From e3cc2590f45c3287dc65bf4520d6aa649188a42b Mon Sep 17 00:00:00 2001
From: devicerandom <devnull@localhost>
Date: Sun, 7 Sep 2008 17:05:44 +0000
Subject: [PATCH] (generalvclamp.py, hooke.conf) autopeak WLC fit interval -
 now also in nanometers

---
 generalvclamp.py | 48 ++++++++++++++++++++++++++++++++++++++----------
 hooke.conf       |  2 +-
 2 files changed, 39 insertions(+), 11 deletions(-)

diff --git a/generalvclamp.py b/generalvclamp.py
index 4f0f0a0..78ee849 100644
--- a/generalvclamp.py
+++ b/generalvclamp.py
@@ -318,6 +318,8 @@ class generalvclampCommands:
         reclick : redefines by hand the contact point, if noauto has been used before
                   but the user is unsatisfied of the previously choosen contact point.
         
+        usepoints : fit interval by number of points instead than by nanometers
+        
         When you first issue the command, it will ask for the filename. If you are giving the filename
         of an existing file, autopeak will resume it and append measurements to it. If you are giving
         a new filename, it will create the file and append to it until you close Hooke.
@@ -332,9 +334,14 @@ class generalvclampCommands:
         pl_value=None
         T=self.config['temperature']
         
-        fit_points=int(self.config['auto_fit_points'])
+        if 'usepoints' in args.split():
+            fit_points=int(self.config['auto_fit_points'])
+            usepoints=True
+        else:
+            fit_points=None
+            usepoints=False
+            
         slope_span=int(self.config['auto_slope_span'])
-        
         delta_force=10
         rebase=False #if true=we select rebase
         
@@ -356,23 +363,24 @@ class generalvclampCommands:
                 t_expression=arg.split('=')
                 T=float(t_expression[1])
                
+                
         #Handle contact point arguments
-        #FIXME: code duplication
-        if 'reclick' in args.split():
-            print 'Click contact point'
+        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
+                
+        if 'reclick' in args.split():
+            print 'Click contact point'
+            contact_point, contact_point_index = 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=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
+                contact_point , contact_point_index = pickup_contact_point()
             else:
                 contact_point=self.wlccontact_point
                 contact_point_index=self.wlccontact_index
@@ -413,6 +421,22 @@ class generalvclampCommands:
         forces=[]
         slopes=[]
         
+        def fit_interval_nm(start_index,plot):
+            '''
+            Calculates the number of points to fit, given a fit interval in nm
+            '''
+            nm=self.config['auto_fit_nm']
+            x_vect=plot.vectors[1][0]
+            
+            c=0
+            i=start_index
+            start=x_vect[start_index]
+            while abs(x_vect[i]-x_vect[start_index])*(10**9) < nm:
+                i-=1
+                c+=1
+            
+            return c
+        
         #Cycle between peaks and do analysis.
         for peak in peak_location:
             #Do WLC fits.
@@ -421,6 +445,10 @@ class generalvclampCommands:
             peak_point=ClickedPoint()
             peak_point.absolute_coords=displayed_plot.vectors[1][0][peak], displayed_plot.vectors[1][1][peak]
             peak_point.find_graph_coords(displayed_plot.vectors[1][0], displayed_plot.vectors[1][1])    
+            
+            if not usepoints:
+                fit_points=fit_interval_nm(peak, displayed_plot)
+            
             #-create a clicked point for the other fit point
             other_fit_point=ClickedPoint()
             other_fit_point.absolute_coords=displayed_plot.vectors[1][0][peak-fit_points], displayed_plot.vectors[1][1][peak-fit_points]
diff --git a/hooke.conf b/hooke.conf
index 67c0753..3a60662 100755
--- a/hooke.conf
+++ b/hooke.conf
@@ -2,7 +2,7 @@
 <!-- To comment something, put dashes and ! like here -->
 <config>
 <!-- Internal variabls. -->
-    <display ext="1" colour_ext="None" ret="1" colour_ret="None" correct="1" colour_correct="None" contact_point="0" medfilt="0" xaxes="0" yaxes="0" flatten="1" temperature="293" auto_fit_points="50" auto_slope_span="20" auto_delta_force="10" fc_showphase="0" fc_showimposed="0" fc_interesting="0"/>
+    <display ext="1" colour_ext="None" ret="1" colour_ret="None" correct="1" colour_correct="None" contact_point="0" medfilt="0" xaxes="0" yaxes="0" flatten="1" temperature="293" auto_fit_points="50" auto_slope_span="20" auto_delta_force="10" auto_fit_nm="5" fc_showphase="0" fc_showimposed="0" fc_interesting="0"/>
 
 <!-- 
 The following section defines your own work directory. Substitute your work directory.
-- 
2.26.2