Merged with trunk

[hooke.git] / hooke / plugin / flatfilts.py

diff --git a/flatfilts.py b/hooke/plugin/flatfilts.py
old mode 100755 (executable)
new mode 100644 (file)
similarity index 90%
rename from flatfilts.py
rename to hooke/plugin/flatfilts.py
index 0843481..e19964c
--- a/flatfilts.py
+++ b/hooke/plugin/flatfilts.py
@@ -10,37 +10,29 @@ Licensed under the GNU LGPL version 2
 Other plugin dependencies:
 procplots.py (plot processing plugin)
 '''
 Other plugin dependencies:
 procplots.py (plot processing plugin)
 '''

-from libhooke import WX_GOOD
+
+from hooke.libhooke import WX_GOOD
+

 import wxversion
 wxversion.select(WX_GOOD)
 import wxversion
 wxversion.select(WX_GOOD)

-

 import xml.dom.minidom
 import xml.dom.minidom

-

 import wx
 import scipy
 import numpy
 from numpy import diff
 import wx
 import scipy
 import numpy
 from numpy import diff

-

 #import pickle
 
 #import pickle
 

-import libpeakspot as lps
-import libhookecurve as lhc
+from .. import libpeakspot as lps
+from .. import libhookecurve as lhc

 
 
 
 

-class flatfiltsCommands:
-    
+class flatfiltsCommands(object):
+

     def _plug_init(self):
         #configurate convfilt variables
         convfilt_configurator=ConvfiltConfig()
     def _plug_init(self):
         #configurate convfilt variables
         convfilt_configurator=ConvfiltConfig()

-        
-        #different OSes have different path conventions
-        if self.config['hookedir'][0]=='/':
-            slash='/' #a Unix or Unix-like system
-        else:
-            slash='\\' #it's a drive letter, we assume it's Windows
-        
-        self.convfilt_config=convfilt_configurator.load_config(self.config['hookedir']+slash+'convfilt.conf')
-    
+        self.convfilt_config=convfilt_configurator.load_config('convfilt.conf')
+

     def do_flatfilt(self,args):
         '''
         FLATFILT
     def do_flatfilt(self,args):
         '''
         FLATFILT


@@ -64,33 +56,33 @@ class flatfiltsCommands:
         median_filter=7
         min_npks=4
         min_deviation=9
         median_filter=7
         min_npks=4
         min_deviation=9

-        
+

         args=args.split(' ')
         if len(args) == 2:
             min_npks=int(args[0])
             min_deviation=int(args[1])
         else:
             pass
         args=args.split(' ')
         if len(args) == 2:
             min_npks=int(args[0])
             min_deviation=int(args[1])
         else:
             pass

-        
+

         print 'Processing playlist...'
         notflat_list=[]
         print 'Processing playlist...'
         notflat_list=[]

-        
+

         c=0
         for item in self.current_list:
             c+=1
         c=0
         for item in self.current_list:
             c+=1

-                                   
+

             try:
                 notflat=self.has_features(item, median_filter, min_npks, min_deviation)
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': features are ',notflat
             except:
                 notflat=False
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'
             try:
                 notflat=self.has_features(item, median_filter, min_npks, min_deviation)
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': features are ',notflat
             except:
                 notflat=False
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'

-            
+

             if notflat:
                 item.features=notflat
                 item.curve=None #empty the item object, to further avoid memory leak
                 notflat_list.append(item)
             if notflat:
                 item.features=notflat
                 item.curve=None #empty the item object, to further avoid memory leak
                 notflat_list.append(item)

-        
+

         if len(notflat_list)==0:
             print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
             return
         if len(notflat_list)==0:
             print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
             return


@@ -101,28 +93,28 @@ class flatfiltsCommands:
             self.current_list=notflat_list
             self.current=self.current_list[self.pointer]
             self.do_plot(0)
             self.current_list=notflat_list
             self.current=self.current_list[self.pointer]
             self.do_plot(0)

-                 
+

     def has_features(self,item,median_filter,min_npks,min_deviation):
         '''
         decides if a curve is flat enough to be rejected from analysis: it sees if there
         are at least min_npks points that are higher than min_deviation times the absolute value
         of noise.
     def has_features(self,item,median_filter,min_npks,min_deviation):
         '''
         decides if a curve is flat enough to be rejected from analysis: it sees if there
         are at least min_npks points that are higher than min_deviation times the absolute value
         of noise.

