[vtkusers] Re: BioImageXD's vtk extensions

[Gaetan Lehmann]

Hi,

The LSM reader works just fine with my images - I no more need to convert  
them with imagej :-)
Mathieu, it would be really nice if it can be integrated in VTK. Is it  
possible ?

I have seen some deconvolution related classes in the C++ directory, but  
haven't found the feature in the GUI. Are they already usable ?

Thanks a lot,

Gaetan


On Thu, 08 Jun 2006 14:16:38 +0200, Dan White <dan at chalkie.org.uk> wrote:

> Hi Gaetan,
>
> if you get the  source code for bioimagexd public beta release 0.9 from
>
> http://modeling.bio.jyu.fi/dl.php?file=source_targz
>
> you will see in the C++ dir that there is our vtkLSMreader and some  
> other of our custom classes
>
> these can be asses to a fresh VTK sources CVS download tree
> using the shell script below  (hopefully you can see how it works, and  
> fix it if it doesnt work for you 1st time)
>
> then when you build this version of VTK with our bits added, the LSM  
> reader functionality will be there.
> Cmake options to use:
> shared libraries on
> python wrapping on (use python2.4 make sure to use t to see the advanced  
> options in ccmake and check 2.4 is being used not 2.3 for some bits)
>
> configure and generate make files in cmake,
> then make and make install
>
> then bioimagexd sould work with
> python2.4 BioImageXD.py
> from in the bioiamgexd pytohn sources you downloaded.
>
> and also our vtkLSMReader should be available to use from python scripts  
> and c++ progs etc using VTK.
>
> we will try to make full source build and install instructions for  
> bioimagexd-VTK available when we do our next public beta release...
>
> cheers
>
> Dan
>
>
>
> #! /bin/sh
> if [ "$2" = "" ]; then
> echo "Usage: install_classes.sh <BioImageXD directory> <VTK directory>"
> exit
> fi
>
> INSTALL="IO Imaging Filtering Widgets"
>
> CPPDIR=$1/C++
> IMAGING=$2/Imaging
> FILTERING=$2/Filtering
> WIDGETS=$2/Widgets
> IO=$2/IO
>
> function insert_to_cmakelists {
>    cxxfile=$1
>    cmakefile=$2/CMakeLists.txt
>    cat $cmakefile|sed s/"SET.*Kit_SRCS"/"SET( Kit_SRCS\n$cxxfile"/ >  
> CMakeLists.new
>    mv -f CMakeLists.new $cmakefile
> }
>
> if [ "`echo $INSTALL|grep Imaging`" ]
> then
>    for i in vtkImageColorMerge vtkImageAlphaFilter  
> vtkImageColocalizationFilter vtkImageColocalizationTest \
>    vtkImageMapToIntensities vtkImageSimpleMIP vtkImageSolitaryFilter
>    do
>      echo "Copying $i.cxx..."
>      cp $CPPDIR/$i.cxx $IMAGING
>      cp $CPPDIR/$i.h $IMAGING
>      if [ "`grep $i $IMAGING/CMakeLists.txt`" = "" ]; then
>         echo "Inserting $i.cxx to CMakeLists.txt"
>         insert_to_cmakelists $i.cxx $IMAGING
>      else
>         echo "$i.cxx already in CMakeLists.txt"
>      fi
>    done
> fi
>
> if [ "`echo $INSTALL|grep Filtering`" ]
>    then
>    for i in vtkIntensityTransferFunction  
> vtkImageAutoThresholdColocalization
>    do
>      echo "Copying $i.cxx..."
>      cp $CPPDIR/$i.cxx $FILTERING
>      cp $CPPDIR/$i.h $FILTERING
>      if [ "`grep $i $FILTERING/CMakeLists.txt`" = "" ]; then
>         echo "Inserting $i.cxx to CMakeLists.txt"
>         insert_to_cmakelists $i.cxx $FILTERING
>      else
>         echo "$i.cxx already in CMakeLists.txt"
>      fi
>    done
> fi
>
> if [ "`echo $INSTALL|grep Widgets`" ]
> then
>    for i in vtkDistanceRepresentationScaled2D
>    do
>      echo "Copying $i.cxx..."
>      cp $CPPDIR/$i.cxx $WIDGETS
>      cp $CPPDIR/$i.h $WIDGETS
>      if [ "`grep $i $WIDGETS/CMakeLists.txt`" = "" ]; then
>         echo "Inserting $i.cxx to CMakeLists.txt"
>         insert_to_cmakelists $i.cxx $WIDGETS
>      else
>         echo "$i.cxx already in CMakeLists.txt"
>      fi
>    done
> fi
>
> if [ "`echo $INSTALL|grep IO`" ]
> then
>    for i in vtkExtTIFFReader vtkLSMReader
>    do
>      echo "Copying $i.cxx..."
>      cp $CPPDIR/$i.cxx $IO
>      cp $CPPDIR/$i.h $IO
>      if [ "`grep $i $IO/CMakeLists.txt`" = "" ]; then
>         echo "Inserting $i.cxx to CMakeLists.txt"
>         insert_to_cmakelists $i.cxx $IO
>      else
>         echo "$i.cxx already in CMakeLists.txt"
>      fi
>    done
> fi
>
>
>
>
> On 8 Jun 2006, at 14:58, Gaetan Lehmann wrote:
>
>>
>> Dan, Kalle,
>>
>> LSM reader is still not usable in ITK (with several channels), I still  
>> lack a good GUI and it seems that it is possible to integrate some itk  
>> filters in BioImageXD, so I'm looking again at BioImageXD.
>> My problem is quite simple (for now): What is the procedure to build  
>> vtk extensions you wrote, so they can be used in BioImageXD ? I can't  
>> find any Makefile, any CMakeLists.txt or setup.py. build_app.py only  
>> declares some functions, but nothing to call it.
>>
>> Can you tell me how you build that code ?
>>
>> Also, it seems that we are interested in the same domains - confocal  
>> miscroscopy, image analysis, and python - so perhaps would you find  
>> useful the development I (and others) have made for ITK. Most of them  
>> are used for confocal microscopy image analysis, and are fully usable  
>> with WrapITK.
>> http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi
>>
>> Regards,
>>
>> Gaetan
>>
>>
>> --Gaëtan Lehmann
>> Biologie du Développement et de la Reproduction
>> INRA de Jouy-en-Josas (France)
>> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
>> http://voxel.jouy.inra.fr
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Bioimaging Coordinator
> Nanoscience Centre and Department of Biological and Environmental  
> Sciences
> Division of Molecular Recognition
> Ambiotica C242
> PO Box 35
> University of Jyväskylä
> Jyväskylä
> FIN 40014
> Finland
>
> +358 14 260 4183 (work)
> +358 468102840 (mobile)
> http://www.bioimagexd.org
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> white at cc.jyu.fi
>



-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr