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Revision 66 - (view) (annotate) - [select for diffs]
Modified Thu Oct 13 19:49:53 2011 UTC (8 years, 1 month ago) by clausted
File length: 11559 byte(s)
Diff to previous 65
Add methods BiosensorArray.save(filename) and .load(filename) which save serialized data files with the sba extension.
Revision 65 - (view) (annotate) - [select for diffs]
Modified Fri May 20 16:33:02 2011 UTC (8 years, 6 months ago) by clausted
File length: 10126 byte(s)
Diff to previous 64
Added much testing to all modules using docstrings and doctest.  To help this, I also added two optional parameters to mclma(), verbose and maxiter.  For example, use "mclma(rois, verbose=False, maxiter=99)" to run the regression up to 99 iterations without echoing progress to the standard output.

Revision 64 - (view) (annotate) - [select for diffs]
Modified Fri May 20 00:27:06 2011 UTC (8 years, 6 months ago) by clausted
File length: 10157 byte(s)
Diff to previous 61
More doctests in docstrings.
Revision 61 - (view) (annotate) - [select for diffs]
Modified Thu May 19 21:39:02 2011 UTC (8 years, 6 months ago) by clausted
File length: 9635 byte(s)
Diff to previous 59
Update docstrings so html looks nice.
Revision 59 - (view) (annotate) - [select for diffs]
Modified Wed May 11 21:27:16 2011 UTC (8 years, 6 months ago) by clausted
File length: 9547 byte(s)
Diff to previous 58
Work on doctest material for ba_class and cal_module.
Now ba_class has built-in 1:1 interaction model simulator.
This is used for testing functions and methods in this and other modules.
Also change bgset() function so zero refers to first ROI.
This is necessary for consistency--but old user scripts might need updating.
Revision 58 - (view) (annotate) - [select for diffs]
Modified Wed May 11 21:25:10 2011 UTC (8 years, 6 months ago) by clausted
File length: 9547 byte(s)
Diff to previous 50
Updated docstring usage examples for doctest.
Revision 50 - (view) (annotate) - [select for diffs]
Modified Wed Feb 9 00:32:35 2011 UTC (8 years, 9 months ago) by clausted
File length: 7591 byte(s)
Diff to previous 48
Remove deprecated matplotlib graph from ba_class.  Other minor changes.
Revision 48 - (view) (annotate) - [select for diffs]
Modified Fri Feb 4 19:09:24 2011 UTC (8 years, 10 months ago) by clausted
File length: 8821 byte(s)
Diff to previous 47
Minor formatting.
Revision 47 - (view) (annotate) - [select for diffs]
Modified Fri Feb 4 19:06:37 2011 UTC (8 years, 10 months ago) by clausted
File length: 8820 byte(s)
Diff to previous 28
Changes only to the docstrings of four modules so that Sphinx can use them.  Update references in mainapi.rst.  
Revision 28 - (view) (annotate) - [select for diffs]
Modified Wed May 19 06:06:07 2010 UTC (9 years, 6 months ago) by clausted
File length: 8162 byte(s)
Diff to previous 27
Changes to params dictionary.  Valid values for 'fixed' are 'fixed' 'float' or an integer.  True and False are no longer acceptable.  Now mutli-ROI curve fitting seems to work!
Revision 27 - (view) (annotate) - [select for diffs]
Modified Wed May 19 01:49:52 2010 UTC (9 years, 6 months ago) by clausted
File length: 8159 byte(s)
Diff to previous 17
New LMA function in fit_module allows us to simultaneously fit parameters to the data in several ROIs that share that parameter.  This is not yet fully tested.  More comments have been added to ba_class.  The __all__ variable has been added to osprai_one to assist the automatic documentation.
Revision 17 - (view) (annotate) - [select for diffs]
Modified Thu Apr 22 00:22:37 2010 UTC (9 years, 7 months ago) by clausted
File length: 6244 byte(s)
Diff to previous 13
Start work on curve fitting.  Added two properties, model and params, to ba.roi in ba_class.  Add mdl_module which will hold functions that model SPR interactions.  
Revision 13 - (view) (annotate) - [select for diffs]
Modified Tue Apr 13 06:48:56 2010 UTC (9 years, 7 months ago) by clausted
File length: 5833 byte(s)
Diff to previous 12
Fixed bugs in cal_module and ba_class where arrays of zeros--empty ROIs--would cause errors.
Revision 12 - (view) (annotate) - [select for diffs]
Modified Tue Apr 13 01:33:13 2010 UTC (9 years, 7 months ago) by clausted
File length: 5710 byte(s)
Diff to previous 9
Addition of cal_module to provide a calibration tool and related features.  Added the time2val function to the ba class.  It has a bug now, but it will be useful for the calibration tool.
Revision 9 - (view) (annotate) - [select for diffs]
Modified Sat Apr 10 00:21:02 2010 UTC (9 years, 8 months ago) by clausted
File length: 5440 byte(s)
Diff to previous 7
Add readbiosensor() and writebiosensor() capabilities to io_module.  
Revision 7 - (view) (annotate) - [select for diffs]
Added Fri Apr 9 17:11:42 2010 UTC (9 years, 8 months ago) by clausted
File length: 6934 byte(s)
Initial addition of ba_class, an alternative to SPRdataclass.  This class, ba or Biosensor Array, has one internal structure rather than different internal structures depending on whether SPRit or Biacore or other data was imported.  This makes the code smaller and more readable.  It provides default values, usually 0 or null text, that make it easier to import and export different file formats.  We also add io_module to provide import and export features.  We also add test.py as a convenience for testing and demonstration.

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