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
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.. 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
-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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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