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.
99 The 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.
203 Because the playlist name is usually saved in the playlist file
204 itself, there is a ``name_playlist`` command that allows you to rename
205 playlists on the fly.
207 hooke> name_playlist 'my old playlist'
212 You can take notes about the curves you are looking at. Just type
213 ``set_note`` followed by the text you want to attach to that curve.
214 Hooke will save the text in your current playlist and in an external
217 .. todo:: No external file yet. Is this important?
219 The output will look like this::
221 Notes taken at Sun Sep 17 20:42:07 2006
222 /home/cyclopia/work/tris/20060620a.041 | This is a note
223 /home/cyclopia/work/tris/20060620a.207 | This is another note
224 /home/cyclopia/work/tris/20060620a.286 | This is a third one
226 The log file name can be configured (:doc:`config`), but it defaults
227 to :file:`hooke.log`.
229 Usually curves you annotated are useful later. You can create a
230 playlist for only annotated curves with
232 hooke> note_filter_playlist --output_playlist nice_list
234 will create sub-playlist `nice_list`. Remember to save the new list
237 If you change your mind about a note, you can remove it by setting a
238 blank note string with ``set_note ''``.
243 You can export Hooke curves as images and as text columns. To export
244 as images or text, use the ``export_block`` command. Supported
245 formats are PNG (Portable Network Graphic, raster) and EPS
246 (Encapsulated Postscript, vector). The export format is determined by
247 the filename extension, so ``export_block --output foo.png``,
248 ``export_block --output foo.eps``, and ``export_block --output
249 foo.txt`` will save PNG, EPS, and TAB-delimited text files
252 .. todo:: Currently no PNG or EPS output, use the GUI and the plot
253 panel's toolbar for non-text exports.
255 .. todo:: Multiple cycles in exported data? Solution: blank lines for
256 "breaks", add option to extract specific sections using Python's
259 If you don't want the entire block, try the ``cut`` command.
264 The commands we have covered so far allow basic bookkeeping. The
265 point of Hooke, though, is to allow you to easily analyze force
266 spectroscopy data. We cover those analysis commands in this section.
268 Measuring distances and forces
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
271 To measure the distance between points, use the ``delta`` command.
276 will measure the distance between the 300th point and the 500th point.
277 One difficulty with the command line interface is that is difficult
278 to know which points you're interested without seeing the plot. The
279 two ways around this are:
281 1) Export the block (with ``export_block``), and graph the exported
282 file with a program of your choice (e.g. Gnuplot_). Use the
283 resulting graph to determine the indices of the points you are
285 2) Run Hooke's GUI instead of the command line when you need to make
286 manual measurements. See :doc:`gui` for details.
288 .. _Gnuplot: http://gnuplot.sourceforge.net/
290 Worm like chain and freely jointed chain fitting
291 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 Polymer model fitting is a complicated beast. To correctly fit your
294 chosen model (WLC, FJC, etc.), you need to execute a multi-step
295 analysis. Hooke provides a flexible chain of curve analyisis commands
296 that create new data columns (e.g. `deflection (N)`) or store
297 information in a curve's `info` dictionary (e.g. `flat filter peaks`).
