From: W. Trevor King <wking@drexel.edu>
Date: Sat, 28 Aug 2010 12:42:19 +0000 (-0400)
Subject: Document fit parameter extraction via PyYAML.
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=42967aa382f2a629371b71b5da716918effe32de;p=hooke.git

Document fit parameter extraction via PyYAML.
---

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 65d288e..f8f06c3 100644
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -308,9 +308,64 @@ ways.::
     hooke> remove_cantilever_from_extension --block retract
     hooke> flat_peaks_to_polymer_peaks --block retract
     hooke> polymer_fit_peaks --block retract
-    hooke> export_block --block retract --output myblock.dat
 
-See each command's `Help`_ for details.
+This stores the fit parameters in the block's
+:attr:`~hooke.curve.Data.info` dictionary (see each command's `Help`_
+for details).  To access the parameters, save the playlist,::
+
+    hooke> save_playlist --output mylist.hkp
+
+load it with PyYAML_::
+
+    $ python
+    >>> import yaml
+    >>> import hooke.util.yaml
+    >>> mylist = yaml.load(open('mylist.hkp', 'r'))
+
+navigate to your curve,::
+
+    >>> mylist.jump(1234)
+
+and extract your parameter.::
+
+    >>> mylist.current().data[1].info['polymer peak 0']['contour length (m)']
+    2.124...e-08
+
+You can also get a list of all available parameters::
+
+    >>> mylist.current().data[1].info['polymer peak 0'].keys()
+    ['model', 'contour length (m)', 'temperature (K)', 'fit',
+     'persistence length (m)']
+
+or just pprint_ the whole thing::
+
+    >>> from pprint import pprint
+    >>> pprint(mylist.current().data[1].info['polymer peak 0'])
+    {'contour length (m)': 2.1248220207858103e-08,
+     'fit': {'active fitted parameters': 3.7024307200788127,
+             'active parameters': 3.7024307200788127,
+             'convergence flag': 1,
+             'covariance matrix': None,
+             'data scale factor': 5.2716380732198972e-10,
+             'fitted parameters': -2.5663294148411571,
+             'info': {'fjac': None,
+                      'fvec': None,
+                      'ipvt': None,
+                      'nfev': 16,
+                      'qtf': None},
+             'initial parameters': [-0.69314718055994529],
+             'message': 'Both actual and predicted relative reductions in the sum of squares\n  are at most 0.000000',
+             'rescaled': True,
+             'scale': None},
+     'model': u'WLC',
+     'persistence length (m)': 4.0000000000000001e-10,
+     'temperature (K)': 301.0}
+
+.. _PyYAML: http://pyyaml.org/
+.. _pprint: http://docs.python.org/library/pprint.html
+
+.. todo:: UI access to block (and curve?) info dicts.  Someone should
+   make a tree-based object browser ;).
 
 Command stacks
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