Close parenthesis on column append in DifferenceCommand

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

diff --git a/hooke/plugin/convfilt.py b/hooke/plugin/convfilt.py
index b85348a6feae57a679a2e41de7980a45b6f2e290..b8d967ae6be224b92d1252af6bd0503e0219b84d 100644 (file)
--- a/hooke/plugin/convfilt.py
+++ b/hooke/plugin/convfilt.py
@@ -7,15 +7,15 @@
 #
 # 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
@@ -45,6 +45,7 @@ from ..plugin import Plugin, argument_to_setting
 from ..plugin.curve import CurveArgument
 from ..plugin.playlist import FilterCommand
 from ..plugin.vclamp import scale
+from ..util.fit import PoorFit
 from ..util.peak import find_peaks, find_peaks_arguments, Peak, _kwargs
 
 
@@ -54,7 +55,7 @@ class ConvFiltPlugin (Plugin):
     def __init__(self):
         super(ConvFiltPlugin, self).__init__(name='convfilt')
         self._arguments = [ # for Command initialization
-            Argument('convolution', type='float', count='-1',
+            Argument('convolution', type='float', count=-1,
                      default=[11.0]+[-1.0]*11, help="""
 Convolution vector roughly matching post-peak cantilever rebound.
 This should roughly match the shape of the feature you're looking for.
@@ -74,7 +75,7 @@ Minimum number of peaks for curve acceptance.
                           ('max cut', 0.2),
                           ('min deviations', 5.0),
                           ('min points', 1),
-                          ('see double', 10e-9),
+                          ('see double', 10), # TODO: points vs. meters. 10e-9),
                           ]:
             argument = [a for a in self._arguments if a.name == key][0]
             argument.default = value
@@ -130,7 +131,7 @@ class ConvolutionPeaksCommand (Command):
             help=self.__doc__, plugin=plugin)
 
     def _run(self, hooke, inqueue, outqueue, params):
-        z_data,d_data,params = self._setup(params)
+        z_data,d_data,params = self._setup(hooke, params)
         start_index = 0
         while z_data[start_index] < params['bind window']:
             start_index += 1
@@ -144,7 +145,7 @@ class ConvolutionPeaksCommand (Command):
             peak.index += start_index
         outqueue.put(peaks)
 
-    def _setup(self, params):
+    def _setup(self, hooke, params):
         """Setup `params` from config and return the z piezo and
         deflection arrays.
         """
@@ -152,9 +153,9 @@ class ConvolutionPeaksCommand (Command):
         if curve.info['experiment'] != VelocityClamp:
             raise Failure('%s operates on VelocityClamp experiments, not %s'
                           % (self.name, curve.info['experiment']))
-        for col in ['surface z piezo (m)', 'deflection (N)']:
+        for col in ['surface distance (m)', 'deflection (N)']:
             if col not in curve.data[0].info['columns']:
-                scale(curve)
+                scale(hooke, curve)
         data = None
         for block in curve.data:
             if block.info['name'].startswith('retract'):
@@ -162,7 +163,7 @@ class ConvolutionPeaksCommand (Command):
                 break
         if data == None:
             raise Failure('No retraction blocks in %s.' % curve)
-        z_data = data[:,data.info['columns'].index('surface z piezo (m)')]
+        z_data = data[:,data.info['columns'].index('surface distance (m)')]
         if 'flattened deflection (N)' in data.info['columns']:
             params['deflection column name'] = 'flattened deflection (N)'
         else:
@@ -204,16 +205,22 @@ class ConvolutionFilterCommand (FilterCommand):
         self.arguments.extend(plugin._arguments)
 
     def filter(self, curve, hooke, inqueue, outqueue, params):
+        params['curve'] = curve
         inq = Queue()
         outq = Queue()
         conv_command = [c for c in self.hooke.commands
                         if c.name=='convolution peaks'][0]
         conv_command.run(hooke, inq, outq, **params)
         peaks = outq.get()
+        if isinstance(peaks, UncaughtException) \
+                and isinstance(peaks.exception, PoorFit):
+            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)
         ret = outq.get()
         if not isinstance(ret, Success):
             raise ret
+        if params['min peaks'] == None: # Use configured default value.
+            params['min peaks'] = self.plugin.config['min peaks']
         return len(peaks) >= params['min peaks']