Add 'scaled column addition' command.

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

diff --git a/hooke/plugin/vclamp.py b/hooke/plugin/vclamp.py
index d741173da573ebf2dcc6fad033d239e7cf766b55..c6c57344c685b1345851ae6fe077b61f37dc2c96 100644 (file)
--- a/hooke/plugin/vclamp.py
+++ b/hooke/plugin/vclamp.py
@@ -102,7 +102,7 @@ Minimum `fit-contact-slope/guessed-contact-slope` ratio for a "good" fit.
         """
         p = params  # convenient alias
         rNC_ignore = self.info['ignore non-contact before index']
-        if self.info['force zero non-contact slope'] == True:
+        if self.info['force zero non-contact slope'] is True:
             p = list(p)
             p.append(0.)  # restore the non-contact slope parameter
         r2 = numpy.round(abs(p[2]))
@@ -296,6 +296,11 @@ point (for the `wtk` algorithm).
                          help="""
 As an alternative to 'ignore index', ignore after the last peak in the
 peak list stored in the `.info` dictionary.
+""".strip()),
+                Argument(name='force zero non-contact slope', type='bool',
+                         default=False, count=1,
+                         help="""
+Fix the fitted non-contact slope at zero.
 """.strip()),
                 Argument(name='distance info name', type='string',
                          default='surface distance offset',
@@ -476,7 +481,8 @@ Name (without units) for storing fit parameters in the `.info` dictionary.
         if reverse == True:    # approaching, contact region on the right
             d_data = d_data[::-1]
         s = SurfacePositionModel(d_data, info={
-                'force zero non-contact slope':True},
+                'force zero non-contact slope':
+                    params['force zero non-contact slope']},
                                  rescale=True)
         for argument in self._wtk_fit_check_arguments:
             s.info[argument.name] = params[argument.name]
@@ -494,6 +500,10 @@ Name (without units) for storing fit parameters in the `.info` dictionary.
             s.info['ignore non-contact before index'] = ignore_index
         offset,contact_slope,surface_index,non_contact_slope = s.fit(
             outqueue=outqueue)
+        deflection_offset = offset + contact_slope*surface_index
+        delta_pos_per_point = z_data[1] - z_data[0]
+        contact_slope /= delta_pos_per_point  # ddef/point -> ddev/dpos
+        non_contact_slope /= delta_pos_per_point
         info = {
             'offset': offset,
             'contact slope': contact_slope,
@@ -501,7 +511,6 @@ Name (without units) for storing fit parameters in the `.info` dictionary.
             'non-contact slope': non_contact_slope,
             'reversed': reverse,
             }
-        deflection_offset = offset + contact_slope*surface_index,
         if reverse == True:
             surface_index = len(d_data)-1-surface_index
         return (numpy.round(surface_index), deflection_offset, info)
@@ -535,6 +544,7 @@ Name of the spring constant in the `.info` dictionary.
     def _run(self, hooke, inqueue, outqueue, params):
         self._add_to_command_stack(params)
         params = self._setup_params(hooke=hooke, params=params)
+        # TODO: call .curve.ScaledColumnAdditionCommand
         def_data = self._get_column(hooke=hooke, params=params,
                                     column_name='deflection column')
         out = def_data * def_data.info[params['spring constant info name']]