Commit ff4dae18 authored by Sebastian Eichelbaum's avatar Sebastian Eichelbaum
Browse files

[ADD #380] added Qt5 gui. Not yet compiling properly.

parent 34291e7c
OpenWalnut is an open source tool for multi-modal medical
and brain data visualization. Its universality allows it
to be easily extended and used in a large variety of application
cases. It is both, a tool for the scientific user and a
powerful framework for the visualization researcher.
OpenWalnut is licensed under the terms of the GNU Lesser
General Public License. Written entirely in Standard C++
and using a number of portable libraries (e.g. OpenSceneGraph and Qt)
it runs on all Windows platforms, OSX and GNU/Linux operating systems. <br />
<br />
Copyright 2009-2014 OpenWalnut community, Nemtics, BSV@Uni-Leipzig, and
CNCF@MPI-CBS. For more information see
<a href=""></a>.<br><br>
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under the terms of the GNU Lesser General Public License.
You should have received a copy of the GNU Lesser General Public License
along with OpenWalnut. If not, see
&lt;<a href=""></a>&gt;.
Website: <a href=""></a><br>
Email: <a href=""></a>
<i>Thank you for using OpenWalnut!</i>
<p>Visualization is our business! Visualization makes data perceptible and imaginable to the mind.
It is the interface between the user and imaging systems, measurement hardware, processing software,
simulation systems, and so much more. Accordingly, visualization's importance can't be
ranked high enough!
We provide software, frameworks, training and consulting on visualization. As a major developer
and maintainer of OpenWalnut, we
provide professional user- and developer-support to it. This allows our customers and users of OpenWalnut
to rely on professional support and a vivid development of the project.
You need help, require features to be implemented or simply need training? Get in touch with us!</p>
Website: <a href=""></a><br>
Email: <a href=""></a>
<i>Thank you for using OpenWalnut!</i>
<body bgcolor="#fff">
<h1>OpenWalnut Help <img src="images/openwalnut.png"/></h1>
<li><a href="#Introduction">Introduction</a></li>
<li><a href="#FirstSteps">First Steps</a></li>
<li><a href="#MainWindow">Main Window</a></li>
<li><a href="#Navigation">Navigation</a></li>
<li><a href="#Keyboard">Keyboard Shortcuts</a></li>
<li><a href="#Toolbar">Toolbar</a></li>
<li><a href="#ROIs">Regions of Interest</a></li>
<li><a href="#Config">Customizing OpenWalnut</a></li>
<h2><a name="Introduction" />Introduction</h2>
The intention of this help document is to give a short overview of how to use the current version
of OpenWalnut. Although it is not at all comprehensive,
it provides a description of the most commonly used features and GUI elements.
As described <a href="#Config">below</a>, the appearance of the GUI is customizable. This help document
assumes the standard configuration. Additionally, some described features may not be available
in every instance of OpenWalnut because they belong to special modules.
<h2><a name="FirstSteps" />First Steps</h2>
<a href="">This</a> tutorial shows you the basic usage of OpenWalnut. You should consider reading this if you are a first time user.
<h2><a name="MainWindow" />Main Window</h2>
This is the main window of OpenWalnut. It is divided into three parts. The navigation views, the main view and the data manipulation GUI.
<img src="images/2_overview.png"/>
<li> 1,2, and 3 - The navigation windows. Use them for orientation and
to select the <i>current</i> position.
<li> 4 - The main view. The main view allows interaction with the visualization and the camera in 3D.
<li> 5 - The module tree. This shows the current setup of your data flow. Use this to process data and to apply visualization.
