I have a bvh file found here and I want to import it to blender, then export it again so that both the original (imported) and exported bvh files are identical. I'm not sure what options I should choose to import and export the bvh files so if anyone could please advise.

When I keep the default options to import and export, then open the bvh files, they are totally different, this is the resulted bvh file.

So if anyone could please advise.

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    $\begingroup$ Blender uses the Z axis for up, whereas many other 3D software packages use the Y axis. This looks like a confusion between these conventions. This is quite possibly a bug, where Blender compensates for its own different convention on import, but "forgets" to do so on export. $\endgroup$ – user7952 Feb 15 '15 at 1:42
  • $\begingroup$ @SixthOfFour so would you please advise me with a way on how to import the original and export it to be the same? $\endgroup$ – Tak Feb 15 '15 at 1:46
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    $\begingroup$ Thanks for accepting. I made a small edit after you accepted, about a possible workaround for the rotation. $\endgroup$ – user7952 Feb 15 '15 at 2:14
  • $\begingroup$ @SixthOfFour Thank you very much! you are a legend :D $\endgroup$ – Tak Feb 15 '15 at 2:19

I looked a little closer and found a solution. On importing, there's an option to set which axes point up and forward. Set those to Z up and Y forward.
BVH import options

Here's the original file with the axes set like that:
Original file

And here's after exporting it and re-importing it with the axes set like that:
Exported then re-imported file

As you can see the entire scene gets rotated when you do this, but the files are essentially identical. A possible workaround would be to import with the axes set to their defaults, and when you're done working with it, select everything and rotating it by -90° around the X axis before exporting. Snap the 3D cursor to the world centre (ShiftS > R) and set the pivot point to 3D cursor before rotating.
Set pivot point

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    $\begingroup$ Related, blender.stackexchange.com/q/471/12 $\endgroup$ – iKlsR Feb 15 '15 at 2:17
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    $\begingroup$ @iKlsR To me Blender's convention is what comes naturally (most likely because of my math background), and I never even considered Y-up before I started using 3D software. A link in a comment to that question explained to me why some software uses Y-up. Thank you for that. $\endgroup$ – user7952 Feb 15 '15 at 2:33

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