Imported Upstream version 1.3.1

parent 766b60a3
language: cpp
compiler:
- gcc
- clang
before_install:
- sudo apt-get update
install:
- sudo apt-get install libboost-all-dev libhdf5-serial-dev h5utils doxygen
before_script:
- mkdir build
- cd build
- cmake ..
script: make && make check
......@@ -50,10 +50,10 @@ endif (WIN32)
#the flexible header. The micro number changes when there are small changes
#in the utility libraries, that don't affect the data format itself.
set(ISMRMRD_VERSION_MAJOR 1)
set(ISMRMRD_VERSION_MINOR 2)
set(ISMRMRD_VERSION_PATCH 3)
set(ISMRMRD_VERSION_MINOR 3)
set(ISMRMRD_VERSION_PATCH 1)
set(ISMRMRD_XML_SCHEMA_SHA1 "99a63f4e8cf08ffc268f5ee8b8c8b2a1edf69412")
set(ISMRMRD_XML_SCHEMA_SHA1 "9b899c6ad806bc2388c70461d6e5affe5cc6d750")
#Remove line breaks and white space that does not change the meaning of the schema
file(STRINGS ${CMAKE_SOURCE_DIR}/schema/ismrmrd.xsd SCHEMA_STRINGS) #Read all strings from file
......@@ -91,6 +91,19 @@ endif()
set(ISMRMRD_VERSION_STRING ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR}.${ISMRMRD_VERSION_PATCH})
set(ISMRMRD_SOVERSION ${ISMRMRD_VERSION_MAJOR}.${ISMRMRD_VERSION_MINOR})
# Find HDF5 for dataset support
find_package(HDF5 1.8 COMPONENTS C)
if (HDF5_FOUND)
set (ISMRMRD_DATASET_SUPPORT true)
set (ISMRMRD_DATASET_SOURCES libsrc/dataset.c libsrc/dataset.cpp)
set (ISMRMRD_DATASET_INCLUDE_DIR ${HDF5_C_INCLUDE_DIR})
set (ISMRMRD_DATASET_LIBRARIES ${HDF5_LIBRARIES})
else (HDF5_FOUND)
set (ISMRMRD_DATASET_SUPPORT false)
message (WARNING "HDF5 not found. Dataset and file support unavailable!")
endif (HDF5_FOUND)
# Generate the version.h header file
find_package(Git)
if (GIT_FOUND)
......@@ -111,43 +124,35 @@ install(FILES ${CMAKE_BINARY_DIR}/include/ismrmrd/version.h DESTINATION include/
# remember to add ${CMAKE_BINARY_DIR}/include to the include path
# --- VERSIONING (end) ----
# --- Main Library (begin) ----
# required packages for main library
find_package(HDF5 1.8 COMPONENTS C REQUIRED)
# --- Main Library (begin) ----
# in windows, install the HDF5 dependencies
if (WIN32)
if (ISMRMRD_INSTALL_DEPENDENCIES)
if ( HDF5_FOUND )
if(DEFINED ENV{HDF5_ROOT})
set(HDF5_BIN_DIR $ENV{HDF5_ROOT}/bin)
else (DEFINED ENV{HDF5_ROOT})
set(HDF5_BIN_DIR ${HDF5_C_INCLUDE_DIR}/../bin)
endif (DEFINED ENV{HDF5_ROOT})
message("Install hdf5 libraries from ${HDF5_BIN_DIR} ")
install( DIRECTORY ${HDF5_BIN_DIR} DESTINATION bin/.. FILES_MATCHING PATTERN "*.dll" )
endif (HDF5_FOUND)
endif (ISMRMRD_INSTALL_DEPENDENCIES)
endif (WIN32)
if (HDF5_FOUND AND WIN32 AND ISMRMRD_INSTALL_DEPENDENCIES)
if(DEFINED ENV{HDF5_ROOT})
set(HDF5_BIN_DIR $ENV{HDF5_ROOT}/bin)
else (DEFINED ENV{HDF5_ROOT})
set(HDF5_BIN_DIR ${HDF5_C_INCLUDE_DIR}/../bin)
endif (DEFINED ENV{HDF5_ROOT})
message("Install hdf5 libraries from ${HDF5_BIN_DIR} ")
install( DIRECTORY ${HDF5_BIN_DIR} DESTINATION bin/.. FILES_MATCHING PATTERN "*.dll" )
endif (HDF5_FOUND AND WIN32 AND ISMRMRD_INSTALL_DEPENDENCIES)
# include directories for main library
set(ISMRMRD_TARGET_INCLUDE_DIRS
include
