Update WLC/FJC fitting section of doc/tutorial.txt

[hooke.git] / doc / tutorial.txt

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 6a85383faa3ba4dfbeb9b78725ee1b3f6f5dc9a1..80dfb53bb9e1288165dd1edb17e07d1d741cbe8b 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -42,16 +42,23 @@ to run the Hooke shell.::
 If you are running hooke from the source directory (see
 :doc:`install`), the equivalent command is::
 
 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::
 
 
 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>
 
     ----
     hooke>
 


@@ -74,16 +81,23 @@ Or see specific help on ``TOPIC`` with::
 
 for example::
 
 
 for example::
 

-    hooke> help current
+    hooke> help load_playlist
+
+will give help on the ``load_playlist`` command.

 
 

-will give help on the ``current`` command.
+Leaving Hooke
+-------------
+
+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
 -------------------
 
 
 Creating a playlist
 -------------------
 

-To start analyzing your curves, you first have to build a playlist. The
-playlist is just an index of the force curve files you want to
-analyze. Imagine it as a music playlist (that’s why it is called a
+To start analyzing your curves, you first have to build a playlist.
+The playlist is just an index of the force curve files you want to
+analyze.  Imagine it as a music playlist (that’s why it is called a

 playlist), but with data files instead of audio files.
 
 Suppose you have 100 PicoForce curve files in your curves directory,
 playlist), but with data files instead of audio files.
 
 Suppose you have 100 PicoForce curve files in your curves directory,


@@ -92,7 +106,7 @@ 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.::
 


@@ -103,155 +117,200 @@ You can list the files in the directory using ``ls`` or ``dir``
 (they’re synonyms).::
 
     hooke> ls
 (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>
+
+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.

 
 

-Now you are ready to generate the playlist. The command to use is
-``genlist``.::
+.. _optparse module:
+  http://docs.python.org/library/optparse.html#callback-example-6-variable-arguments

 
 

-    hooke> genlist mycurve.*
+.. [#POSIX] `Guideline 10 of POSIX:2008's section 12.2 <http://www.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap12.html#tag_12_02>`_ states:

 
 

-You can also generate a playlist containing all what you find in the
-directory by typing:
+    "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."

 
 

-    hooke> genlist c:\curves
+Then glob your curves onto the new list::

 
 

-If you want to select what curves to see, based on the filename, you
-can use wildcards.  For example::
+    hooke> glob_curves_to_playlist mycurve.*

 
 

-    hooke> genlist mycurve.05*
+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`.
 
 
 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
 
 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
 
 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
 -----------------------
 
 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::
 
 
 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
 
 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
 
     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`.
 
 
 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
 ----------------
 
 
 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.
+You can export Hooke curves as images and as text columns.  To export
+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
--------------------------
+Analysis
+--------

 
 

-(no plots in command line mode...)
+The commands we have covered so far allow basic bookkeeping.  The
+point of Hooke, though, is to allow you to easily analyze force
+spectroscopy data.  We cover those analysis commands in this section.

 
 Measuring distances and forces
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
 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.
+To measure the distance between points, use the ``delta`` command.
+For example,::
+
+    hooke> delta 300 500

 
 

-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``.
+will measure the distance between the 300th point and the 500th point.
+One difficulty with the command line interface is that is difficult
+to know which points you're interested without seeing the plot.  The
+two ways around this are:

 
 

-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.
+1) Export the block (with ``export_block``), and graph the exported
+   file with a program of your choice (e.g. Gnuplot_).  Use the
+   resulting graph to determine the indices of the points you are
+   interested in.
+2) Run Hooke's GUI instead of the command line when you need to make
+   manual measurements.  See :doc:`gui` for details.

 
 

-The commands ``force`` and ``distance`` are present in the
-``generalvclamp`` plugin.
+.. _Gnuplot: http://gnuplot.sourceforge.net/

 
 Worm like chain and freely jointed chain fitting
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 
 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
-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
-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.
+Polymer model fitting is a complicated beast.  To correctly fit your
+chosen model (WLC, FJC, etc.), you need to execute a multi-step
+analysis.  Hooke provides a flexible chain of curve analyisis commands
+that create new data columns (e.g. `deflection (N)`) or store
+information in a curve's `info` dictionary (e.g. `flat filter peaks`).
+You can, if necessary, adjust the names of input and output columns
+and `info` values to combine the available commands in new and useful
+ways.
+
+    hooke> zero_surface_contact_point --block retract
+    hooke> flat_filter_peaks --block retract --min_points 1
+    hooke> zero_surface_contact_point --block retract
+    ...        --ignore_after_last_peak_info_name 'flat filter peaks'
+    hooke> convert_distance_to_force --block retract
+    ...        --deflection_column 'surface deflection (m)'
+    hooke> remove_cantilever_from_extension --block retract
+    hooke> flat_peaks_to_polymer_peaks --block retract
+    hooke> polymer_fit_peaks --block retract
+    hooke> export_block --block retract --output myblock.dat
+
+See each command's `Help`_ for details.
+
+.. todo:: Discuss command stacks and polymer model fitting.

 
 Multiple curve fitting and measuring
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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
 
 You can cycle through all your current playlist obtaining WLC fit, FJC
 fit, rupture force and slope (loading rate) information from each


@@ -264,6 +323,8 @@ current curve before fitting all the files in your playlist, use
 Fast curve reviewing and saving
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 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
 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


@@ -273,9 +334,9 @@ directory.
 Configuring Hooke
 -----------------
 
 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.
 details.