Update PolymerFitCommand to use flexible column names.

This allows you to fit multiple WLCs, etc. (by changing the 'output
tension column' name), so you can fit multiple peaks and/or multiple models.

diff --git a/hooke/plugin/polymer_fit.py b/hooke/plugin/polymer_fit.py
index 09b9909f2365851dcb129bfb7a716ca9d7063a62..2bdb440ac241361a8a94bd11279290304c954d17 100644 (file)
--- a/hooke/plugin/polymer_fit.py
+++ b/hooke/plugin/polymer_fit.py
@@ -38,8 +38,9 @@ from ..command import Command, Argument, Failure
 from ..config import Setting
 from ..curve import Data
 from ..plugin import Plugin
-from ..util.fit import PoorFit, ModelFitter
 from ..util.callback import is_iterable
+from ..util.fit import PoorFit, ModelFitter
+from ..util.si import join_data_label, split_data_label
 from .curve import CurveArgument
 from .vclamp import scale
 
@@ -945,6 +946,26 @@ approach/retract force curve, `0` selects the approaching curve and
                 Argument(name='bounds', type='point', optional=False, count=2,
                          help="""
 Indicies of points bounding the selected data.
+""".strip()),
+                Argument(name='input distance column', type='string',
+                         default='cantilever adjusted extension (m)',
+                         help="""
+Name of the column to use as the surface positioning 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 tension column', type='string',
+                         default='polymer tension',
+                         help="""
+Name of the column (without units) to use as the polymer tension output.
+""".strip()),
+                Argument(name='fit parameters info name', type='string',
+                         default='surface deflection offset',
+                         help="""
+Name (without units) for storing the fit parameters in the `.info` dictionary.
 """.strip()),
                 ],
             help=self.__doc__, plugin=plugin)
@@ -961,14 +982,17 @@ Indicies of points bounding the selected data.
         new = Data((data.shape[0], data.shape[1]+1), dtype=data.dtype)
         new.info = copy.deepcopy(data.info)
         new[:,:-1] = data
-        new.info['columns'].append('%s tension (N)' % model)  # TODO: WLC fit for each peak, etc.
+        new.info['columns'].append(
+            join_data_label(params['output tension column'], 'N'))
         z_data = data[:,data.info['columns'].index(
-                'cantilever adjusted extension (m)')]
-        d_data = data[:,data.info['columns'].index('deflection (N)')]
+                params['input distance column'])]
+        d_data = data[:,data.info['columns'].index(
+                params['input deflection column'])]
         start,stop = params['bounds']
         tension_data,ps = self.fit_polymer_model(
             params['curve'], z_data, d_data, start, stop, outqueue)
-        new.info['%s polymer fit parameters' % model] = ps
+        new.info[params['fit parameters info name']] = ps
+        new.info[params['fit parameters info name']]['model'] = model
         new[:,-1] = tension_data
         params['curve'].data[params['block']] = new
 

diff --git a/hooke/plugin/vclamp.py b/hooke/plugin/vclamp.py
index 77887db22a6b14894506a20cc15db038a34cb7f6..a676e31ba9415fe0cf90563afb4a904950d52f0a 100644 (file)
--- a/hooke/plugin/vclamp.py
+++ b/hooke/plugin/vclamp.py
@@ -284,7 +284,7 @@ Name (without units) for storing the deflection offset in the `.info` dictionary
                 Argument(name='fit parameters info name', type='string',
                          default='surface deflection offset',
                          help="""
-Name (without units) for storing the deflection offset in the `.info` dictionary.
+Name (without units) for storing fit parameters in the `.info` dictionary.
 """.strip()),
                 ],
             help=self.__doc__, plugin=plugin)