From: W. Trevor King Date: Wed, 11 Aug 2010 21:11:18 +0000 (-0400) Subject: Updated FlatPeaksCommand to ColumnAddingCommand. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=5785ae8b9ceb51c796df46c7831520cb196ebed4;p=hooke.git Updated FlatPeaksCommand to ColumnAddingCommand. --- diff --git a/hooke/plugin/flatfilt.py b/hooke/plugin/flatfilt.py index ed08a34..7c0b534 100644 --- a/hooke/plugin/flatfilt.py +++ b/hooke/plugin/flatfilt.py @@ -35,15 +35,15 @@ See Also 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.curve import ColumnAddingCommand from ..plugin.playlist import FilterCommand from ..util.fit import PoorFit from ..util.peak import (find_peaks, peaks_to_mask, @@ -84,33 +84,6 @@ Minimum number of peaks for curve acceptance. 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 list of peaks in the `.info` dictionary. -""".strip()), - ]) self._commands = [FlatPeaksCommand(self), FlatFilterCommand(self)] def dependencies(self): @@ -120,7 +93,7 @@ Name for storing the list of peaks in the `.info` dictionary. return self._settings -class FlatPeaksCommand (Command): +class FlatPeaksCommand (ColumnAddingCommand): """Detect peaks in velocity clamp data using noise statistics. Notes @@ -144,63 +117,73 @@ class FlatPeaksCommand (Command): # 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. +""".split()), + ], arguments=[ - CurveArgument, + Argument(name='peak info name', type='string', + default='flat filter peaks', + help=""" +Name (without units) 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']) + 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'] + curve = self._curve(hooke=hooke, params=params) 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'])] for key,value in params.items(): if value == None: # 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) + params['peak info name'] = join_data_label( + params['peak info name'], 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): @@ -228,7 +211,7 @@ class FlatFilterCommand (FilterCommand): def __init__(self, plugin): super(FlatFilterCommand, self).__init__( plugin, name='flat filter playlist') - self.arguments.extend(plugin._arguments) + self.arguments.extend(plugin._arguments) # TODO: curve & block arguments def filter(self, curve, hooke, inqueue, outqueue, params): params['curve'] = curve diff --git a/test/flat_filter_peaks.py b/test/flat_filter_peaks.py new file mode 100644 index 0000000..fd8a578 --- /dev/null +++ b/test/flat_filter_peaks.py @@ -0,0 +1,51 @@ +# Copyright (C) 2010 W. Trevor King +# +# 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 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 +# . + +""" +>>> from hooke.hooke import Hooke, HookeRunner +>>> h = Hooke() +>>> r = HookeRunner() +>>> h = r.run_lines(h, ['load_playlist test/data/test']) # doctest: +ELLIPSIS + +Success + +>>> h = r.run_lines(h, +... ['zero_surface_contact_point --block retract'] +... ) # doctest: +ELLIPSIS, +REPORT_UDIFF +{'info':...} +Success + +>>> h = r.run_lines(h, ['flat_filter_peaks --block retract'] +... ) # doctest: +ELLIPSIS +[] +Success + +>>> curve = h.playlists.current().current() +>>> retract = curve.data[-1] +>>> retract.info['flat filter peaks (m)'] # doctest: +ELLIPSIS +[] +>>> retract.info['columns'] +['z piezo (m)', 'deflection (m)', 'surface distance (m)', 'surface deflection (m)', 'flat filter peaks (m)'] +>>> retract[:5,-1] # doctest: +ELLIPSIS +Data([-0., -0., -0., -0., -0.]) +>>> retract[609:615,-1] # doctest: +ELLIPSIS +Data([ 0.000...e+00, 2.380...e-09, 9.747...e-10, + -2.266...e-10, 9.071...e-11, -0.000...e+00]) +>>> retract[-5:,-1] # doctest: +ELLIPSIS +Data([-0., -0., -0., -0., -0.]) +""" diff --git a/test/flat_filter.py b/test/flat_filter_playlist.py similarity index 100% rename from test/flat_filter.py rename to test/flat_filter_playlist.py