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

Fri May 25 12:04:14 EDT 2012

The data is probably already on the points, (see information tab, is it a
dot or a cube next to the array name), in which case the filter is
inapplicable and won't help you.

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 11:55 AM, Tom Schoenemann <toms at indiana.edu> wrote:

> CellDataToPointData filter option is grayed out - it won't let me apply
> this to my stat data.  The online help says: "Cell Data to Point Data
> filter operates on any type of data set", so I don't know why it wouldn't.
> I'm clearly missing something here.
>
> On May 25, 2012, at 11:18 AM, David E DeMarle wrote:
>
> 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:
>>
>> <example-smooth-mesh-plus-data.png>
>>
>> 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:
>> <example-smooth-mesh-only.png>
>>
>> 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
>>
>> http://www.kitware.com/opensource/opensource.html
>>
>>
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>>
>> http://paraview.org/Wiki/ParaView
>>
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>> _________________________________________________
>>
>>
>> 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:
>>
>> http://paraview.org/Wiki/ParaView
>>
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>> _______________________________________________
>>
>>
>> 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
>>
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>>
>> _________________________________________________
>>
>> 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
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>> _________________________________________________
>>
>> 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
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>> _________________________________________________
>>
>> 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
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>>
>> _________________________________________________
>>
>> 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
>>
>>
>> Follow this link to subscribe/unsubscribe:
>>
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>> <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:
>> http://paraview.org/Wiki/ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.paraview.org/mailman/listinfo/paraview
>>
>>
>
>       _________________________________________________
> 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/
>
>
>
>
>
>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20120525/67651127/attachment-0001.htm>