(pcluster.py) now accepts fixed persistent length

diff --git a/fit.py b/fit.py
index b843419afbbd4fea6a2242f322dd3630143958f1..096f923e6c1f05d02215a192a9f75a7b5f0786a1 100755 (executable)
--- a/fit.py
+++ b/fit.py
@@ -141,7 +141,6 @@ class fitCommands:
                 pii=1/pl_value
         
             Kb=(1.38065e-23) #boltzmann constant
-            #T=293 #temperature FIXME:should be user-modifiable!
             therm=Kb*T #so we have thermal energy
         
             return ( (therm*pii/4.0) * (((1-(x*lambd))**-2.0) - 1 + (4.0*x*lambd)) )

diff --git a/pcluster.py b/pcluster.py
index 08222c6eeaee3228427dd13852ff9cd0adcb40cb..011c9738a6db3d564acae9afa2e018d7253ecbea 100644 (file)
--- a/pcluster.py
+++ b/pcluster.py
@@ -17,14 +17,27 @@ warnings.simplefilter('ignore',np.RankWarning)
 class pclusterCommands:
 
                def do_pcluster(self,args):
+                                
                                '''
                                pCLUSTER
                                (pcluster.py)
+                                
+                                Automatically measures peaks for further clustering
+                                
+                                (c)Paolo Pancaldi, Massimo Sandal 2009
                                '''
-                               
+                               #--Custom persistent length
+                                for arg in args.split():
+                                    #look for a persistent length argument.
+                                    if 'pl=' in arg:
+                                        pl_expression=arg.split('=')
+                                        pl_value=float(pl_expression[1]) #actual value
+                                    else:
+                                        pl_value=None
+                                    
                                #configuration variables
-                               min_npks = 5
-                               min_deviation = 5
+                               min_npks = self.convfilt_config['minpeaks']
+                               min_deviation = self.convfilt_config['mindeviation']
                                
                                # ------ FUNCTION ------
                                def fit_interval_nm(start_index,plot,nm,backwards):
@@ -63,7 +76,7 @@ class pclusterCommands:
                                                fit_errors                                                                                      [6.5817195369767644e-010, 2.4415923138871498e-011]
                                                '''
                                                fit_points=int(self.config['auto_fit_points']) # number of points to fit before the peak maximum <50>
-                                               pl_value=None # persistent length <None>
+                                               
                                                T=self.config['temperature'] #temperature of the system in kelvins. By default it is 293 K. <301.0>
                                                cindex=self.find_contact_point() #Automatically find contact point <158, libhooke.ClickedPoint>
                                                contact_point=self._clickize(itplot[0].vectors[1][0], itplot[0].vectors[1][1], cindex)
@@ -167,15 +180,6 @@ class pclusterCommands:
                                                     for var, vector in zip([c_leng, p_leng, sigma_c_leng, sigma_p_leng, force, slope],[c_lengths, p_lengths, sigma_c_lengths, sigma_p_lengths, forces, slopes]):
                                                         if var is not None:
                                                             vector.append(var)
-                                                    
-                                                    '''
-                                                    c_lengths.append(c_leng)
-                                                    p_lengths.append(p_leng)
-                                                    sigma_c_lengths.append(sigma_c_leng)
-                                                   sigma_p_lengths.append(sigma_p_leng)
-                                                   forces.append(force)
-                                                   slopes.append(slope)
-                                                    '''
                                                                                                
                                                print 'Measurements for all peaks detected:'
                                                print 'contour (nm)', c_lengths