Merged with trunk

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

diff --git a/hooke/plugin/autopeak.py b/hooke/plugin/autopeak.py
index bbea952e34cc5761b730f119dfdb919ca3b9b460..50dc9e303280dbcdc9ee9c145daea342bc40ea1e 100644 (file)
--- a/hooke/plugin/autopeak.py
+++ b/hooke/plugin/autopeak.py
@@ -83,51 +83,6 @@ class autopeakCommands(object):
                                 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']
@@ -176,11 +131,11 @@ class autopeakCommands(object):
         #--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
@@ -189,10 +144,10 @@ class autopeakCommands(object):
             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
@@ -201,24 +156,8 @@ class autopeakCommands(object):
 
         #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
@@ -235,7 +174,7 @@ class autopeakCommands(object):
             #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)
 
@@ -311,8 +250,7 @@ class autopeakCommands(object):
 
         #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