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imikejacksonimikejackson
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Initial Commit of code that can parse a Zeiss Montage data set. We are only creating the Data Containers and the meta AttributeMatrix at this point. No attempt to create the Bundles or read the actual image data from the image files. No attempt to read more than a single slice of data.
0 parents  commit 659ccb6

23 files changed

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‎CMakeLists.txt‎

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#--////////////////////////////////////////////////////////////////////////////
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#-- Your License or copyright can go here
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#--////////////////////////////////////////////////////////////////////////////
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project(ZeissImport)
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set(PLUGIN_NAME ZeissImport)
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# --------------------------------------------------------------------
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# Look for Qt 4 as we need it for the plugin GUI to be generated
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if(NOT QT4_FOUND)
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message(FATAL_ERROR "Qt 4 is Needed for this ${PLUGIN_NAME}Plugin.")
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endif()
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include( ${QT_USE_FILE} )
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set(${PLUGIN_NAME}_Project_SRCS "")
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include(${DREAM3DProj_SOURCE_DIR}/Source/DREAM3DLib/DREAM3DLibMacros.cmake)
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#-------
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# Start writing this header file
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set(AllFiltersHeaderFile ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/${PLUGIN_NAME}Filters.h_tmp)
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file(WRITE ${AllFiltersHeaderFile} "#ifndef _${PLUGIN_NAME}_Filters_H_\n#define _${PLUGIN_NAME}_Filters_H_\n\n")
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# --------------------------------------------------------------------
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# Create a File that will register all of the DREAM3D Filters
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set(RegisterKnownFiltersFile ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/RegisterKnownFilters.cpp_tmp)
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file(WRITE ${RegisterKnownFiltersFile} "/* This file was AUTO GENERATED During the CMake Run. DO NOT EDIT THIS FILE. Edit the CMake files that generate this file */\n")
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file(APPEND ${RegisterKnownFiltersFile} "/* The CMake code that generates this file is located in ${CMAKE_CURRENT_LIST_FILE}*/\n")
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file(APPEND ${RegisterKnownFiltersFile} "/* This file will be directly included in another source file. */\n")
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file(APPEND ${RegisterKnownFiltersFile} "#include \"${PLUGIN_NAME}Filters.h\"\n\n")
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file(APPEND ${RegisterKnownFiltersFile} "\nvoid ${PLUGIN_NAME}Plugin::registerFilters(FilterManager* fm)\n{\n")
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# --------------------------------------------------------------------
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# Generate a file with all of our MOC'ed sources and headers
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set(FilterWidget_GEN_HDRS_File ${${PLUGIN_NAME}_BINARY_DIR}/FilterWidget_GEN_HDRS_File.cmake)
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set(FilterWidget_GEN_SRCS_File ${${PLUGIN_NAME}_BINARY_DIR}/FilterWidget_GEN_SRCS_File.cmake)
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file(WRITE ${FilterWidget_GEN_HDRS_File})
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file(WRITE ${FilterWidget_GEN_SRCS_File})
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set(Project_SRCS "")
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# Add in our Filter classes
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include(${${PLUGIN_NAME}_SOURCE_DIR}/${PLUGIN_NAME}Filters/SourceList.cmake)
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# Add in our Plugin Specific FilterParameterWidgets
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include(${${PLUGIN_NAME}_SOURCE_DIR}/FilterParameterWidgets/SourceList.cmake)
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#-----------------------------------------------------
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# Include any extra Widgets that this plugin needs
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include(${${PLUGIN_NAME}_SOURCE_DIR}/Widgets/SourceList.cmake)
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set(${PLUGIN_NAME}_Project_SRCS ${Project_SRCS})
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#-----------------------------------------------------
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# Close up all the files that we just generated
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file(APPEND ${AllFiltersHeaderFile} "\n#endif\n")
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file(APPEND ${RegisterKnownFiltersFile} "\n }\n")
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cmpReplaceFileIfDifferent(OLD_FILE_PATH ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/${PLUGIN_NAME}Filters.h
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NEW_FILE_PATH ${AllFiltersHeaderFile} )
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cmpReplaceFileIfDifferent(OLD_FILE_PATH ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/RegisterKnownFilters.cpp
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NEW_FILE_PATH ${RegisterKnownFiltersFile} )
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set(AllFiltersHeaderFile ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/${PLUGIN_NAME}Filters.h)
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set(RegisterKnownFiltersFile ${${PLUGIN_NAME}_BINARY_DIR}/${PLUGIN_NAME}Filters/RegisterKnownFilters.cpp)
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#--------------------------
