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):
+ 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
+
+ auto_fit_nm = number of nm to fit before the peak maximum, for WLC (if usepoints false)
+ auto_fit_points = number of points to fit before the peak maximum, for WLC (if usepoints true)
+
+ baseline_clicks = 0: automatic baseline
+ 1: decide baseline with a single click and length defined in auto_left_baseline
+ 2: let user click points of baseline
+ auto_left_baseline = length in nm to use as baseline from the right point (if baseline_clicks=0 , 1)
+ auto_right_baseline = distance in nm of peak-most baseline point from last peak (if baseline_clicks = 0)
'''
+ 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: #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']
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=[]
- 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:
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)
+ 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()
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]
#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('')
projects / hooke.git / commitdiff