testing.txt
-Architecture
+Dependencies
============
To clean up the internals, were going to go crazy on the
.. _Scipy: http://www.scipy.org/
To make a responsive user interface in parallel with data processing
-and possible GUIs, we'll use Python's multiprocessing_ and queue_
-modules. These modules are both new in Python 2.6, but 2.6 usage is
-becoming fairly widespread. Certainly more widespread than any
-alternative queue module that I know of. Since we're leveraging the
-power of the standard library, we use configparser_ for the config
-files.
+and possible GUIs, we'll use Python's multiprocessing_ module. This
+module is new in Python 2.6, but 2.6 usage is becoming fairly
+widespread. Certainly more widespread than any alternative queue
+module that I know of. Since we're leveraging the power of the
+standard library, we use configparser_ for the config files.
.. _multiprocessing: http://docs.python.org/dev/library/multiprocessing.html
-.. _queue: http://docs.python.org/library/queue.html
.. _configparser: http://docs.python.org/library/configparser.html
On the testing side, the need to stick to the standard library relaxes
.. _nose: http://somethingaboutorange.com/mrl/projects/nose/0.11.3/
.. _Testing: testing.txt
+
+
+Architecture
+============
+
+Hooke's main entry point is :class:`hooke.hooke.Hooke`. `Hooke` reads
+in the configuration files and loads Plugins_ and Drivers_. Then it
+forks off a :class:`hooke.engine.CommandEngine` instance to execute
+Commands_, and a :class:`hooke.ui.UserInterface` instance to connect
+the `CommandEngine` with the user. The `CommandEngine` runs in a
+subprocess, which allows command execution to occur in parallel with
+`UserInterface` interaction. The two processes communicate via two
+:class:`multiprocessing.Queue`\s.
+
+There are a number of special classes availiable to structure queue
+communications. See :mod:`hooke.interaction` and
+:class:`hooke.command.CommandExit` for details.
+
+Plugins
+-------
+
+:class:`hooke.plugin.Plugin`\s contain bundles of Commands_,
+representing the various operations a user can carry out through the
+Hooke interface.
+
+`Plugin`\s can depend on other `Plugin`\s, so you shouldn't need to
+repeat code. One central `Plugin` can provide useful functionality
+to several dependent `Plugin`\s.
+
+There is a `Plugin` subtype :class:`hooke.plugin.Builtin` which is
+just like a `Plugin`, but is considered fundamental enough to not be
+optional. `Builtin`\s are always loaded.
+
+Commands
+~~~~~~~~
+
+:class:`hooke.command.Command`\s specify user-actions in an
+interface-agnostic manner. This makes writing
+:class:`hooke.ui.UserInterface`\s easier, because you don't need to
+know anything about particular `Plugin`\s or `Command`\s, you just
+need to be able to explain the base classes for you user and then
+speak the language of :mod:`hooke.interaction` and
+:class:`hooke.command.CommandExit` with the
+:class:`hooke.engine.CommandEngine` process.
+
+Drivers
+-------
+
+:class:`hooke.driver.Driver`\s are responsible for reading assorted
+data files into Hooke's Data_ structure.
+
+Data
+----
+
+Experiments
+~~~~~~~~~~~
+
+Force spectroscopy experiments come in several major flavors. Each
+flavor gets its own subclass of :class:`hooke.experiment.Experiment`
+in :mod:`hooke.experiment`. For example, force clamp experiments are
+:class:`hooke.experiment.ForceClamp`. This gives Drivers_ a way to
+tag experimental data so Commands_ know what they are working with.
+
+Curves
+~~~~~~
+
+Experiments_ tags need a data-holding container to tag, and
+:class:`hooke.curve.Curve`\s are that container. Each `Curve` can
+hole several blocks of :class:`hooke.curve.Data` (for example approach
+and retract curves in a :class:`hooke.experiment.VelocityClamp`
+experiment would be seperate blocks). `Curve`\s also have an
+:attr:`~hooke.curve.Curve.info` attribute for persistently storing
+arbitrary data.
+
+Playlists
+~~~~~~~~~
+
+Normally you'll want to analyze multiple Curves_ in one session.
+:class:`hooke.playlist.Playlist`\s provide a convenient container for
+Curves_, and the subclass :class:`hooke.playlist.FilePlaylist` add
+persistant file backing (save, load, etc.).
