Use cantilever adjusted extension in polymer fitting.

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

diff --git a/hooke/plugin/flatfilt.py b/hooke/plugin/flatfilt.py
index ca9b1b89e8cc5ef761a6476b05877486f6999e0e..4e77f3cc647f8dc289c69af5efa93d166bfbd7f0 100644 (file)
--- a/hooke/plugin/flatfilt.py
+++ b/hooke/plugin/flatfilt.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
@@ -38,13 +38,14 @@ from multiprocessing import Queue
 from numpy import diff
 from scipy.signal.signaltools import medfilt
 
-from ..command import Command, Argument, Success, Failure
+from ..command import Command, Argument, Success, Failure, UncaughtException
 from ..config import Setting
 from ..experiment import VelocityClamp
 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
 
 
@@ -71,7 +72,7 @@ Minimum number of peaks for curve acceptance.
                           ('max cut', 0.2),
                           ('min deviations', 9.0),
                           ('min points', 4),
-                          ('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
@@ -121,9 +122,10 @@ class FlatPeaksCommand (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['blind window']:
+        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'])
         deriv = diff(median)
@@ -134,7 +136,7 @@ class FlatPeaksCommand (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.
         """
@@ -142,17 +144,17 @@ class FlatPeaksCommand (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:
+        for i,block in enumerate(curve.data):
             if block.info['name'].startswith('retract'):
                 data = block
                 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:
@@ -196,16 +198,22 @@ class FlatFilterCommand (FilterCommand):
         self.arguments.extend(plugin._arguments)
 
     def filter(self, curve, hooke, inqueue, outqueue, params):
+        params['curve'] = curve
         inq = Queue()
         outq = Queue()
         filt_command = [c for c in hooke.commands
                         if c.name=='flat filter peaks'][0]
         filt_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) >= int(params['min peaks'])