Add support for multicompartment models

images.qrc

@@ -2146,7 +2146,7 @@
         <file>images/material-icons/toggle/svg/production/ic_star_border_24px.svg</file>
         <file>images/material-icons/toggle/svg/production/ic_star_half_24px.svg</file>
         <file>images/material-icons/toggle/svg/production/ic_star_half_48px.svg</file>
-        <file>qml/hud/TopCreationItem.qml</file>
         <file>images/dashboard/integrate-and-fire.png</file>
+        <file>images/meters/amperemeter.png</file>
     </qresource>
 </RCC>

neuronify.pro

@@ -15,14 +15,11 @@ HEADERS += \
     src/core/graphengine.h \
     src/core/nodebase.h \
     src/core/nodeengine.h \
-    src/neurons/current.h \
     src/neurons/neuronengine.h \
     src/retina/androidmultimediautils.h \
     src/retina/retinaengine.h \
     src/retina/retinapainter.h \
     src/retina/videosurface.h \
-    src/neurons/leakcurrent.h \
-    src/neurons/adaptationcurrent.h \
     src/retina/kernel.h \
     src/retina/kernels/gaborkernelengine.h \
     src/retina/kernels/abstractkernelengine.h \
@@ -36,22 +33,25 @@ HEADERS += \
     src/core/edgebase.h \
     src/core/edgeengine.h \
     src/io/downloadmanager.h \
-    src/io/neuronifyfile.h
+    src/io/neuronifyfile.h \
+    src/currents/current.h \
+    src/currents/leakcurrent.h \
+    src/currents/potassiumcurrent.h \
+    src/currents/sodiumcurrent.h \
+    src/currents/adaptationcurrent.h \
+    src/compartments/compartmentengine.h
 
 SOURCES += \
     src/io/fileio.cpp \
     src/main.cpp \
     src/core/nodebase.cpp \
     src/core/nodeengine.cpp \
     src/core/graphengine.cpp \
-    src/neurons/current.cpp \
     src/neurons/neuronengine.cpp \
     src/retina/retinaengine.cpp \
     src/retina/retinapainter.cpp \
     src/retina/videosurface.cpp \
     src/retina/androidmultimediautils.cpp \
-    src/neurons/adaptationcurrent.cpp \
-    src/neurons/leakcurrent.cpp \
     src/retina/kernel.cpp \
     src/retina/kernels/gaborkernelengine.cpp \
     src/retina/kernels/abstractkernelengine.cpp \
@@ -65,7 +65,13 @@ SOURCES += \
     src/core/edgebase.cpp \
     src/core/edgeengine.cpp \
     src/io/downloadmanager.cpp \
-    src/io/neuronifyfile.cpp
+    src/io/neuronifyfile.cpp \
+    src/currents/leakcurrent.cpp \
+    src/currents/potassiumcurrent.cpp \
+    src/currents/sodiumcurrent.cpp \
+    src/currents/adaptationcurrent.cpp \
+    src/compartments/compartmentengine.cpp \
+    src/currents/current.cpp
 
 
 RESOURCES += qml.qrc \

qml.qrc

@@ -122,6 +122,13 @@
         <file>qml/menus/filemenu/AccountView.qml</file>
         <file>qml/menus/filemenu/NewView.qml</file>
         <file>qml/menus/filemenu/MySimulations.qml</file>
+        <file>qml/edges/CompartmentConnection.qml</file>
+        <file>qml/hud/TopCreationItem.qml</file>
+        <file>qml/compartments/SimpleCompartment.qml</file>
+        <file>qml/hud/CompartmentsList.qml</file>
+        <file>qml/compartments/CompartmentEngine.qml</file>
+        <file>qml/meters/Amperemeter.qml</file>
+        <file>qml/compartments/HHCompartment.qml</file>
         <file>qml/menus/filemenu/AboutView.qml</file>
     </qresource>
 </RCC>

