Mercurial > hg > minc-tools

changeset 2592:b25a2deca01c

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small bug fixes
author Vladimir Fonov <vladimir.fonov@gmail.com>
date Wed, 18 Jan 2012 16:52:13 -0500 (2012-01-18)
parents 7980090d445e
children 6c85a80d4692
files CMakeLists.txt UseMINC2.cmake.in cmake-modules/FindBISON.cmake cmake-modules/FindFLEX.cmake cmake-modules/FindMINC.cmake
diffstat 5 files changed, 2 insertions(+), 326 deletions(-) [+]
line wrap: on
line diff
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,7 +8,7 @@
 
 PROJECT(minc2)
 
-#SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules")
+SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake-modules")
 ENABLE_TESTING()
 INCLUDE(CTest)
 
--- a/UseMINC2.cmake.in
+++ b/UseMINC2.cmake.in
@@ -11,7 +11,7 @@
   INCLUDE_DIRECTORIES( ${HDF5_INCLUDE_DIR} )
   
   SET(MINC2 "1")
-  ADD_DEFINITIONS( -DMINC2 )
+  ADD_DEFINITIONS( -DMINC2=1 )
   
   SET(MINC_LIBRARIES volume_io2 minc2 netcdf hdf5 z)
 else(HAVE_MINC2)
deleted file mode 100644
--- a/cmake-modules/FindBISON.cmake
+++ /dev/null
@@ -1,162 +0,0 @@
-# - Find bison executable and provides macros to generate custom build rules
-# The module defined the following variables:
-#  BISON_EXECUTABLE - path to the bison program
-#  BISON_VERSION - version of bison
-#  BISON_FOUND - true if the program was found
-# If bison is found, the module defines the macros:
-#  BISON_TARGET(<Name> <YaccInput> <CodeOutput> [VERBOSE <file>]
-#              [COMPILE_FLAGS <string>])
-# which will create  a custom rule to generate  a parser. <YaccInput> is
-# the path to  a yacc file. <CodeOutput> is the name  of the source file
-# generated by bison.  A header file is also  be generated, and contains
-# the  token  list.  If  COMPILE_FLAGS  option is  specified,  the  next
-# parameter is  added in the bison  command line.  if  VERBOSE option is
-# specified, <file> is created  and contains verbose descriptions of the
-# grammar and parser. The macro defines a set of variables:
-#  BISON_${Name}_DEFINED - true is the macro ran successfully
-#  BISON_${Name}_INPUT - The input source file, an alias for <YaccInput>
-#  BISON_${Name}_OUTPUT_SOURCE - The source file generated by bison
-#  BISON_${Name}_OUTPUT_HEADER - The header file generated by bison
-#  BISON_${Name}_OUTPUTS - The sources files generated by bison
-#  BISON_${Name}_COMPILE_FLAGS - Options used in the bison command line
-#
-# Example:
-# FIND_PACKAGE(BISON)
-# BISON_TARGET(MyParser parser.y ${PROJECT_BINARY_DIR}/parser.cpp)
-# ADD_EXECUTABLE(Foo main.cpp ${BISON_MyParser_OUTPUTS})
-#
-
-# Copyright (c) 2006, Tristan Carel
-# All rights reserved.
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-#     * Redistributions of source code must retain the above copyright
-#       notice, this list of conditions and the following disclaimer.
-#     * Redistributions in binary form must reproduce the above copyright
-#       notice, this list of conditions and the following disclaimer in the
-#       documentation and/or other materials provided with the distribution.
