Merge remote-tracking branch 'upstream/master'

Author: jessdtate

README.md

@@ -33,25 +33,24 @@ For documentation, please see: http://sciinstitute.github.io/SCIRun/
 
 ### Platform Notes
 #### Build requirements
-* OS X (tested on 10.7 and 10.8)
+* 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)
-  - Visual Studio 2013
+* 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)
-  - gcc 4.6, 4.7
+* 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/src/CMakeLists.txt.
+    + 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).
-    + BUILD_WITH_PYTHON works on Windows, not yet (easily) on MacOS.
 
 #### CMake Build Generators
 * Windows
@@ -63,9 +62,8 @@ For documentation, please see: http://sciinstitute.github.io/SCIRun/
   - Unix Makefiles
 
 #### Unix Makefiles notes
-* Boost must be built before the SCIRun libraries.
-* Parallel make builds can be used as long the Boost target is built first, for example:
-  - make -j4 Boost_external && make -j4
+* 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.
@@ -78,7 +76,7 @@ For help, email the testing mailing list at [email protected].
 
   The MIT License
 
-  Copyright (c) 2015 Scientific Computing and Imaging Institute,
+  Copyright (c) 2016 Scientific Computing and Imaging Institute,
   University of Utah.
 
 

TODO.md

@@ -9,20 +9,14 @@ User Requests
     + better network parameter editing
     + maybe a network wizard?
     + show what files are being used, network file name
-    + better network parameter editing
 
   - more example nets
   - more documentation, more sample networks (very useful for demonstrating module functionality)
-  - must work with clipboard (through Qt support?)
   - search modules, networks for keywords
 
     + see Matlab descriptors at the top of source files as an example
     + when searching for modules, can we have the option of searching within the module text (i.e. search module GUI component names, variable names etc.)
 
-  - error reporting should not kill SCIRun
-
-    + For example, if you end up with an empty field in your network, and you have a bounding box displayed for that field, the bounding box calculation asserts that the diagonal is zero and aborts the program, which is bad. Instead, an error should be displayed and the user should be able to change the network to fix the problem.
-
   - port colors: change intensities, not just colors
 
     + get updated palette from Nathan
@@ -46,11 +40,7 @@ User Requests
 
 * UI
 
-  - select (highlight with mouse?) and copy multiple modules - connections between modules will have to be propagated as well
-  - adjust GUI scale so it doesn't flow over bottom of screen
   - collapse network preview window
-  - zoom or center network in editor
-  - hover or hot key to expose some module parameters
   - side pane to expose some module parameters
 
     + expose important dataset parameters too (size, dims, data info etc.)
@@ -68,34 +58,28 @@ User Requests
     + line up modules
     + expose-like (OS X)
 
-  - Change exponential widget behavior to be more intuitive
   - Add GUI element for indicating result of "Clear Output" button of module CollectMatrices
   - Add string port to Read / Write Nrrd
   - Add support for newer Matlab file format
   - Add cylinder to vector glyph types
   - ShowMatrix module should detect matrix dimensions
-  - reinterpret_cast from pointer-to-object to pointer-to-function not portable
   - IO plugin for Meshalyzer binary mesh format
   - IO plugin for a binary node index matrix
 
 * Networks
 
   - halt network without killing SCIRun
-  - stop module in network
 
 * Subnets
 
   - subnets must work (currently broken) - should be an easy select and create operation in GUI
-  - offer common network fragments as subnets (i.e. ShowField, ColorMap etc., ViewScene)
   - better views for subnets: dockable widgets, tabs etc.
   - duplicate entire subnet
   - import network into other network
 
     + choice to import as subnet or register network
     + choice to save subnet as separate file
 
-  - 'Duplicate' should work on multiply-selected modules
-
 Qt Migration
 ============
 
@@ -125,23 +109,10 @@ Qt Migration
 
   - All menu options/preferences work
   - Can walk through entire SCIRun tutorial!
-  - At this point, all essential modules should be converted. Can begin converting other individual modules.
-
-* Core
-
-  - Discuss memory model for Matrix/Arrays/etc.
-  - Move namespace SCIRunAlgo into SCIRun::Algo to remove need for using directives in headers.
-  - Replace Thread library with Boost.
-  - Boost threading notes.
 