qml/MainDesktop.qml

@@ -68,7 +68,8 @@ Item {
     }
 
     function firstLoad() {
-        neuronify.loadSimulation("qrc:/simulations/tutorial/tutorial_1_intro/tutorial_1_intro.nfy") // TODO replace with open
+//        neuronify.loadSimulation("qrc:/simulations/tutorial/tutorial_1_intro/tutorial_1_intro.nfy") // TODO replace with open
+        open("file:///home/svenni/tmp/test.neuronify")
     }
 
     function tryClose() {
@@ -328,6 +329,12 @@ Item {
                         imageSource: "qrc:/images/generators/current_clamp.png"
                         listSource: "qrc:/qml/hud/GeneratorsList.qml"
                     }
+                    ListElement  {
+                        name: "Compartments"
+                        source: "qrc:/qml/compartments/HHCompartment.qml"
+                        imageSource: "qrc:/images/generators/current_clamp.png"
+                        listSource: "qrc:/qml/hud/CompartmentsList.qml"
+                    }
                     ListElement  {
                         name: "Annotation"
                         source: "qrc:/qml/annotations/Note.qml"

qml/compartments/CompartmentEngine.qml

@@ -0,0 +1,9 @@
+import Neuronify 1.0
+
+CompartmentEngineBase {
+    id: engine
+    savedProperties: PropertyGroup {
+//        property alias voltage: engine.voltage
+//        property alias capacitance: engine.capacitance
+    }
+}

qml/compartments/HHCompartment.qml

@@ -0,0 +1,148 @@
+import QtQuick 2.0
+import Neuronify 1.0
+import QtQuick.Controls 2.1
+import QtQuick.Controls.Material 2.1
+import QtQuick.Layouts 1.1
+
+import ".."
+import "../edges"
+import "../controls"
+
+Node {
+    id: root
+    filename: "compartments/HHCompartment.qml"
+    name: "Hodgkin-Huxley compartment"
+
+    readonly property real voltage: engine.voltage
+    readonly property real leakCurrent: leakCurrent.current
+    readonly property real sodiumCurrent: sodiumCurrent.current
+    readonly property real potassiumCurrent: potassiumCurrent.current
+
+    width: 64
+    height: 64
+    color: "#dd5900"
+    canReceiveConnections: true
+    preferredEdge: CompartmentConnection {}
+
+    engine: CompartmentEngine {
+        id: engine
+
+        savedProperties: PropertyGroup {
+//            property alias currentOutput: engine.currentOutput
+        }
+
+        capacitance: 1e-6 * engine.area * 1e4
+
+        LeakCurrent {
+            id: leakCurrent
+            property real conductance: 0.3e-3 * engine.area * 1e4
+            resistance: (1.0 / conductance)
+            voltage: engine.voltage
+            restingPotential: -54.4e-3
+        }
+
+        SodiumCurrent {
+            id: sodiumCurrent
+            meanSodiumConductance: 120e-3 * engine.area * 1e4
+            voltage: engine.voltage
+        }
+
+        PotassiumCurrent {
+            id: potassiumCurrent
+            meanPotassiumConductance: 36e-3 * engine.area * 1e4
+            voltage: engine.voltage
+        }
+    }
+
+    controls: Rectangle {
+        color: Material.background
+        width: 480
+        height: 360
+
+        ColumnLayout {
+            anchors {
+                fill: parent
+                margins: 16
+            }
+
+            BoundSlider {
+                target: engine
+                property: "length"
+                text: "Length"
+                unit: "μm"
+                minimumValue: 1.0e-6
+                maximumValue: 300.0e-6
+                stepSize: 1.0e-6
+                unitScale: 1e-6
+                precision: 1
+            }
+            BoundSlider {
+                target: engine
+                property: "radiusA"
+                text: "Radius A"
+                unit: "μm"
+                minimumValue: 1.0e-6
+                maximumValue: 300.0e-6
+                stepSize: 1.0e-6
+                unitScale: 1e-6
+                precision: 1
+            }
+            BoundSlider {
+                target: engine
+                property: "radiusB"
+                text: "Radius B"
+                unit: "μm"
+                minimumValue: 1.0e-6
+                maximumValue: 300.0e-6
+                stepSize: 1.0e-6
+                unitScale: 1e-6
+                precision: 1
+            }
+
+            Item {
+                Layout.fillHeight: true
+                Layout.fillWidth: true
+            }
+        }
+    }
+
+
+    Rectangle {
+        anchors.fill: parent
+        radius: Math.min(width, height) / 10
+        color: "#6baed6"
+        border.color: selected ? "#08306b" : "#2171b5"
+        border.width: selected ? 3.0 : 1.0
+    }
+
+    Rectangle {
+        anchors.fill: parent
+        anchors.margins: 2.0
+        radius: Math.min(width, height) / 10
+        color: "#f7fbff"
+        opacity: (engine.voltage * 1e3 + 100) / (150)
+    }
+
+    Text {
+        anchors.centerIn: parent
+        text: (engine.voltage * 1e3).toFixed(1)
+        font.pixelSize: 14
+    }
+
+    DropArea {
+        id: dropArea
+        anchors {
+            fill: parent
+            margins: -16
+        }
+        keys: ["connector"]
+        onDropped: {
+            receivedDrop(drop.source.node)
+        }
+    }
+
+    Connector {
+        color: "#dd5000"
+        connectorColor: "#dd5000"
+    }
+}