${CMAKE_BINARY_DIR}/include
${HDF5_C_INCLUDE_DIR}
${ISMRMRD_DATASET_INCLUDE_DIR}
)
set(ISMRMRD_TARGET_SOURCES
libsrc/ismrmrd.c
libsrc/ismrmrd.cpp
libsrc/dataset.c
libsrc/dataset.cpp
libsrc/xml.cpp
libsrc/meta.cpp
${ISMRMRD_DATASET_SOURCES}
)
set(ISMRMRD_TARGET_LINK_LIBS ${HDF5_LIBRARIES})
set(ISMRMRD_TARGET_LINK_LIBS ${ISMRMRD_DATASET_LIBRARIES})
# optional handling of system-installed pugixml
if(USE_SYSTEM_PUGIXML)
......@@ -183,40 +188,35 @@ install(TARGETS ismrmrd DESTINATION lib)
install(DIRECTORY include/ismrmrd DESTINATION include)
# install the schema file
install(FILES schema/ismrmrd.xsd
DESTINATION share/ismrmrd/schema)
install(FILES schema/ismrmrd.xsd DESTINATION share/ismrmrd/schema)
# install the cmake modules
install(FILES
cmake/FindIsmrmrd.cmake
cmake/FindFFTW3.cmake
cmake/FindNumPy.cmake
DESTINATION
share/ismrmrd/cmake
)
install(FILES cmake/FindIsmrmrd.cmake cmake/FindFFTW3.cmake DESTINATION share/ismrmrd/cmake)
# --- Main Library (end) ----
# turn on testing
enable_testing()
# process subdirectories
add_subdirectory(doc)
add_subdirectory(examples/c)
add_subdirectory(utilities)
if (HDF5_FOUND)
add_subdirectory(examples/c)
endif (HDF5_FOUND)
# TODO: make this work on Windows
if (NOT WIN32)
add_subdirectory(tests)
endif (NOT WIN32)
# install the matlab api
install(DIRECTORY matlab DESTINATION share/ismrmrd)
# TODO build and install the python bindings
# Create package
string(TOLOWER ${PROJECT_NAME} PROJECT_NAME_LOWER)
include(${ISMRMRD_CMAKE_DIR}/ismrmrd_cpack.cmake)
if(CPACK_GENERATOR)
message(STATUS "Found CPack generators: ${CPACK_GENERATOR}")
configure_file("${ISMRMRD_CMAKE_DIR}/cpack_options.cmake.in"
${ISMRMRD_CPACK_CFG_FILE} @ONLY)
configure_file("${ISMRMRD_CMAKE_DIR}/cpack_options.cmake.in" ${ISMRMRD_CPACK_CFG_FILE} @ONLY)
set(CPACK_PROJECT_CONFIG_FILE ${ISMRMRD_CPACK_CFG_FILE})
include (CPack)
endif()
include(CPack)
endif(CPACK_GENERATOR)
[![Build Status](https://travis-ci.org/ismrmrd/ismrmrd.svg?branch=master)](https://travis-ci.org/ismrmrd/ismrmrd)
ISMRM Raw Data Format (ISMRMRD)
===============================
......@@ -12,7 +14,7 @@ To download the source code, clone the git archive:
API Documentation can be found at https://ismrmrd.github.io/api/.
You will need CMake, HDF5, Boost and optionally Doxygen and FFTW to build the C/C++ code. Please see the ISMRMRD documentation for specific installation instructions for [Linux](https://ismrmrd.github.io/index.html#linux-installation), [Mac OS X](https://ismrmrd.github.io/index.html#mac-osx-installation), and [Windows](https://ismrmrd.github.io/index.html#windows-installation).
You will need CMake, HDF5, and optionally Boost and FFTW to build the C/C++ code. To generate the API documentation you will need Doxygen. Please see the ISMRMRD documentation for specific installation instructions for [Linux](https://ismrmrd.github.io/index.html#linux-installation), [Mac OS X](https://ismrmrd.github.io/index.html#mac-osx-installation), and [Windows](https://ismrmrd.github.io/index.html#windows-installation).
