4 Force spectroscopy curves filtering of flat curves
5 Licensed under the GNU LGPL version 2
7 Other plugin dependencies:
8 procplots.py (plot processing plugin)
10 from libhooke import WX_GOOD
12 wxversion.select(WX_GOOD)
14 import xml.dom.minidom
19 from numpy import diff
23 import libpeakspot as lps
24 import libhookecurve as lhc
27 class flatfiltsCommands(object):
30 #configurate convfilt variables
31 convfilt_configurator=ConvfiltConfig()
33 #different OSes have different path conventions
34 if self.config['hookedir'][0]=='/':
35 slash='/' #a Unix or Unix-like system
37 slash='\\' #it's a drive letter, we assume it's Windows
39 self.convfilt_config=convfilt_configurator.load_config(self.config['hookedir']+slash+'convfilt.conf')
41 def do_flatfilt(self,args):
45 Filters out flat (featureless) curves of the current playlist,
46 creating a playlist containing only the curves with potential
50 flatfilt [min_npks min_deviation]
52 min_npks = minmum number of points over the deviation
55 min_deviation = minimum signal/noise ratio
58 If called without arguments, it uses default values, that
59 should work most of the times.
68 min_deviation=int(args[1])
72 print 'Processing playlist...'
76 for item in self.current_list:
80 notflat=self.has_features(item, median_filter, min_npks, min_deviation)
81 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': features are ',notflat
84 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'
88 item.curve=None #empty the item object, to further avoid memory leak
89 notflat_list.append(item)
91 if len(notflat_list)==0:
92 print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
95 print 'Found ',len(notflat_list),' potentially interesting curves'
96 print 'Regenerating playlist...'
98 self.current_list=notflat_list
99 self.current=self.current_list[self.pointer]
102 def has_features(self,item,median_filter,min_npks,min_deviation):
104 decides if a curve is flat enough to be rejected from analysis: it sees if there
105 are at least min_npks points that are higher than min_deviation times the absolute value
108 Algorithm original idea by Francesco Musiani, with my tweaks and corrections.
112 item.identify(self.drivers)
113 #we assume the first is the plot with the force curve
114 #do the median to better resolve features from noise
115 flat_plot=self.plotmanip_median(item.curve.default_plots()[0], item, customvalue=median_filter)
116 flat_vects=flat_plot.vectors
117 item.curve.close_all()
118 #needed to avoid *big* memory leaks!
122 #absolute value of derivate
123 yretdiff=diff(flat_vects[1][1])
124 yretdiff=[abs(value) for value in yretdiff]
125 #average of derivate values
126 diffmean=numpy.mean(yretdiff)
130 for value in yretdiff:
131 if value/diffmean > min_deviation:
139 del flat_plot, flat_vects, yretdiff
143 ################################################################
144 #-----CONVFILT-------------------------------------------------
145 #-----Convolution-based peak recognition and filtering.
146 #Requires the libpeakspot.py library
148 def has_peaks(self, plot, abs_devs=None):
150 Finds peak position in a force curve.
151 FIXME: should be moved in libpeakspot.py
154 abs_devs=self.convfilt_config['mindeviation']
157 xret=plot.vectors[1][0]
158 yret=plot.vectors[1][1]
159 #Calculate convolution.
160 convoluted=lps.conv_dx(yret, self.convfilt_config['convolution'])
162 #surely cut everything before the contact point
163 cut_index=self.find_contact_point(plot)
164 #cut even more, before the blind window
165 start_x=xret[cut_index]
167 for value in xret[cut_index:]:
168 if abs((value) - (start_x)) > self.convfilt_config['blindwindow']*(10**-9):
171 cut_index+=blind_index
172 #do the dirty convolution-peak finding stuff
173 noise_level=lps.noise_absdev(convoluted[cut_index:], self.convfilt_config['positive'], self.convfilt_config['maxcut'], self.convfilt_config['stable'])
174 above=lps.abovenoise(convoluted,noise_level,cut_index,abs_devs)
175 peak_location,peak_size=lps.find_peaks(above,seedouble=self.convfilt_config['seedouble'])
178 for i in range(len(peak_location)):
179 peak=peak_location[i]
180 maxpk=min(yret[peak-10:peak+10])
181 index_maxpk=yret[peak-10:peak+10].index(maxpk)+(peak-10)
182 peak_location[i]=index_maxpk
184 return peak_location,peak_size
187 def exec_has_peaks(self,item,abs_devs):
189 encapsulates has_peaks for the purpose of correctly treating the curve objects in the convfilt loop,
190 to avoid memory leaks
192 item.identify(self.drivers)
193 #we assume the first is the plot with the force curve
194 plot=item.curve.default_plots()[0]
196 if 'flatten' in self.config['plotmanips']:
197 #If flatten is present, use it for better recognition of peaks...
198 flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
199 plot=flatten(plot, item, customvalue=1)
201 peak_location,peak_size=self.has_peaks(plot,abs_devs)
202 #close all open files
203 item.curve.close_all()
204 #needed to avoid *big* memory leaks!
207 return peak_location, peak_size
209 #------------------------
210 #------commands----------
211 #------------------------
212 def do_peaks(self,args):
216 Test command for convolution filter / test.
218 Syntax: peaks [deviations]
219 absolute deviation = number of times the convolution signal is above the noise absolute deviation.
