From 8d319b7731dbab6ae3e4e5efb0838ca206d54f1a Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@drexel.edu>
Date: Mon, 17 May 2010 09:18:28 -0400
Subject: [PATCH] Started translating hooke.plugin.multifit to new
 Plugin/Command architecture.

---
 hooke/command.py         |   1 +
 hooke/plugin/multifit.py | 584 ++++++++++++++++-----------------------
 2 files changed, 246 insertions(+), 339 deletions(-)

diff --git a/hooke/command.py b/hooke/command.py
index fcea13e..c822cc5 100644
--- a/hooke/command.py
+++ b/hooke/command.py
@@ -100,6 +100,7 @@ class Command (object):
     <BLANKLINE>
     """
     def __init__(self, name, aliases=None, arguments=[], help=''):
+        # TODO: see_also=[other,command,instances,...]
         self.name = name
         if aliases == None:
             aliases = []
diff --git a/hooke/plugin/multifit.py b/hooke/plugin/multifit.py
index 483bf37..986b781 100644
--- a/hooke/plugin/multifit.py
+++ b/hooke/plugin/multifit.py
@@ -17,379 +17,285 @@
 # License along with Hooke.  If not, see
 # <http://www.gnu.org/licenses/>.
 
-#FIXME clean this, probably some dependencies are not needed
+"""The ``multifit`` module provides :class:`MultifitPlugin` and
+several associated :class:`hooke.command.Command`\s for fitting
+all sorts of :class:`hooke.experiment.VelocityClamp` parameters.
+"""
 
-from ..libhooke import WX_GOOD, ClickedPoint
-import wxversion
-wxversion.select(WX_GOOD)
-from wx import PostEvent
-import numpy as np
-import scipy as sp
-import copy
-import os.path
-import time
-import tempfile
-import warnings
-warnings.simplefilter('ignore',np.RankWarning)
-import Queue
+from ..command import Command, Argument, Failure
+from ..playlist import FilePlaylist
+from ..plugin import Plugin
+from ..plugin.playlist import PlaylistArgument
 
-global measure_wlc
-global EVT_MEASURE_WLC
 
-global events_from_fit
-events_from_fit=Queue.Queue() #GUI ---> CLI COMMUNICATION
+class MultifitPlugin (Plugin):
+    def __init__(self):
+        super(MultifitPlugin, self).__init__(name='multifit')
 
+    def commands(self):
+        return [MultifitCommand()]
 
-class multifitCommands:
+class MultifitCommand (Command):
+    """Presents curves for interactive manual analysis.
 
-    def do_multifit(self,args):
-        '''
-        MULTIFIT
-        (multifit.py)
-        Presents curves for manual analysis in a comfortable mouse-only fashion.
-        Obtains contour length, persistance length, rupture force and 
-        slope - loading rate.
-        WLC is shown in red, eFJC in blue.
-        -------------
-        Syntax:
-        multifit [pl=value] [kl=value] [t=value] [slopew=value] [basew=value]
-                [slope2p] [justone]
+    Obtains contour length, persistance length, rupture force and 
+    slope (loading rate).
 
-        pl=[value] and kl=[value]: Use a fixed persistent length (WLC) or Kuhn
-                length (eFJC) 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.
-                eFJC fit works better with a fixed kl
-                The value must be in nanometers. 
+    See :class:`hooke.plugin.fit.FitCommand` help for more information
+    on the options and fit procedures.
+    """
+    #NOTE: centerzero plot modifier should be activated (set centerzero
+    #1).
+    def __init__(self):
+        super(MultifitCommand, self).__init__(
+            name='multifit',
+            arguments=[
+                PlaylistArgument,
+                Argument(name='persistence length', type='float',
+                    help="""
+Persistence length in meters for WLC fits.  If not given, the fit will
+be a 2-variable fit.
+""".strip()),
+                Argument(name='Kuhn length', type='float',
+                    help="""
+Kuhn length in meters for eFJC fits.  If not given, the fit will be a
+2-variable fit.  The eFJC fit works better with a fixed Kuhn length
+(citation?).
+""".strip()),
+                Argument(name='temperature', type='float', default=293.0,
+                    help="""
+Temperature in Kelvin.  Defaults to 293 K.
+""".strip()),
+                Argument(name='slope width', type='int',
+                    help="""
+Width in points for slope fitting (points leading up to the rupture).
+If not given, the routine will prompt for an extra point to fit the
+slope.
+""".strip()),
+                Argument(name='base width', type='int', default=15,
+                    help="""
+Width in points for slope fitting (points following the rupture?).
+""".strip()),
+            Argument(name='point slope', type='bool', default=False,
+                     help="""
+Calculate the slope from the two selected points instead of fitting
+data between them.
+""".strip()),
+            Argument(name='just one', type='bool', default=False,
+                     help="""
+Perform the fits on the current curve instead of iterating.
+""".strip()),
+                ],
+            help=self.__doc__)
 