Overview
---------
......@@ -26,3 +28,8 @@ A raw data set consist mainly of 2 sections:
1. Raw data section. This section contains all the acquired data in the experiment. Each data item is preceded by a C-struct with encoding numbers, etc. Following this data header is a channel header and data for each acquired channel. The raw data headers are defined in a C/C++ header file (ismrmrd.h). Please see the [C header](https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h) and the [documentation](https://ismrmrd.github.io/index.html#fixed-data-structures) for more information.
In addition to these sections, the ISMRMRD format also specifies an image header for storing reconstructed images and the accompanying C/C++ library provides a convenient way of writing such images into HDF5 files along with generic arrays for storing less well defined data structures, e.g. coil sensitivity maps or other calibration data.
Other Resources
---------------
- [Python implementation](https://www.github.com/ismrmrd/ismrmrd-python)
# - Find Java
# This module finds if Java is installed and determines where the
# include files and libraries are. This code sets the following
# variables:
#
# Java_JAVA_EXECUTABLE = the full path to the Java runtime
# Java_JAVAC_EXECUTABLE = the full path to the Java compiler
# Java_JAVAH_EXECUTABLE = the full path to the Java header generator
# Java_JAVADOC_EXECUTABLE = the full path to the Java documention generator
# Java_XJC_EXECUTABLE = the full path to the Java JAXB generator
# Java_JAR_EXECUTABLE = the full path to the Java archiver
# Java_VERSION_STRING = Version of the package found (java version), eg. 1.6.0_12
# Java_VERSION_MAJOR = The major version of the package found.
# Java_VERSION_MINOR = The minor version of the package found.
# Java_VERSION_PATCH = The patch version of the package found.
# Java_VERSION_TWEAK = The tweak version of the package found (after '_')
# Java_VERSION = This is set to: $major.$minor.$patch(.$tweak)
#
# The minimum required version of Java can be specified using the
# standard CMake syntax, e.g. find_package(Java 1.5)
#
# NOTE: ${Java_VERSION} and ${Java_VERSION_STRING} are not guaranteed to be
# identical. For example some java version may return:
# Java_VERSION_STRING = 1.5.0_17
# and
# Java_VERSION = 1.5.0.17
#
# another example is the Java OEM, with:
# Java_VERSION_STRING = 1.6.0-oem
# and
# Java_VERSION = 1.6.0
#
# For these components the following variables are set:
#
# Java_FOUND - TRUE if all components are found.
# Java_INCLUDE_DIRS - Full paths to all include dirs.
# Java_LIBRARIES - Full paths to all libraries.
# Java_<component>_FOUND - TRUE if <component> is found.
#
# Example Usages:
# find_package(Java)
# find_package(Java COMPONENTS Runtime)
# find_package(Java COMPONENTS Development)
#
#=============================================================================
# Copyright 2002-2009 Kitware, Inc.
# Copyright 2009-2011 Mathieu Malaterre <mathieu.malaterre@gmail.com>
#
# Distributed under the OSI-approved BSD License (the "License");
# see accompanying file Copyright.txt for details.
#
# This software is distributed WITHOUT ANY WARRANTY; without even the
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the License for more information.
#=============================================================================
# (To distribute this file outside of CMake, substitute the full
# License text for the above reference.)
# The HINTS option should only be used for values computed from the system.
set(_JAVA_HINTS
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\2.0;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.9;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.8;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.7;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.6;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.5;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/bin"
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/bin"
$ENV{JAVA_HOME}/bin
)
