[Paraview] combining a voxel-based stat file with a surface mesh?

Fri May 25 11:18:21 EDT 2012

Apply the CellDataToPointData filter to your stats volume first, that will
give the resample filter something to interpolate with inside of each cell.

David E DeMarle
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Fri, May 25, 2012 at 9:45 AM, Tom Schoenemann <toms at indiana.edu> wrote:

> Got that to work, thanks!
>
> However, my ultimate goal is to display stats smoothly on a smooth mesh.
>  The problem here is that the data are calculated on voxel data, which are
> inherently unsmooth (unless the size of the voxels is tiny enough).  When I
> put the data on the smooth mesh with ResampleWithDataset, the unsmooth data
> gets placed on the smooth mesh, such that the image isn't accomplishing
> what I'd hoped.  Here is the result of data + smooth mesh:
>
>
> You can see how the data coloring highlights the step-function as a result
> of the data being voxel based.
>
> Here is the smooth mesh by itself:
>
> This smooth mesh was created by ITK-SNAP, which based it on voxel data.
>  So there is a way to smooth voxel data, but it may not be in Paraview?  Or
> is there some way to accomplish my goal in Paraview?
>
> Thanks for any suggestions, if anyone has any!  And thanks for getting me
> this far.
>
> -Tom
>
> On May 24, 2012, at 3:30 PM, David E DeMarle wrote:
>
> Not sure if this is what you are trying but you can always sample
> values from a field onto a mesh by using the ResampleWithDataset
> filter.
>
> See the attached state file for a demo.
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
> On Thu, May 24, 2012 at 3:01 PM, Tom Schoenemann <toms at indiana.edu> wrote:
>
> Just wondering if anyone had any hints they could give me about things to
>
> try.
>
>
> -Tom
>
>
> On May 19, 2012, at 10:16 AM, Tom Schoenemann wrote:
>
>
> So, how would one "layer" a stat (voxel data) file over a mesh file, to
>
> color code the surface of the mesh?
>
>
> -Tom
>
>
> On May 18, 2012, at 7:14 PM, Tom Schoenemann wrote:
>
>
> I have figured out how to get my surface meshes (from ITK-SNAP) to line up
>
> perfectly with my stat data (calculated originally on the same image). Here
>
> is how I did it:
>
>
> 1) reflected the ITK-SNAP surface mesh about the X axis:
>
> With the surface mesh highlighted in the pipeline browser, select
>
> Filters>Alphabetical>Reflect
>
> set:
>
> Plane: X
>
> Center: 0
>
> Press "apply"
>
>
> 2) load the stat data file (press "apply")
>
> Go to the Information tab for this file and note the X, Y, and Z range
>
> bounds for this file.  The bounds for my image say, for example:
>
> X range: 109 to 218 (delta: 109)
>
> Y range: -107 to -0.5 (delta: 106)
>
> Z range: 136 to 272 (delta: 136)
>
>
> 3) return to the ITK-SNAP surface mesh, reflected version (click on the
>
> "Reflect" object in the pipeline browser listed just below your ITK-SNAP
>
> surface mesh file, so that it is highlighted).  Then select:
>
> Filters>Alphabetical>Transform
>
> In the "Translate" boxes of the Transform properties tab, enter the first
>
> number for each of your X, Y, and Z ranges, that you noted in step 2 above,
>
> in each of the boxes (unfortunately not labeled "X", "Y" and "Z").
>
> E.g., for my data, the boxes for the "Translate" row would read:
>
> Translate:    109    -107    136
>
> Leave the "Rotate" and "Scale" at their default values.
>
> Press "apply"
>
>
> This moves the mesh to perfectly overlap my stat data.
