Update SurfaceContactCommand to use flexible column/info names.

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

diff --git a/hooke/plugin/vclamp.py b/hooke/plugin/vclamp.py
index 21f078a8c3bc82a8d7b14e17a17a8528662e24ba..40c1ecb543b20a697768e6b20171271d1780e117 100644 (file)
--- a/hooke/plugin/vclamp.py
+++ b/hooke/plugin/vclamp.py
@@ -35,6 +35,7 @@ from ..config import Setting
 from ..curve import Data
 from ..plugin import Plugin
 from ..util.fit import PoorFit, ModelFitter
+from ..util.si import join_data_label, split_data_label
 from .curve import CurveArgument
 
 
@@ -75,7 +76,7 @@ def scale(hooke, curve, block=None):
     return curve
 
 class SurfacePositionModel (ModelFitter):
-    """
+    """Bilinear surface position model.
 
     The bilinear model is symmetric, but the parameter guessing and
     sanity checks assume the contact region occurs for lower indicies
@@ -96,9 +97,6 @@ class SurfacePositionModel (ModelFitter):
     should be enough data in the off-surface region that interactions
     due to proteins, etc. will not seriously skew the fit in the
     off-surface region.
-
-
-    We guess
     """
     def model(self, params):
         """A continuous, bilinear model.
@@ -168,7 +166,6 @@ class SurfacePositionModel (ModelFitter):
 
         Notes
         -----
-
         We guess offset scale (:math:`p_0`) as one tenth of the total
         deflection range, the kink scale (:math:`p_2`) as one tenth of
         the total index range, the initial (contact) slope scale
@@ -234,14 +231,6 @@ class VelocityClampPlugin (Plugin):
 class SurfaceContactCommand (Command):
     """Automatically determine a block's surface contact point.
 
-    Uses the block's `z piezo (m)` and `deflection (m)` arrays.
-    Stores the contact parameters in `block.info`'s `surface distance
-    offset (m)` and `surface deflection offset (m)`.  Model-specific
-    fitting information is stored in `surface detection parameters`.
-
-    The adjusted data columns `surface distance (m)` and `surface
-    adjusted deflection (m)` are also added to the block.
-
     You can select the contact point algorithm with the creatively
     named `surface contact point algorithm` configuration setting.
     Currently available options are:
@@ -260,6 +249,41 @@ class SurfaceContactCommand (Command):
 Data block for which the force should be calculated.  For an
 approach/retract force curve, `0` selects the approaching curve and `1`
 selects the retracting curve.
+""".strip()),
+                Argument(name='input distance column', type='string',
+                         default='z piezo (m)',
+                         help="""
+Name of the column to use as the surface positioning input.
+""".strip()),
+                Argument(name='input deflection column', type='string',
+                         default='deflection (m)',
+                         help="""
+Name of the column to use as the deflection input.
+""".strip()),
+                Argument(name='output distance column', type='string',
+                         default='surface distance',
+                         help="""
+Name of the column (without units) to use as the surface positioning output.
+""".strip()),
+                Argument(name='output deflection column', type='string',
+                         default='surface deflection',
+                         help="""
+Name of the column (without units) to use as the deflection output.
+""".strip()),
+                Argument(name='distance info name', type='string',
+                         default='surface distance offset',
+                         help="""
+Name of the column (without units) for storing the distance offset in the `.info` dictionary.
+""".strip()),
+                Argument(name='deflection info name', type='string',
+                         default='surface deflection offset',
+                         help="""
+Name of the column (without units) for storing the deflection offset in the `.info` dictionary.
+""".strip()),
+                Argument(name='fit parameters info name', type='string',
+                         default='surface deflection offset',
+                         help="""
+Name of the column (without units) for storing the deflection offset in the `.info` dictionary.
 """.strip()),
                 ],
             help=self.__doc__, plugin=plugin)
@@ -274,18 +298,26 @@ selects the retracting curve.
         new = Data((data.shape[0], data.shape[1]+2), dtype=data.dtype)
         new.info = copy.deepcopy(data.info)
         new[:,:-2] = data
-        new.info['columns'].extend(
-            ['surface distance (m)', 'surface adjusted deflection (m)'])
-        z_data = data[:,data.info['columns'].index('z piezo (m)')]
-        d_data = data[:,data.info['columns'].index('deflection (m)')]
-        i,deflection_offset,ps = self.find_contact_point(
-            params['curve'], z_data, d_data, outqueue)
-        surface_offset = z_data[i]
-        new.info['surface distance offset (m)'] = surface_offset
-        new.info['surface deflection offset (m)'] = deflection_offset
-        new.info['surface detection parameters'] = ps
-        new[:,-2] = z_data - surface_offset
-        new[:,-1] = d_data - deflection_offset
+        name,dist_units = split_data_label(params['input distance column'])
+        name,def_units = split_data_label(params['input deflection column'])
+        new.info['columns'].extend([
+                join_data_label(params['output distance column'], dist_units),
+                join_data_label(params['output deflection column'], def_units),
+                ])
+        dist_data = data[:,data.info['columns'].index(
+                params['input distance column'])]
+        def_data = data[:,data.info['columns'].index(
+                params['input deflection column'])]
+        i,def_offset,ps = self.find_contact_point(
+            params['curve'], dist_data, def_data, outqueue)
+        dist_offset = dist_data[i]
+        new.info[join_data_label(params['distance info name'], dist_units
+                                 )] = dist_offset
+        new.info[join_data_label(params['deflection info name'], def_units
+                                 )] = def_offset
+        new.info[params['fit parameters info name']] = ps
+        new[:,-2] = dist_data - dist_offset
+        new[:,-1] = def_data - def_offset
         params['curve'].data[params['block']] = new
 
     def find_contact_point(self, curve, z_data, d_data, outqueue=None):