# Hard-coded guesses should still go in PATHS. This ensures that the user
# environment can always override hard guesses.
set(_JAVA_PATHS
/usr/lib/java/bin
/usr/share/java/bin
/usr/local/java/bin
/usr/local/java/share/bin
/usr/java/j2sdk1.4.2_04
/usr/lib/j2sdk1.4-sun/bin
/usr/java/j2sdk1.4.2_09/bin
/usr/lib/j2sdk1.5-sun/bin
/opt/sun-jdk-1.5.0.04/bin
)
find_program(Java_JAVA_EXECUTABLE
NAMES java
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
if(Java_JAVA_EXECUTABLE)
execute_process(COMMAND ${Java_JAVA_EXECUTABLE} -version
RESULT_VARIABLE res
OUTPUT_VARIABLE var
ERROR_VARIABLE var # sun-java output to stderr
OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_STRIP_TRAILING_WHITESPACE)
if( res )
if(${Java_FIND_REQUIRED})
message( FATAL_ERROR "Error executing java -version" )
else()
message( STATUS "Warning, could not run java --version")
endif()
else()
# extract major/minor version and patch level from "java -version" output
# Tested on linux using
# 1. Sun / Sun OEM
# 2. OpenJDK 1.6
# 3. GCJ 1.5
# 4. Kaffe 1.4.2
if(var MATCHES "java version \"[0-9]+\\.[0-9]+\\.[0-9_.]+.*\".*")
# This is most likely Sun / OpenJDK, or maybe GCJ-java compat layer
string( REGEX REPLACE ".* version \"([0-9]+\\.[0-9]+\\.[0-9_.]+.*)\".*"
"\\1" Java_VERSION_STRING "${var}" )
elseif(var MATCHES "java full version \"kaffe-[0-9]+\\.[0-9]+\\.[0-9_]+\".*")
# Kaffe style
string( REGEX REPLACE "java full version \"kaffe-([0-9]+\\.[0-9]+\\.[0-9_]+).*"
"\\1" Java_VERSION_STRING "${var}" )
else()
if(NOT Java_FIND_QUIETLY)
message(WARNING "regex not supported: ${var}. Please report")
endif()
endif()
string( REGEX REPLACE "([0-9]+).*" "\\1" Java_VERSION_MAJOR "${Java_VERSION_STRING}" )
string( REGEX REPLACE "[0-9]+\\.([0-9]+).*" "\\1" Java_VERSION_MINOR "${Java_VERSION_STRING}" )
string( REGEX REPLACE "[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" Java_VERSION_PATCH "${Java_VERSION_STRING}" )
# warning tweak version can be empty:
string( REGEX REPLACE "[0-9]+\\.[0-9]+\\.[0-9]+[_\\.]?([0-9]*).*$" "\\1" Java_VERSION_TWEAK "${Java_VERSION_STRING}" )
if( Java_VERSION_TWEAK STREQUAL "" ) # check case where tweak is not defined
set(Java_VERSION ${Java_VERSION_MAJOR}.${Java_VERSION_MINOR}.${Java_VERSION_PATCH})
else()
set(Java_VERSION ${Java_VERSION_MAJOR}.${Java_VERSION_MINOR}.${Java_VERSION_PATCH}.${Java_VERSION_TWEAK})
endif()
endif()
endif()
find_program(Java_JAR_EXECUTABLE
NAMES jar
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
find_program(Java_JAVAC_EXECUTABLE
NAMES javac
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
find_program(Java_XJC_EXECUTABLE
NAMES xjc
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
find_program(Java_JAVAH_EXECUTABLE
NAMES javah
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
find_program(Java_JAVADOC_EXECUTABLE
NAMES javadoc
HINTS ${_JAVA_HINTS}
PATHS ${_JAVA_PATHS}
)
include(FindPackageHandleStandardArgs)
if(Java_FIND_COMPONENTS)
foreach(component ${Java_FIND_COMPONENTS})
# User just want to execute some Java byte-compiled
if(component STREQUAL "Runtime")
find_package_handle_standard_args(Java
REQUIRED_VARS Java_JAVA_EXECUTABLE
VERSION_VAR Java_VERSION
)
elseif(component STREQUAL "Development")
find_package_handle_standard_args(Java
REQUIRED_VARS Java_JAVA_EXECUTABLE Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE
Java_XJC_EXECUTABLE Java_JAVAH_EXECUTABLE Java_JAVADOC_EXECUTABLE
VERSION_VAR Java_VERSION
)
else()
message(FATAL_ERROR "Comp: ${component} is not handled")
endif()
set(Java_${component}_FOUND TRUE)
endforeach()
else()
# Check for everything
find_package_handle_standard_args(Java
REQUIRED_VARS Java_JAVA_EXECUTABLE Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE
Java_XJC_EXECUTABLE Java_JAVAH_EXECUTABLE Java_JAVADOC_EXECUTABLE
VERSION_VAR Java_VERSION
)
endif()
mark_as_advanced(
Java_JAVA_EXECUTABLE
Java_JAR_EXECUTABLE
Java_JAVAC_EXECUTABLE
Java_XJC_EXECUTABLE
Java_JAVAH_EXECUTABLE
Java_JAVADOC_EXECUTABLE
)
# LEGACY
set(JAVA_RUNTIME ${Java_JAVA_EXECUTABLE})
set(JAVA_ARCHIVE ${Java_JAR_EXECUTABLE})
set(JAVA_COMPILE ${Java_JAVAC_EXECUTABLE})
