5 `A short video showing Hooke in action`_! (courtesy of Fabrizio
6 Benedetti, EPFL, Lausanne)
8 .. _A short video showing Hooke in action:
9 https://documents.epfl.ch/users/f/fb/fbenedet/www/hooke_short_demostration.ogv
19 This tutorial will focus on the command-line interface as the most
20 powerful, and leave the :doc:`gui` interface to another document.
22 .. _command-line: `Command-line interface`_
27 See :doc:`install` for details on downloading and installing Hooke.
30 Command-line interface
31 ======================
33 Running the hooke shell
34 -----------------------
36 Hooke has a set of commands that depend on the loaded
37 :class:`hooke.plugin.Plugin`\s. To access these commands, you'll need
38 to run the Hooke shell.::
42 If you are running hooke from the source directory (see
43 :doc:`install`), the equivalent command is::
47 You may need to give the full path for Python on Windows systems, and
48 also check that the current working directory (`.`) is in your
49 `PYTHONPATH`. See :manpage:`python(1)` for details.
51 As Hooke launches, you should see something like the following in your
54 Hooke version 0.9.0.devel (Kenzo)
56 Copyright (C) 2006-2010 A. Seeholzer, Alberto Gomez-Casado, Allen
57 Chen, Fabrizio Benedetti, Francesco Musiani, Marco Brucale, Massimo
58 Sandal, Pancaldi Paolo, Richard Naud, Rolf Schmidt, W. Trevor King
60 Hooke comes with ABSOLUTELY NO WARRANTY and is licensed under the GNU
61 Lesser General Public License. For details, run `license`.
65 The final line, ``hooke>``, is the Hooke prompt. It allows you to
66 enter commands to interact with the interpreter.
71 All commands have help text explaining their purpose and usage. The
72 text is stored in the code itself, and therefore more likely to be up
73 to date than this tutorial. You can get a list of commands and topics
78 Or see specific help on ``TOPIC`` with::
84 hooke> help load_playlist
86 will give help on the ``load_playlist`` command.
91 When you're done with an interactive Hooke session, you can close the
92 session with ``exit`` or its aliases ``quit`` and ``EOF`` (``EOF`` is
93 the end of the stdin stream, which is Ctrl-d in many shells).
98 To start analyzing your curves, you first have to build a playlist. The
99 playlist is just an index of the force curve files you want to
100 analyze. Imagine it as a music playlist (that’s why it is called a
101 playlist), but with data files instead of audio files.
103 Suppose you have 100 PicoForce curve files in your curves directory,
104 starting from :file:`mycurve.000` and ending in :file:`mycurve.100`
105 and you want to analyze them all.
107 You then can ``cd`` (change directory) to the directory::
109 hooke> cd --path c:\curves
111 Type ``pwd`` (print working directory) to check the directory is correct.::
116 You can list the files in the directory using ``ls`` or ``dir``
117 (they’re synonyms).::
124 Now you are ready to generate the playlist. First, create a blank playlist::
126 hooke> new_playlist --output_playlist mylist
128 Ensure that the new playlist is active::
130 hooke> jump_to_playlist -- -1
132 <FilePlaylist mylist>
134 The ``--`` in the ``jump_to_playlist`` command lets
135 ``jump_to_playlist`` know that ``-1`` is an argument and not an
136 option. Using the bare ``--`` is a POSIX specification [#POSIX]_
137 supported by the `optparse module`_. You don't need to jump if
138 the new playlist is your only loaded playlist.
141 http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments
143 .. [#POSIX] `Guideline 10 of POSIX:2008's section 12.2 <http://www.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap12.html#tag_12_02>`_ states:
145 "The first ``--`` argument that is not an option-argument should be
146 accepted as a delimiter indicating the end of options. Any
147 following arguments should be treated as operands, even if they
148 begin with the ``-`` character."
150 Then glob your curves onto the new list::
152 hooke> glob_curves_to_playlist mycurve.*
154 You can also be more specific with wildcards. For example::
156 hooke> glob_curve_to_playlist mycurve.05*
158 will take only curves from :file:`mycurve.050` to :file:`mycurve.059`.
160 Note that by using ``glob_curves_to_playlist`` you just generate the
161 playlist in the local session. To save your playlist to a file for
164 hooke> save_playlist --output mylist
166 In this example, the list will be saved in the file
167 :file:`mylist.hkp`. Hooke will add the extension ``.hkp`` (Hooke
168 playlist) to the playlist if you forget to. The ``.hkp`` file is an
169 XML file you can read and edit with any text editor (i.e. Wordpad), if
170 needed. If you want to load it, simply issue ``load_playlist
171 mylist.hkp`` or ``load_playlist mylist``, Hooke will add ``.hkp`` if
174 If, generating the playlist, you are including by chance a non-force
175 curve file that Hooke cannot open, Hooke will log a warning and
178 Navigating the playlist
179 -----------------------
181 Now you can navigate through your playlist using the commands
182 ``next_curve`` and ``previous_curve``. You don’t need to type
183 ``next_curve`` every time to run along a list of curves. You can
184 navigate through the command history by using the up and down arrows,
185 or auto-complete partial commands with TAB. From the last curve of
186 your playlist, ``next_curve`` will wrap around to the first curve.
