[Paraview] Xdmf Polyvertex, Only First Half Visible

Tue Aug 21 17:32:15 EDT 2012

I think your topology is written incorrectly. Every other cell refers
to point 0.
See the spreadsheet view.

00000000: 0000 0000 0000 0000 0100 0000 0000 0000  ................
00000010: 0200 0000 0000 0000 0300 0000 0000 0000  ................
00000020: 0400 0000 0000 0000 0500 0000 0000 0000  ................
00000030: 0600 0000 0000 0000 0700 0000 0000 0000  ................
00000040: 0800 0000 0000 0000 0900 0000 0000 0000  ................
00000050: 0a00 0000 0000 0000 0b00 0000 0000 0000  ................
00000060: 0c00 0000 0000 0000 0d00 0000 0000 0000  ................
00000070: 0e00 0000 0000 0000                      ........

Should be something like:
00000000: 0000 0000 0100 0000 0200 0000 0300 0000  ................
00000010: 0400 0000 0500 0000 0600 0000 0700 0000  ................
00000020: 0800 0000 0900 0000 0a00 0000 0b00 0000  ................
00000030: 0c00 0000 0d00 0000 0e00 0000 ............

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

On Tue, Aug 21, 2012 at 5:19 PM, Cory Quammen <cquammen at cs.unc.edu> wrote:
> David,
>
> I loaded the testTwoFile.xdmf in ParaView 3.14.1. I counted 8 points
> in the surface and points representations. Upon applying a Glyph
> filter to the data set, I see all 15 points.
>
> I've seen similar problems when loading point data from Xdmf files.
> Perhaps there is a bug in how the surface and points representations
> renders point data?
>
> Interestingly, if you apply a Mask Points filter to your file data,
> set the On Ratio to 1 and check the "Generate Vertices" option, you
> will see all 15 points in the points and surface representations.
>
> I know this doesn't answer your question about why only some of your
> points are displayed, but hopefully I've presented some workarounds.
>
> Cory
>
> On Tue, Aug 21, 2012 at 4:59 PM, David Zemon <david.zemon at mst.edu> wrote:
>> Summary
>> I'm creating a translator from CSV to Xdmf. My Xdmf file points to binary
>> files with the heavy data. When I open the file in ParaView, only the first
>> half of my data is visible.
>>
>> Question
>> Why am I only seeing half of the data?
>>
>> Details
>> Dataset
>> The first 3 lines of my dataset look like this. Columns 1-3 are XYZ, column
>> 4 is an attribute. I have two files with the same format, the first 3
>> columns of both files hold identical values, the 4th column different. This
>> gives me 5 columns: 3 for XYZ, and 1 for each of 2 attributes. Each file is
>> 125,000 rows (making a cube that is 50x50x50).
>>
>>           0.80000000          0.80000000          3.14154793
>> -34815.54578017
>>           0.80000000          0.80000000          2.89352122
>> -34815.61573156
>>           0.80000000          0.80000000          2.78985515
>> -34815.59134643
>>
>> Translator
>> Python is my language of choice and the Xdmf file is written by hand, not
>> the Xdmf python library. I read a single line from both files, split those
>> lines into lists, assign each field to a dictionary {"X": [0.8000000], "Y":
>> ...., "Energy1": [-34815.54578017], "Energy2": [-34962.99394561]}. I then
>> loop through the dictionary and write the fields to their appropriate files,
>> erasing the dictionary as I go, and increment a row counter. When both files
>> are done, I create the topology file based on the row counter. When all
>> binary files are written, I write the Xdmf file.
>>
>> Debugging Efforts
>> In the "Information" tab of ParaView, under "Statistics", "Data Arrays", and
>> "Bounds" I see all of the correct information. It shows the expected number
>> of cells and the correct ranges for all 5 columns. If I turn on "Show cube
>> axes" in "Display", the axes extend to the full range of the data, not just
>> the half that is shown.
>> In a small, 15 row sample, I tried printing to the screen every piece of
>> information before writing to the files. The screen shows every valid field
>> of all 15 rows in both files.
>>
>> Attachment
>> I've attached the output files from a small sample set (15 rows in each
>> file) - one Xdmf and 4 binary files (geometry, topology, attribute 1 and 2),
>> and 2 CSV files (two 15 row datasets).
>>
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>
>
>
> --
> Cory Quammen
> Research Associate
> Department of Computer Science
> The University of North Carolina at Chapel Hill
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>
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