Merge branch 'release/18.03.00'

.gitignore

@@ -2,3 +2,4 @@ build*
 BUILD*
 .dir-locals.el
 *.pyc
+TAGS

CMakeLists.txt

@@ -53,6 +53,8 @@ include(GenerateExportHeader)
 
 include(py.test)
 
+include(python_module)
+
 include(WarningLevels)
 
 find_package(Conduit)

cmake/python_module.cmake

@@ -0,0 +1,93 @@
+#-------------------------------------------------------------------------------
+# 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.
+#-------------------------------------------------------------------------------
+
+function(ADD_PYTHON_MODULE)
+  # parse arguments
+  set(options )
+  set(oneValueArgs NAME OUTPUT_DIRECTORY)
+  set(multiValueArgs
+    SOURCES HEADERS PYTHON_SOURCES INCLUDE_DIRECTORIES LINK_LIBRARIES)
+  cmake_parse_arguments(ADD_PYTHON_MODULE
+    "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  python_add_module(${ADD_PYTHON_MODULE_NAME}
+    ${ADD_PYTHON_MODULE_SOURCES}
+    ${ADD_PYTHON_MODULE_HEADERS}
+    )
+
+  target_include_directories(${ADD_PYTHON_MODULE_NAME}
+    PRIVATE ${Boost_INCLUDE_DIRS}
+    PRIVATE ${PYTHON_INCLUDE_DIRS}
+    ${ADD_PYTHON_MODULE_INCLUDE_DIRECTORIES}
+    )
+
+  target_link_libraries(${ADD_PYTHON_MODULE_NAME}
+    ${Boost_LIBRARIES}
+    ${PYTHON_LIBRARIES}
+    ${ADD_PYTHON_MODULE_LINK_LIBRARIES}
+    )
+
+  set_warning_levels_RWTH(${ADD_PYTHON_MODULE_NAME}
+    SUPPRESS_WARNINGS_HEADER ${CMAKE_CURRENT_BINARY_DIR}/include/pyniv/suppress_warnings.hpp
+    )
+
+  add_test_cpplint(NAME "${ADD_PYTHON_MODULE_NAME}--cpplint"
+    ${ADD_PYTHON_MODULE_SOURCES}
+    ${ADD_PYTHON_MODULE_HEADERS}
+    )
+
+  add_custom_command(TARGET ${ADD_PYTHON_MODULE_NAME}
+    POST_BUILD
+    #OUTPUT ${ADD_PYTHON_MODULE_OUTPUT_DIRECTORY}/$<TARGET_FILE_NAME:${ADD_PYTHON_MODULE_NAME}>
+    #DEPENDS $<TARGET_FILE:${ADD_PYTHON_MODULE_NAME}>
+    COMMAND ${CMAKE_COMMAND}
+    -E copy_if_different
+    $<TARGET_FILE:${ADD_PYTHON_MODULE_NAME}>
+    ${ADD_PYTHON_MODULE_OUTPUT_DIRECTORY}/$<TARGET_FILE_NAME:${ADD_PYTHON_MODULE_NAME}>
+    )
+
+  foreach (ADD_PYTHON_MODULE_PYTHON_INPUT ${ADD_PYTHON_MODULE_PYTHON_SOURCES})
+    get_filename_component(ADD_PYTHON_MODULE_PYTHON_INPUT_NAME
+      ${ADD_PYTHON_MODULE_PYTHON_INPUT}
+      NAME)
+    set(ADD_PYTHON_MODULE_PYTHON_OUTPUT
+      "${ADD_PYTHON_MODULE_OUTPUT_DIRECTORY}/${ADD_PYTHON_MODULE_PYTHON_INPUT_NAME}"
+      )
+    set(ADD_PYTHON_MODULE_CUSTOM_TARGET_NAME
+      "${ADD_PYTHON_MODULE_NAME}_COPY_${ADD_PYTHON_MODULE_PYTHON_INPUT_NAME}"
+      )
+    add_custom_command(
+      OUTPUT ${ADD_PYTHON_MODULE_PYTHON_OUTPUT}
+      DEPENDS ${ADD_PYTHON_MODULE_PYTHON_INPUT}
+      COMMAND ${CMAKE_COMMAND}
+      -E copy_if_different 
+      ${ADD_PYTHON_MODULE_PYTHON_INPUT}
+      ${ADD_PYTHON_MODULE_PYTHON_OUTPUT}
+      )
+    add_custom_target(${ADD_PYTHON_MODULE_CUSTOM_TARGET_NAME}
+      DEPENDS
+      ${ADD_PYTHON_MODULE_PYTHON_OUTPUT}
+      )
+    add_dependencies(${ADD_PYTHON_MODULE_NAME}
+      ${ADD_PYTHON_MODULE_CUSTOM_TARGET_NAME}
+      )
+  endforeach(ADD_PYTHON_MODULE_PYTHON_INPUT)
+endfunction()