>
>
> However, now I can't figure out how to have the stat data attach to my
>
> beautiful ITK-SNAP surface mesh.  I tried
>
> Filters>Alphabetical>Append Attributes
>
> with both the translated (and previously reflected) mesh highlighted along
>
> with the stat data file, but this doesn't seem to work.  The
>
> AppendAttributes object now claims to have my stat data attached
> (Properties
>
> shows them as scalars), but there is no option to display them.  The "color
>
> by" option under the display tab for this object only has "solid color" as
>
> an option.  Any ideas how I might be able to get these scalars to display
> on
>
> my beautiful mesh?
>
>
> -Tom
>
>
> On May 18, 2012, at 12:38 PM, Tom Schoenemann wrote:
>
>
> OK, so Paraview screws up NIFTI coordinates, or doesn't read the header
>
> right?  The surface mesh that ITK-SNAP makes is in vtk format, so it must
> be
>
> that ITK-SNAP doesn't put the orientation info into the right format?
>
>
> Looking closely at my image, I can see that the vtk mesh in Paraview is
>
> indeed left-right reversed compared to the original in ITK-SNAP (in
> addition
>
> to being shifted in various ways out of alignment inexplicably).
>
>
> Here are the bounds in Paraview for the mesh:
>
>
> X range: -98.9 to -9.78 (delta: 89.1)
>
>
> If I put the following for Reflect:
>
> plane: X
>
> center: 50
>
>
> Then the images are no longer left-right reversed from each other, but they
>
> are still not overlapping.  There is some kind of Y and Z shift also going
>
> on.
>
>
> -Tom
>
>
>
> On May 17, 2012, at 11:51 AM, Philip A Cook wrote:
>
>
> Trying this out on some actual data - it seems the reflection should
>
> actually be about the boundary of the image, not the center. Here the
>
> x-bounds of my image are 114 to 337 in Paraview (note this does not agree
>
> with the NIFTI or ITK coordinates), so I reflected the mesh (blue) about
> 114
>
> in the x-axis, giving me what I think is a correctly oriented mesh.
>
>
> Unfortunately, there appear to be other transformations at play as well.
> You
>
> can't see it in this view but the red mesh is offset in the Z-axis. I think
>
> this is because of the disagreement between the NIFTI and Paraview
>
> coordinates.
>
>
> <PastedGraphic-1.png>
>
>
> On May 17, 2012, at 10:36 AM, Philip A Cook wrote:
>
>
> Hi,
>
>
>
> I have had some success with the Reflect filter. Often the SNAP meshes are
>
> reflected about the origin of the image. Thus I do Reflect on the mesh (I
>
> always find it easier to transform the mesh rather than the image in
>
> Paraview), with Plane set to X / Y / Z as appropriate, and Center set to
> the
>
> Center of the image.
>
>
>
> The Center of the image in Paraview might not agree with what's in the
> image
>
> header, at least not for NIFTI files. You can figure out the Center in
>
> Paraview by selecting the image and then looking at the Information tab.
> The
>
> Bounds box will tell you the min and max in each coordinate. For the
> Reflect
>
> filter, you want the Center to be halfway between the min and max bound of
>
> the image.
>
>
>
> This usually solves my problems with meshes and images not lining up. I'm
>
> assuming here that you are loading the same image from which the mesh was
>
> defined.
>
>
>
>
> Phil
>
>
>
>
> On May 16, 2012, at 11:53 PM, Tom Schoenemann wrote:
>
>
>
> OK, that worked. I've figured out how it works, following what you
>
> suggested.
>
>
>
> Unfortunately, Paraview didn't just shift the data over, leaving it in the
>
> same orientation, it also inexplicably changed the orientation by several
>
> degrees (??).  Even if I am able to get the two boxes in basically the same
>
> location, the shifted orientation makes it impossible to be confident the
>
> data are overlaid in the right places.  This is very frustrating.
>
>  Apparently Paraview makes random changes to the orientation??  Why on
> earth
>
> would it do that?
>
>
>
> -Tom
>
>
>
> On May 16, 2012, at 5:18 PM, Scott, W Alan wrote:
>
>
>
> So, I just tried the following:
>
>
> *Sources/ Wavelet.  Apply.  Display this by Outline.
