generalvclamp.py

   1 #!/usr/bin/env python
   2
   3 '''
   4 generalvclamp.py
   5
   6 Plugin regarding general velocity clamp measurements
   7 '''
   8
   9 from libhooke import WX_GOOD, ClickedPoint
  10 import wxversion
  11 wxversion.select(WX_GOOD)
  12 from wx import PostEvent
  13 import numpy as np
  14 import scipy as sp
  15 import copy
  16 import os.path
  17 import time
  18
  19 import warnings
  20 warnings.simplefilter('ignore',np.RankWarning)
  21
  22
  23 class generalvclampCommands:
  24
  25     def _plug_init(self):
  26         self.basecurrent=None
  27         self.basepoints=None
  28         self.autofile=''
  29
  30     def do_distance(self,args):
  31         '''
  32         DISTANCE
  33         (generalvclamp.py)
  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
  37         an alias of zpiezo)
  38         -----------------
  39         Syntax: distance
  40         '''
  41         if self.current.curve.experiment == 'clamp':
  42             print 'You wanted to use zpiezo perhaps?'
  43             return
  44         else:
  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)
  49
  50
  51     def do_force(self,args):
  52         '''
  53         FORCE
  54         (generalvclamp.py)
  55         Measure the force difference (in pN) between two points
  56         ---------------
  57         Syntax: force
  58         '''
  59         if self.current.curve.experiment == 'clamp':
  60             print 'This command makes no sense for a force clamp experiment.'
  61             return
  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)
  66
  67
  68     def do_forcebase(self,args):
  69         '''
  70         FORCEBASE
  71         (generalvclamp.py)
  72         Measures the difference in force (in pN) between a point and a baseline
  73         took as the average between two points.
  74
  75         The baseline is fixed once for a given curve and different force measurements,
  76         unless the user wants it to be recalculated
  77         ------------
  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
  82         '''
  83         rebase=False #if true=we select rebase
  84         maxpoint=False #if true=we measure the maximum peak
  85
  86         plot=self._get_displayed_plot()
  87         whatset=1 #fixme: for all sets
  88         if 'rebase' in args or (self.basecurrent != self.current.path):
  89             rebase=True
  90         if 'max' in args:
  91             maxpoint=True
  92
  93         if rebase:
  94             print 'Select baseline'
  95             self.basepoints=self._measure_N_points(N=2, whatset=whatset)
  96             self.basecurrent=self.current.path
  97
  98         if maxpoint:
  99             print 'Select two points'
 100             points=self._measure_N_points(N=2, whatset=whatset)
 101             boundpoints=[points[0].index, points[1].index]
 102             boundpoints.sort()
 103             try:
 104                 y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
 105             except ValueError:
 106                 print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
 107         else:
 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]
 112
 113         #fixme: code duplication
 114         boundaries=[self.basepoints[0].index, self.basepoints[1].index]
 115         boundaries.sort()
 116         to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
 117
 118         avg=np.mean(to_average)
 119         forcebase=abs(y-avg)
 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)
 123
 124
 125     def plotmanip_flatten(self, plot, current, customvalue=False):
 126         '''
 127         Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
 128         the best polynomial fit is chosen among polynomials of degree 1 to n, where n is
 129         given by the configuration file or by the customvalue.
 130
 131         customvalue= int (>0) --> starts the function even if config says no (default=False)
 132         '''
 133
 134         #not a smfs curve...
 135         if current.curve.experiment != 'smfs':
 136             return plot
 137
 138         #only one set is present...