-        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.
-
-        slopew and basew : width in points for slope fitting (points to the
-                right of clicked rupture) and base level fitting (points to
-                the left of clicked top of rupture).
-                If slopew is not provided, the routine will ask for a 5th
-                point to fit the slope.
-                DO NOT put spaces between 'slopew' or 'basew', '=' value.
-        
-        slope2p : calculates the slope from the two clicked points, 
-                instead of fitting data between them        
-                
-        justone : performs the fits over current curve instead of iterating
-
-        See fit command help for more information on the options and fit 
-        procedures.
-        NOTE: centerzero plot modifier should be activated (set centerzero 1).
-        '''
-
-		#NOTE duplicates a lot of code from do_fit in fit.py, a call to it could be used directly
-		#but it is easier to control the program flow bypassing it
-	
-        pl_value=None
-        kl_value=None
-        T=self.config['temperature']
-        slopew=None
-        basew=15
-        justone=False
-        twops=False
-        
-        #FIXME spaces are not allowed between pl or t and value
-        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
-            if 'kl=' in arg:
-                kl_expression=arg.split('=')
-                kl_value=float(kl_expression[1]) #actual value
-            #look for a T argument.
-            if ('t=' in arg) or ('T=' in arg):
-                t_expression=arg.split('=')
-                T=float(t_expression[1])
-            #look for a basew argument.
-            if ('basew=' in arg):
-                basew_expression=arg.split('=')
-                basew=int(basew_expression[1])
-            #look for a slopew argument.
-            if ('slopew=' in arg):
-                slopew_expression=arg.split('=')
-                slopew=int(slopew_expression[1])
-            if('justone' in arg):
-                justone=True
-            if('slope2p' in arg):
-                twops=True
-		
+    def _run(self, hooke, inqueue, outqueue, params):
         counter=0
         savecounter=0
         curveindex=0
         
-        if not justone:
-            print 'What curve no. you would like to start? (enter for ignoring)'
-            skip=raw_input()
-
-            if skip.isdigit()==False:
-                skip=0
-            else:
-                skip=int(skip)-1
-                print 'Skipping '+str(skip)+ ' curves'
-        else:
-            skip=0
-        #begin presenting curves for analysis
-        while curveindex <len(self.current_list):
-            if not justone:
-                counter+=1
-                curve=self.current_list[curveindex]
-                if skip>curveindex:
-                    curveindex+=1
-                    continue	
-
-            #give periodically the opportunity to stop the analysis
-                if counter%20==0 and counter>0:
-                    print '\nYou checked '+str(counter)+' curves. Do you want to continue?'
-                    self.current=curve
-                    self.do_plot(0)
-                    if self.YNclick():
-                        print 'Going on...'
-                    else:
-                        break
-                else:
-                    self.current=curve
-                    self.do_plot(0)
-            else:
-                curve=self.current
-                self.do_plot(0)
-            if not justone:
-                print '\nCurve '+str(curveindex+1)+' of '+str(len(self.current_list))       
-            print 'Click contact point or left end (red area)of the curve to skip'
-            #hightlights an area dedicated to reject current curve
-            sizeret=len(self.plots[0].vectors[1][0])
-            noarea=self.plots[0].vectors[1][0][-sizeret/6:-1]                
-            noareaplot=copy.deepcopy(self._get_displayed_plot())
-            #noise dependent slight shift to improve visibility
-            noareaplot.add_set(noarea,np.ones_like(noarea)*5.0*np.std(self.plots[0].vectors[1][1][-sizeret/6:-1]))
-            noareaplot.styles+=['scatter']
-            noareaplot.colors+=["red"]
-            self._send_plot([noareaplot])
-            contact_point=self._measure_N_points(N=1, whatset=1)[0]
-            contact_point_index=contact_point.index
-            noareaplot.remove_set(-1)
-            #remove set leaves some styles disturbing the next graph, fixed by doing do_plot
-            self.do_plot(0)
-            if contact_point_index>5.0/6.0*sizeret:
-                if justone:
-                    break
-                curveindex+=1
-                continue				
-                
-            self.wlccontact_point=contact_point
-            self.wlccontact_index=contact_point.index
-            self.wlccurrent=self.current.path
-                
-            print 'Now click two points for the fitting area (one should be the rupture point)'
-            wlcpoints=self._measure_N_points(N=2,whatset=1)
-            print 'And one point of the top of the jump'
-            toppoint=self._measure_N_points(N=1,whatset=1)
-            slopepoint=ClickedPoint()
-            if slopew==None:
-                print 'Click a point to calculate slope'
-                slopepoint=self._measure_N_points(N=1,whatset=1)
+        start_curve = params['playlist'].current()
+        curve = start_curve
+        while True:
+            outqueue.put('TODO to end %s execution' % self.name)
+            self._fit_curve(hooke, inqueue, outqueue, params, curve)
+            if params['just one'] == True:
+                break
+            params['playlist'].next()
+            next_curve = params['playlist'].current()
+            if next_curve == start_curve:
+                break # loop through playlist complete
+            curve = next_curve
 
