Update to inviwo commit 1abb2b923c51d684af8b6205c3b3e8ece2f86c6a

* CI: Use vcpkg 
* Disable Python in CMakePresets.json
* Update to inviwo commit 1abb2b923c51d684af8b6205c3b3e8ece2f86c6a
* Fix uppdated include path for inviwocommondefines.h
* Fix packaging setup CMakePresets.json
* MacOS 13 packaging fix actions/runner-images#7522 (comment)

.github/workflows/test-installer.yml

@@ -43,7 +43,7 @@ jobs:
         # launch the nsis installer in "silent mode" (/S), should run without user interaction
         Invoke-expression "./'$exe' /S"
         # this will spawn the installer in the background so we need to wait for it to finish
-        $proc = Get-Process | where {$_.ProcessName -like "Visual Neuro-*"} | Select-Object -First 1
+        $proc = Get-Process | where {$_.ProcessName -like "VisualNeuro*"} | Select-Object -First 1
         if ($proc) { 
           Wait-Process -Id $proc.id
         }
@@ -52,8 +52,8 @@ jobs:
       if: runner.os == 'Windows'
       shell: pwsh
       run: |
-        $ver = (Get-ChildItem -Name C:/"Program Files/Visual Neuro"/*)
-        Invoke-expression "C:/'Program Files/Visual Neuro/$ver/bin/Visual Neuro.exe' --logconsole --quit"
+        $ver = (Get-ChildItem -Name C:/"Program Files/VisualNeuroApp"/*)
+        Invoke-expression "C:/'Program Files/VisualNeuroApp/$ver/bin/VisualNeuro.exe' --logconsole --quit"
     
     ###############################################################################
     # Macos
@@ -67,15 +67,15 @@ jobs:
         # Mount installer image
         hdiutil attach "$DMG"
         # Install by copying Visual Neuro.app to applications folder
-        cp -r "/Volumes/${DMG%%.dmg}/Visual Neuro.app" /Applications/
+        cp -r "/Volumes/${DMG%%.dmg}/VisualNeuroApp.app" /Applications/
         hdiutil detach "/Volumes/${DMG%%.dmg}/"
 
     - name: Run Visual Neuro
       if: runner.os == 'macOS'
       shell: bash
       run: |
-        cd "/Applications/Visual Neuro.app/Contents/MacOS/"
-        ./"Visual Neuro" --logconsole --quit
+        cd "/Applications/VisualNeuroApp.app/Contents/MacOS/"
+        ./"VisualNeuro" --logconsole --quit
 
     ###############################################################################
     # Linux
@@ -90,4 +90,4 @@ jobs:
         tar zxvf "$TGZ"
         # Get folder name and move into the folder 
         cd "${TGZ%.tar.gz}"
-        ./"bin/Visual Neuro" --logconsole --quit
+        ./"bin/VisualNeuro" --logconsole --quit

.github/workflows/visualneuro.yml

@@ -21,6 +21,7 @@ jobs:
       matrix:
         system: [windows, macos, linux]
         linkage: [dynamic]
+        cmake_linkage: ['ON']
         configuration: [Release]
 
         include:
@@ -31,23 +32,23 @@ jobs:
             preset: msvc-visualneuro
             targets: 'ALL_BUILD package'
             installer: 'visualneuro-installer-win'
-            artifact: 'build/Visual Neuro-v*.exe'
+            artifact: 'build/VisualNeuroApp-v*.exe'
           - system: macos
             os: 'macos-13' # for now macos-latest == macos-12 since macos-13 is still "beta"
             triplet: 'x64-osx'
             cmake: '-DVCPKG_APPLOCAL_DEPS=OFF'
             preset: ninja-visualneuro
             targets: 'all package'
             installer: 'visualneuro-installer-macos'
-            artifact: 'build/Visual Neuro-v*.dmg'
+            artifact: 'build/VisualNeuroApp-v*.dmg'
           - system: linux
             os: 'ubuntu-22.04'
             triplet: 'x64-linux'
             cmake: '-DIVW_PACKAGE_INSTALLER=OFF' 
             preset: ninja-visualneuro
             targets: 'all package'
             installer: 'visualneuro-installer-ubuntu'
-            artifact: 'build/Visual Neuro-v*.tar.gz'
+            artifact: 'build/VisualNeuroApp-v*.tar.gz'
       fail-fast: false
 
     runs-on: ${{ matrix.os }}
@@ -131,6 +132,7 @@ jobs:
       uses: actions/checkout@v4
       with:
         repository: 'inviwo/inviwo'
+        ref: '1abb2b923c51d684af8b6205c3b3e8ece2f86c6a'
         path: 'inviwo' 
         submodules: recursive
 

