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Revision 83 - Directory Listing
Modified Tue Mar 18 00:16:14 2014 UTC (2 years, 1 month ago) by clausted

Revision 82 - Directory Listing
Modified Tue Mar 18 00:11:22 2014 UTC (2 years, 1 month ago) by clausted
Inside comments, add new potential features that still need testing. 1) Read Plexera data analysis SAN file format. 2) Concatenate ba objects.
Revision 81 - Directory Listing
Modified Sat Feb 1 00:29:25 2014 UTC (2 years, 2 months ago) by clausted
No comment.
Revision 80 - Directory Listing
Modified Sat Feb 1 00:27:02 2014 UTC (2 years, 2 months ago) by clausted
Check in script to test tutorials.
Revision 79 - Directory Listing
Modified Sat Feb 1 00:25:03 2014 UTC (2 years, 2 months ago) by clausted
Updated tutorial01 so it is now checked by doctest.  It contains new figures and examples.
Revision 78 - Directory Listing
Modified Sat Feb 1 00:20:58 2014 UTC (2 years, 2 months ago) by clausted
Less verbose mclma() output.
Revision 77 - Directory Listing
Modified Wed Dec 4 07:39:26 2013 UTC (2 years, 4 months ago) by clausted
Activate readclamp() function.
Revision 76 - Directory Listing
Modified Thu Nov 21 07:11:45 2013 UTC (2 years, 5 months ago) by clausted
Insert comments regarding reading files exported by Plexera's data analysis module.
Revision 75 - Directory Listing
Modified Thu Mar 7 00:02:34 2013 UTC (3 years, 1 month ago) by clausted
Improve io_module.readicmtxt() so that it will work on files containing blank lines. 
Revision 74 - Directory Listing
Modified Mon Aug 20 23:13:37 2012 UTC (3 years, 8 months ago) by clausted
Utilize Numpy genfromtxt() to simplify readcsv().  Might want to deprecate TsvTable.
Revision 73 - Directory Listing
Modified Mon Aug 20 19:38:52 2012 UTC (3 years, 8 months ago) by clausted
Created class TsvTable to convert between strings and lists.
This will help with CSV or TSV file import and export.
Changed function readcsv() to use this class.
The string form has data in columns separated by a delimiter.
The list form is a list of lists of strings like data[column][row]
Revision 72 - Directory Listing
Modified Sat Aug 18 01:40:04 2012 UTC (3 years, 8 months ago) by clausted
Add example-20spot.gal and example-csv.csv files.
Add class TsvTable to io_module.py; it will be used to simplify data import/export.
Revision 71 - Directory Listing
Modified Fri Aug 17 18:58:07 2012 UTC (3 years, 8 months ago) by clausted
Add example code to most io_module docstrings for doctest.
Put some more example files in exampledata folder.
Revision 70 - Directory Listing
Modified Wed Aug 15 19:47:15 2012 UTC (3 years, 8 months ago) by clausted
Make automatic code testing of every module available by running `python osprai_one.py`
Revision 69 - Directory Listing
Modified Wed May 16 18:00:28 2012 UTC (3 years, 11 months ago) by clausted
Change mdl_module.py range() to xrange() to increase speeds 5%.
Revision 68 - Directory Listing
Modified Fri May 11 22:43:32 2012 UTC (3 years, 11 months ago) by clausted
Add _demo function to support more testing.  Invoke it with 'python mdl_module.py demo'.
Baseline stabilization phase of sensorgrams now modelled with a linear regression instead of running average.
Revision 67 - Directory Listing
Modified Thu Apr 26 00:15:50 2012 UTC (4 years ago) by clausted
Fix bug in numbering ROIs in io_module.readicmtext().
Enhance vu_module.dualgraph() to automatically show modeled data along with read data.
Increase running average length in mdl_module; this isn't a good solution.
Change private function names from double-undescore to single-underscore prefixes.
Revision 66 - Directory Listing
Modified Thu Oct 13 19:49:53 2011 UTC (4 years, 6 months ago) by clausted
Add methods BiosensorArray.save(filename) and .load(filename) which save serialized data files with the sba extension.
Revision 65 - Directory Listing
Modified Fri May 20 16:33:02 2011 UTC (4 years, 11 months ago) by clausted
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 - Directory Listing
Modified Fri May 20 00:27:06 2011 UTC (4 years, 11 months ago) by clausted
More doctests in docstrings.
