diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index af96791fc63ed27af167ba8856d2a0088506d0cc..0000000000000000000000000000000000000000
--- a/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-.vscode
-build
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 31220fe87030cc1f0658c3b2fa2e13ab736c0fcd..a1ea9f56542c851155ec9eb1199fd9a1ce1d89c2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -40,7 +40,7 @@ set( MODULE_NAME ${SHORT_NAME}module )
# 2) Add all your sources here
set( MODULE_SOURCES
streamingmodule.h streamingmodule.cpp
- streaming_recording_backend.h streaming_recording_backend.cpp
+ recording_backend_nesci_contra.h recording_backend_nesci_contra.cpp
)
# 3) We require a header name like this:
@@ -179,17 +179,6 @@ execute_process(
OUTPUT_STRIP_TRAILING_WHITESPACE
)
-#--------------------------------------------------------------------
-set(CMAKE_CXX_STANDARD 14)
-
-if (NOT CONTRA_TRANSPORT)
- set(CONTRA_TRANSPORT shared_memory)
-endif()
-
-find_package(contra COMPONENTS contra ${CONTRA_TRANSPORT} REQUIRED)
-find_package(nesci COMPONENTS producer REQUIRED)
-#--------------------------------------------------------------------
-
# on OS X
set( CMAKE_MACOSX_RPATH ON )
@@ -242,13 +231,14 @@ add_custom_target( dist
COMMENT "Creating a source distribution from ${MODULE_NAME}..."
)
-add_subdirectory(demos)
+include(${CMAKE_BINARY_DIR}/conanbuildinfo.cmake)
+conan_basic_setup( TARGETS )
if ( BUILD_SHARED_LIBS )
# When building shared libraries, also create a module for loading at runtime
# with the `Install` command.
add_library( ${MODULE_NAME}_module MODULE ${MODULE_SOURCES} )
- target_link_libraries( ${MODULE_NAME}_module nesci::producer contra::${CONTRA_TRANSPORT} )
+ target_link_libraries( ${MODULE_NAME}_module CONAN_PKG::nesci CONAN_PKG::contra )
set_target_properties( ${MODULE_NAME}_module
PROPERTIES
COMPILE_FLAGS "${NEST_CXXFLAGS} -DLTX_MODULE"
@@ -262,7 +252,7 @@ endif ()
# Build dynamic/static library for standard linking from NEST.
add_library( ${MODULE_NAME}_lib ${MODULE_SOURCES} )
-target_link_libraries( ${MODULE_NAME}_lib nesci::producer contra::${CONTRA_TRANSPORT} )
+target_link_libraries( ${MODULE_NAME}_lib CONAN_PKG::nesci CONAN_PKG::contra )
if ( BUILD_SHARED_LIBS )
# Dynamic libraries are initiated by a `global` variable of the `SLIModule`,
# which is included, when the flag `LINKED_MODULE` is set.
@@ -306,6 +296,7 @@ if ( NOT CMAKE_CROSSCOMPILING )
)
endif ()
+
message( "" )
message( "-------------------------------------------------------" )
message( "${MODULE_NAME} Configuration Summary" )
diff --git a/CPPLINT.cfg b/CPPLINT.cfg
deleted file mode 100644
index ce7c7e4c264e5a39da61062cc86686e28865fee8..0000000000000000000000000000000000000000
--- a/CPPLINT.cfg
+++ /dev/null
@@ -1,4 +0,0 @@
-set noparent
-filter=-readability/check,-build/c++tr1,-build/c++11,-build/c++14
-linelength=80
-headers=h,hpp
diff --git a/README.md b/README.md
index 959031604698864c49194136ac7276d464606bde..84571b76334196e2989fe88346b6f463b5ff2476 100644
--- a/README.md
+++ b/README.md
@@ -3,15 +3,15 @@
## Prerequisites
* CMake >= 3.6.0 (https://cmake.org/)
* Python 2.7 (https://www.python.org/)
-* NEST: the latest release of NEST does currently not support modules. Thus, a custom version is required that can be found [here](https://github.com/jougs/nest-simulator/tree/feature/custom-recording-backend). You need to checkout and build the branch `feature/custom-recording-backend`
+* Conan (`pip install conan`)
+* NEST: the latest release of NEST does currently not support modules. Thus, a custom version is required that can be found [here](https://github.com/jougs/nest-simulator/tree/feature/custom-recording-backend).
## Building
1. Create a build directory
2. Open terminal in build directory
3. Run CMake: `cmake -Dwith-nest=${PATH_TO_NEST_INSTALLATION} ${PATH_TO_NEST_STREAMING_MODULE_SOURCE}`
-4. Run Conan: `conan install ${PATH_TO_NEST_STREAMING_MODULE_SOURCE} --build=missing`
-5. Build: `cmake --build .`
-6. Install: `cmake --build . --target install`
+4. Build: `cmake --build .`
+5. Install: `cmake --build . --target install`
## How to use the nest-streaming-module?
The *nest-streaming-module* registers a new RecordingBackend to the simulator. When registering a `RecordingDevice` using PyNEST the used recording backend can be specified in the `record_to` parameter. If you want to stream the data, set this parameter to `['streaming']`. Clients that receive the data can be either written in Python or C++. See https://devhub.vr.rwth-aachen.de/VR-Group/nesci-contra-demos for examples.
\ No newline at end of file
diff --git a/conanfile.py b/conanfile.py
new file mode 100644
index 0000000000000000000000000000000000000000..89c81b32798f259395ba22372cca213e4b43691e
--- /dev/null
+++ b/conanfile.py
@@ -0,0 +1,37 @@
+# conanfile.py
+#
+# This file is part of NEST.
+#
+# Copyright (C) 2004 The NEST Initiative
+#
+# NEST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# NEST 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with NEST. If not, see <http://www.gnu.org/licenses/>
+
+from conans import ConanFile, CMake
+
+class nest(ConanFile):
+ name = "NEST"
+ version = "18.05"
+ license = "GNU General Public License, Version 2"
+ description = """NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons."""
+ settings = "os", "compiler", "build_type", "arch"
+
+ requires = (("contra/18.05@RWTH-VR/develop"),
+ ("nesci/18.05@RWTH-VR/develop"))
+ generators = "cmake"
+
+ def configure(self):
+ pass
+
+ def imports(self):
+ pass
diff --git a/demos/CMakeLists.txt b/demos/CMakeLists.txt
deleted file mode 100644
index 406fe9e6e986f14f50b815e53eacb80d1dafea05..0000000000000000000000000000000000000000
--- a/demos/CMakeLists.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-#-------------------------------------------------------------------------------
-# nest-streaming-module
-#
-# Copyright (c) 2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualization Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#-------------------------------------------------------------------------------
-
-option(BUILD_BRUNEL_SIMULATION "Build the brunel simulation" ON)
-option(BUILD_QVTK_DEMO "Build the QVTK visualization demo" OFF)
-
-if (${BUILD_BRUNEL_SIMULATION})
- add_subdirectory(brunel_simulation)
-endif (${BUILD_BRUNEL_SIMULATION})
-
-if (${BUILD_QVTK_DEMO})
- add_subdirectory(QVTK-Demo)
-endif (${BUILD_QVTK_DEMO})
-
-
diff --git a/demos/QVTK-Demo/CMakeLists.txt b/demos/QVTK-Demo/CMakeLists.txt
deleted file mode 100644
index 492be448f7d430f12d10ca085c0e18ce7c72454e..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/CMakeLists.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-#-------------------------------------------------------------------------------
-# QVTK-Demo
-#
-# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualization Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#-------------------------------------------------------------------------------
-
-add_subdirectory(qvtk-app)
-add_subdirectory(qvtk-lib)
-
diff --git a/demos/QVTK-Demo/Readme.txt b/demos/QVTK-Demo/Readme.txt
deleted file mode 100644
index 8602ac1f9b151f31187404906c1cbde5b65e521d..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/Readme.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-#-------------------------------------------------------------------------------
-# QVTK-Demo
-#
-# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualization Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#-------------------------------------------------------------------------------
-
-This is a brief summary on how to get the QVTK-Demo running.
-
-Prerequisites:
- -QT (Version 5.9 or higher is advised! -older versions might work aswell but havent been tested).
- -Get this first and build it.
- -The Visualization Toolkit(VTK) (The demo was originally build with version 8.0.1. Newer versions should work too but havent been tested).
- -Ŵhen building VTK with CMake make sure you enable VTK_BUILD_QT_DESIGNER_PLUGIN, VTK_Group_Qt and set VTK_QT_VERSION to 5.
-
-Installing:
-When running CMake enable BUILD_QVTK_DEMO and BUILD_BRUNEL_SIMULATION.
-
-Running the Demo:
-To run the Demo start both, the QVTK-Demo(qvtk-app) and the Brunel Simulation(run_sim.sh) from your build folder.
-
-
diff --git a/demos/QVTK-Demo/qvtk-app/CMakeLists.txt b/demos/QVTK-Demo/qvtk-app/CMakeLists.txt
deleted file mode 100644
index aa8b8c96f551b878ec5dfbbb749c9b7d9e5c0009..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-app/CMakeLists.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-#-------------------------------------------------------------------------------
-# QVTK-Demo
-#
-# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualisation Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# This framework 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.
-#
-# In the future, we may decide to add a commercial license
-# at our own discretion without further notice.
