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-rw-r--r--.gitignore5
-rw-r--r--Makefile.am2
-rw-r--r--build-aux/snippet/arg-nonnull.h (renamed from build-aux/arg-nonnull.h)2
-rw-r--r--build-aux/snippet/c++defs.h (renamed from build-aux/c++defs.h)2
-rw-r--r--build-aux/snippet/warn-on-use.h (renamed from build-aux/warn-on-use.h)2
-rw-r--r--doc/twin-calculator.odtbin22080 -> 21250 bytes
-rw-r--r--doc/twin-calculator.pdfbin63106 -> 48169 bytes
-rw-r--r--lib/Makefile.am188
-rw-r--r--lib/dummy.c2
-rw-r--r--lib/stddef.in.h19
-rw-r--r--lib/string.in.h72
-rw-r--r--lib/strndup.c5
-rw-r--r--lib/strnlen.c5
-rw-r--r--libcrystfel/Makefile.am2
-rw-r--r--libcrystfel/src/cell.c28
-rw-r--r--libcrystfel/src/dirax.c22
-rw-r--r--libcrystfel/src/hdf5-file.c29
-rw-r--r--libcrystfel/src/index.c52
-rw-r--r--libcrystfel/src/mosflm.c20
-rw-r--r--libcrystfel/src/render.c69
-rw-r--r--libcrystfel/src/statistics.c37
-rw-r--r--m4/00gnulib.m42
-rw-r--r--m4/extensions.m411
-rw-r--r--m4/gnulib-cache.m426
-rw-r--r--m4/gnulib-common.m4150
-rw-r--r--m4/gnulib-comp.m453
-rw-r--r--m4/gnulib-tool.m42
-rw-r--r--m4/include_next.m454
-rw-r--r--m4/lib-ignore.m42
-rw-r--r--m4/onceonly.m425
-rw-r--r--m4/stddef_h.m42
-rw-r--r--m4/string_h.m414
-rw-r--r--m4/strndup.m418
-rw-r--r--m4/strnlen.m412
-rw-r--r--m4/warn-on-use.m414
-rw-r--r--m4/wchar_t.m42
-rw-r--r--src/check_hkl.c17
-rw-r--r--src/cl-utils.c87
-rw-r--r--src/compare_hkl.c22
-rw-r--r--src/get_hkl.c22
-rw-r--r--src/hdfsee.c23
-rw-r--r--src/partial_sim.c30
-rw-r--r--src/partialator.c24
-rw-r--r--src/pattern_sim.c34
-rw-r--r--src/post-refinement.c24
-rw-r--r--src/powder_plot.c57
-rw-r--r--src/render_hkl.c58
47 files changed, 871 insertions, 477 deletions
diff --git a/.gitignore b/.gitignore
index fba1c515..30a8bdee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -46,4 +46,7 @@ build-aux/missing
build-aux/config.guess
build-aux/depcomp
build-aux/ltmain.sh
-/nbproject/private/ \ No newline at end of file
+/nbproject/private/
+lib/.libs/
+lib/dummy.lo
+lib/libgnu.la
diff --git a/Makefile.am b/Makefile.am
index 6460d8fb..f093d39a 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -28,7 +28,7 @@ endif
AM_CFLAGS = -Wall @MAIN_CFLAGS@
AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
AM_CPPFLAGS += -I$(top_srcdir)/lib
-LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
+LDADD = $(top_builddir)/lib/libgnu.la @IGNORE_UNUSED_LIBRARIES_CFLAGS@
LDADD += $(top_builddir)/libcrystfel/libcrystfel.la @MAIN_LIBS@
src_partial_sim_SOURCES = src/partial_sim.c
diff --git a/build-aux/arg-nonnull.h b/build-aux/snippet/arg-nonnull.h
index 6c2f1e82..3a9dd266 100644
--- a/build-aux/arg-nonnull.h
+++ b/build-aux/snippet/arg-nonnull.h
@@ -1,5 +1,5 @@
/* A C macro for declaring that specific arguments must not be NULL.
- Copyright (C) 2009-2011 Free Software Foundation, Inc.
+ Copyright (C) 2009-2012 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published
diff --git a/build-aux/c++defs.h b/build-aux/snippet/c++defs.h
index b6821a64..96da94b9 100644
--- a/build-aux/c++defs.h
+++ b/build-aux/snippet/c++defs.h
@@ -1,5 +1,5 @@
/* C++ compatible function declaration macros.
- Copyright (C) 2010-2011 Free Software Foundation, Inc.
+ Copyright (C) 2010-2012 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published
diff --git a/build-aux/warn-on-use.h b/build-aux/snippet/warn-on-use.h
index 2cdeec3e..d4cb94f3 100644
--- a/build-aux/warn-on-use.h
+++ b/build-aux/snippet/warn-on-use.h
@@ -1,5 +1,5 @@
/* A C macro for emitting warnings if a function is used.
- Copyright (C) 2010-2011 Free Software Foundation, Inc.
+ Copyright (C) 2010-2012 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published
diff --git a/doc/twin-calculator.odt b/doc/twin-calculator.odt
index 16e43495..108aac55 100644
--- a/doc/twin-calculator.odt
+++ b/doc/twin-calculator.odt
Binary files differ
diff --git a/doc/twin-calculator.pdf b/doc/twin-calculator.pdf
index 9f4735a7..1559fc96 100644
--- a/doc/twin-calculator.pdf
+++ b/doc/twin-calculator.pdf
Binary files differ
diff --git a/lib/Makefile.am b/lib/Makefile.am
index 835dc32b..238cd918 100644
--- a/lib/Makefile.am
+++ b/lib/Makefile.am
@@ -1,15 +1,27 @@
## DO NOT EDIT! GENERATED AUTOMATICALLY!
## Process this file with automake to produce Makefile.in.
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
#
-# This file is free software, distributed under the terms of the GNU
-# General Public License. As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file 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 3 of the License, or
+# (at your option) any later version.
+#
+# This file 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 file. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
# the same distribution terms as the rest of that program.
#
# Generated by gnulib-tool.
-# Reproduce by: gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-libtool --macro-prefix=gl lib-ignore strndup
+# Reproduce by: gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-conditional-dependencies --libtool --macro-prefix=gl lib-ignore strndup
AUTOMAKE_OPTIONS = 1.5 gnits
@@ -29,14 +41,16 @@ MAINTAINERCLEANFILES =
AM_CPPFLAGS =
AM_CFLAGS =
-noinst_LIBRARIES += libgnu.a
+noinst_LTLIBRARIES += libgnu.la
-libgnu_a_SOURCES =
-libgnu_a_LIBADD = $(gl_LIBOBJS)
-libgnu_a_DEPENDENCIES = $(gl_LIBOBJS)
-EXTRA_libgnu_a_SOURCES =
+libgnu_la_SOURCES =
+libgnu_la_LIBADD = $(gl_LTLIBOBJS)
+libgnu_la_DEPENDENCIES = $(gl_LTLIBOBJS)
+EXTRA_libgnu_la_SOURCES =
+libgnu_la_LDFLAGS = $(AM_LDFLAGS)
+libgnu_la_LDFLAGS += -no-undefined
-## begin gnulib module arg-nonnull
+## begin gnulib module snippet/arg-nonnull
# The BUILT_SOURCES created by this Makefile snippet are not used via #include
# statements but through direct file reference. Therefore this snippet must be
@@ -45,22 +59,23 @@ EXTRA_libgnu_a_SOURCES =
BUILT_SOURCES += arg-nonnull.h
# The arg-nonnull.h that gets inserted into generated .h files is the same as
-# build-aux/arg-nonnull.h, except that it has the copyright header cut off.
-arg-nonnull.h: $(top_srcdir)/build-aux/arg-nonnull.h
+# build-aux/snippet/arg-nonnull.h, except that it has the copyright header cut
+# off.
+arg-nonnull.h: $(top_srcdir)/build-aux/snippet/arg-nonnull.h
$(AM_V_GEN)rm -f $@-t $@ && \
sed -n -e '/GL_ARG_NONNULL/,$$p' \
- < $(top_srcdir)/build-aux/arg-nonnull.h \
+ < $(top_srcdir)/build-aux/snippet/arg-nonnull.h \
> $@-t && \
mv $@-t $@
MOSTLYCLEANFILES += arg-nonnull.h arg-nonnull.h-t
ARG_NONNULL_H=arg-nonnull.h
-EXTRA_DIST += $(top_srcdir)/build-aux/arg-nonnull.h
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/arg-nonnull.h
-## end gnulib module arg-nonnull
+## end gnulib module snippet/arg-nonnull
-## begin gnulib module c++defs
+## begin gnulib module snippet/c++defs
# The BUILT_SOURCES created by this Makefile snippet are not used via #include
# statements but through direct file reference. Therefore this snippet must be
@@ -69,20 +84,40 @@ EXTRA_DIST += $(top_srcdir)/build-aux/arg-nonnull.h
BUILT_SOURCES += c++defs.h
# The c++defs.h that gets inserted into generated .h files is the same as
-# build-aux/c++defs.h, except that it has the copyright header cut off.
-c++defs.h: $(top_srcdir)/build-aux/c++defs.h
+# build-aux/snippet/c++defs.h, except that it has the copyright header cut off.
+c++defs.h: $(top_srcdir)/build-aux/snippet/c++defs.h
$(AM_V_GEN)rm -f $@-t $@ && \
sed -n -e '/_GL_CXXDEFS/,$$p' \
- < $(top_srcdir)/build-aux/c++defs.h \
+ < $(top_srcdir)/build-aux/snippet/c++defs.h \
> $@-t && \
mv $@-t $@
MOSTLYCLEANFILES += c++defs.h c++defs.h-t
CXXDEFS_H=c++defs.h
-EXTRA_DIST += $(top_srcdir)/build-aux/c++defs.h
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/c++defs.h
+
+## end gnulib module snippet/c++defs
+
+## begin gnulib module snippet/warn-on-use
+
+BUILT_SOURCES += warn-on-use.h
+# The warn-on-use.h that gets inserted into generated .h files is the same as
+# build-aux/snippet/warn-on-use.h, except that it has the copyright header cut
+# off.
