from ..curve import Data
from ..plugin import Plugin
from ..util.fit import PoorFit, ModelFitter
+from ..util.si import join_data_label, split_data_label
from .curve import CurveArgument
params = {'curve':curve, 'block':block}
b = curve.data[block]
if ('surface distance (m)' not in b.info['columns']
- or 'surface adjusted deflection (m)' not in b.info['columns']):
+ or 'surface deflection (m)' not in b.info['columns']):
try:
- contact._run(hooke, inqueue, outqueue, params)
+ contact.run(hooke, inqueue, outqueue, **params)
except PoorFit, e:
raise PoorFit('Could not fit %s %s: %s'
% (curve.path, block, str(e)))
if ('deflection (N)' not in b.info['columns']):
- force._run(hooke, inqueue, outqueue, params)
+ force.run(hooke, inqueue, outqueue, **params)
if ('cantilever adjusted extension (m)' not in b.info['columns']):
- cant_adjust._run(hooke, inqueue, outqueue, params)
+ cant_adjust.run(hooke, inqueue, outqueue, **params)
return curve
class SurfacePositionModel (ModelFitter):
- """
+ """Bilinear surface position model.
The bilinear model is symmetric, but the parameter guessing and
sanity checks assume the contact region occurs for lower indicies
should be enough data in the off-surface region that interactions
due to proteins, etc. will not seriously skew the fit in the
off-surface region.
-
-
- We guess
"""
def model(self, params):
"""A continuous, bilinear model.
Notes
-----
-
We guess offset scale (:math:`p_0`) as one tenth of the total
deflection range, the kink scale (:math:`p_2`) as one tenth of
the total index range, the initial (contact) slope scale
class SurfaceContactCommand (Command):
"""Automatically determine a block's surface contact point.
- Uses the block's `z piezo (m)` and `deflection (m)` arrays.
- Stores the contact parameters in `block.info`'s `surface distance
- offset (m)` and `surface deflection offset (m)`. Model-specific
- fitting information is stored in `surface detection parameters`.
-
- The adjusted data columns `surface distance (m)` and `surface
- adjusted deflection (m)` are also added to the block.
-
You can select the contact point algorithm with the creatively
named `surface contact point algorithm` configuration setting.
Currently available options are:
Data block for which the force should be calculated. For an
approach/retract force curve, `0` selects the approaching curve and `1`
selects the retracting curve.
+""".strip()),
+ Argument(name='input distance column', type='string',
+ default='z piezo (m)',
+ help="""
+Name of the column to use as the surface positioning input.
+""".strip()),
+ Argument(name='input deflection column', type='string',
+ default='deflection (m)',
+ help="""
+Name of the column to use as the deflection input.
+""".strip()),
+ Argument(name='output distance column', type='string',
+ default='surface distance',
+ help="""
+Name of the column (without units) to use as the surface positioning output.
+""".strip()),
+ Argument(name='output deflection column', type='string',
+ default='surface deflection',
+ help="""
+Name of the column (without units) to use as the deflection output.
+""".strip()),
+ Argument(name='distance info name', type='string',
+ default='surface distance offset',
+ help="""
+Name (without units) for storing the distance offset in the `.info` dictionary.
+""".strip()),
+ Argument(name='deflection info name', type='string',
+ default='surface deflection offset',
+ help="""
+Name (without units) for storing the deflection offset in the `.info` dictionary.
+""".strip()),
+ Argument(name='fit parameters info name', type='string',
+ default='surface deflection offset',
+ help="""
+Name (without units) for storing the deflection offset in the `.info` dictionary.
