[Insight-developers] ITKv4 Modularization Plan
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Tue Feb 8 10:57:29 EST 2011
Le 8 févr. 11 à 15:59, Xiaoxiao Liu a écrit :
> Inside each module, there is a itk-module.cmake file, which lists
> the module dependency in one line.
> For example, in itk-io-tiff/itk-module.cmake, you will find:
> itk_module(itk-io-tiff DEPENDS itk-tiff itk-io-base)
>
are they created by hande, after once the modularization script has
been run?
>
> 2011/2/8 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> I forgot a question: where are the dependencies between modules?
>
> Thanks,
>
> Gaëtan
>
>
> Le 8 févr. 11 à 15:49, Gaëtan Lehmann a écrit :
>
>
>
> Hi Xiaoxiao,
>
> I'm giving a closer look at the modularization. First I've tried to
> compute a quick summary of the number of classes by module:
>
> [glehmann at marvin Modularization]$ egrep '/[a-zA-Z]*\.h' Manifest.txt
> | awk '{print $3}' | sort | uniq -c | sort -n
> 1 itk-anti-alias
> 1 itk-eigen
> 1 itk-io-raw
> 1 itk-polynomials
> 1 itk-spatial-function
> 1 itk-test-kernel
> 1 itk-xml
> 2 itk-io-biorad
> 2 itk-io-bmp
> 2 itk-io-gipl
> 2 itk-io-jpeg
> 2 itk-io-lsm
> 2 itk-io-mesh
> 2 itk-io-png
> 2 itk-io-siemens
> 2 itk-io-stimulate
> 2 itk-io-tiff
> 2 itk-io-vtk
> 2 itk-narrow-band
> 3 itk-io-analyze
> 3 itk-io-deprecated
> 3 itk-io-gdcm
> 3 itk-io-ge
> 3 itk-io-ipl
> 3 itk-io-nifti
> 3 itk-io-nrrd
> 3 itk-io-spatialobjects
> 3 itk-signed-distance-function
> 3 itk-vtk
> 4 itk-bias-correction
> 4 itk-io-meta
> 4 itk-markov-random-fields-classifiers
> 4 itk-voronoi
> 5 itk-deformation-field
> 5 itk-fem-registration
> 5 itk-label-voting
> 5 itk-region-growing
> 6 itk-classifiers
> 6 itk-curvature-flow
> 6 itk-edge-detection
> 6 itk-finite-difference
> 6 itk-image-compare
> 6 itk-region-growing-klm
> 6 itk-smoothing
> 7 itk-bio-cell
> 8 itk-fft
> 9 itk-connected-components
> 9 itk-thresholding
> 10 itk-deprecated
> 10 itk-pde-deformable-registration
> 12 itk-anisotropic-smoothing
> 12 itk-distance-map
> 13 itk-watersheds
> 14 itk-io-base
> 15 itk-image-filter-base
> 15 itk-path
> 16 itk-meta-spatial-objects
> 20 itk-image-statistics
> 20 itk-mesh
> 21 itk-quad-edge-mesh-filtering
> 25 itk-image-grid
> 25 itk-quad-edge-mesh
> 27 itk-blox
> 27 itk-image-function
> 28 itk-optimizers
> 33 itk-transform
> 35 itk-registration-common
> 38 itk-neural-networks
> 41 itk-spatial-objects
> 44 itk-fem
> 46 itk-level-sets
> 61 itk-mathematical-morphology
> 61 itk-statistics
> 99 itk-intensity-math
> 271 itk-common
>
> and the total number of modules:
>
> [glehmann at marvin Modularization]$ egrep '/[a-zA-Z]*\.h' Manifest.txt
> | awk '{print $3}' | sort | uniq -c | sort -n | wc -l
> 75
>
>
> And a few comments — sometimes only questions, as I don't know the
> answer ;-)
>
> * no itk-fftw? As for the io modules, I guess this would simplify
> the management of the dependency on FFTW. I'm not sure how we can
> ensure that FFTW will be used if it is available however - is it
> possible to ensure that behavior with the itk factories?
>
> * MedianImageFilter .h and .txx files are not in the same module
>
> * VectorImageToImagePixelAccessor in itk-intensity-math?
>
> * ChangeLabelImageFilter and RelabelImageFilter are not restricted
> to connected components
>
> * ReflectiveImageRegion[Const]Iterator in itk-distance-map?
>
> * AbsoluteValueDifferenceImageFilter in image-compare? I would
> rather put it in itk-intensity-math
>
> * I don't get immediately the meaning of itk-image-grid.
> Unfortunately, I'm not sure to have something better to propose. In
> WrapITK, the closest library is named Resize
>
> * itk-image-statistics contains mostly the filters for the
> projection. Those projections use some statistics to compute the
> projected value, that's right, but many filters are also using some
> statistics internally, like the Otsu threshold for example. In
> WrapITK, the projection filters are in the Resize library.
>
> * the compose filters in itk-intensity-math?
>
> * Gradient, Gaussian, Laplacian filters in itk-intensity-math?
> Clearly, I won't look there to find them!
