[ADD] Now the fiberStipple and isoLine modules are living inside this toolbox,...

[ADD] Now the fiberStipple and isoLine modules are living inside this toolbox, not polluting our pristine sources for our framework

FiberStippleToolbox/COPYING

+You are free to copy, modify and re-distribute these files as you like.

FiberStippleToolbox/README

+* This is an example of how to create your own module toolbox
+  for OpenWalnut (http://www.openwalnut.org).
+
+* You should have a look at our WIKI for further details under
+  http://www.openwalnut.org/projects/openwalnut/wiki/Module_ExternalDevelopment
+
+* It basically creates one library with two modules in it.
+  You can use this example as your basic development setup
+  and extend it as you need.
+
+* Please contact us if you have trouble or if you have added
+  platform support to the OpenWalnut.cmake script. We 
+  appreciate your help!
+
+
+Happy coding!
+- The OpenWalnut Team -

FiberStippleToolbox/VERSION

+# OW Version File. This file specifies the version. The line VERSION=X.Y.Z is
+# used and parsed. This file has to be here everytime. The VERSION needs to be
+# set properly or CMake will fail.
+#
+# SYNTAX: The version string always is 1.2.3 with an optional postfix of "+hg1234".
+#         This is useful if building is done by scripts. If you want to automatically
+#         add the correct HG revision, use only +hgX without number.
+#
+# IMPORTANT: If you modify the file, cmake re-creates the version header. But
+#            it is not able to set all library version. Please re-run cmake if
+#            you change something here.
+#
+# NOTE: do not add a space after #. The current CMake script will fail.
+# Examples:
+#VERSION=1.2.0
+#VERSION=1.2.0+hgX  -> replaces the X with the current revision number
+#VERSUIB=1.2.0+hg1234 -> here, revision number was set by the build scripts for example.
+VERSION=0.1.0+hgX

FiberStippleToolbox/doc/developer/doxygenLayout.xml

+<doxygenlayout version="1.0">
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title=""/>
+    <tab type="pages" visible="yes" title=""/>
+    <tab type="modules" visible="yes" title="Groups"/>
+    <tab type="namespaces" visible="yes" title="">
+      <tab type="namespaces" visible="yes" title=""/>
+      <tab type="namespacemembers" visible="yes" title=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="">
+      <tab type="classes" visible="yes" title=""/>
+      <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="hierarchy" visible="yes" title=""/>
+      <tab type="classmembers" visible="yes" title=""/>
+    </tab>
+    <tab type="files" visible="yes" title="">
+      <tab type="files" visible="yes" title=""/>
+      <tab type="globals" visible="yes" title=""/>
+    </tab>
+    <tab type="dirs" visible="yes" title=""/>
+    <tab type="examples" visible="yes" title=""/>  
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <allmemberslink visible="yes"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <typedefs title=""/>
+      <enums title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <briefdescription visible="yes"/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <briefdescription visible="yes"/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <briefdescription visible="yes"/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <nestedgroups visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+    <memberdef>
+      <pagedocs/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <briefdescription visible="yes"/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+    <detaileddescription title=""/>
+  </directory>
+</doxygenlayout>

FiberStippleToolbox/resources/MyGlobalResources/share/openwalnut/modules/MyOpenWalnutToolbox/some_global_resource_file

+example global resource file

FiberStippleToolbox/src/CMakeLists.txt

+#---------------------------------------------------------------------------
+#
+# Project: OpenWalnut ( http://www.openwalnut.org )
+#
+# Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+# For more information see http:#www.openwalnut.org/copying
+#
+# This file is part of OpenWalnut.
+#
+# OpenWalnut is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# OpenWalnut is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with OpenWalnut. If not, see <http:#www.gnu.org/licenses/>.
+#
+#---------------------------------------------------------------------------
+
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+#
+# General CMake Setup
+#
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+PROJECT( FiberStippleToolbox )
+
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+#
+# Include the OpenWalnut build system.
+#
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+
+# where to find our utils and cmake modules?
+SET( OW_TOOLS_DIR ${PROJECT_SOURCE_DIR}/../tools )
+
+# append search path for FindModules:
+LIST( APPEND CMAKE_MODULE_PATH ${OW_TOOLS_DIR}/cmake )
+
+# These scripts contains all the needed tools to setup the build:
+# * Compiler Setup
+# * Common OpenWalnut Options
+# * Third-party Dependencies Setup
+# * Unit Testing Setup if found
+# * Doxygen Setup if found
+INCLUDE( OpenWalnut )
+
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+#
+# Setup your additional dependencies and tools
+#
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+
+# IMPORTANT: NEVER add any commands bore the line INCLUDE( OpenWalnut ). This might cause problems!
+
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+#
+# Setup all modules
+#
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+
+# Here, you can add your own targets, call ADD_MODULE provided by OpenWalnut or a combination of it. When using ADD_MODULE or SETUP_MODULE, the
+# OpenWalnut CMake scripts manages proper resource handling, test compilation and similar. You should use it whenever possible. More details on
+# how to develop external modules, have a look at http://www.openwalnut.org. You can have a look at OpenWalnut.cmake if you want to modify
+# the default behaviour.
+
+# Please see the documentation of SETUP_MODULE as it shows how to add custom dependencies (third-party libs)
+
+SETUP_MODULE( 
+    ${PROJECT_NAME}   # use project name as module(-toolbox) name
+    "."               # where to find the sources
+    ""                # no additonal dependencies
+    ""                # no sources to exclude
+)
+
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+#
+# Additional Setup
+#
+# ---------------------------------------------------------------------------------------------------------------------------------------------------
+
+# Add the files under ../resources/MyGlobalResources as additional, global resources
+# The first parameter is the directory name, the second parameter is the component name. This is used during installation to identify to which
+# install component this belongs. The name is arbitrary but must be unique.
+#
+# NOTE: The first parameter of SETUP_MODULE is not allowed as component name here because SETUP_MODULE already registers this component. Simply
+# append some string.
+SETUP_GLOBAL_RESOURCES( "MyGlobalResources" ${PROJECT_NAME}_Global )