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include_directories( ${HDF5_INCLUDE_DIR} )
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include_directories( ${PROJECT_CODE_DIR} )
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include_directories( ${QtSupport_BINARY_DIR} )
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include_directories( ${QtSupport_SOURCE_DIR} )
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get_filename_component(PLUGINS_SOURCE_DIR ${${PLUGIN_NAME}_SOURCE_DIR} DIRECTORY)
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get_filename_component(PLUGINS_BINARY_DIR ${${PLUGIN_NAME}_BINARY_DIR} DIRECTORY)
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include_directories( ${${PLUGIN_NAME}_BINARY_DIR} )
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include_directories( ${${PLUGIN_NAME}_SOURCE_DIR})
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include_directories( ${PLUGINS_SOURCE_DIR} )
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include_directories( ${PLUGINS_BINARY_DIR} )
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# ******************************************************************************
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# Create our custom executable that will generate most of our QFilterWidget
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# classes from information stored in the Filters themselves.
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# Read the file back into a string so we can configure our file
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file(READ ${FilterWidget_GEN_HDRS_File} ${PLUGIN_NAME}Widget_GEN_HDRS)
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file(READ ${FilterWidget_GEN_SRCS_File} ${PLUGIN_NAME}Widget_GEN_SRCS)
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# Remove the temp files that we no longer need
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file(REMOVE ${FilterWidget_GEN_HDRS_File})
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file(REMOVE ${FilterWidget_GEN_SRCS_File})
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set(FILTER_HEADERS "#include \"${AllFiltersHeaderFile}\"")
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set(FILTER_WIDGETS_TEMP_DIR ${${PLUGIN_NAME}_BINARY_DIR}/Temp)
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set(FILTER_WIDGETS_BINARY_DIR ${${PLUGIN_NAME}_BINARY_DIR})
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set(FILTER_WIDGETS_SOURCE_DIR ${${PLUGIN_NAME}_SOURCE_DIR})
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set(FILTER_WIDGETS_DOCS_DIR ${${PLUGIN_NAME}_SOURCE_DIR}/Documentation/Filters)
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set(FILTER_INCLUDE_PREFIX "${PLUGIN_NAME}")
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# --------------------------------------------------------------------
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# On Linux we need -fPIC for linking static and shared libraries
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if(UNIX AND NOT APPLE)
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set_source_files_properties(${${PLUGIN_NAME}_Project_SRCS} PROPERTIES COMPILE_FLAGS -fPIC)
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endif()
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# --------------------------------------------------------------------
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# These headers will be MOC'ed by the build system. They should all inherit from QObject
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# --------------------------------------------------------------------
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set(${PLUGIN_NAME}_HDRS
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${PROJECT_SOURCE_DIR}/${PLUGIN_NAME}Plugin.h
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${PROJECT_SOURCE_DIR}/${PLUGIN_NAME}Constants.h
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)
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set(${PLUGIN_NAME}_SRCS
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${PROJECT_SOURCE_DIR}/${PLUGIN_NAME}Plugin.cpp
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)
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set(${PLUGIN_NAME}_MISC_HDRS
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${PROJECT_SOURCE_DIR}/${PLUGIN_NAME}Constants.h
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)
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cmp_IDE_SOURCE_PROPERTIES( "${PLUGIN_NAME}/" "${${PLUGIN_NAME}_HDRS};${${PLUGIN_NAME}_MISC_HDRS}" "${${PLUGIN_NAME}_SRCS}" "0")
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# -----------------------------------------------------------------------------
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# Collect all of our Generated header and source files so that they show up in the various projects
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set(${PLUGIN_NAME}_GEN_HDRS
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${AllFiltersHeaderFile}
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${RegisterKnownFiltersFile}
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${AllFilterParameterWidgetsHeaderFile}
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${RegisterKnownFilterParameterWidgetsFile}
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)
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# --------------------------------------------------------------------
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#
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# --------------------------------------------------------------------
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set_source_files_properties( ${${PLUGIN_NAME}_MODULE_MOC_SRCS} PROPERTIES HEADER_FILE_ONLY TRUE)
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set_source_files_properties( ${RegisterKnownFiltersFile} PROPERTIES HEADER_FILE_ONLY TRUE)
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set_source_files_properties( ${RegisterKnownFilterParameterWidgetsFile} PROPERTIES HEADER_FILE_ONLY TRUE)
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# --------------------------------------------------------------------
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# Group all the generated source files in IDE's that support it. Makes it clear
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# to the user of the IDE what is generated and what is not.
