Initial public release

.gitignore

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+wiki/

CMakeLists.txt

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+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+#                                                                     #
+# Copyright (c) 2019, De Graef Group, Carnegie Mellon University      #
+# All rights reserved.                                                #
+#                                                                     #
+# Author: William C. Lenthe                                           #
+#                                                                     #
+# This package is free software; you can redistribute it and/or       #
+# modify it under the terms of the GNU General Public License as      #
+# published by the Free Software Foundation; either version 2 of the  #
+# License, or (at your option) any later version.                     #
+#                                                                     #
+# This program is distributed in the hope that it will be useful,     #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of      #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the       #
+# GNU General Public License for more details.                        #
+#                                                                     #
+# You should have received a copy of the GNU General Public License   #
+# along with this program; if not, check the Free Software Foundation #
+# website: <https://www.gnu.org/licenses/old-licenses/gpl-2.0.html>   #
+#                                                                     #
+#                                                                     #
+# Interested in a commercial license? Contact:                        #
+#                                                                     #
+# Center for Technology Transfer and Enterprise Creation              #
+# 4615 Forbes Avenue, Suite 302                                       #
+# Pittsburgh, PA 15213                                                #
+#                                                                     #
+# phone. : 412.268.7393                                               #
+# email  : innovation@cmu.edu                                         #
+# website: https://www.cmu.edu/cttec/                                 #
+#                                                                     #
+# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
+
+project(EMSphInx)
+# cmake_minimum_required(VERSION 3.12) # 3.12 for the parallel option for cmake --build
+cmake_minimum_required(VERSION 3.14) # for FetchContent_MakeAvailable (could fall back to 3.12 with alternate pattern but it is now deprecated)
+
+set(CMAKE_CXX_STANDARD 11) # apparently you still need to explicitly request 2011 conformance in 2019...
+
+################################
+#       package options        #
+################################
+
+option(EMSPHINX_BUILD_SHARED "should shared or static libraries be preferred"                                           OFF)
+option(EMSPHINX_FFTW_F       "enable float templates by linking against fftw_f"                                         OFF)
+option(EMSPHINX_FFTW_D       "enable double templates by linking against fftw"                                          ON )
+option(EMSPHINX_FFTW_L       "enable long double templates by linking against fftw_l"                                   OFF)
+option(EMSPHINX_BUILD_FFTW   "fetch and build FFTW instead of using an existing system installation"                    ON )
+option(EMSPHINX_FFTW_SIMD    "should SSE/SSE2/AVX instructions be enabled for fftw build (faster run, slower compiler)" ON )
+option(EMSPHINX_FFTW_AVX2    "should AVX2 instructions be enabled for fftw build (not supported on all processors)    " OFF)
+option(EMSPHINX_BUILD_HDF5   "fetch and build HDF5 instead of using an existing system installation"               ON )
+option(EMSPHINX_BUILD_TESTS  "should test programs (/test/*) be built"                                             ON )
+option(EMSPHINX_BUILD_GUIS   "should the GUI programs be built (experimental)"                                     OFF)
+if(EMSPHINX_BUILD_GUIS)
+	option(EMSPHINX_BUILD_wxWidgets "should wxWidgets be built from source" ON)
+endif()
+
+################################
+#     multicore compiling      #
+################################
+
+include(ProcessorCount)
+ProcessorCount(NCORES)
+if(NOT NCORES EQUAL 0)
+	set(CMAKE_BUILD_PARALLEL_LEVEL NCORES)
+endif()
+
+################################
+# compiler specific adjustment #
+################################
+
+# visual studio
+if(MSVC)
+	add_definitions(-D_SCL_SECURE_NO_WARNINGS) # these warnings are annoying and not critical
+	add_definitions(-D_CRT_SECURE_NO_WARNINGS) # these warnings are annoying and not critical
