unfold-protein.git
12 years agoAdd .update-copyright.conf.
W. Trevor King [Fri, 11 May 2012 18:21:40 +0000 (14:21 -0400)]
Add .update-copyright.conf.

Use my update-copyright project to manage copyright blurbs.

http://pypi.python.org/pypi/update-copyright/

12 years agoChange my email address from drexel.edu to tremily.us.
W. Trevor King [Wed, 18 Apr 2012 17:24:54 +0000 (13:24 -0400)]
Change my email address from drexel.edu to tremily.us.

12 years agoUpdate unfold_protein to use the new pyafm.storage._load_afm.
W. Trevor King [Fri, 11 May 2012 17:42:47 +0000 (13:42 -0400)]
Update unfold_protein to use the new pyafm.storage._load_afm.

This is a messy commit to get my Git repo in sync with the version I'm
currently using in the lab, but most of the changes have to do with
the nested-config overhaul starting with pypiezo's:

  commit de497a3734372f5fa7c92d6ff7bdb6b2e327c345
  Author: W. Trevor King <wking@drexel.edu>
  Date:   Thu Mar 15 10:13:20 2012 -0400

    Optional config-based-setup for PiezoAxis, OutputChannel, and InputChannel.

    See the module docstring for details on why this is useful.

12 years agoRemove TemperatureConfig from unfold_protein.config.UnfoldCycleConfig.
W. Trevor King [Mon, 26 Mar 2012 18:53:32 +0000 (14:53 -0400)]
Remove TemperatureConfig from unfold_protein.config.UnfoldCycleConfig.

Replaced by pyafm.config.AFMConfig['temperature'].

12 years agoRemove unfold_protein.temperature (replaced by pyafm.temperature).
W. Trevor King [Mon, 26 Mar 2012 18:50:51 +0000 (14:50 -0400)]
Remove unfold_protein.temperature (replaced by pyafm.temperature).

12 years agoRemove unfold_protein.afm now that there is a configurable default AFM in pyafm.
W. Trevor King [Mon, 26 Mar 2012 18:32:02 +0000 (14:32 -0400)]
Remove unfold_protein.afm now that there is a configurable default AFM in pyafm.

Now you can use pyafm.storage.load_afm() and instead of hardcoding your
configuration in the unfold_protein.afm module.

12 years agoUpdate unfold.py config to show temp in Kelvin.
W. Trevor King [Wed, 25 Jan 2012 15:33:43 +0000 (10:33 -0500)]
Update unfold.py config to show temp in Kelvin.

By default, `calibcant.config.TemperatureConfig` assumes you'll give
temperatures in Celsius, but in
`unfold_python.temperature.Temperature.get_temperature`, we convert
the backend temperature from Celsius to Kelvin.

12 years agoAssorted plots and bug-fixes in unfolder.py.
W. Trevor King [Tue, 24 Jan 2012 13:08:42 +0000 (08:08 -0500)]
Assorted plots and bug-fixes in unfolder.py.

* Updated `ExceptionTooFar` plot and `Unfolder._plot` to use `FIGURE`
  and `_pyplot`.
* Fix configs used in `Unfolder._unfold`'s bit/meter conversions.
* Remove unrecognized keyword `dtype` from the `.astype` call.
* Reshape `out` so it is 2D (as required by `Piezo.ramp`).
* Don't force unfold log values to be integers.
* Fix filename generation in `Unfolder._save`.
* Removed trailing whitespace.

12 years agoMake ExceptionTooFar check more robust with .max().
W. Trevor King [Tue, 24 Jan 2012 13:02:08 +0000 (08:02 -0500)]
Make ExceptionTooFar check more robust with .max().

12 years agoStylistic cleanups in UnfoldScanner.move_far_from_surface.
W. Trevor King [Tue, 24 Jan 2012 12:59:04 +0000 (07:59 -0500)]
Stylistic cleanups in UnfoldScanner.move_far_from_surface.

12 years agoIncrease 'far' in ApproachConfig to 30 microns.
W. Trevor King [Tue, 24 Jan 2012 12:57:50 +0000 (07:57 -0500)]
Increase 'far' in ApproachConfig to 30 microns.

12 years agoRemove buggy self argument from Temperature self() call.
W. Trevor King [Mon, 23 Jan 2012 19:29:05 +0000 (14:29 -0500)]
Remove buggy self argument from Temperature self() call.

12 years agoMerge irrelevant "Update to data_logger v0.4." by dropping the changes.
W. Trevor King [Tue, 17 Jan 2012 22:53:03 +0000 (17:53 -0500)]
Merge irrelevant "Update to data_logger v0.4." by dropping the changes.

The new h5config framework no longer uses data_logger to locate or
save data.

12 years agoUpdate to use new h5config, pycomedi, etc.
W. Trevor King [Tue, 17 Jan 2012 22:49:26 +0000 (17:49 -0500)]
Update to use new h5config, pycomedi, etc.

12 years agoAdd .gitignore.
W. Trevor King [Tue, 17 Jan 2012 22:04:34 +0000 (17:04 -0500)]
Add .gitignore.

14 years agoUpdate to data_logger v0.4.
W. Trevor King [Tue, 9 Nov 2010 20:14:58 +0000 (15:14 -0500)]
Update to data_logger v0.4.

15 years agoAvoid banded non-contact region by reducing default stepsize.
W. Trevor King [Mon, 6 Jul 2009 20:23:26 +0000 (16:23 -0400)]
Avoid banded non-contact region by reducing default stepsize.

See bug 18dd6d0a-3c45-4aba-80da-fa32ffaaf5db for example banded data.
(plot deflection without lines to see why I call it "banded").  Reducing
the stepsize reduces the jolt on the cantilever, and reducing the
points-per-step accordingly means we don't have to change the
card-clock rate.  It might be worth adding "target-clock-rate" option,
and letting the stepsize be determined automatically (as an
alternative to setting the stepsize explicitly) but we'll
put that off for now...

15 years agoAdded README file.
W. Trevor King [Fri, 26 Jun 2009 18:55:20 +0000 (14:55 -0400)]
Added README file.

Also a bug/thoughts on packaging trouble (blocked by temperature).

15 years agoUpdated to work with newly bundled pizeo package.
W. Trevor King [Fri, 26 Jun 2009 18:32:20 +0000 (14:32 -0400)]
Updated to work with newly bundled pizeo package.

15 years agoAdded EFILE debugging output to ExceptionTooClose case.
W. Trevor King [Wed, 3 Jun 2009 19:22:41 +0000 (15:22 -0400)]
Added EFILE debugging output to ExceptionTooClose case.

15 years agoBegan versioning.
W. Trevor King [Wed, 3 Jun 2009 19:19:40 +0000 (15:19 -0400)]
Began versioning.