>
>
> * Filters/ Alphabetical/ Transform.  Translate X by 10.  Apply.
>
>
> * Leaving the Transform filter highlighted in the pipeline browser,
> Filters/
>
> Common/ Contor.  Apply.
>
>
> * Now, if you turn on visibility of the original Wavelet, you see that the
>
> wavelet has moved along with the contour.
>
>
>
> Or are you saying you want to move the two different files?  Then, you use
>
> two transforms – one per file.
>
>
>
> Alan
>
>
>
> From: paraview-bounces at paraview.org [mailto:paraview-bounces at paraview.org]
>
> On Behalf Of Tom Schoenemann
>
>
> Sent: Wednesday, May 16, 2012 2:41 PM
>
>
> To: Samuel Key
>
>
> Cc: paraview at paraview.org
>
>
> Subject: [EXTERNAL] Re: [Paraview] different orientation of input files
>
>
>
> I must be missing something.  It only seems to move the bounding box, but
>
> not the location of the contour itself.. Not sure what that would be useful
>
> for, but in any case, I need to move the contour and/or data within the
>
> workspace, so the two overlap.  Transform is only changing the box, not
>
> changing the location of the object within the box.  Again, maybe I'm
>
> missing something.
>
>
>
> -Tom
>
>
>
> On May 16, 2012, at 2:32 PM, Samuel Key wrote:
>
>
>
>
> Tom,
>
>
>
> Will the Transform filter work for you? (Filters>Alphabetical>Transform)
>
>
>
> It works for me with unstructured meshes. I don't know if it will work with
>
> a surface mesh produced ITK-SNAP.
>
>
>
> Sam Key
>
>
>
> On 5/16/2012 10:29 AM, Tom Schoenemann wrote:
>
>
> Hi everyone,
>
>
>
> I have a question about changing/editing the orientation and origin
>
> information about an input file.  Basically, the problem is this: I have a
>
> 3D volume (originally voxel data) file that contains statistics on its
>
> surface that I want to display color-coded.  I can create a nice smoothed
>
> version of the surface using a different piece of software (ITK-SNAP), and
>
> this is the surface I'd like to use to display my stats (Paraview does not
>
> allow you to smooth the surface in the same way that ITK-SNAP does,
>
> eliminating the stair-step surface artifacts).  I can indeed read both the
>
> stats file and the surface file from ITK-SNAP into Paraview, but
>
> unfortunately they now have different origins. That is, they don't overlap
>
> (the bounding box for the stats is completely outside the surface model
> that
>
> ITK-SNAP created.
>
>
>
> Originally, both files had the same orientation and origin: ITK-SNAP used
>
> the same file to create the beautiful surface that the stats were created
>
> with.
>
>
>
> So Paraview apparently does not read the header info the same way for the
>
> two types of files, even though ITK-SNAP does.
>
>
>
> Is there a way to change the origin and/or orientation of files in
> Paraview?
>
>  I'm assuming there is a simple transform I could figure out by trial and
>
> error to get them to overlap again, but I don't know how or where I would
> do
>
> this.
>
>
>
> Thanks for any suggestions!
