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 #AUTOMATIC ANALYSES
 286 #====================
 287     '''
 288     def do_autopeak(self,args):
 289         #FIXME: this function is too long. split it and make it rational.
 290         #FIXME: also, *generalize fits* to allow FJC and any other model in the future!
 291
 292         def fit_interval_nm(start_index,plot,nm,backwards):
 293     '''
 294
 295     '''
 296             Calculates the number of points to fit, given a fit interval in nm
 297             start_index: index of point
 298             plot: plot to use
 299             backwards: if true, finds a point backwards.
 300     '''
 301
 302     '''
 303             x_vect=plot.vectors[1][0]
 304
 305             c=0
 306             i=start_index
 307             start=x_vect[start_index]
 308             maxlen=len(x_vect)
 309             while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
 310                 if i==0 or i==maxlen-1: #we reached boundaries of vector!
 311                     return c
 312
 313                 if backwards:
 314                     i-=1
 315                 else:
 316                     i+=1
 317                 c+=1
 318             return c
 319
 320
 321         pl_value=None
 322         T=self.config['temperature']
 323
 324         if 'usepoints' in args.split():
 325             fit_points=int(self.config['auto_fit_points'])
 326             usepoints=True
 327         else:
 328             fit_points=None
 329             usepoints=False
 330
 331         slope_span=int(self.config['auto_slope_span'])
 332         delta_force=10
 333         rebase=False #if true=we select rebase
 334
 335         #Pick up plot
 336         displayed_plot=self._get_displayed_plot(0)
 337
 338         if self.current.curve.experiment != 'smfs' or len(displayed_plot.vectors) < 2:
 339             print 'Cannot work on this curve.'
 340             return
 341
 342         #Look for custom persistent length / custom temperature
 343         for arg in args.split():
 344             #look for a persistent length argument.
 345             if 'pl=' in arg:
 346                 pl_expression=arg.split('=')
 347                 pl_value=float(pl_expression[1]) #actual value
 348             #look for a T argument. FIXME: spaces are not allowed between 'pl' and value
 349             if ('t=' in arg[0:2]) or ('T=' in arg[0:2]):
 350                 t_expression=arg.split('=')
 351                 T=float(t_expression[1])
 352
 353         #Handle contact point arguments
 354         def pickup_contact_point():
 355             #macro to pick up the contact point by clicking
 356             contact_point=self._measure_N_points(N=1, whatset=1)[0]
 357             contact_point_index=contact_point.index
 358             self.wlccontact_point=contact_point
 359             self.wlccontact_index=contact_point.index
 360             self.wlccurrent=self.current.path
 361             return contact_point, contact_point_index
 362
 363         if 'reclick' in args.split():
 364             print 'Click contact point'
 365             contact_point, contact_point_index = pickup_contact_point()
 366         elif 'noauto' in args.split():
 367             if self.wlccontact_index==None or self.wlccurrent != self.current.path:
 368                 print 'Click contact point'
 369                 contact_point , contact_point_index = pickup_contact_point()
 370             else:
 371                 contact_point=self.wlccontact_point
 372                 contact_point_index=self.wlccontact_index
 373         else:
 374             #Automatically find contact point
 375             cindex=self.find_contact_point()
 376             contact_point=ClickedPoint()
 377             contact_point.absolute_coords=displayed_plot.vectors[1][0][cindex], displayed_plot.vectors[1][1][cindex]
 378             contact_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 379             contact_point.is_marker=True
 380
 381
 382         #Find peaks.
 383         defplot=self.current.curve.default_plots()[0]
 384         flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
 385         defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
 386         peak_location,peak_size=self.has_peaks(defplot, self.convfilt_config['mindeviation'])
 387
 388         #Create a new plot to send
 389         fitplot=copy.deepcopy(displayed_plot)
 390
 391         #Pick up force baseline
 392         whatset=1 #fixme: for all sets
 393         if 'rebase' in args or (self.basecurrent != self.current.path):
 394             rebase=True
 395         if rebase:
 396             clicks=self.config['baseline_clicks']
 397             if clicks==0:
 398                 self.basepoints=[]
 399                 self.basepoints.append(ClickedPoint())
 400                 self.basepoints.append(ClickedPoint())
 401                 self.basepoints[0].index=peak_location[-1]+fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
 402                 self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
 403                 for point in self.basepoints:
 404                     #for graphing etc. purposes, fill-in with coordinates
 405                     point.absolute_coords=displayed_plot.vectors[1][0][point.index], displayed_plot.vectors[1][1][point.index]
 406                     point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 407             elif clicks>0:
 408                 print 'Select baseline'
 409                 if clicks==1:
 410                     self.basepoints=self._measure_N_points(N=1, whatset=whatset)
 411                     self.basepoints.append(ClickedPoint())
 412                     self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
 413                     #for graphing etc. purposes, fill-in with coordinates
 414                     self.basepoints[1].absolute_coords=displayed_plot.vectors[1][0][self.basepoints[1].index], displayed_plot.vectors[1][1][self.basepoints[1].index]
 415                     self.basepoints[1].find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 416                 else:
 417                     self.basepoints=self._measure_N_points(N=2, whatset=whatset)
 418
 419             self.basecurrent=self.current.path
 420
 421         boundaries=[self.basepoints[0].index, self.basepoints[1].index]
 422         boundaries.sort()
 423         to_average=displayed_plot.vectors[1][1][boundaries[0]:boundaries[1]] #y points to average
 424         avg=np.mean(to_average)
 425
 426
 427         #Initialize data vectors
 428         c_lengths=[]
 429         p_lengths=[]
 430         forces=[]
 431         slopes=[]
 432
 433
 434
 435         #Cycle between peaks and do analysis.
