=============  BUILD ODIN FROM SCRATCH ON WINDOWS ===================

Please note that the following instructions are for building ODIN from
scratch on Windows using MinGW and to create a binary distribution of ODIN.
If you just want to use ODIN on Windows, possibly in combination with IDEA,
I strongly recommend that you download and install the binary distribution
from the ODIN Download page, since the installation described here is pretty
tedious.

Uninstall any ODIN binary distributions before continuing.

Download and install "Qt 5.1.1 for Windows 32-bit (MinGW 4.8, OpenGL)" from
http://qt-project.org/downloads and check "Tools -> MinGW 4.8" during install
Ignore errors during install?
Set the environment variables QTDIR and PATH manually,
i.e. set QTDIR to the directory which contains bin\qmake.exe
and append %QTDIR%\bin to PATH.


Download and install MSYS-1.0.11.exe
Specify the location of the Qt-included MinGW when asked for the path
(e.g. c:/Qt/qt5.1.1/Tools/mingw48_32)


Create a directory (e.g. c:\MR-Software) to put all the ODIN-related stuff.
Use the MSYS shell to install all further stuff. Please note: A drive
letter X: in this shell can be used usin /X/, e.g. c: is /c/ in the MSYS shell.

Download recent GSL source code, unpack and do a
./configure --prefix=/c/MR-Software --disable-shared --enable-static
make
make install

Compile and install Blitz++ from source:
./configure --prefix=/c/MR-Software --disable-shared --enable-static
make lib
make install


Download and unpack qwt5/6. In qwtconfig.pri, modify
INSTALLBASE/QWT_INSTALL_PREFIX = C:\MR-Software
headers.path = $$INSTALLBASE/include/qwt
and comment out
#CONFIG           += QwtDll
#CONFIG           += QwtDesigner
#CONFIG           += QwtSvg
#CONFIG           += QwtMathML
then do a
qmake
(mingw32-)make install


Compile dcmtk source:
0) Hack dcmtk (3.5.4) to be used with MinGW 4.8 from Qt:
  a) Insert a lot of 'this->' as required by the compiler
1) ./configure --prefix=/c/MR-Software
2) First 'make' (for libofstd)
3) create a built-in dictionary by going into dcmdata/libsrc
   and do a 'make builtindict'. Fix 'mkdictbi.cc:getUserName' if necessaray.
4) Compile and install the libraries by 'make install-lib'


For LAPACK support using ACML:
Get the g77 version of the AMD Core Math Library from
http://developer.amd.com/acml.jsp and install it.
Use a short installation path without dots, e.g. c:/acml,
otherwise configure fails.
Use the -a option of install.win (see below) to specify
the location of libacml.a.


For NIfTI/zlib support:
1) Download and unpack zlib-1.2.7 from http://www.zlib.net/
   do a
   INCLUDE_PATH=/c/MR-Software/include/ LIBRARY_PATH=/c/MR-Software/lib/ BINARY_PATH=/c/MR-Software/bin make -f win32/Makefile.gcc install
2) Download nifticlib from http://niftilib.sourceforge.net/
   Hack Makefile:
   Add
   -Ic:/MR-Software/include to ZLIB_INC
   and
   -Lc:/MR-Software/lib to ZLIB_PATH
   Use mingw32-make to compile, ignore errors in utils
   Install manually:
   cp lib/*.a /c/MR-Software/lib/
   cp include/*.h /c/MR-Software/include/


For PNG support:
Download and unpack source from
http://www.libpng.org/pub/png/libpng.html
configure with
LDFLAGS=-L/C/MR-Software/lib CPPFLAGS=-I/c/MR-Software/include ./configure --disable-shared --enable-static --prefix=/c/MR-Software/
and then
make LDFLAGS="-all-static"
make install
Delete all libpng* stuff, except libpng.a, from /c/MR-Software/bin and /c/MR-Software/lib


Download the notepad++ minimalist package from http://notepad-plus-plus.org/
and copy all *.exe *.dll *.xml files to /c/MR-Software/bin


Download and install doxygen-1.8.2-setup.exe for Windows from http://www.stack.nl/~dimitri/doxygen/download.html

Download graphviz-2.8.exe (the newer MSI installer does not work with vmware)
and select C:\Programme  for installation (ignore warning)

Download and install NSIS with default settings to c:/Programme/NSIS/

Create dist of ODIN under Linux/UNIX using 'make dist'.
Unpack and compile the resulting odin-x.y.z.tar.gz using the script 'install.win'.