""".strip()),
],
help=self.__doc__, plugin=plugin)
new = Data((data.shape[0], data.shape[1]+2), dtype=data.dtype)
new.info = copy.deepcopy(data.info)
new[:,:-2] = data
- new.info['columns'].extend(
- ['surface distance (m)', 'surface adjusted deflection (m)'])
- z_data = data[:,data.info['columns'].index('z piezo (m)')]
- d_data = data[:,data.info['columns'].index('deflection (m)')]
- i,deflection_offset,ps = self.find_contact_point(
- params['curve'], z_data, d_data, outqueue)
- surface_offset = z_data[i]
- new.info['surface distance offset (m)'] = surface_offset
- new.info['surface deflection offset (m)'] = deflection_offset
- new.info['surface detection parameters'] = ps
- new[:,-2] = z_data - surface_offset
- new[:,-1] = d_data - deflection_offset
+ name,dist_units = split_data_label(params['input distance column'])
+ name,def_units = split_data_label(params['input deflection column'])
+ new.info['columns'].extend([
+ join_data_label(params['output distance column'], dist_units),
+ join_data_label(params['output deflection column'], def_units),
+ ])
+ dist_data = data[:,data.info['columns'].index(
+ params['input distance column'])]
+ def_data = data[:,data.info['columns'].index(
+ params['input deflection column'])]
+ i,def_offset,ps = self.find_contact_point(
+ params['curve'], dist_data, def_data, outqueue)
+ dist_offset = dist_data[i]
+ new.info[join_data_label(params['distance info name'], dist_units
+ )] = dist_offset
+ new.info[join_data_label(params['deflection info name'], def_units
+ )] = def_offset
+ new.info[params['fit parameters info name']] = ps
+ new[:,-2] = dist_data - dist_offset
+ new[:,-1] = def_data - def_offset
params['curve'].data[params['block']] = new
def find_contact_point(self, curve, z_data, d_data, outqueue=None):
surface_index = len(d_data)-1-surface_index
return (numpy.round(surface_index), deflection_offset, info)
-class ForceCommand (Command):
- """Calculate a block's `deflection (N)` array.
- Uses the block's `deflection (m)` array and
- `spring constant (N/m)`.
+class ForceCommand (Command):
+ """Convert a deflection column from meters to newtons.
"""
def __init__(self, plugin):
super(ForceCommand, self).__init__(
Data block for which the force should be calculated. For an
approach/retract force curve, `0` selects the approaching curve and `1`
selects the retracting curve.
+""".strip()),
+ Argument(name='input deflection column', type='string',
+ default='surface deflection (m)',
+ help="""
+Name of the column to use as the deflection input.
+""".strip()),
+ Argument(name='output deflection column', type='string',
+ default='deflection',
+ help="""
+Name of the column (without units) to use as the deflection output.
+""".strip()),
+ Argument(name='spring constant info name', type='string',
+ default='spring constant (N/m)',
+ help="""
+Name of the spring constant in the `.info` dictionary.
""".strip()),
],
help=self.__doc__, plugin=plugin)
new = Data((data.shape[0], data.shape[1]+1), dtype=data.dtype)
new.info = copy.deepcopy(data.info)
new[:,:-1] = data
- new.info['columns'].append('deflection (N)')
- d_data = data[:,data.info['columns'].index('surface adjusted deflection (m)')]
- new[:,-1] = d_data * data.info['spring constant (N/m)']
+ new.info['columns'].append(
+ join_data_label(params['output deflection column'], 'N'))
+ d_data = data[:,data.info['columns'].index(
+ params['input deflection column'])]
+ new[:,-1] = d_data * data.info[params['spring constant info name']]
params['curve'].data[params['block']] = new
class CantileverAdjustedExtensionCommand (Command):
- """Calculate a block's `cantilever adjusted extension (m)` array.
-
- Uses the block's `deflection (m)` and `surface distance offset (m)`
- arrays and `spring constant (N/m)`.
+ """Remove cantilever extension from a total extension column.
"""
def __init__(self, plugin):
super(CantileverAdjustedExtensionCommand, self).__init__(
Data block for which the adjusted extension should be calculated. For
an approach/retract force curve, `0` selects the approaching curve and
`1` selects the retracting curve.
+""".strip()),
+ Argument(name='input distance column', type='string',
+ default='surface distance (m)',
+ help="""
+Name of the column to use as the distance input.
