Pyafm is a set of tools for controlling atomic force microscopes. It
provides control of AFM postition using both short-range (piezo) and
long range (stepper) vertical positioning. There are separate modules
-for controlling the piezo (`pypiezo`) and stepper (`stepper`), this
+for controlling the piezo (pypiezo_) and stepper (stepper_), this
module mostly contains methods that require the capabilities of both.
+This module can optionally include temperature sensing via a pypid_
+backend.
+
Packages
========
I've packaged pyafm for Gentoo. You need layman_ and my `wtk
overlay`_. Install with::
- # emerge -av app-portage/layman
- # layman --add wtk
- # emerge -av sci-physics/pyafm
+ # emerge -av app-portage/layman
+ # layman --add wtk
+ # emerge -av sci-physics/pyafm
Although it is not strictly required (thanks to `duck typing`_) you'll
probably also want my `stepper`_ package or an equivalent
stepper implementation.
-.. _layman: http://layman.sourceforge.net/
-.. _wtk overlay: http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/Gentoo_overlay/
-.. _duck typing: http://en.wikipedia.org/wiki/Duck_typing
-.. _stepper: http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/stepper/
-
Dependencies
============
Pyafm requires the following Python modules:
+* Pycomedi_ (required directly, and via ``pypiezo``)
* Pypiezo_
* Stepper_ (or equivalent stepper implementation)
-
-.. _stepper: http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/stepper/
-.. _pypiezo: http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/pypiezo/
-
+* Pypid_ (optional temperature monitoring and control)
+* H5config_ (required directly, and via ``pypiezo``)
+* SciPy_
Getting the source
==================
Pyafm is available as a Git_ repository::
- $ git clone http://www.physics.drexel.edu/~wking/code/git/pyafm.git
+ $ git clone git://tremily.us/pyafm.git
There are also periodic bundled releases. For example, get version
-0.1 as a gzipped tarball with::
+0.3 as a gzipped tarball with::
- $ wget http://www.physics.drexel.edu/~wking/code/python/pyafm-0.1.tar.gz
- $ tar -xzvf pyafm-0.1.tar.gz
-
-.. _Git: http://git-scm.com/
+ $ wget 'http://git.tremily.us/?p=pyafm.git;a=snapshot;h=v0.3;sf=tgz'
+ $ tar -xzvf pyafm-0.1.tar.gz
Installation
After downloading, change to the source directory and run::
- $ python setup.py install
+ $ python setup.py install
to install pyafm. Run::
- $ python setup.py install --help
+ $ python setup.py install --help
to see a list of installation options you may want to configure.
Usage
=====
-TODO
+The docstrings include some pretty detailed tests to get you started.
+``dir()`` and ``help()`` are your friends ;). One neat feature that
+I've added recently (2012-03-16) is the ability to store and load
+complete AFM configurations via h5config_. For example, when you
+first use pyafm, it may take you a bit to dig up all the necessary
+calibration constants, etc. and plug them into your config::
+
+ >>> import pycomedi.constant
+ >>> import pypiezo.config
+ >>> import pyafm.config
+ >>> config = pyafm.config.AFMConfig()
+ >>> config['name'] = '1B3D9'
+ >>> config['main-axis'] = 'z'
+ >>> config['piezo'] = pypiezo.config.PiezoConfig()
+ >>> config['piezo']['name'] = '2253E'
+ >>> config['piezo']['axes'] = [
+ ... pypiezo.config.AxisConfig(), pypiezo.config.AxisConfig()]
+ >>> config['piezo']['axes'][0]['gain'] = 20
+ >>> config['piezo']['axes'][0]['sensitivity'] = 8.8e-9
+ >>> config['piezo']['axes'][0]['channel'] = pypiezo.config.OutputChannelConfig()
+ >>> config['piezo']['axes'][0]['channel']['analog-reference] = pycomedi.constant.AREF.ground
+ >>> config['piezo']['axes'][0]['channel']['analog-reference] = pycomedi.constant.AREF.ground
+
+and on, and on ;). Don't worry though, once you finish telling Python
+about your particular AFM configuration, you can get a working ``AFM``
+instance quite easily::
+
+ >>> devices = []
+ >>> afm = AFM(config=config, devices=devices)
+
+That takes care of opening all the channels and initializing all the
+pieces you configured above. ``devices`` will end up full of any
+``pycomedi.device.Device`` instances that you need. Once you're happy
+with your setup, make sure the ``config`` object is up-to-date with::
+
+ >>> afm.setup_config()
+
+Which copies any new object state into the ``.config`` attribute
+(e.g. bit-to-volt conversion polynomials). Then save your
+configuration with::
+
+ >>> import pyafm.storage
+ >>> pyafm.storage.save_afm(afm=afm, filename='whatever', group='/optional')
+
+Which will create a HDF5 file at the specified path, and store the AFM
+configutaion under the specified group. Both ``filename`` and
+``group`` are optional. If you leave them out, they will default to
+``~/.config/pyafm-default.h5`` and ``/`` respectively.
+
+The next time you need to do something with the AFM, just load your
+old config file. If you used the default location, that's as easy
+as::
+
+ >>> import pyafm.storage
+ >>> devices = []
+ >>> afm = pyafm.storage.load_afm(devices=devices)
+ >>> afm.load_from_config()
+
+When you're done using them, it's good practice to close any devices
+in ``devices``::
+
+ >>> for device in devices:
+ ... device.close()
+
+Using ``load_afm`` with the default path is a good way to keep your
+AFM configuration synchronized across several applications. That way,
+there's only one place you need to update if you recalibrate your
+piezo or rebuild an amplifier.
+
+
+.. _layman: http://layman.sourceforge.net/
+.. _wtk overlay: http://blog.tremily.us/posts/Gentoo_overlay/
+.. _duck typing: http://en.wikipedia.org/wiki/Duck_typing
+.. _pycomedi: http://blog.tremily.us/posts/pycomedi/
+.. _pypiezo: http://blog.tremily.us/posts/pypiezo/
+.. _stepper: http://blog.tremily.us/posts/stepper/
+.. _pypid: http://blog.tremily.us/posts/pypid/
+.. _h5config: http://blog.tremily.us/posts/h5config/
+.. _SciPy: http://www.scipy.org/
+.. _Git: http://git-scm.com/
projects / pyafm.git / blobdiff