CMakePresets.json

@@ -10,6 +10,7 @@
         "IVW_EXTERNAL_PROJECTS" : "${sourceParentDir}/visualneuro/apps;",
 
         "BUILD_SHARED_LIBS":                { "type": "BOOL", "value": "ON"},
+        "IVW_ENABLE_PYTHON":                { "type": "BOOL", "value": "OFF"},
         "IVW_CFG_CMAKE_DEBUG":              { "type": "BOOL", "value": "ON"},
         "IVW_CFG_PROFILING":                { "type": "BOOL", "value": "OFF"},
         "IVW_CFG_PRECOMPILED_HEADERS":      { "type": "BOOL", "value": "OFF"},
@@ -28,7 +29,7 @@
         "IVW_TEST_INTEGRATION_TESTS":       { "type": "BOOL", "value": "OFF"},
 
         "IVW_PACKAGE_INSTALLER":            { "type": "BOOL", "value": "ON"},
-        "IVW_APP_INSTALL_NAME":             "Visual Neuro",
+        "IVW_APP_INSTALL_NAME":             "VisualNeuroApp",
         "IVW_PACKAGE_SELECT_APP":           "VisualNeuroApp",
 
         "IVW_USE_OPENMP":                   { "type": "BOOL", "value": "OFF"},
@@ -56,20 +57,20 @@
       "name": "msvc-visualneuro",
       "displayName": "MSVC Visual Neuro",
       "description": "Visual Studio configuration",
-      "inherits": ["msvc", "user", "vcpkg", "visualneuro"]
+      "inherits": ["visualneuro", "msvc", "user", "vcpkg"]
     },
     {
       "name": "ninja-visualneuro",
       "displayName": "Ninja Visual Neuro",
       "description": "Ninja configuration",
-      "inherits": ["ninja", "user", "vcpkg", "visualneuro"]
+      "inherits": ["visualneuro", "ninja", "user", "vcpkg"]
     },
     {
       "name": "xcode-visualneuro",
       "displayName": "Visual Neuro XCode",
       "description": "XCode development configuration",
       "generator": "Xcode",
-      "inherits": ["user", "visualneuro"]
+      "inherits": ["visualneuro", "user"]
     }  
   ]
 }

apps/visualneuro/CMakeLists.txt

@@ -1,5 +1,6 @@
 #--------------------------------------------------------------------
 # Brain Cohort Analyzer
+# Do not name the CMake project VisualNeuro because it can be confused with the module
 project(VisualNeuroApp)
 
 include(version.cmake)
@@ -58,7 +59,7 @@ add_executable(${PROJECT_NAME} MACOSX_BUNDLE WIN32
     ${RES_FILES})
 # Do not name the CMake project VisualNeuro because it can be confused with the module
 # However, we still want the the executable to be called VisualNeuro
-set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME "Visual Neuro")
+#set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME "VisualNeuroApp")
 target_link_libraries(${PROJECT_NAME} PUBLIC
     inviwo::core
     inviwo::module-system
@@ -83,19 +84,19 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # https://cmake.org/cmake/help/v3.15/prop_tgt/MACOSX_BUNDLE_INFO_PLIST.html
     string(TIMESTAMP YEAR "%Y")
     set_target_properties(${PROJECT_NAME} PROPERTIES
-        MACOSX_BUNDLE_INFO_STRING "Visual Neuro ${VISUALNEURO_VERSION}"
+        MACOSX_BUNDLE_INFO_STRING "${IVW_APP_INSTALL_NAME} ${VISUALNEURO_VERSION}"
         MACOSX_BUNDLE_ICON_FILE "favicon.icns"
         MACOSX_BUNDLE_GUI_IDENTIFIER "com.VisualNeuro"
         MACOSX_BUNDLE_LONG_VERSION_STRING "${VISUALNEURO_VERSION}"
-        MACOSX_BUNDLE_BUNDLE_NAME "Visual Neuro"
+        MACOSX_BUNDLE_BUNDLE_NAME "${IVW_APP_INSTALL_NAME}"
         MACOSX_BUNDLE_SHORT_VERSION_STRING "${VISUALNEURO_VERSION}"
         MACOSX_BUNDLE_BUNDLE_VERSION "${VISUALNEURO_VERSION}"
         MACOSX_BUNDLE_COPYRIGHT "C) 2012-${YEAR} Daniel Jönsson"
     )
 
     install(
         DIRECTORY   ${IVW_ROOT_DIR}/data/
-        DESTINATION VisualNeuro.app/Contents/Resources/data
+        DESTINATION ${IVW_APP_INSTALL_NAME}.app/Contents/Resources/data
         COMPONENT   Application
     )
 