-#     * Neither the name of the University of California, Berkeley nor the
-#       names of its contributors may be used to endorse or promote products
-#       derived from this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY
-# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE REGENTS AND CONTRIBUTORS BE LIABLE FOR ANY
-# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-# $Id: FindBISON.cmake,v 1.1 2007-10-16 23:21:42 rotor Exp $
-
-SET(BISON_FOUND FALSE)
-
-FIND_PROGRAM(BISON_EXECUTABLE bison DOC "path to the bison executable")
-MARK_AS_ADVANCED(BISON_EXECUTABLE)
-
-IF(BISON_EXECUTABLE)
-  SET(BISON_FOUND TRUE)
-
-  EXECUTE_PROCESS(COMMAND ${BISON_EXECUTABLE} --version
-    OUTPUT_VARIABLE BISON_version_output
-    ERROR_VARIABLE BISON_version_error
-    RESULT_VARIABLE BISON_version_result
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-  IF(NOT ${BISON_version_result} EQUAL 0)
-    MESSAGE(SEND_ERROR "Command \"${BISON_EXECUTABLE} --version\" failed with output:\n${BISON_version_error}")
-  ELSE(NOT ${BISON_version_result} EQUAL 0)
-    STRING(REGEX REPLACE "^bison \\(GNU Bison\\) ([^\n]+)\n.*" "\\1"
-      BISON_VERSION "${BISON_version_output}")
-  ENDIF(NOT ${BISON_version_result} EQUAL 0)
-
-  # internal macro
-  MACRO(BISON_TARGET_option_verbose Name BisonOutput filename)
-    LIST(APPEND BISON_TARGET_cmdopt "--verbose")
-    GET_FILENAME_COMPONENT(BISON_TARGET_output_path "${BisonOutput}" PATH)
-    GET_FILENAME_COMPONENT(BISON_TARGET_output_name "${BisonOutput}" NAME_WE)
-    ADD_CUSTOM_COMMAND(OUTPUT ${filename}
-      COMMAND ${CMAKE_COMMAND} -E copy
-      "${BISON_TARGET_output_path}/${BISON_TARGET_output_name}.output"
-      "${filename}"
-      DEPENDS
-      "${BISON_TARGET_output_path}/${BISON_TARGET_output_name}.output"
-      COMMENT "[BISON][${Name}] Copying bison verbose table to ${filename}"
-      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
-    SET(BISON_${Name}_VERBOSE_FILE ${filename})
-    LIST(APPEND BISON_TARGET_extraoutputs
-      "${BISON_TARGET_output_path}/${BISON_TARGET_output_name}.output")
-  ENDMACRO(BISON_TARGET_option_verbose)
-
-  # internal macro
-  MACRO(BISON_TARGET_option_extraopts Options)
-    SET(BISON_TARGET_extraopts "${Options}")
-    SEPARATE_ARGUMENTS(BISON_TARGET_extraopts)
-    LIST(APPEND BISON_TARGET_cmdopt ${BISON_TARGET_extraopts})
-  ENDMACRO(BISON_TARGET_option_extraopts)
-
-  MACRO(BISON_TARGET Name BisonInput BisonOutput)
-    SET(BISON_TARGET_output_header "")
-    SET(BISON_TARGET_command_opt "")
-    SET(BISON_TARGET_outputs "${BisonOutput}")
-    IF(NOT ${ARGC} EQUAL 3 AND NOT ${ARGC} EQUAL 5 AND NOT ${ARGC} EQUAL 7)
-      MESSAGE(SEND_ERROR "Usage")
-    ELSE(NOT ${ARGC} EQUAL 3 AND NOT ${ARGC} EQUAL 5 AND NOT ${ARGC} EQUAL 7)
-      # Parsing parameters
-      IF(${ARGC} GREATER 5 OR ${ARGC} EQUAL 5)
-	IF("${ARGV3}" STREQUAL "VERBOSE")
-	  BISON_TARGET_option_verbose(${Name} ${BisonOutput} "${ARGV4}")
-	ENDIF("${ARGV3}" STREQUAL "VERBOSE")
-	IF("${ARGV3}" STREQUAL "COMPILE_FLAGS")
-	  BISON_TARGET_option_extraopts("${ARGV4}")
-	ENDIF("${ARGV3}" STREQUAL "COMPILE_FLAGS")