-   
+

         Algorithm original idea by Francesco Musiani, with my tweaks and corrections.
         '''
         retvalue=False
         Algorithm original idea by Francesco Musiani, with my tweaks and corrections.
         '''
         retvalue=False

-        
-        item.identify(self.drivers)        
+
+        item.identify(self.drivers)

         #we assume the first is the plot with the force curve
         #do the median to better resolve features from noise
         flat_plot=self.plotmanip_median(item.curve.default_plots()[0], item, customvalue=median_filter)
         #we assume the first is the plot with the force curve
         #do the median to better resolve features from noise
         flat_plot=self.plotmanip_median(item.curve.default_plots()[0], item, customvalue=median_filter)

-        flat_vects=flat_plot.vectors 
+        flat_vects=flat_plot.vectors

         item.curve.close_all()
         #needed to avoid *big* memory leaks!
         del item.curve
         del item
         item.curve.close_all()
         #needed to avoid *big* memory leaks!
         del item.curve
         del item

-        
-        #absolute value of derivate        
+
+        #absolute value of derivate

         yretdiff=diff(flat_vects[1][1])
         yretdiff=[abs(value) for value in yretdiff]
         #average of derivate values
         yretdiff=diff(flat_vects[1][1])
         yretdiff=[abs(value) for value in yretdiff]
         #average of derivate values


@@ -135,12 +127,12 @@ class flatfiltsCommands:
                 c_pks+=1
             else:
                 break
                 c_pks+=1
             else:
                 break

-                    
+

         if c_pks>=min_npks:
             retvalue = c_pks
         if c_pks>=min_npks:
             retvalue = c_pks

-        
+

         del flat_plot, flat_vects, yretdiff
         del flat_plot, flat_vects, yretdiff

-        
+

         return retvalue
 
     ################################################################
         return retvalue
 
     ################################################################


@@ -155,13 +147,13 @@ class flatfiltsCommands:
         '''
         if abs_devs==None:
             abs_devs=self.convfilt_config['mindeviation']
         '''
         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'])
         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(plot)
         #cut even more, before the blind window
         #surely cut everything before the contact point
         cut_index=self.find_contact_point(plot)
         #cut even more, before the blind window


@@ -173,8 +165,8 @@ class flatfiltsCommands:
             blind_index+=1
         cut_index+=blind_index
         #do the dirty convolution-peak finding stuff
             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)     
+        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,seedouble=self.convfilt_config['seedouble'])
                 
         #take the minimum or the maximum of a peak
         peak_location,peak_size=lps.find_peaks(above,seedouble=self.convfilt_config['seedouble'])
                 
         #take the minimum or the maximum of a peak


@@ -197,22 +189,22 @@ class flatfiltsCommands:
             peak_location[i]=index_pk
             
         return peak_location,peak_size
             peak_location[i]=index_pk
             
         return peak_location,peak_size

-    
-    
+
+

     def exec_has_peaks(self,item,abs_devs):
         '''
         encapsulates has_peaks for the purpose of correctly treating the curve objects in the convfilt loop,
         to avoid memory leaks
         '''
     def exec_has_peaks(self,item,abs_devs):
         '''
         encapsulates has_peaks for the purpose of correctly treating the curve objects in the convfilt loop,
         to avoid memory leaks
         '''

-        item.identify(self.drivers)        
+        item.identify(self.drivers)

         #we assume the first is the plot with the force curve
         plot=item.curve.default_plots()[0]
         #we assume the first is the plot with the force curve
         plot=item.curve.default_plots()[0]

-        
+

         if 'flatten' in self.config['plotmanips']:
                     #If flatten is present, use it for better recognition of peaks...
                     flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
                     plot=flatten(plot, item, customvalue=1)
         if 'flatten' in self.config['plotmanips']:
                     #If flatten is present, use it for better recognition of peaks...
                     flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
                     plot=flatten(plot, item, customvalue=1)

-        
+

         peak_location,peak_size=self.has_peaks(plot,abs_devs)
         #close all open files
         item.curve.close_all()
         peak_location,peak_size=self.has_peaks(plot,abs_devs)
         #close all open files
         item.curve.close_all()


@@ -220,10 +212,10 @@ class flatfiltsCommands:
         del item.curve
         del item
         return peak_location, peak_size
         del item.curve
         del item
         return peak_location, peak_size

-        
+

     #------------------------
     #------commands----------
     #------------------------
     #------commands----------

-    #------------------------    
+    #------------------------

     def do_peaks(self,args):
         '''
         PEAKS
     def do_peaks(self,args):
         '''
         PEAKS


@@ -236,37 +228,37 @@ class flatfiltsCommands:
         '''
         if len(args)==0:
             args=self.convfilt_config['mindeviation']
         '''
         if len(args)==0:
             args=self.convfilt_config['mindeviation']

-        
+

         try:
             abs_devs=float(args)
         except:
             print 'Wrong argument, using config value'
             abs_devs=float(self.convfilt_config['mindeviation'])
         try:
             abs_devs=float(args)
         except:
             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
         defplots=self.current.curve.default_plots()[0] #we need the raw, uncorrected plots

-        
+

         if 'flatten' in self.config['plotmanips']:
             flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
             defplots=flatten(defplots, self.current)
         else:
             print 'You have the flatten plot manipulator not loaded. Enabling it could give you better results.'
         if 'flatten' in self.config['plotmanips']:
             flatten=self._find_plotmanip('flatten') #extract flatten plot manipulator
             defplots=flatten(defplots, self.current)
         else:
             print 'You have the flatten plot manipulator not loaded. Enabling it could give you better results.'

