pyafm.git
12 years agoMerge temperature.py from my unfold_protein repository.
W. Trevor King [Thu, 15 Mar 2012 18:51:49 +0000 (14:51 -0400)]
Merge temperature.py from my unfold_protein repository.

12 years agoAdd `steps` and `sleep` options to `move_just_onto_surface()`.
W. Trevor King [Thu, 15 Mar 2012 11:39:52 +0000 (07:39 -0400)]
Add `steps` and `sleep` options to `move_just_onto_surface()`.

This takes advantage of yesterday's pypiezo commit:

  commit b66d6dbcb8cd381cf7515a42ab0aee4a4841beb3
  Author: W. Trevor King <wking@drexel.edu>
  Date:   Wed Mar 14 16:18:23 2012 -0400

    Add `steps` and `sleep` options for gentler `jump()`s.

and I've bumped the minimum pypiezo version accordingly.

When I was running some calibrations yesterday, I could hear the piezo
clicking, and after the calibration the deflection was shifted half a
volt or so from the initial deflection.  I attribute this to the
violent piezo jumps shaking the cantilever chip from its original
position.  The wimpy spring-loaded wire clips used in the MultiMode
fluid cells probably aren't helping any either ;).

12 years agoUse stepper.single_step instead of stepper.step_relative in AFM methods.
W. Trevor King [Fri, 2 Mar 2012 21:22:08 +0000 (16:22 -0500)]
Use stepper.single_step instead of stepper.step_relative in AFM methods.

This avoids problems with steppers in full-step mode always rounding
the asked-for half step back to the current position.  The drawback to
the new approach is that we loose backlash protection when moving away
from the surface, but the surface fitting condition ...?

12 years agoFix deflection channel config extraction in AFM.move_just_onto_surface().
W. Trevor King [Tue, 28 Feb 2012 20:25:07 +0000 (15:25 -0500)]
Fix deflection channel config extraction in AFM.move_just_onto_surface().

12 years agoFix tremily -> blog.tremily in homepage URL in setup.py.
W. Trevor King [Tue, 28 Feb 2012 14:25:45 +0000 (09:25 -0500)]
Fix tremily -> blog.tremily in homepage URL in setup.py.

12 years agoUpdate URLs from einstein to tremily.
W. Trevor King [Wed, 22 Feb 2012 18:29:51 +0000 (13:29 -0500)]
Update URLs from einstein to tremily.

Also move link targets to the end of the README.

12 years agoComplete setpoint removal started with 1139d17967014ca0fe79773796dda182b3441f9f.
W. Trevor King [Mon, 23 Jan 2012 21:17:46 +0000 (16:17 -0500)]
Complete setpoint removal started with 1139d17967014ca0fe79773796dda182b3441f9f.

12 years agoDon't force integer formatting in AFM._check_target_deflection messages.
W. Trevor King [Mon, 23 Jan 2012 21:14:17 +0000 (16:14 -0500)]
Don't force integer formatting in AFM._check_target_deflection messages.

We're about to raise an exception anyway, so there's no need to be
overly picky here.

12 years agoAFM._check_target_deflection doesn't have access to `setpoint` in volts.
W. Trevor King [Mon, 23 Jan 2012 21:09:20 +0000 (16:09 -0500)]
AFM._check_target_deflection doesn't have access to `setpoint` in volts.

12 years agoFinish target_deflection -> deflection conversion started a few commits ago.
W. Trevor King [Mon, 23 Jan 2012 21:05:45 +0000 (16:05 -0500)]
Finish target_deflection -> deflection conversion started a few commits ago.

Original commit was e5d2a98f662eafacbb26598884f44ba4d3dc341f

12 years agoOops, ._deflection_channel is an AFMPiezo method.
W. Trevor King [Mon, 23 Jan 2012 21:03:22 +0000 (16:03 -0500)]
Oops, ._deflection_channel is an AFMPiezo method.

12 years agoChange AFM._check_target_deflection argument name to `deflection`.
W. Trevor King [Mon, 23 Jan 2012 21:00:23 +0000 (16:00 -0500)]
Change AFM._check_target_deflection argument name to `deflection`.

Also check for negative deflections.  It can't hurt ;).

12 years agoOops, remove trailing colon from `max_def = defc.get_maxdata():`.
W. Trevor King [Mon, 23 Jan 2012 20:55:22 +0000 (15:55 -0500)]
Oops, remove trailing colon from `max_def = defc.get_maxdata():`.

Sloppy copy/paste.

12 years agoOops, `def` is a reserved word in Python. Use `defc` instead.
W. Trevor King [Mon, 23 Jan 2012 20:53:04 +0000 (15:53 -0500)]
Oops, `def` is a reserved word in Python.  Use `defc` instead.

12 years agoAdd AFM._check_target_deflection to avoid approaching forever.
W. Trevor King [Mon, 23 Jan 2012 20:41:52 +0000 (15:41 -0500)]
Add AFM._check_target_deflection to avoid approaching forever.

Also use the deflection channel config to convert `setpoint` to bits,
instead of the output z channel config.

12 years agoOops, fix min_slope_position/min_slope_postion -> min_slope_ratio typo.
W. Trevor King [Mon, 23 Jan 2012 20:21:46 +0000 (15:21 -0500)]
Oops, fix min_slope_position/min_slope_postion -> min_slope_ratio typo.

I need to get more sleep ;).

12 years agoAdd min_slope_ratio argument to AFM.move_just_onto_surface.
W. Trevor King [Mon, 23 Jan 2012 20:02:10 +0000 (15:02 -0500)]
Add min_slope_ratio argument to AFM.move_just_onto_surface.

