[Paraview] Create 4D Animation from sets of 3D Data

Mon Nov 6 15:38:22 EST 2017

Ken,

Unfortunately neither raw or tiff format works. ParaView would crash from
reading 4d tiff formats.For raw format, I couldn't get the volume to be
displayed correctly, and the z-spacing does not work for raw files.

I have 200 stacks. One way seems would work for me is to write a Python
script and read each of the stack and set their visibility at different
frames individually.

On Mon, Nov 6, 2017 at 11:51 AM, Moreland, Kenneth <kmorel at sandia.gov>
wrote:

> It looks like the NRRD reader does not support time series. I wrote up a
> bug (https://gitlab.kitware.com/paraview/paraview/issues/17820), but in
> the mean time you could try a different image format. You could try either
> raw or tiff format.
>
>
>
> -Ken
>
>
>
> *From:* Joe Ping-Lin Hsiao [mailto:phsiao at cs.unc.edu]
> *Sent:* Monday, November 6, 2017 9:21 AM
> *To:* Moreland, Kenneth <kmorel at sandia.gov>
> *Cc:* Quang Ha <qth20 at cam.ac.uk>; DeMarle, David E. (External Contacts) <
> dave.demarle at kitware.com>; paraview at paraview.org
>
> *Subject:* [EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D
> Data
>
>
>
> Hi Ken,
>
>
>
> I I can load a bunch of .nrrd volume scans into ParaView as one unit. But
> when I play the animation, the animation only stays at the first volume and
> would not proceed.
>
>
>
> The reason may be that the files do not have time step information. In the
> "information" tab, the "Time" table of my 4d stack is empty.
>
>
>
> Is there an easy way to fix this? I used ImageJ to create those images.
>
>
>
> -Joe
>
>
>
> On Mon, Jul 28, 2014 at 5:02 PM, Moreland, Kenneth <kmorel at sandia.gov>
> wrote:
>
> Image segmentation is not my specialty, but I don't think there is an easy
> answer. You might be able to use a level set method that starts with the
> mesh from the first image and constrains the topology to be the same, but
> that would probably create artifacts that compound over time.
>
>
>
> -Ken
>
>
>
> *From: *Quang Ha <qth20 at cam.ac.uk>
> *Date: *Monday, July 28, 2014 9:25 AM
> *To: *Kenneth Moreland <kmorel at sandia.gov>, David E DeMarle <
> dave.demarle at kitware.com>
>
>
> *Cc: *paraview-help <paraview-help at sandia.gov>, "paraview at paraview.org" <
> paraview at paraview.org>
> *Subject: *[EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D
> Data
>
>
>
> Hi,
>
> Thank you very much for your reply. It seems that I would have to deal
> with the input data once again.
>
> Is there a way for the surface to be modified in such way that you have
> stated? Would you suggested starting to look at vtk/CGAL codes or something
> similar?
>
> Best regards,
> Quang
>
> On 28/07/14 15:46, Moreland, Kenneth wrote:
>
> Quang,
>
>
>
> First before answering your question, let me alert you to an easier way to
> load your data into ParaView. First, name your files with numbers just
> before the extension (e.g. left_ventricle_00.stl, left_ventricle_01.stl,
> left_ventricle_02.stl, etc.). Then just load this file series as one unit
> (they will be grouped in the ParaView file browser) and ParaView will
> automatically animate them; no need to add them manually with the Animation
> View.
>
>
>
> Now the bad news. I don't think the Temporal Interpolator is going to work
> with your data. The Temporal Interpolator needs a way to register where a
> point in one time step goes to in the next time step. It does this in a
> very simplistic way by assuming the topology is consistent across time
> steps. That is, each data set has the exact same triangles listed in the
> same order connected the same way but at different positions. The surface
> from your segmentation is surely not of this nature.
>
>
>
> -Ken
>
>
>
> *From: *Quang-Thinh Ha <qth20 at cam.ac.uk>
> *Date: *Friday, July 25, 2014 11:34 PM
> *To: *David E DeMarle <dave.demarle at kitware.com>
> *Cc: *paraview-help <paraview-help at sandia.gov>, "paraview at paraview.org" <
> paraview at paraview.org>
> *Subject: *[EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D
> Data
>
>
>
> Hi,
>
> Thanks for your reply.
>
> 1) The data sets are all in STL format.
>
> 2) I am not very sure about this. After using text editor to open the mesh
> file I can say that they are not... Is there anyway to change this?
>
> Quang
>
> On 26 Jul 2014 04:17, David E DeMarle <dave.demarle at kitware.com> wrote:
>
> 1) What file format are the 10 data sets in?
>
> 2) do all meshes have the same number of points and cells and do the come
> in the same order in every timstep? temporal interpolation requires a 1:1
> correspondence so that it knows what to interpolate between.
>
>
>
>
> On Friday, July 25, 2014, Quang Ha <qth20 at cam.ac.uk> wrote:
>
> Hi,
>
> I have a group of 10 data sets of the left ventricle at different cardiac
> phases. They have been 3D reconstructed using segmentation method. Now I am
> trying to use ParaView to see the dynamic changes over different cardiac
> phases.
>
> I have been able to get to the View -> Animation mode and add each 3D data
> at different time, but they only show me a jump from one data to another,
> rather than 'deforming' into another. I have done some searches on the
> internet and found someone suggesting the use of 'Temporal Interpolator'
> but failed to utilise it.
>
> Would anyone be kind enough to give me some advices on this, please?
>
> Thanks,
> Quang
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> --
> David E DeMarle
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> Visit other Kitware open-source projects at http://www.kitware.com/
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