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Tuesday, 11th December 2018 21:58:30 (GMT+1) 

polsoft

sources unter

/home/emmenlau/Diplomarbeit/extsrc
cvs -d ':pserver:emmenlau@falballa.informatik.uni-freiburg.de:/polsoft' login
cvs -d ':pserver:emmenlau@falballa.informatik.uni-freiburg.de:/polsoft' co polsoft
cd $POLSRC/extsrc/
cvs -d :pserver:emmenlau@falballa.informatik.uni-freiburg.de:/lmbsoft login
cvs -d :pserver:emmenlau@falballa.informatik.uni-freiburg.de:/lmbsoft co libcmdline
cvs -d :pserver:emmenlau@falballa.informatik.uni-freiburg.de:/lmbsoft co libfidwid
cvs -d :pserver:emmenlau@falballa.informatik.uni-freiburg.de:/lmbsoft co liblmbcam

Fuer polsoft: ../configure --prefix=$PWD --enable-extras --with-qt4

For more details see: http://lmb.informatik.uni-freiburg.de/lmbwiki/index.php/PollenSoftware

cd $POLSRC/src/pollen_3d_scripts/
moc -o ./moc_volume_render11.hh ./volume_render11.cc

#aufruf:
polrecog2 --no_include \
   --cxxfile $POLSRC/src/pollen_3d_scripts/volume_render11.cc\
   --object_name 72h_THTOTO3_20x_8bit.nc --finish

cmake:

From: http://www.cmake.org/HTML/Download.html Use:

SRCDIR="$HOME/Diplomarbeit/extsrc"
cd $SRCDIR
CMAKEVERSION="cmake-2.4.5"
tar -xvzf $CMAKEVERSION.tar.gz
mkdir $CMAKEVERSION/$HOSTTYPE
cd $CMAKEVERSION/$HOSTTYPE
../configure --prefix=$HOME/Diplomarbeit/ext-$HOSTTYPE
make && make install

Non-Interactive Builds

vtk:

From: http://vtk.org/get-software.php

SRCDIR="$HOME/Diplomarbeit/extsrc"
cd $SRCDIR
VTKVERSION="vtk-5.0.2"
tar -xvzf $VTKVERSION.tar.gz
mv VTK $VTKVERSION
mkdir $VTKVERSION/$HOSTTYPE
cd $VTKVERSION/$HOSTTYPE
cmake ../ \
   -DBUILD_DOCUMENTATION:BOOL=ON \
   -DBUILD_EXAMPLES:BOOL=OFF \
   -DBUILD_SHARED_LIBS:BOOL=ON \
   -DBUILD_TESTING:BOOL=OFF \
   -DCMAKE_BUILD_TYPE:STRING=Release \
   -DCMAKE_INSTALL_PREFIX:FILEPATH=/home/emmenlau/Diplomarbeit/ext-$HOSTTYPE \
   -DOPENGL_xmesa_INCLUDE_DIR:FILEPATH=/usr/include/GL \
   -DVTK_OPENGL_HAS_OSMESA:BOOL=OFF \
   -DVTK_USE_SYSTEM_EXPAT:BOOL=ON \
   -DVTK_USE_SYSTEM_FREETYPE:BOOL=ON \
   -DVTK_USE_SYSTEM_JPEG:BOOL=ON \
   -DVTK_USE_SYSTEM_PNG:BOOL=ON \
   -DVTK_USE_SYSTEM_TIFF:BOOL=ON \
   -DVTK_USE_SYSTEM_ZLIB:BOOL=ON
make -j4 && make install

vxl:

From: Use:

SRCDIR="$HOME/Diplomarbeit/extsrc"
cd $SRCDIR
VXLVERSION="vxl-1.7.0"
tar -xvzf $VXLVERSION.tgz
mkdir $VXLVERSION/$HOSTTYPE
cd $VXLVERSION/$HOSTTYPE
for I in 1 2; do
cmake ../ \
   -DCMAKE_BACKWARDS_COMPATIBILITY:STRING=2.4 \
   -DBUILD_EXAMPLES:BOOL=OFF \
   -DBUILD_SHARED_LIBS:BOOL=ON \
   -DBUILD_TESTING:BOOL=OFF \
   -DCMAKE_BUILD_TYPE:STRING=Release \
   -DCMAKE_INSTALL_PREFIX:FILEPATH=/home/emmenlau/Diplomarbeit/ext-$HOSTTYPE \
   -DOPENGL_xmesa_INCLUDE_DIR:FILEPATH=/usr/include/GL \
   -DVXL_USE_LFS:BOOL=ON
done
make -j4 && make install
   -DDC1394_INCLUDE_DIR:FILEPATH=/usr/include/libdc1394 \
   -DDC1394_LIBRARY:FILEPATH=/usr/lib/libdc1394_control.so.13 \