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cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Moc" "${${PLUGIN_NAME}_GEN_HDRS}" "${${PLUGIN_NAME}_Generated_MOC_SRCS};${${PLUGIN_NAME}_MOC_SRCS};${${PLUGIN_NAME}_GEN_SRCS}" "0")
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cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Uic" "${${PLUGIN_NAME}_Generated_UI_HDRS}" "" "0")
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cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Qrc" "${${PLUGIN_NAME}_Generated_RC_SRCS}" "" "0")
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# --------------------------------------------------------------------
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#
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# --------------------------------------------------------------------
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include(${ZeissImport_SOURCE_DIR}/ZeissXml/SourceList.cmake)
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# --------------------------------------------------------------------
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#
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# --------------------------------------------------------------------
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set(${PLUGIN_NAME}_MODULE_SRCS
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${${PLUGIN_NAME}_Project_SRCS} # These sources come from the SourceList.cmake file and include .h/.cpp/moc/uic files
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${${PLUGIN_NAME}_HDRS}
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${${PLUGIN_NAME}_SRCS}
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${${PLUGIN_NAME}_MODULE_MOC_SRCS}
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${${PLUGIN_NAME}_MISC_HDRS}
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# -- Add in the Filter Parameter Widgets
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${${PLUGIN_NAME}_ParameterWidgets_HDRS}
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${${PLUGIN_NAME}_ParameterWidgets_SRCS}
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${${PLUGIN_NAME}_ParameterWidgets_UIS}
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${${PLUGIN_NAME}_ParameterWidgets_Generated_MOC_SRCS}
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${${PLUGIN_NAME}_ParameterWidgets_Generated_UI_HDRS}
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# -- Add in the plain Widgets
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${${PLUGIN_NAME}_Widgets_HDRS}
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${${PLUGIN_NAME}_Widgets_SRCS}
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${${PLUGIN_NAME}_Widgets_UIS}
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${${PLUGIN_NAME}_Widgets_Generated_MOC_SRCS}
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${${PLUGIN_NAME}_Widgets_Generated_UI_HDRS}
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${${PLUGIN_NAME}_GEN_HDRS}
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${ZeissXml_SRCS}
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${ZeissXml_HDRS}
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)
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# --------------------------------------------------------------------
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# Setup output Directory for the plugin
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if(NOT MSVC)
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set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${DREAM3DProj_BINARY_DIR}/Bin/Plugins )
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endif()
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add_library(${PLUGIN_NAME} MODULE ${${PLUGIN_NAME}_MODULE_SRCS})
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target_link_libraries(${PLUGIN_NAME}
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${QT_QTCORE_LIBRARY}
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DREAM3DLib
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${QT_QTGUI_LIBRARY}
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QtSupport
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DREAM3DWidgetsLib
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${QT_QTXML_LIBRARY}
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)
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SET_TARGET_PROPERTIES(${PLUGIN_NAME} PROPERTIES FOLDER ${PLUGIN_NAME}Plugin)
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# --------------------------------------------------------------------
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# Set some additional properties of the plugin like its output name
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PluginProperties(${PLUGIN_NAME} "_debug" "${DREAM3D_VERSION}"
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"${DREAM3D_BINARY_DIR}" "${CMP_PLUGIN_LIST_FILE}")
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# --------------------------------------------------------------------
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# Put back the output directory
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if(NOT MSVC)
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set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${DREAM3DProj_BINARY_DIR}/Bin )
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endif()
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‎Documentation/ZeissImportFilters/ZeissImportFilter.md‎

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ZeissImportFilter {#zeissimportfilter}
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=====
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## Group (Subgroup) ##
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ZeissImport (ZeissImport)
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## Description ##
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This filter does the following...
