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

Mon Nov 6 11:51:29 EST 2017

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<mailto: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<mailto:qth20 at cam.ac.uk>>
Date: Monday, July 28, 2014 9:25 AM
To: Kenneth Moreland <kmorel at sandia.gov<mailto:kmorel at sandia.gov>>, David E DeMarle <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>>

Cc: paraview-help <paraview-help at sandia.gov<mailto:paraview-help at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto: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<mailto:qth20 at cam.ac.uk>>
Date: Friday, July 25, 2014 11:34 PM
To: David E DeMarle <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>>
Cc: paraview-help <paraview-help at sandia.gov<mailto:paraview-help at sandia.gov>>, "paraview at paraview.org<mailto:paraview at paraview.org>" <paraview at paraview.org<mailto: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<mailto: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<mailto: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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