-# -*- coding: utf-8 -*-
+# Copyright (C) 2008-2012 Fabrizio Benedetti <fabrizio.benedetti.82@gmail.com>
+# Marco Brucale <marco.brucale@unibo.it>
+# Massimo Sandal <devicerandom@gmail.com>
+# W. Trevor King <wking@tremily.us>
+#
+# This file is part of Hooke.
+#
+# Hooke is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# Hooke is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with Hooke. If not, see <http://www.gnu.org/licenses/>.
+
+"""The autopeak module provides :class:`Autopeak`, a
+:class:`hooke.plugin.Plugin` for automatically extracting force peaks
+(unfolding events) from force curves.
+"""
+
+from hooke.libhooke import WX_GOOD
-from libhooke import WX_GOOD, ClickedPoint
import wxversion
wxversion.select(WX_GOOD)
from wx import PostEvent
import warnings
warnings.simplefilter('ignore',np.RankWarning)
+#from .. import ui.gui.results as results
-class autopeakCommands:
- def do_autopeak(self,args):
+class autopeakCommands(object):
+ '''
+ Autopeak carries out force curve fitting with a chosen model:
+ - WLC
+ - FJC
+ - FJC-PEG
+ '''
+ def do_autopeak(self, args):
'''
AUTOPEAK
(autopeak.py)
outside of which the peak is automatically discarded (in nm)
'''
- #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.
- '''
- 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 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(noflatten):
- #Find peaks.
- defplot=self.current.curve.default_plots()[0]
- if not noflatten:
- 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']
#--Contact point arguments
if 'reclick' in args.split():
print 'Click contact point'
- contact_point, contact_point_index = pickup_contact_point()
+ contact_point, contact_point_index = self.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()
+ contact_point , contact_point_index = self.pickup_contact_point()
else:
contact_point=self.wlccontact_point
contact_point_index=self.wlccontact_index
cindex=self.find_contact_point()
contact_point=self._clickize(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1], cindex)
#--END COMMAND LINE PARSING--
-
-
- peak_location, peak_size = find_current_peaks(noflatten)
-
+
+
+ peak_location, peak_size = self.find_current_peaks(noflatten)
+
if len(peak_location) == 0:
print 'No peaks to fit.'
return
#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
-
+ self.basepoints=self.baseline_points(peak_location, displayed_plot)
+
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
#WLC FITTING
#define fit interval
if not usepoints:
- fit_points=fit_interval_nm(peak, displayed_plot, self.config['auto_fit_nm'], True)
+ fit_points=self.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)
#Show wlc fits and peak locations
self._send_plot([fitplot])
- #self.do_peaks('')
-
+
print 'Using fit function: ',self.config['fit_function']
print 'Measurements for all peaks detected:'
print 'contour (nm)', c_lengths
f.close()
self.do_note('autopeak')
+
projects / hooke.git / blobdiff