added a simple program to export files in .vdb format #148
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## master #148 +/- ##
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- Coverage 88.20% 84.46% -3.75%
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Files 5 6 +1
Lines 814 869 +55
Branches 107 113 +6
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+ Hits 718 734 +16
- Misses 56 95 +39
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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).
CHANGELOG
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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
CHANGELOG
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| 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
gridData/OpenVDB.py
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| 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.
gridData/OpenVDB.py
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| 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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fixed the CHANGELOG and OpenVDB.py. I didn't get the time to work on the blender part due to exams. I will surely try do it! |
The first two are for naChR_M2_water.vdb and the last two are for 1jzv.vdb. |
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Good that you're able to load something into Blender. From a first glance I don;t recognize what I'd expect but this may be dependent on how you render in Blender. As I already said on Discord: Try to establish yourself what "correct" means. Load the original data in a program where you can reliably look at it. ChimeraX is probably the best for looking at densities; it can definitely read DX. Btw, the M2 density should look similar to the blue "blobs" on the cover of https://sbcb.bioch.ox.ac.uk/users/oliver/download/Thesis/OB_thesis_2sided.pdf |
The first one is for 1jzv.vdb and second for nAChR_M2_water.vdb (not done the shading/coloring) Can I proceed with the tests part? |
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Mentioned in the Discord but also bringing up here: In your current examples (most obvious with the pore) is that the axis is flipped so that X is "up" compared to atomic coordinates which would have Z as up. |
Thank you for the update! will try to fix this |
3 participants
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.