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):
max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
contact_index=self.find_contact_point()
+
valn=[[] for item in range(max_exponent)]
yrn=[0.0 for item in range(max_exponent)]
errn=[0.0 for item in range(max_exponent)]
for i in range(int(max_cycles)):
+
x_ext=plot.vectors[0][0][contact_index+delta_contact:]
y_ext=plot.vectors[0][1][contact_index+delta_contact:]
x_ret=plot.vectors[1][0][contact_index+delta_contact:]
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))
# 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]
reclick : redefines by hand the contact point, if noauto has been used before
but the user is unsatisfied of the previously choosen contact point.
+ usepoints : fit interval by number of points instead than by nanometers
+
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.
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
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
forces=[]
slopes=[]
+ def fit_interval_nm(start_index,plot):
+ '''
+ Calculates the number of points to fit, given a fit interval in nm
+ '''
+ nm=self.config['auto_fit_nm']
+ x_vect=plot.vectors[1][0]
+
+ c=0
+ i=start_index
+ start=x_vect[start_index]
+ while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
+ i-=1
+ c+=1
+
+ return c
+
#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)
+
#-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]
projects / hooke.git / blobdiff