added a simple program to export files in .vdb format #148
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## master #148 +/- ##
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- Coverage 87.70% 83.20% -4.50%
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Lines 748 804 +56
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@orbeckst , please review the OpenVDB.py file. After that, I will add some more test covering all the missing parts |
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Thank you for contribution. I’m currently on holidays and will come back to reviewing open source contributions in the new year. Am 12/27/25 um 03:16 schrieb Shreejan Dolai ***@***.***>:spyke7 left a comment (MDAnalysis/GridDataFormats#148)
@orbeckst , please review the OpenVDB.py file. After that, I will add some more test covering all the missing parts
—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>
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orbeckst
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orbeckst
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Thank you for your contribution. Before going further, can you please try your own code and demonstrate that it works? For instance, take some of the bundled test files such as 1jzv.ccp4 or nAChR_M2_water.plt, write it to OpenVDB, load it in blender, and show an image of the rendered density?
Once we know that it's working in principle, we'll need proper tests (you can look at PR #147 for good example of minimal testing for writing functionality).
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| * Added `OpenVDB.py` inside `gridData` to simply export and write in .vdb format | ||
| * Added `test_vdb.py` inside `gridData\tests` |
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not needed, too much detail; see other entries for example. Just the user-relevant changes in functionality
| Fixes | ||
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| * Adding openVDB formats (Issue #141) |
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not a fix but an Enhancement – put it into the existing 1.1.0 section and add you name there.
| sufficient to export density data for visualization in Blender. | ||
| The OpenVDB format uses a sparse tree structure to efficiently store | ||
| volumetric data. It is the native format for Blender's volume system. |
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mention and link to the openvdb library/package
| try: | ||
| import pyopenvdb as vdb | ||
| except ImportError: | ||
| vdb = None |
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We may have to make openvdb optional and then this requires more robust handling of missing packages.
| for i in range(self.grid.shape[0]): | ||
| for j in range(self.grid.shape[1]): | ||
| for k in range(self.grid.shape[2]): | ||
| value = float(self.grid[i, j, k]) | ||
| if abs(value) > threshold: | ||
| accessor.setValueOn((i, j, k), value) |
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This looks really slow — iterating over a grid explicitly. For a start, you can find all cells above a threshold with numpy operations (np.abs(g) > threshold) and then ideally use it in a vectorized form to set the accessor.
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These tests are not testing OpenVDB so remove until you have real tests.
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Hm yes
Let me first run the thing on blender and then provide you with more details
I will try my best as I am new in this, so it may take some time also :-)
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Hi @orbeckst
I have added
OpenVDB.pyinside gridData that simply export files in.vdbformat. Also I have addedtest_vdb.pyinside tests and it successfully passes.It resolves issue #141
Required Libraries -
openvdb
conda install -c conda-forge openvdbThere are many things that need to be updated like docs, etc, but I have just provided the file and test so that you can review it, and I can fix the problems. Please let me know if anything needs to be changed and updated.