[Insight-developers] itkVTKPolyDataReader.h reads ascii only --- why?

wanlin wanlinzhu at gmail.com
Sat Oct 23 04:13:16 EDT 2010 

On Sat, Oct 23, 2010 at 4:27 PM, Alexandre GOUAILLARD <agouaillard at gmail.com
> wrote:

> hi wanlin,
>
> I have a design issue with polylinecell.
> I understand the need for vizualization, and why it is in VTK.
> I do not see the need for computation. Do you have algorithms/filters
> that requires polylines?
>
> You are right. I don't have algorithm/filters depends on itkpolyline at the
moment. it is there because
1. there is a vtkPolyline.
2. Support vtk file obtained from MedINRIA (*.fib, but it is vtk binary
file).

In term of structure, it could be possible to add this feature to
> itk::Mesh, but almost impossible to add it to an itk:QuadEdgeMesh. The
> reason is that itk::Mesh has a "polygon soup + links" structure (like
> vtkPolydata) where you can add pretty much whatever you want, while
> QuadEdgeMesh has an edge-based structure which supposes each edge is
> unique and not part of a poly-edge structure.
>
Now, If you have filters that use those polylines, I could take a look
> to see if we can find a better design. With this code anyway, you
> cannot deal with polyline separately as it is identified as a
> polygon_cell at the cell interface level (we would need to add the
> POLYLINE_CELL in the celltype enum, and then return this type in the
> corresponding methods of itkpolylinecell.h).
>
If you just want to be able to read files that contains polylines (vtk
> for example), the reader could read them and pass them through as
> edges.
>

> If you want to write them, the writer could check for aligned edges
> (edges that share a point with another edge, but no other face) and
> pass those edges as polyline (if the output format support them, i.e.
> at the formatWriter level).
>
> Please let me know what is your usage in ITK filters of this feature.
>
> From your suggestion, we could read many edges to represent a polyline, I
think it is doable. But there are some potential problems
1. time-consuming for searching for aligned edges when processing polylines
or write them.
2. How do discriminate the start and end points for a polyline.(sometime may
be the order is useful).


