.. toctree::
:maxdepth: 2
- gui.txt
+ gui
Introduction
============
This tutorial will focus on the command-line interface as the most
-powerful, and leave the GUI interface to another document.
+powerful, and leave the :doc:`gui` interface to another document.
.. _command-line: `Command-line interface`_
-.. _GUI: gui.txt
Installation
============
-See the Installation_ page for details on downloading and installing
-Hooke.
-
-.. _Installation: install.txt
+See :doc:`install` for details on downloading and installing Hooke.
Command-line interface
Running the hooke shell
-----------------------
-Hooke has a set of commands that depend on the loaded plugins_.
-To access these commands, you'll need to run the Hooke shell.::
+Hooke has a set of commands that depend on the loaded
+:class:`hooke.plugin.Plugin`\s. To access these commands, you'll need
+to run the Hooke shell.::
$ hooke
If you are running hooke from the source directory (see
-Installation_), the equivalent command is::
-
- $ python bin/hooke
+:doc:`install`), the equivalent command is::
-You may need to give the full path for Python on Windows systems.
+ $ python bin/hk.py
-.. _plugins: hooke/hooke.plugin.txt
+You may need to give the full path for Python on Windows systems, and
+also check that the current working directory (`.`) is in your
+`PYTHONPATH`. See :manpage:`python(1)` for details.
As Hooke launches, you should see something like the following in your
terminal::
- Hooke version 0.8.0 Seinei
+ Hooke version 0.9.0.devel (Kenzo)
+
+ Copyright (C) 2006-2010 A. Seeholzer, Alberto Gomez-Casado, Allen
+ Chen, Fabrizio Benedetti, Francesco Musiani, Marco Brucale, Massimo
+ Sandal, Pancaldi Paolo, Richard Naud, Rolf Schmidt, W. Trevor King
- COPYRIGHT
+ Hooke comes with ABSOLUTELY NO WARRANTY and is licensed under the GNU
+ Lesser General Public License. For details, run `license`.
----
hooke>
-The final line, `hooke>`, is the Hooke prompt. It allows you to
-enter commans to interact with the interpreter.
+The final line, ``hooke>``, is the Hooke prompt. It allows you to
+enter commands 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
for example::
- hooke> help current
+ hooke> help load_playlist
+
+will give help on the ``load_playlist`` command.
+
+Leaving Hooke
+-------------
-will give help on the `current` command.
+When you're done with an interactive Hooke session, you can close the
+session with ``exit`` or its aliases ``quit`` and ``EOF`` (``EOF`` is
+the end of the stdin stream, which is Ctrl-d in many shells).
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
-want to analyze them all.
+starting from :file:`mycurve.000` and ending in :file:`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
+ hooke> cd --path 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
-synonyms).::
+You can list the files in the directory using ``ls`` or ``dir``
+(they’re synonyms).::
hooke> ls
- [’mycurve.000’, ’mycurve.001’, ...
- ]
+ mycurve.000
+ mycurve.001
+ ...
+
+Now you are ready to generate the playlist. First, create a blank playlist::
+
+ hooke> new_playlist --output_playlist mylist
+
+Ensure that the new playlist is active::
+
+ hooke> jump_to_playlist -- -1
+ hooke> get_playlist
+ <FilePlaylist mylist>
-Now you are ready to generate the playlist. The command to use is
-`genlist`.::
+The ``--`` in the ``jump_to_playlist`` command lets
+``jump_to_playlist`` know that ``-1`` is an argument and not an
+option. Using the bare ``--`` is a POSIX specification [#POSIX]_
+supported by the `optparse module`_. You don't need to jump if
+the new playlist is your only loaded playlist.
- hooke> genlist mycurve.*
+.. _optparse module:
+ http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments
-You can also generate a playlist containing all what you find in the
-directory by typing:
+.. [#POSIX] `Guideline 10 of POSIX:2008's section 12.2 <http://www.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap12.html#tag_12_02>`_ states:
- hooke> genlist c:\curves
+ "The first ``--`` argument that is not an option-argument should be
+ accepted as a delimiter indicating the end of options. Any
+ following arguments should be treated as operands, even if they
+ begin with the ``-`` character."
-If you want to select what curves to see, based on the filename, you
-can use wildcards. For example::
+Then glob your curves onto the new list::
- hooke> genlist mycurve.05*
+ hooke> glob_curves_to_playlist mycurve.*
-will take only curves from mycurve.050 to mycurve.059.
+You can also be more specific with wildcards. For example::
-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> glob_curve_to_playlist mycurve.05*
- hooke> savelist mylist
+will take only curves from :file:`mycurve.050` to :file:`mycurve.059`.
-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.