-            fitpoints=[contact_point]+wlcpoints
-            #use the currently displayed plot for the fit
-            displayed_plot=self._get_displayed_plot()
-
-            #use both fit functions
-            try:
-                wlcparams, wlcyfit, wlcxfit, wlcfit_errors,wlc_qstd = self.wlc_fit(fitpoints, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],pl_value,T, return_errors=True )
-                wlcerror=False	
-            except:
-                print 'WLC fit not possible'
-                wlcerror=True
-
-            try:
-                fjcparams, fjcyfit, fjcxfit, fjcfit_errors,fjc_qstd = self.efjc_fit(fitpoints, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],kl_value,T, return_errors=True )
-                fjcerror=False
-            except:
-                print 'eFJC fit not possible'
-                fjcerror=True
+    def _fit_curve(self, hooke, inqueue, outqueue, params, curve):
+        contact = self._get_point('Mark the contact point of the curve.')
+        #hightlights an area dedicated to reject current curve
+        sizeret=len(self.plots[0].vectors[1][0])
+        noarea=self.plots[0].vectors[1][0][-sizeret/6:-1]                
+        noareaplot=copy.deepcopy(self._get_displayed_plot())
+        #noise dependent slight shift to improve visibility
+        noareaplot.add_set(noarea,np.ones_like(noarea)*5.0*np.std(self.plots[0].vectors[1][1][-sizeret/6:-1]))
+        noareaplot.styles+=['scatter']
+        noareaplot.colors+=["red"]
+        self._send_plot([noareaplot])
+        contact_point=self._measure_N_points(N=1, whatset=1)[0]
+        contact_point_index=contact_point.index
+        noareaplot.remove_set(-1)
+        #remove set leaves some styles disturbing the next graph, fixed by doing do_plot
+        self.do_plot(0)
+        if contact_point_index>5.0/6.0*sizeret:
+            if params['just one']:
+                break
+            curveindex+=1
+            continue				
+        
+        self.wlccontact_point=contact_point
+        self.wlccontact_index=contact_point.index
+        self.wlccurrent=self.current.path
+        
+        print 'Now click two points for the fitting area (one should be the rupture point)'
+        wlcpoints=self._measure_N_points(N=2,whatset=1)
+        print 'And one point of the top of the jump'
+        toppoint=self._measure_N_points(N=1,whatset=1)
+        slopepoint=ClickedPoint()
+        if slopew==None:
+            print 'Click a point to calculate slope'
+            slopepoint=self._measure_N_points(N=1,whatset=1)
+            
+        fitpoints=[contact_point]+wlcpoints
+        #use the currently displayed plot for the fit
+        displayed_plot=self._get_displayed_plot()
+        
+        #use both fit functions
+        try:
+            wlcparams, wlcyfit, wlcxfit, wlcfit_errors,wlc_qstd = self.wlc_fit(fitpoints, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],pl_value,T, return_errors=True )
+            wlcerror=False	
+        except:
+            print 'WLC fit not possible'
+            wlcerror=True
+            
+        try:
+            fjcparams, fjcyfit, fjcxfit, fjcfit_errors,fjc_qstd = self.efjc_fit(fitpoints, displayed_plot.vectors[1][0], displayed_plot.vectors[1][1],kl_value,T, return_errors=True )
+            fjcerror=False
+        except:
+            print 'eFJC fit not possible'
+            fjcerror=True
                 