# - Find the NumPy libraries
# This module finds if NumPy is installed, and sets the following variables
# indicating where it is.
#
# TODO: Update to provide the libraries and paths for linking npymath lib.
#
# NUMPY_FOUND - was NumPy found
# NUMPY_VERSION - the version of NumPy found as a string
# NUMPY_VERSION_MAJOR - the major version number of NumPy
# NUMPY_VERSION_MINOR - the minor version number of NumPy
# NUMPY_VERSION_PATCH - the patch version number of NumPy
# NUMPY_VERSION_DECIMAL - e.g. version 1.6.1 is 10601
# NUMPY_INCLUDE_DIRS - path to the NumPy include files
#============================================================================
# Copyright 2012 Continuum Analytics, Inc.
#
# MIT License
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to permit
# persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
#
#============================================================================
# Finding NumPy involves calling the Python interpreter
if(NumPy_FIND_REQUIRED)
find_package(PythonInterp REQUIRED)
else()
find_package(PythonInterp)
endif()
if(NOT PYTHONINTERP_FOUND)
set(NUMPY_FOUND FALSE)
return()
endif()
execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
"import numpy as n; print(n.__version__); print(n.get_include());"
RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
ERROR_VARIABLE _NUMPY_ERROR_VALUE
OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
if(NumPy_FIND_REQUIRED)
message(FATAL_ERROR
"NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
endif()
set(NUMPY_FOUND FALSE)
return()
endif()
# Convert the process output into a list
string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
list(GET _NUMPY_VALUES 0 NUMPY_VERSION)
list(GET _NUMPY_VALUES 1 NUMPY_INCLUDE_DIRS)
string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
if("${_VER_CHECK}" STREQUAL "")
# The output from Python was unexpected. Raise an error always
# here, because we found NumPy, but it appears to be corrupted somehow.
message(FATAL_ERROR
"Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
return()
endif()
# Make sure all directory separators are '/'
string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
# Get the major and minor version numbers
string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
math(EXPR NUMPY_VERSION_DECIMAL
"(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
find_package_message(NUMPY
"Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
"${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
set(NUMPY_FOUND TRUE)
......@@ -8,7 +8,7 @@ set(CPACK_PACKAGE_VERSION_MAJOR "@ISMRMRD_VERSION_MAJOR@")
set(CPACK_PACKAGE_VERSION_MINOR "@ISMRMRD_VERSION_MINOR@")
set(CPACK_PACKAGE_VERSION_PATCH "@ISMRMRD_VERSION_PATCH@")
set(CPACK_PACKAGE_NAME "@PROJECT_NAME@")
set(CPACK_PACKAGE_VENDOR "https://sourceforge.net/p/ismrmrd")
set(CPACK_PACKAGE_VENDOR "http://ismrmrd.github.io/")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "ISMRM Raw Data Format (ISMRMRD)")
set(CPACK_PACKAGE_INSTALL_DIRECTORY "@PROJECT_NAME_LOWER@")
set(CPACK_RESOURCE_FILE_LICENSE "@CMAKE_SOURCE_DIR@/LICENSE")
......@@ -18,19 +18,13 @@ set(CPACK_PACKAGE_MAINTAINER "Michael S. Hansen <michael.hansen@nih.gov>")
set(CPACK_PACKAGE_CONTACT "Michael S. Hansen <michael.hansen@nih.gov>")
# DEB specific
set(CPACK_DEBIAN_PACKAGE_DEPENDS "@DEBIAN_PACKAGE_DEPENDS@")
set(CPACK_DEBIAN_PACKAGE_SECTION "devel")
set(CPACK_DEBIAN_PACKAGE_PRIORITY "optional")
set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
set(CPACK_DEBIAN_PACKAGE_DESCRIPTION "Implementation of the ISMRMRD format.")
# RPM specific
# TODO: set(CPACK_RPM_PACKAGE_REQUIRES "@RPM_PACKAGE_DEPENDS@")
# TODO: set(CPACK_RPM_PACKAGE_DESCRIPTION "Implementation of the ISMRMRD format.")
# NSIS specific
set(CPACK_NSIS_HELP_LINK "http:\\\\\\\\ismrmrd.sourceforge.net")
set(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\\\\\ismrmrd.sourceforge.net")
set(CPACK_NSIS_HELP_LINK "http://ismrmrd.github.io")
set(CPACK_NSIS_URL_INFO_ABOUT "http://ismrmrd.github.io")
set(CPACK_NSIS_MODIFY_PATH ON)
set(CPACK_NSIS_DISPLAY_NAME "ismrmrd")
......