+
+Utilities
+---------
+
+There are a number of general coding features we need for Hooke that
+are not provided by Python's standard library. We factor those
+features out into :mod:`hooke.utils`.
+
+There are also a number of features who's standard library support
+changes with different versions of Python. :mod:`hooke.compat`
+provides a uniform interface to those tools so that Hooke will work
+with several Python versions.
As Hooke launches, you should see something like the following in your
terminal::
- Starting Hooke.
- Imported plugin fit
- Imported plugin procplots
- Imported plugin flatfilts
- Imported plugin generalclamp
- Imported plugin generalvclamp
- Imported plugin massanalysis
- Imported plugin macro
- Imported driver picoforce
- Imported driver hemingclamp
- Imported driver csvdriver
- Imported driver tutorialdriver
-
- Warning: Invalid work directory.
- This is Hooke, version 0.8.0 Seinei
- (c) Massimo Sandal, 2006. Released under the GNU General Public License Version 2
- Hooke is Free software.
+ Hooke version 0.8.0 Seinei
+
+ COPYRIGHT
----
hooke>
-The final line, ``hooke>``, is the Hooke prompt. It allows you to
+The final line, `hooke>`, is the Hooke prompt. It allows you to
enter commans to interact with the interpreter.
Help
hooke> help
-Or see specific help on ``TOPIC`` with::
+Or see specific help on `TOPIC` with::
hooke> help TOPIC
hooke> help current
-will give help on the ``current`` command.
+will give help on the `current` command.
Creating a playlist
-------------------
playlist), but with data files instead of audio files.
Suppose you have 100 PicoForce curve files in your curves directory,
-starting from ``mycurve.000`` and ending in ``mycurve.100`` and you
+starting from `mycurve.000` and ending in `mycurve.100` and you
want to analyze them all.
-You then can ``cd`` (change directory) to the directory::
+You then can `cd` (change directory) to the directory::
hooke> cd c:\curves
-Type ``pwd`` (print working directory) to check the directory is correct.::
+Type `pwd` (print working directory) to check the directory is correct.::
hooke> pwd
c:\curves
-You can list the files in the directory using ``ls`` or ``dir`` (they’re
+You can list the files in the directory using `ls` or `dir` (they’re
synonyms).::
hooke> ls
]
Now you are ready to generate the playlist. The command to use is
-``genlist``.::
+`genlist`.::
hooke> genlist mycurve.*
will take only curves from mycurve.050 to mycurve.059.
-Note that by using ``genlist`` you just generate the playlist in the
+Note that by using `genlist` you just generate the playlist in the
local session. To save your playlist to a file for future reuse,
type::
hooke> savelist mylist
-In this example, the list will be saved in the file ``mylist.hkp``.
-Hooke will add the extension ``.hkp`` (Hooke playlist) to the playlist
-if you forget to. The ``.hkp`` file is an XML file you can read and
+In this example, the list will be saved in the file `mylist.hkp`.
+Hooke will add the extension `.hkp` (Hooke playlist) to the playlist
+if you forget to. The `.hkp` file is an XML file you can read and
edit with any text editor (i.e. Wordpad), if needed. If you want to
-load it, simply issue ``loadlist mylist.hkp`` or ``loadlist mylist``,
-Hooke will add ``.hkp`` if necessary.
+load it, simply issue `loadlist mylist.hkp` or `loadlist mylist`,
+Hooke will add `.hkp` if necessary.
If, generating the playlist, you are including by chance a non-force
curve file that Hooke cannot open, Hooke will print an error and
Navigating the playlist
-----------------------
-Now you can navigate through your playlist using the commands ``next``
-and ``previous`` or, their aliases ``n`` and ``p``. You don’t need to
-type ``n`` every time to run along a list of curves. If you press
+Now you can navigate through your playlist using the commands `next`
+and `previous` or, their aliases `n` and `p`. You don’t need to
+type `n` every time to run along a list of curves. If you press
Return to an empty prompt, Hooke will repeat the last command you
issued explicitly. You can also navigate through the command history
by using the up and down arrows. From the last curve of your
-playlist, ``n`` will wrap around to the first curve. Analogously,
-issuing ``p`` at the first curve will jump to the last.
+playlist, `n` will wrap around to the first curve. Analogously,
+issuing `p` at the first curve will jump to the last.
