Stop treating a goniometer axis and a grid scan as alternatives
They are not alternatives: a grid is usually collected at a particular head position, so an axis and a grid describe different parts of the same setup. The exclusion was enforced independently in four places - the API converter, the CBOR serializer, the writer and the reader - and each silently dropped the grid scan when an axis was present. Nothing warned. The writer now builds one chain from the base outwards, spindle -> chi -> phi -> helical -> grid translations, instead of two branches. NXmx applies the deepest dependency first, so the sample ends up innermost, which is what it physically is: the grid stage rides on the head and the head rides on the spindle. The grid translations consequently move inside the rotation - identical to before at omega = 0, and right rather than wrong when it is not. A grid scan with no axis at all now writes a stationary omega. NXmx has no way to say "there is no rotation", and a sample chain of translations alone is not something readers accept: dxtbx raises outright on it, so every grid-scan master we have written so far cannot be opened by DIALS. Measured on a file matching the new chain: dials.import reads it. At 0 degrees the rotation is the identity whatever the axis points along, so the conventional vector carries no geometric claim - it only has to be well formed. The API change is deliberately not breaking: no field changes type or cardinality, only the prose saying the two were exclusive, and a request that set both used to lose one silently and now does not. JFJochReader_GridScan asserted the absence of a goniometer; it now asserts the axis is present and stationary, which is the contract that matters - a grid scan must not read back as a sweep. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
Claude Opus 5
@@ -665,9 +665,11 @@ DatasetSettings Convert(const org::openapitools::server::model::Dataset_settings
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ret.TotalFlux(input.getTotalFlux());
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if (input.transmissionIsSet())
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ret.AttenuatorTransmission(input.getTransmission());
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// Not alternatives: a grid scan is often collected at a given head position, so an axis and a
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// grid can both be set. This used to drop the grid scan silently whenever an axis was present.
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if (input.goniometerIsSet())
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ret.Goniometer(Convert(input.getGoniometer()));
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else if (input.gridScanIsSet())
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if (input.gridScanIsSet())
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ret.GridScan(Convert(input.getGridScan()));
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if (input.spaceGroupNumberIsSet())
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@@ -240,7 +240,9 @@ components:
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default: "indigo"
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schemas:
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grid_scan:
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description: Definition of a grid scan (mutually exclusive with `rotation_axis`)
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description: |
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Definition of a grid scan. May be combined with a goniometer axis: a grid is often collected
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at a particular head position, and a stationary axis records where that was.
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type: object
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required:
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- n_fast
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+1
-1
@@ -52,7 +52,7 @@ There are minor differences at the moment:
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| - - axis | Array(float) | Vector for the rotation axis | |
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| - - helical_step | Array(float) | Translation for helical scan for 1 image \[m\] | |
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| - - screening_wedge | Array(float) | Wedge for screening \[deg\] (increment would correspond to difference between screening points) | |
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| grid_scan | object | Grid scan definition (optional and exclusive with rotation axis) | |
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| grid_scan | object | Grid scan definition (optional). May be sent together with `goniometer`: a grid is often collected at a given head position, recorded as a stationary axis (step 0) | |
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| - n_fast | uint64 | Number of elements along fast axis | |
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| - n_slow | uint64 | Number of elements along slow axis | |
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| - step_x_axis | float | Step along X axis, can be negative \[m\] | |
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@@ -15,6 +15,8 @@ This is an UNSTABLE release. It includes many experimental features, as well as
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* rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared directly with an XDS refinement.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* `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.
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@@ -688,9 +688,10 @@ void CBORStream2Serializer::SerializeSequenceStart(const StartMessage& message)
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CBOR_ENC(mapEncoder, "series_id", message.run_number);
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CBOR_ENC(mapEncoder, "fluorescence", message.fluorescence_spectrum);
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// Both, when both are present - the decoder has always read the two keys independently.
