print str(forcebase*(10**12))+' pN'
to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
self.outlet.push(to_dump)
+\r
+ def plotmanip_multiplier(self, plot, current):
+ '''
+ Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'\r
+ configuration variable. Useful for calibrations and other stuff.
+ '''
+
+ #not a smfs curve...
+ if current.curve.experiment != 'smfs':
+ return plot
+
+ #only one set is present...
+ if len(self.plots[0].vectors) != 2:
+ return plot
+ #multiplier is 1...
+ if (self.config['force_multiplier']==1):
+ return plot\r
+\r
+ for i in range(len(plot.vectors[0][1])):
+ plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier'] \r
+\r
+ for i in range(len(plot.vectors[1][1])):
+ plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']\r
+\r
+ return plot \r
+
def plotmanip_flatten(self, plot, current, customvalue=False):
'''
self._send_plot([lineplot])
- def linefit_between(self,index1,index2):
+ def linefit_between(self,index1,index2,whatset=1):
'''
Creates two vectors (xtofit,ytofit) slicing out from the
current return trace a portion delimited by the two indexes
(c) Marco Brucale, Massimo Sandal 2008
'''
# Translates the indexes into two vectors containing the x,y data to fit
- xtofit=self.plots[0].vectors[1][0][index1:index2]
- ytofit=self.plots[0].vectors[1][1][index1:index2]
+ xtofit=self.plots[0].vectors[whatset][0][index1:index2]
+ ytofit=self.plots[0].vectors[whatset][1][index1:index2]
# Does the actual linear fitting (simple least squares with numpy.polyfit)
linefit=[]
-#====================
-#AUTOMATIC ANALYSES
-#====================
- '''
- def do_autopeak(self,args):
- #FIXME: this function is too long. split it and make it rational.
- #FIXME: also, *generalize fits* to allow FJC and any other model in the future!
-
- def fit_interval_nm(start_index,plot,nm,backwards):
- '''
-
- '''
- Calculates the number of points to fit, given a fit interval in nm
- start_index: index of point
- plot: plot to use
- backwards: if true, finds a point backwards.
- '''
-
- '''
- x_vect=plot.vectors[1][0]
-
- c=0
- i=start_index
- start=x_vect[start_index]
- maxlen=len(x_vect)
- while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
- if i==0 or i==maxlen-1: #we reached boundaries of vector!
- return c
-
- if backwards:
- i-=1
- else:
- i+=1
- c+=1
- return c
-
-
- pl_value=None
- T=self.config['temperature']
-
- if 'usepoints' in args.split():
- fit_points=int(self.config['auto_fit_points'])
- usepoints=True
- else:
- fit_points=None
- usepoints=False
-
- slope_span=int(self.config['auto_slope_span'])
- delta_force=10
- rebase=False #if true=we select rebase
-
- #Pick up plot
- displayed_plot=self._get_displayed_plot(0)
-
- if self.current.curve.experiment != 'smfs' or len(displayed_plot.vectors) < 2:
- print 'Cannot work on this curve.'
- return
-
- #Look for custom persistent length / custom temperature
- for arg in args.split():
- #look for a persistent length argument.
- if 'pl=' in arg:
- pl_expression=arg.split('=')
- pl_value=float(pl_expression[1]) #actual value
- #look for a T argument. FIXME: spaces are not allowed between 'pl' and value
- if ('t=' in arg[0:2]) or ('T=' in arg[0:2]):
- t_expression=arg.split('=')
- T=float(t_expression[1])
-
- #Handle contact point arguments
- def pickup_contact_point():
- #macro to pick up the contact point by clicking
- contact_point=self._measure_N_points(N=1, whatset=1)[0]
- contact_point_index=contact_point.index
- self.wlccontact_point=contact_point
- self.wlccontact_index=contact_point.index
- self.wlccurrent=self.current.path
- return contact_point, contact_point_index
-
- if 'reclick' in args.split():
- print 'Click contact point'
- contact_point, contact_point_index = pickup_contact_point()
- elif 'noauto' in args.split():
- if self.wlccontact_index==None or self.wlccurrent != self.current.path:
- print 'Click contact point'
- contact_point , contact_point_index = pickup_contact_point()
- else:
- contact_point=self.wlccontact_point
- contact_point_index=self.wlccontact_index
- else:
- #Automatically find contact point
- cindex=self.find_contact_point()
- contact_point=ClickedPoint()
- contact_point.absolute_coords=displayed_plot.vectors[1][0][cindex], displayed_plot.vectors[1][1][cindex]
- contact_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
- contact_point.is_marker=True
-
-
- #Find peaks.