@@ -110,8 +111,8 @@ endif()
 
 ivw_deploy_qt(${PROJECT_NAME})
 
-set_property(CACHE IVW_PACKAGE_SELECT_APP APPEND PROPERTY STRINGS "Visual Neuro")
+set_property(CACHE IVW_PACKAGE_SELECT_APP APPEND PROPERTY STRINGS "VisualNeuroApp")
 
-if(IVW_PACKAGE_SELECT_APP STREQUAL "Visual Neuro")
+if(IVW_PACKAGE_SELECT_APP STREQUAL "VisualNeuroApp")
     include(packaging/packaging.cmake) # Package creation
 endif()

apps/visualneuro/consolewidget.h

@@ -44,6 +44,7 @@
 #include <warn/pop>
 
 #include <chrono>
+#include <mutex>
 
 class QLabel;
 class QKeyEvent;

apps/visualneuro/packaging/packaging.cmake

@@ -31,7 +31,16 @@ set(CMAKE_INSTALL_OPENMP_LIBRARIES TRUE)
 set(CMAKE_INSTALL_SYSTEM_RUNTIME_COMPONENT Application)
 include (InstallRequiredSystemLibraries)
 
-set(CPACK_PACKAGE_NAME                "Visual Neuro")
+
+if(APPLE)
+    # Fix for CPack Error on MacOS 13
+    # Error generating temporary disk image.
+    # hdiutil: create failed - Resource busy
+    # https://github.com/actions/runner-images/issues/7522#issuecomment-1564467252
+    set(CPACK_COMMAND_HDIUTIL "/usr/bin/sudo /usr/bin/hdiutil")
+endif()
+
+set(CPACK_PACKAGE_NAME                "VisualNeuroApp")
 set(CPACK_PACKAGE_CONTACT             "Daniel Jönsson <info@visualneuro.com>")
 set(CPACK_PACKAGE_VENDOR              "Daniel Jönsson")
 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Interactive brain cohort analysis")

apps/visualneuro/resources/visualneuro.rc

@@ -1 +1 @@
-id ICON "favicon.ico"
+IDI_ICON1 ICON "favicon.ico"

apps/visualneuro/splashscreen.cpp

@@ -28,7 +28,7 @@
  *********************************************************************************/
 
 #include "splashscreen.h"
-#include <inviwo/core/inviwocommondefines.h>
+#include <inviwo/core/common/inviwocommondefines.h>
 #include <inviwo/core/util/commandlineparser.h>
 #include <inviwo/core/util/stringconversion.h>
 #include <modules/qtwidgets/inviwoqtutils.h>

modules/visualneuro/src/datastructures/volumeatlas.cpp

@@ -120,7 +120,7 @@ int VolumeAtlas::getLabelId(vec3 worldPos) const {
 }
 
 double VolumeAtlas::getLabelIdNormalized(int labelId) const {
-    return atlas_->dataMap_.mapFromValueToNormalized(static_cast<double>(labelId));
+    return atlas_->dataMap.mapFromValueToNormalized(static_cast<double>(labelId));
 }
 
