From: W. Trevor King Date: Tue, 17 Aug 2010 10:57:44 +0000 (-0400) Subject: Update distance-measurement sections of doc/tutorial.txt and doc/gui.txt X-Git-Url: http://git.tremily.us/?p=hooke.git;a=commitdiff_plain;h=efb1f76427c4d4dfd950cf7ed6643808693c4022 Update distance-measurement sections of doc/tutorial.txt and doc/gui.txt --- diff --git a/doc/gui.txt b/doc/gui.txt index f8ee894..17ec5f4 100644 --- a/doc/gui.txt +++ b/doc/gui.txt @@ -43,6 +43,27 @@ the `y column(s)` button and checking interesting columns. We suggest you stick to columns with a single unit, and not try and dispay, for example, both meters and newtons on the same y axis. +You can move about the plot using its navigation toolbar. See the +`Matplotlib manual`_ for details. + +.. _Matplotlib manual: + http://matplotlib.sourceforge.net/users/navigation_toolbar.html + +You can measure distances and forces directly in the plot. If you +want to know the coordinates of a single point, left click on it. The +index and coordinates of the nearest data point will be displayed in +the status bar along with the x and y coordinates of your click. + +To find the distance between two points, 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. 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. + +.. todo:: Implement blue dots and click handler. + Folders ======= Here you can navigate your file system and double click on a saved diff --git a/doc/tutorial.txt b/doc/tutorial.txt index 714c597..89a1919 100644 --- a/doc/tutorial.txt +++ b/doc/tutorial.txt @@ -95,9 +95,9 @@ the end of the stdin stream, which is Ctrl-d in many shells). 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, @@ -234,7 +234,7 @@ blank note string with ``set_note ''``. 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 @@ -260,23 +260,24 @@ Interacting with the plot 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -290,7 +291,7 @@ 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 +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. @@ -321,9 +322,9 @@ directory. 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.