qml/compartments/SimpleCompartment.qml

@@ -0,0 +1,93 @@
+import QtQuick 2.0
+import Neuronify 1.0
+
+import ".."
+import "../edges"
+
+Node {
+    id: root
+    filename: "compartments/SimpleCompartment.qml"
+    name: "Simple compartment"
+
+    readonly property real voltage: engine.voltage
+    readonly property real leakCurrent: leakCurrent.current
+
+    width: 64
+    height: 64
+    color: "#dd5900"
+    canReceiveConnections: true
+    preferredEdge: CompartmentConnection {}
+
+    engine: CompartmentEngine {
+        id: engine
+
+        savedProperties: PropertyGroup {
+//            property alias currentOutput: engine.currentOutput
+        }
+
+        capacitance: 1e-6 * engine.area * 1e4
+
+        LeakCurrent {
+            id: leakCurrent
+            property real conductance: 0.3e-3 * engine.area * 1e4
+            resistance: (1.0 / conductance)
+            voltage: engine.voltage
+            restingPotential: -54.4e-3
+        }
+    }
+
+//    controls: Component {
+//        PropertiesPage {
+//            BoundSlider {
+//                target: engine
+//                property: "currentOutput"
+//                text: "Current output"
+//                unit: "nA"
+//                minimumValue: 0.0e-9
+//                maximumValue: 30.0e-9
+//                stepSize: 0.01e-9
+//                unitScale: 1e-9
+//                precision: 2
+//            }
+//        }
+//    }
+
+    Rectangle {
+        anchors.fill: parent
+        radius: Math.min(width, height) / 10
+        color: "#6baed6"
+        border.color: selected ? "#08306b" : "#2171b5"
+        border.width: selected ? 3.0 : 1.0
+    }
+
+    Rectangle {
+        anchors.fill: parent
+        anchors.margins: 2.0
+        radius: Math.min(width, height) / 10
+        color: "#f7fbff"
+        opacity: (engine.voltage * 1e3 + 100) / (150)
+    }
+
+    Text {
+        anchors.centerIn: parent
+        text: (engine.voltage * 1e3).toFixed(1)
+        font.pixelSize: 14
+    }
+
+    DropArea {
+        id: dropArea
+        anchors {
+            fill: parent
+            margins: -16
+        }
+        keys: ["connector"]
+        onDropped: {
+            receivedDrop(drop.source.node)
+        }
+    }
+
+    Connector {
+        color: "#dd5000"
+        connectorColor: "#dd5000"
+    }
+}