-#
-# This program 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 Lesse r General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
-
-set(CMAKE_AUTOMOC ON)
-set(QVTK_APP_API_HEADER_DIR include/qvtk_app)
-
-file(GLOB QVTK_APP_SOURCES src/*.cpp)
-file(GLOB QVTK_APP_HEADERS include/qvtk_app/*.hpp)
-file(GLOB QVTK_APP_API_HEADERS ${QVTK_APP_API_HEADER_DIR}/*.hpp)
-file(GLOB QVTK_APP_SUPPRESS_WARNING_HEADERS include/qvtk_app/suppress_warnings/Qt *.hpp)
-
-add_executable(qvtk_app
- ${QVTK_APP_SOURCES}
- ${QVTK_APP_HEADERS}
- ${QVTK_APP_API_HEADERS}
- ${QVTK_APP_SUPPRESS_WARNING_HEADERS}
-)
-
-target_include_directories(
- qvtk_app PUBLIC
- ${CMAKE_CURRENT_SOURCE_DIR}/include
- ${CMAKE_BINARY_DIR}
-)
-
-#add_test_cpplint(NAME "qvtk_app--cpplint"
-# ${QVTK_APP_SOURCES}
-# ${QVTK_APP_HEADERS}
-# ${QVTK_APP_API_HEADERS}
-# ${QVTK_APP_SUPPRESS_WARNING_HEADERS}
-#)
-
-set_warning_levels_RWTH(qvtk_app
- SUPPRESS_WARNINGS_HEADER ${CMAKE_CURRENT_BINARY_DIR}/include/qt_app/suppress_warnings.hpp
-)
-
-include_directories(include)
-
-# --- dependencies ---
-
-# VTK
-find_package(VTK REQUIRED)
-include(${VTK_USE_FILE})
-target_include_directories(qvtk_app PUBLIC ${VTK_INCLUDE_DIR})
-
-#vtkexperiment
-target_include_directories(qvtk_app PUBLIC ${QVTK_LIB_INCLUDE_DIRS})
-
-target_link_libraries(qvtk_app PUBLIC qvtk-lib debug ${VTK_LIBRARIES} optimized ${VTK_LIBRARIES})
-
diff --git a/demos/QVTK-Demo/qvtk-app/include/qvtk_app/application.hpp b/demos/QVTK-Demo/qvtk-app/include/qvtk_app/application.hpp
deleted file mode 100644
index b2beda8abf3487f26919ba90f914135075bb5e5c..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-app/include/qvtk_app/application.hpp
+++ /dev/null
@@ -1,49 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_APP_INCLUDE_QVTK_APP_APPLICATION_HPP_
-#define QVTK_APP_INCLUDE_QVTK_APP_APPLICATION_HPP_
-
-#include "QApplication"
-
-#include "qvtk-lib/main_window.hpp"
-#include "qvtk-lib/point_data.hpp"
-
-class Application
-{
-public:
- Application(int *argc, char **argv);
- ~Application() {}
-
- int Run();
-
-private:
- QApplication qt_app_;
-
- vtkexp::PointData points_;
- vtkexp::MainWindow window_;
-};
-
-#endif // QVTK_APP_INCLUDE_QVTK_APP_APPLICATION_HPP_
diff --git a/demos/QVTK-Demo/qvtk-app/src/application.cpp b/demos/QVTK-Demo/qvtk-app/src/application.cpp
deleted file mode 100644
index 3b5fd95dab12a074e3b1eb5875cb22666947bb9c..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-app/src/application.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk_app/application.hpp"
-
-Application::Application(int *argc, char **argv)
- : qt_app_{*argc, argv}, points_(6, 6, 1), window_{&points_} {}
-
-int Application::Run()
-{
- window_.show();
- return qt_app_.exec();
-}
diff --git a/demos/QVTK-Demo/qvtk-app/src/main.cpp b/demos/QVTK-Demo/qvtk-app/src/main.cpp
deleted file mode 100644
index 1fc8d5018dc15715da06ac22aace0dd6ab7a78b6..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-app/src/main.cpp
+++ /dev/null
@@ -1,32 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk_app/application.hpp"
-
-int main(int argc, char **argv)
-{
- Application app(&argc, argv);
- return app.Run();
-}
diff --git a/demos/QVTK-Demo/qvtk-lib/CMakeLists.txt b/demos/QVTK-Demo/qvtk-lib/CMakeLists.txt
deleted file mode 100644
index 32ce237d4fbb58314fee48eb5541bf8bc4f9ba4a..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/CMakeLists.txt
+++ /dev/null
@@ -1,83 +0,0 @@
-#-------------------------------------------------------------------------------
-# QVTK-Demo
-#
-# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualisation Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# This framework 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.
-#
-# In the future, we may decide to add a commercial license
-# at our own discretion without further notice.
-#
-# This program 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 Lesse r General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#-------------------------------------------------------------------------------
-
-set(CMAKE_AUTOMOC ON)
-set(QVTK_LIB_API_HEADER_DIR include/qvtk-lib)
-
-file(GLOB QVTK_LIB_SOURCES src/*.cpp)
-file(GLOB QVTK_LIB_HEADERS include/qvtk-lib/*.hpp)
-file(GLOB QVTK_LIB_API_HEADERS ${QVTK_LIB_API_HEADER_DIR}/*.hpp)
-
-set(QVTK_LIB_INCLUDE_DIRS
- ${CMAKE_CURRENT_SOURCE_DIR}/include
- ${PROJECT_SOURCE_DIR}qvtk-lib/include
- ${PROJECT_BINARY_DIR}
- CACHE PATH "Path to public headers in vtk's source tree."
-)
-
-add_library(qvtk-lib
- ${QVTK_LIB_SOURCES}
- ${QVTK_LIB_HEADERS}
-)
-
-target_include_directories(qvtk-lib
- PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
- PUBLIC ${CMAKE_CURRENT_BINARY_DIR}
-)
-
-generate_export_header(qvtk-lib
- EXPORT_FILE_NAME ${CMAKE_CURRENT_BINARY_DIR}/include/qvtk-lib/export.hpp
-)
-
-set_warning_levels_RWTH(qvtk-lib
- SUPPRESS_WARNINGS_HEADER ${CMAKE_CURRENT_BINARY_DIR}/include/qvtk-lib/suppress_warnings.hpp
-)
-
-#add_test_cpplint(NAME "vtkexperiment--cpplint"
-# ${VTKEXPERIMENT_SOURCES}
-# ${VTKEXPERIMENT_HEADERS}
-#)
-
-include_directories(include)
-
-# --- dependencies ---
-# VTK
-find_package(VTK REQUIRED)
-include(${VTK_USE_FILE})
-target_include_directories(qvtk-lib PUBLIC ${VTK_INCLUDE_DIR})
-
-target_include_directories(qvtk-lib PUBLIC
- ${CONAN_INCLUDE_DIRS}
-)
-
-target_link_libraries(qvtk-lib
- PUBLIC ${CONAN_OR_CMAKE_contra}
- PUBLIC ${CONAN_OR_CMAKE_nesci}
- PUBLIC ${CONAN_OR_CMAKE_conduit}
- PUBLIC ${CONAN_OR_CMAKE_Qt}
- PUBLIC ${CONAN_OR_CMAKE_VTK}
- debug ${VTK_LIBRARIES}
- optimized ${VTK_LIBRARIES}
-)
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/animate.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/animate.hpp
deleted file mode 100644
index bdedbbb2a48fbb1af8ebc09ba19d67a7ce51dad8..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/animate.hpp
+++ /dev/null
@@ -1,76 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_ANIMATE_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_ANIMATE_HPP_
-
-#include "QObject"
-#include "QTimer"
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#include "qvtk-lib/point_data.hpp"
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-class Animate : public QObject
-{
- Q_OBJECT
-
-public:
- explicit Animate(PointData *points);
- ~Animate() {}
-
- void StartTimer();
-
-signals:
- void DataChanged();
- void DataChanged(int time_step);
- void NextStep();
- void LastStep();
- void SwitchRealtime();
- void SwitchPlayPause();
-
-public slots: // NOLINT
- void ChangeData(int timestep = -1);
- void IncreaseSpeed();
- void DecreaseSpeed();
- void Iterate();
- void RealtimeButton();
- void PlayButton();
- void SpeedMenu(int index);
-
-private:
- PointData *points_;
- QTimer *rt_timer_;
- QTimer *play_timer_;
- int play_speed_ = 1000;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_ANIMATE_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/data_stream.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/data_stream.hpp
deleted file mode 100644
index 7254ccf5045a38be1e1a0289dda4fd2773c25ec0..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/data_stream.hpp
+++ /dev/null
@@ -1,64 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_DATA_STREAM_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_DATA_STREAM_HPP_
-
-#include <vector>
-
-#include "conduit/conduit_node.hpp"
-//#include "contra/boost-shmem/shared_memory_transport.hpp"
-#include "contra/relay.hpp"
-#include "contra/zmq/zeromq_transport.hpp"
-
-#include "nesci/consumer/nest_multimeter.hpp"
-
-namespace vtkexp
-{
-
-class DataStream
-{
-public:
- DataStream();
- ~DataStream() {}
-
- std::vector<double> GetMultValuesAt(int time_step);
- std::vector<double> GetTimeSteps();
-
-private:
- void SetUpStream();
- void Update(int time_step);
-
- std::vector<double> mult_values_;
-
- contra::Relay<contra::ZMQTransport> *relay_;
- nesci::consumer::NestMultimeter *multimeter_;
-
- conduit::Node node_;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_DATA_STREAM_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/interaction.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/interaction.hpp
deleted file mode 100644
index cfc6b51abc9a946416fdae1aac9885ac5eef47fa..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/interaction.hpp
+++ /dev/null
@@ -1,87 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_INTERACTION_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_INTERACTION_HPP_
-
-#include <string>
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#include <vtkActor.h>
-#include <vtkDataSetMapper.h>
-#include <vtkMapper.h>
-#include <vtkPointGaussianMapper.h>
-#include <vtkPointPicker.h>
-#include <vtkUnstructuredGrid.h>
-#include "vtkInteractorStyleTrackballCamera.h"
-#include "vtkPolyData.h"
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-class Interaction : public vtkInteractorStyleTrackballCamera
-{
- public:
- static Interaction *New();
- vtkTypeMacro(Interaction, vtkInteractorStyleTrackballCamera)
-
- Interaction();
-
- virtual void OnLeftButtonUp();
-
- void SetUpShaders();
- void SetUpActor();
- void SetUpMapper();
-
- double GetNeuronValue();
- vtkIdType GetNeuronId();
-
- void SetData(vtkSmartPointer<vtkPolyData> data);
- void SwitchMapper(int rendertype);
- void ExtractSelection();
- void HighlightSelection();
- void Deselect();
- void Pick();
-
- private:
- double neuron_value_;
- vtkIdType id_;
- vtkSmartPointer<vtkUnstructuredGrid> selected_;
-
- vtkSmartPointer<vtkPolyData> data_;
-
- vtkSmartPointer<vtkActor> actor_;
- vtkSmartPointer<vtkPointGaussianMapper> mapper_;
- vtkSmartPointer<vtkPointPicker> picker_;
-
- std::string point_shader_;
- std::string sphere_shader_;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_INTERACTION_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_widget.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_widget.hpp
deleted file mode 100644
index fd0ec97094735bb488f0a6ff010f87d9e7a80968..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_widget.hpp
+++ /dev/null
@@ -1,71 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WIDGET_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WIDGET_HPP_
-
-#include "qvtk-lib/visualize.hpp"
-
-#include "qvtk-lib/interaction.hpp"
-
-#include "QObject"
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wpedantic"
-#include "QVTKOpenGLWidget.h"
-#include "vtkGenericOpenGLRenderWindow.h"
-#pragma GCC diagnostic pop
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-class MainWidget : public QVTKOpenGLWidget
-{
- Q_OBJECT
-
-public:
- explicit MainWidget(PointData *points, QVTKOpenGLWidget *parent = 0);
- ~MainWidget() {}
-
- void Rerender();
-
-public slots: // NOLINT
- void ChangeRendertype(int rendertype);
-
-protected:
- void mouseReleaseEvent(QMouseEvent *event) override;
-
-private:
- Visualize *vispoints_;
- vtkSmartPointer<Interaction> style_;
- vtkSmartPointer<vtkGenericOpenGLRenderWindow> renderwindow_;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WIDGET_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_window.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_window.hpp