187 Analogously, issuing ``previous_curve`` at the first curve will jump
190 You can also jump to a given curve::
192 hooke> jump_to_curve 14
194 will jump to the 14th curve in the zero-indexed playlist.
196 .. todo:: ``jump_to_curve <PATH>``, where the path can be either an
197 absolute path or a path relative to the directory holding the
200 Replace ``curve`` with ``playlist`` in the above commands to navigate
201 around through the list of loaded playlists.
206 You can take notes about the curves you are looking at. Just type
207 ``set_note`` followed by the text you want to attach to that curve.
208 Hooke will save the text in your current playlist and in an external
211 .. todo:: No external file yet. Is this important?
213 The output will look like this::
215 Notes taken at Sun Sep 17 20:42:07 2006
216 /home/cyclopia/work/tris/20060620a.041 | This is a note
217 /home/cyclopia/work/tris/20060620a.207 | This is another note
218 /home/cyclopia/work/tris/20060620a.286 | This is a third one
220 The log file name can be configured (:doc:`config`), but it defaults
221 to :file:`hooke.log`.
223 Usually curves you annotated are useful later. You can create a
224 playlist for only annotated curves with
226 hooke> note_filter_playlist --name c:\curves\nice.hkp
228 will create sub-playlist :file:`c:\curves\nice.hkp`. Make sure that
229 the target directory (here :file:`c:\curves\`) already exists before
232 If you change your mind about a note, you can remove it by setting a
233 blank note string with ``set_note ''``.
238 You can export Hooke curves as images and as text columns. To export
239 as images or text, use the ``export_block`` command. Supported
240 formats are PNG (Portable Network Graphic, raster) and EPS
241 (Encapsulated Postscript, vector). The export format is determined by
242 the filename extension, so ``export_block foo.png``, ``export_block
243 foo.eps``, and ``export_block foo.txt`` will save PNG, EPS, and
244 TAB-delimited text files respectively.
246 .. todo:: Multiple cycles in exported data? Solution: blank lines for
247 "breaks", add option to extract specific sections using Python's
250 If you don't want the entire block, try the ``cut`` command.
252 Interacting with the plot
253 -------------------------
255 (no plots in command line mode...)
257 Measuring distances and forces
258 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
260 You can move about the plot using its navigation toolbar. See the
261 `Matplotlib manual`_ for details.
263 .. _Matplotlib manual:
264 http://matplotlib.sourceforge.net/users/navigation_toolbar.html
266 You can measure distances and forces directly in the plot. Just issue
267 the command ``delta``. You will be asked to click two points. When
268 you click a point, a blue dot should appear. When you click the
269 second point, the distances will appear in the output panel. If you
270 want to know the coordinates of a single point, left click on it.
272 Hooke automatically adjusts the position of the clicked point to the
273 nearest point in the graph, so you will be always measuring distances
274 and forces between points in the graph.
276 Worm like chain and freely jointed chain fitting
277 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
279 You can measure by hand the parameters relative to a force peak using
280 a worm-like chain fitting with the ``fit`` command. The command by
281 default automatically finds the contact point, asks for two points
282 delimiting the portion to fit, and performs a two-variable fit, with
283 contour length, persistence length, and their relative errors as
284 output. If desired, one can use the ``noauto`` option to manually
285 click the contact point, and/or the ``pl=NUMBER`` options to impose a
286 specific persistence or Kuhn length (in nanometers). You can choose
287 which model to use with ``set fit_function wlc`` or ``set fit_function
288 fjc``. See the help of the ``fit`` command from the Hooke command
291 Multiple curve fitting and measuring
292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 You can cycle through all your current playlist obtaining WLC fit, FJC
295 fit, rupture force and slope (loading rate) information from each
296 curve using the ``multifit`` command. The collected data can be saved
297 in a text file for further analysis in your favourite spreadsheet or
298 statistical program. If you want to check your parameters on the
299 current curve before fitting all the files in your playlist, use
300 ``multifit justone``. See the ``multifit`` help for more options.
302 Fast curve reviewing and saving
303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
305 When automatic routines are not good enough to filter your data, use
306 ``review`` command to cycle through your playlist presenting ten
307 curves in the same graph. You can then enter the numbers of the
308 interesting curves and automatically save a copy of them into another
314 You can set environment variables to influence the behaviour of
315 Hooke. The command to use is ``set_config``. Use ``get_config`` to
316 read a particular option and ``print_config`` to display the entire
317 configuration file. Any changes to the configuration will be saved
318 when you exit Hooke, see :doc:`config` for details.