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Initial public release
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wlenthe committed Oct 16, 2019
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1 change: 1 addition & 0 deletions .gitignore
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wiki/
199 changes: 199 additions & 0 deletions 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 : [email protected] #
# 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
74 changes: 74 additions & 0 deletions 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
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