......@@ -8,31 +8,33 @@ if(UNIX)
if(EXISTS ${DPKG_PROGRAM})
list(APPEND CPACK_GENERATOR "DEB")
endif(EXISTS ${DPKG_PROGRAM})
# TODO: RPM
#find_program(RPMBUILD_PROGRAM rpmbuild)
#if(EXISTS ${RPMBUILD_PROGRAM})
# list(APPEND CPACK_GENERATOR "RPM")
#endif(EXISTS ${RPMBUILD_PROGRAM})
endif(UNIX)
if(WIN32)
# NSLS
list(APPEND CPACK_GENERATOR "NSIS")
endif(WIN32)
# Enable/Disable automatic search for dependencies:
set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON)
# TODO: list(APPEND CPACK_SOURCE_GENERATOR "TGZ")
# TODO: list(APPEND CPACK_SOURCE_GENERATOR "ZIP")
list(APPEND CPACK_SOURCE_IGNORE_FILES ";.git;.gitignore;todo.txt;_clang-format;build/")
# Enable/Disable component install for CPack generator DEB
set(CPACK_DEB_COMPONENT_INSTALL OFF)
set(CPACK_DEB_PACKAGE_COMPONENT OFF)
# set dependencies explicitly
include(InstallRequiredSystemLibraries)
set(DEBIAN_PACKAGE_DEPENDS "libhdf5-7, libfftw3-3, libboost-program-options-dev")
# TODO: set(RPM_PACKAGE_DEPENDS "hdf5-devel")
# Set dependencies explicitly
set(CPACK_DEBIAN_PACKAGE_DEPENDS "libhdf5-7, libfftw3-3, libboost-program-options-dev")
# where the package metadata are
# Where the package metadata are
set(ISMRMRD_CPACK_CFG_FILE "${PROJECT_BINARY_DIR}/cpack_options.cmake")
# Where the package to be installed
#set(CPACK_PACKAGE_INSTALL_DIRECTORY ${CMAKE_INSTALL_PREFIX})
# Where the package to be installed
set(CPACK_PACKAGING_INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX})
message("CPACK_PACKAGING_INSTALL_PREFIX: " ${CPACK_PACKAGING_INSTALL_PREFIX})
if(WIN32)
# NSLS
list(APPEND CPACK_GENERATOR "NSIS")
endif(WIN32)
list(APPEND CPACK_SOURCE_GENERATOR "TGZ")
list(APPEND CPACK_SOURCE_GENERATOR "ZIP")
list(APPEND CPACK_SOURCE_IGNORE_FILES ";.git;.gitignore;todo.txt;_clang-format;build/")
# set dependencies explicitly
include(InstallRequiredSystemLibraries)
include_directories(${CMAKE_SOURCE_DIR}/include)
cmake_minimum_required(VERSION 2.8)
project(ISMRMRD-C-EXAMPLE)
add_executable(ismrmrd_c_demo main.c)
target_link_libraries(ismrmrd_c_demo ismrmrd)
install(TARGETS ismrmrd_c_demo DESTINATION bin)
# if building this example as a standalone project
if(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
if(NOT DEFINED ENV{ISMRMRD_HOME})
message(FATAL_ERROR "ISMRMRD_HOME environment variable must be defined")
endif(NOT DEFINED ENV{ISMRMRD_HOME})
list(APPEND CMAKE_MODULE_PATH "$ENV{ISMRMRD_HOME}/share/ismrmrd/cmake")
find_package(Ismrmrd REQUIRED)
# otherwise, building it as part of ISMRMRD itself
else(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
set(ISMRMRD_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR}/include")
set(ISMRMRD_LIBRARIES ismrmrd)
endif(CMAKE_SOURCE_DIR STREQUAL CMAKE_CURRENT_SOURCE_DIR)
include_directories(${ISMRMRD_INCLUDE_DIR})
add_executable(ismrmrd_c_example main.c)
target_link_libraries(ismrmrd_c_example ${ISMRMRD_LIBRARIES})
install(TARGETS ismrmrd_c_example DESTINATION bin)
This is an example of a simple C project that is built on ISMRMRD.