deleted file mode 100644
index a9bf28246dd4a41fcfff408052b1315bd10761f2..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/main_window.hpp
+++ /dev/null
@@ -1,99 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WINDOW_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WINDOW_HPP_
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-
-#include "qvtk-lib/animate.hpp"
-#include "qvtk-lib/main_widget.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#include "qvtk-lib/point_data.hpp"
-SUPPRESS_WARNINGS_END
-
-#include "QComboBox"
-#include "QGridLayout"
-#include "QLabel"
-#include "QLineEdit"
-#include "QMainWindow"
-#include "QPushButton"
-#include "QSlider"
-#include "QTimer"
-
-namespace vtkexp
-{
-
-class MainWindow : public QMainWindow
-{
- Q_OBJECT
-
-public:
- explicit MainWindow(PointData *points);
- ~MainWindow() {}
-
- QLineEdit *slider_line_edit_;
-
-public slots: // NOLINT
- void Rerender();
- void Realtime();
- void PlayPause();
- void IncrementSlider();
- void UpdateSlider();
- void AdjustSlider();
- void SliderValue();
- void SliderValue(int time_step);
-
-private:
- void ConnectSignals();
- void InitSlider(QSlider *slider);
- void SetUpButtons();
- void SetUpContent();
- void SetUpLayout();
- void SetUpLineEdit();
- void SetUpSliders();
- void SetUpVisualization();
- void StartAnimation();
-
- Animate *animation_;
- PointData *points_;
-
- QWidget *dummywidget_;
- MainWidget *mainwidget_;
- QComboBox *render_type_;
- QComboBox *speed_menu_;
- QPushButton *rt_button_;
- QPushButton *play_button_;
- QGridLayout *grid_;
- QLabel *time_label_;
- QSlider *time_slider_;
-
- bool realtime_{true};
- bool play_{true};
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_MAIN_WINDOW_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/point_data.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/point_data.hpp
deleted file mode 100644
index 934ccb63c71b959d625599c0d47165c43f71e4c8..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/point_data.hpp
+++ /dev/null
@@ -1,73 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_POINT_DATA_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_POINT_DATA_HPP_
-
-#include <vector>
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#include "qvtk-lib/data_stream.hpp"
-
-#include "vtkDataObject.h"
-#include "vtkFloatArray.h"
-#include "vtkPolyData.h"
-#include "vtkSmartPointer.h"
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-class PointData
-{
-public:
- PointData(int num_x, int num_y, int num_z);
- ~PointData() {}
-
- void Update(int time_step = -1);
- vtkSmartPointer<vtkPolyData> GetPolyPoints();
- vtkSmartPointer<vtkFloatArray> GetColors() const;
-
- int GetEndTime() const;
- int GetStartTime() const;
-
-private:
- void AttachColorsToPoints(const std::vector<double> &colors);
- static vtkSmartPointer<vtkPoints> CreatePoints(int num_x, int num_y,
- int num_z);
- void Initialize(int x, int y, int z);
- void ColorsModified();
-
- DataStream *stream_;
-
- int num_points_;
- vtkSmartPointer<vtkPolyData> points_polydata_;
- vtkSmartPointer<vtkFloatArray> pointcolors_;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_POINT_DATA_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/visualize.hpp b/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/visualize.hpp
deleted file mode 100644
index 9b0fc750c88a364b742638dfca86b0cfaef2a5bc..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/include/qvtk-lib/visualize.hpp
+++ /dev/null
@@ -1,98 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#ifndef QVTK_LIB_INCLUDE_QVTK_LIB_VISUALIZE_HPP_
-#define QVTK_LIB_INCLUDE_QVTK_LIB_VISUALIZE_HPP_
-
-#include <string>
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wpedantic"
-#include "qvtk-lib/interaction.hpp"
-#include "qvtk-lib/point_data.hpp"
-
-#include "vtkActor.h"
-#include "vtkAxesActor.h"
-#include "vtkColorTransferFunction.h"
-#include "vtkGenericOpenGLRenderWindow.h"
-#include "vtkOrientationMarkerWidget.h"
-#include "vtkPointGaussianMapper.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkRenderer.h"
-#include "vtkScalarBarActor.h"
-#include "vtkScalarBarWidget.h"
-#include "vtkSmartPointer.h"
-#pragma GCC diagnostic pop
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-class Visualize
-{
-public:
- explicit Visualize(PointData *points);
- ~Visualize() {}
-
- void Initialize(vtkSmartPointer<vtkGenericOpenGLRenderWindow> renderwindow,
- vtkSmartPointer<vtkRenderWindowInteractor> interactor);
- vtkSmartPointer<vtkRenderer> GetRenderer();
-
- void SwitchMapper(int rendertype);
-
-private:
- void SetUpAxes();
- void SetUpInteractor();
- void SetUpLegend();
- void SetUpMapper();
- void SetUpRenderer();
- void SetUpScene();
- void SetUpShaders();
- void SetUpTransferFunction();
-
- PointData *points_;
-
- std::string point_shader_;
- std::string sphere_shader_;
-
- vtkSmartPointer<vtkActor> actor_;
- vtkSmartPointer<vtkRenderer> renderer_;
- vtkSmartPointer<vtkRenderWindowInteractor> interactor_;
- vtkSmartPointer<vtkGenericOpenGLRenderWindow> renderwindow_;
-
- vtkSmartPointer<vtkPointGaussianMapper> mapper_;
- vtkSmartPointer<vtkColorTransferFunction> transfer_function_;
-
- vtkSmartPointer<vtkAxesActor> axes_;
- vtkSmartPointer<vtkOrientationMarkerWidget> axes_widget_;
- vtkSmartPointer<vtkScalarBarWidget> scalar_bar_widget_;
- vtkSmartPointer<vtkScalarBarActor> scalar_bar_;
-};
-
-} // namespace vtkexp
-
-#endif // QVTK_LIB_INCLUDE_QVTK_LIB_VISUALIZE_HPP_
diff --git a/demos/QVTK-Demo/qvtk-lib/src/animate.cpp b/demos/QVTK-Demo/qvtk-lib/src/animate.cpp
deleted file mode 100644
index fb736464121e7be169c2964721cefc1bc50b45fa..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/animate.cpp
+++ /dev/null
@@ -1,107 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk-lib/animate.hpp"
-
-namespace vtkexp
-{
-
-Animate::Animate(PointData *points) : points_(points)
-{
- rt_timer_ = new QTimer(this);
- play_timer_ = new QTimer(this);
- connect(rt_timer_, SIGNAL(timeout()), this, SLOT(ChangeData()));
- connect(play_timer_, SIGNAL(timeout()), this, SLOT(Iterate()));
-}
-
-void Animate::ChangeData(int time_step)
-{
- points_->Update(time_step);
- emit DataChanged();
-}
-
-void Animate::IncreaseSpeed() { play_speed_ += 1; }
-
-void Animate::DecreaseSpeed() { play_speed_ -= 1; }
-
-void Animate::Iterate()
-{
- rt_timer_->isActive() ? emit LastStep() : emit NextStep();
-}
-
-void Animate::StartTimer()
-{
- rt_timer_->start(1);
- play_timer_->start(play_speed_);
-}
-
-void Animate::RealtimeButton()
-{
- if (rt_timer_->isActive())
- {
- rt_timer_->stop();
- emit SwitchRealtime();
- }
- else
- {
- rt_timer_->start(1);
- emit SwitchRealtime();
- }
-}
-
-void Animate::SpeedMenu(int index)
-{
- switch (index)
- {
- case 0:
- play_speed_ = 1000;
- break;
- case 1:
- play_speed_ = 1000 / 5;
- break;
- case 2:
- play_speed_ = 1000 / 10;
- break;
- case 3:
- play_speed_ = 1000 / 50;
- break;
- case 4:
- play_speed_ = 1000 / 100;
- break;
- default:
- play_speed_ = 1000;
- break;
- }
- play_timer_->setInterval(play_speed_);
-}
-
-void Animate::PlayButton()
-{
- play_timer_->isActive() ? play_timer_->stop()
- : play_timer_->start(play_speed_);
- emit SwitchPlayPause();
-}
-
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/data_stream.cpp b/demos/QVTK-Demo/qvtk-lib/src/data_stream.cpp
deleted file mode 100644
index 16d39ab583025c37bb8a81023f361835eb6ec853..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/data_stream.cpp
+++ /dev/null
@@ -1,78 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk-lib/data_stream.hpp"
-
-#include <vector>
-
-namespace vtkexp
-{
-
-DataStream::DataStream() { SetUpStream(); }
-
-void DataStream::SetUpStream()
-{
- relay_ = new contra::Relay<contra::ZMQTransport>(
- contra::ZMQTransport::Type::CLIENT, "tcp://localhost:5555");
-
- multimeter_ = new nesci::consumer::NestMultimeter("recordingNode51");
- multimeter_->SetNode(&node_);
-}
-
-void DataStream::Update(int time_step)
-{
- auto time_step_string = std::to_string(static_cast<double>(time_step));
-
- const auto received_nodes = relay_->Receive();
- for (auto node : received_nodes)
- {
- node_.update(node);
- }
-
- if (time_step == -1 && !multimeter_->GetTimesteps().empty())
- {
- time_step_string = multimeter_->GetTimesteps().back();
- }
-
- mult_values_ = multimeter_->GetTimestepData(time_step_string, "V_m");
-}
-
-std::vector<double> DataStream::GetMultValuesAt(int time_step)
-{
- Update(time_step);
- return mult_values_;
-}
-
-std::vector<double> DataStream::GetTimeSteps()
-{
- std::vector<double> ret;
- for (auto value : multimeter_->GetTimesteps())
- {
- ret.push_back(std::stod(value));
- }
- return ret;
-}
-
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/interaction.cpp b/demos/QVTK-Demo/qvtk-lib/src/interaction.cpp
deleted file mode 100644
index d6554811cb363e5cf50c4f4e98e7f648ac146c31..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/interaction.cpp
+++ /dev/null
@@ -1,242 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk-lib/interaction.hpp"
-
-#include <string>
-
-SUPPRESS_WARNINGS_BEGIN
-#include "vtkExtractSelection.h"
-#include "vtkGeometryFilter.h"
-#include "vtkHardwareSelector.h"
-#include "vtkIdTypeArray.h"
-#include "vtkPointData.h"
-#include "vtkProperty.h"
-#include "vtkRenderWindow.h"
-#include "vtkRenderWindowInteractor.h"
-#include "vtkRendererCollection.h"
-#include "vtkSelection.h"
-#include "vtkSelectionNode.h"
-#include "vtkSmartPointer.h"
-#include "vtkVertexGlyphFilter.h"
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-vtkStandardNewMacro(Interaction)
-
- Interaction::Interaction()
-{
- SetUpShaders();
- SetUpMapper();
- SetUpActor();
-}
-
-void Interaction::SetUpMapper()
-{
- mapper_ = vtkSmartPointer<vtkPointGaussianMapper>::New();
- mapper_->SetSplatShaderCode(point_shader_.c_str());
- mapper_->ScalarVisibilityOff();
- mapper_->SetScaleFactor(0.35);
- mapper_->UseLookupTableScalarRangeOn();
- mapper_->EmissiveOff();
- mapper_->Update();
-}
-
-void Interaction::SetUpActor()
-{
- actor_ = vtkSmartPointer<vtkActor>::New();
- actor_->SetMapper(mapper_);
- actor_->GetProperty()->SetColor(0.0, 1.0, 0.0);
- actor_->GetProperty()->SetEdgeVisibility(1);
-}
-
-void Interaction::OnLeftButtonUp()
-{
- Pick();
-
- vtkSmartPointer<vtkHardwareSelector> selector =
- vtkSmartPointer<vtkHardwareSelector>::New();
- selector->SetRenderer(
- this->Interactor->GetRenderWindow()->GetRenderers()->GetFirstRenderer());
- int *temp = this->Interactor->GetRenderWindow()->GetSize();
- unsigned int windowSize[4];
- windowSize[0] = temp[2];
- windowSize[1] = temp[3];
- windowSize[2] = temp[0];
- windowSize[3] = temp[1];
- /*
- for(unsigned int i = 0; i < 4; i++)
- {
- windowSize[i] = temp[i];
- }
- */
- selector->SetArea(windowSize);
- selector->SetFieldAssociation(vtkDataObject::FIELD_ASSOCIATION_POINTS);
- vtkSelection *selection = selector->Select();
- std::cout << "Selection has " << selection->GetNumberOfNodes() << " nodes."