+Note that by using ``glob_curves_to_playlist`` you just generate the
+playlist in the local session. To save your playlist to a file for
+future reuse, type::
+
+ hooke> save_playlist --output mylist
+
+In this example, the list will be saved in the file
+: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 ``load_playlist
+mylist.hkp`` or ``load_playlist 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
-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.
+Now you can navigate through your playlist using the commands
+``next_curve`` and ``previous_curve``. You don’t need to type
+``next_curve`` every time to run along a list of curves. You can
+navigate through the command history by using the up and down arrows,
+or auto-complete partial commands with TAB. From the last curve of
+your playlist, ``next_curve`` will wrap around to the first curve.
+Analogously, issuing ``previous_curve`` at the first curve will jump
+to the last.
You can also jump to a given curve::
- hooke> jump c:\curves\mycurve.012
+ hooke> jump_to_curve 14
+
+will jump to the 14th curve in the playlist.
-where the path can be either an absolute path, or a path relative to
-the directory holding the playlist file.
+.. todo:: ``jump_to_curve <PATH>``, where the path can be either an
+ absolute path or a path relative to the directory holding the
+ playlist file.
Taking notes
------------
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
-will save the text in your current playlist and in an external log
-file. The output will look like this:
+``set_note`` followed by the text you want to attach to that curve.
+Hooke will save the text in your current playlist and in an external
+log file.
-Notes taken at Sun Sep 17 20:42:07 2006
-/home/cyclopia/work/tris/20060620a.041 | This is a note
-/home/cyclopia/work/tris/20060620a.207 | This is another note
-/home/cyclopia/work/tris/20060620a.286 | This is a third one
+.. todo:: No external file yet. Is this important?
-The log file name can be configured_, but it defaults to hooke.log.
+The output will look like this::
-.. _configured: config.txt
+ Notes taken at Sun Sep 17 20:42:07 2006
+ /home/cyclopia/work/tris/20060620a.041 | This is a note
+ /home/cyclopia/work/tris/20060620a.207 | This is another note
+ /home/cyclopia/work/tris/20060620a.286 | This is a third one
-Usually curves you annotated are useful later. You can copy the curves
-you annotated to a different directory by using the `copylog`
-command.
+The log file name can be configured (:doc:`config`), but it defaults
+to :file:`hooke.log`.
- hooke> copylog c:\nicecurves
+Usually curves you annotated are useful later. You can create a
+playlist for only annotated curves with
-will copy all curves you have annotated to the c:\nicecurves
-directory. Make sure that the directory already exists before doing
-that. TODO: replace with::
+ hooke> note_filter_playlist --name c:\curves\nice.hkp
- hooke> copylist --log c:\curves\nice.hkp
+will create sub-playlist :file:`c:\curves\nice.hkp`. Make sure that
+the target directory (here :file:`c:\curves\`) already exists before
+doing that.
+
+If you change your mind about a note, you can remove it by setting a
+blank note string with ``set_note ''``.
Exporting curves
----------------
You can export Hooke curves as images and as text columns. To export
-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
-PNG and EPS files respectively.
-
-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).
+as images or text, use the ``export_block`` command. Supported
+formats are PNG (Portable Network Graphic, raster) and EPS
+(Encapsulated Postscript, vector). The export format is determined by
+the filename extension, so ``export_block foo.png``, ``export_block
+foo.eps``, and ``export_block foo.txt`` will save PNG, EPS, and
+TAB-delimited text files respectively.
-TODO: multiple cycles? Solution: blank lines for "breaks", add option
-to extract specific sections using Python's slice notation.
+.. todo:: Multiple cycles in exported data? Solution: blank lines for
+ "breaks", add option to extract specific sections using Python's
+ slice notation.
+If you don't want the entire block, try the ``cut`` command.
Interacting with the plot
-------------------------
Measuring distances and forces
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-You can easily zoom in the plot by dragging a rectangle on it with the
-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.
+You can move about the plot using its navigation toolbar. See the
+`Matplotlib manual`_ for details.
+
+.. _Matplotlib manual:
+ http://matplotlib.sourceforge.net/users/navigation_toolbar.html
You can measure distances and forces directly in the plot. Just issue
-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,
-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`.
+the command ``delta``. 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 will appear in the output panel. If you
+want to know the coordinates of a single point, left click on it.
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.
-
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
-command line for details.
+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.
Configuring Hooke
-----------------
-You can set environment variables to influence the behaviour of
-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`_
-section for details.
-
-.. _Configuring Hooke: config.txt
+You can set environment variables to influence the behaviour of
+Hooke. The command to use is ``set_config``. Use ``get_config`` to
+read a particular option and ``print_config`` to display the entire
+configuration file. Any changes to the configuration will be saved
+when you exit Hooke, see :doc:`config` for details.
projects / hooke.git / blobdiff