+warn-on-use.h: $(top_srcdir)/build-aux/snippet/warn-on-use.h
+ $(AM_V_GEN)rm -f $@-t $@ && \
+ sed -n -e '/^.ifndef/,$$p' \
+ < $(top_srcdir)/build-aux/snippet/warn-on-use.h \
+ > $@-t && \
+ mv $@-t $@
+MOSTLYCLEANFILES += warn-on-use.h warn-on-use.h-t
+
+WARN_ON_USE_H=warn-on-use.h
-## end gnulib module c++defs
+EXTRA_DIST += $(top_srcdir)/build-aux/snippet/warn-on-use.h
+
+## end gnulib module snippet/warn-on-use
## begin gnulib module stddef
@@ -94,7 +129,8 @@ if GL_GENERATE_STDDEF_H
stddef.h: stddef.in.h $(top_builddir)/config.status
$(AM_V_GEN)rm -f $@-t $@ && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
- sed -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
+ sed -e 's|@''GUARD_PREFIX''@|GL|g' \
+ -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|@PRAGMA_SYSTEM_HEADER@|g' \
-e 's|@''PRAGMA_COLUMNS''@|@PRAGMA_COLUMNS@|g' \
-e 's|@''NEXT_STDDEF_H''@|$(NEXT_STDDEF_H)|g' \
@@ -122,47 +158,52 @@ BUILT_SOURCES += string.h
string.h: string.in.h $(top_builddir)/config.status $(CXXDEFS_H) $(ARG_NONNULL_H) $(WARN_ON_USE_H)
$(AM_V_GEN)rm -f $@-t $@ && \
{ echo '/* DO NOT EDIT! GENERATED AUTOMATICALLY! */' && \
- sed -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
+ sed -e 's|@''GUARD_PREFIX''@|GL|g' \
+ -e 's|@''INCLUDE_NEXT''@|$(INCLUDE_NEXT)|g' \
-e 's|@''PRAGMA_SYSTEM_HEADER''@|@PRAGMA_SYSTEM_HEADER@|g' \
-e 's|@''PRAGMA_COLUMNS''@|@PRAGMA_COLUMNS@|g' \
-e 's|@''NEXT_STRING_H''@|$(NEXT_STRING_H)|g' \
- -e 's|@''GNULIB_MBSLEN''@|$(GNULIB_MBSLEN)|g' \
- -e 's|@''GNULIB_MBSNLEN''@|$(GNULIB_MBSNLEN)|g' \
- -e 's|@''GNULIB_MBSCHR''@|$(GNULIB_MBSCHR)|g' \
- -e 's|@''GNULIB_MBSRCHR''@|$(GNULIB_MBSRCHR)|g' \
- -e 's|@''GNULIB_MBSSTR''@|$(GNULIB_MBSSTR)|g' \
- -e 's|@''GNULIB_MBSCASECMP''@|$(GNULIB_MBSCASECMP)|g' \
- -e 's|@''GNULIB_MBSNCASECMP''@|$(GNULIB_MBSNCASECMP)|g' \
- -e 's|@''GNULIB_MBSPCASECMP''@|$(GNULIB_MBSPCASECMP)|g' \
- -e 's|@''GNULIB_MBSCASESTR''@|$(GNULIB_MBSCASESTR)|g' \
- -e 's|@''GNULIB_MBSCSPN''@|$(GNULIB_MBSCSPN)|g' \
- -e 's|@''GNULIB_MBSPBRK''@|$(GNULIB_MBSPBRK)|g' \
- -e 's|@''GNULIB_MBSSPN''@|$(GNULIB_MBSSPN)|g' \
- -e 's|@''GNULIB_MBSSEP''@|$(GNULIB_MBSSEP)|g' \
- -e 's|@''GNULIB_MBSTOK_R''@|$(GNULIB_MBSTOK_R)|g' \
- -e 's|@''GNULIB_MEMCHR''@|$(GNULIB_MEMCHR)|g' \
- -e 's|@''GNULIB_MEMMEM''@|$(GNULIB_MEMMEM)|g' \
- -e 's|@''GNULIB_MEMPCPY''@|$(GNULIB_MEMPCPY)|g' \
- -e 's|@''GNULIB_MEMRCHR''@|$(GNULIB_MEMRCHR)|g' \
- -e 's|@''GNULIB_RAWMEMCHR''@|$(GNULIB_RAWMEMCHR)|g' \
- -e 's|@''GNULIB_STPCPY''@|$(GNULIB_STPCPY)|g' \
- -e 's|@''GNULIB_STPNCPY''@|$(GNULIB_STPNCPY)|g' \
- -e 's|@''GNULIB_STRCHRNUL''@|$(GNULIB_STRCHRNUL)|g' \
- -e 's|@''GNULIB_STRDUP''@|$(GNULIB_STRDUP)|g' \
- -e 's|@''GNULIB_STRNCAT''@|$(GNULIB_STRNCAT)|g' \
- -e 's|@''GNULIB_STRNDUP''@|$(GNULIB_STRNDUP)|g' \
- -e 's|@''GNULIB_STRNLEN''@|$(GNULIB_STRNLEN)|g' \
- -e 's|@''GNULIB_STRPBRK''@|$(GNULIB_STRPBRK)|g' \
- -e 's|@''GNULIB_STRSEP''@|$(GNULIB_STRSEP)|g' \
- -e 's|@''GNULIB_STRSTR''@|$(GNULIB_STRSTR)|g' \
- -e 's|@''GNULIB_STRCASESTR''@|$(GNULIB_STRCASESTR)|g' \
- -e 's|@''GNULIB_STRTOK_R''@|$(GNULIB_STRTOK_R)|g' \
- -e 's|@''GNULIB_STRERROR''@|$(GNULIB_STRERROR)|g' \
- -e 's|@''GNULIB_STRERROR_R''@|$(GNULIB_STRERROR_R)|g' \
- -e 's|@''GNULIB_STRSIGNAL''@|$(GNULIB_STRSIGNAL)|g' \
- -e 's|@''GNULIB_STRVERSCMP''@|$(GNULIB_STRVERSCMP)|g' \
+ -e 's/@''GNULIB_FFSL''@/$(GNULIB_FFSL)/g' \
+ -e 's/@''GNULIB_FFSLL''@/$(GNULIB_FFSLL)/g' \
+ -e 's/@''GNULIB_MBSLEN''@/$(GNULIB_MBSLEN)/g' \
+ -e 's/@''GNULIB_MBSNLEN''@/$(GNULIB_MBSNLEN)/g' \
+ -e 's/@''GNULIB_MBSCHR''@/$(GNULIB_MBSCHR)/g' \
+ -e 's/@''GNULIB_MBSRCHR''@/$(GNULIB_MBSRCHR)/g' \
+ -e 's/@''GNULIB_MBSSTR''@/$(GNULIB_MBSSTR)/g' \
+ -e 's/@''GNULIB_MBSCASECMP''@/$(GNULIB_MBSCASECMP)/g' \
+ -e 's/@''GNULIB_MBSNCASECMP''@/$(GNULIB_MBSNCASECMP)/g' \
+ -e 's/@''GNULIB_MBSPCASECMP''@/$(GNULIB_MBSPCASECMP)/g' \
+ -e 's/@''GNULIB_MBSCASESTR''@/$(GNULIB_MBSCASESTR)/g' \
+ -e 's/@''GNULIB_MBSCSPN''@/$(GNULIB_MBSCSPN)/g' \
+ -e 's/@''GNULIB_MBSPBRK''@/$(GNULIB_MBSPBRK)/g' \
+ -e 's/@''GNULIB_MBSSPN''@/$(GNULIB_MBSSPN)/g' \
+ -e 's/@''GNULIB_MBSSEP''@/$(GNULIB_MBSSEP)/g' \
+ -e 's/@''GNULIB_MBSTOK_R''@/$(GNULIB_MBSTOK_R)/g' \
+ -e 's/@''GNULIB_MEMCHR''@/$(GNULIB_MEMCHR)/g' \
+ -e 's/@''GNULIB_MEMMEM''@/$(GNULIB_MEMMEM)/g' \
+ -e 's/@''GNULIB_MEMPCPY''@/$(GNULIB_MEMPCPY)/g' \
+ -e 's/@''GNULIB_MEMRCHR''@/$(GNULIB_MEMRCHR)/g' \
+ -e 's/@''GNULIB_RAWMEMCHR''@/$(GNULIB_RAWMEMCHR)/g' \
+ -e 's/@''GNULIB_STPCPY''@/$(GNULIB_STPCPY)/g' \
+ -e 's/@''GNULIB_STPNCPY''@/$(GNULIB_STPNCPY)/g' \
+ -e 's/@''GNULIB_STRCHRNUL''@/$(GNULIB_STRCHRNUL)/g' \
+ -e 's/@''GNULIB_STRDUP''@/$(GNULIB_STRDUP)/g' \
+ -e 's/@''GNULIB_STRNCAT''@/$(GNULIB_STRNCAT)/g' \
+ -e 's/@''GNULIB_STRNDUP''@/$(GNULIB_STRNDUP)/g' \
+ -e 's/@''GNULIB_STRNLEN''@/$(GNULIB_STRNLEN)/g' \
+ -e 's/@''GNULIB_STRPBRK''@/$(GNULIB_STRPBRK)/g' \
+ -e 's/@''GNULIB_STRSEP''@/$(GNULIB_STRSEP)/g' \
+ -e 's/@''GNULIB_STRSTR''@/$(GNULIB_STRSTR)/g' \
+ -e 's/@''GNULIB_STRCASESTR''@/$(GNULIB_STRCASESTR)/g' \
+ -e 's/@''GNULIB_STRTOK_R''@/$(GNULIB_STRTOK_R)/g' \
+ -e 's/@''GNULIB_STRERROR''@/$(GNULIB_STRERROR)/g' \
+ -e 's/@''GNULIB_STRERROR_R''@/$(GNULIB_STRERROR_R)/g' \
+ -e 's/@''GNULIB_STRSIGNAL''@/$(GNULIB_STRSIGNAL)/g' \
+ -e 's/@''GNULIB_STRVERSCMP''@/$(GNULIB_STRVERSCMP)/g' \
< $(srcdir)/string.in.h | \
- sed -e 's|@''HAVE_MBSLEN''@|$(HAVE_MBSLEN)|g' \
+ sed -e 's|@''HAVE_FFSL''@|$(HAVE_FFSL)|g' \
+ -e 's|@''HAVE_FFSLL''@|$(HAVE_FFSLL)|g' \
+ -e 's|@''HAVE_MBSLEN''@|$(HAVE_MBSLEN)|g' \
-e 's|@''HAVE_MEMCHR''@|$(HAVE_MEMCHR)|g' \
-e 's|@''HAVE_DECL_MEMMEM''@|$(HAVE_DECL_MEMMEM)|g' \
-e 's|@''HAVE_MEMPCPY''@|$(HAVE_MEMPCPY)|g' \
@@ -213,7 +254,7 @@ EXTRA_DIST += string.in.h
EXTRA_DIST += strndup.c
-EXTRA_libgnu_a_SOURCES += strndup.c
+EXTRA_libgnu_la_SOURCES += strndup.c
## end gnulib module strndup
@@ -222,32 +263,13 @@ EXTRA_libgnu_a_SOURCES += strndup.c
EXTRA_DIST += strnlen.c
-EXTRA_libgnu_a_SOURCES += strnlen.c
+EXTRA_libgnu_la_SOURCES += strnlen.c
## end gnulib module strnlen
-## begin gnulib module warn-on-use
-
-BUILT_SOURCES += warn-on-use.h
-# The warn-on-use.h that gets inserted into generated .h files is the same as
-# build-aux/warn-on-use.h, except that it has the copyright header cut off.
-warn-on-use.h: $(top_srcdir)/build-aux/warn-on-use.h
- $(AM_V_GEN)rm -f $@-t $@ && \
- sed -n -e '/^.ifndef/,$$p' \
- < $(top_srcdir)/build-aux/warn-on-use.h \
- > $@-t && \
- mv $@-t $@
-MOSTLYCLEANFILES += warn-on-use.h warn-on-use.h-t
-
-WARN_ON_USE_H=warn-on-use.h
-
-EXTRA_DIST += $(top_srcdir)/build-aux/warn-on-use.h
-
-## end gnulib module warn-on-use
-
## begin gnulib module dummy
-libgnu_a_SOURCES += dummy.c
+libgnu_la_SOURCES += dummy.c
## end gnulib module dummy
diff --git a/lib/dummy.c b/lib/dummy.c
index c958ea05..6e4b76e0 100644
--- a/lib/dummy.c
+++ b/lib/dummy.c
@@ -1,5 +1,5 @@
/* A dummy file, to prevent empty libraries from breaking builds.
- Copyright (C) 2004, 2007, 2009-2011 Free Software Foundation, Inc.
+ Copyright (C) 2004, 2007, 2009-2012 Free Software Foundation, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
diff --git a/lib/stddef.in.h b/lib/stddef.in.h
index 62a91a7a..17fcaea2 100644
--- a/lib/stddef.in.h
+++ b/lib/stddef.in.h
@@ -1,6 +1,6 @@
/* A substitute for POSIX 2008 <stddef.h>, for platforms that have issues.
- Copyright (C) 2009-2011 Free Software Foundation, Inc.
+ Copyright (C) 2009-2012 Free Software Foundation, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -13,8 +13,7 @@
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, write to the Free Software Foundation,
- Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */
+ along with this program; if not, see <http://www.gnu.org/licenses/>. */
/* Written by Eric Blake. */
@@ -38,9 +37,9 @@
remember if special invocation has ever been used to obtain wint_t,
in which case we need to clean up NULL yet again. */
-# if !(defined _GL_STDDEF_H && defined _GL_STDDEF_WINT_T)
+# if !(defined _@GUARD_PREFIX@_STDDEF_H && defined _GL_STDDEF_WINT_T)
# ifdef __need_wint_t
-# undef _GL_STDDEF_H
+# undef _@GUARD_PREFIX@_STDDEF_H
# define _GL_STDDEF_WINT_T
# endif
# @INCLUDE_NEXT@ @NEXT_STDDEF_H@
@@ -49,14 +48,14 @@
#else
/* Normal invocation convention. */
-# ifndef _GL_STDDEF_H
+# ifndef _@GUARD_PREFIX@_STDDEF_H
/* The include_next requires a split double-inclusion guard. */
# @INCLUDE_NEXT@ @NEXT_STDDEF_H@
-# ifndef _GL_STDDEF_H
-# define _GL_STDDEF_H
+# ifndef _@GUARD_PREFIX@_STDDEF_H
+# define _@GUARD_PREFIX@_STDDEF_H
/* On NetBSD 5.0, the definition of NULL lacks proper parentheses. */
#if @REPLACE_NULL@
@@ -82,6 +81,6 @@
# define wchar_t int
#endif
-# endif /* _GL_STDDEF_H */
-# endif /* _GL_STDDEF_H */
+# endif /* _@GUARD_PREFIX@_STDDEF_H */
+# endif /* _@GUARD_PREFIX@_STDDEF_H */
#endif /* __need_XXX */
diff --git a/lib/string.in.h b/lib/string.in.h
index 76d26ed3..f8d7520e 100644
--- a/lib/string.in.h
+++ b/lib/string.in.h
@@ -1,6 +1,6 @@
/* A GNU-like <string.h>.
- Copyright (C) 1995-1996, 2001-2011 Free Software Foundation, Inc.
