#
# This file is part of Hooke.
#
-# Hooke is free software: you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation, either
-# version 3 of the License, or (at your option) any later version.
+# Hooke is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
#
-# Hooke is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Lesser General Public License for more details.
+# Hooke is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
+# Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with Hooke. If not, see
import copy
import numpy
+import scipy
from ..command import Command, Argument, Failure, NullQueue
from ..config import Setting
from ..curve import Data
-from ..plugin import Builtin
+from ..plugin import Plugin
from ..util.fit import PoorFit, ModelFitter
+from ..util.si import join_data_label, split_data_label
from .curve import CurveArgument
-def scale(hooke, curve):
+def scale(hooke, curve, block=None):
+ """Run 'add block force array' on `block`.
+
+ Runs 'zero block surface contact point' first, if necessary. Does
+ not run either command if the columns they add to the block are
+ already present.
+
+ If `block` is `None`, scale all blocks in `curve`.
+ """
commands = hooke.commands
contact = [c for c in hooke.commands
if c.name == 'zero block surface contact point'][0]
force = [c for c in hooke.commands if c.name == 'add block force array'][0]
+ cant_adjust = [c for c in hooke.commands
+ if c.name == 'add block cantilever adjusted extension array'][0]
inqueue = None
outqueue = NullQueue()
- for i,block in enumerate(curve.data):
- params = {'curve':curve, 'block':i}
- contact._run(hooke, inqueue, outqueue, params)
- force._run(hooke, inqueue, outqueue, params)
+ if block == None:
+ for i in range(len(curve.data)):
+ scale(hooke, curve, block=i)
+ else:
+ params = {'curve':curve, 'block':block}
+ b = curve.data[block]
+ if ('surface distance (m)' not in b.info['columns']
+ or 'surface deflection (m)' not in b.info['columns']):
+ try:
+ 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)
+ if ('cantilever adjusted extension (m)' not in b.info['columns']):
+ 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.
if self.info.get('force zero non-contact slope', None) == True:
p = list(p)
p.append(0.) # restore the non-contact slope parameter
- r2 = numpy.round(p[2])
+ r2 = numpy.round(abs(p[2]))
if r2 >= 1:
self._model_data[:r2] = p[0] + p[1] * numpy.arange(r2)
if r2 < len(self._data)-1:
- self._model_data[r2:] = p[0] + p[1]*p[2] + p[3] * numpy.arange(len(self._data)-r2)
+ self._model_data[r2:] = \
+ p[0] + p[1]*p[2] + p[3] * numpy.arange(len(self._data)-r2)
return self._model_data
def set_data(self, data, info=None):
produces the maximum deflection at the left-most point, and the
final (non-contact) slope (:math:`p_3`) is zero.
"""
- left_offset = self.info['max deflection']
- left_slope = 2*(-self.info['deflection range']
- /self.info['position range'])
+ left_offset = self.info['min deflection']
+ left_slope = 2*(self.info['deflection range']
+ /self.info['position range'])
kink_position = (self.info['max position']
+self.info['min position'])/2.0
right_slope = 0
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
def fit(self, *args, **kwargs):
self.info['guessed contact slope'] = None
params = super(SurfacePositionModel, self).fit(*args, **kwargs)
+ params[2] = abs(params[2])
if self.info.get('force zero non-contact slope', None) == True:
params = list(params)
params.append(0.) # restore the non-contact slope parameter
# check that the fit is reasonable, see the :meth:`model` docstring
- # for parameter descriptions.
+ # for parameter descriptions. HACK: hardcoded cutoffs.
if abs(params[3]*10) > abs(params[1]) :
raise PoorFit('Slope in non-contact region, or no slope in contact')
if params[2] < self.info['min position']+0.02*self.info['position range']:
- raise poorFit(
+ raise PoorFit(
'No kink (kink %g less than %g, need more space to left)'
% (params[2],
self.info['min position']+0.02*self.info['position range']))
% (params[2],
self.info['max position']-0.02*self.info['position range']))
if (self.info['guessed contact slope'] != None
- and params[3] < 0.5 * self.info['guessed contact slope']):
- raise PoorFit('Too far')
+ and abs(params[1]) < 0.5 * abs(self.info['guessed contact slope'])):
+ raise PoorFit('Too far (contact slope %g, but expected ~%g'
+ % (params[3], self.info['guessed contact slope']))
return params
-class VelocityClampPlugin (Builtin):
+class VelocityClampPlugin (Plugin):
def __init__(self):
super(VelocityClampPlugin, self).__init__(name='vclamp')
self._commands = [
SurfaceContactCommand(self), ForceCommand(self),
+ CantileverAdjustedExtensionCommand(self),
]
def default_settings(self):
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`.
