Rebase from master

.github/workflows/build.yml

@@ -4,66 +4,45 @@ on:
   push:
   pull_request:
   workflow_dispatch:
-    inputs:
-      forceMacBuild:
-        description: 'If set true override the ENABLE_MACOS_BUILD to force a build'
-        type: boolean
-        default: false
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
-  MACENABLED: ${{ inputs.forceMacBuild }}
 
 # for matrix check https://docs.github.com/en/actions/reference/specifications-for-github-hosted-runners
 jobs:
+  prepare_matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.matrix_setup.outputs.matrix }}
+    steps:
+    - name: Get matrix from file
+      id: matrix_setup
+      uses: ManiVaultStudio/github-actions/matrix_setup@main
+
   cross-platform-build:
     name: Cross platform build
+    needs: prepare_matrix
     # The CMake configure and build commands are platform agnostic and should work equally
     # well on Windows or Mac.  You can convert this to a matrix build if you need
     # cross-platform coverage.
     # See: https://docs.github.com/en/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        include:
-          - name: Windows-msvc2019
-            os: windows-2019
-            compiler: msvc-2019
-            build-cversion: 16
-            build-runtime: MD
-            build-config: Release
-
-          - name: Linux_gcc11
-            os: ubuntu-22.04
-            build-cc: gcc
-            build-cxx: g++
-            build-compiler: gcc
-            build-cversion: 11
-            build-config: Release
-            build-os: Linux
-            build-libcxx: libstdc++
-
-          - name: Macos_xcode13.4
-            os: macos-12
-            build-compiler: apple-clang
-            build-cversion: 13
-            build-config: Release
-            build-os: Macos
-            build-xcode-version: 13.4
-            build-libcxx: libc++
+        include: ${{ fromJson(needs.prepare_matrix.outputs.matrix) }}
 
     steps:
       - name: Checkout the source
         if: github.event_name != 'pull_request'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
 
       - name: Checkout the source - pull request
         if: github.event_name == 'pull_request'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           submodules: recursive
           fetch-depth: 0
@@ -75,12 +54,12 @@ jobs:
           sudo xcode-select -switch /Applications/Xcode_${{matrix.build-xcode-version}}.app
 
       - name: Setup python version
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
       - name: Start ssh key agent
-        uses: webfactory/ssh-agent@v0.7.0
+        uses: webfactory/ssh-agent@v0.9.0
         with:
           ssh-private-key: ${{ secrets.RULESSUPPORT_DEPLOY_KEY }}
 
@@ -111,21 +90,23 @@ jobs:
           conan-libcxx-version: ${{matrix.build-libcxx}}
           conan-build-type: ${{matrix.build-config}}
           conan-build-os: ${{matrix.build-os}}
+          build-arch: ${{matrix.build-arch}}
           conan-user: ${{secrets.LKEB_UPLOAD_USER}}
           conan-password: ${{secrets.LKEB_UPLOAD_USER_PASSWORD}}
           conan-pem: ${{secrets.LKEB_UPLOAD_CERT_CHAIN}}
           conan-cc: gcc-${{matrix.build-cversion}}
           conan-cxx: g++-${{matrix.build-cversion}}
 
       - name: Mac build
-        if: startsWith(matrix.os, 'macos') &&  (env.MACENABLED == 'true' || vars.ENABLE_MACOS_BUILD == 'True')
+        if: startsWith(matrix.os, 'macos')
         uses: ManiVaultStudio/github-actions/conan_linuxmac_build@main
         with:
           conan-compiler: ${{matrix.build-compiler}}
           conan-compiler-version: ${{matrix.build-cversion}}
           conan-libcxx-version: ${{matrix.build-libcxx}}
           conan-build-type: ${{matrix.build-config}}
           conan-build-os: ${{matrix.build-os}}
+          build-arch: ${{matrix.build-arch}}
           conan-user: ${{secrets.LKEB_UPLOAD_USER}}
           conan-password: ${{secrets.LKEB_UPLOAD_USER_PASSWORD}}
           conan-pem: ${{secrets.LKEB_UPLOAD_CERT_CHAIN}}