- << std::endl;
-
- vtkSmartPointer<vtkExtractSelection> extractSelection =
- vtkSmartPointer<vtkExtractSelection>::New();
- extractSelection->SetInputData(0, data_);
- extractSelection->Update();
-
- vtkSmartPointer<vtkDataSetMapper> mapper =
- vtkSmartPointer<vtkDataSetMapper>::New();
- mapper->SetInputConnection(extractSelection->GetOutputPort());
-
- vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
- actor->SetMapper(mapper);
- actor->GetProperty()->SetColor(1, 0, 0);
- GetDefaultRenderer()->AddActor(actor);
-
- if (id_ != -1)
- {
- ExtractSelection();
- HighlightSelection();
- }
- else
- {
- Deselect();
- }
- vtkInteractorStyleTrackballCamera::OnLeftButtonUp();
-}
-
-void Interaction::Pick()
-{
- int *pos = GetInteractor()->GetEventPosition();
-
- picker_ = vtkSmartPointer<vtkPointPicker>::New();
- picker_->SetTolerance(0.015);
-
- picker_->Pick(pos[0], pos[1], 0, GetDefaultRenderer());
- id_ = picker_->GetPointId();
- std::cout << id_ << std::endl;
-}
-
-void Interaction::ExtractSelection()
-{
- vtkSmartPointer<vtkIdTypeArray> ids = vtkSmartPointer<vtkIdTypeArray>::New();
- ids->SetNumberOfComponents(1);
- ids->InsertNextValue(picker_->GetPointId());
-
- vtkSmartPointer<vtkSelectionNode> selectionNode =
- vtkSmartPointer<vtkSelectionNode>::New();
- selectionNode->SetFieldType(vtkSelectionNode::POINT);
- selectionNode->SetContentType(vtkSelectionNode::INDICES);
- selectionNode->SetSelectionList(ids);
-
- vtkSmartPointer<vtkSelection> selection =
- vtkSmartPointer<vtkSelection>::New();
- selection->AddNode(selectionNode);
-
- vtkSmartPointer<vtkExtractSelection> extract_selection =
- vtkSmartPointer<vtkExtractSelection>::New();
- extract_selection->SetInputData(0, data_);
- extract_selection->SetInputData(1, selection);
- extract_selection->Update();
-
- selected_ = vtkSmartPointer<vtkUnstructuredGrid>::New();
- selected_->ShallowCopy(extract_selection->GetOutput());
-
- neuron_value_ = selected_->GetPointData()->GetScalars()->GetComponent(0, 0);
-}
-
-void Interaction::HighlightSelection()
-{
- vtkSmartPointer<vtkGeometryFilter> geometryFilter =
- vtkSmartPointer<vtkGeometryFilter>::New();
- geometryFilter->SetInputData(selected_);
- geometryFilter->Update();
-
- vtkSmartPointer<vtkVertexGlyphFilter> glyphFilter =
- vtkSmartPointer<vtkVertexGlyphFilter>::New();
- glyphFilter->SetInputData(geometryFilter->GetOutput());
- glyphFilter->Update();
-
- mapper_->SetInputData(glyphFilter->GetOutput());
-
- CurrentRenderer->AddActor(actor_);
- GetInteractor()->GetRenderWindow()->Render();
-}
-
-void Interaction::Deselect()
-{
- vtkSmartPointer<vtkPolyData> empty = vtkSmartPointer<vtkPolyData>::New();
-
- mapper_->SetInputData(empty);
- mapper_->Update();
-
- CurrentRenderer->AddActor(actor_);
- GetInteractor()->GetRenderWindow()->Render();
-}
-
-void Interaction::SetData(vtkSmartPointer<vtkPolyData> data) { data_ = data; }
-
-void Interaction::SwitchMapper(int rendertype)
-{
- if (rendertype == 0)
- {
- mapper_->SetSplatShaderCode(point_shader_.c_str());
- }
- else if (rendertype == 1)
- {
- mapper_->SetSplatShaderCode(sphere_shader_.c_str());
- }
-}
-
-double Interaction::GetNeuronValue() { return neuron_value_; }
-
-vtkIdType Interaction::GetNeuronId() { return id_; }
-
-void Interaction::SetUpShaders()
-{
- sphere_shader_ =
- "//VTK::Color::Impl\n"
- "float dist = dot(offsetVCVSOutput.xy,offsetVCVSOutput.xy);\n"
- "if (dist > 0.9) {\n"
- " discard;\n"
- "} else {\n"
- " float scale = (1.0 - dist);\n"
- " ambientColor *= 0.5;\n"
- " diffuseColor *= 0.7;\n"
- "}\n";
-
- point_shader_ =
- "//VTK::Color::Impl\n"
- "ambientColor *= 0.5;\n"
- "diffuseColor *= 0.7;\n"
- "if (abs(offsetVCVSOutput.x) > 0.3 || abs(offsetVCVSOutput.y) > 0.3) "
- "{\n"
- " discard;\n"
- "}\n"
- "if (abs(offsetVCVSOutput.x) < 0.0 && abs(offsetVCVSOutput.y) < 0.0) "
- "{\n"
- " discard;\n"
- "}\n";
-}
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/main_widget.cpp b/demos/QVTK-Demo/qvtk-lib/src/main_widget.cpp
deleted file mode 100644
index dcc6f6cf638bb7153e63d7cac1d99fc9f63e2c67..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/main_widget.cpp
+++ /dev/null
@@ -1,68 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------
-
-#include "qvtk-lib/main_widget.hpp"
-
-#include "vtkGenericOpenGLRenderWindow.h"
-
-#include "QString"
-#include "QtWidgets"
-
-namespace vtkexp
-{
-
-MainWidget::MainWidget(PointData *points, QVTKOpenGLWidget *parent)
- : QVTKOpenGLWidget(parent)
-{
- renderwindow_ = vtkSmartPointer<vtkGenericOpenGLRenderWindow>::New();
- this->SetRenderWindow(renderwindow_.Get());
-
- style_ = vtkSmartPointer<Interaction>::New();
- style_->SetData(points->GetPolyPoints());
- this->GetInteractor()->SetInteractorStyle(style_);
-
- vispoints_ = new Visualize(points);
- vispoints_->Initialize(renderwindow_, this->GetInteractor());
-}
-
-void MainWidget::mouseReleaseEvent(QMouseEvent *event)
-{
- QVTKOpenGLWidget::mouseReleaseEvent(event);
- if (event->button() == Qt::LeftButton && style_->GetNeuronId() != -1)
- {
- QToolTip::showText(this->mapToGlobal(event->pos()),
- QString::number(style_->GetNeuronValue()));
- }
-}
-
-void MainWidget::ChangeRendertype(int rendertype)
-{
- vispoints_->SwitchMapper(rendertype);
- style_->SwitchMapper(rendertype);
-}
-
-void MainWidget::Rerender() { renderwindow_->Render(); }
-
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/main_window.cpp b/demos/QVTK-Demo/qvtk-lib/src/main_window.cpp
deleted file mode 100644
index 980eb8afc59c25bff71de6222b5a2fa810fb21e2..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/main_window.cpp
+++ /dev/null
@@ -1,208 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk-lib/main_window.hpp"
-
-namespace vtkexp
-{
-
-MainWindow::MainWindow(PointData *points) : points_(points)
-{
- setWindowTitle("QVTK-Neuron-Viewer");
- SetUpVisualization();
- SetUpContent();
- setCentralWidget(dummywidget_);
- ConnectSignals();
- StartAnimation();
-}
-
-void MainWindow::SetUpVisualization()
-{
- animation_ = new Animate(points_);
- mainwidget_ = new MainWidget(points_);
-}
-
-void MainWindow::SetUpContent()
-{
- SetUpSliders();
- SetUpLineEdit();
- SetUpButtons();
- SetUpLayout();
-}
-
-void MainWindow::SetUpLayout()
-{
- dummywidget_ = new QWidget;
- grid_ = new QGridLayout;
- grid_->addWidget(mainwidget_, 0, 0, 1, -1);
- grid_->addWidget(time_label_, 1, 0, 1, 1);
- grid_->addWidget(time_slider_, 1, 1, 1, 1);
- grid_->addWidget(slider_line_edit_, 1, 2, 1, 10);
- grid_->addWidget(render_type_, 1, 14, 1, 1);
- grid_->addWidget(rt_button_, 1, 15, 1, 1);
- grid_->addWidget(play_button_, 1, 13, 1, 1);
- grid_->addWidget(speed_menu_, 1, 12, 1, 1);
- dummywidget_->setLayout(grid_);
-
- resize(800, 600);
-}
-
-void MainWindow::SetUpLineEdit()
-{
- slider_line_edit_ = new QLineEdit();
- slider_line_edit_->setText(std::to_string(0).c_str());
-}
-
-void MainWindow::SetUpSliders()
-{
- time_slider_ = new QSlider(Qt::Horizontal);
- time_label_ = new QLabel("Time:");
- InitSlider(time_slider_);
- time_slider_->setEnabled(0);
-}
-
-void MainWindow::InitSlider(QSlider *slider)
-{
- slider->setFocusPolicy(Qt::StrongFocus);
- slider->setTickPosition(QSlider::TicksAbove);
- slider->setTickInterval(50);
- slider->setSingleStep(20);
- slider->setMinimum(0);
- slider->setMaximum(100);
- slider->setValue(100);
-}
-
-void MainWindow::SetUpButtons()
-{
- rt_button_ = new QPushButton("Replay", this);
- rt_button_->setFixedSize(QSize(80, 32));
- play_button_ = new QPushButton("⏸", this);
- play_button_->setFixedSize(QSize(32, 32));
- render_type_ = new QComboBox(this);
- render_type_->setFixedSize(QSize(80, 32));
- render_type_->addItems({"Points", "Spheres"});
- speed_menu_ = new QComboBox(this);
- speed_menu_->addItems({"1/sec", "5/sec", "10/sec", "50/sec", "100/sec"});
-}
-
-void MainWindow::StartAnimation() { animation_->StartTimer(); }
-
-void MainWindow::ConnectSignals()
-{
- connect(speed_menu_, SIGNAL(activated(int)), animation_,
- SLOT(SpeedMenu(int)));
- connect(rt_button_, SIGNAL(clicked()), animation_, SLOT(RealtimeButton()));
- connect(play_button_, SIGNAL(clicked()), animation_, SLOT(PlayButton()));
- connect(time_slider_, SIGNAL(valueChanged(int)), animation_,
- SLOT(ChangeData(int)));
- connect(time_slider_, SIGNAL(valueChanged(int)), SLOT(SliderValue(int)));
- connect(slider_line_edit_, SIGNAL(editingFinished()), SLOT(SliderValue()));
- connect(render_type_, SIGNAL(currentIndexChanged(int)), mainwidget_,
- SLOT(ChangeRendertype(int)));
- connect(animation_, SIGNAL(SwitchRealtime()), this, SLOT(Realtime()));
- connect(animation_, SIGNAL(SwitchPlayPause()), this, SLOT(PlayPause()));
- connect(animation_, SIGNAL(DataChanged()), this, SLOT(Rerender()));
- connect(animation_, SIGNAL(DataChanged()), this, SLOT(AdjustSlider()));
- connect(animation_, SIGNAL(NextStep()), SLOT(IncrementSlider()));
- connect(animation_, SIGNAL(LastStep()), SLOT(UpdateSlider()));
-}
-
-void MainWindow::Rerender() { mainwidget_->Rerender(); }
-
-void MainWindow::IncrementSlider()
-{
- int newval;
- if (time_slider_->value() + 1 < time_slider_->maximum())
- {
- newval = time_slider_->value() + 1;
- }
- else
- {
- newval = time_slider_->maximum();
- }
-
- time_slider_->setValue(newval);
- slider_line_edit_->setText(std::to_string(newval).c_str());
-}
-
-void MainWindow::UpdateSlider()
-{
- time_slider_->setValue(points_->GetEndTime());
- slider_line_edit_->setText(std::to_string(time_slider_->value()).c_str());
-}
-
-void MainWindow::AdjustSlider()
-{
- time_slider_->setMinimum(points_->GetStartTime());
- time_slider_->setMaximum(points_->GetEndTime());
-}
-
-void MainWindow::SliderValue(int time_step)
-{
- slider_line_edit_->setText(std::to_string(time_step).c_str());