Revision 63 - Directory Listing
Modified Thu May 19 21:45:15 2011 UTC (4 years, 11 months ago) by clausted
Update html manual.
Revision 62 - Directory Listing
Modified Thu May 19 21:41:02 2011 UTC (4 years, 11 months ago) by clausted
Add readme.txt.
Revision 61 - Directory Listing
Modified Thu May 19 21:39:02 2011 UTC (4 years, 11 months ago) by clausted
Update docstrings so html looks nice.
Revision 60 - Directory Listing
Modified Thu May 19 20:13:13 2011 UTC (4 years, 11 months ago) by clausted
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 59 - Directory Listing
Modified Wed May 11 21:27:16 2011 UTC (4 years, 11 months ago) by clausted
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 - Directory Listing
Modified Wed May 11 21:25:10 2011 UTC (4 years, 11 months ago) by clausted
Updated docstring usage examples for doctest.
Revision 57 - Directory Listing
Modified Tue Apr 19 23:11:55 2011 UTC (5 years ago) by clausted
We are starting to implement automatic code testing using doctest.  The example code in the main docstring of cal_module was modified for compliance.
Revision 56 - Directory Listing
Modified Mon Mar 21 23:51:57 2011 UTC (5 years, 1 month ago) by clausted
Change to field names printed by writebiosensor() function.
Revision 55 - Directory Listing
Modified Tue Feb 22 00:27:41 2011 UTC (5 years, 2 months ago) by clausted
Improve mdl_module to avoid SPR responses that overshoot Rmax.
Revision 54 - Directory Listing
Modified Wed Feb 16 21:29:02 2011 UTC (5 years, 2 months ago) by clausted
Added fit_module and mdl_module to sphinx documentation.
Revision 53 - Directory Listing
Modified Wed Feb 16 01:56:39 2011 UTC (5 years, 2 months ago) by clausted
Add mdl_module documentation.  Also add sphinx html output to svn repository.
Revision 52 - Directory Listing
Modified Fri Feb 11 22:11:13 2011 UTC (5 years, 2 months ago) by clausted
Add some hyperlinks to the documentation.
Revision 51 - Directory Listing
Modified Wed Feb 9 01:09:05 2011 UTC (5 years, 2 months ago) by clausted
Fix minor docstring error.
Revision 50 - Directory Listing
Modified Wed Feb 9 00:32:35 2011 UTC (5 years, 2 months ago) by clausted
Remove deprecated matplotlib graph from ba_class.  Other minor changes.
Revision 49 - Directory Listing
Modified Tue Feb 8 01:38:34 2011 UTC (5 years, 2 months ago) by clausted
Add readcsv() function to io_module since sometimes we might have data in a spreadsheet with the left column containing time data and the rest of the columns containing sensorgram data.  
Add a flattenlist() function to cal_module.  It might be useful when using the ba.roi.bgroi property. Sometimes it is a single number, but sometimes we'd like it to be a list of roi numbers.  
Revision 48 - Directory Listing
Modified Fri Feb 4 19:09:24 2011 UTC (5 years, 2 months ago) by clausted
Minor formatting.
Revision 47 - Directory Listing
Modified Fri Feb 4 19:06:37 2011 UTC (5 years, 2 months ago) by clausted
Changes only to the docstrings of four modules so that Sphinx can use them.  Update references in mainapi.rst.  
Revision 46 - Directory Listing
Modified Fri Feb 4 00:29:01 2011 UTC (5 years, 2 months ago) by clausted
Update the sphinx documentation.  Add a new file called mainapi.rst to join tutorial01.rst and index.rst.  
Revision 45 - Directory Listing
Modified Thu Feb 3 02:52:40 2011 UTC (5 years, 2 months ago) by clausted
Create a reST version of the tutorial, called tutorial01.rst, based on a html version.  Add a reference to it in index.rst. 
Revision 44 - Directory Listing
Modified Wed Feb 2 22:17:09 2011 UTC (5 years, 2 months ago) by clausted
First, all public functions now have a standard format for their docstrings.  They use reStructuredText and symbols recognized by Sphinx automatic documentation. More comments describing internal design is placed at the end of the function.
Second, functions that do not need to be public have been made private by prefixing double-underscore to their names.  This will help prevent name collisions in the future and it also serves to exclude them from the Sphinx autodocumentation.
Revision 43 - Directory Listing
Modified Wed Feb 2 01:11:43 2011 UTC (5 years, 2 months ago) by clausted
Fix debian package name; change scipy to python-scipy.
