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This was previously being used as a kind of check for correctness of the
indexing solution. However, the threshold only made sense for large
unit cells. It breaks indexing for small cells, which we are
increasingly seeing in applications.
Now, the threshold is reduced to the theoretical minimum below which the
refinement is strictly underdetermined. We (currently!) refine 9
parameters and have three data points per pair (fs,ss,excitation error).
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While compiling CrystFEL using musl, this error message popped up:
In file included from ../libcrystfel/src/indexers/pinkindexer.c:36:
x86_64-unknown-linux-musl/sys-include/sys/errno.h:1:2:
warning: #warning redirecting incorrect #include <sys/errno.h> to <errno.h> [-Wcpp]
1 | #warning redirecting incorrect #include <sys/errno.h> to <errno.h>
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So I removed sys/errno.h completely (since I couldn't figure out where
it was used in the file anyways), and the result still compiled.
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The Mac runner and Seedee source aren't available elsewhere, so these
will always fail for merge requests.
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This is a simple but unsophisticated way of getting the numbers out.
There's no way to change the geometry if required.
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Prevously, it disabled the resend timeout, but still sent the
acknowledgements.
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This was out of date, referring to the old detector-shift which doesn't
work any more.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/97
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Previously, there was a missing function argument here.
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I was trying to be too clever. The old version breaks if the G6
distance is exactly zero, which happens e.g. in one of the unit tests.
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The previous behaviour gave biased cell distributions in some
situations, because it preferred not to overrule the indexing algorithm.
Some indexing algorithms (xgandalf) always return a certain cell
variant, e.g. gamma > 90. To make the histograms interpretable, we have
to randomise our choice of reduced cell in all cases.
However, we need to be careful that the cells we randomise between are
really equivalent. The previous behaviour here was to look only at the
axis lengths. We must look at the angles as well.
But that's not the end of the story. We would have to choose some
weighting factor between axis lengths and angles when deciding if a new
cell is "better". That would be hard. Instead, compare_rcp now
compares the G6 vectors directly, which consider lengths and angles on
an even footing.
Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/95
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Previously, there was a bad bug here. We would still try to write a
top-level coffset even if panels have moved such that the coffset is no
longer a single value.
One possibility is to unset panel->cnz_offset_default when moving a
panel. This works, but we have to do it on every translation, or accept
a floating-point comparison with zero and associated non-determinism.
It's very likely that if we move one panel, we'll be moving all panels,
even if only by a small amount. So, a more stable way seems to just
write separate coffset values all the time. The coffset values aren't
really meant to be used at the top level anyway (that's what clen is
for!), so this fits pretty well.
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With thanks to biochem-fan.
Fixes: https://github.com/taw10/crystfel/issues/12
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Two problems:
1. Didn't take into account that bad->name already includes the prefix
"bad".
2. Didn't convert the panel-relative coordinates back to slab-relative.
Fixes: https://github.com/taw10/crystfel/issues/11
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Otherwise, we end up acknowledging the previous message ID after
receiving something like kEndOfStream.
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Something strange is going on here, need to debug.
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See 79bda19687e425818888ce17cc6e2239744ee640
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Fixes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/96
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Also mention this when complaining about the geometry file.
Fixes: https://github.com/taw10/crystfel/issues/10
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Fixes: https://github.com/taw10/crystfel/issues/9
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The type of the list needs to be correct, otherwise we can't push to it
later.
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Fixes: https://github.com/taw10/crystfel/issues/8
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In some rare cases, the cell changes from right to left handed during
the vector refinement stage of asdf, while ending up at an apparently
correct indexing solution. This commit just flips the axis round when
necessary, in the same way that asdf already does in an earlier stage.
I haven't done a proper survey, but I can say that the image I used to
isolate and test this issue had very low resolution while still being
what we would call "indexable". The left-handed cells appeared for six
out of the 12173 hits in that run, or slightly below 0.05%. So, it's
rare but not totally impossible.
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It's hardly needed for re-use, and invites problems with the volume
going out of sync with the vectors. Better just to calculate it when
needed.
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1) Remove MacOS native build job and build-brew-macos the only job for MacOS.
2) Make container builds manual.
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build is done.
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Needs to be a raw download.
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