- time_slider_->setMinimum(points_->GetStartTime());
- time_slider_->setMaximum(points_->GetEndTime());
-}
-
-void MainWindow::SliderValue()
-{
- time_slider_->setValue(slider_line_edit_->text().toInt());
-}
-
-void MainWindow::Realtime()
-{
- if (realtime_)
- {
- realtime_ = false;
- rt_button_->setText("Realtime");
- time_slider_->setMinimum(points_->GetStartTime());
- time_slider_->setMaximum(points_->GetEndTime());
- time_slider_->setEnabled(1);
- }
- else
- {
- realtime_ = true;
- time_slider_->setValue(points_->GetEndTime());
- rt_button_->setText("Replay");
- time_slider_->setEnabled(0);
- }
-}
-
-void MainWindow::PlayPause()
-{
- if (play_)
- {
- play_ = false;
- play_button_->setText("▶");
- SliderValue(slider_line_edit_->text().toInt());
- }
- else
- {
- play_ = true;
- play_button_->setText("⏸");
- }
-}
-
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/point_data.cpp b/demos/QVTK-Demo/qvtk-lib/src/point_data.cpp
deleted file mode 100644
index 263c7bc1d82a35fcb489f6fc975d98ad7c22edfc..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/point_data.cpp
+++ /dev/null
@@ -1,133 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include <vector>
-
-#include "include/qvtk-lib/suppress_warnings.hpp"
-SUPPRESS_WARNINGS_BEGIN
-#include "qvtk-lib/point_data.hpp"
-
-#include "vtkCellArray.h"
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wpedantic"
-#include "vtkPointData.h"
-#pragma GCC diagnostic pop
-SUPPRESS_WARNINGS_END
-
-namespace vtkexp
-{
-
-PointData::PointData(int num_x, int num_y, int num_z)
- : num_points_(num_x * num_y * num_z)
-{
- Initialize(num_x, num_y, num_z);
-}
-
-void PointData::Initialize(int x, int y, int z)
-{
- points_polydata_ = vtkSmartPointer<vtkPolyData>::New();
- points_polydata_->SetPoints(CreatePoints(x, y, z));
-
- pointcolors_ = vtkSmartPointer<vtkFloatArray>::New();
- pointcolors_->SetName("colors");
- pointcolors_->SetNumberOfTuples(num_points_);
-
- std::vector<double> init(num_points_);
- std::fill(init.begin(), init.end(), 0);
- AttachColorsToPoints(init);
-
- stream_ = new DataStream();
-}
-
-vtkSmartPointer<vtkPoints> PointData::CreatePoints(int num_x, int num_y,
- int num_z)
-{
- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
- for (int i = 0; i < num_x; ++i)
- {
- for (int j = 0; j < num_y; ++j)
- {
- for (int k = 0; k < num_z; ++k)
- {
- points->InsertNextPoint(i, j, k);
- }
- }
- }
- return points;
-}
-
-void PointData::ColorsModified()
-{
- points_polydata_->GetPointData()->GetScalars()->Modified();
-}
-
-void PointData::AttachColorsToPoints(const std::vector<double> &scalars)
-{
- if (!scalars.empty())
- {
- for (int i = 0; i < num_points_; ++i)
- {
- pointcolors_->SetValue(
- i, static_cast<float>(scalars.at(static_cast<int>(i))));
- }
- points_polydata_->GetPointData()->SetScalars(pointcolors_);
- }
-}
-
-void PointData::Update(int time_step)
-{
- AttachColorsToPoints(stream_->GetMultValuesAt(time_step));
- ColorsModified();
-}
-
-vtkSmartPointer<vtkPolyData> PointData::GetPolyPoints()
-{
- return points_polydata_;
-}
-
-vtkSmartPointer<vtkFloatArray> PointData::GetColors() const
-{
- return pointcolors_;
-}
-
-int PointData::GetStartTime() const
-{
- if (!stream_->GetTimeSteps().empty())
- {
- return static_cast<int>(stream_->GetTimeSteps().front());
- }
- return 0;
-}
-
-int PointData::GetEndTime() const
-{
- if (!stream_->GetTimeSteps().empty())
- {
- return static_cast<int>(stream_->GetTimeSteps().back());
- }
- return 100;
-}
-
-} // namespace vtkexp
diff --git a/demos/QVTK-Demo/qvtk-lib/src/visualize.cpp b/demos/QVTK-Demo/qvtk-lib/src/visualize.cpp
deleted file mode 100644
index 614c74b13507c2eb05468c8c82d0c27f60686e96..0000000000000000000000000000000000000000
--- a/demos/QVTK-Demo/qvtk-lib/src/visualize.cpp
+++ /dev/null
@@ -1,157 +0,0 @@
-//------------------------------------------------------------------------------
-// QVTK-Demo
-//
-// Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-// Virtual Reality & Immersive Visualisation Group.
-//------------------------------------------------------------------------------
-// License
-//
-// This framework 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.
-//
-// In the future, we may decide to add a commercial license
-// at our own discretion without further notice.
-//
-// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
-//------------------------------------------------------------------------------
-
-#include "qvtk-lib/visualize.hpp"
-
-#include <string>
-
-namespace vtkexp
-{
-
-Visualize::Visualize(PointData *points) { points_ = points; }
-
-vtkSmartPointer<vtkRenderer> Visualize::GetRenderer() { return renderer_; }
-
-void Visualize::Initialize(
- vtkSmartPointer<vtkGenericOpenGLRenderWindow> renderwindow,
- vtkSmartPointer<vtkRenderWindowInteractor> interactor)
-{
- renderwindow_ = renderwindow;
- interactor_ = interactor;
- SetUpTransferFunction();
- SetUpMapper();
- SetUpScene();
- SetUpRenderer();
- SetUpAxes();
- SetUpLegend();
-}
-
-void Visualize::SetUpLegend()
-{
- scalar_bar_widget_ = vtkSmartPointer<vtkScalarBarWidget>::New();
- scalar_bar_widget_->SetInteractor(interactor_);
- scalar_bar_widget_->SetEnabled(true);
-
- scalar_bar_ = scalar_bar_widget_->GetScalarBarActor();
- // scalar_bar_->SetTitle("Legend");
- scalar_bar_->SetLookupTable(transfer_function_);
- scalar_bar_->SetOrientationToVertical();
- scalar_bar_->SetNumberOfLabels(0);
-
- scalar_bar_->SetPosition2(0, 0);
- scalar_bar_->SetBarRatio(0.6);
-}
-
-void Visualize::SetUpAxes()
-{
- axes_ = vtkSmartPointer<vtkAxesActor>::New();
-
- axes_widget_ = vtkSmartPointer<vtkOrientationMarkerWidget>::New();
- axes_widget_->SetOutlineColor(0.9300, 0.5700, 0.1300);
- axes_widget_->SetOrientationMarker(axes_);
- axes_widget_->SetInteractor(interactor_);
- axes_widget_->SetViewport(0.0, 0.0, 0.2, 0.2);
- axes_widget_->SetEnabled(1);
- axes_widget_->InteractiveOn();
-
- renderer_->ResetCamera();
-}
-
-void Visualize::SetUpScene()
-{
- actor_ = vtkSmartPointer<vtkActor>::New();
- actor_->SetMapper(mapper_);
-}
-
-void Visualize::SetUpRenderer()
-{
- renderer_ = vtkSmartPointer<vtkRenderer>::New();
- renderwindow_->AddRenderer(renderer_);
- renderer_->AddActor(actor_);
- interactor_->GetInteractorStyle()->SetDefaultRenderer(renderer_);
-
- renderer_->GradientBackgroundOn();
- renderer_->SetBackground(0.3, 0.4, 0.5);
- renderer_->SetBackground2(0.1, 0.2, 0.3);
-}
-
-void Visualize::SetUpTransferFunction()
-{
- transfer_function_ = vtkSmartPointer<vtkColorTransferFunction>::New();
- transfer_function_->SetColorSpaceToDiverging();
- transfer_function_->AddRGBPoint(-15, 0, 0, 1);
- transfer_function_->AddRGBPoint(5, 1, 0, 0);
-}
-
-void Visualize::SetUpMapper()
-{
- SetUpShaders();
-
- mapper_ = vtkSmartPointer<vtkPointGaussianMapper>::New();
- mapper_->SetInputData(points_->GetPolyPoints());
- mapper_->SetSplatShaderCode(point_shader_.c_str());
- mapper_->SetLookupTable(transfer_function_);
- mapper_->SetScaleFactor(0.35);
- mapper_->UseLookupTableScalarRangeOn();
- mapper_->EmissiveOff();
- mapper_->Update();
-}
-
-void Visualize::SetUpShaders()
-{
- point_shader_ =
- "//VTK::Color::Impl\n"
- "ambientColor *= 1.0;\n"
- "diffuseColor *= 1.0;\n"
- "if (abs(offsetVCVSOutput.x) > 0.2 || abs(offsetVCVSOutput.y) > 0.2) "
- "{\n"
- " discard;\n"
- "}\n";
-
- sphere_shader_ =
- "//VTK::Color::Impl\n"
- "float dist = dot(offsetVCVSOutput.xy,offsetVCVSOutput.xy);\n"
- "if (dist > 0.8) {\n"
- " discard;\n"
- "} else {\n"
- " float scale = (1.0 - dist);\n"
- " ambientColor *= scale;\n"
- " diffuseColor *= scale;\n"
- "}\n";
-}
-
-void Visualize::SwitchMapper(int rendertype)
-{
- if (rendertype == 0)
- {
- mapper_->SetSplatShaderCode(point_shader_.c_str());
- }
- else if (rendertype == 1)
- {
- mapper_->SetSplatShaderCode(sphere_shader_.c_str());
- }
-}
-
-} // namespace vtkexp
diff --git a/demos/brunel_simulation/CMakeLists.txt b/demos/brunel_simulation/CMakeLists.txt
deleted file mode 100644
index 6fd813ebf9dbf4b4c0e2db0852fcc1879ec51b1a..0000000000000000000000000000000000000000
--- a/demos/brunel_simulation/CMakeLists.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-#-------------------------------------------------------------------------------
-# nest-streaming-module
-#
-# Copyright (c) 2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualization Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#-------------------------------------------------------------------------------
-
-get_filename_component(NEST_DIR ${with-nest} DIRECTORY)
-
-set(SCRIPT_FILENAME "${CMAKE_CURRENT_BINARY_DIR}/run_sim.sh")
-execute_process(
- COMMAND ${NEST_CONFIG} --python-executable
- RESULT_VARIABLE RES_VAR
- OUTPUT_VARIABLE PYTHON_EXECUTABLE
- OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-message(STATUS "PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE}")
-
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/run_sim.sh.in ${SCRIPT_FILENAME})
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/brunel_example.py ${CMAKE_CURRENT_SOURCE_DIR}/nest_sim.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-add_custom_target(brunel_simulation ALL chmod "+x" "run_sim.sh"
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- DEPENDS ${SCRIPT_FILENAME} ${CMAKE_CURRENT_BINARY_DIR}/brunel_example.py ${CMAKE_CURRENT_SOURCE_DIR}/nest_sim.py)
diff --git a/demos/brunel_simulation/brunel_example.py b/demos/brunel_simulation/brunel_example.py
deleted file mode 100644
index 4c59b60dbaa9fd1c84c694131ef9825f736d9a3c..0000000000000000000000000000000000000000
--- a/demos/brunel_simulation/brunel_example.py
+++ /dev/null
@@ -1,265 +0,0 @@
-
-"""
-Definition of spatially extended Brunel network.