 * IO
 
   - is there a way we can display a brief blurb describing file importer and exporter plugin information (i.e. show a short description of the file types supported, file extensions etc.)?
-  - change file importer and exporter plugin function pointer table to functors
-
-* Dataflow
-
-  - Execute all button in network editor: triggers execution even if network is currently executing. Queue (or block?) request for execution until current execution is done.
 
 * Graphics and Visualization
 
@@ -156,11 +127,6 @@ Qt Migration
   - verify that libpng and zlib are still needed, if so, update
   - better XML parsing library (libxml2 is overly complex and buggy)
 
-* Boost
-
-  - Boost is an external project in the CMake build
-  - In case Boost needs to be built outside of SCIRun: Boost build notes
-
 * Build
 
   - merge all generated headers into a single generated header file

src/Core/Application/Application.cc

@@ -162,27 +162,36 @@ namespace
   class HardCodedPythonTestCommand : public ParameterizedCommand
   {
   public:
+    HardCodedPythonTestCommand(const std::string& script, bool enabled) : script_(script), enabled_(enabled) {}
     virtual bool execute() override
     {
-      auto script = Preferences::Instance().postModuleAddScript_temporarySolution.val();
-      if (!script.empty())
+      if (!enabled_)
+        return false;
+
+      if (!script_.empty())
       {
         PythonInterpreter::Instance().run_string("import SCIRunPythonAPI; from SCIRunPythonAPI import *");
-        PythonInterpreter::Instance().run_string(script);
+        PythonInterpreter::Instance().run_string(script_);
       }
       return true;
     }
+  private:
+    std::string script_;
+    bool enabled_;
   };
 
   class HardCodedPythonFactory : public NetworkEventCommandFactory
   {
   public:
     virtual CommandHandle create(NetworkEventCommands type) const override
     {
+      const auto& prefs = Preferences::Instance();
       switch (type)
       {
       case NetworkEventCommands::PostModuleAdd:
-        return boost::make_shared<HardCodedPythonTestCommand>();
+        return boost::make_shared<HardCodedPythonTestCommand>(prefs.postModuleAddScript_temporarySolution.val(), prefs.postModuleAddScriptEnabled_temporarySolution.val());
+      case NetworkEventCommands::OnNetworkLoad:
+        return boost::make_shared<HardCodedPythonTestCommand>(prefs.onNetworkLoadScript_temporarySolution.val(), prefs.onNetworkLoadScriptEnabled_temporarySolution.val());
       }
       return nullptr;
     }
@@ -297,141 +306,3 @@ bool Application::get_user_name( std::string& user_name ) const
 {
   return applicationHelper.get_user_name(user_name);
 }
-
-/*
-int Application::GetMajorVersion()
-{
-	return CORE_APPLICATION_MAJOR_VERSION;
-}
-
-int Application::GetMinorVersion()
-{
-	return CORE_APPLICATION_MINOR_VERSION;
-}
-
-int Application::GetPatchVersion()
-{
-	return CORE_APPLICATION_PATCH_VERSION;
-}
-
-bool Application::Is64Bit()
-{
-	return ( sizeof(void *) == 8 );
-}
-
-bool Application::Is32Bit()
-{
-	return ( sizeof(void *) == 4 );
-}
-
-std::string Application::GetApplicationName()
-{
-	return CORE_APPLICATION_NAME;
-}
-
-std::string Application::GetReleaseName()
-{
-	return CORE_APPLICATION_RELEASE;
-}
-
-std::string Application::GetApplicationNameAndVersion()
-{
-	return GetApplicationName() + " " + GetReleaseName() + " " + GetVersion();
-}
-
-std::string Application::GetAbout()
-{
-	return CORE_APPLICATION_ABOUT;
-}
-*/
-
-#if 0 //shouldn't need this anymore
-// Services start up...
-void ApplicationPrivate::start_eai()
-{
-  // Create a database of all available services. The next piece of code
-  // scans both the SCIRun as well as the Packages directories to find
-  // services that need to be started. Services allow communication with
-  // thirdparty software and are Threads that run asychronously with
-  // with the rest of SCIRun. Since the thirdparty software may be running
-  // on a different platform it allows for connecting to remote machines
-  // and running the service on a different machine
-  ServiceDBHandle servicedb(new ServiceDB);
-  // load all services and find all makers
-  servicedb->loadpackages();
-  // activate all services
-  servicedb->activateall();
-
-  // Services are started and created by the ServiceManager,
-  // which will be launched here
-  // Two competing managers will be started,
-  // one for purely internal usage and one that
-  // communicates over a socket.
-  // The latter will only be created if a port is set.
-  // If the current instance of SCIRun should not provide any services
-  // to other instances of SCIRun over the internet,
-  // the second manager will not be launched
-
-  IComAddressHandle internaladdress(new IComAddress("internal","servicemanager"));
-
-// Only build log file if needed for debugging
-#ifdef DEBUG
-  const char *chome = sci_getenv("HOME");
-  std::string scidir("");
-  if (chome)
-    scidir = chome+std::string("/SCIRun/");
-
-  // A log file is not necessary but handy for debugging purposes
-  ServiceLogHandle internallogfile(new ServiceLog(scidir+"scirun_internal_servicemanager.log"));
-
-  ServiceManagerHandle internal_service_manager(new ServiceManager(servicedb, internaladdress, internallogfile));
-#else
-  ServiceManager internal_service_manager(servicedb, internaladdress);
-#endif
-
-  boost::thread t_int(internal_service_manager);
-  t_int.detach();
-
-
-#ifdef SCIRUN4_CODE_TO_BE_ENABLED_LATER
-  // Use the following environment setting to switch on IPv6 support
-  // Most machines should be running a dual-host stack for the internet
-  // connections, so it should not hurt to run in IPv6 mode. In most case
-  // ipv4 address will work as well.
-  // It might be useful
-  std::string ipstr(sci_getenv_p("SCIRUN_SERVICE_IPV6")?"ipv6":"");
-
-  // Start an external service as well
-  const char *serviceport_str = sci_getenv("SCIRUN_SERVICE_PORT");
-  // If its not set in the env, we're done
-  if (!serviceport_str) return;
-
-  // The protocol for conencting has been called "scirun"
-  // In the near future this should be replaced with "sciruns" for
-  // a secure version which will run over ssl.
-
-  // A log file is not necessary but handy for debugging purposes
-
-  IComAddress externaladdress("scirun","",serviceport_str,ipstr);
-
-#ifdef DEBUG
-  ServiceLogHandle externallogfile =
-    new ServiceLog(scidir+"scirun_external_servicemanager.log");
-
-  ServiceManager* external_service_manager =
-    new ServiceManager(servicedb,externaladdress,externallogfile);
-#else
-  ServiceManager* external_service_manager =
-    new ServiceManager(servicedb,externaladdress);
-
-#endif
-
-  Thread* t_ext =
-    new Thread(external_service_manager,"external service manager",
-		  0, Thread::NotActivated);
-  t_ext->setStackSize(1024*20);
-  t_ext->activate(false);
-  t_ext->detach();
-#endif
-}
-#endif