AVIFILE_AVIPLAY_LIBRARY=/usr/lib/libaviplay.so
AVIFILE_INCLUDE_DIR=/usr/include/avifile-0.7
BUILD_EXAMPLES=OFF
BUILD_SHARED_LIBS=ON
BUILD_TESTING=OFF
BUILD_UNMAINTAINED_LIBRARIES=ON ??
//BUILD_VGUI=OFF ??
CMAKE_BUILD_TYPE=Release
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext
DC1394_INCLUDE_DIR=/usr/include/libdc1394
DC1394_LIBRARY=/usr/lib/libdc1394_control.so.13
DCMTK_DIR=
DCMTK_config_INCLUDE_DIR=/usr/include/dcmtk
DCMTK_dcmdata_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/dcmdata
DCMTK_dcmdata_LIBRARY=/usr/lib/libdcmdata.so
DCMTK_dcmimgle_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/dcmimgle
DCMTK_dcmimgle_LIBRARY=/usr/lib/libdcmimgle.so
DCMTK_ofstd_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/ofstd
DCMTK_ofstd_LIBRARY=/usr/lib/libofstd.so
DESIRED_QT_VERSION=3
ECW_INCLUDE_DIR=
FFMPEG_INCLUDE_DIR=/usr/include/ffmpeg
MPEG2_INCLUDE_DIR=/usr/include/mpeg2dec
MPEG2_mpeg2_LIBRARY=/usr/lib/libmpeg2.so
MPEG2_vo_LIBRARY=/usr/lib/libmpeg2.so
OPENGL_xmesa_INCLUDE_DIR=/usr/include/GL
VXL_BUILD_DCMTK=ON
VXL_UPDATE_CONFIGURATION=ON
VXL_USE_LFS=ON
XERCES_BXML_INCLUDE_PATH=/usr/include/xercesc
XERCES_BXML_LIBRARY_PATH=/usr/lib/libxerces-c.so
XERCES_NEW_BXML_INCLUDE_PATH=
XERCES_NEW_BXML_LIBRARY_PATH=

InsightToolkit:

From: http://www.itk.org/index.htm Use:

SRCDIR="$HOME/Diplomarbeit/extsrc"
TRGTDIR="$HOME/Diplomarbeit/ext-$HOSTTYPE"
cd $SRCDIR
ITKVERSION="InsightToolkit-3.0.0"
tar -xvzf $ITKVERSION.tar.gz
mkdir $ITKVERSION/$HOSTTYPE
cd $ITKVERSION/$HOSTTYPE
$TRGTDIR/bin/cmake ../ \
   -DCMAKE_BACKWARDS_COMPATIBILITY:STRING=2.4 \
   -DBUILD_DOXYGEN:BOOL=ON \
   -DBUILD_EXAMPLES:BOOL=OFF \
   -DBUILD_SHARED_LIBS:BOOL=ON \
   -DBUILD_TESTING:BOOL=OFF \
   -DCMAKE_BUILD_TYPE:STRING=Release \
   -DCMAKE_INSTALL_PREFIX:FILEPATH=$TRGTDIR \
   -DITK_EXPLICIT_INSTANTIATION:BOOL=OFF \
   -DITK_USE_CONCEPT_CHECKING:BOOL=OFF \
   -DITK_USE_KWSTYLE:BOOL=OFF \
   -DITK_USE_PATENTED:BOOL=OFF \
   -DITK_USE_REVIEW:BOOL=OFF \
   -DITK_USE_SYSTEM_GDCM:BOOL=OFF \
   -DITK_USE_SYSTEM_PNG:BOOL=ON \
   -DITK_USE_SYSTEM_TIFF:BOOL=ON \
   -DITK_USE_SYSTEM_VXL:BOOL=OFF \
   -DITK_USE_SYSTEM_ZLIB:BOOL=ON \
   -DUSE_FFTWD:BOOL=ON \
   -DUSE_FFTWF:BOOL=ON \
   -DUSE_SCSL:BOOL=OFF
make -j4 && make install

InsightApplication:

From: http://www.itk.org/index.htm Use:

