# 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
projects / hooke.git / commitdiff