Merge branch 'master' into issues_A

Author: dcwhite

README.md

@@ -12,10 +12,8 @@ https://github.com/SCIInstitute/SCIRun
 	- [Summary](#user-content-summary)
 	- [Goals](#user-content-goals)
 	- [Documentation](#user-content-documentation)
-	- [Platform Notes](#user-content-platform-notes)
-		- [Build requirements](#user-content-build-requirements)
-		- [CMake Build Generators](#user-content-cmake-build-generators)
-		- [Unix Makefiles notes](#user-content-unix-makefiles-notes)
+ 	  - [Build](#user-content-build)
+ 	  - [Python API](#user-content-python-api)
 	- [Questions and Answers](#user-content-questions-and-answers)
 	- [License and Credits](#user-content-license-and-credits)
 
@@ -24,49 +22,18 @@ https://github.com/SCIInstitute/SCIRun
 | Warning! |  SCIRun 5 is alpha software, you may use for real science but beware of instability.  |
 |:--------:|:-------------------------------------------------------------------------------------:|
 
-###Goals
+### Goals
 SCIRun 5 is a complete rewrite of the GUI front end and graphical components of SCIRun 4, including a more stable and
 efficient middle layer, with support for Python scripting.
 
 ### Documentation
-For documentation, please see: http://sciinstitute.github.io/SCIRun/
-
-### Platform Notes
-#### Build requirements
-* OS X (tested on 10.7-10.11)
-  - Apple clang 5.1
-  - Qt 4.8
-    + Download from http://releases.qt-project.org/qt4/source/qt-mac-opensource-4.8.4.dmg.
-    + The above dmg will not work if using OS X 10.11. In this case Qt 4.8 can be acquired through macports using the command 'sudo port install qt4-mac' - more on macports here: https://www.macports.org/install.php
-* Windows (tested on Windows 7, 8, 10)
-  - Visual Studio 2013, 2015
-  - Qt 4.8
-    + Build from source (see http://scirundocwiki.sci.utah.edu/SCIRunDocs/index.php/CIBC:Seg3D2:Building_Releases#Installing_Qt_on_your_system_and_building_from_scratch for instructions), but be sure to download http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz.
-* Linux (tested on Ubuntu 12.10, OpenSUSE Leap)
-  - gcc 4.6, 4.7, 4.8
-  - Qt 4.8
-    + Build from source (http://releases.qt-project.org/qt4/source/qt-everywhere-opensource-src-4.8.4.tar.gz), or use system libraries if available.
-* All platforms
-  - CMake 2.8
-    + Root cmake file is SCIRun/Superbuild/CMakeLists.txt.
-    + Building in the source directory is not permitted.
-    + Make sure BUILD_SHARED_LIBS is on (default setting).
-
-#### CMake Build Generators
-* Windows
-  - Visual Studio 2013
-* OS X (tested on 10.7 and 10.8 and 10.10)
-  - Unix Makefiles
-  - Xcode
-* Linux (tested on Ubuntu 12.10)
-  - Unix Makefiles
-
-#### Unix Makefiles notes
-* Build Superbuild first (src/Superbuild), then subsequently, SCIRun can be built by itself (src/).
-* Included `build.sh` takes care of all this for you.
-
-### Tagging releases
-On an OSX system, run script `release.sh` in the `src` directory with the release name in format `alpha.XX` as a parameter.
+For documentation, please see: http://sciinstitute.github.io/scirun.pages
+
+#### Build
+Please see http://sciinstitute.github.io/scirun.pages/build.html
+
+#### Python API
+Please see http://sciinstitute.github.io/scirun.pages/python.html
 
 ### Questions and Answers
 For help, email the testing mailing list at [email protected].

src/Core/IEPlugin/CMakeLists.txt

@@ -32,7 +32,7 @@ SET(Core_IEPlugin_SRCS
   CurveField_Plugin.cc
   #DIF_Plugin.cc
   EcgsimFileToMatrix_Plugin.cc
-  #IgbFileToMatrix_Plugin.cc
+  IgbFileToMatrix_Plugin.cc
   #EcgsimFileToTriSurf_Plugin.cc
   #HexVolField_Plugin.cc
   IEPluginInit.cc

src/Core/IEPlugin/IEPluginInit.cc

@@ -32,7 +32,7 @@
 #include <Core/IEPlugin/SimpleTextFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/EcgsimFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/PointCloudField_Plugin.h>
-#include <Core/IEPlugin/IGBFileToMatrix_Plugin.h>
+#include <Core/IEPlugin/IgbFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/CurveField_Plugin.h>
 #include <Core/IEPlugin/TriSurfField_Plugin.h>
 #include <Core/IEPlugin/TetVolField_Plugin.h>
@@ -66,7 +66,7 @@ void IEPluginManager::Initialize()
   static FieldIEPluginLegacyAdapter CurveField_plugin("CurveField", "*.pts *.pos *.edge", "", TextToCurveField_reader, CurveFieldToTextBaseIndexZero_writer);
 
