X-Git-Url: http://git.tremily.us/?a=blobdiff_plain;f=doc%2Ftutorial.txt;h=714c59716e60fc5c8d238e0c72bd78766525af81;hb=226c1eeae314e3148c4d25074794c86d947129fd;hp=6bfe3e0ce54f45a8e6d34dadd311e9d4cb14e764;hpb=67d118cf221744a832ead64a560f384869e39cea;p=hooke.git diff --git a/doc/tutorial.txt b/doc/tutorial.txt index 6bfe3e0..714c597 100644 --- 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 ``, 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.