-This module provides layer and projections declarations suitable for
-use with the NEST Topology Module.
-It defines a Brunel-style network with neurons placed on a regular grid.
-Connectivity is probabilitstic from the entire network, i.e., connectivity
-is not structured spatially.
-"""
-
-from copy import deepcopy
-from math import sqrt
-import numpy as np
-from mpl_toolkits.mplot3d import Axes3D
-import matplotlib.pyplot as plt
-
-import nest
-import nest.raster_plot
-import nest.topology as tp
-
-
-class Brunel3D:
-
- def __init__(self):
- self.layer_dict = {}
- nest.Install("streamingmodule")
- # nest.SetKernelStatus({'print_time': True})
-
- class Parameters:
- """
- Define model parameters.
- """
- order = 9 # must be square
- NE = 4 * order # number of excitatory neurons.
- NI = 1 * order # number of inhibitory neurons
-
- lengthE = int(sqrt(NE))
- lengthI = int(sqrt(NI))
-
- if not (lengthE**2 == NE and lengthI**2 == NI):
- raise ValueError('Order must be a square number (order = n**2)')
-
- # neuron_model = 'iaf_psc_alpha'
- neuron_model = 'mat2_psc_exp'
-
- g = 5.0 # ratio inhibitory weight/excitatory weight
- eta = 2.0 # external rate relative to threshold rate
- epsilon = 0.1 # connection probability
-
- delay = 1.5 # synaptic delay in ms
-
- tauMem = 20.0 # time constant of membrane potential in ms
- theta = 20.0 # membrane threshold potential in mV
-
- J = 0.1 # postsynaptic amplitude in mV
- J_ex = J # amplitude of excitatory postsynaptic potential
- J_in = -g * J_ex # amplitude of inhibitory postsynaptic potential
-
- CE = int(epsilon * NE) # number of excitatory synapses per neuron
-
- nu_th = theta / (J * CE * tauMem)
- nu_ex = eta * nu_th
- p_rate = 1.0 * nu_ex * CE
-
- neuron_params = {"C_m": 1.0,
- "tau_m": tauMem,
- "t_ref": 2.0,
- "E_L": 0.0,
- # "V_reset": 0.0, # doesn't work with mat2_psc_exp
- # "V_th": theta, # doesn't work with mat2_psc_exp
- "V_m": 0.0
- }
- mm_params = {'record_from': ['V_m', 'V_th'],
- 'record_to': ['streaming']}
- poisson_params = {"rate": p_rate}
-
- def modified_copy(self, orig, diff):
- """
- Returns a deep copy of dictionary with changes applied.
- @param orig original dictionary, will be deep-copied
- @param diff copy will be updated with this dict
- """
-
- tmp = deepcopy(orig)
- tmp.update(diff)
- return tmp
-
- def make_layer_specs(self):
- """
- Returns lists of dictionaries with model, layer, and synapse model
- specifications.
- """
-
- P = self.Parameters
-
- self.models = [(P.neuron_model, 'excitatory', P.neuron_params),
- (P.neuron_model, 'inhibitory', P.neuron_params),
- ('poisson_generator', 'noise', P.poisson_params),
- ('multimeter', 'recordingNode', P.mm_params)]
-
- self.syn_models = [('static_synapse', 'static_excitatory', {})]
-
- dE = 1.0 / float(P.lengthE)
- limE = (1.0 - dE) / 2.0
- posE = np.linspace(-limE, limE, num=P.lengthE)
-
- dI = 1.0 / float(P.lengthI)
- limI = (1.0 - dI) / 2.0
- posI = np.linspace(-limI, limI, num=P.lengthI)
-
- self.layers = [('Excitatory', {'positions': [[x, y, 0.4]
- for x in posE
- for y in posE],
- 'edge_wrap': True,
- 'elements': 'excitatory'}),
- ('Inhibitory', {'positions': [[x, y, -0.4]
- for x in posI
- for y in posI],
- 'edge_wrap': True,
- 'elements': 'inhibitory'})]
- self.layers.append(('PoissonGenerator',
- {'positions': [[0.0, 0.0, 0.0]],
- 'elements': 'noise'}))
- self.layers.append(('Multimeter',
- {'positions': [[0.0, 0.0, 0.0]],
- 'elements': 'recordingNode'}))
- self.layers.append(('SpikeDetector',
- {'positions': [[0.0, 0.0, 0.0]],
- 'elements': 'spike_detector'}))
-
- def make_connection_specs(self):
- """
- Returns list of dictionaries specifying projections for Brunel network.
- """
-
- P = self.Parameters
-
- self.projections = [('Excitatory', 'Excitatory',
- {'connection_type': 'convergent',
- 'synapse_model': 'static_synapse',
- 'kernel': P.epsilon,
- 'weights': P.J_ex,
- 'delays': P.delay}),
- ('Excitatory', 'Inhibitory',
- {'connection_type': 'convergent',
- 'synapse_model': 'static_synapse',
- 'kernel': P.epsilon,
- 'weights': P.J_ex,
- 'delays': P.delay}),
- ('Inhibitory', 'Excitatory',
- {'connection_type': 'convergent',
- 'synapse_model': 'static_synapse',
- 'kernel': P.epsilon,
- 'weights': P.J_in,
- 'delays': P.delay}),
- ('Inhibitory', 'Excitatory',
- {'connection_type': 'convergent',
- 'synapse_model': 'static_synapse',
- 'kernel': P.epsilon,
- 'weights': P.J_in,
- 'delays': P.delay}),
- ('Multimeter', 'Excitatory',
- {'connection_type': 'convergent'}),
- ('Excitatory', 'SpikeDetector',
- {'connection_type': 'convergent'}),
- ('Inhibitory', 'SpikeDetector',
- {'connection_type': 'convergent'}),
- ('PoissonGenerator', 'Excitatory',
- {'connection_type': 'convergent'})]
-
- def make_layers(self):
- # First, we copy the models with custom specifications
- # Neuron models
- for model in self.models:
- old_name, new_name, spec = model
- nest.CopyModel(old_name, new_name, spec)
- # Synapse models
- for model in self.syn_models:
- old_name, new_name, spec = model
- nest.CopyModel(old_name, new_name, spec)
-
- # Next we make the layers
- for l in self.layers:
- name = l[0]
- specs = l[1]
- self.layer_dict.update({name: tp.CreateLayer(specs)})
-
- def make_connections(self):
- # Connect layers
- for proj in self.projections:
- pre_layer = self.layer_dict[proj[0]]
- post_layer = self.layer_dict[proj[1]]
- conn_specs = proj[2]
- tp.ConnectLayers(pre_layer, post_layer, conn_specs)
-
- def simulate(self):
- nest.Simulate(1000)
-
- def plot_positions(self):
- ex_pos = self.layers[0][1]['positions']
- in_pos = self.layers[1][1]['positions']
- fig = plt.figure()
- ax = Axes3D(fig)
- for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
- ax.scatter([x for x, y, z in positions],
- [y for x, y, z in positions],
- [z for x, y, z in positions],
- c=c, marker=m)
-
- def get_results(self):
- mm = (self.layer_dict['Multimeter'][0] + 1,)
- sd = (self.layer_dict['SpikeDetector'][0] + 1,)
- mm_status = nest.GetStatus(mm)[0]
- sd_status = nest.GetStatus(sd)[0]
-
- nest.raster_plot.from_device(sd, hist=True)
-
- senders = mm_status['events']['senders']
- times = mm_status['events']['times']
- v_m = mm_status['events']['V_m']
- v_th = mm_status['events']['V_th']
- step = int(max(senders)/100 + 1) # Only plot results from some GIDs
-
- mm_events = []
- for i in range(1, max(senders) + 1, step):
- if i in senders:
- indices = np.argwhere(senders == i)
- mm_events.append({'GID': i,
- 'times': [times[n] for n in indices],
- 'V_m': [v_m[n] for n in indices],
- 'V_th': [v_th[n] for n in indices]})
-
- return {'multimeter': mm_events,
- 'spike_detector': nest.GetStatus(sd)[0]}
-
-
-if __name__ == '__main__':
- nest.ResetKernel()
-
- print('Making specifications')
- brunel = Brunel3D()
- brunel.make_layer_specs()
- brunel.make_connection_specs()
-
- print('Making layers')
- brunel.make_layers()
- nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
- 'brunel_nodes.txt')
-
- print('Making connections')
- brunel.make_connections()
-
- brunel.simulate()
-
- print('Getting results')
- brunel.plot_positions()
- results = brunel.get_results()
-
- for value in ['V_m', 'V_th']:
- plt.figure()
- for n in results['multimeter'][::20]:
- plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
- plt.legend()
- plt.title(value)
- plt.show()
diff --git a/demos/brunel_simulation/nest_sim.py b/demos/brunel_simulation/nest_sim.py
deleted file mode 100644
index 65788db7fdfa3b6b407bc8f91ba08e04e1dc8dfc..0000000000000000000000000000000000000000
--- a/demos/brunel_simulation/nest_sim.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#-------------------------------------------------------------------------------
-# nest in situ vis
-#
-# Copyright (c) 2017-2018 RWTH Aachen University, Germany,
-# Virtual Reality & Immersive Visualisation Group.