-      ENDIF(${ARGC} GREATER 5 OR ${ARGC} EQUAL 5)
-      IF(${ARGC} EQUAL 7)
-	IF("${ARGV5}" STREQUAL "VERBOSE")
-	  BISON_TARGET_option_verbose(${Name} ${BisonOutput} "${ARGV6}")
-	ENDIF("${ARGV5}" STREQUAL "VERBOSE")
-	IF("${ARGV5}" STREQUAL "COMPILE_FLAGS")
-	  BISON_TARGET_option_extraopts("${ARGV6}")
-	ENDIF("${ARGV5}" STREQUAL "COMPILE_FLAGS")
-      ENDIF(${ARGC} EQUAL 7)
-
-      # Header's name generated by bison (see option -d)
-      LIST(APPEND BISON_TARGET_cmdopt "-d")
-      STRING(REGEX REPLACE "^(.*)\\.c([^.]*)$" "\\1.h\\2"
-	BISON_${Name}_OUTPUT_HEADER "${ARGV2}")
-      LIST(APPEND BISON_TARGET_outputs "${BISON_${Name}_OUTPUT_HEADER}")
-
-      ADD_CUSTOM_COMMAND(OUTPUT ${BISON_TARGET_outputs}
-	${BISON_TARGET_extraoutputs}
-	COMMAND ${BISON_EXECUTABLE} ${BISON_TARGET_cmdopt} -o ${ARGV2} ${ARGV1}
-	DEPENDS ${ARGV1}
-	COMMENT "[BISON][${Name}] Building parser with bison ${BISON_VERSION}"
-	WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
-
-      # define target variables
-      SET(BISON_${Name}_DEFINED TRUE)
-      SET(BISON_${Name}_INPUT ${ARGV1})
-      SET(BISON_${Name}_OUTPUTS ${BISON_TARGET_outputs})
-      SET(BISON_${Name}_COMPILE_FLAGS ${BISON_TARGET_cmdopt})
-      SET(BISON_${Name}_OUTPUT_SOURCE "${BisonOutput}")
-
-    ENDIF(NOT ${ARGC} EQUAL 3 AND NOT ${ARGC} EQUAL 5 AND NOT ${ARGC} EQUAL 7)
-  ENDMACRO(BISON_TARGET)
-
-ENDIF(BISON_EXECUTABLE)
-
-
-IF(NOT BISON_FOUND)
-  IF(NOT BISON_FIND_QUIETLY)
-    MESSAGE(STATUS "BISON was not found.")
-  ELSE(NOT BISON_FIND_QUIETLY)
-    IF(BISON_FIND_REQUIRED)
-      MESSAGE(FATAL_ERROR "BISON was not found.")
-    ENDIF(BISON_FIND_REQUIRED)
-  ENDIF(NOT BISON_FIND_QUIETLY)
-ENDIF(NOT BISON_FOUND)
-
-# FindBISON.cmake ends here
deleted file mode 100644
--- a/cmake-modules/FindFLEX.cmake
+++ /dev/null
@@ -1,134 +0,0 @@
-# - Find flex executable and provides a macro to generate custom build rules
-# The module defines the following variables:
-#  FLEX_FOUND - true is flex executable is found
-#  FLEX_VERSION - the version of flex
-# If flex is found on the system, the module provides the macro:
-#  FLEX_TARGET(Name FlexInput FlexOutput [COMPILE_FLAGS <string>])
-# which creates a custom command  to generate the <FlexOutput> file from
-# the <FlexInput> file.  If  COMPILE_FLAGS option is specified, the next
-# parameter is added to the flex  command line. Name is an alias used to
-# get  details of  this custom  command.  Indeed the  macro defines  the
-# following variables:
-#  FLEX_${Name}_DEFINED - true is the macro ran successfully
-#  FLEX_${Name}_OUTPUTS - the source file generated by the custom rule, an
-#  alias for FlexOutput
-#  FLEX_${Name}_INPUT - the flex source file, an alias for ${FlexInput}
-#
-# Flex scanners oftenly use tokens  defined by Bison: the code generated
-# by Flex  depends of the header  generated by Bison.   This module also
-# defines a macro:
-#  ADD_FLEX_BISON_DEPENDENCY(FlexTarget BisonTarget)
-# which  adds the  required dependency  between a  scanner and  a parser
-# where  <FlexTarget>  and <BisonTarget>  are  the  first parameters  of
-# respectively FLEX_TARGET and BISON_TARGET macros.