.gitignore

@@ -534,3 +534,4 @@ FodyWeavers.xsd
 
 Build/
 .DS_Store
+*.bak

CMakeLists.txt

@@ -1,30 +1,40 @@
-cmake_minimum_required(VERSION 3.17)
+cmake_minimum_required(VERSION 3.22)
 
-set(SVPLUGIN "SpectralViewPlugin")
+option(MV_UNITY_BUILD "Combine target source files into batches for faster compilation" OFF)
 
-PROJECT(${SVPLUGIN})
+# -----------------------------------------------------------------------------
+# SpectralView Plugin
+# -----------------------------------------------------------------------------
+set(SVPLUGIN "SpectralViewPlugin")
+PROJECT(${SVPLUGIN}
+        DESCRIPTION "View plugin for ManiVault for spectral data"
+        LANGUAGES CXX
+)
 
+# -----------------------------------------------------------------------------
+# CMake Options
+# -----------------------------------------------------------------------------
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
 set(CMAKE_AUTOMOC ON)
 set(CMAKE_AUTORCC ON)
-set(CMAKE_AUTOUIC ON)
-
-if(MSVC)
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /DWIN32 /EHsc /MP /permissive- /Zc:__cplusplus /W3")
-	set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /LTCG /NODEFAULTLIB:LIBCMT")
-	set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /MDd")
-	set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} /MD")
-endif(MSVC)
-
-# Check if the directory to the ManiVault installation has been provided
-if(NOT DEFINED MV_INSTALL_DIR)
-    set(MV_INSTALL_DIR "" CACHE PATH "Directory where ManiVault is installed")
-    message(FATAL_ERROR "Please set MV_INSTALL_DIR to the directory where ManiVault is installed")
+
+if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /DWIN32 /EHsc /MP /permissive- /Zc:__cplusplus /W3")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /MDd")
+    set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} /MD")
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} /MD")
 endif()
-file(TO_CMAKE_PATH ${MV_INSTALL_DIR} MV_INSTALL_DIR)
 
-find_package(Qt6 6.3.1 COMPONENTS Widgets WebEngineWidgets Concurrent REQUIRED)
+# -----------------------------------------------------------------------------
+# Dependencies
+# -----------------------------------------------------------------------------
+find_package(Qt6 COMPONENTS Widgets WebEngineWidgets Concurrent REQUIRED)
+
+find_package(ManiVault COMPONENTS Core PointData ClusterData ImageData CONFIG QUIET)
 
+# -----------------------------------------------------------------------------
+# Source files
+# -----------------------------------------------------------------------------
 set(PLUGIN
     src/SpectralViewPlugin.h
     src/SpectralViewPlugin.cpp
@@ -34,10 +44,6 @@ set(PLUGIN
     src/Endmember.h
 )
 
-set(PLUGIN_MOC_HEADERS
-	src/SpectralViewPlugin.h
-)
-
 set(ACTIONS
     src/SettingsAction.h
     src/SettingsAction.cpp
@@ -82,7 +88,7 @@ set(WEB
 
 set(AUX
 	res/lineplot_resources.qrc
-	src/SpectralViewPlugin.json
+	PluginInfo.json
 )
 
 qt6_add_resources(RESOURCE_FILES res/lineplot_resources.qrc)
@@ -95,34 +101,40 @@ source_group(Widget FILES ${WIDGETS})
 source_group(Web FILES ${WEB})
 source_group(Aux FILES ${AUX})
 
+# -----------------------------------------------------------------------------
+# CMake Target
+# -----------------------------------------------------------------------------
 add_library(${SVPLUGIN} SHARED ${SOURCES} ${WEB} ${AUX} ${RESOURCE_FILES})
 
-qt_wrap_cpp(SV_PARAMETERS_MOC ${PLUGIN_MOC_HEADERS} TARGET ${SVPLUGIN})
-target_sources(${SVPLUGIN} PRIVATE ${SV_PARAMETERS_MOC})
+# -----------------------------------------------------------------------------
+# Target include directories
+# -----------------------------------------------------------------------------
+target_include_directories(${SVPLUGIN} PRIVATE "${ManiVault_INCLUDE_DIR}")
 
