Before this commit, many files are using std::string without including
<string>. It can work accidentally but causes issues when refactoring,
especially if using operator <<() which is included implicitly by some
compilers.

To find guilty header files, I used:

    grep -l "^ *std::string" $(grep -L "#include <string>" $(find . -type f -name "*.h"))

which finds all files containing "std::string" at the beginning of a line
(usually a member or variable declaration), but not "#include <string>".
And then this script to add the includes (plus some manual ediing):

    #!/usr/bin/env python3

    import re
    import argparse

    def fix_file(filename, header):

        with open(filename, "r") as f:
            content = f.read()

        matches = list(re.finditer(r"(#include .*\n)\n", content))
        if len(matches) == 0:
            print("no include!")
            sys.exit(-1)

        pos = matches[-1].end(1)
        open(filename, "w").write(content[:pos] + "#include <{}>\n".format(header) + content[pos:])

    if __name__ == "__main__":
        parser = argparse.ArgumentParser()
        parser.add_argument('--header', type=str, required=True)
        parser.add_argument('files', type=str, nargs='+')
        args = parser.parse_args()

        for filename in args.files:
            fix_file(filename, args.header)

find \( -name "*.hxx" -or -name "*.h" -or -name "*.cxx" \) -not -path "*ThirdParty*" -print0 | xargs -0 sed -sri "s/([^<])vcl_(adjacent_find|and|binary|binary_search|copy|copy_|count|count_if|equal|equal_range|fill|fill_n|find|find_end|find_first_of|find_if|for_each|generate|generate_n|generators_|heap|includes|inplace_merge|iter_swap|lexicographical_compare|lower_bound|make_heap|max|min|max_element|merge|merge_|min_element|mismatch|next_permutation|nth_element|partial_sort|partial_sort_copy|partition|stable_partition|partitions_|pop_heap|prev_permutation|push_heap|random_shuffle|remove|remove_copy|remove_copy_if|remove_if|replace|replace_copy|replace_copy_if|replace_if|reverse|reverse_copy|rotate|rotate_copy|search|search_n|set_difference|set_intersection|set_symmetric_difference|set_union|sort|sort_|sort_heap|stable_sort|swap|swap_|swap_ranges|transform|unique|unique_copy|upper_bound|bitset|abs|acos|asin|atan|atan2|ceil|cos|cosh|exp|fabs|floor|fmod|frexp|ldexp|log|log10|modf|pow|sin|sinh|sqrt|tan|tanh|complex|real|imag|arg|norm|conj|polar|jmp_buf|longjmp|sig_atomic_t|raise|signal|va_list|ptrdiff_t|size_t|FILE|fpos_t|fopen|fclose|feof|ferror|fflush|fgetc|fgetpos|fgets|fwrite|fread|fseek|ftell|perror|clearerr|rename|fputc|fputs|freopen|fsetpos|getc|getchar|gets|putc|putchar|puts|rewind|setbuf|setvbuf|tmpfile|tmpnam|ungetc|printf|sprintf|fprintf|vprintf|vsprintf|vfprintf)/\1std::\2/g"

find \( -name "*.hxx" -or -name "*.h" -or -name "*.cxx" \) -not -path "*ThirdParty*" -print0 | xargs -0 sed -sri "s/<<vcl_log/<<std::log/g"

OTB followed since the beginning the ITK convention and use .txx extension for all
template classes. Nevertheless, some development tools do not recognize .txx
file extension. Other tool like GitHub can't do in-browser syntax highlighting for
txx files I think.

The root problem is the use of the txx which should be changed to hxx (or hpp).

In 2011, after an in-depth discussion near April 20, 2011 on the
Insight-Developers mailing list, ITK rename all txx files to hxx (and event
prevent the push of .txx files with a pre-commit hook). It happens is major release v4.

You can find some arguments in the discussion about the change and also in other
projects related to ITK which applied the same modification, see for instance VXL:

https://github.com/vxl/vxl/issues/209

This commit apply now the same modification for OTB.