-#-------------------------------------------------------------------------------
-# License
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#-------------------------------------------------------------------------------
-
-import sys
-import nest
-import numpy
-
-from PyQt5.QtWidgets import QApplication, QPushButton
-from PyQt5.QtCore import QTimer
-
-import brunel_example
-
-class Simulation:
- def __init__(self):
- self.SetupSim()
-
- def SetupSim(self):
- nest.ResetKernel()
-
- print('Making specifications')
- self.brunel = brunel_example.Brunel3D()
- self.brunel.make_layer_specs()
- self.brunel.make_connection_specs()
-
- print('Making layers')
- self.brunel.make_layers()
- nest.topology.DumpLayerNodes([l[0] for l in self.brunel.layer_dict.values()][:2],
- 'brunel_nodes.txt')
-
- print('Making connections')
- self.brunel.make_connections()
-
- def Simulate(self, steps):
- nest.Simulate(steps)
-
-
-class MainWindow:
- def __init__(self, screen_resolution):
- self.screen_resolution = screen_resolution
- self.SetupWindow()
- self.simulation = Simulation()
-
- def SetupWindow(self):
- self.simulate_button = QPushButton("nest.Simulate(1000)")
- self.simulate_button.clicked.connect(self.SimulateButtonClicked)
-
- def SimulateButtonClicked(self):
- self.simulate_button.setEnabled(False)
- QApplication.processEvents()
-
- self.simulation.Simulate(1000)
-
- QApplication.processEvents()
- self.simulate_button.setEnabled(True)
-
- def Show(self):
- self.simulate_button.show()
- button_geometry = self.simulate_button.geometry()
- self.simulate_button.setGeometry(
- self.screen_resolution.width() - button_geometry.width(),
- self.screen_resolution.height() - button_geometry.height(),
- button_geometry.width(),
- button_geometry.height())
-
-
-def main(argv):
- app = QApplication(argv)
- screen_resolution = app.desktop().screenGeometry()
-
- w = MainWindow(screen_resolution)
- w.Show()
-
- return app.exec_()
-
-if __name__ == "__main__":
- main(sys.argv)
diff --git a/demos/brunel_simulation/run_sim.sh.in b/demos/brunel_simulation/run_sim.sh.in
deleted file mode 100644
index dd5c5c1b65105d5bd99b67e3b61314d2e362be64..0000000000000000000000000000000000000000
--- a/demos/brunel_simulation/run_sim.sh.in
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash
-source ${NEST_DIR}/nest_vars.sh
-LD_LIBRARY_PATH=$NEST_MODULE_PATH:$LD_LIBRARY_PATH ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/nest_sim.py
\ No newline at end of file
diff --git a/recording_backend_nesci_contra.cpp b/recording_backend_nesci_contra.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..57b97e96d44390f5afacace84631e3d9a7069efa
--- /dev/null
+++ b/recording_backend_nesci_contra.cpp
@@ -0,0 +1,230 @@
+/*
+ * recording_backend_stream_niv.cpp
+ *
+ * This file is part of NEST.
+ *
+ * Copyright (C) 2004 The NEST Initiative
+ *
+ * NEST is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * NEST 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with NEST. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include "recording_backend_nesci_contra.h"
+
+#include "recording_device.h"
+
+#include <iostream>
+#include <memory>
+#include <sstream>
+
+streamingnest::RecordingBackendNesciContra::RecordingBackendNesciContra()
+ : num_buffered_steps_( 0 ), datum_(0, std::string{}, std::vector<double>{})
+{
+ datum_.values.reserve(10);
+}
+
+void
+streamingnest::RecordingBackendNesciContra::enroll( const nest::RecordingDevice& device )
+{
+ enroll( device, std::vector< Name >() );
+}
+
+
+void
+streamingnest::RecordingBackendNesciContra::enroll( const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names )
+{
+ if ( !is_enrolled_( device ) )
+ {
+ do_enroll_( device, value_names );
+ }
+}
+
+bool
+streamingnest::RecordingBackendNesciContra::is_enrolled_( const nest::RecordingDevice& device )
+{
+ return recorders_.find( device.get_gid() ) != recorders_.end();
+}
+
+void
+streamingnest::RecordingBackendNesciContra::do_enroll_( const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names )
+{
+ std::unique_ptr< nesci::producer::Device > recorder{ create_recorder_(
+ device, value_names ) };
+
+
+ recorders_[ device.get_gid() ] = std::move( recorder );
+}
+
+std::unique_ptr< nesci::producer::Device >
+streamingnest::RecordingBackendNesciContra::create_recorder_(
+ const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names )
+{
+ if ( device.get_type() == nest::RecordingDevice::MULTIMETER )
+ {
+ const std::vector< std::string > converted_value_names{ convert_value_names(
+ value_names ) };
+ return std::unique_ptr< nesci::producer::Device >(
+ new nesci::producer::NestMultimeter(
+ generate_device_identifier_( device ), converted_value_names ) );
+ }
+ // Spike detector is currently not supported
+ // else if ( device.get_type() == nest::RecordingDevice::SPIKE_DETECTOR )
+ // {
+ // return std::unique_ptr< nesci::producer::Device >(
+ // new nesci::producer::SpikeDetector(
+ // generate_device_identifier_( device ) ) );
+ // }
+ return std::unique_ptr< nesci::producer::Device >( nullptr );
+}
+
+std::vector< std::string >
+streamingnest::RecordingBackendNesciContra::convert_value_names(
+ const std::vector< Name >& value_names ) const
+{
+ std::vector< std::string > converted_value_names;
+ std::for_each( value_names.begin(),
+ value_names.end(),
+ [&converted_value_names]( const Name& name ) {
+ converted_value_names.push_back( name.toString() );
+ } );
+ return converted_value_names;
+}
+
+std::string
+streamingnest::RecordingBackendNesciContra::generate_device_identifier_(
+ const nest::RecordingDevice& device ) const
+{
+ if ( device.get_label().size() == 0 )
+ {
+ std::stringstream device_identifier;
+ device_identifier << device.get_name();
+ device_identifier << device.get_gid();
+ return device_identifier.str();
+ }
+
+ return device.get_label();
+}
+
+void
+streamingnest::RecordingBackendNesciContra::initialize()
+{
+ num_buffered_steps_ = 0;
+}
+
+void
+streamingnest::RecordingBackendNesciContra::finalize()
+{
+}
+
+void
+streamingnest::RecordingBackendNesciContra::synchronize()
+{
+#pragma omp barrier
+#pragma omp master
+ {
+ ++num_buffered_steps_;
+ if ( num_buffered_steps_ == 10 )
+ {
+ send_and_reset_node_();
+ num_buffered_steps_ = 0;
+ }
+ }
+}
+
+void
+streamingnest::RecordingBackendNesciContra::send_and_reset_node_()
+{
+ for ( const auto& indexRecorder : recorders_ )
+ {
+ relay_.Send( indexRecorder.second->node() );
+ indexRecorder.second->node().reset();
+ }
+}
+
+void
+streamingnest::RecordingBackendNesciContra::write( const nest::RecordingDevice& device,
+ const nest::Event& event )
+{
+ if ( !is_enrolled_( device ) )
+ {
+ return;
+ }
+
+ // nesci does currently not support spike detectors
+ // const auto time = event.get_stamp().get_ms() - event.get_offset();
+ // auto& recorder = recorders_[ device.get_gid() ];
+ // recorder->Record(
+ // niv::producer::SpikeDetector::Datum( time, event.get_sender_gid() ) );
+}
+
+void
+streamingnest::RecordingBackendNesciContra::write( const nest::RecordingDevice& device,
+ const nest::Event& event,
+ const std::vector< double >& values )
+{
+ if ( !is_enrolled_( device ) )
+ {
+ return;
+ }
+
+ const auto time = event.get_stamp().get_ms() - event.get_offset();
+ auto& recorder = recorders_[ device.get_gid() ];
+ datum_.time = time;
+ datum_.neuron_id = std::to_string(event.get_sender_gid());
+ datum_.values = values;
+ recorder->Record( datum_ );
+}
+
+void
+streamingnest::RecordingBackendNesciContra::set_status( const DictionaryDatum& d )
+{
+ Parameters_ ptmp = P_; // temporary copy in case of errors
+ ptmp.set( *this, d ); // throws if BadProperty
+
+ // if we get here, temporaries contain consistent set of properties
+ P_ = ptmp;
+}
+
+void
+streamingnest::RecordingBackendNesciContra::get_status( DictionaryDatum& d ) const
+{
+ P_.get( *this, d );
+}
+
+streamingnest::RecordingBackendNesciContra::Parameters_::Parameters_()
+ : stream_interval_( 10 )
+{
+}
+
+void
+streamingnest::RecordingBackendNesciContra::Parameters_::get(
+ const RecordingBackendNesciContra&,
+ DictionaryDatum& d ) const
+{
+ ( *d )[ "stream_interval" ] = stream_interval_;
+}
+
+void
+streamingnest::RecordingBackendNesciContra::Parameters_::set(
+ const RecordingBackendNesciContra&,
+ const DictionaryDatum& d )
+{
+ if ( updateValue< long >( d, "stream_interval", stream_interval_ ) )
+ {
+ // do nothing for now
+ }
+}
diff --git a/recording_backend_nesci_contra.h b/recording_backend_nesci_contra.h
new file mode 100644
index 0000000000000000000000000000000000000000..70389b7a85439a8cbe5e17441141d1d4e9634f69
--- /dev/null
+++ b/recording_backend_nesci_contra.h
@@ -0,0 +1,102 @@
+/*
+ * recording_backend_stream_niv.h
+ *
+ * This file is part of NEST.
+ *
+ * Copyright (C) 2004 The NEST Initiative
+ *
+ * NEST is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * NEST 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with NEST. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef RECORDING_BACKEND_STREAM_NIV_H
+#define RECORDING_BACKEND_STREAM_NIV_H
+
+#include <map>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "conduit/conduit_node.hpp"
+
+#include "nest_types.h"
+#include "recording_backend.h"
+
+#include "contra/relay.hpp"
+#include "contra/boost-shmem/shared_memory_transport.hpp"
+#include "nesci/producer/device.hpp"
+#include "nesci/producer/nest_multimeter.hpp"
+
+namespace streamingnest
+{
+
+class RecordingBackendNesciContra : public nest::RecordingBackend
+{
+public:
+ RecordingBackendNesciContra();
+ ~RecordingBackendNesciContra() throw()
+ {
+ }
+
+ void enroll( const nest::RecordingDevice& device );
+ void enroll( const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names );
+ void initialize();
+ void finalize();
+ void synchronize();
+ void write( const nest::RecordingDevice& device, const nest::Event& event );
+ void write( const nest::RecordingDevice& device,
+ const nest::Event& event,
+ const std::vector< double >& );
+
+ void set_status( const DictionaryDatum& );
+ void get_status( DictionaryDatum& ) const;
+
+private:
+ bool is_enrolled_( const nest::RecordingDevice& device );
+ void do_enroll_( const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names );
+ std::string generate_device_identifier_(
+ const nest::RecordingDevice& device ) const;
+ std::unique_ptr< nesci::producer::Device > create_recorder_(
+ const nest::RecordingDevice& device,
+ const std::vector< Name >& value_names );
+ void send_and_reset_node_();
+
+ struct Parameters_
+
+ {
+ long stream_interval_;
+
+ Parameters_();
+
+ void get( const RecordingBackendNesciContra&, DictionaryDatum& ) const;
+ void set( const RecordingBackendNesciContra&, const DictionaryDatum& );
+ };
+
+ Parameters_ P_;
+
+ std::size_t num_buffered_steps_;
+
+ std::vector< std::string > convert_value_names(
+ const std::vector< Name >& value_names ) const;
+
+
+ contra::Relay< contra::SharedMemoryTransport > relay_;
+ std::map< nest::index, std::unique_ptr< nesci::producer::Device > > recorders_;
+ nesci::producer::NestMultimeter::Datum datum_;
+};
+}
+
+#endif // RECORDING_BACKEND_STREAM_NIV_H
diff --git a/sli/streamingmodule-init.sli b/sli/mymodule-init.sli
similarity index 100%
rename from sli/streamingmodule-init.sli
rename to sli/mymodule-init.sli
diff --git a/streaming_recording_backend.cpp b/streaming_recording_backend.cpp
deleted file mode 100644
index f6cf26da6dcd3eb83c68d0473b96bc68a737c5b3..0000000000000000000000000000000000000000
--- a/streaming_recording_backend.cpp
+++ /dev/null
@@ -1,139 +0,0 @@
-/*
- * recording_backend_stream_niv.cpp
- *
- * This file is part of NEST.