SRCDIR="$HOME/Diplomarbeit/extsrc"
cd $SRCDIR
ITKAPPVERSION="InsightApplications-3.0.0"
tar -xvzf $ITKAPPVERSION.tar.gz
mkdir $ITKAPPVERSION/$HOSTTYPE
cd $ITKAPPVERSION/$HOSTTYPE
cmake ../ \
   -DCMAKE_BACKWARDS_COMPATIBILITY:STRING=2.4 \
   -DBUILD_DOXYGEN:BOOL=ON \
   -DBUILD_TESTING:BOOL=OFF \
   -DBUILD_SHARED_LIBS:BOOL=On \
   -DCMAKE_BUILD_TYPE:STRING=Release \
   -DCMAKE_INSTALL_PREFIX:FILEPATH=/home/emmenlau/Diplomarbeit/ext-$HOSTTYPE \
   -DITK_DIR:FILEPATH=/home/emmenlau/Diplomarbeit/ext-$HOSTTYPE/lib/InsightToolkit \
   -DOPENGL_xmesa_INCLUDE_DIR:FILEPATH=/usr/include/GL \
   -DUSE_VTK:BOOL=ON
make -j4 && make install

ImageJ:

From: http://rsb.info.nih.gov/ij/ Addons: http://www.uhnresearch.ca/facilities/wcif/fdownload.html Use:

unzip ImageJ-1.36.zip
cd ImageJ/plugins/ && unzip ../../ImageJ_WCIF_plugins_only.zip
cp /misc/database/ronneber/ImageJ_plugins/NetCDF_.jar ImageJ/plugins/

to run: java -Xmx256m -cp ./ij.jar ij.ImageJ

PanoplyJ:

amide:

From: http://amide.sourceforge.net/packages.html Needs: http://xmedcon.sourceforge.net/ Use:

XMEDCONDIR="xmedcon-0.9.9.3"
tar -xvzf $XMEDCONDIR.tar.gz
mkdir $XMEDCONDIR/$HOSTTYPE
cd $XMEDCONDIR/$HOSTTYPE
../configure --prefix=/home/emmenlau/Diplomarbeit/ext
make && make install

VOLPACKDIR="volpack-1.0c4"
tar -xvzf $VOLPACKDIR.tgz
mkdir $VOLPACKDIR/$HOSTTYPE
cd $VOLPACKDIR/$HOSTTYPE
../configure --prefix=/home/emmenlau/Diplomarbeit/ext
make && make install

AMIDEDIR="amide-0.8.18"
tar -xvzf $AMIDEDIR.tgz
mkdir $AMIDEDIR/$HOSTTYPE
cd $AMIDEDIR/$HOSTTYPE
../configure --prefix=/home/emmenlau/Diplomarbeit/ext
make && make install

Interactive

vtk:

From: http://vtk.org/get-software.php

VTKDIR="vtk-5.0.2"
tar -xvzf $VTKDIR.tar.gz
mv VTK $VTKDIR
mkdir $VTKDIR/$HOSTTYPE
cd $VTKDIR/$HOSTTYPE
ccmake ../
# press 'c' then 't', set params, then press 'c' - 'c' - 'g'
make install
BUILD_DOCUMENTATION=ON
BUILD_EXAMPLES=OFF
BUILD_SHARED_LIBS=ON
BUILD_TESTING=OFF
CMAKE_BUILD_TYPE=Release
# echo "ext-$HOSTTYPE"
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext-i486
OPENGL_xmesa_INCLUDE_DIR=/usr/include/GL
VTK_OPENGL_HAS_OSMESA=OFF
VTK_USE_SYSTEM_EXPAT=ON
VTK_USE_SYSTEM_FREETYPE=ON
VTK_USE_SYSTEM_JPEG=ON
VTK_USE_SYSTEM_PNG=ON
VTK_USE_SYSTEM_TIFF=ON
VTK_USE_SYSTEM_ZLIB=ON

InsightToolkit:

From: http://www.itk.org/index.htm Use:

ITKDIR="InsightToolkit-3.0.0"
tar -xvzf $ITKDIR.tar.gz
mkdir $ITKDIR/$HOSTTYPE
cd $ITKDIR/$HOSTTYPE
ccmake ../
# press 'c' then 't', set params, then press 'c' - 'c' - 'g'
make install
BUILD_DOXYGEN=ON
BUILD_EXAMPLES=OFF
BUILD_SHARED_LIBS=ON
BUILD_TESTING=OFF
CMAKE_BUILD_TYPE=Release
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext-i486
ITK_EXPLICIT_INSTANTIATION=OFF ??
ITK_USE_CONCEPT_CHECKING=OFF ??
ITK_USE_KWSTYLE=OFF ??
ITK_USE_PATENTED=OFF ??
ITK_USE_REVIEW=OFF ??
ITK_USE_SYSTEM_GDCM=OFF
ITK_USE_SYSTEM_PNG=ON
ITK_USE_SYSTEM_TIFF=ON
ITK_USE_SYSTEM_VXL=OFF
ITK_USE_SYSTEM_ZLIB=ON
USE_FFTWD=ON
USE_FFTWF=ON
USE_SCSL=OFF