-        
+

         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
         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.
         if len(peak_location)==0:
             return
         #if no peaks, we have nothing to plot. exit.
         if len(peak_location)==0:
             return

-        
+

         #otherwise, we plot the peak locations.
         xplotted_ret=self.plots[0].vectors[1][0]
         yplotted_ret=self.plots[0].vectors[1][1]
         xgood=[xplotted_ret[index] for index in peak_location]
         ygood=[yplotted_ret[index] for index in peak_location]
         #otherwise, we plot the peak locations.
         xplotted_ret=self.plots[0].vectors[1][0]
         yplotted_ret=self.plots[0].vectors[1][1]
         xgood=[xplotted_ret[index] for index in peak_location]
         ygood=[yplotted_ret[index] for index in peak_location]

-        
+

         recplot=self._get_displayed_plot()
         recplot.vectors.append([xgood,ygood])
         if recplot.styles==[]:
         recplot=self._get_displayed_plot()
         recplot.vectors.append([xgood,ygood])
         if recplot.styles==[]:


@@ -275,9 +267,9 @@ class flatfiltsCommands:
         else:
             recplot.styles+=['scatter']
             recplot.colors+=[None]
         else:
             recplot.styles+=['scatter']
             recplot.colors+=[None]

-        
+

         self._send_plot([recplot])
         self._send_plot([recplot])

-        
+

     def do_convfilt(self,args):
         '''
         CONVFILT
     def do_convfilt(self,args):
         '''
         CONVFILT


@@ -297,26 +289,26 @@ class flatfiltsCommands:
 
         If called without arguments, it uses default values.
         '''
 
         If called without arguments, it uses default values.
         '''

-        
+

         min_npks=self.convfilt_config['minpeaks']
         min_deviation=self.convfilt_config['mindeviation']
         min_npks=self.convfilt_config['minpeaks']
         min_deviation=self.convfilt_config['mindeviation']

-        
+

         args=args.split(' ')
         if len(args) == 2:
             min_npks=int(args[0])
             min_deviation=int(args[1])
         else:
             pass
         args=args.split(' ')
         if len(args) == 2:
             min_npks=int(args[0])
             min_deviation=int(args[1])
         else:
             pass

-        
+

         print 'Processing playlist...'
         print '(Please wait)'
         notflat_list=[]
         print 'Processing playlist...'
         print '(Please wait)'
         notflat_list=[]

-        
+

         c=0
         for item in self.current_list:
             c+=1
         c=0
         for item in self.current_list:
             c+=1

-                                   
-            try:    
+
+            try:

                 peak_location,peak_size=self.exec_has_peaks(item,min_deviation)
                 if len(peak_location)>=min_npks:
                     isok='+'
                 peak_location,peak_size=self.exec_has_peaks(item,min_deviation)
                 if len(peak_location)>=min_npks:
                     isok='+'


@@ -326,7 +318,7 @@ class flatfiltsCommands:
             except:
                 peak_location,peak_size=[],[]
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'
             except:
                 peak_location,peak_size=[],[]
                 print 'Curve',item.path, 'is',c,'of',len(self.current_list),': cannot be filtered. Probably unable to retrieve force data from corrupt file.'

-            
+

             if len(peak_location)>=min_npks:
                 item.peak_location=peak_location
                 item.peak_size=peak_size
             if len(peak_location)>=min_npks:
                 item.peak_location=peak_location
                 item.peak_size=peak_size


@@ -340,7 +332,7 @@ class flatfiltsCommands:
         if not ('flatten' in self.config['plotmanips']):
             print 'Flatten manipulator was not found. Processing was done without flattening.'
             print 'Try to enable it in your configuration file for better results.'
         if not ('flatten' in self.config['plotmanips']):
             print 'Flatten manipulator was not found. Processing was done without flattening.'
             print 'Try to enable it in your configuration file for better results.'