demo/CMakeLists.txt

@@ -19,5 +19,6 @@
 # limitations under the License.
 #-------------------------------------------------------------------------------
 
-add_subdirectory(nest_python_vis)
+add_subdirectory(arbor_miniapp-niv)
 add_subdirectory(brunel_example)
+add_subdirectory(nest_python_vis)

demo/arbor_miniapp-niv/CMakeLists.txt

@@ -0,0 +1,35 @@
+#-------------------------------------------------------------------------------
+# 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.
+#-------------------------------------------------------------------------------
+
+set(PYTHON_DUMP_SOURCE dump_to_stdout.py)
+set(PYTHON_VIS_SOURCE vis.py)
+
+if(NOT CMAKE_MAKE_PROGRAM STREQUAL "/usr/bin/xcodebuild")
+
+file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_dump.sh
+  CONTENT "PYTHONPATH=${PYNIV_OUTPUT_DIR}/..:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${PYTHON_DUMP_SOURCE}"
+  )
+
+file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_vis.sh
+  CONTENT "PYTHONPATH=${PYNIV_OUTPUT_DIR}/..:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${PYTHON_VIS_SOURCE}"
+  )
+
+endif()

demo/arbor_miniapp-niv/dump_to_stdout.py

@@ -0,0 +1,92 @@
+#-------------------------------------------------------------------------------
+# 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 matplotlib.pyplot as plt
+import numpy as np
+import seaborn as sns
+
+import pyniv
+
+from PyQt5.QtWidgets import QApplication, QWidget, QLabel, QGridLayout, QPushButton
+from PyQt5.QtCore import QTimer
+
+class MainWindow:
+    def __init__(self):
+        self.SetupStreaming()
+        self.SetupWindow()
+        self.SetupUpdateTimer()
+
+    def SetupStreaming(self):
+        self.receiver = pyniv.consumer.Receiver()
+
+        self.multimeter = pyniv.consumer.ArborMultimeter("multimeter")
+
+        self.backend = pyniv.consumer.Backend();
+        self.backend.Connect(self.receiver);
+        self.backend.Connect(self.multimeter);
+
+    def SetupWindow(self):
+        self.print_button = QPushButton("Print")
+        self.print_button.clicked.connect(self.PrintButtonClicked)
+
+    def SetupUpdateTimer(self):
+        self.update_timer = QTimer()
+        self.update_timer.timeout.connect(self.Receive)
+        self.update_timer.start(1)
+
+    def PrintButtonClicked(self):
+        print 60 * '='
+        timesteps = self.multimeter.GetTimestepsString()
+        for t in timesteps:
+            print 't = {}'.format(t)
+            attributes = self.multimeter.GetAttributes(t)
+            for a in attributes:
+                values = self.multimeter.GetTimestepData(t, a)
+                print a + ': ' + ', '.join(['{}'.format(v) for v in values])
+            print 40 * '-'
+
+    def Show(self):
+        self.print_button.show()
+        button_geometry = self.print_button.geometry()
+        self.print_button.setGeometry(
+            0, 0,
+            button_geometry.width(),
+            button_geometry.height())
+
+    def Receive(self):
+        self.backend.Receive()
+
+    def Dump(self):
+        print("DUMP")
+
+
+def main(argv):
+    app = QApplication(argv)
+
+    w = MainWindow()
+    w.Show()
+
+    return app.exec_()
+
+if __name__ == "__main__":
+    main(sys.argv)