-            #Measure rupture force
-            ruptpoint=ClickedPoint()    
-            if wlcpoints[0].graph_coords[1]<wlcpoints[1].graph_coords[1]:
-                ruptpoint=wlcpoints[0]
-            else:
-                ruptpoint=wlcpoints[1]
-            tpindex=toppoint[0].index
-            toplevel=np.average(displayed_plot.vectors[1][1][tpindex:tpindex+basew])
-            force=toplevel-ruptpoint.graph_coords[1]					
-         
-            #Measure the slope - loading rate
+        #Measure rupture force
+        ruptpoint=ClickedPoint()    
+        if wlcpoints[0].graph_coords[1]<wlcpoints[1].graph_coords[1]:
+            ruptpoint=wlcpoints[0]
+        else:
+            ruptpoint=wlcpoints[1]
+        tpindex=toppoint[0].index
+        toplevel=np.average(displayed_plot.vectors[1][1][tpindex:tpindex+basew])
+        force=toplevel-ruptpoint.graph_coords[1]					
+        
+        #Measure the slope - loading rate
             
-            if slopew==None:
-                if twops:
-                    xint=ruptpoint.graph_coords[0]-slopepoint[0].graph_coords[0]
-                    yint=ruptpoint.graph_coords[1]-slopepoint[0].graph_coords[1]
-                    slope=yint/xint
-                    slopeplot=self._get_displayed_plot(0) #get topmost displayed plot
-                    slopeplot.add_set([ruptpoint.graph_coords[0],slopepoint[0].graph_coords[0]],[ruptpoint.graph_coords[1],slopepoint[0].graph_coords[1]])
-                    if slopeplot.styles==[]:
-                        slopeplot.styles=[None,None,'scatter']
-                        slopeplot.colors=[None,None,'red']
-                    else:
-                        slopeplot.styles+=['scatter']
-                        slopeplot.colors+=['red']
-                else:    
-                    slope=self._slope([ruptpoint]+slopepoint,slopew)
-            else:
-                slope=self._slope([ruptpoint],slopew)
+        if slopew==None:
+            if twops:
+                xint=ruptpoint.graph_coords[0]-slopepoint[0].graph_coords[0]
+                yint=ruptpoint.graph_coords[1]-slopepoint[0].graph_coords[1]
+                slope=yint/xint
+                slopeplot=self._get_displayed_plot(0) #get topmost displayed plot
+                slopeplot.add_set([ruptpoint.graph_coords[0],slopepoint[0].graph_coords[0]],[ruptpoint.graph_coords[1],slopepoint[0].graph_coords[1]])
+                if slopeplot.styles==[]:
+                    slopeplot.styles=[None,None,'scatter']
+                    slopeplot.colors=[None,None,'red']
+                else:
+                    slopeplot.styles+=['scatter']
+                    slopeplot.colors+=['red']
+            else:    
+                slope=self._slope([ruptpoint]+slopepoint,slopew)
+        else:
+            slope=self._slope([ruptpoint],slopew)
          
-            #plot results (_slope already did)
+        #plot results (_slope already did)
             
-            #now we have the fit, we can plot it
-            #add the clicked points in the final PlotObject
-            clickvector_x, clickvector_y=[], []
-            for item in wlcpoints:
-                clickvector_x.append(item.graph_coords[0])
-                clickvector_y.append(item.graph_coords[1])
+        #now we have the fit, we can plot it
+        #add the clicked points in the final PlotObject
+        clickvector_x, clickvector_y=[], []
+        for item in wlcpoints:
+            clickvector_x.append(item.graph_coords[0])
+            clickvector_y.append(item.graph_coords[1])
             
