Adaptahop support improvement #551
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apontzen
reviewed
Jan 19, 2020
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Looks good! I just had one query flagged inline... |
apontzen
reviewed
Jan 21, 2020
nose/adaptahop_test.py
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| # - obtained from get_group_array masking | ||
| # are the same (in term of sets) | ||
| assert len(np.setdiff1d(iord[mask], h[halo_id]['iord'])) == 0 |
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Should you also be checking the reverse? I think setdiff1d is asymmetric
cphyc
commented
Oct 14, 2020
pynbody/halo/adaptahop.py
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| for halo_id, halo in self._halos.items(): | ||
| fpu.seek(halo.properties['file_offset']) | ||
| fpu.skip(1) # number of particles | ||
| particle_ids = fpu.read_vector('i') |
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After #584 is merged, this should be fixed to take into account cases where particle_ids is not sorted and/or is not a 32bit integer.
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@apontzen do you think this is ready to go? |
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Is there any way to test this? Happy to add a small file to the testdata tar if needed. |
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I can generate one of about ~50Mio (snapshot + simulation), would that suffice? |
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Sounds good, thank you! |
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We can use the following halo catalog (very minimalistic, only two halos and linked to the |
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Thanks! |
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This PR improves the support of adaptahop in pynbody (see #546 for the original PR).
It changes the following behaviour:
np.searchsortedfunction. This was used to generate anIndexedSubSnapfrom a list of particle ids,iord_argsortwhich is the result ofnp.argsort(sim['iord']),get_group_arrayfor adaptahop, to make it usable with https://github.com/pynbody/tangos (see TypeError error when linking tangos#112).