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## Parameters ##
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| Name | Type |
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|------------------|------|
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| Feature Array Name | String |
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## Required Arrays ##
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| Type | Default Array Name | Description | Comment |
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|------|--------------------|-------------|---------|
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| Int | SomeName | .... | other |
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## Created Arrays ##
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| Type | Default Array Name | Description | Comment |
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|------|--------------------|-------------|---------|
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| Int | SomeName | .... | other |
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## Authors: ##
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**Copyright:** Who holds the copyright for the code
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**Contact Info:** email address
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**Version:** x.y.z
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**License:** What is the license for this code
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‎FilterParameterWidgets/SourceList.cmake‎

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set(${PLUGIN_NAME}_ParameterWidgets_HDRS "")
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set(${PLUGIN_NAME}_ParameterWidgets_SRCS "")
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set(${PLUGIN_NAME}_ParameterWidgets_UIS "")
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# --------------------------------------------------------------------
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# List the name of your custom FilterParameter Widgets in this section
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set(${PLUGIN_NAME}_PARAMETER_WIDGETS
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# SomeCustomWidget
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)
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# --------------------------------------------------------------------
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# Create a File that has all the headers for the various Filter Parameter Widgets
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set(AllFilterParameterWidgetsHeaderFile ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/FilterParameterWidgets.h_tmp)
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file(WRITE ${AllFilterParameterWidgetsHeaderFile} "#ifndef _${PLUGIN_NAME}_FilterParameterWidgets_H_\n#define _${PLUGIN_NAME}_FilterParameterWidgets_H_\n\n")
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# --------------------------------------------------------------------
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# Create a File that will register all of the DREAM3D Filter Parameter Widgets
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set(RegisterKnownFilterParameterWidgetsFile ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/RegisterKnownFilterParameterWidgets.cpp_tmp)
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file(WRITE ${RegisterKnownFilterParameterWidgetsFile} "/* This file was AUTO GENERATED During the CMake Run. DO NOT EDIT THIS FILE. Edit the CMake files that generate this file */\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "/* The CMake code that generates this file is located in ${CMAKE_CURRENT_LIST_FILE}*/\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "/* This file will be directly included in another source file. */\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "#include \"DREAM3DWidgetsLib/FilterWidgetManager.h\"\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "#include \"DREAM3DWidgetsLib/PipelineFilterWidgetFactory.hpp\"\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "#include \"${PLUGIN_NAME}/FilterParameterWidgets/FilterParameterWidgets.h\"\n\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "\nvoid ${PLUGIN_NAME}Plugin::registerFilterWidgets(FilterWidgetManager* idManager)\n{\n")
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# --------------------------------------------------------------------
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# Loop through all the FilterParameterWidgets that this plugin is going to compile and make available.