=============  INSTALLING ODIN ON LINUX/UNIX  =======================

Prerequisites:
==============

The following programs and libraries are required to compile ODIN for Linux/UNIX
(In parenthesis are the version numbers of the packages with which ODIN
has been tested successfully):

* Qt library (3.0.* or later)

* Qwt library (4.2.0 or later)

* Blitz++ template library (0.8 or later)

* GNU Scientific Library (0.9.3 or later)

* optional: Vista/Lipsia library (http://www.cbs.mpg.de/institute/software/lipsia/download.html
            or vista-2.2.0 from ODIN download page),
            use configure option --enable-vistasupport to activate Vista support in ODIN

* optional: NIFTI library  (http://nifti.nimh.nih.gov), use configure option
            --enable-niftisupport to activate NIFTI support in ODIN

* optional: vtk library (4.2.5 or later), use configure option --enable-vtksupport
            to activate VTK support in ODIN

* optional: dcmtk library (3.5.4 or later), use configure option --enable-dcmtksupport
            to activate DICOM support in ODIN

* optional: PNG library (1.2.27 or later), use configure option --enable-pngsupport
            to activate PNG support in ODIN

* optional: gdb debugger and xterm terminal to attach debugger to running
            ODIN process

* optional: LAPACK for fast linear algebra. Since the NetLib implementation is currently
            not thread safe, we recommend using the thread-safe ACML (http://developer.amd.com/cpu/Libraries/acml/).
            Download the GFORTRAN version, and use --with-lapack-libname=acml during configure.



A note for GRAPPA users:
If no LAPACK is found during configure, Odin will fall back to using GSL
for linear algebra. However, the GSL implementation is very slow
(several orders of magnitude compared to LAPACK) which makes GRAPPA
reconstruction impractical. So, please:
MAKE SURE TO USE LAPACK FOR GRAPPA RECONSTRUCTION.
At the best, use a thread-safe LAPACK implementation, like ACML.
The actual library name can be given by --with-lapack-libname.




A short HOWTO (for the impatient):
==================================

After you've unpacked the archive go into the directory where this file
resides and issue:

./configure && make

After compilation log in as root and type

make install

After that you should be able to start Odin by

odin

on the command line.


To configure/compile ODIN with other settings, enter

./configure --help

to get a list of options.



Platform Specific Notes:
========================


  * Debian 9/10/11 (stretch/buster/bullseye):
  Required packages for building from scratch:
  autoconf automake libtool g++ help2man doxygen libblitz0-dev libgsl-dev libdcmtk-dev libnifti-dev libpng-dev libvtk6/7-dev libismrmrd-dev qt5-default/qtbase5-dev libqwt-qt5-dev xterm gdb

  * Ubuntu 14: Required packages for building from scratch:
    autoconf automake libtool g++ libgsl0-dev libblitz0-dev libqt4-dev libqt4-dev-bin libqwt-dev libatlas-base-dev libnifti-dev libvtk5-dev libdcmtk2-dev libpng12-dev help2man

  * Debian 8 (jessie):
  The dault GCC version 4.9 throws a message: 
  "internal compiler error: in possible_polymorphic_call_targets, at ipa-devirt.c".
  Workaround: An older version of GCC (4.8), e.g.
  CXX=g++-4.8 ./configure && make install

  * Red Hat Enterprise Linux 3 (hosting Brukers Paravision 3)
  ODIN was successfully installed with the following libraries and configure options:
  gsl-1.6:     ./configure --enable-shared=yes --enable-static=no
  blitz-0.8:   ./configure --enable-shared=yes --enable-static=no
  vista-2.2.0: ./configure --enable-shared=yes --enable-static=no
  ODIN can be compiled with following options:
  ./configure --enable-shared=yes --enable-static=no


* MacOS X 10.4(Tiger), 10.5(Leopard)
  -Install the development tools from Apple, i.e. XCode 2.4 or later
  -Use fink 0.8.0 and set the following environment variables:
   export FINKDIR=/sw
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FINKDIR/lib
   export LIBRARY_PATH=$LIBRARY_PATH:$FINKDIR/lib
   export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$FINKDIR/include
  -Install qt-mac-opensource, 4.1.x or later, use the source code distribution,
   otherwise qwt cannot be compiled (with the qmake of the dmg binary distribution)
   For a minimal Qt sufficient for Odin, configure Qt with
   ./configure -prefix $QT_INSTALL_DIR -no-qt3support -release -no-xmlpatterns -no-phonon -no-webkit -no-nis -no-cups -no-dbus -nomake "tools examples demos docs"
   Set the variable QTDIR to point to the source-code directory of Qt
  -Additionally, install the following libraries:
   -qwt5 (adapt qwtconfig.pri: INSTALLBASE and headers.path = $$INSTALLBASE/include/qwt, comment out QwtDesigner, QwtSvg, QwtMathML, QwtFramework)
   -gsl (fink package)
   -blitz++ (current CVS checkout with CVSROOT=:pserver:anonymous@blitz.cvs.sourceforge.net:/cvsroot/blitz cvs co blitz),
    for configuration,use 'LIBTOOLIZE=glibtoolize autoreconf -fiv' (aborts with error, but creates configure which works fine)
    If necessary, create directory blitz/apple and therein link to blitz/gnu/bzconfig.h (also in the installed blitz headers)
   -Optionally, install the following libraries:
    -vista-2.2.0 (from ODIN download page)
    -dcmtk 3.5.4 (run make install-lib install-support, run ranlib manually, as requested)
  -Use the script ./install.macos to configure/compile/install ODIN




