From ba1f60a1b909e28a5af5c6b169cbe2449641710a Mon Sep 17 00:00:00 2001
From: marcobrucale <devnull@localhost>
Date: Thu, 30 Apr 2009 10:21:49 +0000
Subject: [PATCH] Added a small feature in the 'autopeak' command. If the
 variable 'baseline_clicks' is set to -1, no baseline is calculated. Rather,
 the ordinate of the contact point (either hand-picked or automatically found
 depending on other autopeak arguments) is taken as the zero force point.

---
 autopeak.py | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/autopeak.py b/autopeak.py
index 2474add..1eabb18 100644
--- a/autopeak.py
+++ b/autopeak.py
@@ -66,9 +66,10 @@ class autopeakCommands:
         auto_fit_nm = number of nm to fit before the peak maximum, for WLC (if usepoints false)
         auto_fit_points = number of points to fit before the peak maximum, for WLC (if usepoints true)
         
-        baseline_clicks = 0: automatic baseline
-                          1: decide baseline with a single click and length defined in auto_left_baseline
-                          2: let user click points of baseline
+        baseline_clicks = -1: no baseline, f=0 at the contact point (whether hand-picked or automatically found)
+                           0: automatic baseline
+                           1: decide baseline with a single click and length defined in auto_left_baseline
+                           2: let user click points of baseline
         auto_left_baseline = length in nm to use as baseline from the right point (if baseline_clicks=0 , 1)
         auto_right_baseline = distance in nm of peak-most baseline point from last peak (if baseline_clicks = 0)
         '''
@@ -106,7 +107,7 @@ class autopeakCommands:
             contact_point_index=contact_point.index
             self.wlccontact_point=contact_point
             self.wlccontact_index=contact_point.index
-            self.wlccurrent=self.current.path
+            self.wlccurrent=self.current.path
             return contact_point, contact_point_index
         
         def find_current_peaks():
@@ -186,7 +187,7 @@ class autopeakCommands:
         
         #Pick up force baseline
         if rebase:
-            clicks=self.config['baseline_clicks']
+            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)
@@ -207,8 +208,14 @@ class autopeakCommands:
         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
-        avg=np.mean(to_average)
-        
+        avg=np.mean(to_average)
+        
+        clicks=self.config['baseline_clicks']
+        if clicks==-1:
+            try:
+                avg=displayed_plot.vectors[1][1][contact_point_index]
+            except:
+                avg=displayed_plot.vectors[1][1][cindex]
         
         for peak in peak_location:
             #WLC FITTING
-- 
2.26.2