grid scan: say how the stationary spindle angle is stated, and pin it
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.
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@@ -3365,6 +3365,24 @@ TEST_CASE("JFJochReader_AxisRecovery", "[HDF5][Full]") {
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cleanup("test_ax_grid");
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}
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// A grid scan is taken at a stationary spindle, and the angle it stood at is what relates one
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// grid to another taken elsewhere on the circle. It is stated by sending the axis with step 0;
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// send nothing and the spindle is recorded at 0, which says only that nobody told us.
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SECTION("a grid scan at a stationary head position") {
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DiffractionExperiment x(DetJF(1));
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x.ImagesPerTrigger(6).GridScan(GridScanSettings(3, 10.0f, 20.0f, false, false).ImageNum(6))
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.Goniometer(GoniometerAxis("omega", 90.0f, 0.0f, Coord(-1,0,0), {}));
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const auto out = round_trip(x, "test_ax_gridstill");
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REQUIRE(out.GetGridScan().has_value());
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CHECK(out.GetGridScan()->GetNFast() == 3);
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REQUIRE(out.GetGoniometer().has_value());
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CHECK(out.GetGoniometer()->GetName() == "omega");
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CHECK(!out.GetGoniometer()->IsScanning());
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CHECK(out.GetGoniometer()->GetStart_deg() == Catch::Approx(90).margin(1e-3));
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CHECK(out.GetGoniometer()->GetAxis() == Coord(-1,0,0));
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cleanup("test_ax_gridstill");
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}
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SECTION("a grid scan under a turning spindle") {
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DiffractionExperiment x(DetJF(1));
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x.ImagesPerTrigger(6).GridScan(GridScanSettings(3, 10.0f, 20.0f, false, false).ImageNum(6))
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