<li> 6 - The control panel. This shows parameters and further information of the currently selected module. Use this to interact with your
<h2><a name="Navigation" />Navigation</h2>
<h3>Navigation in Main View</h3>
<tr><td><b><i>Mouse Button&nbsp;&nbsp;</i></b></td><td><b><i>Action</i></b></td></tr>
<tr><td>Right</td><td>Pick, move <a href="#ROIs">ROI</a> box, or move slice</td></tr>
<tr><td>Right + [Shift]</td><td>Resize <a href="#ROIs">ROI</a> box</td></tr>
<tr><td>+</td><td>Zoom in</td></tr>
<tr><td>-</td><td>Zoom out</td></tr>
<tr><td>[Space]</td><td>Reset view</td></tr>
<h3>Navigation in EEG View</h3>
<tr><td><b><i>Mouse Button</i></b></td><td><b><i>Action</i></b></td></tr>
<tr><td>Left</td><td>Mark event position</td></tr>
<tr><td>Right</td><td>Zoom in time</td></tr>
<tr><td>Wheel</td><td>Scale voltage</td></tr>
<tr><td>Wheel + Right</td><td>Change spacing between graphs</td></tr>
<tr><td>Wheel + Left</td><td>Change sensitivity of the coloring of the head surface</td></tr>
<h2><a name="Keyboard" />Keyboard Shortcuts</h2>
<h3>Program-wide Keyboard Shortcuts</h3>
<tr><td>[Ctrl] + q</td><td>Quit</td></tr>
<tr><td>[Esc]</td><td>Resets main view</td></tr>
<tr><td>[F1]</td><td>Opens help window</td></tr>
<h3>ROI Tree</h3>
<tr><td>[Delete]</td><td>Removes <a href="#ROIs">ROI</a></td></tr>
<h3>Module Tree</h3>
<tr><td>[Delete]</td><td>Removes module</td></tr>
<h2><a name="Toolbar" />Toolbar</h2>
<tr><td><img src="images/new.png" width="20"></td><td>New
Project</td><td>Removes all modules, including the data modules,
to provide a clean OpenWalnut session for a new project.
<tr><td><img src="images/load.png" width="20"></td><td>Load
Dataset or Project</td><td>Loads data given in various formats or
project files. Data files can be fibers (.fib), NIfTI
images (.nii, .nii.gz) or EEG data (.cnt). Not all supported file formats
are available through this button and the dialog behind it. For some file
formats there are special modules for reading and/or writing them. Project
files (.owp, .owproj) instantiate modules, set their
connections and orient the scene accordingly.</td></tr>
<tr><td><img src="images/save.png" width="20"></td><td>Save Project</td><td>Saves the current state (modules, connections, orientation of
the scene) of OpenWalnut to a project file (.owp, .owproj).</td></tr>
<tr><td><img src="images/image.png"
width="20"></td><td>Screenshot</td><td>Stores a snapshot image of
the main view.</td></tr>
<tr><td><img src="images/camera.png" width="20"></td><td>Reset</td><td>Rotates
and scales the scene in the central 3D view to show the same orientation as
after program startup but zoomed to show all contents of the
<tr><td><img src="images/roi.png" width="20"></td><td>ROI</td><td>Adds a new ROI box to the 3D scene and the ROI browser. See also: <a href="#ROIs">ROIs</a>.</td></tr>
<tr><td><img src="images/question.png" width="20"></td><td>Missing
module?</td><td>Opens the dialog that allows to customize the list of
modules that are allowed to appear in the <i>Compatible Modules</i> toolbar.</td></tr>
<h2><a name="ROIs" />Regions of Interest</h2>
A ROI (<b>r</b>egion <b>o</b>f <b>i</b>nterest) is usually used to specify a
certain area (2D) or volume (3D) that can then be accessed by
modules. Different modules will use ROIs for different purposes. The most
important purpose of ROI boxes in OpenWalnut is the selection of fibers in
conjunction with fiber display modules. This is described in a separate
section below.
The ROIs can be moved around by dragging them with the right mouse
button. Their size can be changed by dragging one of their faces with the right
mouse button while the [Shift] key is pressed.
<h3>ROIs for Selecting Fibers</h3>
For the special task of selecting fiber bundles from larger sets of fibers, ROIs can be
combined in the ROI tree widget. All ROIs in the same branch of the tree are
combined using a Boolean "and" operation. The result will be a bundle
consisting only of fibers that pass through all boxes in the branch. The branches themselves are combined
using a Boolean "or" operation. This means that the bundles selected by the
different branches will be visible/selected at the same time.
<h2><a name="Config" />Customizing OpenWalnut</h2>
OpenWalnut allows you to configure several features. Most of these options are
only useful to advanced users. Have a look into the <i>View</i>, <i>Camera</i> and <i>Settings</i>
menus for what you can adapt. If you would like to configure which modules are
allowed to be shown in the toolbar click on the <tt>Missing Module?</tt> button
with the three question marks. The appearing dialog will provide enough information
and the possibility to customize which modules may appear. This can be useful
to maintain a not too crowded toolbar.
<br />
<br />
<font color="#aaa">
<small><b>For more information on OpenWalnut
visit <a href=""></a>.</b></small>
<h1>Need Support?</h1>
Do you need professional support? We can provide training, development courses, and contract-based feature implementations.