 139         if len(self.plots[0].vectors) != 2:
 140             return plot
 141
 142         #config is not flatten, and customvalue flag is false too
 143         if (not self.config['flatten']) and (not customvalue):
 144             return plot
 145
 146         max_exponent=12
 147         delta_contact=0
 148
 149         if customvalue:
 150             max_cycles=customvalue
 151         else:
 152             max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
 153
 154         contact_index=self.find_contact_point()
 155
 156         valn=[[] for item in range(max_exponent)]
 157         yrn=[0.0 for item in range(max_exponent)]
 158         errn=[0.0 for item in range(max_exponent)]
 159
 160         for i in range(int(max_cycles)):
 161
 162             x_ext=plot.vectors[0][0][contact_index+delta_contact:]
 163             y_ext=plot.vectors[0][1][contact_index+delta_contact:]
 164             x_ret=plot.vectors[1][0][contact_index+delta_contact:]
 165             y_ret=plot.vectors[1][1][contact_index+delta_contact:]
 166             for exponent in range(max_exponent):
 167                 try:
 168                     valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
 169                     yrn[exponent]=sp.polyval(valn[exponent],x_ret)
 170                     errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
 171                 except Exception,e:
 172                     print 'Cannot flatten!'
 173                     print e
 174                     return plot
 175
 176             best_exponent=errn.index(min(errn))
 177
 178             #extension
 179             ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
 180             yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
 181             #retraction
 182             ycorr_ret=y_ret-yrn[best_exponent]+y_ext[0] #noncontact part
 183             yjoin_ret=np.array(plot.vectors[1][1][0:contact_index+delta_contact]) #contact part
 184
 185             ycorr_ext=np.concatenate((yjoin_ext, ycorr_ext))
 186             ycorr_ret=np.concatenate((yjoin_ret, ycorr_ret))
 187
 188             plot.vectors[0][1]=list(ycorr_ext)
 189             plot.vectors[1][1]=list(ycorr_ret)
 190
 191         return plot
 192
 193     #---SLOPE---
 194     def do_slope(self,args):
 195         '''
 196         SLOPE
 197         (generalvclamp.py)
 198         Measures the slope of a delimited chunk on the return trace.
 199         The chunk can be delimited either by two manual clicks, or have
 200         a fixed width, given as an argument.
 201         ---------------
 202         Syntax: slope [width]
 203                 The facultative [width] parameter specifies how many
 204                 points will be considered for the fit. If [width] is
 205                 specified, only one click will be required.
 206         (c) Marco Brucale, Massimo Sandal 2008
 207         '''
 208
 209         # Reads the facultative width argument
 210         try:
 211             fitspan=int(args)
 212         except:
 213             fitspan=0
 214
 215         # Decides between the two forms of user input, as per (args)
 216         if fitspan == 0:
 217             # Gets the Xs of two clicked points as indexes on the current curve vector
 218             print 'Click twice to delimit chunk'
 219             clickedpoints=[]
 220             points=self._measure_N_points(N=2,whatset=1)
 221             clickedpoints=[points[0].index,points[1].index]
 222             clickedpoints.sort()
 223         else:
 224             print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
 225             clickedpoints=[]
 226             points=self._measure_N_points(N=1,whatset=1)
 227             clickedpoints=[points[0].index-fitspan,points[0].index]
 228
 229         # Calls the function linefit_between
 230         parameters=[0,0,[],[]]
 231         parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
 232
 233         # Outputs the relevant slope parameter
 234         print 'Slope:'
 235         print str(parameters[0])
 236         to_dump='slope '+self.current.path+' '+str(parameters[0])
 237         self.outlet.push(to_dump)
 238
 239         # Makes a vector with the fitted parameters and sends it to the GUI
 240         xtoplot=parameters[2]
 241         ytoplot=[]
 242         x=0
 243         for x in xtoplot:
 244             ytoplot.append((x*parameters[0])+parameters[1])
 245
 246         clickvector_x, clickvector_y=[], []
 247         for item in points:
 248             clickvector_x.append(item.graph_coords[0])
 249             clickvector_y.append(item.graph_coords[1])
 250
 251         lineplot=self._get_displayed_plot(0) #get topmost displayed plot
 252
 253         lineplot.add_set(xtoplot,ytoplot)
 254         lineplot.add_set(clickvector_x, clickvector_y)
 255
 256         if lineplot.styles==[]:
 257             lineplot.styles=[None,None,None,'scatter']
 258         else:
 259             lineplot.styles+=[None,'scatter']
 260
 261         self._send_plot([lineplot])
 262
 263     def linefit_between(self,index1,index2):
 264         '''
 265         Creates two vectors (xtofit,ytofit) slicing out from the
 266         current return trace a portion delimited by the two indexes
 267         given as arguments.