To match the following calibcant commit:

  commit 7c934e1f5f0838a42a7a0b1d5a392e3f0686e1c4
  Author: W. Trevor King <wking@drexel.edu>
  Date:   Mon Jan 23 14:41:10 2012 -0500

    Add min-slope-ratio option to BumpConfig.

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 agoBreak AFM.stepper_approach out of ._stepper_approach_again.
W. Trevor King [Tue, 17 Jan 2012 22:38:54 +0000 (17:38 -0500)]
Break AFM.stepper_approach out of ._stepper_approach_again.

12 years agoFix get -> get_temperature typo in AFM.get_temperature.
W. Trevor King [Fri, 13 Jan 2012 18:05:19 +0000 (13:05 -0500)]
Fix get -> get_temperature typo in AFM.get_temperature.

13 years agoImport missing SurfaceError from pypiezo.surface.
W. Trevor King [Fri, 30 Sep 2011 18:34:53 +0000 (14:34 -0400)]
Import missing SurfaceError from pypiezo.surface.

13 years agoImport missing FlatFit from pypiezo.surface.
W. Trevor King [Tue, 27 Sep 2011 20:30:04 +0000 (16:30 -0400)]
Import missing FlatFit from pypiezo.surface.

13 years agoUpdate config arguments to bit/volt/meter conversion functions.
W. Trevor King [Tue, 27 Sep 2011 20:22:58 +0000 (16:22 -0400)]
Update config arguments to bit/volt/meter conversion functions.

13 years agoAdd bit/volt/meter converter imports to pyafm.afm.
W. Trevor King [Tue, 27 Sep 2011 20:19:24 +0000 (16:19 -0400)]
Add bit/volt/meter converter imports to pyafm.afm.

13 years agoRemove unneccessary inputs from pyafm.afm.
W. Trevor King [Tue, 27 Sep 2011 19:50:50 +0000 (15:50 -0400)]
Remove unneccessary inputs from pyafm.afm.

13 years agoUpdate setup.py to reflect the fact that we're no longer a single module.
W. Trevor King [Tue, 27 Sep 2011 19:40:40 +0000 (15:40 -0400)]
Update setup.py to reflect the fact that we're no longer a single module.

13 years agoRestructure and convert to new, nestable h5config. v0.3
W. Trevor King [Thu, 15 Sep 2011 12:18:39 +0000 (08:18 -0400)]
Restructure and convert to new, nestable h5config.

13 years agoClarify stepper motion during additional surface location attempts.
W. Trevor King [Wed, 20 Apr 2011 20:04:15 +0000 (16:04 -0400)]
Clarify stepper motion during additional surface location attempts.

13 years agoDon't set handler log level; just use the logger log level.
W. Trevor King [Wed, 20 Apr 2011 19:13:03 +0000 (15:13 -0400)]
Don't set handler log level; just use the logger log level.

13 years agoFix typo target_def -> target_deflection.
W. Trevor King [Wed, 20 Apr 2011 18:46:04 +0000 (14:46 -0400)]
Fix typo target_def -> target_deflection.

13 years agoCatch FlatFit errors from all .get_surface_position calls.
W. Trevor King [Wed, 20 Apr 2011 18:34:43 +0000 (14:34 -0400)]
Catch FlatFit errors from all .get_surface_position calls.

13 years agoAdd optional temperature controller attribute.
W. Trevor King [Tue, 19 Apr 2011 23:42:17 +0000 (19:42 -0400)]
Add optional temperature controller attribute.

13 years agoFix typos pyiezo -> piezo.
W. Trevor King [Tue, 19 Apr 2011 20:57:57 +0000 (16:57 -0400)]
Fix typos pyiezo -> piezo.

13 years agoAdd self to _stepper_approach_again arguments :p.
W. Trevor King [Tue, 19 Apr 2011 20:55:09 +0000 (16:55 -0400)]
Add self to _stepper_approach_again arguments :p.

13 years agoAdd /posts/ to homepage URL in setup.py.
W. Trevor King [Tue, 19 Apr 2011 20:32:36 +0000 (16:32 -0400)]
Add /posts/ to homepage URL in setup.py.

13 years agoMinor rewrite of README intro section.
W. Trevor King [Tue, 19 Apr 2011 18:56:06 +0000 (14:56 -0400)]
Minor rewrite of README intro section.

13 years agoMinor rewrite of README intro section.
W. Trevor King [Tue, 19 Apr 2011 18:52:34 +0000 (14:52 -0400)]
Minor rewrite of README intro section.

13 years agoCorrect setpoint -> target_deflection typo.
W. Trevor King [Tue, 19 Apr 2011 17:58:47 +0000 (13:58 -0400)]
Correct setpoint -> target_deflection typo.

13 years agoCorrect axis.channel_config -> axis.axis_channel_config typo.
W. Trevor King [Tue, 19 Apr 2011 17:54:48 +0000 (13:54 -0400)]
Correct axis.channel_config -> axis.axis_channel_config typo.

13 years agoSet `axis = ...` earlier in AFM.move_just_onto_surface().
W. Trevor King [Tue, 19 Apr 2011 17:51:17 +0000 (13:51 -0400)]
Set `axis = ...` earlier in AFM.move_just_onto_surface().

13 years agoFix LOG formatting error.
W. Trevor King [Tue, 19 Apr 2011 14:30:32 +0000 (10:30 -0400)]
Fix LOG formatting error.

13 years agoFix pymodules typo in setup.py.
W. Trevor King [Tue, 19 Apr 2011 14:28:40 +0000 (10:28 -0400)]
Fix pymodules typo in setup.py.

13 years agoBegin versioning. 0.1
W. Trevor King [Tue, 19 Apr 2011 14:18:02 +0000 (10:18 -0400)]
Begin versioning.

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