Revision 42 - Directory Listing
Modified Tue Feb 1 08:07:06 2011 UTC (5 years, 3 months ago) by clausted
Begin to use Sphinx and reStructuredText for documentation.  This provides comprehensive documentation as well as automatic API documentation.  This does not preclude the use of Epydoc, another simple autodocumentation tool.
Revision 41 - Directory Listing
Modified Tue Jan 18 00:35:23 2011 UTC (5 years, 3 months ago) by clausted
Moved old data class "SPRdataclass" and accompanying surface interaction model modules to /models2010 subdirectory.  The plan is to implement these models for use with the "ba_class" and the modules in the parent directory.  

Should all the models be added to mdl_module or should they each go in their own module?  I am undecided.  
Revision 40 - Directory Listing
Modified Tue Jan 18 00:22:07 2011 UTC (5 years, 3 months ago) by clausted
Move two html documentation files into /help subdirectory.
Revision 39 - Directory Listing
Modified Tue Jan 18 00:12:02 2011 UTC (5 years, 3 months ago) by clausted
Moved example data files into /exampledata 
Revision 38 - Directory Listing
Modified Tue Jan 18 00:10:49 2011 UTC (5 years, 3 months ago) by clausted
Move example data files to \exampledata 
Revision 37 - Directory Listing
Modified Tue Jan 18 00:01:49 2011 UTC (5 years, 3 months ago) by clausted
New folder "exampledata" will hold data files used for testing and for tutorial demonstrations.
Revision 36 - Directory Listing
Modified Sat Nov 20 01:12:26 2010 UTC (5 years, 5 months ago) by clausted
Add zerotime() and zerovalue() to cal_module for zeroing the initial values of sensorgrams.
Revision 35 - Directory Listing
Modified Thu Aug 19 07:31:59 2010 UTC (5 years, 8 months ago) by clausted
Updates to the documentation.  Mention the online help.  Add hyperlinks to SVN clients.
Revision 34 - Directory Listing
Modified Sat Jul 31 00:08:34 2010 UTC (5 years, 9 months ago) by clausted
Use CSS numbering to simulated the IPython prompt in the documentation. Added benefit: User can now select code in web browser and paste it into IPython--the prompt is left off.
Revision 33 - Directory Listing
Modified Fri Jul 23 19:08:00 2010 UTC (5 years, 9 months ago) by clausted
Added more documentation and the images figure05*.png.  This explains the mclma() curve fitting.
Revision 32 - Directory Listing
Modified Fri Jul 23 01:23:44 2010 UTC (5 years, 9 months ago) by clausted
Add a new directory to contain Osprai documentation files.  Help files consist of html and css.
Revision 31 - Directory Listing
Modified Tue Jul 13 09:51:41 2010 UTC (5 years, 9 months ago) by ywan
Removal of a temporary file used to test svn.
Revision 30 - Directory Listing
Modified Tue Jul 13 09:50:19 2010 UTC (5 years, 9 months ago) by ywan
just for test
Revision 29 - Directory Listing
Modified Thu May 20 01:14:55 2010 UTC (5 years, 11 months ago) by clausted
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 - Directory Listing
Modified Wed May 19 06:06:07 2010 UTC (5 years, 11 months ago) by clausted
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 - Directory Listing
Modified Wed May 19 01:49:52 2010 UTC (5 years, 11 months ago) by clausted
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 - Directory Listing
Modified Fri May 14 22:36:12 2010 UTC (5 years, 11 months ago) by clausted
Added mass-transport limitation model simple1to1_mtl.

Revision 25 - Directory Listing
Modified Wed Apr 28 20:22:24 2010 UTC (6 years ago) by rjaynes
Add py and obj files to allow modeling of more SPR experiments with converter and curvefitting modules.  This is the work of Yuhang Wan and Rui Hou.

1. In "converter.py": 
      Add the saving and reading function for the sprclass data object.
      Also add function "keyfile_read_fake" to provide default information for SPRit and ICM formats in case of the bug when do background_subtract.
      Fix the bugs in "background_subtract".
      Tested by DAM and ICM formats.
2. In model modules:
      "modelclass.py" is the parent class for all the other model classes that performs the theoretical simulating, loading and saving of the parameter or simulated data. Rui and I also add some other model modules like competing model, twostate model, parallel model, and the time variable concentrated models, where the simulated result is compared with Clamp's simulation to make sure the equations are correct. 