+ You can select the contact point algorithm with the creatively
+ named `surface contact point algorithm` configuration setting.
+ Currently available options are:
- The adjusted data columns `surface distance (m)` and `surface
- adjusted deflection (m)` are also added to the block.
+ * fmms (:meth:`find_contact_point_fmms`)
+ * ms (:meth:`find_contact_point_ms`)
+ * wtk (:meth:`find_contact_point_wtk`)
"""
def __init__(self, plugin):
super(SurfaceContactCommand, 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 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)
def _run(self, hooke, inqueue, outqueue, params):
- data = params['curve'].data[int(params['block'])] # HACK, int() should be handled by ui
+ 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
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(
- 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
- data = params['curve'].data[int(params['block'])] # HACK, int() should be handled by ui
- params['curve'].data[int(params['block'])] = new # HACK, int() should be handled by ui
-
- def _find_contact_point(self, z_data, d_data, outqueue=None):
- fn = getattr(self, '_find_contact_point_%s'
+ 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):
+ """Railyard for the `find_contact_point_*` family.
+
+ Uses the `surface contact point algorithm` configuration
+ setting to call the appropriate backend algorithm.
+ """
+ fn = getattr(self, 'find_contact_point_%s'
% self.plugin.config['surface contact point algorithm'])
- return fn(z_data, d_data, outqueue)
+ return fn(curve, z_data, d_data, outqueue)
- def _find_contact_point_fmms(self, z_data, d_data, outqueue=None):
+ def find_contact_point_fmms(self, curve, z_data, d_data, outqueue=None):
"""Algorithm by Francesco Musiani and Massimo Sandal.
Notes
-----
Algorithm:
- * take care of the PicoForce trigger bug - exclude retraction portions with too high standard deviation
- * fit the second half of the retraction curve to a line
- * if the fit is not almost horizontal, take a smaller chunk and repeat
- * otherwise, we have something horizontal
- * so take the average of horizontal points and use it as a baseline
-
- Then, start from the rise of the retraction curve and look at
- the first point below the baseline.
+ 0) Driver-specific workarounds, e.g. deal with the PicoForce
+ trigger bug by excluding retraction portions with excessive
+ deviation.
+ 1) Select the second half (non-contact side) of the retraction
+ curve.
+ 2) Fit the selection to a line.
+ 3) If the fit is not almost horizontal, halve the selection
+ and retrun to (2).
+ 4) Average the selection and use it as a baseline.
+ 5) Slide in from the start (contact side) of the retraction
+ curve, until you find a point with greater than baseline
+ deflection. That point is the contact point.
"""
- if not plot:
- plot=self.plots[0]
-
- outplot=self.subtract_curves(1)
- xret=outplot.vectors[1][0]
- ydiff=outplot.vectors[1][1]
-
- xext=plot.vectors[0][0]
- yext=plot.vectors[0][1]
- xret2=plot.vectors[1][0]
- yret=plot.vectors[1][1]
-
- #taking care of the picoforce trigger bug: we exclude portions of the curve that have too much
- #standard deviation. yes, a lot of magic is here.
- monster=True
- monlength=len(xret)-int(len(xret)/20)
- finalength=len(xret)
- while monster:
- monchunk=scipy.array(ydiff[monlength:finalength])
- if abs(np.std(monchunk)) < 2e-10:
- monster=False
- else: #move away from the monster
- monlength-=int(len(xret)/50)
- finalength-=int(len(xret)/50)
-
-
- #take half of the thing
- endlength=int(len(xret)/2)
-
- ok=False
-
- while not ok:
- xchunk=yext[endlength:monlength]
- ychunk=yext[endlength:monlength]
- regr=scipy.stats.linregress(xchunk,ychunk)[0:2]
- #we stop if we found an almost-horizontal fit or if we're going too short...
- #FIXME: 0.1 and 6 here are "magic numbers" (although reasonable)
- if (abs(regr[1]) > 0.1) and ( endlength < len(xret)-int(len(xret)/6) ) :
- endlength+=10
- else:
- ok=True
-
-
- ymean=np.mean(ychunk) #baseline
-
- index=0
- point = ymean+1
-
- #find the first point below the calculated baseline
- while point > ymean:
- try:
- point=yret[index]
- index+=1
- except IndexError:
- #The algorithm didn't find anything below the baseline! It should NEVER happen
- index=0
- return index
-
- return index
-
- def _find_contact_point_ms(self, z_data, d_data, outqueue=None):
+ if curve.info['filetype'] == 'picoforce':
+ # Take care of the picoforce trigger bug (TODO: example
+ # data file demonstrating the bug). We exclude portions
+ # of the curve that have too much standard deviation.