+""".strip()),
+ Argument(name='input deflection column', type='string',
+ default='deflection (N)',
+ help="""
+Name of the column to use as the deflection input.
+""".strip()),
+ Argument(name='output distance column', type='string',
+ default='cantilever adjusted extension',
+ help="""
+Name of the column (without units) to use as the deflection output.
+""".strip()),
+ Argument(name='spring constant info name', type='string',
+ default='spring constant (N/m)',
+ help="""
+Name of the spring constant in the `.info` dictionary.
""".strip()),
],
help=self.__doc__, plugin=plugin)
new = Data((data.shape[0], data.shape[1]+1), dtype=data.dtype)
new.info = copy.deepcopy(data.info)
new[:,:-1] = data
- new.info['columns'].append('cantilever adjusted extension (m)')
- z_data = data[:,data.info['columns'].index('surface distance (m)')]
- d_data = data[:,data.info['columns'].index('deflection (N)')]
- new[:,-1] = z_data - d_data / data.info['spring constant (N/m)']
+ new.info['columns'].append(
+ join_data_label(params['output distance column'], 'm'))
+ z_data = data[:,data.info['columns'].index(
+ params['input distance column'])]
+ d_data = data[:,data.info['columns'].index(
+ params['input deflection column'])]
+ k = data.info[params['spring constant info name']]
+
+ z_name,z_unit = split_data_label(params['input distance column'])
+ assert z_unit == 'm', params['input distance column']
+ d_name,d_unit = split_data_label(params['input deflection column'])
+ assert d_unit == 'N', params['input deflection column']
+ k_name,k_unit = split_data_label(params['spring constant info name'])
+ assert k_unit == 'N/m', params['spring constant info name']
+
+ new[:,-1] = z_data - d_data / k
params['curve'].data[params['block']] = new
class generalvclampCommands(object):
- def _plug_init(self):
- self.basecurrent=None
- self.basepoints=None
- self.autofile=''
-
- def do_distance(self,args):
- '''
- DISTANCE
- (generalvclamp.py)
- Measure the distance (in nm) between two points.
- For a standard experiment this is the delta X distance.
- For a force clamp experiment this is the delta Y distance (actually becomes
- an alias of zpiezo)
- -----------------
- Syntax: distance
- '''
- if self.current.curve.experiment == 'clamp':
- print 'You wanted to use zpiezo perhaps?'
- return
- else:
- dx,unitx,dy,unity=self._delta(set=1)
- print str(dx*(10**9))+' nm'
- to_dump='distance '+self.current.path+' '+str(dx*(10**9))+' nm'
- self.outlet.push(to_dump)
-
-
- def do_force(self,args):
- '''
- FORCE
- (generalvclamp.py)
- Measure the force difference (in pN) between two points
- ---------------
- Syntax: force
- '''
- if self.current.curve.experiment == 'clamp':
- print 'This command makes no sense for a force clamp experiment.'
- return
- dx,unitx,dy,unity=self._delta(set=1)
- print str(dy*(10**12))+' pN'
- to_dump='force '+self.current.path+' '+str(dy*(10**12))+' pN'
- self.outlet.push(to_dump)
-
-
- def do_forcebase(self,args):
- '''
- FORCEBASE
- (generalvclamp.py)
- Measures the difference in force (in pN) between a point and a baseline
- took as the average between two points.
-
- The baseline is fixed once for a given curve and different force measurements,
- unless the user wants it to be recalculated
- ------------
- Syntax: forcebase [rebase]
- rebase: Forces forcebase to ask again the baseline
- max: Instead of asking for a point to measure, asks for two points and use
- the maximum peak in between
- '''
- rebase=False #if true=we select rebase
- maxpoint=False #if true=we measure the maximum peak
-
- plot=self._get_displayed_plot()
- whatset=1 #fixme: for all sets
- if 'rebase' in args or (self.basecurrent != self.current.path):
- rebase=True
- if 'max' in args:
- maxpoint=True
-
- if rebase:
- print 'Select baseline'
- self.basepoints=self._measure_N_points(N=2, whatset=whatset)
- self.basecurrent=self.current.path
-
- if maxpoint:
- print 'Select two points'
- points=self._measure_N_points(N=2, whatset=whatset)
- boundpoints=[points[0].index, points[1].index]
- boundpoints.sort()
- try:
- y=min(plot.vectors[whatset][1][boundpoints[0]:boundpoints[1]])
- except ValueError:
- print 'Chosen interval not valid. Try picking it again. Did you pick the same point as begin and end of interval?'