-#
-# Example:
-#  FIND_PACKAGE(BISON)
-#  FIND_PACKAGE(FLEX)
-#  BISON_TARGET(MyParser parser.y ${PROJECT_BINARY_DIR}/parser.cpp
-#  FLEX_TARGET(MyScanner lexer.l ${PROJECT_BINARY_DIR}/lexer.cpp)
-#  ADD_FLEX_BISON_DEPENDENCY(MyScanner MyParser)
-#
-
-# Copyright (c) 2006, Tristan Carel
-# All rights reserved.
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-#     * Redistributions of source code must retain the above copyright
-#       notice, this list of conditions and the following disclaimer.
-#     * Redistributions in binary form must reproduce the above copyright
-#       notice, this list of conditions and the following disclaimer in the
-#       documentation and/or other materials provided with the distribution.
-#     * Neither the name of the University of California, Berkeley nor the
-#       names of its contributors may be used to endorse or promote products
-#       derived from this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY
-# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE REGENTS AND CONTRIBUTORS BE LIABLE FOR ANY
-# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-# $Id: FindFLEX.cmake,v 1.1 2007-10-16 23:21:42 rotor Exp $
-
-SET(FLEX_FOUND FALSE)
-
-FIND_PROGRAM(FLEX_EXECUTABLE flex DOC "path to the flex executable")
-MARK_AS_ADVANCED(FLEX_EXECUTABLE)
-
-FIND_LIBRARY(FL_LIBRARY NAMES fl
-  PATHS /usr/lib DOC "path to the fl library")
-SET(FLEX_LIBRARIES ${FL_LIBRARY})
-
-IF(FLEX_EXECUTABLE)
-  SET(FLEX_FOUND TRUE)
-
-  EXECUTE_PROCESS(COMMAND ${FLEX_EXECUTABLE} --version
-    OUTPUT_VARIABLE FLEX_version_output
-    ERROR_VARIABLE FLEX_version_error
-    RESULT_VARIABLE FLEX_version_result
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-  IF(NOT ${FLEX_version_result} EQUAL 0)
-    MESSAGE(SEND_ERROR "Command \"${FLEX_EXECUTABLE} --version\" failed with output:\n${FLEX_version_error}")
-  ELSE(NOT ${FLEX_version_result} EQUAL 0)
-    STRING(REGEX REPLACE "^flex (.*)$" "\\1"
-      FLEX_VERSION "${FLEX_version_output}")
-  ENDIF(NOT ${FLEX_version_result} EQUAL 0)
-
-  MACRO(FLEX_TARGET Name Input Output)
-    SET(FLEX_TARGET_usage "FLEX_TARGET(<Name> <Input> <Output> [COMPILE_FLAGS <string>]")
-    IF(${ARGC} GREATER 3)
-      IF(${ARGC} EQUAL 5)
-	IF("${ARGV3}" STREQUAL "COMPILE_FLAGS")
-	  SET(FLEX_EXECUTABLE_opts  "${ARGV4}")
-	  SEPARATE_ARGUMENTS(FLEX_EXECUTABLE_opts)
-	ELSE("${ARGV3}" STREQUAL "COMPILE_FLAGS")
-	  MESSAGE(SEND_ERROR ${FLEX_TARGET_usage})
-	ENDIF("${ARGV3}" STREQUAL "COMPILE_FLAGS")
-      ELSE(${ARGC} EQUAL 5)
-	MESSAGE(SEND_ERROR ${FLEX_TARGET_usage})
-      ENDIF(${ARGC} EQUAL 5)
-    ENDIF(${ARGC} GREATER 3)
-    ADD_CUSTOM_COMMAND(OUTPUT ${Output}
-      COMMAND ${FLEX_EXECUTABLE} ${FLEX_EXECUTABLE_opts} -o${Output} ${Input}
-      DEPENDS ${Input}
-      COMMENT "[FLEX][${Name}] Building scanner with flex ${FLEX_VERSION}"
-      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
-
-    SET(FLEX_${Name}_DEFINED TRUE)
-    SET(FLEX_${Name}_OUTPUTS ${Output})
-    SET(FLEX_${Name}_INPUT ${Input})
-    SET(FLEX_${Name}_COMPILE_FLAGS ${FLEX_EXECUTABLE_opts})
-  ENDMACRO(FLEX_TARGET)
-
-  MACRO(ADD_FLEX_BISON_DEPENDENCY FlexTarget BisonTarget)
-    IF(NOT FLEX_${FlexTarget}_TARGET)
-      MESSAGE(SEND_ERROR "Flex target `${FlexTarget}' does not exists.")