 std::optional<VolumeAtlas::Label> VolumeAtlas::getLabel(int id) const {

modules/visualneuro/src/processors/fmritransferfunctioncontroller.cpp

@@ -255,7 +255,7 @@ fMRITransferFunctionController::fMRITransferFunctionController()
     tTestVolume_.onChange([this]() {
         if (tTestVolume_.hasData()) {
             NetworkLock lock(this);
-            auto dataMap = tTestVolume_.getData()->dataMap_;
+            auto dataMap = tTestVolume_.getData()->dataMap;
             double maxValueRange =
                 std::max(glm::abs(dataMap.valueRange).x, glm::abs(dataMap.valueRange).y);
             thresholdtTestTF_.setMaxValue(maxValueRange);
@@ -353,30 +353,30 @@ void fMRITransferFunctionController::updateTFs(ActiveInput input) {
     if (input == ActiveInput::Mean && meanVolume_.hasData()) {
         if (TFtype(*inputDataTFtype_) == TFtype::Linear) {
             updateLinearTF(linearTF2D_.get(), true, thresholdLinearTF_.get(),
-                           opacityLinearTF_.get(), meanVolume_.getData()->dataMap_);
+                           opacityLinearTF_.get(), meanVolume_.getData()->dataMap);
             updateLinearTF(linearTF3D_.get(), false, thresholdLinearTF_.get(),
-                           opacityLinearTF_.get(), meanVolume_.getData()->dataMap_);
+                           opacityLinearTF_.get(), meanVolume_.getData()->dataMap);
         } else if (TFtype(*inputDataTFtype_) == TFtype::Symmetric && meanVolume_.hasData()) {
             updateSymmetricTF(symmetricTF2D_.get(), true, thresholdSymmetricTF_.get(),
-                              opacitySymmetricTF_.get(), meanVolume_.getData()->dataMap_);
+                              opacitySymmetricTF_.get(), meanVolume_.getData()->dataMap);
             updateSymmetricTF(symmetricTF3D_.get(), false, thresholdSymmetricTF_.get(),
-                              opacitySymmetricTF_.get(), meanVolume_.getData()->dataMap_);
+                              opacitySymmetricTF_.get(), meanVolume_.getData()->dataMap);
         }
     } else if (input == ActiveInput::Correlation && correlationVolume_.hasData()) {
-        if (correlationVolume_.getData()->dataMap_.valueRange.x < 0) {
+        if (correlationVolume_.getData()->dataMap.valueRange.x < 0) {
             updateSymmetricTF(correlationTF2D_.get(), true, thresholdCorrelationTF_.get(),
-                              opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap_);
+                              opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap);
             updateSymmetricTF(correlationTF3D_.get(), false, thresholdCorrelationTF_.get(),
-                              opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap_);
+                              opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap);
         } else {
             updateLinearTF(correlationTF2D_.get(), true, thresholdCorrelationTF_.get(),
-                           opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap_);
+                           opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap);
             updateLinearTF(correlationTF3D_.get(), false, thresholdCorrelationTF_.get(),
-                           opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap_);
+                           opacityCorrelationTF_.get(), correlationVolume_.getData()->dataMap);
         }
 
     } else if (input == ActiveInput::tTest && tTestVolume_.hasData()) {
-        if (tTestVolume_.getData()->dataMap_.valueRange.x < 0) {
+        if (tTestVolume_.getData()->dataMap.valueRange.x < 0) {
             // Colormap, reversed, PuOr_8
             auto leftColors = {vec3(0.32941176470588235, 0.15294117647058825, 0.5333333333333333),
                                vec3(0.5019607843137255, 0.45098039215686275, 0.6745098039215687),
@@ -389,16 +389,16 @@ void fMRITransferFunctionController::updateTFs(ActiveInput input) {
                 vec3(0.7019607843137254, 0.34509803921568627, 0.023529411764705882)};
 
             updateSymmetricTF(tTestTF2D_.get(), true, thresholdtTestTF_.get(),
-                              opacitytTestTF_.get(), tTestVolume_.getData()->dataMap_, leftColors,
+                              opacitytTestTF_.get(), tTestVolume_.getData()->dataMap, leftColors,
                               rightColors);
             updateSymmetricTF(tTestTF3D_.get(), false, thresholdtTestTF_.get(),
-                              opacitytTestTF_.get(), tTestVolume_.getData()->dataMap_, leftColors,
+                              opacitytTestTF_.get(), tTestVolume_.getData()->dataMap, leftColors,
                               rightColors);
         } else {
             updateLinearTF(tTestTF2D_.get(), true, thresholdtTestTF_.get(), opacitytTestTF_.get(),
-                           tTestVolume_.getData()->dataMap_);
+                           tTestVolume_.getData()->dataMap);
             updateLinearTF(tTestTF3D_.get(), false, thresholdtTestTF_.get(), opacitytTestTF_.get(),
-                           tTestVolume_.getData()->dataMap_);
+                           tTestVolume_.getData()->dataMap);
         }
     }
 }  // namespace inviwo
@@ -472,7 +472,7 @@ void fMRITransferFunctionController::updateSymmetricTF(TransferFunction &tf, con
 void fMRITransferFunctionController::updateMeanVolumeSliders(const bool updateSetValue) {
     if (meanVolume_.hasData()) {
         NetworkLock lock(this);
-        auto dataMap = meanVolume_.getData()->dataMap_;
+        auto dataMap = meanVolume_.getData()->dataMap;
         thresholdLinearTF_.set(thresholdLinearTF_.get(), dataMap.valueRange.x, dataMap.valueRange.y,
                                abs(dataMap.valueRange.y - dataMap.valueRange.x) * 0.01);
         double maxValueRange =

modules/visualneuro/src/processors/parametervolumesequencecorrelation.cpp

@@ -100,7 +100,7 @@ void ParameterVolumeSequenceCorrelation::process() {
             for (size_t index = 0; index < volumeRAMs.size(); index++) {
                 if (filter[index]) continue;
 
