else:
dx,unitx,dy,unity=self._delta(set=1)
print str(dx*(10**9))+' nm'
+ to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
+ self.outlet.push(to_dump)
def do_force(self,args):
return
dx,unitx,dy,unity=self._delta(set=1)
print str(dy*(10**12))+' pN'
+ to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
+ self.outlet.push(to_dump)
def do_forcebase(self,args):
avg=np.mean(to_average)
forcebase=abs(y-avg)
print str(forcebase*(10**12))+' pN'
+ to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
+ self.outlet.push(to_dump)
def plotmanip_flatten(self, plot, current, customvalue=False):
valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
yrn[exponent]=sp.polyval(valn[exponent],x_ret)
errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
- except TypeError:
+ except Exception,e:
print 'Cannot flatten!'
+ print e
return plot
best_exponent=errn.index(min(errn))
# Calls the function linefit_between
parameters=[0,0,[],[]]
- parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
+ try:
+ parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
+ except:
+ print 'Cannot fit. Did you click twice the same point?'
+ return
# Outputs the relevant slope parameter
print 'Slope:'
print str(parameters[0])
+ to_dump='slope '+self.current.path+' '+str(parameters[0])
+ self.outlet.push(to_dump)
# Makes a vector with the fitted parameters and sends it to the GUI
xtoplot=parameters[2]
return (linefit[0],linefit[1],xtofit,ytofit)
+
+
#====================
#AUTOMATIC ANALYSES
#====================
+ '''
def do_autopeak(self,args):
- '''
- AUTOPEAK
- (generalvclamp.py)
- Automatically performs a number of analyses on the peaks of the given curve.
- Currently it automatically:
- - fits peaks with WLC function
- - measures peak maximum forces with a baseline
- - measures slope in proximity of peak maximum
- Requires flatten plotmanipulator , fit.py plugin , flatfilts.py plugin with convfilt
-
- Syntax:
- autopeak [rebase] [pl=value] [t=value] [noauto] [reclick]
+ #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!
- rebase : Re-asks baseline interval
-
- pl=[value] : Use a fixed persistent length for the fit. If pl is not given,
- the fit will be a 2-variable
- fit. DO NOT put spaces between 'pl', '=' and the value.
- The value must be in meters.
- Scientific notation like 0.35e-9 is fine.
-
- t=[value] : Use a user-defined temperature. The value must be in
- kelvins; by default it is 293 K.
- DO NOT put spaces between 't', '=' and the value.
-
- noauto : allows for clicking the contact point by
- hand (otherwise it is automatically estimated) the first time.
- If subsequent measurements are made, the same contact point
- clicked the first time is used
-
- reclick : redefines by hand the contact point, if noauto has been used before
- but the user is unsatisfied of the previously choosen contact point.
-
- When you first issue the command, it will ask for the filename. If you are giving the filename
- of an existing file, autopeak will resume it and append measurements to it. If you are giving
- a new filename, it will create the file and append to it until you close Hooke.
-
- Useful variables (to set with SET command):
-
- temperature= temperature of the system for wlc fit (in K)
- auto_fit_points = number of points to fit before the peak maximum, for wlc
- auto_slope_span = number of points on which measure the slope, for slope
- '''
+ 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']
- fit_points=int(self.config['auto_fit_points'])
+ 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
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
- #FIXME: code duplication
- if 'reclick' in args.split():
- print 'Click contact point'
+ 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=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
+ contact_point , contact_point_index = pickup_contact_point()
else:
contact_point=self.wlccontact_point
contact_point_index=self.wlccontact_index
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:
- print 'Select baseline'
- self.basepoints=self._measure_N_points(N=2, whatset=whatset)
+ 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)
- #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)
#Initialize data vectors
c_lengths=[]
forces=[]
slopes=[]
+
+
#Cycle between peaks and do analysis.
for peak in peak_location:
#Do WLC fits.
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))
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)
#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('')
#Save file info
if self.autofile=='':
- self.autofile=raw_input('Filename? (return to ignore) ')
+ self.autofile=raw_input('Autopeak filename? (return to ignore) ')
if self.autofile=='':
print 'Not saved.'
return
f.close()
self.do_note('autopeak')
-
\ No newline at end of file
+ '''
\ No newline at end of file
projects / hooke.git / blobdiff