 268         Then does a least squares linear fit on that slice.
 269         Finally returns [0]=the slope, [1]=the intercept of the
 270         fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
 271         used for the fit.
 272         (c) Marco Brucale, Massimo Sandal 2008
 273         '''
 274         # Translates the indexes into two vectors containing the x,y data to fit
 275         xtofit=self.plots[0].vectors[1][0][index1:index2]
 276         ytofit=self.plots[0].vectors[1][1][index1:index2]
 277
 278         # Does the actual linear fitting (simple least squares with numpy.polyfit)
 279         linefit=[]
 280         linefit=np.polyfit(xtofit,ytofit,1)
 281
 282         return (linefit[0],linefit[1],xtofit,ytofit)
 283
 284
 285
 286 #====================
 287 #AUTOMATIC ANALYSES
 288 #====================
 289     '''
 290     def do_autopeak(self,args):
 291         #FIXME: this function is too long. split it and make it rational.
 292         #FIXME: also, *generalize fits* to allow FJC and any other model in the future!
 293
 294         def fit_interval_nm(start_index,plot,nm,backwards):
 295     '''
 296
 297     '''
 298             Calculates the number of points to fit, given a fit interval in nm
 299             start_index: index of point
 300             plot: plot to use
 301             backwards: if true, finds a point backwards.
 302     '''
 303
 304     '''
 305             x_vect=plot.vectors[1][0]
 306
 307             c=0
 308             i=start_index
 309             start=x_vect[start_index]
 310             maxlen=len(x_vect)
 311             while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
 312                 if i==0 or i==maxlen-1: #we reached boundaries of vector!
 313                     return c
 314
 315                 if backwards:
 316                     i-=1
 317                 else:
 318                     i+=1
 319                 c+=1
 320             return c
 321
 322
 323         pl_value=None
 324         T=self.config['temperature']
 325
 326         if 'usepoints' in args.split():
 327             fit_points=int(self.config['auto_fit_points'])
 328             usepoints=True
 329         else:
 330             fit_points=None
 331             usepoints=False
 332
 333         slope_span=int(self.config['auto_slope_span'])
 334         delta_force=10
 335         rebase=False #if true=we select rebase
 336
 337         #Pick up plot
 338         displayed_plot=self._get_displayed_plot(0)
 339
 340         if self.current.curve.experiment != 'smfs' or len(displayed_plot.vectors) < 2:
 341             print 'Cannot work on this curve.'
 342             return
 343
 344         #Look for custom persistent length / custom temperature
 345         for arg in args.split():
 346             #look for a persistent length argument.
 347             if 'pl=' in arg:
 348                 pl_expression=arg.split('=')
 349                 pl_value=float(pl_expression[1]) #actual value
 350             #look for a T argument. FIXME: spaces are not allowed between 'pl' and value
 351             if ('t=' in arg[0:2]) or ('T=' in arg[0:2]):
 352                 t_expression=arg.split('=')
 353                 T=float(t_expression[1])
 354
 355         #Handle contact point arguments
 356         def pickup_contact_point():
 357             #macro to pick up the contact point by clicking
 358             contact_point=self._measure_N_points(N=1, whatset=1)[0]
 359             contact_point_index=contact_point.index
 360             self.wlccontact_point=contact_point
 361             self.wlccontact_index=contact_point.index
 362             self.wlccurrent=self.current.path
 363             return contact_point, contact_point_index
 364
 365         if 'reclick' in args.split():
 366             print 'Click contact point'
 367             contact_point, contact_point_index = pickup_contact_point()
 368         elif 'noauto' in args.split():
 369             if self.wlccontact_index==None or self.wlccurrent != self.current.path:
 370                 print 'Click contact point'
 371                 contact_point , contact_point_index = pickup_contact_point()
 372             else:
 373                 contact_point=self.wlccontact_point
 374                 contact_point_index=self.wlccontact_index
 375         else:
 376             #Automatically find contact point
 377             cindex=self.find_contact_point()
 378             contact_point=ClickedPoint()
 379             contact_point.absolute_coords=displayed_plot.vectors[1][0][cindex], displayed_plot.vectors[1][1][cindex]
 380             contact_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 381             contact_point.is_marker=True
 382
 383
 384         #Find peaks.