- else:
- print 'Select point to measure'
- points=self._measure_N_points(N=1, whatset=whatset)
- #whatplot=points[0].dest
- y=points[0].graph_coords[1]
-
- #fixme: code duplication
- boundaries=[self.basepoints[0].index, self.basepoints[1].index]
- boundaries.sort()
- to_average=plot.vectors[whatset][1][boundaries[0]:boundaries[1]] #y points to average
-
- avg=np.mean(to_average)
- forcebase=abs(y-avg)
- print str(forcebase*(10**12))+' pN'
- to_dump='forcebase '+self.current.path+' '+str(forcebase*(10**12))+' pN'
- self.outlet.push(to_dump)
-
- def plotmanip_multiplier(self, plot, current):
- '''
- Multiplies all the Y values of an SMFS curve by a value stored in the 'force_multiplier'
- configuration variable. Useful for calibrations and other stuff.
- '''
-
- #not a smfs curve...
- if current.curve.experiment != 'smfs':
- return plot
-
- #only one set is present...
- if len(self.plots[0].vectors) != 2:
- return plot
-
- #multiplier is 1...
- if (self.config['force_multiplier']==1):
- return plot
-
- for i in range(len(plot.vectors[0][1])):
- plot.vectors[0][1][i]=plot.vectors[0][1][i]*self.config['force_multiplier']
-
- for i in range(len(plot.vectors[1][1])):
- plot.vectors[1][1][i]=plot.vectors[1][1][i]*self.config['force_multiplier']
-
- return plot
-
-
def plotmanip_flatten(self, plot, current, customvalue=False):
'''
Subtracts a polynomial fit to the non-contact part of the curve, as to flatten it.
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']
- try:
- abs_devs=float(a)
- except:
- print "Bad input, using default."
- abs_devs=self.convfilt_config['mindeviation']
-
- defplot=self.current.curve.default_plots()[0]
- if not noflatten:
- flatten=self._find_plotmanip('flatten') #Extract flatten plotmanip
- defplot=flatten(defplot, self.current, customvalue=1) #Flatten curve before feeding it to has_peaks
- pk_location,peak_size=self.has_peaks(defplot, abs_devs, maxpeak)
- return pk_location, peak_size
-
-
- def pickup_contact_point(self,N=1,whatset=1):
- '''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
- self.wlccontact_index=contact_point.index
- self.wlccurrent=self.current.path
- return contact_point, contact_point_index
-
-
- def baseline_points(self,peak_location, displayed_plot):
- clicks=self.config['baseline_clicks']
- if clicks==0:
- self.basepoints=[]
- base_index_0=peak_location[-1]+self.fit_interval_nm(peak_location[-1], displayed_plot, self.config['auto_right_baseline'],False)
- self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_0))
- base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'],False)
- self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
- elif clicks>0:
- print 'Select baseline'
- if clicks==1:
- self.basepoints=self._measure_N_points(N=1, whatset=1)
- base_index_1=self.basepoints[0].index+self.fit_interval_nm(self.basepoints[0].index, displayed_plot, self.config['auto_left_baseline'], False)
- self.basepoints.append(self._clickize(displayed_plot.vectors[1][0],displayed_plot.vectors[1][1],base_index_1))
- else:
- self.basepoints=self._measure_N_points(N=2, whatset=1)
-
- self.basecurrent=self.current.path
- return self.basepoints
projects / hooke.git / blobdiff