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Write the grid stage as a base stage, not head-mounted

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The grid translations went innermost, i.e. mounted on the head, so a grid
position turned with the spindle. At SLS the grid is an Aerotech xyz that the
spindle is mounted ON, so the mounting order is base -> grid -> omega -> chi ->
phi -> sample and a grid position is independent of omega.

Identical to the previous chain at omega = 0, which is every grid scan collected
so far, and correct rather than incorrect when it is not.

A head-mounted stage exists too - the Smargon translates, and that is what
helical uses - and would sit on the other side of omega. Only the base stage is
modelled for now, which is the one actually used; the comment says so.

Measured: dials.import reads a master with the new chain.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-08-22 22:41:51 +02:00
co-authored by Claude Opus 5
parent cc334c5c55
commit 5e05515165
2 changed files with 22 additions and 17 deletions
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docs/CHANGELOG.md
+1 -1
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@@ -16,7 +16,7 @@ This is an UNSTABLE release. It includes many experimental features, as well as
* HDF5: a data file missing next to a VDS master now reads as the error-pixel marker instead of zero counts, so those frames are masked rather than silently integrated as blank.
* The writer refuses a stream whose start message declares a different pixel format than its images carry, instead of writing a master that does not describe its own data.
* A grid scan and a goniometer axis are no longer alternatives - both can be set, and the grid scan is no longer silently dropped when an axis is present.
* HDF5: a grid-scan file now records the (stationary) spindle, so it can be opened by programs that require a rotation axis; DIALS refused the previous files outright.
* HDF5: a grid-scan file now records the (stationary) spindle, so it can be opened by programs that require a rotation axis; DIALS refused the previous files outright. The grid stage is written as a base stage, so a grid position does not turn with the spindle.
* The rotation axis is read back from HDF5 under whatever name it carries; only `omega` was recognised before, so a sweep recorded as e.g. `phi` re-opened as stills with nothing to say so.
* A goniometer axis that does not turn is now kept rather than discarded, and is distinguished from a rotation sweep - it records where the head was for a still or a grid scan.
* `images_per_file` is now chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000.
writer/HDF5NXmx.cpp
+21 -16
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@@ -766,9 +766,13 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
};
// One chain, built from the base outwards, rather than the goniometer and the grid scan being
// alternatives. NXmx applies the deepest dependency first, so writing spindle -> chi -> phi ->
// grid translations makes the sample sit at the innermost end, which is what it physically is:
// the grid stage rides on the head, and the head rides on the spindle.
// alternatives. NXmx applies the deepest dependency first, so the order here is the mounting
// order: the grid stage is a BASE stage (an Aerotech xyz at SLS) that the spindle is mounted on,
// the spindle carries the head, and the head carries the sample. So
// base -> grid -> omega -> chi -> phi -> sample
// and a grid position therefore does NOT turn with omega. (A head-mounted grid stage exists too
// - the Smargon can translate - and would sit on the other side of omega; only the base stage is
// modelled for now, which is what is actually used.)
const bool write_goniometer = (end.max_image_number > 0) && start.goniometer.has_value();
const bool write_grid_scan = start.grid_scan.has_value();
@@ -788,6 +792,20 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
transformations.NXClass("NXtransformations");
hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");
// Base stage first: everything else is mounted on it. The position containers hold one entry
// per image and are empty if the scan stopped at the first image.
if (write_grid_scan && (end.max_image_number > 0)) {
SaveVector(transformations,"grid_scan_x", start.grid_scan->GetXContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {1, 0, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_x";
SaveVector(transformations,"grid_scan_y", start.grid_scan->GetYContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {0, 1, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_y";
}
if (write_goniometer) {
// Prefer the rotation axis refined by the offline analysis (rugnux); the broker leaves it empty
// and the user-provided goniometer axis stands.
@@ -852,19 +870,6 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
}
}
// The grid stage is mounted on the head, so its translations are innermost. The position
// containers hold one entry per image and are empty if the scan stopped at the first image.
if (write_grid_scan && (end.max_image_number > 0)) {
SaveVector(transformations,"grid_scan_x", start.grid_scan->GetXContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {1, 0, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_x";
SaveVector(transformations,"grid_scan_y", start.grid_scan->GetYContainer_m(end.max_image_number))
->Transformation("m", depends_on, "", "",
"translation", {0, 1, 0}, {0,0,0}, "");
depends_on = "/entry/sample/transformations/grid_scan_y";
}
}
group.SaveScalar("depends_on", depends_on);