- *
- * Copyright (C) 2004 The NEST Initiative
- *
- * NEST is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 2 of the License, or
- * (at your option) any later version.
- *
- * NEST 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 General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with NEST. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#include "streaming_recording_backend.h"
-
-#include "recording_device.h"
-
-#include <iostream>
-#include <memory>
-#include <sstream>
-#include <thread>
-
-namespace streamingnest {
-
-StreamingRecordingBackend::StreamingRecordingBackend() {}
-
-void StreamingRecordingBackend::initialize() {
- // Called once
- std::cout << "initialize()" << std::endl;
-}
-
-void StreamingRecordingBackend::enroll(
- const nest::RecordingDevice &device,
- const std::vector<Name> &double_value_names,
- const std::vector<Name> &long_value_names) {
- // Called per thread
- std::lock_guard<std::mutex> lock_guard(enroll_mutex_);
-
- std::vector<std::string> double_parameter_names;
- double_parameter_names.reserve(double_value_names.size());
- for (const auto &value_name : double_value_names) {
- double_parameter_names.push_back(value_name.toString());
- }
-
- std::vector<std::string> long_parameter_names;
- long_parameter_names.reserve(long_value_names.size());
- for (const auto &value_name : long_value_names) {
- long_parameter_names.push_back(value_name.toString());
- }
-
- if (device.get_type() == nest::RecordingDevice::Type::MULTIMETER) {
- devices_[std::this_thread::get_id()][device.get_name()] =
- std::make_unique<nesci::producer::NestMultimeter>(
- device.get_name(), double_parameter_names, long_parameter_names);
- }
-
- std::cout << std::this_thread::get_id() << ' ';
- std::cout << device.get_name() << ' ';
- std::cout << "double_value_names: ";
- for (const auto &name : double_value_names) {
- std::cout << name << ' ';
- }
- std::cout << ", long_value_names: ";
- for (const auto &name : long_value_names) {
- std::cout << name << ' ';
- }
- std::cout << std::endl;
-}
-
-void StreamingRecordingBackend::write(const nest::RecordingDevice &device,
- const nest::Event &event,
- const std::vector<double> &double_values,
- const std::vector<long> &long_values) {
- // Called per thread
- // std::lock_guard<std::mutex> lock_guard(write_mutex_);
- // std::cout << std::this_thread::get_id() << ' ';
- // std::cout << device.get_name() << ' ';
- // std::cout << event.get_sender_gid() << ' ';
- // std::cout << event.get_stamp() << ' ';
- // for (const auto value : double_values) {
- // std::cout << value << ' ';
- // }
- // std::cout << ' ';
- // for (const auto value : long_values) {
- // std::cout << value << ' ';
- // }
- // std::cout << std::endl;
-
- const auto thread_devices = devices_.find(std::this_thread::get_id());
- if (thread_devices == devices_.end()) {
- // std::cout << "Error: no devices assigned to this thread!" << std::endl;
- return;
- }
-
- const auto thread_device = thread_devices->second.find(device.get_name());
- if (thread_device == thread_devices->second.end()) {
- // std::cout << "Error: device not found in this thread (device = "
- // << device.get_name() << ")" << std::endl;
-
- return;
- }
-
- auto &nesci_device = thread_device->second;
-
- if (device.get_type() == nest::RecordingDevice::Type::MULTIMETER) {
- auto multimeter =
- static_cast<nesci::producer::NestMultimeter *>(nesci_device.get());
- multimeter->Record(event.get_stamp().get_ms(), event.get_sender_gid(),
- double_values.data(), long_values.data());
- }
-}
-
-void StreamingRecordingBackend::synchronize() {
- // Called per thread
- for (const auto &device : devices_.at(std::this_thread::get_id())) {
- {
- std::lock_guard<std::mutex> lock_guard(relay_mutex_);
- relay_.Send(device.second->node(), false);
- }
- static_cast<nesci::producer::NestMultimeter *>(device.second.get())
- ->Clear();
- }
-}
-
-void StreamingRecordingBackend::finalize() {
- // Called once
- std::cout << "finalize()" << std::endl;
-}
-
-} // namespace streamingnest
diff --git a/streaming_recording_backend.h b/streaming_recording_backend.h
deleted file mode 100644
index ede20e6b3761b28fb4be86f4d6a153c2fae85778..0000000000000000000000000000000000000000
--- a/streaming_recording_backend.h
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * recording_backend_stream_niv.h
- *
- * This file is part of NEST.
- *
- * Copyright (C) 2004 The NEST Initiative
- *
- * NEST is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 2 of the License, or
- * (at your option) any later version.
- *
- * NEST 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 General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with NEST. If not, see <http://www.gnu.org/licenses/>.
- *
- */
-
-#ifndef RECORDING_BACKEND_STREAM_NIV_H
-#define RECORDING_BACKEND_STREAM_NIV_H
-
-#include <map>
-#include <memory>
-#include <mutex>
-#include <string>
-#include <vector>
-
-#include "nest_types.h"
-#include "recording_backend.h"
-
-#include "contra/relay.hpp"
-#include "contra/shared_memory/shared_memory_transport.hpp"
-#include "nesci/producer/device.hpp"
-#include "nesci/producer/nest_multimeter.hpp"
-
-namespace streamingnest {
-
-class StreamingRecordingBackend : public nest::RecordingBackend {
- public:
- StreamingRecordingBackend();
- ~StreamingRecordingBackend() throw() {}
-
- void enroll(const nest::RecordingDevice &, const std::vector<Name> &,
- const std::vector<Name> &) override;
-
- void initialize() override;
-
- void finalize() override;
- void synchronize() override;
-
- void write(const nest::RecordingDevice &, const nest::Event &,
- const std::vector<double> &, const std::vector<long> &) override;
-
- private:
- std::mutex relay_mutex_;
- contra::Relay<contra::SharedMemoryTransport> relay_;
-
- std::mutex write_mutex_;
-
- std::map<std::thread::id,
- std::map<std::string, std::unique_ptr<nesci::producer::Device>>>
- devices_;
- std::mutex enroll_mutex_;
-};
-} // namespace streamingnest
-
-#endif // RECORDING_BACKEND_STREAM_NIV_H
diff --git a/streamingmodule.cpp b/streamingmodule.cpp
index f5c95340db7ce0b102dbd5dbfc5ea168dbe4a2ad..0b0a1948e0839237f4e35c6887dc8de9984b06fe 100644
--- a/streamingmodule.cpp
+++ b/streamingmodule.cpp
@@ -26,7 +26,7 @@
#include "config.h"
// include headers with your own stuff
-#include "streaming_recording_backend.h"
+#include "recording_backend_nesci_contra.h"
// Includes from nestkernel:
#include "connection_manager_impl.h"
@@ -35,10 +35,10 @@
#include "exceptions.h"
#include "genericmodel.h"
#include "genericmodel_impl.h"
-#include "io_manager_impl.h"
#include "kernel_manager.h"
#include "model.h"
#include "model_manager_impl.h"
+#include "io_manager_impl.h"
#include "nestmodule.h"
#include "target_identifier.h"
@@ -70,38 +70,45 @@
* registration will take place in the file `static_modules.h`, which is
* generated by cmake.
*/
-#if defined(LTX_MODULE) | defined(LINKED_MODULE)
+#if defined( LTX_MODULE ) | defined( LINKED_MODULE )
streamingnest::StreamingModule streamingmodule_LTX_mod;
#endif
// -- DynModule functions ------------------------------------------------------
-streamingnest::StreamingModule::StreamingModule() {
-#if defined(LINKED_MODULE) && defined(HAVE_LIBLTDL)
+streamingnest::StreamingModule::StreamingModule()
+{
+#ifdef LINKED_MODULE
// register this module at the dynamic loader
// this is needed to allow for linking in this module at compile time
// all registered modules will be initialized by the main app's dynamic loader
- nest::DynamicLoaderModule::registerLinkedModule(this);
+ nest::DynamicLoaderModule::registerLinkedModule( this );
#endif
}
-streamingnest::StreamingModule::~StreamingModule() {}
+streamingnest::StreamingModule::~StreamingModule()
+{
+}
-const std::string streamingnest::StreamingModule::name(void) const {
- return std::string("Streaming NEST Module"); // Return name of the module
+const std::string
+streamingnest::StreamingModule::name( void ) const
+{
+ return std::string( "Streaming NEST Module" ); // Return name of the module
}
-const std::string streamingnest::StreamingModule::commandstring(void) const {
+const std::string
+streamingnest::StreamingModule::commandstring( void ) const
+{
// Instruct the interpreter to load streamingmodule-init.sli
- return std::string("(streamingmodule-init) run");
+ return std::string( "(streamingmodule-init) run" );
}
//-------------------------------------------------------------------------------------
-void streamingnest::StreamingModule::init(SLIInterpreter *i) {
+void
+streamingnest::StreamingModule::init( SLIInterpreter* i )
+{
// Register recording backend.
- nest::kernel()
- .io_manager
- .register_recording_backend<streamingnest::StreamingRecordingBackend>(
- "streaming");
+ nest::kernel().io_manager.register_recording_backend< streamingnest::RecordingBackendNesciContra >(
+ "streaming" );
-} // StreamingModule::init()
+} // StreamingModule::init()
diff --git a/streamingmodule.h b/streamingmodule.h
index e06646c49b23d97b89cae5e84075ad665a00df70..bb1309340d476351783618fe548f4ff22a9d27e8 100644
--- a/streamingmodule.h
+++ b/streamingmodule.h
@@ -28,14 +28,16 @@
#include "slimodule.h"
// Put your stuff into your own namespace.
-namespace streamingnest {
+namespace streamingnest
+{
/**
* Class defining your model.
* @note For each model, you must define one such class, with a unique name.
*/
-class StreamingModule : public SLIModule {
- public:
+class StreamingModule : public SLIModule
+{
+public:
// Interface functions ------------------------------------------
/**
@@ -53,20 +55,20 @@ class StreamingModule : public SLIModule {
* Initialize module.
* @param SLIInterpreter* SLI interpreter
*/
- void init(SLIInterpreter *);
+ void init( SLIInterpreter* );
/**
* Return the name of your model.
*/
- const std::string name(void) const;
+ const std::string name( void ) const;
/**
* Return the name of a sli file to execute when streamingmodule is loaded.
* This mechanism can be used to define SLI commands associated with your
* module, in particular, set up type tries for functions you have defined.
*/
- const std::string commandstring(void) const;
+ const std::string commandstring( void ) const;
};
-} // namespace streamingnest
+} // namespace streamingnest
#endif