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,
Exporting curves
----------------
-You can export Hooke curves as images and as text columns. To export
+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
Measuring distances and forces
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-You can move about the plot using its navigation toolbar. See the
-`Matplotlib manual`_ for details.
+To measure the distance between points, use the ``delta`` command.
+For example,::
-.. _Matplotlib manual:
- http://matplotlib.sourceforge.net/users/navigation_toolbar.html
+ hooke> delta 300 500
-You can measure distances and forces directly in the plot. Just issue
-the command ``delta``. 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 will appear in the output panel. If you
-want to know the coordinates of a single point, left click on it.
+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:
-.. todo:: Add description of ``delta``'s command line interface.
+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.
-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.
+.. _Gnuplot: http://gnuplot.sourceforge.net/
Worm like chain and freely jointed chain fitting
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
+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.
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
+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.
projects / hooke.git / blobdiff