 385         defplot=self.current.curve.default_plots()[0]
 386         flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
 387         defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
 388         peak_location,peak_size=self.has_peaks(defplot, self.convfilt_config['mindeviation'])
 389
 390         #Create a new plot to send
 391         fitplot=copy.deepcopy(displayed_plot)
 392
 393         #Pick up force baseline
 394         whatset=1 #fixme: for all sets
 395         if 'rebase' in args or (self.basecurrent != self.current.path):
 396             rebase=True
 397         if rebase:
 398             clicks=self.config['baseline_clicks']
 399             if clicks==0:
 400                 self.basepoints=[]
 401                 self.basepoints.append(ClickedPoint())
 402                 self.basepoints.append(ClickedPoint())
 403                 self.basepoints[0].index=peak_location[-1]+fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
 404                 self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
 405                 for point in self.basepoints:
 406                     #for graphing etc. purposes, fill-in with coordinates
 407                     point.absolute_coords=displayed_plot.vectors[1][0][point.index], displayed_plot.vectors[1][1][point.index]
 408                     point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 409             elif clicks>0:
 410                 print 'Select baseline'
 411                 if clicks==1:
 412                     self.basepoints=self._measure_N_points(N=1, whatset=whatset)
 413                     self.basepoints.append(ClickedPoint())
 414                     self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
 415                     #for graphing etc. purposes, fill-in with coordinates
 416                     self.basepoints[1].absolute_coords=displayed_plot.vectors[1][0][self.basepoints[1].index], displayed_plot.vectors[1][1][self.basepoints[1].index]
 417                     self.basepoints[1].find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 418                 else:
 419                     self.basepoints=self._measure_N_points(N=2, whatset=whatset)
 420
 421             self.basecurrent=self.current.path
 422
 423         boundaries=[self.basepoints[0].index, self.basepoints[1].index]
 424         boundaries.sort()
 425         to_average=displayed_plot.vectors[1][1][boundaries[0]:boundaries[1]] #y points to average
 426         avg=np.mean(to_average)
 427
 428
 429         #Initialize data vectors
 430         c_lengths=[]
 431         p_lengths=[]
 432         forces=[]
 433         slopes=[]
 434
 435
 436
 437         #Cycle between peaks and do analysis.
 438         for peak in peak_location:
 439             #Do WLC fits.