- defplot=self.current.curve.default_plots()[0]
- flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
- defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
- peak_location,peak_size=self.has_peaks(defplot, self.convfilt_config['mindeviation'])
-
- #Create a new plot to send
- fitplot=copy.deepcopy(displayed_plot)
-
- #Pick up force baseline
- whatset=1 #fixme: for all sets
- if 'rebase' in args or (self.basecurrent != self.current.path):
- rebase=True
- if rebase:
- clicks=self.config['baseline_clicks']
- if clicks==0:
- self.basepoints=[]
- self.basepoints.append(ClickedPoint())
- self.basepoints.append(ClickedPoint())
- self.basepoints[0].index=peak_location[-1]+fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
- self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
- for point in self.basepoints:
- #for graphing etc. purposes, fill-in with coordinates
- point.absolute_coords=displayed_plot.vectors[1][0][point.index], displayed_plot.vectors[1][1][point.index]
- point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
- elif clicks>0:
- print 'Select baseline'
- if clicks==1:
- self.basepoints=self._measure_N_points(N=1, whatset=whatset)
- self.basepoints.append(ClickedPoint())
- self.basepoints[1].index=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
- #for graphing etc. purposes, fill-in with coordinates
- self.basepoints[1].absolute_coords=displayed_plot.vectors[1][0][self.basepoints[1].index], displayed_plot.vectors[1][1][self.basepoints[1].index]
- self.basepoints[1].find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
- else:
- self.basepoints=self._measure_N_points(N=2, whatset=whatset)
-
- self.basecurrent=self.current.path
-
- boundaries=[self.basepoints[0].index, self.basepoints[1].index]
- boundaries.sort()
- to_average=displayed_plot.vectors[1][1][boundaries[0]:boundaries[1]] #y points to average
- avg=np.mean(to_average)
-
-
- #Initialize data vectors
- c_lengths=[]
- p_lengths=[]
- forces=[]
- slopes=[]
-
-
-
- #Cycle between peaks and do analysis.
- for peak in peak_location:
- #Do WLC fits.
- #FIXME: clean wlc fitting, to avoid this clickedpoint hell
- #-create a clicked point for the peak point
- peak_point=ClickedPoint()
- peak_point.absolute_coords=displayed_plot.vectors[1][0][peak], displayed_plot.vectors[1][1][peak]
- peak_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
-
- if not usepoints:
- fit_points=fit_interval_nm(peak, displayed_plot, self.config['auto_fit_nm'], True)
-
- #-create a clicked point for the other fit point
- other_fit_point=ClickedPoint()
- other_fit_point.absolute_coords=displayed_plot.vectors[1][0][peak-fit_points], displayed_plot.vectors[1][1][peak-fit_points]
- other_fit_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])
- #do the fit
- points=[contact_point, peak_point, other_fit_point]
-
- #Check if we have enough points for a fit. If not, wlc_fit could crash
- if abs(peak_point.index-other_fit_point.index) < 2:
- continue
-
- params, yfit, xfit = self.wlc_fit(points, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],pl_value,T)
- #save wlc values (nm)
- c_lengths.append(params[0]*(1.0e+9))
- if len(params)==2: #if we did choose 2-value fit
- p_lengths.append(params[1]*(1.0e+9))
- else:
- p_lengths.append(pl_value)
- #Add WLC fit lines to plot
- fitplot.add_set(xfit,yfit)
-
- if len(fitplot.styles)==0:
- fitplot.styles=[]
- else:
- fitplot.styles.append(None)
-
- #Measure forces
- delta_to_measure=displayed_plot.vectors[1][1][peak-delta_force:peak+delta_force]
- y=min(delta_to_measure)
- #save force values (pN)
- forces.append(abs(y-avg)*(1.0e+12))
-
- #Measure slopes
- slope=self.linefit_between(peak-slope_span,peak)[0]
- slopes.append(slope)
-
- #--DEBUG STUFF--
- 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]])
- fitplot.styles.append('scatter')
-
- #Show wlc fits and peak locations
- self._send_plot([fitplot])
- self.do_peaks('')
-
- #Ask the user what peaks to ignore from analysis.
- print 'Peaks to ignore (0,1...n from contact point,return to take all)'
- print 'N to discard measurement'
- exclude_raw=raw_input('Input:')
- if exclude_raw=='N':
- print 'Discarded.'
- return
- if not exclude_raw=='':
- exclude=exclude_raw.split(',')
- try:
- exclude=[int(item) for item in exclude]
- for i in exclude:
- c_lengths[i]=None
- p_lengths[i]=None
- forces[i]=None
- slopes[i]=None
- except:
- print 'Bad input, taking all...'
- #Clean data vectors from ignored peaks
- c_lengths=[item for item in c_lengths if item != None]
- p_lengths=[item for item in p_lengths if item != None]
- forces=[item for item in forces if item != None]
- slopes=[item for item in slopes if item != None]
- print 'contour (nm)',c_lengths
- print 'p (nm)',p_lengths
- print 'forces (pN)',forces
- print 'slopes (N/m)',slopes
-
- #Save file info
- if self.autofile=='':
- self.autofile=raw_input('Autopeak filename? (return to ignore) ')
- if self.autofile=='':
- print 'Not saved.'
- return
-
- if not os.path.exists(self.autofile):
- f=open(self.autofile,'w+')
- f.write('Analysis started '+time.asctime()+'\n')
- f.write('----------------------------------------\n')
- f.write('; Contour length (nm) ; Persistence length (nm) ; Max.Force (pN) ; Slope (N/m) \n')
- f.close()
-
- print 'Saving...'
- f=open(self.autofile,'a+')
-
- f.write(self.current.path+'\n')
- for i in range(len(c_lengths)):
- f.write(' ; '+str(c_lengths[i])+' ; '+str(p_lengths[i])+' ; '+str(forces[i])+' ; '+str(slopes[i])+'\n')
-
- f.close()
- self.do_note('autopeak')
- '''
\ No newline at end of file
projects / hooke.git / blobdiff