 436         for peak in peak_location:
 437             #Do WLC fits.
 438             #FIXME: clean wlc fitting, to avoid this clickedpoint hell
 439             #-create a clicked point for the peak point
 440             peak_point=ClickedPoint()
 441             peak_point.absolute_coords=displayed_plot.vectors[1][0][peak], displayed_plot.vectors[1][1][peak]
 442             peak_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 443
 444             if not usepoints:
 445                 fit_points=fit_interval_nm(peak, displayed_plot, self.config['auto_fit_nm'], True)
 446
 447             #-create a clicked point for the other fit point
 448             other_fit_point=ClickedPoint()
 449             other_fit_point.absolute_coords=displayed_plot.vectors[1][0][peak-fit_points], displayed_plot.vectors[1][1][peak-fit_points]
 450             other_fit_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
 451             #do the fit
 452             points=[contact_point, peak_point, other_fit_point]
 453
 454             #Check if we have enough points for a fit. If not, wlc_fit could crash
 455             if abs(peak_point.index-other_fit_point.index) < 2:
 456                 continue
 457
 458             params, yfit, xfit = self.wlc_fit(points, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],pl_value,T)
 459             #save wlc values (nm)
 460             c_lengths.append(params[0]*(1.0e+9))
 461             if len(params)==2: #if we did choose 2-value fit
 462                 p_lengths.append(params[1]*(1.0e+9))
 463             else:
 464                 p_lengths.append(pl_value)
 465             #Add WLC fit lines to plot
 466             fitplot.add_set(xfit,yfit)
 467
 468             if len(fitplot.styles)==0:
 469                 fitplot.styles=[]
 470             else:
 471                 fitplot.styles.append(None)
 472
 473             #Measure forces
 474             delta_to_measure=displayed_plot.vectors[1][1][peak-delta_force:peak+delta_force]
 475             y=min(delta_to_measure)
 476             #save force values (pN)
 477             forces.append(abs(y-avg)*(1.0e+12))
 478
 479             #Measure slopes
 480             slope=self.linefit_between(peak-slope_span,peak)[0]
 481             slopes.append(slope)
 482
 483         #--DEBUG STUFF--
 484         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]])
 485         fitplot.styles.append('scatter')
 486
 487         #Show wlc fits and peak locations
 488         self._send_plot([fitplot])
 489         self.do_peaks('')
 490
 491         #Ask the user what peaks to ignore from analysis.
 492         print 'Peaks to ignore (0,1...n from contact point,return to take all)'
 493         print 'N to discard measurement'
 494         exclude_raw=raw_input('Input:')
 495         if exclude_raw=='N':
 496             print 'Discarded.'
 497             return
 498         if not exclude_raw=='':
 499             exclude=exclude_raw.split(',')
 500             try:
 501                 exclude=[int(item) for item in exclude]
 502                 for i in exclude:
 503                     c_lengths[i]=None
 504                     p_lengths[i]=None
 505                     forces[i]=None
 506                     slopes[i]=None
 507             except:
 508                  print 'Bad input, taking all...'
 509         #Clean data vectors from ignored peaks
 510         c_lengths=[item for item in c_lengths if item != None]
 511         p_lengths=[item for item in p_lengths if item != None]
 512         forces=[item for item in forces if item != None]
 513         slopes=[item for item in slopes if item != None]
 514         print 'contour (nm)',c_lengths
 515         print 'p (nm)',p_lengths
 516         print 'forces (pN)',forces
 517         print 'slopes (N/m)',slopes
 518
 519         #Save file info
 520         if self.autofile=='':
 521             self.autofile=raw_input('Autopeak filename? (return to ignore) ')
 522             if self.autofile=='':
 523                 print 'Not saved.'
 524                 return
 525
 526         if not os.path.exists(self.autofile):
 527             f=open(self.autofile,'w+')
 528             f.write('Analysis started '+time.asctime()+'\n')
 529             f.write('----------------------------------------\n')
 530             f.write('; Contour length (nm)  ;  Persistence length (nm) ;  Max.Force (pN)  ;  Slope (N/m) \n')
 531             f.close()
 532
 533         print 'Saving...'
 534         f=open(self.autofile,'a+')
 535
 536         f.write(self.current.path+'\n')
 537         for i in range(len(c_lengths)):
 538             f.write(' ; '+str(c_lengths[i])+' ; '+str(p_lengths[i])+' ; '+str(forces[i])+' ; '+str(slopes[i])+'\n')
 539
 540         f.close()
 541         self.do_note('autopeak')
 542         '''