# License along with Hooke. If not, see
# <http://www.gnu.org/licenses/>.
-"""The ``flatfilt`` module provides :class:`~FlatFiltPlugin` and
+"""The ``flatfilt`` module provides :class:`FlatFiltPlugin` and
several associated :class:`~hooke.command.Command`\s for removing flat
(featureless) :mod:`~hooke.curve.Curve`\s from
:class:`~hooke.playlist.Playlist`\s.
See Also
--------
-:mod:`~hooke.plugin.convfilt` for a convolution-based filter for
-:class:`~hooke.experiment.VelocityClamp` experiments.
+:mod:`~hooke.plugin.convfilt` for a convolution-based filter.
"""
import copy
from Queue import Queue
-from numpy import diff
+from numpy import absolute, diff
from scipy.signal.signaltools import medfilt
-from ..command import Command, Argument, Success, Failure, UncaughtException
+from ..command import Argument, Success, Failure, UncaughtException
from ..config import Setting
from ..curve import Data
-from ..experiment import VelocityClamp
-from ..plugin import Plugin, argument_to_setting
-from ..plugin.curve import CurveArgument
-from ..plugin.playlist import FilterCommand
from ..util.fit import PoorFit
from ..util.peak import (find_peaks, peaks_to_mask,
find_peaks_arguments, Peak, _kwargs)
from ..util.si import join_data_label, split_data_label
+from . import Plugin, argument_to_setting
+from .curve import ColumnAddingCommand
+from .playlist import FilterCommand
class FlatFiltPlugin (Plugin):
self._settings.append(argument_to_setting(
self.setting_section, argument))
argument.default = None # if argument isn't given, use the config.
- self._arguments.extend([ # Non-configurable arguments
- Argument(name='retract block', type='string',
- default='retract',
- help="""
-Name of the retracting data block.
-""".strip()),
- Argument(name='input distance column', type='string',
- default='surface distance (m)',
- help="""
-Name of the column to use as the surface position 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 peak column', type='string',
- default='peak deflection',
- help="""
-Name of the column (without units) to use as the peak-maske deflection output.
-""".strip()),
- Argument(name='peak info name', type='string',
- default='flat filter peaks',
- help="""
-Name for storing the distance offset in the `.info` dictionary.
-""".strip()),
- ])
- self._commands = [FlatPeaksCommand(self), FlatFilterCommand(self)]
+ self._commands = [FlatPeaksCommand(self)]
+ # append FlatFilterCommand so it can steal arguments from
+ # FlatPeaksCommand.
+ self._commands.append(FlatFilterCommand(self))
def dependencies(self):
return ['vclamp']
return self._settings
-class FlatPeaksCommand (Command):
+class FlatPeaksCommand (ColumnAddingCommand):
"""Detect peaks in velocity clamp data using noise statistics.
Notes
# function, just detecting peaks.
super(FlatPeaksCommand, self).__init__(
name='flat filter peaks',
+ columns=[
+ ('distance column', 'surface distance (m)', """
+Name of the column to use as the surface position input.
+""".strip()),
+ ('deflection column', 'surface deflection (m)', """
+Name of the column to use as the deflection input.
+""".strip()),
+ ],
+ new_columns=[
+ ('output peak column', 'flat filter peaks', """
+Name of the column (without units) to use as the peak output.
+""".strip()),
+ ],
arguments=[
- CurveArgument,
+ Argument(name='peak info name', type='string',
+ default='flat filter peaks',
+ help="""
+Name for storing the list of peaks in the `.info` dictionary.