+	# add_compile_options($<$<CXX_COMPILER_ID:MSVC>:/MP>) # use multi core compiling
+	add_compile_options(/MP) # the generator expression version breaks wxWidgets
+endif()
+
+# gcc
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+	set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-pthread" )# std::thread requires pthreads on gcc
+endif()
+
+# non clang osx
+# if(APPLE AND NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang") # only for gcc, not clang
+	# set(CMAKE_INSTALL_RPATH_USE_LINK_PATH OFF) # there seems to be an rpath issue on apple + GCC
+# endif()
+set(MACOSX_RPATH ON) # still haven't fully resolved this...
+
+################################
+#   dynamic library copying    #
+################################
+
+# get prefix/extension for built libraries
+if(EMSPHINX_BUILD_SHARED)
+	set(LIB_PRE ${CMAKE_SHARED_LIBRARY_PREFIX})
+	set(LIB_EXT ${CMAKE_SHARED_LIBRARY_SUFFIX})
+else()
+	set(LIB_PRE ${CMAKE_STATIC_LIBRARY_PREFIX})
+	set(LIB_EXT ${CMAKE_STATIC_LIBRARY_SUFFIX})
+endif()
+
+# determine name of files to link against (windows makes .dll for runtime but also keeps .lib for linking) and copy into build directory
+if(MSVC)
+	set(LNK_EXT ${CMAKE_STATIC_LIBRARY_SUFFIX}) # link against the .lib
+	set(CPY_DIR bin) # location to copy shared libraries from
+else()
+	set(LNK_EXT ${LIB_EXT}) # link against static or dynamic as appropriate
+	set(CPY_DIR lib) # location to copy shared libraries from
+endif()
+
+################################
+#        git versioning        #
+################################
+
+find_package(Git REQUIRED)
+execute_process( # get branch name
+	COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
+	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+	OUTPUT_VARIABLE EMSPHINX_GIT_BRANCH
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+execute_process( # get abbreviated hash
+	COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
+	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+	OUTPUT_VARIABLE EMSPHINX_GIT_HASH
+	OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+if("${EMSPHINX_GIT_BRANCH}" STREQUAL "")
+	message(FATAL_ERROR "failed to determine git branch)")
+endif()
+if("${EMSPHINX_GIT_HASH}" STREQUAL "")
+	message(FATAL_ERROR "failed to determine git hash)")
+endif()
+
+add_definitions("-DEMSPHINX_GIT_HASH=${EMSPHINX_GIT_HASH}")
+add_definitions("-DEMSPHINX_GIT_BRANCH=${EMSPHINX_GIT_BRANCH}")
+
+################################
+#         dependencies         #
+################################
+
+# fetch SHT file format content
+# this could be done with a git submodule but the user would have to call:
+#   git submodule update
+#   git clone --recursive
+# which is a bit annoying
+include(FetchContent)
+FetchContent_Declare(
+	SHTfile
+	GIT_REPOSITORY "https://github.com/EMsoft-org/SHTfile"
+	GIT_TAG        "cfd13df"
+	# GIT_TAG        "v3.1.2" # just get the most recent version for now
+	# GIT_PROGRESS   TRUE # its currently only 1 file, we probably don't need to print out progress
+)
+# set(FETCHCONTENT_QUIET NO) # again only 1 file
+FetchContent_MakeAvailable(SHTfile)
+FetchContent_GetProperties(SHTfile BINARY_DIR SHTfile_BINARY_DIR)
+include_directories(${SHTfile_BINARY_DIR})
+
+# compiled dependencies
+include(${CMAKE_CURRENT_LIST_DIR}/depends/FFTW.cmake) # build or find existing FFTW
+include(${CMAKE_CURRENT_LIST_DIR}/depends/HDF5.cmake) # build or find existing HDF5
+
+if(EMSPHINX_BUILD_GUIS)
+	include(${CMAKE_CURRENT_LIST_DIR}/depends/wxWidgets.cmake) # build or find existing HDF5
+endif()
+
+# png support, for now I've included these files directly due to download issues on some versions of cmake (if libcurl doesn't support https)
+set(BuildMiniZ OFF)
+if(BuildMiniZ)
+	set(MINIZ_VERSION "2.0.8")
+	ExternalProject_Add(
+		miniz PREFIX "miniz"
+		URL https://github.com/richgel999/miniz/releases/download/${MINIZ_VERSION}/miniz-${MINIZ_VERSION}.zip
+		URL_HASH MD5=0692c3f080267b24419ab67c1eefc881 # make sure the download wasn't corrupted (/ someone hasn't injected a different version)
+		CONFIGURE_COMMAND "" ${CMAKE_COMMAND} -E copy_directory ${CMAKE_BINARY_DIR}/miniz/src/miniz/ ${CMAKE_SOURCE_DIR}/include/miniz # copy everything (source + license are most critical)
+		BUILD_COMMAND "" INSTALL_COMMAND ""
+	)
+endif(BuildMiniZ)
+
+################################
+#     add actual components    #
+################################
+
+# include headers
+include_directories(${CMAKE_CURRENT_LIST_DIR}/include)
+include_directories(${CMAKE_CURRENT_LIST_DIR}/icons)
+
+# add test programs if needed
+if(EMSPHINX_BUILD_TESTS)
+	add_subdirectory(${CMAKE_CURRENT_LIST_DIR}/test ${CMAKE_BINARY_DIR}/test) # don't put in /cpp/test
+endif()
+
+# add actual programs
+include(${CMAKE_CURRENT_LIST_DIR}/programs/CMakeLists.txt) # include instead of add_subdirectory so we don't get a subfolder in the build