-target_include_directories(${SVPLUGIN} PRIVATE "${MV_INSTALL_DIR}/$<CONFIGURATION>/include/")
+# -----------------------------------------------------------------------------
+# Target properties
+# -----------------------------------------------------------------------------
+target_compile_features(${SVPLUGIN} PRIVATE cxx_std_20)
 
-# Request C++17
-target_compile_features(${SVPLUGIN} PRIVATE cxx_std_17)
+if(MV_UNITY_BUILD)
+    set_target_properties(${SVPLUGIN} PROPERTIES UNITY_BUILD ON)
+endif()
 
+# -----------------------------------------------------------------------------
+# Target library linking
+# -----------------------------------------------------------------------------
 target_link_libraries(${SVPLUGIN} PRIVATE Qt6::Widgets)
 target_link_libraries(${SVPLUGIN} PRIVATE Qt6::WebEngineWidgets)
 target_link_libraries(${SVPLUGIN} PRIVATE Qt6::Concurrent)
 
-set(MV_LINK_PATH "${MV_INSTALL_DIR}/$<CONFIGURATION>/lib")
-set(PLUGIN_LINK_PATH "${MV_INSTALL_DIR}/$<CONFIGURATION>/$<IF:$<CXX_COMPILER_ID:MSVC>,lib,Plugins>")
-set(MV_LINK_SUFFIX $<IF:$<CXX_COMPILER_ID:MSVC>,${CMAKE_LINK_LIBRARY_SUFFIX},${CMAKE_SHARED_LIBRARY_SUFFIX}>)
-
-set(MV_LINK_LIBRARY "${MV_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}MV_Public${MV_LINK_SUFFIX}")
-set(POINTDATA_LINK_LIBRARY "${PLUGIN_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}PointData${MV_LINK_SUFFIX}") 
-set(IMAGEDATA_LINK_LIBRARY "${PLUGIN_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}ImageData${MV_LINK_SUFFIX}") 
-set(CLUSTERDATA_LINK_LIBRARY "${PLUGIN_LINK_PATH}/${CMAKE_SHARED_LIBRARY_PREFIX}ClusterData${MV_LINK_SUFFIX}") 
-
-target_link_libraries(${SVPLUGIN} PRIVATE "${MV_LINK_LIBRARY}")
-target_link_libraries(${SVPLUGIN} PRIVATE "${POINTDATA_LINK_LIBRARY}")
-target_link_libraries(${SVPLUGIN} PRIVATE "${IMAGEDATA_LINK_LIBRARY}")
-target_link_libraries(${SVPLUGIN} PRIVATE "${CLUSTERDATA_LINK_LIBRARY}")
+target_link_libraries(${SVPLUGIN} PRIVATE ManiVault::Core)
+target_link_libraries(${SVPLUGIN} PRIVATE ManiVault::PointData)
+target_link_libraries(${SVPLUGIN} PRIVATE ManiVault::ClusterData)
+target_link_libraries(${SVPLUGIN} PRIVATE ManiVault::ImageData)
 
+# -----------------------------------------------------------------------------
+# Target installation
+# -----------------------------------------------------------------------------
 install(TARGETS ${SVPLUGIN}
     RUNTIME DESTINATION Plugins COMPONENT PLUGINS # Windows .dll
     LIBRARY DESTINATION Plugins COMPONENT PLUGINS # Linux/Mac .so
@@ -132,11 +144,16 @@ add_custom_command(TARGET ${SVPLUGIN} POST_BUILD
 	COMMAND "${CMAKE_COMMAND}"
 	--install ${CMAKE_CURRENT_BINARY_DIR}
 	--config $<CONFIGURATION>
-	--prefix ${MV_INSTALL_DIR}/$<CONFIGURATION>
+	--prefix ${ManiVault_INSTALL_DIR}/$<CONFIGURATION>
 )
 