298 You can, if necessary, adjust the names of input and output columns
299 and `info` values to combine the available commands in new and useful
302 hooke> zero_surface_contact_point --block retract
303 hooke> flat_filter_peaks --block retract --min_points 1
304 hooke> zero_surface_contact_point --block retract
305 ... --ignore_after_last_peak_info_name 'flat filter peaks'
306 hooke> convert_distance_to_force --block retract
307 ... --deflection_column 'surface deflection (m)'
308 hooke> remove_cantilever_from_extension --block retract
309 hooke> flat_peaks_to_polymer_peaks --block retract
310 hooke> polymer_fit_peaks --block retract
312 This stores the fit parameters in the block's
313 :attr:`~hooke.curve.Data.info` dictionary (see each command's `Help`_
314 for details). To access the parameters, save the playlist,::
316 hooke> save_playlist --output mylist.hkp
318 load it with PyYAML_::
322 >>> import hooke.util.yaml
323 >>> mylist = yaml.load(open('mylist.hkp', 'r'))
325 navigate to your curve,::
327 >>> mylist.jump(1234)
329 and extract your parameter.::
331 >>> mylist.current().data[1].info['polymer peak 0']['contour length (m)']
334 You can also get a list of all available parameters::
336 >>> mylist.current().data[1].info['polymer peak 0'].keys()
337 ['model', 'contour length (m)', 'temperature (K)', 'fit',
338 'persistence length (m)']
340 or just pprint_ the whole thing::
342 >>> from pprint import pprint
343 >>> pprint(mylist.current().data[1].info['polymer peak 0'])
344 {'contour length (m)': 2.1248220207858103e-08,
345 'fit': {'active fitted parameters': 3.7024307200788127,
346 'active parameters': 3.7024307200788127,
347 'convergence flag': 1,
348 'covariance matrix': None,
349 'data scale factor': 5.2716380732198972e-10,
350 'fitted parameters': -2.5663294148411571,
351 'info': {'fjac': None,
356 'initial parameters': [-0.69314718055994529],
357 'message': 'Both actual and predicted relative reductions in the sum of squares\n are at most 0.000000',
361 'persistence length (m)': 4.0000000000000001e-10,
362 'temperature (K)': 301.0}
364 .. _PyYAML: http://pyyaml.org/
365 .. _pprint: http://docs.python.org/library/pprint.html
367 .. todo:: UI access to block (and curve?) info dicts. Someone should
368 make a tree-based object browser ;).
370 .. todo:: Playlists currently drop all :class:`~hooke.curve.Data`
371 instances when they are unloaded, so you can't extract the fitted
372 parameters from unloaded curves. We'll need a way to export chosen
373 curve attributes to file.
378 Since you are likely to apply similar analysis to several curves,
379 Hooke provides :mod:`command stacks <hooke.command_stack>` for
380 bundling groups of commands.::
382 hooke> start_command_capture
383 hooke> zero_surface_contact_point --block retract
384 hooke> flat_filter_peaks --block retract --min_points 1
386 hooke> stop_command_capture
388 You can check the state of the command stack with
389 ``get_command_stack`` and the state of capture with
390 ``get_command_capture_state``. If you make mistakes, you can pop
391 commands from the stack with ``pop_command_from_stack``. If you stop
392 capturing a command stack (e.g. to test a complicated command before
393 continuing), you can continue adding to the same stack with
394 ``restart_command_capture.``
396 To execute a command stack, run::
398 hooke> execute_command_stack
400 To execute a command stack on every curve in a playlist, run::
402 hooke> apply_command_stack_to_playlist
404 If you decide that there are commands in a curve's stack that you
405 don't want, you can clear the stack with::
407 hooke> clear_curve_command_stack
409 You can also save command stacks to disk (and reload them later,
410 potentially in a different Hooke session).::
412 hooke> save_command_stack --output my_stack
413 hooke> load_command_stack --input my_stack
415 Multiple curve analysis
416 ~~~~~~~~~~~~~~~~~~~~~~~
418 You can analyze multiple curves by combining `Worm like chain and
419 freely jointed chain fitting`_ and `Command stacks`_.::
421 hooke> start_command_capture
422 hooke> zero_surface_contact_point --block retract
423 hooke> flat_filter_peaks --block retract --min_points 1
424 hooke> zero_surface_contact_point --block retract
425 ... --ignore_after_last_peak_info_name 'flat filter peaks'
426 hooke> convert_distance_to_force --block retract
427 ... --deflection_column 'surface deflection (m)'
428 hooke> remove_cantilever_from_extension --block retract
429 hooke> flat_peaks_to_polymer_peaks --block retract
430 hooke> polymer_fit_peaks --block retract
431 hooke> export_block --block retract --output myblock.dat
432 hooke> stop_command_capture
433 hooke> apply_command_stack_to_playlist
438 You can set environment variables to influence the behaviour of Hooke.
439 The command to use is ``set_config``. Use ``get_config`` to read a
440 particular option and ``print_config`` to display the entire
441 configuration file. To save changes, either run ``save_config`` or
442 start Hooke with the ``--save-config`` option. See :doc:`config` for