Get in touch with us!
Website: <a href=""></a><br>
Email: <a href=""></a>
<i>Thank you for using OpenWalnut!</i>
<div style='font-family:sans-serif;'>
<div style='padding:10px; border:0px solid #000; border-bottom-width: 10px;color:#fff;background:#0c67a8;'>
Welcome to OpenWalnut!
<div style='padding:10px; background:#ddd;'>
<h3>Version Information</h3>
This is %OW_VERSION%. You can check out the
<a href="">Release Notes</a> and the
<a href="">Changelog</a> for detailled information on fixed bugs, new features and other
<div style='padding:10px; background:#eee;'>
<h3>Further Information</h3>
<div style='padding:10px; ;'>
Hello User! You see this dialog because you have started this version of OpenWalnut the first time.
Are you new to OpenWalnut? Have a look at <a href=""></a>!
We provide
<li> <a href="">a first steps tutorial</a>,
<li> a user documentation,
<li> programming tutorials,
<li> and the latest information on OpenWalnut.
Do you have problems using OpenWalnut? Do not hesitate to ask:
<li><a href="">Mailing list</a>
<li>IRC Chat on, channel #ow
Found a bug? Do you have ideas for improvements? Please <a href="">report</a> these issues! We can improve OpenWalnut only with your help and ideas.
<i>Thank you for using OpenWalnut!</i>
# get path of this script
BINDIR=`dirname "$0"`
# IMPORTANT: The following code is not compatible with many specifics of certain Linux Distros.
# We disable it. If you having trouble running multiple locally installed versions of OW, you can use
# this code again.
# You might need to adapt the LIBDIR variable. Some systems use "lib32", "lib64" and similar. Debian
# uses lib/x86_64-linux-gnu for amd64 systems.
# strip "bin" to get base directory
# BASEDIR=`dirname "$BINDIR"`
# We want to avoid that multiple system installations of OpenWalnut cause some weird loading of libs. We want ours (relative to our executable) to be loaded:
# Well, this one needs to be there! If not, your installation is wrong.
# We need to ensure the libs are there. If not, do not add them to the preloads variable
#for lib in $Libs
# libfile=$LIBDIR/$lib
# if [ -e "$libfile" ]; then
# Preloads=$Preloads:$libfile
# fi
# Finally, export it
#export LD_PRELOAD=$Preloads
# If the user has installed OSG manually into a non-standard location, we need to set some OSG paths.
# This command uses libopenwalnuts dependencies to find the libosgDB directory.
# NOTE: if this command fails, script will continue execution
#export OSG_LIBRARY_PATH=$(dirname `ldd lib/ | grep "libosgDB" | awk '{print $3;}'` 2> /dev/null)
# Force C locale. This fixes an issue with newer boost versions. See ticket #130.
export LC_ALL=C
# Check if the user has set $OPENWALNUT_USEOPTIMUS to an executable
if [ -x "$OPENWALNUT_USEOPTIMUS" ]; then
echo "Optimus implementation found. Using "$OPENWALNUT_USEOPTIMUS""
# Run OpenWalnut
$runner $BINDIR/openwalnut-qt5 "$@"
[Desktop Entry]
Keywords=visualization;medical data;neuroscience;
:: Add lib and bin to PATH to allow all the libs to be found properly
set PATH=./lib/;./bin/;%PATH%
:: Add externals to PATH
set PATH=./ext;%PATH%
:: Finally, run OpenWalnut
## A list of modules that will be provided through the GUI. Modules not
## listed here, will be hidden in the GUI but still available in scripts
## and project files.
## recommendation list:
recommended = Arbitrary Plane,Coordinate System,Image Extractor,Paint Texture,Arbitrary Rois,Bounding Box,Distance Map Isosurface,Gauss Filtering,HUD,Isosurface,Isosurface Raytracer,LIC,Read Mesh,Voxelizer,Superquadric Glyphs,Triangle Mesh Renderer,Vector Plot,Write NIfTI,Fiber Display,Fiber Display Simple,Read Spherical Harmonics,Navigation Slices,Deterministic Tract Clustering using Gaussian Processes,Deterministic Tract to Gaussian Process Converter,Cluster Param Display,Write Tracts,Fiber Resampling,Grid Renderer,Spatial Derivative,Scalar Operator,Vector Operator,Colormapper
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