# Calls the function linefit_between
parameters=[0,0,[],[]]
- parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
+ try:
+ parameters=self.linefit_between(clickedpoints[0],clickedpoints[1])
+ except:
+ print 'Cannot fit. Did you click twice the same point?'
+ return
# Outputs the relevant slope parameter
print 'Slope:'
return (linefit[0],linefit[1],xtofit,ytofit)
+
+
#====================
#AUTOMATIC ANALYSES
#====================
+ '''
def do_autopeak(self,args):
- '''
- AUTOPEAK
- (generalvclamp.py)
- Automatically performs a number of analyses on the peaks of the given curve.
- Currently it automatically:
- - fits peaks with WLC function
- - measures peak maximum forces with a baseline
- - measures slope in proximity of peak maximum
- Requires flatten plotmanipulator , fit.py plugin , flatfilts.py plugin with convfilt
-
- Syntax:
- autopeak [rebase] [pl=value] [t=value] [noauto] [reclick]
-
- rebase : Re-asks baseline interval
-
- pl=[value] : Use a fixed persistent length for the fit. If pl is not given,
- the fit will be a 2-variable
- fit. DO NOT put spaces between 'pl', '=' and the value.
- The value must be in meters.
- Scientific notation like 0.35e-9 is fine.
-
- t=[value] : Use a user-defined temperature. The value must be in
- kelvins; by default it is 293 K.
- DO NOT put spaces between 't', '=' and the value.
-
- noauto : allows for clicking the contact point by
- hand (otherwise it is automatically estimated) the first time.
- If subsequent measurements are made, the same contact point
- clicked the first time is used
-
- 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.
-
-
- Useful variables (to set with SET command):
- ---
- temperature= temperature of the system for wlc fit (in K)
-
- auto_slope_span = number of points on which measure the slope, for slope
-
- 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
- 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)
- '''
+ #FIXME: this function is too long. split it and make it rational.
+ #FIXME: also, *generalize fits* to allow FJC and any other model in the future!
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.
- '''
+ '''
+
+ '''
x_vect=plot.vectors[1][0]
c=0
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: #we reached boundaries of vector!
+ if i==0 or i==maxlen-1: #we reached boundaries of vector!
return c
if backwards:
if ('t=' in arg[0:2]) or ('T=' in arg[0:2]):
t_expression=arg.split('=')
T=float(t_expression[1])
-
-
+
#Handle contact point arguments
def pickup_contact_point():
- '''macro to pick up the contact point by clicking'''
+ #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
f.close()
self.do_note('autopeak')
-
\ No newline at end of file
+ '''
\ No newline at end of file
projects / hooke.git / blobdiff