-            #create a custom PlotObject to gracefully plot the fit along the curves
+        #create a custom PlotObject to gracefully plot the fit along the curves
             
-            #first fix those irritating zoom-destroying fits
-            lowestpoint=min(displayed_plot.vectors[1][1])
-            for i in np.arange(0,len(wlcyfit)):
-                if wlcyfit[i] < 1.2*lowestpoint:
-                    wlcyfit[i]=toplevel    
-            for i in np.arange(0,len(fjcyfit)):
-                if fjcyfit[i] < 1.2*lowestpoint:
-                    fjcyfit[i]=toplevel
+        #first fix those irritating zoom-destroying fits
+        lowestpoint=min(displayed_plot.vectors[1][1])
+        for i in np.arange(0,len(wlcyfit)):
+            if wlcyfit[i] < 1.2*lowestpoint:
+                wlcyfit[i]=toplevel    
+        for i in np.arange(0,len(fjcyfit)):
+            if fjcyfit[i] < 1.2*lowestpoint:
+                fjcyfit[i]=toplevel
             
-            fitplot=copy.deepcopy(displayed_plot)
-            fitplot.add_set(wlcxfit,wlcyfit)
-            fitplot.add_set(fjcxfit,fjcyfit) 
-            fitplot.add_set(clickvector_x,clickvector_y)
+        fitplot=copy.deepcopy(displayed_plot)
+        fitplot.add_set(wlcxfit,wlcyfit)
+        fitplot.add_set(fjcxfit,fjcyfit) 
+        fitplot.add_set(clickvector_x,clickvector_y)
 
-            fitplot.styles+=[None,None,'scatter']
-            fitplot.colors+=["red","blue",None]
-            
-            self._send_plot([fitplot])
+        fitplot.styles+=[None,None,'scatter']
+        fitplot.colors+=["red","blue",None]
             
+        self._send_plot([fitplot])
+        
 
-             #present results of measurement
-            if len(wlcparams)==1:
-                wlcparams.append(pl_value*1e-9)
-            if len(fjcparams)==1:
-                fjcparams.append(kl_value*1e-9)
+        #present results of measurement
+        if len(wlcparams)==1:
+            wlcparams.append(pl_value*1e-9)
+        if len(fjcparams)==1:
+            fjcparams.append(kl_value*1e-9)
                 
-            if fjcfit_errors:
-                fjcfit_nm=[i*(10**9) for i in fjcfit_errors]
-                if len(fjcfit_nm)==1:
-                    fjcfit_nm.append(0)
-            else:
-                fjcfit_errors=[0,0]        
-            if wlcfit_errors:
-                wlcfit_nm=[i*(10**9) for i in wlcfit_errors]
-                if len(wlcfit_nm)==1:
-                    wlcfit_nm.append(0)
-            else:
-                wlcfit_errors=[0,0]
+        if fjcfit_errors:
+            fjcfit_nm=[i*(10**9) for i in fjcfit_errors]
+            if len(fjcfit_nm)==1:
+                fjcfit_nm.append(0)
+        else:
+            fjcfit_errors=[0,0]        
+        if wlcfit_errors:
+            wlcfit_nm=[i*(10**9) for i in wlcfit_errors]
+        if len(wlcfit_nm)==1:
+            wlcfit_nm.append(0)
+        else:
+            wlcfit_errors=[0,0]
             
-            wlc_fitq=wlc_qstd/np.std(displayed_plot.vectors[1][1][-20:-1])
-            fjc_fitq=fjc_qstd/np.std(displayed_plot.vectors[1][1][-20:-1])
+        wlc_fitq=wlc_qstd/np.std(displayed_plot.vectors[1][1][-20:-1])
+        fjc_fitq=fjc_qstd/np.std(displayed_plot.vectors[1][1][-20:-1])
             
