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Revision 65 - (view) (annotate) - [select for diffs]
Modified Fri May 20 16:33:02 2011 UTC (7 years, 2 months ago) by clausted
File length: 8958 byte(s)
Diff to previous 60
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 60 - (view) (annotate) - [select for diffs]
Modified Thu May 19 20:13:13 2011 UTC (7 years, 2 months ago) by clausted
File length: 7576 byte(s)
Diff to previous 29
First, add a function to model multiple (up to eight) injections called simple1to1_series().  Second, add functions to return dictionaries with default parameters, called simple1to1_def_params(), simple1to1_mtl_def_params(), and simple1to1_series_def_params().  Also add doctest examples to mdl_module.py.
Revision 29 - (view) (annotate) - [select for diffs]
Modified Thu May 20 01:14:55 2010 UTC (8 years, 2 months ago) by clausted
File length: 5417 byte(s)
Diff to previous 28
Add a parameter ('cofa') to the 1to1 models that represents a concentration factor.  This allows for easier analysis of a dilution series.  For example, if two ROIs contain data for the same sample but at a dilutions of 1:2 and 1:4, the set 'conc' value to the molar stock concentration and set the two 'cofa' values to 0.5 and 0.25.
Revision 28 - (view) (annotate) - [select for diffs]
Modified Wed May 19 06:06:07 2010 UTC (8 years, 3 months ago) by clausted
File length: 5218 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 (8 years, 3 months ago) by clausted
File length: 4503 byte(s)
Diff to previous 26
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 26 - (view) (annotate) - [select for diffs]
Modified Fri May 14 22:36:12 2010 UTC (8 years, 3 months ago) by clausted
File length: 2695 byte(s)
Diff to previous 24
Added mass-transport limitation model simple1to1_mtl.

Revision 24 - (view) (annotate) - [select for diffs]
Modified Wed Apr 28 01:00:17 2010 UTC (8 years, 3 months ago) by clausted
File length: 2656 byte(s)
Diff to previous 23
Added copyinterval() to cal_module.  This cuts out a slice of SPR data between two timepoints and puts it in a new ba object.  
Revision 23 - (view) (annotate) - [select for diffs]
Modified Tue Apr 27 07:18:13 2010 UTC (8 years, 3 months ago) by clausted
File length: 2585 byte(s)
Diff to previous 20
The new module osprai_one provides access to the important functions in all of the other modules.  Documentation has been started with osprai_one.html.
Revision 20 - (view) (annotate) - [select for diffs]
Modified Mon Apr 26 21:59:45 2010 UTC (8 years, 3 months ago) by clausted
File length: 2701 byte(s)
Diff to previous 19
Added clma(), a constrained LMA fitting function.  We can now set a lower and upper bound for fitting.  Be sure that the initial estimate is between, not at, the bounds.  It transforms the parameters using x1 = ((b-a)*tanh(x0)+b+a)/2 for the interval (a,b).  
Revision 19 - (view) (annotate) - [select for diffs]
Modified Fri Apr 23 01:45:38 2010 UTC (8 years, 3 months ago) by clausted
File length: 2702 byte(s)
Diff to previous 14
Introduction of the fit_module.  This provides ordinary Levenberg-Marquart curvefitting.  The user can choose which model parameters are fixed and which are allowed to float.  Next, we can add a constrained version.

Revision 14 - (view) (annotate) - [select for diffs]
Modified Wed Apr 14 00:40:11 2010 UTC (8 years, 4 months ago) by clausted
File length: 1320 byte(s)
Diff to previous 12
Added features to select time points for measuring binding responses and to output that data to a file or scatterplot.  Added the background subtraction feature to cal_module.  Also a few bug fixes. --CGL
Revision 12 - (view) (annotate) - [select for diffs]
Modified Tue Apr 13 01:33:13 2010 UTC (8 years, 4 months ago) by clausted
File length: 865 byte(s)
Diff to previous 11
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 11 - (view) (annotate) - [select for diffs]
Modified Mon Apr 12 22:59:57 2010 UTC (8 years, 4 months ago) by clausted
File length: 760 byte(s)
Diff to previous 9
Introduce vu_module.py for viewing ba objects.  This GUI uses Tk and has buttons to allow users to move through the sensorgrams six-at-a-time.  The traces can be dotted or continuous lines or both.  Specify two ba objects and the first will be dotted while the second will be continuous.  This could be useful for comparing real and simulated data. --CGL 
Revision 9 - (view) (annotate) - [select for diffs]
Modified Sat Apr 10 00:21:02 2010 UTC (8 years, 4 months ago) by clausted
File length: 595 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 (8 years, 4 months ago) by clausted
File length: 525 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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