223 args=self.convfilt_config['mindeviation']
228 print 'Wrong argument, using config value'
229 abs_devs=float(self.convfilt_config['mindeviation'])
231 defplots=self.current.curve.default_plots()[0] #we need the raw, uncorrected plots
233 if 'flatten' in self.config['plotmanips']:
234 flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
235 defplots=flatten(defplots, self.current)
237 print 'You have the flatten plot manipulator not loaded. Enabling it could give you better results.'
239 peak_location,peak_size=self.has_peaks(defplots,abs_devs)
240 print 'Found '+str(len(peak_location))+' peaks.'
241 to_dump='peaks '+self.current.path+' '+str(len(peak_location))
242 self.outlet.push(to_dump)
245 #if no peaks, we have nothing to plot. exit.
246 if len(peak_location)==0:
249 #otherwise, we plot the peak locations.
250 xplotted_ret=self.plots[0].vectors[1][0]
251 yplotted_ret=self.plots[0].vectors[1][1]
252 xgood=[xplotted_ret[index] for index in peak_location]
253 ygood=[yplotted_ret[index] for index in peak_location]
255 recplot=self._get_displayed_plot()
256 recplot.vectors.append([xgood,ygood])
257 if recplot.styles==[]:
258 recplot.styles=[None,None,'scatter']
259 recplot.colors=[None,None,None]
261 recplot.styles+=['scatter']
262 recplot.colors+=[None]
264 self._send_plot([recplot])
266 def do_convfilt(self,args):
270 Filters out flat (featureless) curves of the current playlist,
271 creating a playlist containing only the curves with potential
275 convfilt [min_npks min_deviation]
277 min_npks = minmum number of peaks
278 (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
280 min_deviation = minimum signal/noise ratio *in the convolution*
281 (to set the default, see convfilt.conf file; CONVCONF and SETCONF commands)
283 If called without arguments, it uses default values.
286 min_npks=self.convfilt_config['minpeaks']
287 min_deviation=self.convfilt_config['mindeviation']
291 min_npks=int(args[0])
292 min_deviation=int(args[1])
296 print 'Processing playlist...'
297 print '(Please wait)'
301 for item in self.current_list:
305 peak_location,peak_size=self.exec_has_peaks(item,min_deviation)
306 if len(peak_location)>=min_npks:
310 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': found '+str(len(peak_location))+' peaks.'+isok
312 peak_location,peak_size=[],[]
313 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'
315 if len(peak_location)>=min_npks:
316 item.peak_location=peak_location
317 item.peak_size=peak_size
318 item.curve=None #empty the item object, to further avoid memory leak
319 notflat_list.append(item)
321 #Warn that no flattening had been done.
322 if not ('flatten' in self.config['plotmanips']):
323 print 'Flatten manipulator was not found. Processing was done without flattening.'
324 print 'Try to enable it in your configuration file for better results.'
326 if len(notflat_list)==0:
327 print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
330 print 'Found ',len(notflat_list),' potentially interesting curves'
331 print 'Regenerating playlist...'
333 self.current_list=notflat_list
334 self.current=self.current_list[self.pointer]
338 def do_setconv(self,args):
342 Sets the convfilt configuration variables
344 Syntax: setconv variable value
347 #FIXME: a general "set dictionary" function has to be built
349 print self.convfilt_config
351 if not (args[0] in self.convfilt_config.keys()):
352 print 'This is not an internal convfilt variable!'
353 print 'Run "setconv" without arguments to see a list of defined variables.'
357 print self.convfilt_config[args[0]]
360 self.convfilt_config[args[0]]=eval(args[1])
361 except NameError: #we have a string argument
362 self.convfilt_config[args[0]]=args[1]
365 #########################
366 #HANDLING OF CONFIGURATION FILE
367 class ConvfiltConfig(object):
369 Handling of convfilt configuration file
371 Mostly based on the simple-yet-useful examples of the Python Library Reference
372 about xml.dom.minidom
374 FIXME: starting to look a mess, should require refactoring
381 def load_config(self, filename):
382 myconfig=file(filename)
383 #the following 3 lines are needed to strip newlines. otherwise, since newlines
384 #are XML elements too, the parser would read them (and re-save them, multiplying
386 #yes, I'm an XML n00b
387 the_file=myconfig.read()
388 the_file_lines=the_file.split('\n')
389 the_file=''.join(the_file_lines)
391 self.config_tree=xml.dom.minidom.parseString(the_file)
393 def getText(nodelist):
394 #take the text from a nodelist
395 #from Python Library Reference 13.7.2
397 for node in nodelist:
398 if node.nodeType == node.TEXT_NODE:
402 def handleConfig(config):
403 noiseabsdev_elements=config.getElementsByTagName("noise_absdev")
404 convfilt_elements=config.getElementsByTagName("convfilt")
405 handleAbsdev(noiseabsdev_elements)
406 handleConvfilt(convfilt_elements)
408 def handleAbsdev(noiseabsdev_elements):
409 for element in noiseabsdev_elements:
410 for attribute in element.attributes.keys():
411 self.config[attribute]=element.getAttribute(attribute)
413 def handleConvfilt(convfilt_elements):
414 for element in convfilt_elements:
415 for attribute in element.attributes.keys():
416 self.config[attribute]=element.getAttribute(attribute)
418 handleConfig(self.config_tree)
419 #making items in the dictionary machine-readable
420 for item in self.config.keys():
422 self.config[item]=eval(self.config[item])
423 except NameError: #if it's an unreadable string, keep it as a string