   static MatrixIEPluginLegacyAdapter EcgsimFileMatrix_plugin("ECGSimFile", "", "", EcgsimFileMatrix_reader, EcgsimFileMatrix_writer);
-  //static MatrixIEPluginLegacyAdapter IgbFileMatrix_plugin("IGBFile", "*.igb", "*.igb", IgbFileMatrix_reader, IgbFileMatrix_writer);
+  static MatrixIEPluginLegacyAdapter IgbFileMatrix_plugin("IGBFile", "*.igb", "*.igb", IgbFileMatrix_reader, IgbFileMatrix_writer);
 
   static FieldIEPluginLegacyAdapter TriSurfField_plugin("TriSurfField", "*.fac *.tri *.pts *.pos", "", TextToTriSurfField_reader, TriSurfFieldToTextBaseIndexZero_writer);
   static FieldIEPluginLegacyAdapter TriSurfFieldBaseIndexOne_plugin("TriSurfField[BaseIndex 1]", "*.fac *.pts", "", nullptr, TriSurfFieldToTextBaseIndexOne_writer);

src/Core/IEPlugin/IgbFileToMatrix_Plugin.cc

@@ -38,7 +38,7 @@
 
 
 #include <Core/ImportExport/Matrix/MatrixIEPlugin.h>
-#include <Core/IEPlugin/IgbmFileToMatrix_Plugin.h>
+#include <Core/IEPlugin/IgbFileToMatrix_Plugin.h>
 #include <Core/Datatypes/DenseMatrix.h>
 #include <Core/Datatypes/MatrixTypeConversions.h>
 #include <Core/Utils/Legacy/StringUtil.h>

src/Documentation/Manuals/BasicTutorial/BasicTutorial.pdf

@@ -46,24 +46,6 @@ \subsection{SCIRun  \SCIRunVersion}
 
 %%\subsection{SCIRun SVN}
 
-\chapter{User Interface}
-
-\begin{introduction}
-Scope: \hyperref[datalayer]{Data Layers} - \hyperref[favorites]{Favorite Modules} -
-\hyperref[visualize]{Saved Subnetworks} - \hyperref[convert4]{Converting Networks from SCIRun 4} 
-\end{introduction}
-
-\subsection{Data Layers}\label{datalayer}
-
-\subsection{Favorite Modules}\label{favorites}
-
-\subsection{Saved Subnetworks and Snippets}\label{subnets}
-
-\subsection{Converting Networks from SCIRun 4}\label{convert4}
-
-
-
-
 \chapter{Simple Dataflow Network}
 
 \begin{introduction}

src/Documentation/Manuals/BasicTutorial/BasicTutorial.tex

@@ -54,6 +54,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="1" column="0">
@@ -68,6 +71,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="2" column="0">
@@ -82,6 +88,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
          </layout>
@@ -370,6 +379,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="1" column="0">
@@ -384,6 +396,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="2" column="0">
@@ -398,6 +413,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
          </layout>
@@ -459,22 +477,6 @@
             </property>
            </widget>
           </item>
-          <item row="2" column="1">
-           <widget class="QDoubleSpinBox" name="rotateZAxisDoubleSpinBox_">
-            <property name="minimum">
-             <double>-1.000000000000000</double>
-            </property>
-            <property name="maximum">
-             <double>1.000000000000000</double>
-            </property>
-            <property name="singleStep">
-             <double>0.010000000000000</double>
-            </property>
-            <property name="value">
-             <double>1.000000000000000</double>
-            </property>
-           </widget>
-          </item>
           <item row="3" column="0">
            <widget class="QLabel" name="label_22">
             <property name="text">
@@ -498,6 +500,22 @@
             </property>
            </widget>
           </item>
+          <item row="2" column="1">
+           <widget class="QDoubleSpinBox" name="rotateZAxisDoubleSpinBox_">
+            <property name="minimum">
+             <double>-1.000000000000000</double>
+            </property>
+            <property name="maximum">
+             <double>1.000000000000000</double>
+            </property>
+            <property name="singleStep">
+             <double>0.010000000000000</double>
+            </property>
+            <property name="value">
+             <double>1.000000000000000</double>
+            </property>
+           </widget>
+          </item>
          </layout>
         </widget>
        </item>
@@ -539,6 +557,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="1" column="0">
@@ -553,6 +574,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
           <item row="2" column="0">
@@ -567,6 +591,9 @@
             <property name="decimals">
              <number>6</number>
             </property>
+            <property name="minimum">
+             <double>-99.989999999999995</double>
+            </property>
            </widget>
           </item>
          </layout>

src/Interface/Modules/Math/CreateGeometricTransform.ui

@@ -157,7 +157,7 @@ class CoreBootstrap : public es::EmptySystem
 
     // Add static world light.
     StaticWorldLight worldLight;
-    worldLight.lightDir = glm::vec3(1.0f, 0.0f, 0.0f);
+    //worldLight.lightDir = glm::vec3(1.0f, 0.0f, 0.0f);
     core.addStaticComponent(worldLight);
     core.addExemptComponent<StaticWorldLight>();
 

src/Interface/Modules/Render/ES/CoreBootstrap.cc

@@ -109,6 +109,7 @@ namespace SCIRun {
       // Construct ESCore. We will need to bootstrap the core. We should also
       // probably add utility static classes.
       setupCore();
+      setupLights();
     }
 
     //------------------------------------------------------------------------------
@@ -153,6 +154,18 @@ namespace SCIRun {
 
     }
 
+    void SRInterface::setupLights()
+    {
+      //mLightPosition;
+      mLightsOn.push_back(true);
+      mLightPosition.push_back(glm::vec3(0, 0, 1));
+      for (int i = 1; i < LIGHT_NUM; ++i)
+      {
+        mLightsOn.push_back(false);
+        mLightPosition.push_back(glm::vec3(0, 0, 1));
+      }
+    }
+
     //------------------------------------------------------------------------------
     void SRInterface::setMouseMode(MouseMode mode)
     {
@@ -1365,15 +1378,86 @@ namespace SCIRun {
     //------------------------------------------------------------------------------
     void SRInterface::updateWorldLight()
     {
+      /*
+      getWorldToProjection() const;
+      getWorldToView() const;
+      getViewToWorld() const;
+      getViewToProjection() const;
+      */
       glm::mat4 viewToWorld = mCamera->getViewToWorld();
+      //glm::mat4 viewToWorld = mCamera->getWorldToView();
+
+      // Set directional light source (in world space).
+      StaticWorldLight* light = mCore.getStaticComponent<StaticWorldLight>();
+      if (light)
+      {
+        for (int i = 0; i < LIGHT_NUM; ++i)
+        {
+          /*
+          glm::vec3 viewDir = glm::vec3(0.0, 0.0, -1.0) - mLightPosition[i];
+          glm::vec4 newDir(viewDir.x, viewDir.y, viewDir.z, 1.0);
+          viewToWorld *= newDir;
+          glm::vec3 lightDir = viewToWorld[4].xyz();
+          */
+
+          glm::vec3 viewDir = viewToWorld[2].xyz();
+          viewDir = -viewDir; // Cameras look down -Z.
+          light->lightDir[i] = mLightsOn[i] ? viewDir - mLightPosition[i] : glm::vec3(0.0, 0.0, 0.0);
+          //light->lightDir[i] = mLightsOn[i] ? lightDir : glm::vec3(0.0, 0.0, 0.0);
+        }
+      }
+    }
+
+    void SRInterface::setLightColor(int index, float r, float g, float b)
+    {
+      if (index >= LIGHT_NUM)
+        return;
+      StaticWorldLight* light = mCore.getStaticComponent<StaticWorldLight>();
+      if (light)
+      {
+        light->lightColor[index] = glm::vec3(r, g, b);
+      }
+    }
+
+
+    void SRInterface::setLightPosition(int index, float x, float y)
+    {
+      if (index >= LIGHT_NUM)
+        return;
 
+      glm::mat4 viewToWorld = mCamera->getViewToWorld();
+      glm::vec3 position = glm::vec3(x, y, 0);
+      if (mLightPosition.size() > 0)
+      {
+        mLightPosition[index] = glm::vec3(x, y, 0.0);
+      }
+      /*
       // Set directional light source (in world space).
       StaticWorldLight* light = mCore.getStaticComponent<StaticWorldLight>();
       if (light)
       {
         glm::vec3 viewDir = viewToWorld[2].xyz();
-        viewDir = -viewDir; // Cameras look down -Z.
-        light->lightDir = viewDir;
+        viewDir = -viewDir; // Cameras look down -Z.        
+        light->lightDir[index] = mLightsOn[index] ? viewDir-position : glm::vec3(0.0, 0.0, 0.0);
+
+        glm::vec3 view1 = viewToWorld[0].xyz();
+        glm::vec3 view2 = viewToWorld[1].xyz();
+        glm::vec3 view4 = viewToWorld[3].xyz();
+        std::cout << "size: " << viewToWorld.length() << std::endl;
+        std::cout << "view1x: " << view1.x << " view1y: " << view1.y << " view1z: " << view1.z << std::endl;
+        std::cout << "view2x: " << view2.x << " view2y: " << view2.y << " view2z: " << view2.z << std::endl;
+        std::cout << "view3x: " << viewDir.x << " view3y: " << viewDir.y << " view3z: " << viewDir.z << std::endl;
+        std::cout << "view4x: " << view4.x << " view4y: " << view4.y << " view4z: " << view4.z << std::endl;
+        std::cout << "x: " << x << " y: " << y << " z: " << 0 << std::endl;
+      }
+      */
+    }
+
+    void SRInterface::setLightOn(int index, bool value)
+    {
+      if (mLightsOn.size() > 0 && index < LIGHT_NUM)
+      {
+        mLightsOn[index] = value;
       }
     }