A grid scan is a set of stills at a stationary spindle, and the angle it stood
at is what relates one grid to another taken elsewhere on the circle. Users were
finding an all-zero omega in the file and concluding the angle could not be
recorded at all.
It already can, and has since the goniometer and the grid scan stopped being
alternatives: send the axis with step 0 and its start angle, and that angle is
written per image into the NXmx sample chain, read back by reader/, and taken by
dials.import as a set of stills. Measured on a generated 12-image grid: the
placeholder file carries omega = 0 x 12, the same file with the axis sent at
step 0 carries omega = 90 x 12, and dials.import reports "still: 1, sweep: 0"
for both. Nothing in the code needed changing, so nothing was; what was missing
was that nobody could tell, and that no test held the behaviour down.
So: the API and the HDF5 documentation now say it in as many words, and three
tests pin the three legs the value crosses - the OpenAPI request (which used to
drop the grid scan whenever an axis was present, unpinned until now), the CBOR
start message, and the file round trip.
Also corrects a claim two comments and the HDF5 page were making. NXmx can
express "no rotation" perfectly well - a sample may depend_on "." - so the
placeholder is not there for the standard's sake. It is there because dxtbx
cannot read a sample chain of translations alone: strip the rotation axis from a
grid scan master and dials.import dies in get_dxtbx_goniometer with a matmul
dimension mismatch. Recorded so nobody removes the placeholder on the strength
of the standard.
One thing the change does not fix, because it cannot: a stationary angle is
invisible to DIALS when a grid scan is present. dxtbx picks the first varying
axis as the scan axis, which is a grid translation, so the oscillation reads
(0, 0); and with exactly one rotation axis in the chain it builds a single-axis
goniometer whose fixed rotation is the identity, never consulting the angle. The
same angle IS visible when it is the only candidate (oscillation reads (90, 0))
or when a Smargon head puts a second rotation axis in the chain (the setting
rotation then carries it). The value is in the file and correct either way.
leonarski_f
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