-                auto dataMap = (*volumeSequence)[index]->dataMap_;
+                auto dataMap = (*volumeSequence)[index]->dataMap;
                 volumeRAMs[index]->dispatch<void, dispatching::filter::Scalars>(
                     [&values, vxlNmbr, &dataMap](auto vr) {
                         auto ptr_first_vxl = vr->getDataTyped();
@@ -207,8 +207,8 @@ void ParameterVolumeSequenceCorrelation::process() {
 
         // Set data range and value range to (-1,1) since that's the range of the Pearson/Spearman
         // correlation.
-        resVol->dataMap_.dataRange = dvec2(-1.0, 1.0);
-        resVol->dataMap_.valueRange = dvec2(-1.0, 1.0);
+        resVol->dataMap.dataRange = dvec2(-1.0, 1.0);
+        resVol->dataMap.valueRange = dvec2(-1.0, 1.0);
 
         resVol->setModelMatrix(volumes->front()->getModelMatrix());
         resVol->setWorldMatrix(volumes->front()->getWorldMatrix());

modules/visualneuro/src/processors/volume4dsequencesource.cpp

@@ -132,7 +132,10 @@ std::shared_ptr<Volume4DSequence> Volume4DSequenceSource::loadFolder(std::filesy
                 if (auto reader1 = rf->getReaderForTypeAndExtension<Volume>(file)) {
                     auto volume = reader1->readData(file, this);
                     volume->setMetaData<StringMetaData>("filename", file.generic_string());
-                    volumes->push_back(std::make_shared<VolumeSequence>(1, volume));
+                    auto tmp = std::vector<std::shared_ptr<Volume>>(1, volume);
+
+                    volumes->push_back(std::make_shared<VolumeSequence>(
+                        std::span<std::shared_ptr<Volume> >{tmp}));
 
                 } else if (auto reader2 = rf->getReaderForTypeAndExtension<VolumeSequence>(file)) {
                     auto volumeSeq = reader2->readData(file, this);
@@ -196,11 +199,11 @@ void Volume4DSequenceSource::process() {
                         if (!volume->hasMetaData<StringMetaData>("filename"))
                             volume->setMetaData<StringMetaData>("filename", file_.get().generic_string());
 
-                        valueRange.x = std::min(valueRange.x, volume->dataMap_.valueRange.x);
-                        valueRange.y = std::max(valueRange.y, volume->dataMap_.valueRange.y);
+                        valueRange.x = std::min(valueRange.x, volume->dataMap.valueRange.x);
+                        valueRange.y = std::max(valueRange.y, volume->dataMap.valueRange.y);
 
-                        dataRange.x = std::min(dataRange.x, volume->dataMap_.dataRange.x);
-                        dataRange.y = std::max(dataRange.y, volume->dataMap_.dataRange.y);
+                        dataRange.x = std::min(dataRange.x, volume->dataMap.dataRange.x);
+                        dataRange.y = std::max(dataRange.y, volume->dataMap.dataRange.y);
                     }
                     if (!volume4d->empty()) {
                         // set basis of first volume
@@ -232,11 +235,11 @@ void Volume4DSequenceSource::process() {
             if (result && !result->empty()) {
                 // Update value range
                 for (auto& volumeSequence : *result) {
-                    for (auto& volume : *volumeSequence) {
-                        volume->dataMap_.dataRange = dvec2(
-                            volume->dataMap_.mapFromValueToData(information_.valueRange.get().x),
-                            volume->dataMap_.mapFromValueToData(information_.valueRange.get().y));
-                        volume->dataMap_.valueRange = information_.valueRange.get();
+                    for (auto volume : *volumeSequence) {
+                        volume->dataMap.dataRange = dvec2(
+                            volume->dataMap.mapFromValueToData(information_.valueRange.get().x),
+                            volume->dataMap.mapFromValueToData(information_.valueRange.get().y));
+                        volume->dataMap.valueRange = information_.valueRange.get();
                     }
                 }
                 outport_.setData(result);