-    ENDIF(NOT FLEX_${FlexTarget}_TARGET)
-    IF(NOT BISON_${BisonTarget}_TARGET)
-      MESSAGE(SEND_ERROR "Bison target `${BisonTarget}' does not exists.")
-    ENDIF(NOT BISON_${BisonTarget}_TARGET)
-
-    SET_SOURCE_FILES_PROPERTIES(${FLEX_${FlexTarget}_OUTPUT}
-      PROPERTIES OBJECT_DEPENDS ${BISON_${BisonTarget}_OUTPUT_HEADER})
-  ENDMACRO(ADD_FLEX_BISON_DEPENDENCY)
-
-ENDIF(FLEX_EXECUTABLE)
-
-IF(NOT FLEX_FOUND)
-  IF(NOT FLEX_FIND_QUIETLY)
-    MESSAGE(STATUS "FLEX was not found.")
-  ELSE(NOT FLEX_FIND_QUIETLY)
-    IF(FLEX_FIND_REQUIRED)
-      MESSAGE(FATAL_ERROR "FLEX was not found.")
-    ENDIF(FLEX_FIND_REQUIRED)
-  ENDIF(NOT FLEX_FIND_QUIETLY)
-ENDIF(NOT FLEX_FOUND)
-
-# FindFLEX.cmake ends here
deleted file mode 100644
--- a/cmake-modules/FindMINC.cmake
+++ /dev/null
@@ -1,28 +0,0 @@
-# FindMINC.cmake module
-
-FIND_PACKAGE(NETCDF)
-FIND_PACKAGE(HDF5)
-
-
-FIND_PATH(MINC_INCLUDE_DIR minc2.h /usr/include /usr/local/include /usr/local/bic/include)
-FIND_LIBRARY(MINC_LIBRARY NAMES libminc2 PATHS /usr/lib /usr/local/lib /usr/local/bic/lib)
-
-
-IF (MINC_INCLUDE_DIR AND MINC_LIBRARY)
-   SET(MINC_FOUND TRUE)
-   
-   LIST(APPEND MINC_INCLUDE_DIR ${NETCDF_INCLUDE_DIR} ${HDF5_INCLUDE_DIR})
-   LIST(APPEND MINC_LIBRARY ${NETCDF_LIBRARY} ${HDF5_LIBRARY})
-   
-ENDIF (MINC_INCLUDE_DIR AND MINC_LIBRARY)
-
-
-IF (MINC_FOUND)
-   IF (NOT Minc_FIND_QUIETLY)
-      MESSAGE(STATUS "Found MINC: ${MINC_LIBRARY}")
-   ENDIF (NOT Minc_FIND_QUIETLY)
-ELSE (MINC_FOUND)
-   IF (Minc_FIND_REQUIRED)
-      MESSAGE(FATAL_ERROR "Cound not find MINC")
-   ENDIF (Minc_FIND_REQUIRED)
-ENDIF (MINC_FOUND)