+ # Yes, a lot of magic is here.
+ check_start = len(d_data)-len(d_data)/20
+ monster_start = len(d_data)
+ while True:
+ # look at the non-contact tail
+ non_monster = d_data[check_start:monster_start]
+ if non_monster.std() < 2e-10: # HACK: hardcoded cutoff
+ break
+ else: # move further away from the monster
+ check_start -= len(d_data)/50
+ monster_start -= len(d_data)/50
+ z_data = z_data[:monster_start]
+ d_data = d_data[:monster_start]
+
+ # take half of the thing to start
+ selection_start = len(d_data)/2
+ while True:
+ z_chunk = z_data[selection_start:]
+ d_chunk = d_data[selection_start:]
+ slope,intercept,r,two_tailed_prob,stderr_of_the_estimate = \
+ scipy.stats.linregress(z_chunk, d_chunk)
+ # We stop if we found an almost-horizontal fit or if we're
+ # getting to small a selection. FIXME: 0.1 and 5./6 here
+ # are "magic numbers" (although reasonable)
+ if (abs(slope) < 0.1 # deflection (m) / surface (m)
+ or selection_start > 5./6*len(d_data)):
+ break
+ selection_start += 10
+
+ d_baseline = d_chunk.mean()
+
+ # find the first point above the calculated baseline
+ i = 0
+ while i < len(d_data) and d_data[i] < ymean:
+ i += 1
+ return (i, d_baseline, {})
+
+ def find_contact_point_ms(self, curve, z_data, d_data, outqueue=None):
"""Algorithm by Massimo Sandal.
Notes
* ?
"""
- #raw_plot=self.current.curve.default_plots()[0]
- raw_plot=self.plots[0]
- '''xext=self.plots[0].vectors[0][0]
- yext=self.plots[0].vectors[0][1]
- xret2=self.plots[0].vectors[1][0]
- yret=self.plots[0].vectors[1][1]
- '''
xext=raw_plot.vectors[0][0]
yext=raw_plot.vectors[0][1]
xret2=raw_plot.vectors[1][0]
else:
return dummy.index
- def _find_contact_point_wtk(self, z_data, d_data, outqueue=None):
+ def find_contact_point_wtk(self, curve, z_data, d_data, outqueue=None):
"""Algorithm by W. Trevor King.
Notes
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)
def _run(self, hooke, inqueue, outqueue, params):
- data = params['curve'].data[int(params['block'])] # HACK, int() should be handled by ui
+ 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
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)']
- params['curve'].data[int(params['block'])] = new # HACK, int() should be handled by ui
-
-
-class generalvclampCommands(object):
-
- def do_subtplot(self, args):
- '''
- SUBTPLOT
- (procplots.py plugin)
- Plots the difference between ret and ext current curve
- -------
- Syntax: subtplot
- '''
- #FIXME: sub_filter and sub_order must be args
-
- if len(self.plots[0].vectors) != 2:
- print 'This command only works on a curve with two different plots.'
- pass
+ 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
- outplot=self.subtract_curves(sub_order=1)
- plot_graph=self.list_of_events['plot_graph']
- wx.PostEvent(self.frame,plot_graph(plots=[outplot]))
-
- 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.
- '''
+class CantileverAdjustedExtensionCommand (Command):
+ """Remove cantilever extension from a total extension column.
+ """
+ def __init__(self, plugin):
+ super(CantileverAdjustedExtensionCommand, self).__init__(
+ name='add block cantilever adjusted extension array',
+ arguments=[
+ CurveArgument,
+ Argument(name='block', aliases=['set'], type='int', default=0,
+ help="""
+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)
- #not a smfs curve...
- if current.curve.experiment != 'smfs':
- return plot
+ 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
+ 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']]
- #only one set is present...
- if len(self.plots[0].vectors) != 2:
- return plot
+ 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']
- #multiplier is 1...
- if (self.config['force_multiplier']==1):
- return plot
+ new[:,-1] = z_data - d_data / k
+ params['curve'].data[params['block']] = new
- 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']
+class generalvclampCommands(object):
- 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