+""".strip()),
] + plugin_arguments,
help=self.__doc__, plugin=plugin)
def _run(self, hooke, inqueue, outqueue, params):
- data,block_index,z_data,d_data,params = self._setup(hooke, params)
- start_index = 0
- while (start_index < len(z_data)
- and z_data[start_index] < params['blind window']):
- start_index += 1
- median = medfilt(d_data[start_index:], params['median window'])
+ self._add_to_command_stack(params)
+ params = self._setup_params(hooke=hooke, params=params)
+ block = self._block(hooke=hooke, params=params)
+ dist_data = self._get_column(hooke=hooke, params=params,
+ column_name='distance column')
+ def_data = self._get_column(hooke=hooke, params=params,
+ column_name='deflection column')
+ start_index = absolute(dist_data-params['blind window']).argmin()
+ median = medfilt(def_data[start_index:], params['median window'])
deriv = diff(median)
peaks = find_peaks(deriv, **_kwargs(params, find_peaks_arguments,
argument_input_keys=True))
- d_name,d_unit = split_data_label(params['input deflection column'])
for i,peak in enumerate(peaks):
- peak.name = 'flat filter peak %d of %s' % (i, d_name)
+ peak.name = self._peak_name(params, i)
peak.index += start_index
- data.info[params['peak info name']] = peaks
-
- # Add a peak-masked deflection column.
- new = Data((data.shape[0], data.shape[1]+1), dtype=data.dtype)
- new.info = copy.deepcopy(data.info)
- new[:,:-1] = data
- d_name,d_unit = split_data_label(params['input deflection column'])
- new.info['columns'].append(
- join_data_label(params['output peak column'], d_unit))
- new[:,-1] = peaks_to_mask(d_data, peaks) * d_data
+ block.info[params['peak info name']] = peaks
+
+ self._set_column(hooke=hooke, params=params,
+ column_name='output peak column',
+ values=peaks_to_mask(def_data, peaks) * def_data)
outqueue.put(peaks)
- params['curve'].data[block_index] = new
- def _setup(self, hooke, params):
+ def _setup_params(self, hooke, params):
"""Setup `params` from config and return the z piezo and
deflection arrays.
"""
- curve = params['curve']
- if curve.info['experiment'] != VelocityClamp:
- raise Failure('%s operates on VelocityClamp experiments, not %s'
- % (self.name, curve.info['experiment']))
- data = None
- for i,block in enumerate(curve.data):
- if block.info['name'].startswith(params['retract block']):
- data = block
- block_index = i
- break
- if data == None:
- raise Failure('No retraction blocks in %s.' % curve)
- z_data = data[:,data.info['columns'].index(
- params['input distance column'])]
- d_data = data[:,data.info['columns'].index(
- params['input deflection column'])]
+ curve = self._curve(hooke=hooke, params=params)
for key,value in params.items():
- if value == None: # Use configured default value.
+ if value == None and key in self.plugin.config:
+ # Use configured default value.
params[key] = self.plugin.config[key]
# TODO: convert 'see double' from nm to points
- return (data, block_index, z_data, d_data, params)
+ name,def_unit = split_data_label(params['deflection column'])
+ params['output peak column'] = join_data_label(
+ params['output peak column'], def_unit)
+ return params
+
+ def _peak_name(self, params, index):
+ d_name,d_unit = split_data_label(params['deflection column'])
+ return 'flat filter peak %d of %s' % (index, d_name)
class FlatFilterCommand (FilterCommand):
FlatPeaksCommand : Underlying flat-based peak detection.
"""
def __init__(self, plugin):
+ flat_peaks = [c for c in plugin._commands
+ if c.name == 'flat filter peaks'][0]
+ flat_peaks_arguments = [a for a in flat_peaks.arguments
+ if a.name not in ['help', 'stack']]
+ flat_peaks_arg_names = [a.name for a in flat_peaks_arguments]
+ plugin_arguments = [a for a in plugin._arguments
+ if a.name not in flat_peaks_arg_names]
+ arguments = flat_peaks_arguments + plugin_arguments
super(FlatFilterCommand, self).__init__(
plugin, name='flat filter playlist')
- self.arguments.extend(plugin._arguments)
+ self.arguments.extend(arguments)
def filter(self, curve, hooke, inqueue, outqueue, params):
params['curve'] = curve
return False
if not (isinstance(peaks, list) and (len(peaks) == 0
or isinstance(peaks[0], Peak))):
- raise Failure('Expected a list of Peaks, not %s' % peaks)
+ raise Failure('Expected a list of Peaks, not %s: %s'
+ % (type(peaks), peaks))
ret = outq.get()
if not isinstance(ret, Success):
raise ret
projects / hooke.git / blobdiff