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foreach(FPW ${${PLUGIN_NAME}_PARAMETER_WIDGETS})
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set(${PLUGIN_NAME}_ParameterWidgets_HDRS
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${${PLUGIN_NAME}_ParameterWidgets_HDRS}
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${${PLUGIN_NAME}_SOURCE_DIR}/FilterParameterWidgets/${FPW}.h
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)
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set(${PLUGIN_NAME}_ParameterWidgets_SRCS
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${${PLUGIN_NAME}_ParameterWidgets_SRCS}
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${${PLUGIN_NAME}_SOURCE_DIR}/FilterParameterWidgets/${FPW}.cpp
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)
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set(${PLUGIN_NAME}_ParameterWidgets_UIS
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${${PLUGIN_NAME}_ParameterWidgets_UIS}
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${${PLUGIN_NAME}_SOURCE_DIR}/FilterParameterWidgets/UI_Files/${FPW}.ui
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)
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} " {\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} " PipelineFilterWidgetFactory<${FPW}>::Pointer factory = PipelineFilterWidgetFactory<${FPW}>::New();\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} " idManager->addFilterWidgetFactory( \"${FPW}\", factory );\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} " }\n")
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file(APPEND ${AllFilterParameterWidgetsHeaderFile} "#include \"${PLUGIN_NAME}/FilterParameterWidgets/${FPW}.h\"\n")
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endforeach()
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# --------------------------------------------------------------------
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# Close off the files with the proper C++
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file(APPEND ${AllFilterParameterWidgetsHeaderFile} "\n#endif\n")
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file(APPEND ${RegisterKnownFilterParameterWidgetsFile} "}\n")
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cmpReplaceFileIfDifferent(OLD_FILE_PATH ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/FilterParameterWidgets.h
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NEW_FILE_PATH ${AllFilterParameterWidgetsHeaderFile} )
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cmpReplaceFileIfDifferent(OLD_FILE_PATH ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/RegisterKnownFilterParameterWidgets.cpp
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NEW_FILE_PATH ${RegisterKnownFilterParameterWidgetsFile} )
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set(AllFilterParameterWidgetsHeaderFile ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/FilterParameterWidgets.h)
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set(RegisterKnownFilterParameterWidgetsFile ${${PLUGIN_NAME}_BINARY_DIR}/FilterParameterWidgets/RegisterKnownFilterParameterWidgets.cpp)
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cmp_IDE_SOURCE_PROPERTIES( "${PLUGIN_NAME}/FilterParameterWidgets" "${${PLUGIN_NAME}_ParameterWidgets_HDRS}" "${${PLUGIN_NAME}_ParameterWidgets_SRCS}" "0")
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cmp_IDE_GENERATED_PROPERTIES("${PLUGIN_NAME}/FilterParameterWidgets/UI_Files" "${${PLUGIN_NAME}_ParameterWidgets_UIS}" "")
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# --------------------------------------------------------------------
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# and finally this will run moc:
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#QT4_WRAP_CPP( ${PLUGIN_NAME}_ParameterWidgets_Generated_MOC_SRCS ${${PLUGIN_NAME}_ParameterWidgets_HDRS} )
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# These generated moc files will be #include in the FilterWidget source file that
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# are generated so we need to tell the build system to NOT compile these files
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set_source_files_properties( ${${PLUGIN_NAME}_ParameterWidgets_Generated_MOC_SRCS} PROPERTIES HEADER_FILE_ONLY TRUE)
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# -- Run MOC and UIC on the necessary files
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# QT4_ADD_RESOURCES( ${PLUGIN_NAME}_Generated_RC_SRCS "${DREAM3DProj_SOURCE_DIR}/Documentation/Filters/Generated_FilterDocs.qrc" )
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# --------------------------------------------------------------------
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# Continue on with our Qt4 section
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QT4_WRAP_UI( ${PLUGIN_NAME}_ParameterWidgets_Generated_UI_HDRS ${${PLUGIN_NAME}_ParameterWidgets_UIS} )
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# --------------------------------------------------------------------
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#-- Put the Qt generated files into their own group for IDEs
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cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Moc" "" "${${PLUGIN_NAME}_ParameterWidgets_Generated_MOC_SRCS}" "0")
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cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Uic" "${${PLUGIN_NAME}_ParameterWidgets_Generated_UI_HDRS}" "" "0")
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#cmp_IDE_SOURCE_PROPERTIES( "Generated/Qt_Qrc" "${${PLUGIN_NAME}_Generated_RC_SRCS}" "" "0")
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