>
>
>
> -Tom
>
>
>
> _________________________________________________
>
>
> P. Thomas Schoenemann
>
>
>
> Associate Professor
>
>
> Department of Anthropology
>
>
> Indiana University
>
>
> Bloomington, IN  47405
>
>
> Phone: 812-855-8800
>
>
> E-mail: toms at indiana.edu
>
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
>
> Consulting Scholar
>
>
> Museum of Archaeology and Anthropology
>
>
> University of Pennsylvania
>
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Powered by www.kitware.com
>
>
>
> Visit other Kitware open-source projects at
>
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>
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>
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>
> _________________________________________________
>
>
> P. Thomas Schoenemann
>
>
>
> Associate Professor
>
>
> Department of Anthropology
>
>
> Indiana University
>
>
> Bloomington, IN  47405
>
>
> Phone: 812-855-8800
>
>
> E-mail: toms at indiana.edu
>
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
>
> Consulting Scholar
>
>
> Museum of Archaeology and Anthropology
>
>
> University of Pennsylvania
>
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
>
> _________________________________________________
>
>
> P. Thomas Schoenemann
>
>
>
> Associate Professor
>
>
> Department of Anthropology
>
>
> Indiana University
>
>
> Bloomington, IN  47405
>
>
> Phone: 812-855-8800
>
>
> E-mail: toms at indiana.edu
>
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
>
> Consulting Scholar
>
>
> Museum of Archaeology and Anthropology
>
>
> University of Pennsylvania
>
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> Powered by www.kitware.com
>
>
>
> Visit other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
>
>
> Please keep messages on-topic and check the ParaView Wiki at:
>
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>
>
>
> Follow this link to subscribe/unsubscribe:
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> _______________________________________________
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>
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>
>
> Visit other Kitware open-source projects at
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>
> _________________________________________________
>
> P. Thomas Schoenemann
>
>
> Associate Professor
>
> Department of Anthropology
>
> Indiana University
>
> Bloomington, IN  47405
>
> Phone: 812-855-8800
>
> E-mail: toms at indiana.edu
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
> Consulting Scholar
>
> Museum of Archaeology and Anthropology
>
> University of Pennsylvania
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Powered by www.kitware.com
>
>
> Visit other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
>
> Please keep messages on-topic and check the ParaView Wiki at:
>
> http://paraview.org/Wiki/ParaView
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>
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>
>
> _________________________________________________
>
> P. Thomas Schoenemann
>
>
> Associate Professor
>
> Department of Anthropology
>
> Indiana University
>
> Bloomington, IN  47405
>
> Phone: 812-855-8800
>
> E-mail: toms at indiana.edu
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
> Consulting Scholar
>
> Museum of Archaeology and Anthropology
>
> University of Pennsylvania
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Powered by www.kitware.com
>
>
> Visit other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
>
> Please keep messages on-topic and check the ParaView Wiki at:
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>
>
> _________________________________________________
>
> P. Thomas Schoenemann
>
>
> Associate Professor
>
> Department of Anthropology
>
> Indiana University
>
> Bloomington, IN  47405
>
> Phone: 812-855-8800
>
> E-mail: toms at indiana.edu
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
> Consulting Scholar
>
> Museum of Archaeology and Anthropology
>
> University of Pennsylvania
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Powered by www.kitware.com
>
>
> Visit other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
>
> Please keep messages on-topic and check the ParaView Wiki at:
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>
>
> _________________________________________________
>
> P. Thomas Schoenemann
>
>
> Associate Professor
>
> Department of Anthropology
>
> Indiana University
>
> Bloomington, IN  47405
>
> Phone: 812-855-8800
>
> E-mail: toms at indiana.edu
>
>
> Open Research Scan Archive (ORSA) Co-Director
>
> Consulting Scholar
>
> Museum of Archaeology and Anthropology
>
> University of Pennsylvania
>
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
> Powered by www.kitware.com
>
>
> Visit other Kitware open-source projects at
>
> http://www.kitware.com/opensource/opensource.html
>
>
> Please keep messages on-topic and check the ParaView Wiki at:
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>
> <resampleexample.pvsm>
>
>
>      _________________________________________________
> P. Thomas Schoenemann
>
> Associate Professor
> Department of Anthropology
> Indiana University
> Bloomington, IN  47405
> Phone: 812-855-8800
> E-mail: toms at indiana.edu
>
> Open Research Scan Archive (ORSA) Co-Director
> Consulting Scholar
> Museum of Archaeology and Anthropology
> University of Pennsylvania
>
> Homepage: http://mypage.iu.edu/~toms/
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
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