I understand that it will change some habit for developers and don't bring new
features but I think that in general it is better to stay align with ITK guidelines.

In my opinion, it always facilitate the use of OTB and ITK together if we share
when we can the same code architecture, directory organization, naming
conventions...

STY: Change ITK_OVERRIDE for override in whole code (find Modules -type f -exec sed -i 's/ITK_OVERRIDE/override/g' {} +)

    Where available, use c++11 features to identify
    potential nullptr usage errors.

    python run-clang-tidy.py -clang-tidy-binary ~/software/clang+llvm-3.8.0-x86_64-linux-gnu-ubuntu-14.04/bin/clang-tidy -checks=-*,modernize-use-nullptr -header-filter=/home/grizonnetm/projets/otb/src/OTB/Modules/.*/.*/include/.* -j8 -fix -p ~/projets/otb/bin/release/OTB-clang3.8/ ~/projets/otb/src/OTB/Modules/*/*/src/*.cxx ~/projets/otb/src/OTB/Modules/*/*/app/*.cxx ~/projets/otb/src/OTB/Examples/*/*.cxx ~/projets/otb/src/OTB/Modules/*/*/test/*.cxx > ~/temporary/run-clang-tidy-nullptr-log.txt

    find . -type f -print -name "*.h" -o -name "*.txx" -o -name "*.cxx" |xargs perl -pi -e 's/nullptr/ITK_NULLPTR/g'

Used the following command:

find . \( -iname *.txx -and ! -path *ThirdParty* \) -exec perl -pi -w -e 's/__otb(.*)_txx/otb$1_txx/g;' {} \;
find . \( -iname *.h -and ! -path *ThirdParty* \) -exec perl -pi -w -e 's/__otb(.*)_h/otb$1_h/g;' {} \;

Fixes many, but not all, clang -Wreserved-id-macro warnings.

    clang-tidy tool can insert missing override keyword as a macro so that missing [optional] virtual identifiers can be easily added.

    build otb with clang 3.8 and use cmake option CMAKE_EXPORT_COMPILE_COMMANDS=ON. Most modules and third parties have been activated.

    #Save override occurences in otb code
    cd src/Modules ; grep -nR "override" * > ~/temporary/override_otb.txt

    #Run clang modernize check using utility script which allow to process the code in parallel
    python run-clang-tidy.py -clang-tidy-binary ~/software/clang+llvm-3.8.0-x86_64-linux-gnu-ubuntu-14.04/bin/clang-tidy -checks=-*,modernize-use-override -header-filter=/home/grizonnetm/projets/otb/src/OTB/Modules/.*/.*/include/.* -j8 -fix -p ~/projets/otb/bin/release/OTB-clang3.8/ ~/projets/otb/src/OTB/Modules/*/*/src/*.cxx ~/projets/otb/src/OTB/Examples/*/*.cxx ~/projets/otb/src/OTB/Modules/*/*/test/*.cxx > ~/temporary/run-clang-tidy-log.txt

    #Replace override by ITK macro (to maintain compat with c++98)
    find . -type f -print -name "*.h" -o -name "*.txx" |xargs perl -pi -e 's/\ override/\ ITK_OVERRIDE/g'

This patch is authored by Bas Couwenberg <sebastic@xs4all.nl>
from DebianGIS team. spelling errors were encountered when
updating OTB debian package for 5.2.1.
https://bugs.orfeo-toolbox.org/view.php?id=1143

This is a big one without much harm. It fixes incorrect spelling
and grammer when packaging OTB 5.0.0 and 5.2.0 for Debian.
Most of these changes are done by developers at DebianGIS.
For more info, I include the original patch header below.
Description: Fix some spelling errors to silence lintian
enabling  to concentrate on the real problem.
Author: Andreas Tille <tille@debian.org>
Author: Rashad Kanavath <rashad.kanavath@c-s.fr>
Author: Bas Couwenberg <sebastic@xs4all.nl>
Last-Update: 2015-12-22