+ Copyright (C) 1995-1996, 2001-2012 Free Software Foundation, Inc.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
@@ -13,10 +13,9 @@
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, write to the Free Software Foundation,
- Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */
+ along with this program; if not, see <http://www.gnu.org/licenses/>. */
-#ifndef _GL_STRING_H
+#ifndef _@GUARD_PREFIX@_STRING_H
#if __GNUC__ >= 3
@PRAGMA_SYSTEM_HEADER@
@@ -26,8 +25,8 @@
/* The include_next requires a split double-inclusion guard. */
#@INCLUDE_NEXT@ @NEXT_STRING_H@
-#ifndef _GL_STRING_H
-#define _GL_STRING_H
+#ifndef _@GUARD_PREFIX@_STRING_H
+#define _@GUARD_PREFIX@_STRING_H
/* NetBSD 5.0 mis-defines NULL. */
#include <stddef.h>
@@ -59,6 +58,36 @@
/* The definition of _GL_WARN_ON_USE is copied here. */
+/* Find the index of the least-significant set bit. */
+#if @GNULIB_FFSL@
+# if !@HAVE_FFSL@
+_GL_FUNCDECL_SYS (ffsl, int, (long int i));
+# endif
+_GL_CXXALIAS_SYS (ffsl, int, (long int i));
+_GL_CXXALIASWARN (ffsl);
+#elif defined GNULIB_POSIXCHECK
+# undef ffsl
+# if HAVE_RAW_DECL_FFSL
+_GL_WARN_ON_USE (ffsl, "ffsl is not portable - use the ffsl module");
+# endif
+#endif
+
+
+/* Find the index of the least-significant set bit. */
+#if @GNULIB_FFSLL@
+# if !@HAVE_FFSLL@
+_GL_FUNCDECL_SYS (ffsll, int, (long long int i));
+# endif
+_GL_CXXALIAS_SYS (ffsll, int, (long long int i));
+_GL_CXXALIASWARN (ffsll);
+#elif defined GNULIB_POSIXCHECK
+# undef ffsll
+# if HAVE_RAW_DECL_FFSLL
+_GL_WARN_ON_USE (ffsll, "ffsll is not portable - use the ffsll module");
+# endif
+#endif
+
+
/* Return the first instance of C within N bytes of S, or NULL. */
#if @GNULIB_MEMCHR@
# if @REPLACE_MEMCHR@
@@ -695,10 +724,14 @@ _GL_WARN_ON_USE (strtok_r, "strtok_r is unportable - "
# if !(defined __cplusplus && defined GNULIB_NAMESPACE)
# define mbslen rpl_mbslen
# endif
-_GL_FUNCDECL_RPL (mbslen, size_t, (const char *string) _GL_ARG_NONNULL ((1)));
+_GL_FUNCDECL_RPL (mbslen, size_t, (const char *string)
+ _GL_ATTRIBUTE_PURE
+ _GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_RPL (mbslen, size_t, (const char *string));
# else
-_GL_FUNCDECL_SYS (mbslen, size_t, (const char *string) _GL_ARG_NONNULL ((1)));
+_GL_FUNCDECL_SYS (mbslen, size_t, (const char *string)
+ _GL_ATTRIBUTE_PURE
+ _GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_SYS (mbslen, size_t, (const char *string));
# endif
_GL_CXXALIASWARN (mbslen);
@@ -708,6 +741,7 @@ _GL_CXXALIASWARN (mbslen);
/* Return the number of multibyte characters in the character string starting
at STRING and ending at STRING + LEN. */
_GL_EXTERN_C size_t mbsnlen (const char *string, size_t len)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1));
#endif
@@ -721,10 +755,12 @@ _GL_EXTERN_C size_t mbsnlen (const char *string, size_t len)
# define mbschr rpl_mbschr /* avoid collision with HP-UX function */
# endif
_GL_FUNCDECL_RPL (mbschr, char *, (const char *string, int c)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_RPL (mbschr, char *, (const char *string, int c));
# else
_GL_FUNCDECL_SYS (mbschr, char *, (const char *string, int c)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_SYS (mbschr, char *, (const char *string, int c));
# endif
@@ -736,15 +772,17 @@ _GL_CXXALIASWARN (mbschr);
and return a pointer to it. Return NULL if C is not found in STRING.
Unlike strrchr(), this function works correctly in multibyte locales with
encodings such as GB18030. */
-# if defined __hpux
+# if defined __hpux || defined __INTERIX
# if !(defined __cplusplus && defined GNULIB_NAMESPACE)
-# define mbsrchr rpl_mbsrchr /* avoid collision with HP-UX function */
+# define mbsrchr rpl_mbsrchr /* avoid collision with system function */
# endif
_GL_FUNCDECL_RPL (mbsrchr, char *, (const char *string, int c)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_RPL (mbsrchr, char *, (const char *string, int c));
# else
_GL_FUNCDECL_SYS (mbsrchr, char *, (const char *string, int c)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1)));
_GL_CXXALIAS_SYS (mbsrchr, char *, (const char *string, int c));
# endif
@@ -757,6 +795,7 @@ _GL_CXXALIASWARN (mbsrchr);
Unlike strstr(), this function works correctly in multibyte locales with
encodings different from UTF-8. */
_GL_EXTERN_C char * mbsstr (const char *haystack, const char *needle)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -768,6 +807,7 @@ _GL_EXTERN_C char * mbsstr (const char *haystack, const char *needle)
different lengths!
Unlike strcasecmp(), this function works correctly in multibyte locales. */
_GL_EXTERN_C int mbscasecmp (const char *s1, const char *s2)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -782,6 +822,7 @@ _GL_EXTERN_C int mbscasecmp (const char *s1, const char *s2)
Unlike strncasecmp(), this function works correctly in multibyte locales.
But beware that N is not a byte count but a character count! */
_GL_EXTERN_C int mbsncasecmp (const char *s1, const char *s2, size_t n)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -795,6 +836,7 @@ _GL_EXTERN_C int mbsncasecmp (const char *s1, const char *s2, size_t n)
Unlike strncasecmp(), this function works correctly in multibyte
locales. */
_GL_EXTERN_C char * mbspcasecmp (const char *string, const char *prefix)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -805,6 +847,7 @@ _GL_EXTERN_C char * mbspcasecmp (const char *string, const char *prefix)
strlen (haystack) < strlen (needle) !
Unlike strcasestr(), this function works correctly in multibyte locales. */
_GL_EXTERN_C char * mbscasestr (const char *haystack, const char *needle)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -815,6 +858,7 @@ _GL_EXTERN_C char * mbscasestr (const char *haystack, const char *needle)
if none exists.
Unlike strcspn(), this function works correctly in multibyte locales. */
_GL_EXTERN_C size_t mbscspn (const char *string, const char *accept)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -828,10 +872,12 @@ _GL_EXTERN_C size_t mbscspn (const char *string, const char *accept)
# define mbspbrk rpl_mbspbrk /* avoid collision with HP-UX function */
# endif
_GL_FUNCDECL_RPL (mbspbrk, char *, (const char *string, const char *accept)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2)));
_GL_CXXALIAS_RPL (mbspbrk, char *, (const char *string, const char *accept));
# else
_GL_FUNCDECL_SYS (mbspbrk, char *, (const char *string, const char *accept)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2)));
_GL_CXXALIAS_SYS (mbspbrk, char *, (const char *string, const char *accept));
# endif
@@ -845,6 +891,7 @@ _GL_CXXALIASWARN (mbspbrk);
if none exists.
Unlike strspn(), this function works correctly in multibyte locales. */
_GL_EXTERN_C size_t mbsspn (const char *string, const char *reject)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2));
#endif
@@ -964,6 +1011,7 @@ _GL_WARN_ON_USE (strsignal, "strsignal is unportable - "
#if @GNULIB_STRVERSCMP@
# if !@HAVE_STRVERSCMP@
_GL_FUNCDECL_SYS (strverscmp, int, (const char *, const char *)
+ _GL_ATTRIBUTE_PURE
_GL_ARG_NONNULL ((1, 2)));
# endif
_GL_CXXALIAS_SYS (strverscmp, int, (const char *, const char *));
@@ -977,5 +1025,5 @@ _GL_WARN_ON_USE (strverscmp, "strverscmp is unportable - "
#endif
-#endif /* _GL_STRING_H */
-#endif /* _GL_STRING_H */
+#endif /* _@GUARD_PREFIX@_STRING_H */
+#endif /* _@GUARD_PREFIX@_STRING_H */
diff --git a/lib/strndup.c b/lib/strndup.c
index 4a3bece4..40538711 100644
--- a/lib/strndup.c
+++ b/lib/strndup.c
@@ -1,6 +1,6 @@
/* A replacement function, for systems that lack strndup.
- Copyright (C) 1996-1998, 2001-2003, 2005-2007, 2009-2011 Free Software
+ Copyright (C) 1996-1998, 2001-2003, 2005-2007, 2009-2012 Free Software
Foundation, Inc.
This program is free software; you can redistribute it and/or modify it
@@ -14,8 +14,7 @@
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, write to the Free Software Foundation,
- Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */
+ along with this program; if not, see <http://www.gnu.org/licenses/>. */
#include <config.h>
diff --git a/lib/strnlen.c b/lib/strnlen.c
index 3cefa978..d36180dc 100644
--- a/lib/strnlen.c
+++ b/lib/strnlen.c
@@ -1,5 +1,5 @@
/* Find the length of STRING, but scan at most MAXLEN characters.
- Copyright (C) 2005-2007, 2009-2011 Free Software Foundation, Inc.
+ Copyright (C) 2005-2007, 2009-2012 Free Software Foundation, Inc.
Written by Simon Josefsson.
This program is free software; you can redistribute it and/or modify
@@ -13,8 +13,7 @@
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, write to the Free Software Foundation,
- Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. */
+ along with this program; if not, see <http://www.gnu.org/licenses/>. */
#include <config.h>
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index d13bbc93..bd84ceff 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -1,5 +1,5 @@
lib_LTLIBRARIES = libcrystfel.la
-libcrystfel_la_LIBADD = @LIBCRYSTFEL_LIBS@
+libcrystfel_la_LIBADD = ../lib/libgnu.la @LIBCRYSTFEL_LIBS@
libcrystfel_la_LDFLAGS = -version-info=0:0:0
libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 2e87b770..b6ea010b 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -424,7 +424,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
switch ( cell->rep ) {
- case CELL_REP_CRYST:
+ case CELL_REP_CRYST:
/* Direct response */
*a = cell->a;
*b = cell->b;
@@ -434,7 +434,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
*gamma = cell->gamma;
return 0;
- case CELL_REP_CART:
+ case CELL_REP_CART:
/* Convert cartesian -> crystallographic */
*a = modulus(cell->ax, cell->ay, cell->az);
*b = modulus(cell->bx, cell->by, cell->bz);
@@ -448,7 +448,7 @@ int cell_get_parameters(UnitCell *cell, double *a, double *b, double *c,
cell->bx, cell->by, cell->bz);
return 0;
- case CELL_REP_RECIP:
+ case CELL_REP_RECIP:
/* Convert reciprocal -> crystallographic.
* Start by converting reciprocal -> cartesian */
cell_invert(cell->axs, cell->ays, cell->azs,
@@ -480,21 +480,21 @@ int cell_get_cartesian(UnitCell *cell,
switch ( cell->rep ) {
- case CELL_REP_CRYST:
+ case CELL_REP_CRYST:
/* Convert crystallographic -> cartesian. */
return cell_crystallographic_to_cartesian(cell,
ax, ay, az,
bx, by, bz,
cx, cy, cz);
- case CELL_REP_CART:
+ case CELL_REP_CART:
/* Direct response */
*ax = cell->ax; *ay = cell->ay; *az = cell->az;
*bx = cell->bx; *by = cell->by; *bz = cell->bz;
*cx = cell->cx; *cy = cell->cy; *cz = cell->cz;
return 0;
- case CELL_REP_RECIP:
+ case CELL_REP_RECIP:
/* Convert reciprocal -> cartesian */
return cell_invert(cell->axs, cell->ays, cell->azs,
cell->bxs, cell->bys, cell->bzs,
@@ -518,7 +518,7 @@ int cell_get_reciprocal(UnitCell *cell,
switch ( cell->rep ) {
- case CELL_REP_CRYST:
+ case CELL_REP_CRYST:
/* Convert crystallographic -> reciprocal */
r = cell_crystallographic_to_cartesian(cell,
&ax, &ay, &az,
@@ -528,7 +528,7 @@ int cell_get_reciprocal(UnitCell *cell,
return cell_invert(ax, ay, az,bx, by, bz, cx, cy, cz,
asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
- case CELL_REP_CART:
+ case CELL_REP_CART:
/* Convert cartesian -> reciprocal */
cell_invert(cell->ax, cell->ay, cell->az,
cell->bx, cell->by, cell->bz,
@@ -536,7 +536,7 @@ int cell_get_reciprocal(UnitCell *cell,
asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
return 0;
- case CELL_REP_RECIP:
+ case CELL_REP_RECIP:
/* Direct response */
*asx = cell->axs; *asy = cell->ays; *asz = cell->azs;
*bsx = cell->bxs; *bsy = cell->bys; *bsz = cell->bzs;
@@ -569,12 +569,16 @@ const char *cell_get_spacegroup(UnitCell *cell)
static const char *cell_rep(UnitCell *cell)
{
switch ( cell->rep ) {
- case CELL_REP_CRYST:
+
+ case CELL_REP_CRYST:
return "crystallographic, direct space";
- case CELL_REP_CART:
+
+ case CELL_REP_CART:
return "cartesian, direct space";
- case CELL_REP_RECIP:
+
+ case CELL_REP_RECIP:
return "cartesian, reciprocal space";
+
}
return "unknown";
diff --git a/libcrystfel/src/dirax.c b/libcrystfel/src/dirax.c
index 20f48bd3..43de6c6e 100644
--- a/libcrystfel/src/dirax.c
+++ b/libcrystfel/src/dirax.c
@@ -226,37 +226,37 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
switch ( dirax->step ) {
- case 1 :
+ case 1 :
dirax_sendline("\\echo off\n", dirax);
break;
- case 2 :
+ case 2 :
snprintf(tmp, 31, "read xfel-%i.drx\n", image->id);
dirax_sendline(tmp, dirax);
break;
- case 3 :
+ case 3 :
dirax_sendline("dmax 1000\n", dirax);
break;
- case 4 :
+ case 4 :
dirax_sendline("indexfit 2\n", dirax);
break;
- case 5 :
+ case 5 :
dirax_sendline("levelfit 1000\n", dirax);
break;
- case 6 :
+ case 6 :
dirax_sendline("go\n", dirax);
dirax->finished_ok = 1;
break;
- case 7 :
+ case 7 :
dirax_sendline("acl\n", dirax);
break;
- case 8 :
+ case 8 :
if ( dirax->best_acl_nh == 0 ) {
/* At this point, DirAx is presenting its ACL prompt
* and waiting for a single number. Use an extra
@@ -270,11 +270,11 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
dirax_sendline(tmp, dirax);
break;
- case 9 :
+ case 9 :
dirax_sendline("cell\n", dirax);
break;
- case 10 :
+ case 10 :
if ( dirax->n_acls_tried == MAX_DIRAX_CELL_CANDIDATES ) {
dirax_sendline("exit\n", dirax);
} else {
@@ -285,7 +285,7 @@ static void dirax_send_next(struct image *image, struct dirax_data *dirax)
}
break;
- default:
+ default:
dirax_sendline("exit\n", dirax);
return;
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 88d11bff..af06c1b4 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -719,6 +719,10 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
hsize_t max_size;
hid_t type;
hid_t class;
+ herr_t r;
+ int buf_i;
+ double buf_f;
+ char *tmp;
dh = H5Dopen2(f->fh, name, H5P_DEFAULT);
if ( dh < 0 ) return NULL;
@@ -761,40 +765,33 @@ char *hdfile_get_string_value(struct hdfile *f, const char *name)
}
switch ( class ) {
- case H5T_FLOAT : {
- herr_t r;
- double buf;
- char *tmp;
+ case H5T_FLOAT :
r = H5Dread(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &buf);
+ H5P_DEFAULT, &buf_f);
if ( r < 0 ) goto fail;
tmp = malloc(256);
- snprintf(tmp, 255, "%f", buf);
+ snprintf(tmp, 255, "%f", buf_f);
return tmp;
- }
- case H5T_INTEGER : {
+ case H5T_INTEGER :
- herr_t r;
- int buf;
- char *tmp;
r = H5Dread(dh, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
- H5P_DEFAULT, &buf);
+ H5P_DEFAULT, &buf_i);
if ( r < 0 ) goto fail;
tmp = malloc(256);
- snprintf(tmp, 255, "%d", buf);
+ snprintf(tmp, 255, "%d", buf_i);
return tmp;
- }
- default : {
+
+ default :
goto fail;
- }
+
}
fail:
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 2baa2644..102a5312 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -83,18 +83,23 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
for ( n=0; n<nm; n++ ) {
switch ( indm[n] ) {
- case INDEXING_NONE :
+
+ case INDEXING_NONE :
ERROR("Tried to prepare INDEXING_NONE!\n");
break;
- case INDEXING_DIRAX :
+
+ case INDEXING_DIRAX :
iprivs[n] = indexing_private(indm[n]);
break;
- case INDEXING_MOSFLM :
+
+ case INDEXING_MOSFLM :
iprivs[n] = indexing_private(indm[n]);
break;
- case INDEXING_REAX :
+
+ case INDEXING_REAX :
iprivs[n] = reax_prepare();
break;
+
}
}
@@ -113,18 +118,23 @@ void cleanup_indexing(IndexingPrivate **priv)
while ( priv[n] != NULL ) {
switch ( priv[n]->indm ) {
- case INDEXING_NONE :
+
+ case INDEXING_NONE :
free(priv[n]);
break;
- case INDEXING_DIRAX :
+
+ case INDEXING_DIRAX :
free(priv[n]);
break;
- case INDEXING_MOSFLM :
+
+ case INDEXING_MOSFLM :
free(priv[n]);
break;
- case INDEXING_REAX :
+
+ case INDEXING_REAX :
reax_cleanup(priv[n]);
break;
+
}
n++;
@@ -173,17 +183,22 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
/* Index as appropriate */
switch ( indm[n] ) {
- case INDEXING_NONE :
+
+ case INDEXING_NONE :
return;
- case INDEXING_DIRAX :
+
+ case INDEXING_DIRAX :
run_dirax(image);
break;
- case INDEXING_MOSFLM :
+
+ case INDEXING_MOSFLM :
run_mosflm(image, cell);
break;
- case INDEXING_REAX :
+
+ case INDEXING_REAX :
reax_index(ipriv[n], image, cell);
break;
+
}
if ( image->ncells == 0 ) {
n++;
@@ -205,20 +220,25 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
/* Match or reduce the cell as appropriate */
switch ( cellr ) {
- case CELLR_NONE :
+
+ case CELLR_NONE :
new_cell = cell_new_from_cell(cand);
break;
- case CELLR_REDUCE :
+
+ case CELLR_REDUCE :
new_cell = match_cell(cand, cell, verbose,
ltl, 1);
break;
- case CELLR_COMPARE :
+
+ case CELLR_COMPARE :
new_cell = match_cell(cand, cell, verbose,
ltl, 0);
break;
- case CELLR_COMPARE_AB :
+
+ case CELLR_COMPARE_AB :
new_cell = match_cell_ab(cand, cell);
break;
+
}
/* No cell? Move on to the next candidate */
diff --git a/libcrystfel/src/mosflm.c b/libcrystfel/src/mosflm.c
index 0032a095..ed118aa4 100644
--- a/libcrystfel/src/mosflm.c
+++ b/libcrystfel/src/mosflm.c
@@ -283,13 +283,13 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
switch ( mosflm->step ) {
- case 1 :
+ case 1 :
mosflm_sendline("DETECTOR ROTATION HORIZONTAL"
" ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL"
" RECTANGULAR\n", mosflm);
break;
- case 2 :
+ case 2 :
if ( mosflm->target_cell != NULL ) {
cell_get_parameters(mosflm->target_cell, &a, &b, &c,
&alpha, &beta, &gamma);
@@ -303,7 +303,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
}
break;
- case 3 :
+ case 3 :
if ( mosflm->target_cell != NULL ) {
sg = cell_get_spacegroup(mosflm->target_cell);
/* Remove white space from space group */
@@ -321,31 +321,31 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
}
break;
- case 4 :
+ case 4 :
mosflm_sendline("DISTANCE 67.8\n", mosflm);
break;
- case 5 :
+ case 5 :
mosflm_sendline("BEAM 0.0 0.0\n", mosflm);
break;
- case 6 :
+ case 6 :
wavelength = image->lambda*1e10;
snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength);
mosflm_sendline(tmp, mosflm);
break;
- case 7 :
+ case 7 :
snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile);
mosflm_sendline(tmp, mosflm);
break;
- case 8 :
+ case 8 :
snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile);
mosflm_sendline(tmp, mosflm);
break;
- case 9 :
+ case 9 :
snprintf(tmp, 255, "AUTOINDEX DPS FILE %s"
" IMAGE 1 MAXCELL 1000 REFINE\n",
mosflm->sptfile);
@@ -357,7 +357,7 @@ static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
mosflm_sendline(tmp, mosflm);
break;
- case 10 :
+ case 10 :
mosflm_sendline("GO\n", mosflm);
mosflm->finished_ok = 1;
break;
diff --git a/libcrystfel/src/render.c b/libcrystfel/src/render.c
index c9e1f01e..5d0cf9e8 100644
--- a/libcrystfel/src/render.c
+++ b/libcrystfel/src/render.c
@@ -64,34 +64,35 @@ static void render_rgb(double val, double max,
s = 6;
}
switch ( s ) {
- case 0 : { /* Black to blue */
- r = 0; g = 0; b = p;
- break;
- }
- case 1 : { /* Blue to pink */
- r = p; g = 0; b = 1.0;
- break;
- }
- case 2 : { /* Pink to red */
- r = 1.0; g = 0; b = (1.0-p)*1.0;
- break;
- }
- case 3 : { /* Red to Orange */
- r = 1.0; g = 0.5*p; b = 0;
- break;
- }
- case 4 : { /* Orange to Yellow */
- r = 1.0; g = 0.5 + 0.5*p; b = 0;
- break;
- }
- case 5 : { /* Yellow to White */
- r = 1.0; g = 1.0; b = 1.0*p;
- break;
- }
- case 6 : { /* Pixel has hit the maximum value */
- r = 1.0; g = 1.0; b = 1.0;
- break;
- }
+
+ case 0 : /* Black to blue */
+ r = 0; g = 0; b = p;
+ break;
+
+ case 1 : /* Blue to pink */
+ r = p; g = 0; b = 1.0;
+ break;
+
+ case 2 : /* Pink to red */
+ r = 1.0; g = 0; b = (1.0-p)*1.0;
+ break;
+
+ case 3 : /* Red to Orange */
+ r = 1.0; g = 0.5*p; b = 0;
+ break;
+
+ case 4 : /* Orange to Yellow */
+ r = 1.0; g = 0.5 + 0.5*p; b = 0;
+ break;
+
+ case 5 : /* Yellow to White */
+ r = 1.0; g = 1.0; b = 1.0*p;
+ break;
+
+ case 6 : /* Pixel has hit the maximum value */
+ r = 1.0; g = 1.0; b = 1.0;
+ break;
+
}
*rp = r;
@@ -144,16 +145,20 @@ void render_scale(double val, double max, int scale,
double *rp, double *gp, double *bp)
{
switch ( scale ) {
- case SCALE_COLOUR :
+
+ case SCALE_COLOUR :
render_rgb(val, max, rp, gp, bp);
break;
- case SCALE_MONO :
+
+ case SCALE_MONO :
render_mono(val, max, rp, gp, bp);
break;
- case SCALE_INVMONO :
+
+ case SCALE_INVMONO :
render_invmono(val, max, rp, gp, bp);
break;
- case SCALE_RATIO :
+
+ case SCALE_RATIO :
render_ratio(val, max, rp, gp, bp);
break;
}
diff --git a/libcrystfel/src/statistics.c b/libcrystfel/src/statistics.c
index 6ddf2850..56273fdb 100644
--- a/libcrystfel/src/statistics.c
+++ b/libcrystfel/src/statistics.c
@@ -407,22 +407,28 @@ static double calc_r(double scale, void *params)
struct r_params *rp = params;
switch ( rp->fom ) {
- case R_1_ZERO :
+
+ case R_1_ZERO :
return internal_r1_negstozero(rp->list1, rp->list2, scale);
- case R_1_IGNORE :
+
+ case R_1_IGNORE :
return internal_r1_ignorenegs(rp->list1, rp->list2, scale);
- case R_2 :
+
+ case R_2 :
return internal_r2(rp->list1, rp->list2, scale);
- case R_1_I :
+ case R_1_I :
return internal_r_i(rp->list1, rp->list2, scale);
- case R_DIFF_ZERO :
+ case R_DIFF_ZERO :
return internal_rdiff_negstozero(rp->list1, rp->list2,scale);
- case R_DIFF_IGNORE :
+
+ case R_DIFF_IGNORE :
return internal_rdiff_ignorenegs(rp->list1, rp->list2, scale);
- case R_DIFF_INTENSITY :
+
+ case R_DIFF_INTENSITY :
return internal_rdiff_intensity(rp->list1, rp->list2, scale);
+
}
ERROR("No such FoM!\n");
@@ -457,17 +463,20 @@ static double r_minimised(RefList *list1, RefList *list2, double *scalep, int fo
/* Initial guess */
switch ( fom ) {
- case R_1_ZERO :
- case R_1_IGNORE :
- case R_DIFF_ZERO :
- case R_DIFF_IGNORE :
+
+ case R_1_ZERO :
+ case R_1_IGNORE :
+ case R_DIFF_ZERO :
+ case R_DIFF_IGNORE :
scale = stat_scale_sqrti(list1, list2);
break;
- case R_2 :
- case R_1_I :
- case R_DIFF_INTENSITY :
+
+ case R_2 :
+ case R_1_I :
+ case R_DIFF_INTENSITY :
scale = stat_scale_intensity(list1, list2);
break;
+
}
//STATUS("Initial scale factor estimate: %5.2e\n", scale);
diff --git a/m4/00gnulib.m4 b/m4/00gnulib.m4
index 7feed466..d978cb89 100644
--- a/m4/00gnulib.m4
+++ b/m4/00gnulib.m4
@@ -1,5 +1,5 @@
# 00gnulib.m4 serial 2
-dnl Copyright (C) 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2009-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/extensions.m4 b/m4/extensions.m4
index 1330503f..0bfaef6f 100644
--- a/m4/extensions.m4
+++ b/m4/extensions.m4
@@ -1,7 +1,7 @@
-# serial 9 -*- Autoconf -*-
+# serial 11 -*- Autoconf -*-
# Enable extensions on systems that normally disable them.
-# Copyright (C) 2003, 2006-2011 Free Software Foundation, Inc.
