--- /dev/null
+#!/usr/bin/env python
+
+from libhooke import WX_GOOD, ClickedPoint
+import wxversion
+wxversion.select(WX_GOOD)
+from wx import PostEvent
+import numpy as np
+import scipy as sp
+import copy
+import os.path
+import time
+
+import warnings
+warnings.simplefilter('ignore',np.RankWarning)
+
+
+class pclusterCommands:
+
+ def do_pcluster(self,args):
+ '''
+ pCLUSTER
+ (pcluster.py)
+ '''
+
+ #configuration variables
+ min_npks = 5
+ min_deviation = 5
+
+ # ------ FUNCTION ------
+ 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.
+ '''
+ whatset=1 #FIXME: should be decidable
+ 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
+
+ def plot_informations(itplot):
+ '''
+ OUR VARIABLES
+ contact_point.absolute_coords (2.4584142802103689e-007, -6.9647135616234017e-009)
+ peak_point.absolute_coords (3.6047748250571423e-008, -7.7142802788854212e-009)
+ other_fit_point.absolute_coords (4.1666139243838867e-008, -7.3759393477579707e-009)
+ peak_location [510, 610, 703, 810, 915, 1103]
+ peak_size [-1.2729111505202212e-009, -9.1632775347399312e-010, -8.1707438353929907e-010, -8.0335812578148904e-010, -8.7483955226387558e-010, -3.6269619757067322e-009]
+ params [2.2433999931959462e-007, 3.3230248825175678e-010]
+ fit_errors [6.5817195369767644e-010, 2.4415923138871498e-011]
+ '''
+ fit_points=int(self.config['auto_fit_points']) # number of points to fit before the peak maximum <50>
+ pl_value=None # persistent length <None>
+ T=self.config['temperature'] #temperature of the system in kelvins. By default it is 293 K. <301.0>
+ cindex=self.find_contact_point() #Automatically find contact point <158, libhooke.ClickedPoint>
+ contact_point=self._clickize(itplot[0].vectors[1][0], itplot[0].vectors[1][1], cindex)
+ self.basepoints=[]
+ base_index_0=peak_location[-1]+fit_interval_nm(peak_location[-1], itplot[0], self.config['auto_right_baseline'],False)
+ self.basepoints.append(self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],base_index_0))
+ base_index_1=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, itplot[0], self.config['auto_left_baseline'],False)
+ self.basepoints.append(self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],base_index_1))
+ self.basecurrent=self.current.path
+ boundaries=[self.basepoints[0].index, self.basepoints[1].index]
+ boundaries.sort()
+ to_average=itplot[0].vectors[1][1][boundaries[0]:boundaries[1]] #y points to average
+ avg=np.mean(to_average)
+ return fit_points, contact_point, pl_value, T, cindex, avg
+
+ def features_peaks(itplot, peak, fit_points, contact_point, pl_value, T, cindex, avg):
+ '''
+ calculate informations for each peak and add they in
+ c_lengths, p_lengths, sigma_c_lengths, sigma_p_lengths, forces, slopes
+ '''
+ c_leng=None
+ p_leng=None
+ sigma_c_leng=None
+ sigma_p_leng=None
+ force=None
+ slope=None
+
+ delta_force=10
+ slope_span=int(self.config['auto_slope_span'])
+
+ peak_point=self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],peak)
+ other_fit_point=self._clickize(itplot[0].vectors[1][0],itplot[0].vectors[1][1],peak-fit_points)
+
+ points=[contact_point, peak_point, other_fit_point]
+
+ params, yfit, xfit, fit_errors = self.wlc_fit(points, itplot[0].vectors[1][0], itplot[0].vectors[1][1], pl_value, T, return_errors=True)
+
+ #Measure forces
+ delta_to_measure=itplot[0].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]
+ #check fitted data and, if right, add peak to the measurement
+ if len(params)==1: #if we did choose 1-value fit
+ p_leng=pl_value
+ c_leng=params[0]*(1.0e+9)
+ sigma_p_lengths=0
+ sigma_c_lengths=fit_errors[0]*(1.0e+9)
+ force = abs(y-avg)*(1.0e+12)
+ else: #2-value fit
+ p_leng=params[1]*(1.0e+9)
+ #check if persistent length makes sense. otherwise, discard peak.
+ if p_leng>self.config['auto_min_p'] and p_leng<self.config['auto_max_p']:
+ '''
+ p_lengths.append(p_leng)
+ c_lengths.append(params[0]*(1.0e+9))
+ sigma_c_lengths.append(fit_errors[0]*(1.0e+9))
+ sigma_p_lengths.append(fit_errors[1]*(1.0e+9))
+ forces.append(abs(y-avg)*(1.0e+12))
+ slopes.append(slope)
+ '''
+ c_leng=params[0]*(1.0e+9)
+ sigma_c_leng=fit_errors[0]*(1.0e+9)
+ sigma_p_leng=fit_errors[1]*(1.0e+9)
+ force=abs(y-avg)*(1.0e+12)
+
+ else:
+ p_leng=None
+ slope=None
+ #return c_lengths, p_lengths, sigma_c_lengths, sigma_p_lengths, forces, slopes
+ return c_leng, p_leng, sigma_c_leng, sigma_p_leng, force, slope
+
+
+ # ------ PROGRAM -------
+ c=0
+ for item in self.current_list:
+ c+=1
+ item.identify(self.drivers)
+ itplot=item.curve.default_plots()
+ peak_location,peak_size=self.exec_has_peaks(item,min_deviation)
+ fit_points, contact_point, pl_value, T, cindex, avg = plot_informations(itplot)
+ print '\n\nCurve',item.path, 'is',c,'of',len(self.current_list),': found '+str(len(peak_location))+' peaks.'
+
+ #initialize output data vectors
+ c_lengths=[]
+ p_lengths=[]
+ sigma_c_lengths=[]
+ sigma_p_lengths=[]
+ forces=[]
+ slopes=[]
+
+ #loop each peak of my curve
+ for peak in peak_location:
+ c_leng, p_leng, sigma_c_leng, sigma_p_leng, force, slope = features_peaks(itplot, peak, fit_points, contact_point, pl_value, T, cindex, avg)
+ for var, vector in zip([c_leng, p_leng, sigma_c_leng, sigma_p_leng, force, slope],[c_lengths, p_lengths, sigma_c_lengths, sigma_p_lengths, forces, slopes]):
+ if var is not None:
+ vector.append(var)
+
+ '''
+ c_lengths.append(c_leng)
+ p_lengths.append(p_leng)
+ sigma_c_lengths.append(sigma_c_leng)
+ sigma_p_lengths.append(sigma_p_leng)
+ forces.append(force)
+ slopes.append(slope)
+ '''
+
+ print 'Measurements for all peaks detected:'
+ print 'contour (nm)', c_lengths
+ print 'sigma contour (nm)',sigma_c_lengths
+ print 'p (nm)',p_lengths
+ print 'sigma p (nm)',sigma_p_lengths
+ print 'forces (pN)',forces
+ print 'slopes (N/m)',slopes
+
+ print ""
+
\ No newline at end of file
projects / hooke.git / commitdiff