FiberStippleToolbox/src/WToolkit.cpp

+#include <boost/shared_ptr.hpp>
+
+#include <core/kernel/WModule.h>
+
+#include "fiberStipples/WMFiberStipples.h"
+#include "isoLines/WMIsoLines.h"
+
+#include "WToolkit.h"
+
+// This file's purpose is to provide a list of modules as entry point for OpenWalnut's module loader.
+// Add your modules here. If you miss this step, OpenWalnut will not be able to load your modules.
+extern "C" void WLoadModule( WModuleList& m ) // NOLINT
+{
+    m.push_back( boost::shared_ptr< WModule >( new WMIsoLines ) );
+    m.push_back( boost::shared_ptr< WModule >( new WMFiberStipples ) );
+}
+

FiberStippleToolbox/src/WToolkit.h

+#ifndef WTOOLKIT_H
+#define WTOOLKIT_H
+
+// nothing to do here. Have a look at WToolkit.cpp for registration of all the modules inside the toolbox.
+
+#endif  // WTOOLKIT_H
+

FiberStippleToolbox/src/fiberStipples/WMFiberStipples.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WMFIBERSTIPPLES_H
+#define WMFIBERSTIPPLES_H
+
+#include <string>
+
+#include "core/kernel/WModule.h"
+
+// forward declarations to reduce compile dependencies
+template< class T > class WModuleInputData;
+class WDataSetScalar;
+class WDataSetVector;
+class WGEManagedGroupNode;
+
+/**
+ * Draws Fiber Stipples on slice in order to visualize probabilistic tractograms.
+ *
+ * \note For further information see http://dx.doi.org/10.1109/BioVis.2011.6094044.
+ *
+ * \ingroup modules
+ */
+class WMFiberStipples: public WModule
+{
+public:
+    /**
+     * Default constructor.
+     */
+    WMFiberStipples();
+
+    /**
+     * Destructor.
+     */
+    virtual ~WMFiberStipples();
+
+    /**
+     * Gives back the name of this module.
+     * \return the module's name.
+     */
+    virtual const std::string getName() const;
+
+    /**
+     * Gives back a description of this module.
+     * \return description to module.
+     */
+    virtual const std::string getDescription() const;
+
+    /**
+     * Due to the prototype design pattern used to build modules, this method returns a new instance of this method. NOTE: it
+     * should never be initialized or modified in some other way. A simple new instance is required.
+     *
+     * \return the prototype used to create every module in OpenWalnut.
+     */
+    virtual boost::shared_ptr< WModule > factory() const;
+
+    /**
+     * Get the icon for this module in XPM format.
+     * \return The icon.
+     */
+    virtual const char** getXPMIcon() const;
+
+protected:
+    /**
+     * Entry point after loading the module. Runs in separate thread.
+     */
+    virtual void moduleMain();
+
+    /**
+     * Initialize the connectors this module is using.
+     */
+    virtual void connectors();
+
+    /**
+     * Initialize the properties for this module.
+     */
+    virtual void properties();
+
+private:
+    /**
+     * Initialize OSG root node for this module. All other nodes from this module should be attached to this root node.
+     *
+     * \param probTract Pointer to dataset containing the connectivity scores or probabilities. We need this for two things:
+     * First, determine the maxium of connectivity scores to, scale the tracts between 0.0...1.0 and secondly to determine the
+     * boundingbox for the scene. (Furthermore it is assumed that the vectors are also available within this BB.)
+     */
+    void initOSG( boost::shared_ptr< WDataSetScalar > probTract );
+
+    /**
+     * The probabilistic tractogram input connector.
+     */
+    boost::shared_ptr< WModuleInputData< WDataSetScalar > > m_probIC;
+
+    /**
+     * Input connector for the largest eigen vector dataset.
+     */
+    boost::shared_ptr< WModuleInputData< WDataSetVector > > m_vectorIC;
+
+    /**
+     * The OSG root node for this module. All other geodes or OSG nodes will be attached on this single node.
+     */
+    osg::ref_ptr< WGEManagedGroupNode > m_output;
+
+    /**
+     * Controls the slice position, only back and forth will be possible.
+     */
+    WPropDouble m_Pos;
+
+    /**
+     * Color for the fiber stipples.
+     */
+    WPropColor m_color;
+
+    /**
+     * Connectivity scores below that threshold will not be rendered.
+     */
+    WPropDouble m_threshold;
+
+    /**
+     * For scale the thickness of the stipples.
+     */
+    WPropDouble m_glyphThickness;
+
+    /**
+     * For initial slice positioning we need to control if the module is in intial state or not.
+     */
+    bool m_first;
+};
+
+#endif  // WMFIBERSTIPPLES_H