+# Copyright (C) 2003, 2006-2012 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
@@ -43,7 +43,7 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
AC_CHECK_HEADER([minix/config.h], [MINIX=yes], [MINIX=])
if test "$MINIX" = yes; then
AC_DEFINE([_POSIX_SOURCE], [1],
- [Define to 1 if you need to in order for `stat' and other
+ [Define to 1 if you need to in order for 'stat' and other
things to work.])
AC_DEFINE([_POSIX_1_SOURCE], [2],
[Define to 2 if the system does not provide POSIX.1 features
@@ -67,6 +67,10 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
#ifndef _ALL_SOURCE
# undef _ALL_SOURCE
#endif
+/* Enable general extensions on MacOS X. */
+#ifndef _DARWIN_C_SOURCE
+# undef _DARWIN_C_SOURCE
+#endif
/* Enable GNU extensions on systems that have them. */
#ifndef _GNU_SOURCE
# undef _GNU_SOURCE
@@ -95,6 +99,7 @@ AC_BEFORE([$0], [AC_RUN_IFELSE])dnl
test $ac_cv_safe_to_define___extensions__ = yes &&
AC_DEFINE([__EXTENSIONS__])
AC_DEFINE([_ALL_SOURCE])
+ AC_DEFINE([_DARWIN_C_SOURCE])
AC_DEFINE([_GNU_SOURCE])
AC_DEFINE([_POSIX_PTHREAD_SEMANTICS])
AC_DEFINE([_TANDEM_SOURCE])
diff --git a/m4/gnulib-cache.m4 b/m4/gnulib-cache.m4
index c93243e0..acc9a4c9 100644
--- a/m4/gnulib-cache.m4
+++ b/m4/gnulib-cache.m4
@@ -1,9 +1,21 @@
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
#
-# This file is free software, distributed under the terms of the GNU
-# General Public License. As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file 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 3 of the License, or
+# (at your option) any later version.
+#
+# This file 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 file. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
# the same distribution terms as the rest of that program.
#
# Generated by gnulib-tool.
@@ -15,7 +27,7 @@
# Specification in the form of a command-line invocation:
-# gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-libtool --macro-prefix=gl lib-ignore strndup
+# gnulib-tool --import --dir=. --lib=libgnu --source-base=lib --m4-base=m4 --doc-base=doc --tests-base=tests --aux-dir=build-aux --no-conditional-dependencies --libtool --macro-prefix=gl lib-ignore strndup
# Specification in the form of a few gnulib-tool.m4 macro invocations:
gl_LOCAL_DIR([])
@@ -31,5 +43,7 @@ gl_DOC_BASE([doc])
gl_TESTS_BASE([tests])
gl_LIB([libgnu])
gl_MAKEFILE_NAME([])
+gl_LIBTOOL
gl_MACRO_PREFIX([gl])
gl_PO_DOMAIN([])
+gl_WITNESS_C_DOMAIN([])
diff --git a/m4/gnulib-common.m4 b/m4/gnulib-common.m4
index c4d7a20e..d62b7677 100644
--- a/m4/gnulib-common.m4
+++ b/m4/gnulib-common.m4
@@ -1,5 +1,5 @@
-# gnulib-common.m4 serial 24
-dnl Copyright (C) 2007-2011 Free Software Foundation, Inc.
+# gnulib-common.m4 serial 32
+dnl Copyright (C) 2007-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
@@ -12,6 +12,20 @@ AC_DEFUN([gl_COMMON], [
AC_REQUIRE([gl_COMMON_BODY])
])
AC_DEFUN([gl_COMMON_BODY], [
+ AH_VERBATIM([_Noreturn],
+[/* The _Noreturn keyword of C11. */
+#if ! (defined _Noreturn \
+ || (defined __STDC_VERSION__ && 201112 <= __STDC_VERSION__))
+# if (3 <= __GNUC__ || (__GNUC__ == 2 && 8 <= __GNUC_MINOR__) \
+ || 0x5110 <= __SUNPRO_C)
+# define _Noreturn __attribute__ ((__noreturn__))
+# elif defined _MSC_VER && 1200 <= _MSC_VER
+# define _Noreturn __declspec (noreturn)
+# else
+# define _Noreturn
+# endif
+#endif
+])
AH_VERBATIM([isoc99_inline],
[/* Work around a bug in Apple GCC 4.0.1 build 5465: In C99 mode, it supports
the ISO C 99 semantics of 'extern inline' (unlike the GNU C semantics of
@@ -34,6 +48,20 @@ AC_DEFUN([gl_COMMON_BODY], [
/* The name _UNUSED_PARAMETER_ is an earlier spelling, although the name
is a misnomer outside of parameter lists. */
#define _UNUSED_PARAMETER_ _GL_UNUSED
+
+/* The __pure__ attribute was added in gcc 2.96. */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 96)
+# define _GL_ATTRIBUTE_PURE __attribute__ ((__pure__))
+#else
+# define _GL_ATTRIBUTE_PURE /* empty */
+#endif
+
+/* The __const__ attribute was added in gcc 2.95. */
+#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 95)
+# define _GL_ATTRIBUTE_CONST __attribute__ ((__const__))
+#else
+# define _GL_ATTRIBUTE_CONST /* empty */
+#endif
])
dnl Preparation for running test programs:
dnl Tell glibc to write diagnostics from -D_FORTIFY_SOURCE=2 to stderr, not
@@ -47,16 +75,49 @@ AC_DEFUN([gl_COMMON_BODY], [
# expands to a C preprocessor expression that evaluates to 1 or 0, depending
# whether a gnulib module that has been requested shall be considered present
# or not.
-AC_DEFUN([gl_MODULE_INDICATOR_CONDITION], [1])
+m4_define([gl_MODULE_INDICATOR_CONDITION], [1])
# gl_MODULE_INDICATOR_SET_VARIABLE([modulename])
# sets the shell variable that indicates the presence of the given module to
# a C preprocessor expression that will evaluate to 1.
AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE],
[
- GNULIB_[]m4_translit([[$1]],
- [abcdefghijklmnopqrstuvwxyz./-],
- [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])=gl_MODULE_INDICATOR_CONDITION
+ gl_MODULE_INDICATOR_SET_VARIABLE_AUX(
+ [GNULIB_[]m4_translit([[$1]],
+ [abcdefghijklmnopqrstuvwxyz./-],
+ [ABCDEFGHIJKLMNOPQRSTUVWXYZ___])],
+ [gl_MODULE_INDICATOR_CONDITION])
+])
+
+# gl_MODULE_INDICATOR_SET_VARIABLE_AUX([variable])
+# modifies the shell variable to include the gl_MODULE_INDICATOR_CONDITION.
+# The shell variable's value is a C preprocessor expression that evaluates
+# to 0 or 1.
+AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE_AUX],
+[
+ m4_if(m4_defn([gl_MODULE_INDICATOR_CONDITION]), [1],
+ [
+ dnl Simplify the expression VALUE || 1 to 1.
+ $1=1
+ ],
+ [gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR([$1],
+ [gl_MODULE_INDICATOR_CONDITION])])
+])
+
+# gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR([variable], [condition])
+# modifies the shell variable to include the given condition. The shell
+# variable's value is a C preprocessor expression that evaluates to 0 or 1.
+AC_DEFUN([gl_MODULE_INDICATOR_SET_VARIABLE_AUX_OR],
+[
+ dnl Simplify the expression 1 || CONDITION to 1.
+ if test "$[]$1" != 1; then
+ dnl Simplify the expression 0 || CONDITION to CONDITION.
+ if test "$[]$1" = 0; then
+ $1=$2
+ else
+ $1="($[]$1 || $2)"
+ fi
+ fi
])
# gl_MODULE_INDICATOR([modulename])
@@ -151,6 +212,83 @@ m4_ifndef([AS_VAR_IF],
[m4_define([AS_VAR_IF],
[AS_IF([test x"AS_VAR_GET([$1])" = x""$2], [$3], [$4])])])
+# gl_PROG_CC_C99
+# Modifies the value of the shell variable CC in an attempt to make $CC
+# understand ISO C99 source code.
+# This is like AC_PROG_CC_C99, except that
+# - AC_PROG_CC_C99 did not exist in Autoconf versions < 2.60,
+# - AC_PROG_CC_C99 does not mix well with AC_PROG_CC_STDC
+# <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00367.html>,
+# but many more packages use AC_PROG_CC_STDC than AC_PROG_CC_C99
+# <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00441.html>.
+# Remaining problems:
+# - When AC_PROG_CC_STDC is invoked twice, it adds the C99 enabling options
+# to CC twice
+# <http://lists.gnu.org/archive/html/bug-gnulib/2011-09/msg00431.html>.
+# - AC_PROG_CC_STDC is likely to change now that C11 is an ISO standard.
+AC_DEFUN([gl_PROG_CC_C99],
+[
+ dnl Change that version number to the minimum Autoconf version that supports
+ dnl mixing AC_PROG_CC_C99 calls with AC_PROG_CC_STDC calls.
+ m4_version_prereq([9.0],
+ [AC_REQUIRE([AC_PROG_CC_C99])],
+ [AC_REQUIRE([AC_PROG_CC_STDC])])
+])
+
+# gl_PROG_AR_RANLIB
+# Determines the values for AR, ARFLAGS, RANLIB that fit with the compiler.
+# The user can set the variables AR, ARFLAGS, RANLIB if he wants to override
+# the values.
+AC_DEFUN([gl_PROG_AR_RANLIB],
+[
+ dnl Minix 3 comes with two toolchains: The Amsterdam Compiler Kit compiler
+ dnl as "cc", and GCC as "gcc". They have different object file formats and
+ dnl library formats. In particular, the GNU binutils programs ar, ranlib
+ dnl produce libraries that work only with gcc, not with cc.
+ AC_REQUIRE([AC_PROG_CC])
+ AC_CACHE_CHECK([for Minix Amsterdam compiler], [gl_cv_c_amsterdam_compiler],
+ [
+ AC_EGREP_CPP([Amsterdam],
+ [
+#ifdef __ACK__
+Amsterdam
+#endif
+ ],
+ [gl_cv_c_amsterdam_compiler=yes],
+ [gl_cv_c_amsterdam_compiler=no])
+ ])
+ if test -z "$AR"; then
+ if test $gl_cv_c_amsterdam_compiler = yes; then
+ AR='cc -c.a'
+ if test -z "$ARFLAGS"; then
+ ARFLAGS='-o'
+ fi
+ else
+ dnl Use the Automake-documented default values for AR and ARFLAGS,
+ dnl but prefer ${host}-ar over ar (useful for cross-compiling).
+ AC_CHECK_TOOL([AR], [ar], [ar])
+ if test -z "$ARFLAGS"; then
+ ARFLAGS='cru'
+ fi
+ fi
+ else
+ if test -z "$ARFLAGS"; then
+ ARFLAGS='cru'
+ fi
+ fi
+ AC_SUBST([AR])
+ AC_SUBST([ARFLAGS])
+ if test -z "$RANLIB"; then
+ if test $gl_cv_c_amsterdam_compiler = yes; then
+ RANLIB=':'
+ else
+ dnl Use the ranlib program if it is available.
+ AC_PROG_RANLIB
+ fi
+ fi
+ AC_SUBST([RANLIB])
+])
+
# AC_PROG_MKDIR_P
# is a backport of autoconf-2.60's AC_PROG_MKDIR_P, with a fix
# for interoperability with automake-1.9.6 from autoconf-2.62.
diff --git a/m4/gnulib-comp.m4 b/m4/gnulib-comp.m4
index 8c573e37..80d7893e 100644
--- a/m4/gnulib-comp.m4
+++ b/m4/gnulib-comp.m4
@@ -1,10 +1,22 @@
# DO NOT EDIT! GENERATED AUTOMATICALLY!
-# Copyright (C) 2002-2011 Free Software Foundation, Inc.
+# Copyright (C) 2002-2012 Free Software Foundation, Inc.
