--- /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 autopeakCommands:
+
+ def do_autopeak(self,args):
+ '''
+ AUTOPEAK
+ (autopeak.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]
+
+ 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.
+
+ 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.
+
+
+ Useful variables (to set with SET command):
+ ---
+ temperature= temperature of the system for wlc fit (in K)
+
+ 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)
+ '''
+
+ #MACROS.
+ #FIXME: to move outside 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.
+ '''
+ 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 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
+
+ def find_current_peaks():
+ #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'])
+ return peak_location, peak_size
+
+
+
+
+ #default fit etc. variables
+ pl_value=None
+ T=self.config['temperature']
+
+ slope_span=int(self.config['auto_slope_span'])
+ delta_force=10
+ rebase=False #if true=we select rebase
+
+ #initialize output data vectors
+ c_lengths=[]
+ p_lengths=[]
+ forces=[]
+ slopes=[]
+
+ #pick up plot
+ displayed_plot=self._get_displayed_plot(0)
+
+ #COMMAND LINE PARSING
+ #--Using points instead of nm interval
+ if 'usepoints' in args.split():
+ fit_points=int(self.config['auto_fit_points'])
+ usepoints=True
+ else:
+ fit_points=None
+ usepoints=False
+ #--Recalculate baseline
+ if 'rebase' in args or (self.basecurrent != self.current.path):
+ rebase=True
+
+ #--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])
+ #--Contact point arguments
+ 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=self._clickize(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1], cindex)
+ '''
+ 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
+ '''
+ #--END COMMAND LINE PARSING--
+
+
+ peak_location, peak_size = find_current_peaks()
+
+ fitplot=copy.deepcopy(displayed_plot)
+
+ #Pick up force baseline
+ if rebase:
+ clicks=self.config['baseline_clicks']
+ if clicks==0:
+ self.basepoints=[]
+ base_index_0=peak_location[-1]+fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
+ self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
+ base_index_1=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
+ self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
+ elif clicks>0:
+ print 'Select baseline'
+ if clicks==1:
+ self.basepoints=self._measure_N_points(N=1, whatset=whatset)
+ base_index_1=self.basepoints[0].index+fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
+ self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_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)
+
+
+ for peak in peak_location:
+ #WLC FITTING
+ #define fit interval
+ if not usepoints:
+ fit_points=fit_interval_nm(peak, displayed_plot, self.config['auto_fit_nm'], True)
+ peak_point=self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],peak)
+ other_fit_point=self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],peak-fit_points)
+
+ #points for the fit
+ points=[contact_point, peak_point, other_fit_point]
+
+ 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)
+
+ #add basepoints to fitplot
+ 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
#====================
#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]
-
- 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.
-
- 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.
-
-
- Useful variables (to set with SET command):
- ---
- temperature= temperature of the system for wlc fit (in K)
-
- 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)
- '''
-
#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
#Handle contact point arguments
def pickup_contact_point():
- '''macro to pick up the contact point by clicking'''
+ #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
f.close()
self.do_note('autopeak')
-
\ No newline at end of file
+ '''
\ No newline at end of file
projects / hooke.git / commitdiff