If you are running hooke from the source directory (see
:doc:`install`), the equivalent command is::
- $ python bin/hooke
+ $ python bin/hk.py
-You may need to give the full path for Python on Windows systems.
+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
+ 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
+
+ Hooke comes with ABSOLUTELY NO WARRANTY and is licensed under the GNU
+ Lesser General Public License. For details, run `license`.
----
hooke>
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
-------------------
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.::
(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
-Now you are ready to generate the playlist. The command to use is
-``genlist``.::
+Ensure that the new playlist is active::
- hooke> genlist mycurve.*
+ hooke> jump_to_playlist -- -1
+ hooke> get_playlist
+ <FilePlaylist mylist>
-You can also generate a playlist containing all what you find in the
-directory by typing:
+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 c:\curves
+.. _optparse module:
+ http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments
-If you want to select what curves to see, based on the filename, you
-can use wildcards. For example::
+.. [#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 mycurve.05*
+ "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."
+
+Then glob your curves onto the new list::
+
+ hooke> glob_curves_to_playlist mycurve.*
+
+You can also be more specific with wildcards. For example::
+
+ hooke> glob_curve_to_playlist mycurve.05*
will take only curves from :file:`mycurve.050` to :file:`mycurve.059`.
-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::
+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> savelist mylist
+ 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 ``loadlist mylist.hkp``
-or ``loadlist mylist``, Hooke will add ``.hkp`` if necessary.
+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
+curve file that Hooke cannot open, Hooke will log a warning and
continue on.
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 zero-indexed 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.
+
+Replace ``curve`` with ``playlist`` in the above commands to navigate
+around through the list of loaded playlists.
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.
+
+.. todo:: No external file yet. Is this important?
+
+The output will look like this::
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
+ /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
The log file name can be configured (:doc:`config`), but it defaults
to :file:`hooke.log`.
-Usually curves you annotated are useful later. You can copy the curves
-you annotated to a different directory by using the ``copylog``
-command.
+Usually curves you annotated are useful later. You can create a
+playlist for only annotated curves with
- hooke> copylog c:\nicecurves
+ hooke> note_filter_playlist --output_playlist nice_list
-will copy all curves you have annotated to the :file:`c:\nicecurves`
-directory. Make sure that the directory already exists before doing
-that. TODO: replace with::
+will create sub-playlist `nice_list`. Remember to save the new list
+if you like it.
- hooke> copylist --log c:\curves\nice.hkp
+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,
-vector). The export format is determined by the filename extension,
-so ``export foo.png`` and ``export foo.eps`` will save PNG and EPS
-files respectively.
+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 --output foo.png``,
+``export_block --output foo.eps``, and ``export_block --output
+foo.txt`` will save PNG, EPS, and TAB-delimited text 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).
+.. todo:: Currently no PNG or EPS output, use the GUI and the plot
+ panel's toolbar for non-text exports.
-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.
+
+.. todo:: Add description of ``delta``'s command line interface.
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. todo:: Update WLC fitting tutorial section.
+
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
default automatically finds the contact point, asks for two points
Multiple curve fitting and measuring
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. todo:: Update multiple curve fitting tutorial section.
You can cycle through all your current playlist obtaining WLC fit, FJC
fit, rupture force and slope (loading rate) information from each
Fast curve reviewing and saving
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. todo:: Update curve review tutorial section.
+
When automatic routines are not good enough to filter your data, use
``review`` command to cycle through your playlist presenting ten
curves in the same graph. You can then enter the numbers of the
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 :doc:`config` for
+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. To save changes, either run ``save_config`` or
+start Hooke with the ``--save-config`` option. See :doc:`config` for
details.
projects / hooke.git / blobdiff