You can also jump to a given curve::
------------
You can take notes about the curves you are looking at. Just type
-``note`` followed by the text you want to append to that curve. Hooke
+`note` followed by the text you want to append to that curve. Hooke
will save the text in your current playlist and in an external log
file. The output will look like this:
.. _configured: config.txt
Usually curves you annotated are useful later. You can copy the curves
-you annotated to a different directory by using the ``copylog``
+you annotated to a different directory by using the `copylog`
command.
hooke> copylog c:\nicecurves
----------------
You can export Hooke curves as images and as text columns. To export
-as images, issue the ``export`` command followed by the filename.
+as images, issue the `export` command followed by the filename.
Supported formats are PNG (raster) and EPS (Encapsulated Postscript,
vectorial). The export format is determined by the filename
-extension, so ``export foo.png`` and ``export foo.eps`` will save
+extension, so `export foo.png` and `export foo.eps` will save
PNG and EPS files respectively.
-To export as text, use the ``txt`` command, followed by the
+To export as text, use the `txt` command, followed by the
filename. The output is a text file containing columns (first two are
X and Y of extension, second two are X and Y of retraction).
left mouse button. To zoom out, click the right mouse
button. Sometimes by zooming in and out too much, you can lose the
picture (this is probably a small bug in Matplotlib). Just type
-``plot`` at the command line and the curve will be refreshed.
+`plot` at the command line and the curve will be refreshed.
You can measure distances and forces directly in the plot. Just issue
-the command ``distance``. You will be asked to click two points.
+the command `distance`. You will be asked to click two points.
When you click a point, a blue dot should appear. When you click the
second point, the distances (in nanometers and piconewtons) will
-appear on the command line. You can use ``delta`` if you prefer,
+appear on the command line. You can use `delta` if you prefer,
which gives meaningful values for every kind of graph (not only force
curves). If you want to know the coordinates of a single point, use
-``point``.
+`point`.
Hooke automatically adjusts the position of the clicked point to the
nearest point in the graph, so you will be always measuring distances
and forces between points in the graph.
-The commands ``force`` and ``distance`` are present in the
-``generalvclamp`` plugin.
+The commands `force` and `distance` are present in the
+`generalvclamp` plugin.
Worm like chain and freely jointed chain fitting
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You can measure by hand the parameters relative to a force peak using
-a worm-like chain fitting with the ``fit`` command. The command by
+a worm-like chain fitting with the `fit` command. The command by
default automatically finds the contact point, asks for two points
delimiting the portion to fit, and performs a two-variable fit, with
contour length, persistence length, and their relative errors as
-output. If desired, one can use the ``noauto`` option to manually
-click the contact point, and/or the ``pl=NUMBER`` options to impose a
+output. If desired, one can use the `noauto` option to manually
+click the contact point, and/or the `pl=NUMBER` options to impose a
specific persistence or Kuhn length (in nanometers). You can choose
-which model to use with ``set fit_function wlc`` or ``set fit_function
-fjc``. See the help of the ``fit`` command from the Hooke
+which model to use with `set fit_function wlc` or `set fit_function
+fjc`. See the help of the `fit` command from the Hooke
command line for details.
Multiple curve fitting and measuring
You can cycle through all your current playlist obtaining WLC fit, FJC
fit, rupture force and slope (loading rate) information from each
-curve using the ``multifit`` command. The collected data can be saved
+curve using the `multifit` command. The collected data can be saved
in a text file for further analysis in your favourite spreadsheet or
statistical program. If you want to check your parameters on the
current curve before fitting all the files in your playlist, use
-``multifit justone``. See the ``multifit`` help for more options.
+`multifit justone`. See the `multifit` help for more options.
Fast curve reviewing and saving
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When automatic routines are not good enough to filter your data, use
-``review`` command to cycle through your playlist presenting ten
+`review` command to cycle through your playlist presenting ten
curves in the same graph. You can then enter the numbers of the
interesting curves and automatically save a copy of them into another
directory.
-----------------
You can set environment variables to influence the behaviour of
-Hooke. The command to use is ``set``.
+Hooke. The command to use is `set`.
You can alter permanently the behaviour of Hooke by setting these
variables in a Hooke configuration file. See the `Configuring Hooke`_
projects / hooke.git / commitdiff