InsightApplication:

From: http://www.itk.org/index.htm Use:

ITKAPPDIR="InsightApplications-3.0.0"
tar -xvzf $ITKAPPDIR.tar.gz
mkdir $ITKAPPDIR/$HOSTTYPE
cd $ITKAPPDIR/$HOSTTYPE
ccmake ../
# press 'c' then 't', set params, then press 'c' - 'c' - 'g'
make install
BUILD_DOXYGEN=ON
BUILD_TESTING=OFF
BUILD_SHARED_LIBS=On
CMAKE_BUILD_TYPE=Release
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext-i486
ITK_DIR=/home/emmenlau/Diplomarbeit/ext-i486/lib/InsightToolkit
OPENGL_xmesa_INCLUDE_DIR=/usr/include/GL
USE_VTK=ON

Outdated:

netCDF:

From: http://www.unidata.ucar.edu/software/netcdf/ Use:

./configure --prefix=/home/emmenlau/Diplomarbeit/ext
make && make install

fftw:

From: http://www.fftw.org/download.html Use:

make clean
./configure --prefix=/home/emmenlau/Diplomarbeit/ext --enable-shared --enable-threads --enable-float --enable-sse
make && make install

make clean
./configure --prefix=/home/emmenlau/Diplomarbeit/ext --enable-shared --enable-threads --enable-double --enable-sse2
make && make install

gdcm:

From: http://www.creatis.insa-lyon.fr/Public/Gdcm/ Use:

BUILD_EXAMPLES=OFF
BUILD_SHARED_LIBS=ON
BUILD_TESTING=OFF
CMAKE_BUILD_TYPE=Release
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext
GDCM_VTK=ON
VTK_DIR=/home/emmenlau/Diplomarbeit/ext/bin/../lib/vtk-5.0

dcmtk:

From: http://dicom.offis.de/dcmtk.php.de Use:

make clean
./configure --prefix=/home/emmenlau/Diplomarbeit/ext
make && make install

vxl:

From: Use:

cp ~/Diplomarbeit/extsrc/cmake-2.4.3/Modules/FindSDL.cmake ~/Diplomarbeit/extsrc/vxl-1.6.0/config/cmake/Modules/NewCMake/

AVIFILE_AVIPLAY_LIBRARY=/usr/lib/libaviplay.so
AVIFILE_INCLUDE_DIR=/usr/include/avifile-0.7
BUILD_EXAMPLES=OFF
BUILD_SHARED_LIBS=ON
BUILD_TESTING=OFF
BUILD_UNMAINTAINED_LIBRARIES=ON ??
//BUILD_VGUI=OFF ??
CMAKE_BUILD_TYPE=Release
CMAKE_INSTALL_PREFIX=/home/emmenlau/Diplomarbeit/ext
DC1394_INCLUDE_DIR=/usr/include/libdc1394
DC1394_LIBRARY=/usr/lib/libdc1394_control.so.13
DCMTK_DIR=
DCMTK_config_INCLUDE_DIR=/usr/include/dcmtk
DCMTK_dcmdata_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/dcmdata
DCMTK_dcmdata_LIBRARY=/usr/lib/libdcmdata.so
DCMTK_dcmimgle_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/dcmimgle
DCMTK_dcmimgle_LIBRARY=/usr/lib/libdcmimgle.so
DCMTK_ofstd_INCLUDE_DIR=/usr/include/dcmtk/dcmtk/ofstd
DCMTK_ofstd_LIBRARY=/usr/lib/libofstd.so
DESIRED_QT_VERSION=3
ECW_INCLUDE_DIR=
FFMPEG_INCLUDE_DIR=/usr/include/ffmpeg
MPEG2_INCLUDE_DIR=/usr/include/mpeg2dec
MPEG2_mpeg2_LIBRARY=/usr/lib/libmpeg2.so
MPEG2_vo_LIBRARY=/usr/lib/libmpeg2.so
OPENGL_xmesa_INCLUDE_DIR=/usr/include/GL
VXL_BUILD_DCMTK=ON
VXL_UPDATE_CONFIGURATION=ON
VXL_USE_LFS=ON
XERCES_BXML_INCLUDE_PATH=/usr/include/xercesc
XERCES_BXML_LIBRARY_PATH=/usr/lib/libxerces-c.so
XERCES_NEW_BXML_INCLUDE_PATH=
XERCES_NEW_BXML_LIBRARY_PATH=
scratch/compile.txt · Last modified: 2014/04/02 22:39 (external edit)