       The basicmodel and basicmodel_varyC class are tested. 
3. In "curvefitting.py":
      Add typical pipeline for operation. The examples are packed with the file. 
      Add function to show the Elapsed time for each fitting.
Revision 24 - Directory Listing
Modified Wed Apr 28 01:00:17 2010 UTC (6 years ago) by clausted
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 - Directory Listing
Modified Tue Apr 27 07:18:13 2010 UTC (6 years ago) by clausted
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 22 - Directory Listing
Modified Tue Apr 27 07:17:58 2010 UTC (6 years ago) by clausted
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 21 - Directory Listing
Modified Tue Apr 27 07:17:13 2010 UTC (6 years ago) by clausted
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 - Directory Listing
Modified Mon Apr 26 21:59:45 2010 UTC (6 years ago) by clausted
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 - Directory Listing
Modified Fri Apr 23 01:45:38 2010 UTC (6 years ago) by clausted
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 18 - Directory Listing
Modified Thu Apr 22 07:36:31 2010 UTC (6 years ago) by clausted
Add a simple 1to1 model function.
Revision 17 - Directory Listing
Modified Thu Apr 22 00:22:37 2010 UTC (6 years ago) by clausted
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 16 - Directory Listing
Modified Sun Apr 18 05:34:10 2010 UTC (6 years ago) by clausted
Fix bug in "Next" button script.
Revision 15 - Directory Listing
Modified Wed Apr 14 07:14:32 2010 UTC (6 years ago) by clausted
Bug fix.
Revision 14 - Directory Listing
Modified Wed Apr 14 00:40:11 2010 UTC (6 years ago) by clausted
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 13 - Directory Listing
Modified Tue Apr 13 06:48:56 2010 UTC (6 years ago) by clausted
Fixed bugs in cal_module and ba_class where arrays of zeros--empty ROIs--would cause errors.
Revision 12 - Directory Listing
Modified Tue Apr 13 01:33:13 2010 UTC (6 years ago) by clausted
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 - Directory Listing
Modified Mon Apr 12 22:59:57 2010 UTC (6 years ago) by clausted
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 10 - Directory Listing
Modified Mon Apr 12 18:33:59 2010 UTC (6 years ago) by clausted
Add example-biosensor.txt as a convenience for testing.
Revision 9 - Directory Listing
Modified Sat Apr 10 00:21:02 2010 UTC (6 years ago) by clausted
Add readbiosensor() and writebiosensor() capabilities to io_module.  
Revision 8 - Directory Listing
Modified Fri Apr 9 17:18:59 2010 UTC (6 years ago) by clausted
Add four example SPR data files to help in testing code.  --CGL
Revision 7 - Directory Listing
Modified Fri Apr 9 17:11:42 2010 UTC (6 years ago) by clausted
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.
Revision 6 - Directory Listing
Modified Fri Apr 9 16:52:52 2010 UTC (6 years ago) by clausted
Added CONSTANTS to represent data file type identification integers.  These should be used throughout the code in the future to make it more readable.  Also added some default injection data to make it possible to convert a SPRit file to a CLAMP file without having an Analyte/injection file.  Also note a changed dictionary key IDcal->ID in one instance. --CGL
Revision 5 - Directory Listing
Modified Wed Apr 7 06:46:26 2010 UTC (6 years ago) by clausted
Changes made to allow use with Linux.  Can now read SPRit and output Clamp formats.  Replace == and != with "in" and "not in" string comparisons.  Change IDcal to ID in line 834.  Add function "method_read_fake" to provide default information.  Change WindowsError exception to OSError exception.  Allow user to specify default pathway for saving files by entering null string "".
Revision 4 - Directory Listing
Modified Tue Apr 6 06:38:33 2010 UTC (6 years ago) by clausted
Example input data files for testing purposes.
Revision 3 - Directory Listing
Modified Tue Apr 6 05:40:47 2010 UTC (6 years ago) by clausted
Functions in converter are renamed to conform to python PEP8 style.  Some uppercase names have been made lowercase.
Revision 2 - Directory Listing
Modified Tue Apr 6 05:35:46 2010 UTC (6 years ago) by clausted
Initial check-in of the html manual for converter.py.
Revision 1 - Directory Listing
Added Wed Mar 17 05:34:43 2010 UTC (6 years, 1 month ago) by clausted
Initial import of Osprai project