Troubleshooting:
================

* During compilation I get a message '/usr/bin/moc: commamd not found'
-> You must specify the directory where the Qt library is installed
by setting the $QTDIR system variable, i.e. the headers should be
found under $QTDIR/include, the libs under $QTDIR/lib and, most important
for this problem the binaries (for example moc) under $QTDIR/bin.



* During configuration I get a message 'configure: error: Can't find ....'
  or 'Please install ...'
-> The configure script knows (mostly) what is needed, please install
the missing packages.




===============================================================================

And here are the generic installation instructions generated by the
GNU autoconf package:



Basic Installation
==================

   These are generic installation instructions.

   The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation.  It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions.  Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, a file
`config.cache' that saves the results of its tests to speed up
reconfiguring, and a file `config.log' containing compiler output
(useful mainly for debugging `configure').

   If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release.  If at some point `config.cache'
contains results you don't want to keep, you may remove or edit it.

   The file `configure.in' is used to create `configure' by a program
called `autoconf'.  You only need `configure.in' if you want to change
it or regenerate `configure' using a newer version of `autoconf'.

The simplest way to compile this package is:

  1. `cd' to the directory containing the package's source code and type
     `./configure' to configure the package for your system.  If you're
     using `csh' on an old version of System V, you might need to type
     `sh ./configure' instead to prevent `csh' from trying to execute
     `configure' itself.

     Running `configure' takes a while.  While running, it prints some
     messages telling which features it is checking for.

  2. Type `make' to compile the package.

  3. Type `make install' to install the programs and any data files and
     documentation.

  4. You can remove the program binaries and object files from the
     source code directory by typing `make clean'.  

Compilers and Options
=====================

   Some systems require unusual options for compilation or linking that
the `configure' script does not know about.  You can give `configure'
initial values for variables by setting them in the environment.  Using
a Bourne-compatible shell, you can do that on the command line like
this:
     CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure

Or on systems that have the `env' program, you can do it like this:
     env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure

Compiling For Multiple Architectures
====================================

   You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory.  To do this, you must use a version of `make' that
supports the `VPATH' variable, such as GNU `make'.  `cd' to the
directory where you want the object files and executables to go and run
the `configure' script.  `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'.

   If you have to use a `make' that does not supports the `VPATH'
variable, you have to compile the package for one architecture at a time
in the source code directory.  After you have installed the package for
one architecture, use `make distclean' before reconfiguring for another
architecture.

Installation Names
==================

   By default, `make install' will install the package's files in
`/usr/local/bin', `/usr/local/man', etc.  You can specify an
installation prefix other than `/usr/local' by giving `configure' the
option `--prefix=PATH'.

   You can specify separate installation prefixes for
architecture-specific files and architecture-independent files.  If you
give `configure' the option `--exec-prefix=PATH', the package will use
PATH as the prefix for installing programs and libraries.
Documentation and other data files will still use the regular prefix.

   If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.

Optional Features
=================

   Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System).  The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.

   For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.

Specifying the System Type
==========================

   There may be some features `configure' can not figure out
automatically, but needs to determine by the type of host the package
will run on.  Usually `configure' can figure that out, but if it prints
a message saying it can not guess the host type, give it the
`--host=TYPE' option.  TYPE can either be a short name for the system
type, such as `sun4', or a canonical name with three fields:
     CPU-COMPANY-SYSTEM

See the file `config.sub' for the possible values of each field.  If
`config.sub' isn't included in this package, then this package doesn't
need to know the host type.

   If you are building compiler tools for cross-compiling, you can also
use the `--target=TYPE' option to select the type of system they will
produce code for and the `--build=TYPE' option to select the type of
system on which you are compiling the package.

Sharing Defaults
================

   If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists.  Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.

Operation Controls
==================

   `configure' recognizes the following options to control how it
operates.

`--cache-file=FILE'
     Use and save the results of the tests in FILE instead of
     `./config.cache'.  Set FILE to `/dev/null' to disable caching, for
     debugging `configure'.

`--help'
     Print a summary of the options to `configure', and exit.

`--quiet'
`--silent'
`-q'
     Do not print messages saying which checks are being made.

`--srcdir=DIR'
     Look for the package's source code in directory DIR.  Usually
     `configure' can determine that directory automatically.

`--version'
     Print the version of Autoconf used to generate the `configure'
     script, and exit.

`configure' also accepts some other, not widely useful, options.