- if customvalue:
- max_cycles=customvalue
- else:
- max_cycles=self.config['flatten'] #Using > 1 usually doesn't help and can give artefacts. However, it could be useful too.
-
- contact_index=self.find_contact_point()
-
- valn=[[] for item in range(max_exponent)]
- yrn=[0.0 for item in range(max_exponent)]
- errn=[0.0 for item in range(max_exponent)]
-
- #Check if we have a proper numerical value
- try:
- zzz=int(max_cycles)
- except:
- #Loudly and annoyingly complain if it's not a number, then fallback to zero
- print '''Warning: flatten value is not a number!
- Use "set flatten" or edit hooke.conf to set it properly
- Using zero.'''
- max_cycles=0
-
- for i in range(int(max_cycles)):
-
- x_ext=plot.vectors[0][0][contact_index+delta_contact:]
- y_ext=plot.vectors[0][1][contact_index+delta_contact:]
- x_ret=plot.vectors[1][0][contact_index+delta_contact:]
- y_ret=plot.vectors[1][1][contact_index+delta_contact:]
- for exponent in range(max_exponent):
- try:
- valn[exponent]=sp.polyfit(x_ext,y_ext,exponent)
- yrn[exponent]=sp.polyval(valn[exponent],x_ret)
- errn[exponent]=sp.sqrt(sum((yrn[exponent]-y_ext)**2)/float(len(y_ext)))
- except Exception,e:
- print 'Cannot flatten!'
- print e
- return plot
-
- best_exponent=errn.index(min(errn))
-
- #extension
- ycorr_ext=y_ext-yrn[best_exponent]+y_ext[0] #noncontact part
- yjoin_ext=np.array(plot.vectors[0][1][0:contact_index+delta_contact]) #contact part
- #retraction
- ycorr_ret=y_ret-yrn[best_exponent]+y_ext[0] #noncontact part
- yjoin_ret=np.array(plot.vectors[1][1][0:contact_index+delta_contact]) #contact part
-
- ycorr_ext=np.concatenate((yjoin_ext, ycorr_ext))
- ycorr_ret=np.concatenate((yjoin_ret, ycorr_ret))
-
- plot.vectors[0][1]=list(ycorr_ext)
- plot.vectors[1][1]=list(ycorr_ret)
-
- return plot
-
- #---SLOPE---
- def do_slope(self,args):
- '''
- SLOPE
- (generalvclamp.py)
- Measures the slope of a delimited chunk on the return trace.
- The chunk can be delimited either by two manual clicks, or have
- a fixed width, given as an argument.
- ---------------
- Syntax: slope [width]
- The facultative [width] parameter specifies how many
- points will be considered for the fit. If [width] is
- specified, only one click will be required.
- (c) Marco Brucale, Massimo Sandal 2008
- '''
-
- # Reads the facultative width argument
- try:
- fitspan=int(args)
- except:
- fitspan=0
-
- # Decides between the two forms of user input, as per (args)
- if fitspan == 0:
- # Gets the Xs of two clicked points as indexes on the current curve vector
- print 'Click twice to delimit chunk'
- points=self._measure_N_points(N=2,whatset=1)
- else:
- print 'Click once on the leftmost point of the chunk (i.e.usually the peak)'
- points=self._measure_N_points(N=1,whatset=1)
-
- slope=self._slope(points,fitspan)
-
- # Outputs the relevant slope parameter
- print 'Slope:'
- print str(slope)
- to_dump='slope '+self.current.path+' '+str(slope)
- self.outlet.push(to_dump)
-
- def _slope(self,points,fitspan):
- # Calls the function linefit_between
- parameters=[0,0,[],[]]
- try:
- clickedpoints=[points[0].index,points[1].index]
- clickedpoints.sort()
- except:
- clickedpoints=[points[0].index-fitspan,points[0].index]
-
- 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:'
- print str(parameters[0])
- to_dump='slope '+self.curve.path+' '+str(parameters[0])
- self.outlet.push(to_dump)
-
- # Makes a vector with the fitted parameters and sends it to the GUI
- xtoplot=parameters[2]
- ytoplot=[]
- x=0
- for x in xtoplot:
- ytoplot.append((x*parameters[0])+parameters[1])
-
- clickvector_x, clickvector_y=[], []
- for item in points:
- clickvector_x.append(item.graph_coords[0])
- clickvector_y.append(item.graph_coords[1])
-
- lineplot=self._get_displayed_plot(0) #get topmost displayed plot
-
- lineplot.add_set(xtoplot,ytoplot)
- lineplot.add_set(clickvector_x, clickvector_y)
-
-
- if lineplot.styles==[]:
- lineplot.styles=[None,None,None,'scatter']
- else:
- lineplot.styles+=[None,'scatter']
- if lineplot.colors==[]:
- lineplot.colors=[None,None,'black',None]
- else:
- lineplot.colors+=['black',None]
-
-
- self._send_plot([lineplot])
-
- return parameters[0]
-
-
- def linefit_between(self,index1,index2,whatset=1):
- '''
- Creates two vectors (xtofit,ytofit) slicing out from the
- current return trace a portion delimited by the two indexes
- given as arguments.
- Then does a least squares linear fit on that slice.
- Finally returns [0]=the slope, [1]=the intercept of the
- fitted 1st grade polynomial, and [2,3]=the actual (x,y) vectors
- used for the fit.
- (c) Marco Brucale, Massimo Sandal 2008
- '''
- # Translates the indexes into two vectors containing the x,y data to fit
- xtofit=self.plots[0].vectors[whatset][0][index1:index2]
- ytofit=self.plots[0].vectors[whatset][1][index1:index2]
-
- # Does the actual linear fitting (simple least squares with numpy.polyfit)
- linefit=[]
- linefit=np.polyfit(xtofit,ytofit,1)
-
- return (linefit[0],linefit[1],xtofit,ytofit)
-
-
- def fit_interval_nm(self,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.
- '''
- whatset=1 #FIXME: should be decidable
- x_vect=plot.vectors[1][0]
-
- c=0
- i=start_index
- 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-1: #we reached boundaries of vector!
- return c
-
- if backwards:
- i-=1
- else:
- i+=1
- c+=1
- return c
-
-
-
- def find_current_peaks(self,noflatten, a=True, maxpeak=True):
- #Find peaks.
- if a==True:
- a=self.convfilt_config['mindeviation']
+ def _run(self, hooke, inqueue, outqueue, params):
+ data = params['curve'].data[params['block']]
+ # HACK? rely on params['curve'] being bound to the local hooke
+ # playlist (i.e. not a copy, as you would get by passing a
+ # curve through the queue). Ugh. Stupid queues. As an
+ # alternative, we could pass lookup information through the
+ # queue.
+ new = Data((data.shape[0], data.shape[1]+1), dtype=data.dtype)
+ new.info = copy.deepcopy(data.info)
+ new[:,:-1] = data
+ z_data = data[:,data.info['columns'].index(
+ params['input distance column'])]
+ d_data = data[:,data.info['columns'].index(
+ params['input deflection column'])]
+
+ d_name,d_unit = split_data_label(params['input deflection column'])
+ new.info['columns'].append(
+ join_data_label(params['output deflection column'], d_unit))
+
+ contact_index = numpy.absolute(z_data).argmin()
+ mask = z_data > 0
+ indices = numpy.argwhere(mask)
+ z_nc = z_data[indices].flatten()
+ d_nc = d_data[indices].flatten()
+
+ min_err = numpy.inf
+ degree = poly_values = None
+ log = logging.getLogger('hooke')
+ for deg in range(params['max degree']):
projects / hooke.git / blobdiff