FiberStippleToolbox/src/fiberStipples/WMFiberStipples.xpm

+/* XPM */
+static const char * WMFiberStipples_xpm[] = {
+"32 32 310 2",
+"  	c #FBFBFB",
+". 	c #FCFCFC",
+"+ 	c #C5C5C5",
+"@ 	c #E4E4E4",
+"# 	c #F3F3F3",
+"$ 	c #FEFEFE",
+"% 	c #FDFDFD",
+"& 	c #2E2E2E",
+"* 	c #474747",
+"= 	c #808080",
+"- 	c #BABABA",
+"; 	c #FFFFFF",
+"> 	c #F8F8F8",
+", 	c #AFAFAF",
+"' 	c #787878",
+") 	c #4C4C4C",
+"! 	c #5C5C5C",
+"~ 	c #929292",
+"{ 	c #D8D8D8",
+"] 	c #E5E5E5",
+"^ 	c #A2A2A2",
+"/ 	c #656565",
+"( 	c #484848",
+"_ 	c #737373",
+": 	c #C9C9C9",
+"< 	c #EBEBEB",
+"[ 	c #BEBEBE",
+"} 	c #717171",
+"| 	c #3E3E3E",
+"1 	c #4B4B4B",
+"2 	c #BDBDBD",
+"3 	c #F1F1F1",
+"4 	c #DCDCDC",
+"5 	c #9D9D9D",
+"6 	c #2A2A2A",
+"7 	c #2C2C2C",
+"8 	c #9F9F9F",
+"9 	c #FAFAFA",
+"0 	c #EFEFEF",
+"a 	c #ADADAD",
+"b 	c #363636",
+"c 	c #0D0D0D",
+"d 	c #FBFCFC",
+"e 	c #FCFBFB",
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+"g 	c #0E0E0E",
+"h 	c #585858",
+"i 	c #C0C0C0",
+"j 	c #FCFAFA",
+"k 	c #FCFDFD",
+"l 	c #757575",
+"m 	c #222222",
+"n 	c #A9A9A9",
+"o 	c #F7F7F7",
+"p 	c #FD9898",
+"q 	c #FD9C9C",
+"r 	c #FD9B9B",
+"s 	c #FDB8B8",
+"t 	c #FCF2F2",
+"u 	c #FBFFFF",
+"v 	c #FDFEFE",
+"w 	c #909090",
+"x 	c #3C3C3C",
+"y 	c #8B8B8B",
+"z 	c #C8C8C8",
+"A 	c #F5F5F5",
+"B 	c #FE3535",
+"C 	c #FE2D2D",
+"D 	c #FE2E2E",
+"E 	c #FE2424",
+"F 	c #FE2C2C",
+"G 	c #FCD1D1",
+"H 	c #FDA0A0",
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+"U 	c #FCE3E3",
+"V 	c #FCDCDC",
+"W 	c #FCDDDD",
+"X 	c #FCD6D6",
+"Y 	c #FCBABA",
+"Z 	c #FCD8D8",
+"` 	c #FD6B6B",
+" .	c #FE3F3F",
+"..	c #FFA0A6",
+"+.	c #FF8990",
+"@.	c #90E7B2",
+"#.	c #C3F2D6",
+"$.	c #FBFDFD",
+"%.	c #CBCBCB",
+"&.	c #707070",
+"*.	c #4D4D4D",
+"=.	c #7D7D7D",
+"-.	c #F6F6F6",
+";.	c #FE2828",
+">.	c #FE5757",
+",.	c #FCE5E5",
+"'.	c #FCDEDE",
+").	c #FCDFDF",
+"!.	c #FDF2F3",
+"~.	c #FEB0B2",
+"{.	c #78B06F",
+"].	c #BACDAC",
+"^.	c #77AE6D",
+"/.	c #C1D7BA",
+"(.	c #FF464E",
+"_.	c #FDEAEA",
+":.	c #FEFFFF",