.__setup_params() -> ._setup_params() in hooke/plugin/*.py.

[hooke.git] / hooke / plugin / flatfilt.py

diff --git a/hooke/plugin/flatfilt.py b/hooke/plugin/flatfilt.py
index 2688bba32dff41b1b531463304de47188197d414..21665fecbc3e6412829deffdd39a123df69209f7 100644 (file)
--- a/hooke/plugin/flatfilt.py
+++ b/hooke/plugin/flatfilt.py
@@ -21,7 +21,7 @@
 # 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.
@@ -42,13 +42,13 @@ 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 ColumnAddingCommand
-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):
@@ -131,20 +131,20 @@ Name of the column to use as the deflection input.
             new_columns=[
                 ('output peak column', 'flat filter peaks', """
 Name of the column (without units) to use as the peak output.
-""".split()),
+""".strip()),
                 ],
             arguments=[
                 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.
+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):
-        params = self.__setup_params(hooke=hooke, params=params)
+        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')
@@ -165,12 +165,12 @@ dictionary.
                          values=peaks_to_mask(def_data, peaks) * def_data)
         outqueue.put(peaks)
 
-    def __setup_params(self, hooke, params):
+    def _setup_params(self, hooke, params):
         """Setup `params` from config and return the z piezo and
         deflection arrays.
         """
         curve = self._curve(hooke=hooke, params=params)
-        if curve.info['experiment'] != VelocityClamp:
+        if not isinstance(curve.info['experiment'], VelocityClamp):
             raise Failure('%s operates on VelocityClamp experiments, not %s'
                           % (self.name, curve.info['experiment']))
         for key,value in params.items():
@@ -181,8 +181,6 @@ dictionary.
         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):
@@ -215,10 +213,12 @@ class FlatFilterCommand (FilterCommand):
     def __init__(self, plugin):
         flat_peaks = [c for c in plugin._commands
                       if c.name == 'flat filter peaks'][0]
-        flat_peaks_arg_names = [a.name for a in flat_peaks.arguments]
+        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
+        arguments = flat_peaks_arguments + plugin_arguments
         super(FlatFilterCommand, self).__init__(
             plugin, name='flat filter playlist')
         self.arguments.extend(arguments)