#
-# This file is free software, distributed under the terms of the GNU
-# General Public License. As a special exception to the GNU General
-# Public License, this file may be distributed as part of a program
-# that contains a configuration script generated by Autoconf, under
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This file is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this file. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception to the GNU General Public License,
+# this file may be distributed as part of a program that
+# contains a configuration script generated by Autoconf, under
# the same distribution terms as the rest of that program.
#
# Generated by gnulib-tool.
@@ -25,28 +37,26 @@ AC_DEFUN([gl_EARLY],
m4_pattern_allow([^gl_ES$])dnl a valid locale name
m4_pattern_allow([^gl_LIBOBJS$])dnl a variable
m4_pattern_allow([^gl_LTLIBOBJS$])dnl a variable
- AC_REQUIRE([AC_PROG_RANLIB])
- # Code from module arg-nonnull:
- # Code from module c++defs:
+ AC_REQUIRE([gl_PROG_AR_RANLIB])
# Code from module extensions:
AC_REQUIRE([gl_USE_SYSTEM_EXTENSIONS])
# Code from module include_next:
# Code from module lib-ignore:
+ # Code from module snippet/arg-nonnull:
+ # Code from module snippet/c++defs:
+ # Code from module snippet/warn-on-use:
# Code from module stddef:
# Code from module string:
# Code from module strndup:
# Code from module strnlen:
- # Code from module warn-on-use:
])
# This macro should be invoked from ./configure.ac, in the section
# "Check for header files, types and library functions".
AC_DEFUN([gl_INIT],
[
- AM_CONDITIONAL([GL_COND_LIBTOOL], [false])
- gl_cond_libtool=false
- gl_libdeps=
- gl_ltlibdeps=
+ AM_CONDITIONAL([GL_COND_LIBTOOL], [true])
+ gl_cond_libtool=true
gl_m4_base='m4'
m4_pushdef([AC_LIBOBJ], m4_defn([gl_LIBOBJ]))
m4_pushdef([AC_REPLACE_FUNCS], m4_defn([gl_REPLACE_FUNCS]))
@@ -59,8 +69,15 @@ gl_IGNORE_UNUSED_LIBRARIES
gl_STDDEF_H
gl_HEADER_STRING_H
gl_FUNC_STRNDUP
+if test $HAVE_STRNDUP = 0 || test $REPLACE_STRNDUP = 1; then
+ AC_LIBOBJ([strndup])
+fi
gl_STRING_MODULE_INDICATOR([strndup])
gl_FUNC_STRNLEN
+if test $HAVE_DECL_STRNLEN = 0 || test $REPLACE_STRNLEN = 1; then
+ AC_LIBOBJ([strnlen])
+ gl_PREREQ_STRNLEN
+fi
gl_STRING_MODULE_INDICATOR([strnlen])
# End of code from modules
m4_ifval(gl_LIBSOURCES_LIST, [
@@ -139,10 +156,6 @@ changequote([, ])dnl
AC_SUBST([gltests_LIBOBJS], [$gltests_libobjs])
AC_SUBST([gltests_LTLIBOBJS], [$gltests_ltlibobjs])
])
- LIBGNU_LIBDEPS="$gl_libdeps"
- AC_SUBST([LIBGNU_LIBDEPS])
- LIBGNU_LTLIBDEPS="$gl_ltlibdeps"
- AC_SUBST([LIBGNU_LTLIBDEPS])
])
# Like AC_LIBOBJ, except that the module name goes
@@ -202,9 +215,9 @@ AC_DEFUN([gltests_LIBSOURCES], [
# This macro records the list of files which have been installed by
# gnulib-tool and may be removed by future gnulib-tool invocations.
AC_DEFUN([gl_FILE_LIST], [
- build-aux/arg-nonnull.h
- build-aux/c++defs.h
- build-aux/warn-on-use.h
+ build-aux/snippet/arg-nonnull.h
+ build-aux/snippet/c++defs.h
+ build-aux/snippet/warn-on-use.h
lib/dummy.c
lib/stddef.in.h
lib/string.in.h
diff --git a/m4/gnulib-tool.m4 b/m4/gnulib-tool.m4
index ed41e9d4..a09ffc1d 100644
--- a/m4/gnulib-tool.m4
+++ b/m4/gnulib-tool.m4
@@ -1,5 +1,5 @@
# gnulib-tool.m4 serial 2
-dnl Copyright (C) 2004-2005, 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2004-2005, 2009-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/include_next.m4 b/m4/include_next.m4
index b3c78491..a60a2614 100644
--- a/m4/include_next.m4
+++ b/m4/include_next.m4
@@ -1,5 +1,5 @@
-# include_next.m4 serial 18
-dnl Copyright (C) 2006-2011 Free Software Foundation, Inc.
+# include_next.m4 serial 23
+dnl Copyright (C) 2006-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
@@ -143,7 +143,7 @@ choke me
# even if the compiler does not support include_next.
# The three "///" are to pacify Sun C 5.8, which otherwise would say
# "warning: #include of /usr/include/... may be non-portable".
-# Use `""', not `<>', so that the /// cannot be confused with a C99 comment.
+# Use '""', not '<>', so that the /// cannot be confused with a C99 comment.
# Note: This macro assumes that the header file is not empty after
# preprocessing, i.e. it does not only define preprocessor macros but also
# provides some type/enum definitions or function/variable declarations.
@@ -175,11 +175,13 @@ AC_DEFUN([gl_NEXT_HEADERS_INTERNAL],
[AC_CHECK_HEADERS_ONCE([$1])
])
+dnl FIXME: gl_next_header and gl_header_exists must be used unquoted
+dnl until we can assume autoconf 2.64 or newer.
m4_foreach_w([gl_HEADER_NAME], [$1],
[AS_VAR_PUSHDEF([gl_next_header],
[gl_cv_next_]m4_defn([gl_HEADER_NAME]))
if test $gl_cv_have_include_next = yes; then
- AS_VAR_SET([gl_next_header], ['<'gl_HEADER_NAME'>'])
+ AS_VAR_SET(gl_next_header, ['<'gl_HEADER_NAME'>'])
else
AC_CACHE_CHECK(
[absolute name of <]m4_defn([gl_HEADER_NAME])[>],
@@ -205,33 +207,57 @@ AC_DEFUN([gl_NEXT_HEADERS_INTERNAL],
aix*) gl_absname_cpp="$ac_cpp -C" ;;
*) gl_absname_cpp="$ac_cpp" ;;
esac
+changequote(,)
+ case "$host_os" in
+ mingw*)
+ dnl For the sake of native Windows compilers (excluding gcc),
+ dnl treat backslash as a directory separator, like /.
+ dnl Actually, these compilers use a double-backslash as
+ dnl directory separator, inside the
+ dnl # line "filename"
+ dnl directives.
+ gl_dirsep_regex='[/\\]'
+ ;;
+ *)
+ gl_dirsep_regex='\/'
+ ;;
+ esac
+ dnl A sed expression that turns a string into a basic regular
+ dnl expression, for use within "/.../".
+ gl_make_literal_regex_sed='s,[]$^\\.*/[],\\&,g'
+changequote([,])
+ gl_header_literal_regex=`echo ']m4_defn([gl_HEADER_NAME])[' \
+ | sed -e "$gl_make_literal_regex_sed"`
+ gl_absolute_header_sed="/${gl_dirsep_regex}${gl_header_literal_regex}/"'{
+ s/.*"\(.*'"${gl_dirsep_regex}${gl_header_literal_regex}"'\)".*/\1/
+changequote(,)dnl
+ s|^/[^/]|//&|
+changequote([,])dnl
+ p
+ q
+ }'
dnl eval is necessary to expand gl_absname_cpp.
dnl Ultrix and Pyramid sh refuse to redirect output of eval,
dnl so use subshell.
- AS_VAR_SET([gl_next_header],
+ AS_VAR_SET(gl_next_header,
['"'`(eval "$gl_absname_cpp conftest.$ac_ext") 2>&AS_MESSAGE_LOG_FD |
- sed -n '\#/]m4_defn([gl_HEADER_NAME])[#{
- s#.*"\(.*/]m4_defn([gl_HEADER_NAME])[\)".*#\1#
- s#^/[^/]#//&#
- p
- q
- }'`'"'])
+ sed -n "$gl_absolute_header_sed"`'"'])
m4_if([$2], [check],
[else
- AS_VAR_SET([gl_next_header], ['<'gl_HEADER_NAME'>'])
+ AS_VAR_SET(gl_next_header, ['<'gl_HEADER_NAME'>'])
fi
])
])
fi
AC_SUBST(
AS_TR_CPP([NEXT_]m4_defn([gl_HEADER_NAME])),
- [AS_VAR_GET([gl_next_header])])
+ [AS_VAR_GET(gl_next_header)])
if test $gl_cv_have_include_next = yes || test $gl_cv_have_include_next = buggy; then
# INCLUDE_NEXT_AS_FIRST_DIRECTIVE='include_next'
gl_next_as_first_directive='<'gl_HEADER_NAME'>'
else
# INCLUDE_NEXT_AS_FIRST_DIRECTIVE='include'
- gl_next_as_first_directive=AS_VAR_GET([gl_next_header])
+ gl_next_as_first_directive=AS_VAR_GET(gl_next_header)
fi
AC_SUBST(
AS_TR_CPP([NEXT_AS_FIRST_DIRECTIVE_]m4_defn([gl_HEADER_NAME])),
diff --git a/m4/lib-ignore.m4 b/m4/lib-ignore.m4
index 1fdfdc07..292c4691 100644
--- a/m4/lib-ignore.m4
+++ b/m4/lib-ignore.m4
@@ -1,6 +1,6 @@
# If possible, ignore libraries that are not depended on.
-dnl Copyright (C) 2006, 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2006, 2009-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/onceonly.m4 b/m4/onceonly.m4
index 223071a2..275d73c4 100644
--- a/m4/onceonly.m4
+++ b/m4/onceonly.m4
@@ -1,9 +1,22 @@
-# onceonly.m4 serial 7
-dnl Copyright (C) 2002-2003, 2005-2006, 2008-2011 Free Software Foundation,
+# onceonly.m4 serial 9
+dnl Copyright (C) 2002-2003, 2005-2006, 2008-2012 Free Software Foundation,
dnl Inc.
-dnl This file is free software, distributed under the terms of the GNU
-dnl General Public License. As a special exception to the GNU General
-dnl Public License, this file may be distributed as part of a program
+dnl
+dnl This file is free software; you can redistribute it and/or modify
+dnl it under the terms of the GNU General Public License as published by
+dnl the Free Software Foundation; either version 3 of the License, or
+dnl (at your option) any later version.
+dnl
+dnl This file is distributed in the hope that it will be useful,
+dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
+dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+dnl GNU General Public License for more details.
+dnl
+dnl You should have received a copy of the GNU General Public License
+dnl along with this file. If not, see <http://www.gnu.org/licenses/>.
+dnl
+dnl As a special exception to the GNU General Public License,
+dnl this file may be distributed as part of a program
dnl that contains a configuration script generated by Autoconf, under
dnl the same distribution terms as the rest of that program.
@@ -67,7 +80,7 @@ AC_DEFUN([AC_CHECK_FUNCS_ONCE], [
[gl_func_list="$gl_func_list gl_FUNC_NAME"])
gl_FUNCS_EXPANSION
AH_TEMPLATE(AS_TR_CPP([HAVE_]m4_defn([gl_FUNC_NAME])),
- [Define to 1 if you have the `]m4_defn([gl_FUNC_NAME])[' function.])
+ [Define to 1 if you have the ']m4_defn([gl_FUNC_NAME])[' function.])
])
AC_REQUIRE([gl_CHECK_FUNC_]m4_defn([gl_FUNC_NAME]))
])
diff --git a/m4/stddef_h.m4 b/m4/stddef_h.m4
index 1ae23443..cc116096 100644
--- a/m4/stddef_h.m4
+++ b/m4/stddef_h.m4
@@ -1,6 +1,6 @@
dnl A placeholder for POSIX 2008 <stddef.h>, for platforms that have issues.
# stddef_h.m4 serial 4
-dnl Copyright (C) 2009-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2009-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
diff --git a/m4/string_h.m4 b/m4/string_h.m4
index df8c4035..5677e092 100644
--- a/m4/string_h.m4
+++ b/m4/string_h.m4
@@ -1,11 +1,11 @@
# Configure a GNU-like replacement for <string.h>.
-# Copyright (C) 2007-2011 Free Software Foundation, Inc.
+# Copyright (C) 2007-2012 Free Software Foundation, Inc.