-            print '\nRESULTS'
-            print 'WLC contour : '+str(1e9*wlcparams[0])+u' \u00b1 '+str(wlcfit_nm[0])+' nm'
-            print 'Per. length : '+str(1e9*wlcparams[1])+u' \u00b1 '+str(wlcfit_nm[1])+' nm'
-            print 'Quality :'+str(wlc_fitq)
-            print '---'
-            print 'eFJC contour : '+str(1e9*fjcparams[0])+u' \u00b1 '+str(fjcfit_nm[0])+' nm'
-            print 'Kuhn length (e): '+str(1e9*fjcparams[1])+u' \u00b1 '+str(fjcfit_nm[1])+' nm' 
-            print 'Quality :'+str(fjc_fitq)   
-            print '---'
-            print 'Force : '+str(1e12*force)+' pN'
-            print 'Slope : '+str(slope)+' N/m'
+        print '\nRESULTS'
+        print 'WLC contour : '+str(1e9*wlcparams[0])+u' \u00b1 '+str(wlcfit_nm[0])+' nm'
+        print 'Per. length : '+str(1e9*wlcparams[1])+u' \u00b1 '+str(wlcfit_nm[1])+' nm'
+        print 'Quality :'+str(wlc_fitq)
+        print '---'
+        print 'eFJC contour : '+str(1e9*fjcparams[0])+u' \u00b1 '+str(fjcfit_nm[0])+' nm'
+        print 'Kuhn length (e): '+str(1e9*fjcparams[1])+u' \u00b1 '+str(fjcfit_nm[1])+' nm' 
+        print 'Quality :'+str(fjc_fitq)   
+        print '---'
+        print 'Force : '+str(1e12*force)+' pN'
+        print 'Slope : '+str(slope)+' N/m'
 
-            try:
-                #FIXME all drivers should provide retract velocity, in SI or homogeneous units    
-                lrate=slope*self.current.curve.retract_velocity
-                print 'Loading rate (UNTESTED):'+str(lrate)
-            except:
-                print 'Loading rate : n/a'
-                lrate='n/a'
+        try:
+            #FIXME all drivers should provide retract velocity, in SI or homogeneous units    
+            lrate=slope*self.current.curve.retract_velocity
+            print 'Loading rate (UNTESTED):'+str(lrate)
+        except:
+            print 'Loading rate : n/a'
+            lrate='n/a'
             
-            if justone:
-                return
-            
-            #save accept/discard/repeat
-            print '\n\nDo you want to save these?'
-            if self.YNclick():
+        #save accept/discard/repeat
+        print '\n\nDo you want to save these?'
+        if self.YNclick():
                     