Instructions for building:
1. Install ISMRMRD
1. Install ISMRMRD and CMake
2. Define the environment variable ISMRMRD_HOME,
e.g. ISMRMRD_HOME=/usr/local/ismrmrd
3. In a directory of your choosing:
mkdir buildcdemo
cmake ${ISMRMRD_HOME}/examples/c
make
./ismrmrd_c_demo
\ No newline at end of file
e.g. `export ISMRMRD_HOME=/usr/local/ismrmrd`
3. Compile the example:
mkdir build
cmake ..
make
./ismrmrd_c_example
......@@ -45,12 +45,9 @@ int main(void)
ismrmrd_write_header(&dataset1, xmlhdr);
/* Append some acquisitions */
/* must initialize an acquisition before you can use it */
ismrmrd_init_acquisition(&acq);
nacq_write = 5;
for (n=0; n < nacq_write; n++) {
/* must free an acquisition before you can reinitialize it */
ismrmrd_init_acquisition(&acq);
/* must initialize an acquisition before you can use it */
ismrmrd_init_acquisition(&acq);
acq.head.number_of_samples = 128;
acq.head.active_channels = 4;
......@@ -76,6 +73,7 @@ int main(void)
ismrmrd_set_flag(&(acq.head.flags), ISMRMRD_ACQ_LAST_IN_SLICE);
}
ismrmrd_append_acquisition(&dataset1, &acq);
ismrmrd_cleanup_acquisition(&acq);
}
/* Close the dataset */
......@@ -91,6 +89,7 @@ int main(void)
/* Read the header */
xmlstring = ismrmrd_read_header(&dataset2);
printf("Header: %s\n", xmlstring);
free(xmlstring);
/* Get the number of acquisitions */
nacq_read = ismrmrd_get_number_of_acquisitions(&dataset2);
......@@ -131,6 +130,8 @@ int main(void)
#else
printf("Data 3: %f\t 2: %f\n", creal(acq3.data[4]), creal(acq2.data[4]));
#endif
ismrmrd_cleanup_acquisition(&acq2);
ismrmrd_cleanup_acquisition(&acq3);
/* Create and store an image */
ismrmrd_init_image(&im);
......@@ -152,6 +153,7 @@ int main(void)
((float*)im.data)[loc] = 2.0;
}
ismrmrd_append_image(&dataset2, "testimages", &im);
ismrmrd_cleanup_image(&im);
numim = ismrmrd_get_number_of_images(&dataset2, "testimages");
printf("Number of images stored = %d\n", numim);
......@@ -160,6 +162,7 @@ int main(void)
ismrmrd_read_image(&dataset2, "testimages", 1, &im2);
printf("Image 1 attribute string = %s\n", im2.attribute_string);
printf("Image 1 at position 10 has value = %f\n", ((float*)im2.data)[10]);
ismrmrd_cleanup_image(&im2);
/* Create and store an array */
ismrmrd_init_ndarray(&arr);
......@@ -174,19 +177,14 @@ int main(void)
}
ismrmrd_append_array(&dataset2, "testarray", &arr);
printf("Number of arrays stored = %d\n", ismrmrd_get_number_of_arrays(&dataset2, "testarray"));
ismrmrd_cleanup_ndarray(&arr);
/* Read it back in */
ismrmrd_init_ndarray(&arr2);
ismrmrd_read_array(&dataset2, "testarray", 0, &arr2);
printf("Array 2 at position 10 has value = %f\n", ((float*)arr2.data)[10]);
ismrmrd_cleanup_ndarray(&arr2);
/* Clean up */
/* This frees the internal memory of the acquisitions */
ismrmrd_cleanup_acquisition(&acq);
ismrmrd_cleanup_acquisition(&acq2);
ismrmrd_cleanup_acquisition(&acq3);
free(xmlstring);
/* Close the dataset */
ismrmrd_close_dataset(&dataset2);
......
*.h5
\ No newline at end of file
ISMRM Raw Data Example files
-----------------------------
Please download the example data files from:
https://sourceforge.net/projects/ismrmrd/files/data/
On Linux command line, simply type:
wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5
wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5
wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5
Put Michaels spiral and gridder example back.
# coding: utf-8
import os
import ismrmrd
import numpy as np
import matplotlib.pyplot as plt
filename = 'testdata.h5'
if os.path.isfile(filename):
os.remove(filename)
# Create an empty ISMRMRD dataset
dset = ismrmrd.Dataset(filename, "dataset")
# Synthesize the object