=x_vect[start_index]
375 while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
376 if i==0 or i==maxlen-1: #we reached boundaries of vector!
388 def find_current_peaks(self,noflatten, a=True, maxpeak=True):
391 a=self.convfilt_config['mindeviation']
395 print "Bad input, using default."
396 abs_devs=self.convfilt_config['mindeviation']
398 defplot=self.current.curve.default_plots()[0]
400 flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
401 defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
402 pk_location,peak_size=self.has_peaks(defplot, abs_devs, maxpeak)
403 return pk_location, peak_size
406 def pickup_contact_point(self,N=1,whatset=1):
407 '''macro to pick up the contact point by clicking'''
408 contact_point=self._measure_N_points(N=1, whatset=1)[0]
409 contact_point_index=contact_point.index
410 self.wlccontact_point=contact_point
411 self.wlccontact_index=contact_point.index
412 self.wlccurrent=self.current.path
413 return contact_point, contact_point_index
417 def baseline_points(self,peak_location, displayed_plot):
418 clicks=self.config['baseline_clicks']
421 base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
422 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
423 base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
424 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
426 print 'Select baseline'
428 self.basepoints=self._measure_N_points(N=1, whatset=1)
429 base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
430 self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
432 self.basepoints=self._measure_N_points(N=2, whatset=1)
434 self.basecurrent=self.current.path
435 return self.basepoints