-        
+

         if len(notflat_list)==0:
             print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
             return
         if len(notflat_list)==0:
             print 'Found nothing interesting. Check your playlist, could be a bug or criteria could be too much stringent'
             return


@@ -351,8 +343,8 @@ class flatfiltsCommands:
             self.current_list=notflat_list
             self.current=self.current_list[self.pointer]
             self.do_plot(0)
             self.current_list=notflat_list
             self.current=self.current_list[self.pointer]
             self.do_plot(0)

-        
-        
+
+

     def do_setconv(self,args):
         '''
         SETCONV
     def do_setconv(self,args):
         '''
         SETCONV


@@ -370,7 +362,7 @@ class flatfiltsCommands:
                 print 'This is not an internal convfilt variable!'
                 print 'Run "setconv" without arguments to see a list of defined variables.'
                 return
                 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:
             if len(args)==1:
                 print self.convfilt_config[args[0]]
             elif len(args)>1:


@@ -382,22 +374,22 @@ class flatfiltsCommands:
 
 #########################
 #HANDLING OF CONFIGURATION FILE
 
 #########################
 #HANDLING OF CONFIGURATION FILE

-class ConvfiltConfig:
+class ConvfiltConfig(object):

     '''
     Handling of convfilt configuration file
     '''
     Handling of convfilt configuration file

-    
+

     Mostly based on the simple-yet-useful examples of the Python Library Reference
     about xml.dom.minidom
     Mostly based on the simple-yet-useful examples of the Python Library Reference
     about xml.dom.minidom

-    
+

     FIXME: starting to look a mess, should require refactoring
     '''
     FIXME: starting to look a mess, should require refactoring
     '''

-    
+

     def __init__(self):
         self.config={}
     def __init__(self):
         self.config={}

-        
-                
+
+

     def load_config(self, filename):
     def load_config(self, filename):

-        myconfig=file(filename)                    
+        myconfig=file(filename)

         #the following 3 lines are needed to strip newlines. otherwise, since newlines
         #are XML elements too, the parser would read them (and re-save them, multiplying
         #newlines...)
         #the following 3 lines are needed to strip newlines. otherwise, since newlines
         #are XML elements too, the parser would read them (and re-save them, multiplying
         #newlines...)


@@ -405,9 +397,9 @@ class ConvfiltConfig:
         the_file=myconfig.read()
         the_file_lines=the_file.split('\n')
         the_file=''.join(the_file_lines)
         the_file=myconfig.read()
         the_file_lines=the_file.split('\n')
         the_file=''.join(the_file_lines)

-                       
-        self.config_tree=xml.dom.minidom.parseString(the_file)  
-        
+
+        self.config_tree=xml.dom.minidom.parseString(the_file)
+

         def getText(nodelist):
             #take the text from a nodelist
             #from Python Library Reference 13.7.2
         def getText(nodelist):
             #take the text from a nodelist
             #from Python Library Reference 13.7.2


@@ -416,23 +408,23 @@ class ConvfiltConfig:
                 if node.nodeType == node.TEXT_NODE:
                     rc += node.data
             return rc
                 if node.nodeType == node.TEXT_NODE:
                     rc += node.data
             return rc

-        
+

         def handleConfig(config):
             noiseabsdev_elements=config.getElementsByTagName("noise_absdev")
             convfilt_elements=config.getElementsByTagName("convfilt")
             handleAbsdev(noiseabsdev_elements)
             handleConvfilt(convfilt_elements)
         def handleConfig(config):
             noiseabsdev_elements=config.getElementsByTagName("noise_absdev")
             convfilt_elements=config.getElementsByTagName("convfilt")
             handleAbsdev(noiseabsdev_elements)
             handleConvfilt(convfilt_elements)

-                        
+

         def handleAbsdev(noiseabsdev_elements):
             for element in noiseabsdev_elements:
                 for attribute in element.attributes.keys():
                     self.config[attribute]=element.getAttribute(attribute)
         def handleAbsdev(noiseabsdev_elements):
             for element in noiseabsdev_elements:
                 for attribute in element.attributes.keys():
                     self.config[attribute]=element.getAttribute(attribute)

-                    
+

         def handleConvfilt(convfilt_elements):
             for element in convfilt_elements:
                 for attribute in element.attributes.keys():
                     self.config[attribute]=element.getAttribute(attribute)
         def handleConvfilt(convfilt_elements):
             for element in convfilt_elements:
                 for attribute in element.attributes.keys():
                     self.config[attribute]=element.getAttribute(attribute)

-            
+

         handleConfig(self.config_tree)
         #making items in the dictionary machine-readable
         for item in self.config.keys():
         handleConfig(self.config_tree)
         #making items in the dictionary machine-readable
         for item in self.config.keys():


@@ -440,5 +432,5 @@ class ConvfiltConfig:
                 self.config[item]=eval(self.config[item])
             except NameError: #if it's an unreadable string, keep it as a string
                 pass
                 self.config[item]=eval(self.config[item])
             except NameError: #if it's an unreadable string, keep it as a string
                 pass

-            
-        return self.config
\ No newline at end of file
+
+        return self.config