The GUI interface
*****************
-by Rolf Schmidt <rschmidt@alcor.concordia.ca>
+Orignially by Rolf Schmidt <rschmidt@alcor.concordia.ca>.
-You can dock/undock all windows except for plot tab (I would like to
-disable docking above the menubar and instead have the windows dock
-beneath the menubar)
+Run the GUI with::
-You can save perspectives (delete perspectives however does not work yet).
+ $ ./bin/hk.py --ui gui
-The 'Navigation' menubar works, the 'Main' menubar does not work yet.
+Alternatively, select `gui` in your config file (see :doc:`config`)::
-Closing plot tabs does not work properly, feedback on specific
-examples and error messages would be much appreciated
+ [user interfaces]
+ command line = False
+ gui = True
-In the 'Folders' pane you can double-click playlists (with hkp
-extension) to open them (you cannot double-click curves to open them)
+Interface
+=========
+Starting Hooke's GUI for the first time, you will see the central plot
+area with the current plot surrounded by the following windows (the `F*`
+key toggles the visibility of the panel):
-Commands in the 'Commands'-pane that work
+* Commands (`F5`)
+* Folders (`F6`)
+* Note (`F7`)
+* Output (`F8`)
+* Playlists (`F9`)
+* Properties (`F10`)
-* autopeak (only partially, everything that has to do with clicking on the plot does not work)
-* genlist
-* loadlist
-* convfilt
-* flatfilt
+.. image:: img/gui_screenshot.jpg
-When you open or generate a playlist, Hooke seems to hang. This is
-actually not the case, just wait. Hooke loads all the curves into
-memory and applies all the plotmanipulators. In the future, there will
-be a progressbar to indicate the progress.
+Initially, the window will be rather small in order to work with small
+screen resolutions. Adjust the size and position to your liking.
+
+Underneath the menus at thte top of the window there is a navigation
+toolbar to switch from one curve to another (next/previous).
+
+Plot area
+=========
+
+The plot area displays the current curve. You can select the data
+column to use as the x axis using the dropdown menu in the plot
+navigation bar (under the plot, not to be confused with the navigation
+bar under the menus). You can select the columns to plot by clicking
+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
+playlist to open it. You can change the initial folder by modifying
+`workdir` in the `preferences` (core plugin).
+
+.. todo:: Implement folders panel.
+
+Playlists
+=========
+You can manage several playlists in this window. As the GUI is rather
+flexible, it is possible to display the curves from different
+playlists side by side to compare them (relatively handy when
+comparing different fit parameters). You can double-click a file in
+the playlist to display it in the plot area. Deleting entire playlists
+or single files can be accomplished by right-clicking and selecting
+`Delete`.
+
+.. todo:: Do we need side-by-side comparison? How did this work in
+ the old GUI?
+
+Commands
+========
+All available commands are listed under their corresponding plugin.
+In order to see a plugin and its commands, you have to edit
+:file:`hooke.conf` and enable th plugin in the plugins section.
+Selecting a plugin or command will display the associated properties
+in the `Properties`_ window. You can edit the properties and click
+`Execute` to run the selected command. If you do not need to modify
+any properties, you can also double-click a command to run it.
+
+Mousing over a plugin or command in the `Commands`_ window will
+display the associated help in a tooltip. The help for the plugin
+should give a general description of the plugin. The help for a
+command should describe the properties available for this command and
+suggest reasonable default values if possible. Feel free to point out
+missing help content.
+
+Properties
+==========
+The properties for the command selected in the `Commands`_ window are
+displayed here. Edit the properties to your satisfaction (some need to
+be confirmed by hitting enter, this seems to be a problem in
+wxPropertyGrid) and click the `Execute` button to run the selected
+command. Floating point values are limited to a certain number of
+decimals (limitation of wxPropertyGrid?) so be careful when using
+floating point values.
+
+.. todo:: Document new, non-PropGrid
+ :mod:`~hooke.ui.gui.panel.propertyeditor`.
+
+Output
+======
+The Output window serves as a log where pertinent information is
+displayed. The output is generally the same as what you would see if
+you were running the commands from the command line.
+
+Note
+====
+A note can be added to every curve: enter your note and click `Update
+note`. With the `note filter playlist` command (`playlist` plugin)
+you can copy all the curves with a note into a new playlist.
+
+General remarks
+===============
+Read :doc:`hacking` for an overview of how Hooke works internally and
+:doc:`config` for more information about configuring Hooke.
+
+Ignore the text on the `Welcome` tab. This tab is more like a proof of
+principle and will contain a short how-to in the future (once the
+howto is written).
+
+Hooke's GUI will remember the size and position of the main window
+(stored in the config file, see :doc:`config`). You can arrange the
+panels any which way you like and save this arrangement as a
+perspective.
+
+.. image:: img/gui_perspective.jpg
+
+Hooke will always start with the last used perspective and you can
+switch from one perspective to another by selecting a perspective from
+the perspectives menu. After deleting a perspective, the radio
+indicator in the perspectives menu disappears (known bug in
+wxPython). This is only a visual problem and does not affect anything
+else.
+
+In order to pan the plot, zoom in and out and export the plot of your
+force curves, use the plot toolbar under the plot. A more detailed
+description is available on the `Matplotlib website`_
+
+.. _Matplotlib website:
+ http://matplotlib.sourceforge.net/users/navigation_toolbar.html
+
+Some plugins and commands
+=========================
+
+* overlay (export): exports all retraction curves in a playlist on the
+ same scale. This is achieved by determining the maximum x window and
+ adding x(max) and x(min) to all curves that are shorter than the
+ maximum x window. Make sure to filter your playlist before running
+ this command!
+
+.. todo:: Implement overlay.
+
+Basic analysis and autopeak
+===========================
+
+.. todo:: Implement autopeak. Bring in autopeak tutorial from the wiki?
+
+Please follow the steps in the :doc:`tutorial`. Instead of typing in
+the command at the command-line, select it in the `Commands`_ window,
+set your properties in the `Properties`_ window and click on
+`Execute` back in the `Commands`_ window.
+
+The :doc:`autopeak` tutorial is also applicable. You need to setup the
+type of fit you want to use: in the Properties of the autopeak command
+(autopeak plugin) select `WLC`, `FJC` or `FJC_PEG` from the dropdown
+list for the `polymer model` argument of `polymer fit`.
+
+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
+interesting curves and automatically save a copy of them into another
+directory.
projects / hooke.git / blobdiff