Added test/tutorial.py. Works until you get to note_filter_playlist

[hooke.git] / doc / tutorial.txt

diff --git a/doc/tutorial.txt b/doc/tutorial.txt
index 6bfe3e0ce54f45a8e6d34dadd311e9d4cb14e764..714c59716e60fc5c8d238e0c72bd78766525af81 100644 (file)
--- a/doc/tutorial.txt
+++ b/doc/tutorial.txt
@@ -42,7 +42,7 @@ to run the Hooke shell.::
 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
@@ -123,7 +123,7 @@ You can list the files in the directory using ``ls`` or ``dir``
 
 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::
 
@@ -134,7 +134,8 @@ 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
@@ -171,7 +172,7 @@ 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
@@ -190,12 +191,15 @@ You can also jump to a given curve::
 
     hooke> jump_to_curve 14
 
-will jump to the 14th curve in the playlist.
+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
 ------------
 
@@ -219,11 +223,10 @@ to :file:`hooke.log`.
 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 ''``.
@@ -235,9 +238,13 @@ 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 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:: 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
@@ -265,6 +272,8 @@ 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.
@@ -272,6 +281,8 @@ 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
@@ -286,6 +297,7 @@ line for details.
 
 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
@@ -298,6 +310,8 @@ current curve before fitting all the files in your playlist, use
 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
@@ -310,5 +324,6 @@ Configuring Hooke
 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.