kind regards

wanlin

regards,
>
> alex.
>
>
>
> On Mon, Oct 18, 2010 at 7:57 PM, wanlin <wanlinzhu at gmail.com> wrote:
> >
> >
> > On Mon, Oct 18, 2010 at 8:29 PM, Alexandre GOUAILLARD
> > <agouaillard at gmail.com> wrote:
> >>
> >> hi wanlin.
> >>
> >> I just reviewed your code.
> >> Everything seems fine from this quick first review and I updated your
> >> IJ paper with it.
> >>
> > Thank you very much.
> >
> >> It's a wonderful contribution, and I will put it as a candidate for
> >> integration in itk v4.
> >>
> > It's cool. Thanks again.
> >
> >>
> >> Before I do that though, can you tell me more about PolylineCell ? The
> >> code seems to be heavily inspired by the triangle cell, any specific
> >> design point (or question) you would have before i go deeper into it?
> >
> >
> > While PolylineCell is almost the same as PolygonCell ( i copied and
> changed
> > from it) except that the topology of this cell is not closed (i know it
> is
> > ugly but a streamline like polyline cell type is useful, at least for
> me).
> > The purpose of this class is to read streamline type data (currently only
> > vtk polydata support it), such as fiber bundles obtained from DTI
> > tractography algorithm. I know the streamline could be represented by
> > DTITubeSpatialObject, but it is not derived from CellInterface, which
> > prevent me from using it. Do you have a better idea so we could not add
> > PolylineCell?
> >
> >>
> >> Also, I will template your tests and examples over the meshtype to
> >> reduce the number of lines by 2, unless you have strong objection
> >> against it.
> >>
> > I totally agree with it.
> >
> >>
> >> Finally, I don't understand the part on the third page about the data
> >> type (pixeltype), could you point me to the example you are mentioning
> >> in the paper?
> >>
> > Do you refer to this sentence "One of tests shows how it works"? in page
> 2?
> > Sorry for the confusion. One of the data type defined in vtk polydata is
> > COLOR_SCALARS dataName nValues
> > c00 c01 ... c0(nValues-1)
> > c10 c11 ... c1(nValues-1)
> > So the number of elements in the pixelType is determined when reading a
> > file. So we use itk::Array or itk::VariableLengthVector as the pixel
> type.
> > In the test PolylineReadWriteTest, we defined
> > itk::VariableLengthVector<float> as pixel type since the test data
> > fibers.vtk contains COLOR_SCALARS.
> >
> > Finally, i have a question in terms of GIFTI data format, which requires
> > gifticlib (http://www.nitrc.org/frs/?group_id=75). I am not sure the
> third
> > party software policy of itk, therefore i didn't include the support into
> > this version of submission. Do you think we could put gifticlib into
> > Utilities for supporting GIFTI IO? Or we could do it latter when this
> > functionality was required.
> >
> >
> > Many thanks for your help
> >
> >
> > wanlin
> >
> >> thanks again for this contribution.
> >>
> >> regards,
> >>
> >> alex.
> >>
> >>
> >> On Thu, Oct 14, 2010 at 12:19 PM, Alexandre GOUAILLARD
> >> <agouaillard at gmail.com> wrote:
> >> > hi wanlin, all,
> >> >
> >> > mesh IO is in my pile of to-be-reviewed. I m goign to put it on the
> >> > top of my pile, and address it early next week. If everything goes
> >> > alright, I would push the code in ITK v4 before the end of next week.
> >> >
> >> > thanks for the contribution.
> >> >
> >> > alex.
> >> >
> >> >
> >> > On Thu, Oct 14, 2010 at 7:26 AM, wanlin <wanlinzhu at gmail.com> wrote:
> >> >> Hi, Brain,
> >> >>             Reading binary legacy vtk polydata has been implemented
> in
> >> >> http://www.insight-journal.org/browse/publication/761
> >> >> Would you like try it?
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Oct 13, 2010 at 11:15 AM, Luis Ibanez <
> luis.ibanez at kitware.com>
> >> >> wrote:
> >> >>>
> >> >>> Hi Brain,
> >> >>>
> >> >>> Since this is an existing class, Jeff could simply
> >> >>>
> >> >>> 1) create a Git branch in his local repository,
> >> >>> 2) make the necessary changes to the class,
> >> >>> 3) add the proper test for reading binary vtk files,
> >> >>> 4) run Experimental build until green,
> >> >>> 5) and then push the branch to Gerrit for review.
> >> >>>
> >> >>>
> >> >>> Please let us now if you or Jeff run into any
> >> >>> problems.
> >> >>>
> >> >>> I'm sure many people will appreciate having
> >> >>> the binary read functionality in this reader.
> >> >>>
> >> >>>
> >> >>>      Luis
> >> >>>
> >> >>>
> >> >>> --------------------------------------------
> >> >>> On Wed, Oct 13, 2010 at 5:00 PM, brian avants <stnava at gmail.com>
> >> >>> wrote:
> >> >>>>
> >> >>>> Luis
> >> >>>>
> >> >>>> I think we can add the binary I/O capabilities to these classes, if
> >> >>>> it's not done elsewhere, already.   Jeff Duda will probably do this
> >> >>>> --- what's the recommended approach, currently, for adding
> >> >>>> functionality like this to the toolkit?
> >> >>>>
> >> >>>> agreed that xml support is a bit ambitious.
> >> >>>>
> >> >>>> Brian
> >> >>>>
> >> >>>> On Wed, Oct 13, 2010 at 4:49 PM, Luis Ibanez
> >> >>>> <luis.ibanez at kitware.com>
> >> >>>> wrote:
> >> >>>> >
> >> >>>> > Hi Brian,
> >> >>>> >
> >> >>>> > This reader was implemented as a helper class for
> >> >>>> > other initiatives.
> >> >>>> >
> >> >>>> > Managing only ASCII was the first easy way to get
> >> >>>> > it done.
> >> >>>> >
> >> >>>> > Binary just need to be added to its capabilities.
> >> >>>> >
> >> >>>> >
> >> >>>> > Would you be interested in modifying the class
> >> >>>> > and adding the Binary reading capability ?
> >> >>>> >
> >> >>>> >
> >> >>>> > -
> >> >>>> >
> >> >>>> > The support for XML is a more difficult proposition.
> >> >>>> > The implementation in VTK relies on a hierarchy
> >> >>>> > of helper classes.  It can certainly be done in ITK
> >> >>>> > but it will require several weeks of effort.
> >> >>>> >
> >> >>>> >
> >> >>>> > I would suggest to deal only with the Binary
> >> >>>> > reading capability initially.
> >> >>>> >
> >> >>>> >
> >> >>>> >      Luis
> >> >>>> >
> >> >>>> >
> >> >>>> > ----------------------------------------------------------------
> >> >>>> > On Wed, Oct 13, 2010 at 2:38 PM, brian avants <stnava at gmail.com>
> >> >>>> > wrote:
> >> >>>> >>
> >> >>>> >> Hi Everyone
> >> >>>> >>
> >> >>>> >> I updated git-itk this morning.  Am trying to read a vtk mesh
> and
> >> >>>> >> apply a transformation to it.  I get the error below that says,
> >> >>>> >> basically, "File format is BINARY but only ASCII files can be
> >> >>>> >> read".
> >> >>>> >> Is there a good reason for this limitation?    Is it not true
> that
> >> >>>> >> vtk
> >> >>>> >> files can be of type ASCII, binary or xml?   Should all of those
> >> >>>> >> be
> >> >>>> >> supported?   Should the filter(s) be named
> >> >>>> >> itkVTKAsciiPolyDataReader/Writer?    Finally, is anyone working
> on
> >> >>>> >> this or is the solution in the software pipeline?
> >> >>>> >>
> >> >>>> >> Thanks!
> >> >>>> >>
> >> >>>> >> Brian
> >> >>>> >>
> >> >>>> >>
> >> >>>> >> Input object: Mesh.vtk
> >> >>>> >> Error during Update()
> >> >>>> >>
> >> >>>> >> itk::ExceptionObject (0x101abc640)
> >> >>>> >> Location: "void
> >> >>>> >> itk::VTKPolyDataReader<TOutputMesh>::GenerateData()
> >> >>>> >> [with TOutputMesh = itk::Mesh<double, 3u,
> >> >>>> >> itk::DefaultStaticMeshTraits<double, 3u, 3u, float, float,
> double>
> >> >>>> >> >]"
> >> >>>> >> File:
> /Users/brianavants/code/ITK/Code/IO/itkVTKPolyDataReader.txx
> >> >>>> >> Line: 107
> >> >>>> >> Description: itk::ERROR: VTKPolyDataReader(0x101abc4b0): Error
> >> >>>> >> reading
> >> >>>> >> file: WM.vtk
> >> >>>> >> File format is BINARY but only ASCII files can be read.
> >> >>>> >> _______________________________________________
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> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> --
> >> >>>> ß®∫∆π
> >> >>>
> >> >>>
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> >> >>
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> >> >>
> >> >> Visit other Kitware open-source projects at
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> >> >>
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> >
> >
>
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