# This file is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.
-# serial 20
+# serial 21
# Written by Paul Eggert.
@@ -27,9 +27,9 @@ AC_DEFUN([gl_HEADER_STRING_H_BODY],
dnl guaranteed by C89.
gl_WARN_ON_USE_PREPARE([[#include <string.h>
]],
- [memmem mempcpy memrchr rawmemchr stpcpy stpncpy strchrnul strdup
- strncat strndup strnlen strpbrk strsep strcasestr strtok_r strerror_r
- strsignal strverscmp])
+ [ffsl ffsll memmem mempcpy memrchr rawmemchr stpcpy stpncpy strchrnul
+ strdup strncat strndup strnlen strpbrk strsep strcasestr strtok_r
+ strerror_r strsignal strverscmp])
])
AC_DEFUN([gl_STRING_MODULE_INDICATOR],
@@ -43,6 +43,8 @@ AC_DEFUN([gl_STRING_MODULE_INDICATOR],
AC_DEFUN([gl_HEADER_STRING_H_DEFAULTS],
[
+ GNULIB_FFSL=0; AC_SUBST([GNULIB_FFSL])
+ GNULIB_FFSLL=0; AC_SUBST([GNULIB_FFSLL])
GNULIB_MEMCHR=0; AC_SUBST([GNULIB_MEMCHR])
GNULIB_MEMMEM=0; AC_SUBST([GNULIB_MEMMEM])
GNULIB_MEMPCPY=0; AC_SUBST([GNULIB_MEMPCPY])
@@ -80,6 +82,8 @@ AC_DEFUN([gl_HEADER_STRING_H_DEFAULTS],
GNULIB_STRVERSCMP=0; AC_SUBST([GNULIB_STRVERSCMP])
HAVE_MBSLEN=0; AC_SUBST([HAVE_MBSLEN])
dnl Assume proper GNU behavior unless another module says otherwise.
+ HAVE_FFSL=1; AC_SUBST([HAVE_FFSL])
+ HAVE_FFSLL=1; AC_SUBST([HAVE_FFSLL])
HAVE_MEMCHR=1; AC_SUBST([HAVE_MEMCHR])
HAVE_DECL_MEMMEM=1; AC_SUBST([HAVE_DECL_MEMMEM])
HAVE_MEMPCPY=1; AC_SUBST([HAVE_MEMPCPY])
diff --git a/m4/strndup.m4 b/m4/strndup.m4
index d8f00cab..bdde5fe1 100644
--- a/m4/strndup.m4
+++ b/m4/strndup.m4
@@ -1,5 +1,5 @@
-# strndup.m4 serial 18
-dnl Copyright (C) 2002-2003, 2005-2011 Free Software Foundation, Inc.
+# strndup.m4 serial 20
+dnl Copyright (C) 2002-2003, 2005-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
@@ -18,13 +18,18 @@ AC_DEFUN([gl_FUNC_STRNDUP],
fi
if test $ac_cv_func_strndup = yes; then
+ HAVE_STRNDUP=1
# AIX 4.3.3, AIX 5.1 have a function that fails to add the terminating '\0'.
AC_CACHE_CHECK([for working strndup], [gl_cv_func_strndup_works],
[AC_RUN_IFELSE([
AC_LANG_PROGRAM([[#include <string.h>
#include <stdlib.h>]], [[
#ifndef HAVE_DECL_STRNDUP
- extern char *strndup (const char *, size_t);
+ extern
+ #ifdef __cplusplus
+ "C"
+ #endif
+ char *strndup (const char *, size_t);
#endif
char *s;
s = strndup ("some longer string", 15);
@@ -42,12 +47,9 @@ changequote(,)dnl
changequote([,])dnl
])])
case $gl_cv_func_strndup_works in
- *no)
- REPLACE_STRNDUP=1
- AC_LIBOBJ([strndup])
- ;;
+ *no) REPLACE_STRNDUP=1 ;;
esac
else
- AC_LIBOBJ([strndup])
+ HAVE_STRNDUP=0
fi
])
diff --git a/m4/strnlen.m4 b/m4/strnlen.m4
index a1c59ac6..d97e3075 100644
--- a/m4/strnlen.m4
+++ b/m4/strnlen.m4
@@ -1,5 +1,5 @@
-# strnlen.m4 serial 12
-dnl Copyright (C) 2002-2003, 2005-2007, 2009-2011 Free Software Foundation,
+# strnlen.m4 serial 13
+dnl Copyright (C) 2002-2003, 2005-2007, 2009-2012 Free Software Foundation,
dnl Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
@@ -16,16 +16,14 @@ AC_DEFUN([gl_FUNC_STRNLEN],
if test $ac_cv_have_decl_strnlen = no; then
HAVE_DECL_STRNLEN=0
else
- AC_FUNC_STRNLEN
+ m4_pushdef([AC_LIBOBJ], [:])
dnl Note: AC_FUNC_STRNLEN does AC_LIBOBJ([strnlen]).
+ AC_FUNC_STRNLEN
+ m4_popdef([AC_LIBOBJ])
if test $ac_cv_func_strnlen_working = no; then
REPLACE_STRNLEN=1
fi
fi
- if test $HAVE_DECL_STRNLEN = 0 || test $REPLACE_STRNLEN = 1; then
- AC_LIBOBJ([strnlen])
- gl_PREREQ_STRNLEN
- fi
])
# Prerequisites of lib/strnlen.c.
diff --git a/m4/warn-on-use.m4 b/m4/warn-on-use.m4
index e0d0f276..a77802eb 100644
--- a/m4/warn-on-use.m4
+++ b/m4/warn-on-use.m4
@@ -1,5 +1,5 @@
-# warn-on-use.m4 serial 2
-dnl Copyright (C) 2010-2011 Free Software Foundation, Inc.
+# warn-on-use.m4 serial 5
+dnl Copyright (C) 2010-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
@@ -18,8 +18,8 @@ dnl with or without modifications, as long as this notice is preserved.
# some systems declare functions in the wrong header, then INCLUDES
# should do likewise.
#
-# If you assume C89, then it is generally safe to assume declarations
-# for functions declared in that standard (such as gets) without
+# It is generally safe to assume declarations for functions declared
+# in the intersection of C89 and C11 (such as printf) without
# needing gl_WARN_ON_USE_PREPARE.
AC_DEFUN([gl_WARN_ON_USE_PREPARE],
[
@@ -27,6 +27,8 @@ AC_DEFUN([gl_WARN_ON_USE_PREPARE],
[AH_TEMPLATE([HAVE_RAW_DECL_]AS_TR_CPP(m4_defn([gl_decl])),
[Define to 1 if ]m4_defn([gl_decl])[ is declared even after
undefining macros.])])dnl
+dnl FIXME: gl_Symbol must be used unquoted until we can assume
+dnl autoconf 2.64 or newer.
for gl_func in m4_flatten([$2]); do
AS_VAR_PUSHDEF([gl_Symbol], [gl_cv_have_raw_decl_$gl_func])dnl
AC_CACHE_CHECK([whether $gl_func is declared without a macro],
@@ -35,8 +37,8 @@ AC_DEFUN([gl_WARN_ON_USE_PREPARE],
[@%:@undef $gl_func
(void) $gl_func;])],
[AS_VAR_SET(gl_Symbol, [yes])], [AS_VAR_SET(gl_Symbol, [no])])])
- AS_VAR_IF(gl_Symbol, [yes],
- [AC_DEFINE_UNQUOTED(AS_TR_CPP([HAVE_RAW_DECL_$gl_func]), [1])
+ AS_VAR_IF(gl_Symbol, [yes],
+ [AC_DEFINE_UNQUOTED(AS_TR_CPP([HAVE_RAW_DECL_$gl_func]), [1])
dnl shortcut - if the raw declaration exists, then set a cache
dnl variable to allow skipping any later AC_CHECK_DECL efforts
eval ac_cv_have_decl_$gl_func=yes])
diff --git a/m4/wchar_t.m4 b/m4/wchar_t.m4
index d2c03c42..534735d8 100644
--- a/m4/wchar_t.m4
+++ b/m4/wchar_t.m4
@@ -1,5 +1,5 @@
# wchar_t.m4 serial 4 (gettext-0.18.2)
-dnl Copyright (C) 2002-2003, 2008-2011 Free Software Foundation, Inc.
+dnl Copyright (C) 2002-2003, 2008-2012 Free Software Foundation, Inc.
dnl This file is free software; the Free Software Foundation
dnl gives unlimited permission to copy and/or distribute it,
dnl with or without modifications, as long as this notice is preserved.
diff --git a/src/check_hkl.c b/src/check_hkl.c
index 649b86af..4927e60e 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -339,43 +339,44 @@ int main(int argc, char *argv[])
while ((c = getopt_long(argc, argv, "hy:p:", longopts, NULL)) != -1) {
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 'p' :
+ case 'p' :
pdb = strdup(optarg);
break;
- case 0 :
+ case 0 :
break;
- case 2 :
+ case 2 :
if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
ERROR("Invalid value for --rmin\n");
return 1;
}
break;
- case 3 :
+ case 3 :
if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
ERROR("Invalid value for --rmax\n");
return 1;
}
break;
- case 4 :
+ case 4 :
if ( sscanf(optarg, "%f", &sigma_cutoff) != 1 ) {
ERROR("Invalid value for --sigma-cutoff\n");
return 1;
}
break;
- default :
+ default :
return 1;
}
diff --git a/src/cl-utils.c b/src/cl-utils.c
index ae146ed0..71ff25b5 100644
--- a/src/cl-utils.c
+++ b/src/cl-utils.c
@@ -46,28 +46,71 @@
const char *clError(cl_int err)
{
switch ( err ) {
- case CL_SUCCESS : return "no error";
- case CL_INVALID_PLATFORM : return "invalid platform";
- case CL_INVALID_KERNEL : return "invalid kernel";
- case CL_INVALID_ARG_INDEX : return "invalid argument index";
- case CL_INVALID_ARG_VALUE : return "invalid argument value";
- case CL_INVALID_MEM_OBJECT : return "invalid memory object";
- case CL_INVALID_SAMPLER : return "invalid sampler";
- case CL_INVALID_ARG_SIZE : return "invalid argument size";
- case CL_INVALID_COMMAND_QUEUE : return "invalid command queue";
- case CL_INVALID_CONTEXT : return "invalid context";
- case CL_INVALID_VALUE : return "invalid value";
- case CL_INVALID_EVENT_WAIT_LIST : return "invalid wait list";
- case CL_MAP_FAILURE : return "map failure";
- case CL_MEM_OBJECT_ALLOCATION_FAILURE : return "object allocation failure";
- case CL_OUT_OF_HOST_MEMORY : return "out of host memory";
- case CL_OUT_OF_RESOURCES : return "out of resources";
- case CL_INVALID_KERNEL_NAME : return "invalid kernel name";
- case CL_INVALID_KERNEL_ARGS : return "invalid kernel arguments";
- case CL_INVALID_WORK_GROUP_SIZE : return "invalid work group size";
- case CL_IMAGE_FORMAT_NOT_SUPPORTED : return "image format not supported";
- case CL_INVALID_WORK_DIMENSION : return "invalid work dimension";
- default :
+
+ case CL_SUCCESS :
+ return "no error";
+
+ case CL_INVALID_PLATFORM :
+ return "invalid platform";
+
+ case CL_INVALID_KERNEL :
+ return "invalid kernel";
+
+ case CL_INVALID_ARG_INDEX :
+ return "invalid argument index";
+
+ case CL_INVALID_ARG_VALUE :
+ return "invalid argument value";
+
+ case CL_INVALID_MEM_OBJECT :
+ return "invalid memory object";
+
+ case CL_INVALID_SAMPLER :
+ return "invalid sampler";
+
+ case CL_INVALID_ARG_SIZE :
+ return "invalid argument size";
+
+ case CL_INVALID_COMMAND_QUEUE :
+ return "invalid command queue";
+
+ case CL_INVALID_CONTEXT :
+ return "invalid context";
+
+ case CL_INVALID_VALUE :
+ return "invalid value";
+
+ case CL_INVALID_EVENT_WAIT_LIST :
+ return "invalid wait list";
+
+ case CL_MAP_FAILURE :
+ return "map failure";
+
+ case CL_MEM_OBJECT_ALLOCATION_FAILURE :
+ return "object allocation failure";
+
+ case CL_OUT_OF_HOST_MEMORY :
+ return "out of host memory";
+
+ case CL_OUT_OF_RESOURCES :
+ return "out of resources";
+
+ case CL_INVALID_KERNEL_NAME :
+ return "invalid kernel name";
+
+ case CL_INVALID_KERNEL_ARGS :
+ return "invalid kernel arguments";
+
+ case CL_INVALID_WORK_GROUP_SIZE :
+ return "invalid work group size";
+
+ case CL_IMAGE_FORMAT_NOT_SUPPORTED :
+ return "image format not supported";
+
+ case CL_INVALID_WORK_DIMENSION :
+ return "invalid work dimension";
+
+ default :
return "unknown error";
}
}
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index 5846682f..b926c3ae 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -331,49 +331,51 @@ int main(int argc, char *argv[])
{
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'o' :
+ case 'o' :
ratiofile = strdup(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 'p' :
+ case 'p' :
pdb = strdup(optarg);
break;
- case 'u' :
+ case 'u' :
config_unity = 1;
break;
- case 0 :
+ case 0 :
break;
- case 2 :
+ case 2 :
if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
ERROR("Invalid value for --rmin\n");
return 1;
}
break;
- case 3 :
+ case 3 :
if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
ERROR("Invalid value for --rmax\n");
return 1;
}
break;
- case 4 :
+ case 4 :
config_shells = get_r_shell(optarg);
break;
- default :
+ default :
return 1;
+
}
}
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 9f86f0f7..de5d74de 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -391,44 +391,46 @@ int main(int argc, char *argv[])
longopts, NULL)) != -1) {
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 't' :
+ case 't' :