+mv_handle_plugin_config(${SVPLUGIN})
+
+# -----------------------------------------------------------------------------
+# Miscellaneous
+# -----------------------------------------------------------------------------
 # Automatically set the debug environment (command + working directory) for MSVC in debug mode
-if(MSVC)
-	set_property(TARGET ${SVPLUGIN} PROPERTY VS_DEBUGGER_WORKING_DIRECTORY $<IF:$<CONFIG:DEBUG>,${MV_INSTALL_DIR}/debug,${MV_INSTALL_DIR}/release>)
-	set_property(TARGET ${SVPLUGIN} PROPERTY VS_DEBUGGER_COMMAND $<IF:$<CONFIG:DEBUG>,"${MV_INSTALL_DIR}/debug/ManiVault Studio.exe","${MV_INSTALL_DIR}/release/ManiVault Studio.exe">)
+if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+    set_property(TARGET ${SVPLUGIN} PROPERTY VS_DEBUGGER_WORKING_DIRECTORY $<IF:$<CONFIG:DEBUG>,${ManiVault_INSTALL_DIR}/Debug,$<IF:$<CONFIG:RELWITHDEBINFO>,${ManiVault_INSTALL_DIR}/RelWithDebInfo,${ManiVault_INSTALL_DIR}/Release>>)
+    set_property(TARGET ${SVPLUGIN} PROPERTY VS_DEBUGGER_COMMAND $<IF:$<CONFIG:DEBUG>,"${ManiVault_INSTALL_DIR}/Debug/ManiVault Studio.exe",$<IF:$<CONFIG:RELWITHDEBINFO>,"${ManiVault_INSTALL_DIR}/RelWithDebInfo/ManiVault Studio.exe","${ManiVault_INSTALL_DIR}/Release/ManiVault Studio.exe">>)
 endif()

PluginInfo.json

@@ -0,0 +1,9 @@
+{
+    "name" : "Spectral View",
+    "version" :  {
+        "plugin" : "1.0.0",
+        "core" : ["1.3"]
+    },
+    "type" : "View",
+    "dependencies" : ["Points", "Cluster", "Images"]
+}

Readme.md

@@ -13,10 +13,14 @@ git clone git@github.com:ManiVaultStudio/SpectralViewPlugin.git
 ## Usage
 How to use:
 
-0. Load a data set, e.g. with the [ENVI](https://github.com/ManiVaultStudio/ENVILoader) or [general image](https://github.com/ManiVaultStudio/ImageLoaderPlugin) loader plugins. **Caveat**: It's encouraged to define dimension names that encode the wavelength of the respective image channel, e.g. "304.7", "1020" or "304.7 nm". This wavelength information will be displayed in the viewer. If no dimension names are given when loading the data, ManiVault automatically numbers the dimensions, i.e. "Dim 0", etc.; in this case, the dimension numbers are displayed on the x-Axis instead of wavelengths.
+0. Load a data set, e.g. with the [ENVI](https://github.com/ManiVaultStudio/ENVILoader) or [general image](https://github.com/ManiVaultStudio/ImageLoaderPlugin) loader plugins.
 1. Open a spectral viewer and drag & drop the point data into the viewer. At this point you will not see anything yet. Open data in another viewer, e.g. an image viewer, and make a selection. Now you'll see the average spectral values for the selected points.
 2. Create cluster for your data set, e.g. using an analysis like [mean shift clustering](https://github.com/ManiVaultStudio/MeanShiftClustering) or through manual annotation in the [scatterplot](https://github.com/ManiVaultStudio/Scatterplot). Drag & drop the cluster data into the main view of the spectral viewer.
 3. Perform a mapping like the "Spectral Angle Mapping" algorithm for a selected cluster. This will cerate a new image data set. 
+> **Caveats**:
+> - This viewer only handles point data sets that have a image data set as a child.
+> - It's encouraged to define dimension names that encode the wavelength of the respective image channel, e.g. "304.7", "1020" or "304.7 nm". This wavelength information will be displayed in the viewer. If no dimension names are given when loading the data, ManiVault automatically numbers the dimensions, i.e. "Dim 0", etc.; in this case, the dimension numbers are displayed on the x-Axis instead of wavelengths. 
+> - This viewer expects positive data values (as is common in spectral intensities); negative values might lead to unwanted behaviour.
 
 ## References
 Based on Popa et al. "Visual Analysis of RIS Data for Endmember Selection" (2022):