ReadMe.md

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+![EMSphInx Logo](icons/sphinx.png)
+
+# EMSphInx
+*EMSphInx* is a collection of modules and programs that can be used to index a variety of diffraction patterns, ranging from EBSD to TKD, ECP, and x-ray Laue patterns. EMSphInx is currently a public beta; please report bugs to the issue tracker. If you use these programs for research, consider citing the corresponding papers:
+
+* [EBSD Indexing](https://doi.org/10.1016/j.ultramic.2019.112841)
+* [Pseudo-symmetry Prediction](https://doi.org/10.1107/S1600576719011233)
+
+## Financial Support 
+The *EMSphInx* code was developed with support from an ONR Vannevar Bush Faculty Fellowship grant, N00014-­16-­1-­2821. The central indexing algorithm is covered by a provisional patent application.
+
+## Build Instructions
+Nightly builds will be available soon for a variety of operating systems
+
+*EMSphInx* requires [CMake 3.14 or higher](https://www.cmake.org/download) to build. All dependencies are downloaded and compiled as part of the build process by default. The easiest way to build a non-default version of *EMSphInx* is with the cmake gui or ccmake. If you are restricted to the command line and only need the default configuration you can build with the following sequence:
+
+Download the source
+
+> git clone https://github.com/EMsoft-org/EMSphInx
+
+Create a build directory and move into it
+
+> mkdir EMSphInxBuild
+
+> cd EMSphInxBuild
+
+Run cmake and build, if you would like to build the GUIs you can optionally set the GUI CMake flag (e.g. -DEMSPHINX_BUILD_GUIS=ON)
+
+> cmake ../EMSphInx
+
+> make -j
+
+FFTW can compile SIMD instructions on some platforms even if they are not available on the current hardware. If you encounter illegal instructions at runtime try compiling with SIMD disabled (-DEMSPHINX_FFTW_SIMD=OFF). AVX2 instructions are disabled by default but can be enabled with EMSPHINX_FFTW_AVX2.
+
+## Utility Program Overview
+
+1. IndexEBSD
+
+   index EBSD patterns on the command line with a namelist file
+
+2. MasterXcorr
+
+   compute spherical cross correlation between 2 spherical master patterns
+
+3. ShtWisdom
+
+   build FFTW wisdom on new systems (reduces initialization time on first execution of other programs)
+
+4. mp2sht
+
+   convert from EMsoft EBSD master patterns to the new SHT file format used by the indexing programs
+
+5. EMSphInxEBSD (only if EMSPHINX_BUILD_GUIS=ON)
+
+   graphical user interface to build namelist files for IndexEBSD and/or index patterns directly
+
+Help files for these programs are available as wiki pages on [github.com:EMsoft-org/EMSphInx/wiki]() or in the documentation folder of this repository.
+
+## New features in 0.1
+- Public Beta
+
+## What's coming in future versions
+- Additional diffraction modalities
+- Python bindings
+
+Feel free to request additional features using the repo's [issue tracker](https://github.com/EMsoft-org/EMSphInx/issues) (please be sure to tag your issue with the 'enhancement flag')
+
+## License ##
+
+*EMSphInx* source files are distributed under GNU General Public License v2.0 (GPL2), see the license.txt file for details.
+
+*EMSphInx* also includes several files from BSD licensed (3-clause) projects (please refer to the individual files for details):
+
+- include/miniz/miniz.c