>
> * ImageToVectorImageFilter, RGBToLuminanceImageFilter and the Join
> filters are grouped with the Compose filter in WrapITK
>
> * itk-intensity-math is quite big. It may be splitted in unary and
> binary and more filters.
>
> * there is a lot of itk-io-*. It may be better to create a module
> only if there is a dependency on another project, like gdcm or tiff?
>
> * itk-common is probably a bit too big for wrapping. If possible, it
> would be nice to split it a bit.
> Here are the classes which are not in the Base library in WrapITK,
> but are in itk-common — note the a library in wrapitk is a module in
> the modularization work.
>
> BSplineInterpolationWeightFunction
> CellInterface
> DataObjectDecorator
> DefaultDynamicMeshTraits
> DefaultStaticMeshTraits
> ExtractImageFilter
> ImageConstIterator
> ImageConstIteratorWithIndex
> ImageDuplicator
> ImageIterator
> ImageIteratorWithIndex
> ImageLinearConstIteratorWithIndex
> ImageLinearIteratorWithIndex
> ImageRandomConstIteratorWithIndex
> ImageRandomIteratorWithIndex
> ImageRandomNonRepeatingConstIteratorWithIndex
> ImageRandomNonRepeatingIteratorWithIndex
> ImageRegionConstIterator
> ImageRegionConstIteratorWithIndex
> ImageRegionIterator
> ImageRegionIteratorWithIndex
> ImageRegionSplitter
> ImportImageFilter
> LineCell
> MinimumMaximumImageCalculator
> PointSet
> SimpleDataObjectDecorator
> SparseFieldLayer
> SparseImage
> SpatialFunction
> StreamingImageFilter
> TreeNode
> TriangleCell
> TriangleHelper
> VertexCell
>
>
> In WrapITK I think we haven't kept anything related to mesh —
> CellInterface, LineCell, TriangleCell, VertexCell,
> DefaultDynamicMeshTraits, DefaultStaticMeshTraits, TriangleHelper
> and PointSet are in the Mesh library.
> All the iterators are in a separate library in WrapITK.
> The Sparse* classes are in the LevelSet library.
> Some are not in Base in WrapITK because they are not widely used,
> but I think they should be in itk-common, like
> SimpleDataObjectDecorator, so that's ok :-)
>
> Gaëtan
>
>
>
> Le 7 févr. 11 à 21:51, Xiaoxiao Liu a écrit :
>
> Dear All,
>
>
>
> During the ITKv4 Boston meeting, we presented the modularization
> progress and planned to push the modularized ITK into the main ITK
> git repository on Feb, 28th. To make this transition easier for
> all of us, please let us know if you have any suggested improvements
> as soon as possible. We would like to get more feedback especially
> on the granularity of the segmentation of the modules and the naming
> of the modules, since it will be harder to move things around once
> everyone starts to contribute to the modularized ITK.
>
>
> So far we have created 90 modules out of the monolithic ITK (not
> including Examples and Reviews). Among the 90 modules, there are 14
> utility modules (such as itk-tiff and itk-xml) , and 21 I/O
> modules (such as itk-io-tiff). The Manifest (located ITK/
> Modularization/Manifest.txt) lists 2352 source code files and
> their locations in the modularized ITK. Here is a spreadsheet
> version of the Manifest for your convinence to explore:
> Manifest.xlsx. You can also get a copy of a modularized ITK
> (produced at Feb. 2nd) from http://itk.org/gitweb?p=tmp/modularITK.git
> to investigate.
>
>
> The current modularization process involves manually editing the
> Manifest file, adding tests for each module and running dashboards
> for modularized ITK every day. This process is done for the
> majority of ITK now and will be done for the entire toolkit by Feb
> 28th. Moreover, this process will continue to be carried out for any
> new contributions into ITKv4. Therefore, it will be extremely
> helpful for developers to get familiar with the new lay-out of the
> toolkit and get ready for the changes.
>
>
> We are working on detailed documentations to help both developers
> and users to adapt to the modularized version of ITK. More details
> about the modularization can be found at this wiki page: http://www.itk.org/Wiki/ITK_Release_4/Modularization
> .
>
>
> Thank you for your attention!
>
>
>
>
> - Best,
>
> Modularization Team (Luis, Bill, Brad, Xiaoxiao)
>
>
>
>
>
>
> ---------------------------------------------
> Xiaoxiao Liu, Ph.D.
> R & D Engineer
> Kitware Inc.
> Clifton Park, NY
> Phone: (518) 881-4924 or (518) 371-3971 x124
>
>
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>
> --
> 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 http://www.itk.org
> http://www.mandriva.org http://www.bepo.fr
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-developers
>
> --
> 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 http://www.itk.org
> http://www.mandriva.org http://www.bepo.fr
>
>
>
>
> --
> ---------------------------------------------
> Xiaoxiao Liu, Ph.D.
> R & D Engineer
> Kitware Inc.
> Clifton Park, NY
> Phone: (518) 881-4924 or (518) 371-3971 x124
>
>
--
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 http://www.itk.org
http://www.mandriva.org http://www.bepo.fr
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