src/Core/Application/Preferences/Preferences.cc

@@ -51,7 +51,10 @@ Preferences::Preferences() :
   autoNotes("autoNotes", false),
   modulesAreDockable("modulesAreDockable", true),
   networkBackgroundColor("backgroundColor", "#808080"),
-  postModuleAddScript_temporarySolution("postModuleAddScript", "")
+  postModuleAddScript_temporarySolution("postModuleAddScript_temporarySolution", ""),
+  postModuleAddScriptEnabled_temporarySolution("postModuleAddScriptEnabled_temporarySolution", false),
+  onNetworkLoadScript_temporarySolution("onNetworkLoadScript_temporarySolution", ""),
+  onNetworkLoadScriptEnabled_temporarySolution("onNetworkLoadScriptEnabled_temporarySolution", false)
 {
 }
 

src/Core/Application/Preferences/Preferences.h

@@ -85,7 +85,12 @@ namespace SCIRun
       BooleanVariable autoNotes;
       TrackedVariable<BooleanVariable> modulesAreDockable;
       StringVariable networkBackgroundColor;
+
+      //super duper ugly.
       StringVariable postModuleAddScript_temporarySolution;
+      BooleanVariable postModuleAddScriptEnabled_temporarySolution;
+      StringVariable onNetworkLoadScript_temporarySolution;
+      BooleanVariable onNetworkLoadScriptEnabled_temporarySolution;
 
       std::string dataDirectoryPlaceholder() const;
 

src/Core/Command/Command.h

@@ -96,7 +96,8 @@ namespace SCIRun
 
       enum class NetworkEventCommands
       {
-        PostModuleAdd
+        PostModuleAdd,
+        OnNetworkLoad
         //TODO: add more based on user request
       };