#!/usr/bin/env python
+# -*- coding: utf-8 -*-
'''
FLATFILTS
#-----Convolution-based peak recognition and filtering.
#Requires the libpeakspot.py library
- def has_peaks(self, plot, abs_devs):
+ def has_peaks(self, plot, abs_devs=None, maxpeak=True, window=10):
'''
Finds peak position in a force curve.
FIXME: should be moved in libpeakspot.py
'''
+ if abs_devs==None:
+ abs_devs=self.convfilt_config['mindeviation']
+
+
xret=plot.vectors[1][0]
yret=plot.vectors[1][1]
#Calculate convolution.
convoluted=lps.conv_dx(yret, self.convfilt_config['convolution'])
#surely cut everything before the contact point
- cut_index=self.find_contact_point()
-
+ cut_index=self.find_contact_point(plot)
#cut even more, before the blind window
start_x=xret[cut_index]
blind_index=0
break
blind_index+=1
cut_index+=blind_index
-
#do the dirty convolution-peak finding stuff
noise_level=lps.noise_absdev(convoluted[cut_index:], self.convfilt_config['positive'], self.convfilt_config['maxcut'], self.convfilt_config['stable'])
above=lps.abovenoise(convoluted,noise_level,cut_index,abs_devs)
- peak_location,peak_size=lps.find_peaks(above)
+ peak_location,peak_size=lps.find_peaks(above,seedouble=self.convfilt_config['seedouble'])
- #take the maximum
+ #take the minimum or the maximum of a peak
for i in range(len(peak_location)):
peak=peak_location[i]
- maxpk=min(yret[peak-10:peak+10])
- index_maxpk=yret[peak-10:peak+10].index(maxpk)+(peak-10)
- peak_location[i]=index_maxpk
+ valpk=min(yret[peak-window:peak+window]) #maximum in force (near the unfolding point)
+ index_pk=yret[peak-window:peak+window].index(valpk)+(peak-window)
+
+ if maxpeak==False:
+ valpk=max(yret[peak:peak+window]) #minimum in force, near the baseline
+ index_pk=yret[peak:peak+window].index(valpk)+(peak)
+
+# Let's explain that for the minimum. Immaging that we know that there is a peak at position/region 100 and you have found its y-value,
+# Now you look in the array, from 100-10 to 100+10 (if the window is 10).
+# This "100-10 to 100+10" is substancially a new array with its index. In this array you have 20
+# elements, so the index of your y-value will be 10.
+# Now to find the index in the TOTAL array you have to add the "position" of the "region" (that in this case
+# correspond to 100) and also substract the window size ---> (+100-10)
+
+ peak_location[i]=index_pk
return peak_location,peak_size
if len(args)==0:
args=self.convfilt_config['mindeviation']
-
-
try:
abs_devs=float(args)
except:
- pass
+ print 'Wrong argument, using config value'
+ abs_devs=float(self.convfilt_config['mindeviation'])
defplots=self.current.curve.default_plots()[0] #we need the raw, uncorrected plots
peak_location,peak_size=self.has_peaks(defplots,abs_devs)
print 'Found '+str(len(peak_location))+' peaks.'
+ to_dump='peaks '+self.current.path+' '+str(len(peak_location))
+ self.outlet.push(to_dump)
#print peak_location
#if no peaks, we have nothing to plot. exit.
recplot.vectors.append([xgood,ygood])
if recplot.styles==[]:
recplot.styles=[None,None,'scatter']
+ recplot.colors=[None,None,None]
else:
recplot.styles+=['scatter']
+ recplot.colors+=[None]
self._send_plot([recplot])
convfilt [min_npks min_deviation]
min_npks = minmum number of peaks
- (default=4)
+ (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
min_deviation = minimum signal/noise ratio *in the convolution*
- (default=4)
+ (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
If called without arguments, it uses default values.
'''
print '(Please wait)'
notflat_list=[]
-
c=0
for item in self.current_list:
c+=1
item.peak_size=peak_size
item.curve=None #empty the item object, to further avoid memory leak
notflat_list.append(item)
-
+
+ for i in range(1000):
+ k=0
+
#Warn that no flattening had been done.
if not ('flatten' in self.config['plotmanips']):
print 'Flatten manipulator was not found. Processing was done without flattening.'
self.current_list=notflat_list
self.current=self.current_list[self.pointer]
self.do_plot(0)
-
- def do_convconf(self,args):
- '''
- CONVCONFIG
- (flatfilts.py)
- Prints the current convfilt configuration variables.
- ------
- Syntax: convconfig
- '''
- print self.convfilt_config
+
def do_setconv(self,args):
'''
Syntax: setconv variable value
'''
args=args.split()
- try:
- self.convfilt_config[args[0]]=eval(args[1])
- except NameError:
- self.convfilt_config[args[0]]=args[1]
+ #FIXME: a general "set dictionary" function has to be built
+ if len(args)==0:
+ print self.convfilt_config
+ else:
+ if not (args[0] in self.convfilt_config.keys()):
+ print 'This is not an internal convfilt variable!'
+ print 'Run "setconv" without arguments to see a list of defined variables.'
+ return
+
+ if len(args)==1:
+ print self.convfilt_config[args[0]]
+ elif len(args)>1:
+ try:
+ self.convfilt_config[args[0]]=eval(args[1])
+ except NameError: #we have a string argument
+ self.convfilt_config[args[0]]=args[1]
#########################
projects / hooke.git / blobdiff