<div dir="ltr"><div>Ken,</div><div><br></div>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.<div><br></div><div>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.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Nov 6, 2017 at 11:51 AM, Moreland, Kenneth <span dir="ltr"><<a href="mailto:kmorel@sandia.gov" target="_blank">kmorel@sandia.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">It looks like the NRRD reader does not support time series. I wrote up a bug (<a href="https://gitlab.kitware.com/paraview/paraview/issues/17820" target="_blank">https://gitlab.kitware.com/<wbr>paraview/paraview/issues/17820</a><wbr>),
but in the mean time you could try a different image format. You could try either raw or tiff format.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">-Ken<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Joe Ping-Lin Hsiao [mailto:<a href="mailto:phsiao@cs.unc.edu" target="_blank">phsiao@cs.unc.edu</a>]
<br>
<b>Sent:</b> Monday, November 6, 2017 9:21 AM<br>
<b>To:</b> Moreland, Kenneth <<a href="mailto:kmorel@sandia.gov" target="_blank">kmorel@sandia.gov</a>><br>
<b>Cc:</b> Quang Ha <<a href="mailto:qth20@cam.ac.uk" target="_blank">qth20@cam.ac.uk</a>>; DeMarle, David E. (External Contacts) <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>>; <a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a></span></p><div><div class="h5"><br>
<b>Subject:</b> [EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data<u></u><u></u></div></div><p></p><div><div class="h5">
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<p class="MsoNormal">Hi Ken,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Is there an easy way to fix this? I used ImageJ to create those images. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">-Joe<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Mon, Jul 28, 2014 at 5:02 PM, Moreland, Kenneth <<a href="mailto:kmorel@sandia.gov" target="_blank">kmorel@sandia.gov</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">-Ken<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Quang Ha <<a href="mailto:qth20@cam.ac.uk" target="_blank">qth20@cam.ac.uk</a>><br>
<b>Date: </b>Monday, July 28, 2014 9:25 AM<br>
<b>To: </b>Kenneth Moreland <<a href="mailto:kmorel@sandia.gov" target="_blank">kmorel@sandia.gov</a>>, David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>><u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black"><br>
<b>Cc: </b>paraview-help <<a href="mailto:paraview-help@sandia.gov" target="_blank">paraview-help@sandia.gov</a>>, "<a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Hi,<br>
<br>
Thank you very much for your reply. It seems that I would have to deal with the input data once again.<br>
<br>
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?<br>
<br>
Best regards,<br>
Quang <u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">On 28/07/14 15:46, Moreland, Kenneth wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Quang,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">-Ken<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:
</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Quang-Thinh Ha <<a href="mailto:qth20@cam.ac.uk" target="_blank">qth20@cam.ac.uk</a>><br>
<b>Date: </b>Friday, July 25, 2014 11:34 PM<br>
<b>To: </b>David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>><br>
<b>Cc: </b>paraview-help <<a href="mailto:paraview-help@sandia.gov" target="_blank">paraview-help@sandia.gov</a>>, "<a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a>" <<a href="mailto:paraview@paraview.org" target="_blank">paraview@paraview.org</a>><br>
<b>Subject: </b>[EXTERNAL] Re: [Paraview] Create 4D Animation from sets of 3D Data<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Hi,<u></u><u></u></span></p>
<p><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Thanks for your reply.
<u></u><u></u></span></p>
<p><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">1) The data sets are all in STL format.
<u></u><u></u></span></p>
<p><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">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?
<u></u><u></u></span></p>
<p><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Quang<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">On 26 Jul 2014 04:17, David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>> wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">1) What file format are the 10 data sets in?
<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><br>
On Friday, July 25, 2014, Quang Ha <<a href="mailto:qth20@cam.ac.uk" target="_blank">qth20@cam.ac.uk</a>> wrote:<u></u><u></u></span></p>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Hi,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Would anyone be kind enough to give me some advices on this, please?<br>
<br>
Thanks,<br>
Quang<br>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><br>
<br>
-- <br>
David E DeMarle<br>
Kitware, Inc.<br>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black"><u></u> <u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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