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, and
also check that the current working directory (`.`) is in your
Now you are ready to generate the playlist. First, create a blank playlist::
- hooke> new_playlist --name mylist
+ hooke> new_playlist --output_playlist mylist
Ensure that the new playlist is active::
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`_.
+supported by the `optparse module`_. You don't need to jump if
+the new playlist is your only loaded playlist.
.. _optparse module:
http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments
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
hooke> jump_to_curve 14
-will jump to the 14th curve in the playlist. 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.
+will jump to the 14th curve in the zero-indexed playlist.
+
+.. 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
``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::
+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
Usually curves you annotated are useful later. You can create a
playlist for only annotated curves with
- hooke> note_filter_playlist --name c:\curves\nice.hkp
+ hooke> note_filter_playlist --output_playlist nice_list
-will create sub-playlist :file:`c:\curves\nice.hkp`. Make sure that
-the target directory (here :file:`c:\curves\`) already exists before
-doing that.
+will create sub-playlist `nice_list`. Remember to save the new list
+if you like it.
If you change your mind about a note, you can remove it by setting a
blank note string with ``set_note ''``.
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.
+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.
-TODO: multiple cycles? Solution: blank lines for "breaks", add option
-to extract specific sections using Python's slice notation.
+.. todo:: Currently no PNG or EPS output, use the GUI and the plot
+ panel's toolbar for non-text exports.
+
+.. 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.
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.
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
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.
+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