 440             #FIXME: clean wlc fitting, to avoid this clickedpoint hell
 441             #-create a clicked point for the peak point
 442             peak_point=ClickedPoint()
 443             peak_point.absolute_coords=displayed_plot.vectors[1][0][peak], displayed_plot.vectors[1][1][peak]
 444             peak_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 445
 446             if not usepoints:
 447                 fit_points=fit_interval_nm(peak, displayed_plot, self.config['auto_fit_nm'], True)
 448
 449             #-create a clicked point for the other fit point
 450             other_fit_point=ClickedPoint()
 451             other_fit_point.absolute_coords=displayed_plot.vectors[1][0][peak-fit_points], displayed_plot.vectors[1][1][peak-fit_points]
 452             other_fit_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 453             #do the fit
 454             points=[contact_point, peak_point, other_fit_point]
 455
 456             #Check if we have enough points for a fit. If not, wlc_fit could crash
 457             if abs(peak_point.index-other_fit_point.index) < 2:
 458                 continue
 459
 460             params, yfit, xfit = self.wlc_fit(points, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],pl_value,T)
 461             #save wlc values (nm)
 462             c_lengths.append(params[0]*(1.0e+9))
 463             if len(params)==2: #if we did choose 2-value fit
 464                 p_lengths.append(params[1]*(1.0e+9))
 465             else:
 466                 p_lengths.append(pl_value)
 467             #Add WLC fit lines to plot
 468             fitplot.add_set(xfit,yfit)
 469
 470             if len(fitplot.styles)==0:
 471                 fitplot.styles=[]
 472             else:
 473                 fitplot.styles.append(None)
 474
 475             #Measure forces
 476             delta_to_measure=displayed_plot.vectors[1][1][peak-delta_force:peak+delta_force]
 477             y=min(delta_to_measure)
 478             #save force values (pN)
 479             forces.append(abs(y-avg)*(1.0e+12))
 480
 481             #Measure slopes
 482             slope=self.linefit_between(peak-slope_span,peak)[0]
 483             slopes.append(slope)
 484
 485         #--DEBUG STUFF--
 486         fitplot.add_set([self.basepoints[0].graph_coords[0],self.basepoints[1].graph_coords[0]],[self.basepoints[0].graph_coords[1],self.basepoints[1].graph_coords[1]])
 487         fitplot.styles.append('scatter')
 488
 489         #Show wlc fits and peak locations
 490         self._send_plot([fitplot])
 491         self.do_peaks('')
 492
 493         #Ask the user what peaks to ignore from analysis.
 494         print 'Peaks to ignore (0,1...n from contact point,return to take all)'
 495         print 'N to discard measurement'
 496         exclude_raw=raw_input('Input:')
 497         if exclude_raw=='N':
 498             print 'Discarded.'
 499             return
 500         if not exclude_raw=='':
 501             exclude=exclude_raw.split(',')
 502             try:
 503                 exclude=[int(item) for item in exclude]
 504                 for i in exclude:
 505                     c_lengths[i]=None
 506                     p_lengths[i]=None
 507                     forces[i]=None
 508                     slopes[i]=None
 509             except:
 510                  print 'Bad input, taking all...'
 511         #Clean data vectors from ignored peaks
 512         c_lengths=[item for item in c_lengths if item != None]
 513         p_lengths=[item for item in p_lengths if item != None]
 514         forces=[item for item in forces if item != None]
 515         slopes=[item for item in slopes if item != None]
 516         print 'contour (nm)',c_lengths
 517         print 'p (nm)',p_lengths
 518         print 'forces (pN)',forces
 519         print 'slopes (N/m)',slopes
 520
 521         #Save file info
 522         if self.autofile=='':
 523             self.autofile=raw_input('Autopeak filename? (return to ignore) ')
 524             if self.autofile=='':
 525                 print 'Not saved.'
 526                 return
 527
 528         if not os.path.exists(self.autofile):
 529             f=open(self.autofile,'w+')
 530             f.write('Analysis started '+time.asctime()+'\n')
 531             f.write('----------------------------------------\n')
 532             f.write('; Contour length (nm)  ;  Persistence length (nm) ;  Max.Force (pN)  ;  Slope (N/m) \n')
 533             f.close()
 534
 535         print 'Saving...'
 536         f=open(self.autofile,'a+')
 537
 538         f.write(self.current.path+'\n')
 539         for i in range(len(c_lengths)):
 540             f.write(' ; '+str(c_lengths[i])+' ; '+str(p_lengths[i])+' ; '+str(forces[i])+' ; '+str(slopes[i])+'\n')
 541
 542         f.close()
 543         self.do_note('autopeak')
 544         '''