demo/arbor_miniapp-niv/vis.py

@@ -0,0 +1,112 @@
+#-------------------------------------------------------------------------------
+# 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 matplotlib.pyplot as plt
+import numpy as np
+import seaborn as sns
+
+import pyniv
+
+from PyQt5.QtWidgets import QApplication, QWidget, QLabel, QGridLayout, QPushButton
+from PyQt5.QtCore import QTimer
+
+class MainWindow:
+    def __init__(self):
+        self.SetupStreaming()
+        self.SetupWindow()
+        self.SetupPlot()
+        self.SetupUpdateTimer()
+
+    def SetupStreaming(self):
+        self.receiver = pyniv.consumer.Receiver()
+
+        self.multimeter = pyniv.consumer.ArborMultimeter("multimeter")
+
+        self.backend = pyniv.consumer.Backend();
+        self.backend.Connect(self.receiver);
+        self.backend.Connect(self.multimeter);
+
+    def SetupWindow(self):
+        self.visualize_button = QPushButton("Visualize")
+        self.visualize_button.clicked.connect(self.VisualizeButtonClicked)
+
+    def SetupUpdateTimer(self):
+        self.update_timer = QTimer()
+        self.update_timer.timeout.connect(self.Visualize)
+
+    def SetupPlot(self):
+        sns.set_style("darkgrid")
+        self.fig = plt.figure()
+        self.ax1 = self.fig.add_subplot(1,1,1)
+
+
+    def VisualizeButtonClicked(self):
+        self.visualize_button.setEnabled(False)
+        self.update_timer.start(250)
+        self.Visualize()
+
+    def Show(self):
+        self.visualize_button.show()
+        button_geometry = self.visualize_button.geometry()
+        self.visualize_button.setGeometry(
+            0, 0,
+            button_geometry.width(),
+            button_geometry.height())
+
+    def Visualize(self):
+        self.backend.Receive()
+        self.Plot();
+
+    def Plot(self):
+        timesteps = self.multimeter.GetTimestepsString()
+        attribute = 'v'
+        neuron_ids = []
+        if len(timesteps) > 0:
+            neuron_ids = self.multimeter.GetNeuronIds(timesteps[0], attribute)
+
+        self.ax1.clear()
+
+        for neuron_id in neuron_ids:
+            values = self.multimeter.GetTimeSeriesData(attribute, neuron_id)
+            times = [float(t) for t in timesteps]
+            self.ax1.plot(times, values)
+
+        self.ax1.set_title("Arbor Miniapp Niv Example")
+        self.ax1.set_xlabel("Time")
+        self.ax1.set_ylabel("v")
+        self.ax1.set_ylim([-80,50])
+
+        plt.show(block=False)
+        self.fig.canvas.draw()
+
+
+def main(argv):
+    app = QApplication(argv)
+
+    w = MainWindow()
+    w.Show()
+
+    return app.exec_()
+
+if __name__ == "__main__":
+    main(sys.argv)

demo/brunel_example/CMakeLists.txt

@@ -20,20 +20,25 @@
 #-------------------------------------------------------------------------------
 
 set(NEST_PYTHON_VIS_SOURCE nest_python_vis.py)
+set(NEST_PYTHON_DUMP_SOURCE dump_to_stdout.py)
 set(NEST_SIM_SOURCE nest_sim.py)
 
 if(NOT CMAKE_MAKE_PROGRAM STREQUAL "/usr/bin/xcodebuild")
 
 file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_vis.sh
-  CONTENT "PYTHONPATH=$<TARGET_FILE_DIR:pyniv>:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_PYTHON_VIS_SOURCE}"
+  CONTENT "PYTHONPATH=${PYNIV_OUTPUT_DIR}/..:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_PYTHON_VIS_SOURCE}"
+  )
+
+file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_dump.sh
+  CONTENT "PYTHONPATH=${PYNIV_OUTPUT_DIR}/..:$<TARGET_FILE_DIR:pytest_utilities> ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_PYTHON_DUMP_SOURCE}"
   )
 
 set(NEST_DIR
   CACHE PATH "Path to installed nest")
 file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/run_sim.sh
   CONTENT
 "source ${NEST_DIR}/bin/nest_vars.sh
-PYTHONPATH=$<TARGET_FILE_DIR:pyniv>:$PYTHONPATH ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_SIM_SOURCE}"
+PYTHONPATH=${PYNIV_OUTPUT_DIR}/..:$PYTHONPATH ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/${NEST_SIM_SOURCE}"
   )
 
 endif()