template = strdup(optarg);
break;
- case 'o' :
+ case 'o' :
output = strdup(optarg);
break;
- case 'i' :
+ case 'i' :
input_file = strdup(optarg);
break;
- case 'y' :
+ case 'y' :
mero_str = strdup(optarg);
break;
- case 'w' :
+ case 'w' :
holo_str = strdup(optarg);
break;
- case 'e' :
+ case 'e' :
expand_str = strdup(optarg);
break;
- case 2 :
+ case 2 :
adu_per_photon = strtof(optarg, NULL);
have_adu_per_photon = 1;
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
+
}
}
diff --git a/src/hdfsee.c b/src/hdfsee.c
index 22302ec8..613572a2 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -151,15 +151,16 @@ int main(int argc, char *argv[])
char *test;
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'p' :
+ case 'p' :
peaks = strdup(optarg);
break;
- case 'i' :
+ case 'i' :
boost = atoi(optarg);
if ( boost < 1 ) {
ERROR("Intensity boost must be a positive"
@@ -168,7 +169,7 @@ int main(int argc, char *argv[])
}
break;
- case 'b' :
+ case 'b' :
binning = atoi(optarg);
if ( binning < 1 ) {
ERROR("Binning must be a positive integer.\n");
@@ -176,19 +177,19 @@ int main(int argc, char *argv[])
}
break;
- case 'c' :
+ case 'c' :
cscale = strdup(optarg);
break;
- case 'e' :
+ case 'e' :
element = strdup(optarg);
break;
- case 'g' :
+ case 'g' :
geometry = strdup(optarg);
break;
- case 2 :
+ case 2 :
ring_size = strtod(optarg, &test);
if ( test == optarg ) {
ERROR("Ring size must be numerical.\n");
@@ -196,7 +197,7 @@ int main(int argc, char *argv[])
}
break;
- case 'r' :
+ case 'r' :
config_showrings = 1;
reslist = strdup(optarg);
int nchar = strlen(reslist);
@@ -219,10 +220,10 @@ int main(int argc, char *argv[])
}
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 31822eca..9e054675 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -341,47 +341,48 @@ int main(int argc, char *argv[])
longopts, NULL)) != -1)
{
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'o' :
+ case 'o' :
output_file = strdup(optarg);
break;
- case 'i' :
+ case 'i' :
input_file = strdup(optarg);
break;
- case 'b' :
+ case 'b' :
beamfile = strdup(optarg);
break;
- case 'p' :
+ case 'p' :
cellfile = strdup(optarg);
break;
- case 'g' :
+ case 'g' :
geomfile = strdup(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 'n' :
+ case 'n' :
n = atoi(optarg);
break;
- case 'r' :
+ case 'r' :
save_file = strdup(optarg);
break;
- case 'j' :
+ case 'j' :
n_threads = atoi(optarg);
break;
- case 'c' :
+ case 'c' :
cnoise = strtod(optarg, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid cell noise value.\n");
@@ -389,15 +390,16 @@ int main(int argc, char *argv[])
}
break;
- case 2 :
+ case 2 :
phist_file = strdup(optarg);
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
+
}
}
diff --git a/src/partialator.c b/src/partialator.c
index 91f2ff99..4fa8c2bd 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -325,35 +325,36 @@ int main(int argc, char *argv[])
{
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'i' :
+ case 'i' :
infile = strdup(optarg);
break;
- case 'g' :
+ case 'g' :
geomfile = strdup(optarg);
break;
- case 'j' :
+ case 'j' :
nthreads = atoi(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 'o' :
+ case 'o' :
outfile = strdup(optarg);
break;
- case 'n' :
+ case 'n' :
n_iter = atoi(optarg);
break;
- case 'b' :
+ case 'b' :
beam = get_beam_parameters(optarg);
if ( beam == NULL ) {
ERROR("Failed to load beam parameters"
@@ -362,15 +363,16 @@ int main(int argc, char *argv[])
}
break;
- case 'r' :
+ case 'r' :
reference_file = strdup(optarg);
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
+
}
}
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index c207e0dc..03b009b4 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -294,15 +294,16 @@ int main(int argc, char *argv[])
longopts, NULL)) != -1) {
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'r' :
+ case 'r' :
config_randomquat = 1;
break;
- case 'n' :
+ case 'n' :
n_images = strtol(optarg, &rval, 10);
if ( *rval != '\0' ) {
ERROR("Invalid number of images.\n");
@@ -310,43 +311,43 @@ int main(int argc, char *argv[])
}
break;
- case 'i' :
+ case 'i' :
intfile = strdup(optarg);
break;
- case 't' :
+ case 't' :
grad_str = strdup(optarg);
break;
- case 'p' :
+ case 'p' :
filename = strdup(optarg);
break;
- case 'o' :
+ case 'o' :
outfile = strdup(optarg);
break;
- case 'w' :
+ case 'w' :
powder_fn = strdup(optarg);
break;
- case 'g' :
+ case 'g' :
geometry = strdup(optarg);
break;
- case 'b' :
+ case 'b' :
beamfile = strdup(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 2 :
+ case 2 :
gpu_dev = atoi(optarg);
break;
- case 3 :
+ case 3 :
min_size = strtod(optarg, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid minimum size.\n");
@@ -355,7 +356,7 @@ int main(int argc, char *argv[])
random_size++;
break;
- case 4 :
+ case 4 :
max_size = strtod(optarg, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid maximum size.\n");
@@ -364,11 +365,12 @@ int main(int argc, char *argv[])
random_size++;
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
+
}
}
diff --git a/src/post-refinement.c b/src/post-refinement.c
index cf7b2576..78c47d07 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -241,7 +241,7 @@ static void apply_shift(struct image *image, int k, double shift)
{
switch ( k ) {
- case REF_DIV :
+ case REF_DIV :
if ( isnan(shift) ) {
ERROR("NaN divergence shift\n");
} else {
@@ -250,23 +250,23 @@ static void apply_shift(struct image *image, int k, double shift)
}
break;
- case REF_R :
+ case REF_R :
image->profile_radius += shift;
break;
- case REF_ASX :
- case REF_ASY :
- case REF_ASZ :
- case REF_BSX :
- case REF_BSY :
- case REF_BSZ :
- case REF_CSX :
- case REF_CSY :
- case REF_CSZ :
+ case REF_ASX :
+ case REF_ASY :
+ case REF_ASZ :
+ case REF_BSX :
+ case REF_BSY :
+ case REF_BSZ :
+ case REF_CSX :
+ case REF_CSY :
+ case REF_CSZ :
apply_cell_shift(image->indexed_cell, k, shift);
break;
- default :
+ default :
ERROR("No shift defined for parameter %i\n", k);
abort();
diff --git a/src/powder_plot.c b/src/powder_plot.c
index 3f49695a..049b9c0e 100644
--- a/src/powder_plot.c
+++ b/src/powder_plot.c
@@ -775,51 +775,51 @@ int main(int argc, char *argv[])
switch (c) {
- case 'h' :
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'i' :
+ case 'i' :
filename = strdup(optarg);
break;
- case 'o' :
+ case 'o' :
output = strdup(optarg);
break;
- case 'g' :
+ case 'g' :
geometry = strdup(optarg);
break;
- case 'b' :
+ case 'b' :
beamf = strdup(optarg);
break;
- case 'p' :
+ case 'p' :
pdb = strdup(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 's' :
+ case 's' :
hist_info.histsize = atoi(optarg);
break;
- case 'e' :
+ case 'e' :
element = strdup(optarg);
break;
- case 1 :
+ case 1 :
hist_info.q_max = atof(optarg);
break;
- case 2 :
+ case 2 :
hist_info.q_min = atof(optarg);
break;
- case 3 :
+ case 3 :
if (strcmp(optarg, "linear") == 0 ) {
hist_info.spacing = LINEAR;
} else if (strcmp(optarg, "wilson") == 0 ) {
@@ -832,14 +832,14 @@ int main(int argc, char *argv[])
}
break;
- case 'd' :
+ case 'd' :
datatype = strdup(optarg);
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
}
@@ -1096,45 +1096,50 @@ int main(int argc, char *argv[])
}
/* Process reflections based on file type and data type */
- switch (file_type) {
- case FILE_H5 :
+ switch ( file_type ) {
+ case FILE_H5 :
n_patterns++;
n_peaks = process_h5(&image, &hist_info, histdata);
free(image.data);
break;
- case FILE_HKL :
+ case FILE_HKL :
n_patterns++; //inc number of patterns used
n_peaks = process_hkl(&image, sym, cell, &hist_info, histdata,
q_scaling, use_redundancy);
break;
- case FILE_STREAM :
- switch (data_type) {
- case PLOT_REFL :
+ case FILE_STREAM :
+ switch ( data_type ) {
+
+ case PLOT_REFL :
n_peaks = process_stream_reflection(fh, &image,
&hist_info, histdata, &n_patterns);
break;
- case PLOT_HKL :
+
+ case PLOT_HKL :
n_peaks = process_stream_hkl(fh, &image, &hist_info,
+
histdata, cell, &n_patterns);
break;
- case PLOT_PEAKS :
+ case PLOT_PEAKS :
n_peaks = process_stream_peaks(fh, &image, &hist_info,
histdata, &n_patterns, only_indexed);
break;
- case PLOT_H5 :
+
+ case PLOT_H5 :
n_peaks = process_stream_h5(fh, &image, &hist_info,
histdata, config_satcorr, only_indexed,
&n_patterns, element);
break;
- default :
+
+ default :
break;
}
fclose(fh);
break;
- default :
+ default :
break;
}
diff --git a/src/render_hkl.c b/src/render_hkl.c
index a63cbad3..a01e7609 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -118,23 +118,29 @@ static double max_value(RefList *list, int wght, const SymOpList *sym)
n = num_equivs(sym, m);
switch ( wght ) {
- case WGHT_I :
+
+ case WGHT_I :
val = get_intensity(refl);
break;
- case WGHT_SQRTI :
+
+ case WGHT_SQRTI :
val = get_intensity(refl);
val = (val>0.0) ? sqrt(val) : 0.0;
break;
- case WGHT_COUNTS :
+
+ case WGHT_COUNTS :
val = get_redundancy(refl);
val /= (double)n;
break;
- case WGHT_RAWCOUNTS :
+
+ case WGHT_RAWCOUNTS :
val = get_redundancy(refl);
break;
- default :
+
+ default :
ERROR("Invalid weighting.\n");
abort();
+
}
if ( val > max ) max = val;
@@ -192,23 +198,29 @@ static void draw_circles(double xh, double xk, double xl,
yi = (h*yh + k*yk + l*yl) / ny;
switch ( wght) {
- case WGHT_I :
+
+ case WGHT_I :
val = get_intensity(refl);
break;
- case WGHT_SQRTI :
+
+ case WGHT_SQRTI :
val = get_intensity(refl);
val = (val>0.0) ? sqrt(val) : 0.0;
break;
- case WGHT_COUNTS :
+
+ case WGHT_COUNTS :
val = get_redundancy(refl);
val /= (double)n;
break;
- case WGHT_RAWCOUNTS :
+
+ case WGHT_RAWCOUNTS :
val = get_redundancy(refl);
break;
- default :
+
+ default :
ERROR("Invalid weighting.\n");
abort();
+
}
/* Absolute location in image based on 2D basis */
@@ -621,43 +633,44 @@ int main(int argc, char *argv[])
longopts, NULL)) != -1) {
switch (c) {
- case 'h' :
+
+ case 'h' :
show_help(argv[0]);
return 0;
- case 'p' :
+ case 'p' :
pdb = strdup(optarg);
break;
- case 'b' :
+ case 'b' :
boost = atof(optarg);
break;
- case 'y' :
+ case 'y' :
sym_str = strdup(optarg);
break;
- case 'w' :
+ case 'w' :
weighting = strdup(optarg);
break;
- case 'c' :
+ case 'c' :
cscale = strdup(optarg);
break;
- case 'd' :
+ case 'd' :
down = strdup(optarg);
break;
- case 'r' :
+ case 'r' :
right = strdup(optarg);
break;
- case 'o' :
+ case 'o' :
outfile = strdup(optarg);
break;
- case 2 :
+ case 2 :
errno = 0;
scale_top = strtod(optarg, &endptr);
if ( !( (optarg[0] != '\0') && (endptr[0] == '\0') )
@@ -672,11 +685,12 @@ int main(int argc, char *argv[])
}
break;
- case 0 :
+ case 0 :
break;
- default :
+ default :
return 1;
+
}
}