-                #Save file info
+        #Save file info
+            if self.autofile=='':
+                self.autofile=raw_input('Results filename? (press enter for a random generated name)')
                 if self.autofile=='':
-                    self.autofile=raw_input('Results filename? (press enter for a random generated name)')
-                    if self.autofile=='':
-                        [osf,name]=tempfile.mkstemp(prefix='analysis-',suffix='.txt',text=True,dir=self.config['hookedir'])
-                        print 'saving in '+name
-                        self.autofile=name
-                        os.close(osf)
-                        f=open(self.autofile,'a+')
-                        f.write('Analysis started '+time.asctime()+'\n')
-                        f.write('----------------------------------------\n')
-                        f.write(' File ; WLC Cont. length (nm) ; Sigma WLC cl;  Per. Length (nm) ; Sigma pl ; WLC-Q ; eFJC Cont. length (nm) ; Sigma eFJC cl ; Kuhn length (nm); Sigma kl ; FJC-Q ;Force (pN) ; Slope (N/m) ; (untested) Loading rate (pN/s)\n')
-                        f.close()
-        
-                if not os.path.exists(self.autofile):
+                    [osf,name]=tempfile.mkstemp(prefix='analysis-',suffix='.txt',text=True,dir=self.config['hookedir'])
+                    print 'saving in '+name
+                    self.autofile=name
+                    os.close(osf)
                     f=open(self.autofile,'a+')
                     f.write('Analysis started '+time.asctime()+'\n')
                     f.write('----------------------------------------\n')
-                    f.write(' File ; WLC Cont. length (nm) ; Sigma WLC cl;  Per. Length (nm) ; Sigma pl; WLC-Q ;eFJC Cont. length (nm) ; Sigma eFJC cl ; Kuhn length (nm); Sigma kl ; FJC-Q ;Force (pN) ; Slope (N/m) ; (untested) Loading rate (pN/s)\n')
+                    f.write(' File ; WLC Cont. length (nm) ; Sigma WLC cl;  Per. Length (nm) ; Sigma pl ; WLC-Q ; eFJC Cont. length (nm) ; Sigma eFJC cl ; Kuhn length (nm); Sigma kl ; FJC-Q ;Force (pN) ; Slope (N/m) ; (untested) Loading rate (pN/s)\n')
                     f.close()
-                
-                print 'Saving...'
-                savecounter+=1
+                    
+            if not os.path.exists(self.autofile):
                 f=open(self.autofile,'a+')
-                f.write(self.current.path)
-                f.write(' ; '+str(1e9*wlcparams[0])+' ; '+str(wlcfit_nm[0])+' ; '+str(1e9*wlcparams[1])+' ; '+str(wlcfit_nm[1])+' ; '+ str(wlc_fitq)+' ; '+str(1e9*fjcparams[0])+' ; '+str(fjcfit_nm[0])+' ; '+str(1e9*fjcparams[1])+' ; '+str(fjcfit_nm[1])+' ; '+str(fjc_fitq)+' ; '+str(1e12*force)+' ; '+ str(slope)+' ; '+str(lrate)+'\n')
+                f.write('Analysis started '+time.asctime()+'\n')
+                f.write('----------------------------------------\n')
+                f.write(' File ; WLC Cont. length (nm) ; Sigma WLC cl;  Per. Length (nm) ; Sigma pl; WLC-Q ;eFJC Cont. length (nm) ; Sigma eFJC cl ; Kuhn length (nm); Sigma kl ; FJC-Q ;Force (pN) ; Slope (N/m) ; (untested) Loading rate (pN/s)\n')
                 f.close()
-            else:
-                print '\nWould you like to try again on this same curve?'
-                if self.YNclick():
-                    continue
-            curveindex+=1
-
-        if not justone:
-            print 'You saved '+str(savecounter)+' out of '+str(len(self.current_list))+' total curves.'
-            
-            
-            
-    def YNclick(self):
-        #shows something in the graph to indicate we expect YNclick
-        #FIXME is there an easy way to write in the graph?
-        askplot=self._get_displayed_plot()
-        center=np.min(askplot.vectors[1][0])+15e-9
-        scale=np.std(askplot.vectors[1][1][-50:-1])
-        hscale=np.mean(np.diff(askplot.vectors[1][0][-10:-1]))
-        xhline=[center-20*hscale,center-10*hscale,center+10*hscale,center+20*hscale]
-        ytopline=[15*scale,20*scale,20*scale,15*scale]
-        ybotline=[-15*scale,-20*scale,-20*scale,-15*scale]
-        yvline=np.arange(-25*scale,26*scale,scale/2)
-        xvline=np.ones_like(yvline)*center
-        xshow=np.concatenate((xvline,xhline,xhline))
-        yshow=np.concatenate((yvline,ytopline,ybotline))    
-        askplot.add_set(xshow,yshow)
-        askplot.styles+=['scatter']
-        askplot.colors+=["black"]
-        self._send_plot([askplot])
-        print 'Click any point over y=0 for Yes, under it for No'
-        point=self._measure_N_points(N=1,whatset=1)[0]
-        value=point.absolute_coords[1]
-        askplot.remove_set(-1)
-        self._send_plot([askplot])
-        if value<0:
-            return False
+                
+            print 'Saving...'
+            savecounter+=1
+            f=open(self.autofile,'a+')
+            f.write(self.current.path)
+            f.write(' ; '+str(1e9*wlcparams[0])+' ; '+str(wlcfit_nm[0])+' ; '+str(1e9*wlcparams[1])+' ; '+str(wlcfit_nm[1])+' ; '+ str(wlc_fitq)+' ; '+str(1e9*fjcparams[0])+' ; '+str(fjcfit_nm[0])+' ; '+str(1e9*fjcparams[1])+' ; '+str(fjcfit_nm[1])+' ; '+str(fjc_fitq)+' ; '+str(1e12*force)+' ; '+ str(slope)+' ; '+str(lrate)+'\n')
+            f.close()
         else:
-            return True
-
-
-
-
+            print '\nWould you like to try again on this same curve?'
+            if self.YNclick():
+                continue
+        curveindex+=1
-- 
2.26.2