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if (message.goniometer)
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CBOR_ENC_GONIOMETER_MAP(mapEncoder, "goniometer", message);
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else if (message.grid_scan)
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if (message.grid_scan)
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CBOR_ENC_GRID_SCAN(mapEncoder, "grid_scan", message.grid_scan.value());
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CBOR_ENC(mapEncoder, "jungfrau_conversion_enabled", message.jungfrau_conversion_enabled);
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@@ -490,7 +490,11 @@ TEST_CASE("JFJochReader_GridScan", "[HDF5][Full]") {
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auto dataset = reader.GetDataset();
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REQUIRE(!dataset->experiment.GetGoniometer().has_value());
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// A grid scan carries a stationary spindle: NXmx cannot say "no rotation", and a chain of
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// translations alone is not readable (dxtbx raises on it). It must not read back as a sweep.
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REQUIRE(dataset->experiment.GetGoniometer().has_value());
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CHECK(!dataset->experiment.GetGoniometer()->IsScanning());
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CHECK(dataset->experiment.GetGoniometer()->GetIncrement_deg() == 0.0f);
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REQUIRE(dataset->experiment.GetGridScan().has_value());
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CHECK(dataset->experiment.GetGridScan()->IsSnakeScan());
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+76
-58
@@ -762,60 +762,14 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
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depends_on = "/entry/sample/transformations/phi";
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};
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if ((end.max_image_number > 0) && start.goniometer) {
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HDF5Group transformations(group, "transformations");
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transformations.NXClass("NXtransformations");
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hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");
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// One chain, built from the base outwards, rather than the goniometer and the grid scan being
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// alternatives. NXmx applies the deepest dependency first, so writing spindle -> chi -> phi ->
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// grid translations makes the sample sit at the innermost end, which is what it physically is:
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// the grid stage rides on the head, and the head rides on the spindle.
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const bool write_goniometer = (end.max_image_number > 0) && start.goniometer.has_value();
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const bool write_grid_scan = start.grid_scan.has_value();
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// Prefer the rotation axis refined by the offline analysis (rugnux); the broker leaves it empty
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// and the user-provided goniometer axis stands.
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const std::vector<double> axis_vector = end.refined_rotation_axis
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? std::vector<double>{end.refined_rotation_axis->x, end.refined_rotation_axis->y,
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end.refined_rotation_axis->z}
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: start.goniometer->GetAxisVector();
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SaveVector(transformations, start.goniometer->GetName(),
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start.goniometer->GetAngleContainer(end.max_image_number))->
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Transformation("deg", depends_on, "", "",
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"rotation", axis_vector, {0,0,0}, "");
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SaveVector(transformations, start.goniometer->GetName() + "_end",
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start.goniometer->GetAngleContainerEnd(end.max_image_number))
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->Units("deg");
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SaveScalar(transformations, start.goniometer->GetName() + "_range_average",
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start.goniometer->GetIncrement_deg())
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->Units("deg");
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SaveScalar(transformations, start.goniometer->GetName() + "_range_total",
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start.goniometer->GetIncrement_deg() * end.max_image_number)
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->Units("deg");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName();
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write_smargon(transformations, depends_on);
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auto helical = start.goniometer->GetHelicalStep();
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if (helical.has_value()) {
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_x",
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start.goniometer->GetXContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {1, 0, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_x";
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_y",
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start.goniometer->GetYContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {0, 1, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_y";
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_z",
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start.goniometer->GetZContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {0, 0, 1}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_z";
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}
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} else if (start.grid_scan.has_value()) {
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if (write_grid_scan) {
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HDF5Group grid_scan_group(group, "grid_scan");
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grid_scan_group.NXClass("NXcollection");
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@@ -824,14 +778,80 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
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SaveScalar(grid_scan_group, "n_fast", start.grid_scan->GetNFast());
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SaveScalar(grid_scan_group, "step_x", start.grid_scan->GetGridStepX_um() * 1e-6)->Units("m");
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SaveScalar(grid_scan_group, "step_y", start.grid_scan->GetGridStepY_um() * 1e-6)->Units("m");
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}
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if (write_goniometer || write_grid_scan || start.smargon_position) {
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HDF5Group transformations(group, "transformations");
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transformations.NXClass("NXtransformations");
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hdf5_file->HardLink("/entry/sample/transformations","/entry/sample/goniometer");
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// The position containers hold one entry per image; they are empty when the scan
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// stopped at the first image (max_image_number == 0), so only write them otherwise.
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if (end.max_image_number > 0) {
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if (write_goniometer) {
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// Prefer the rotation axis refined by the offline analysis (rugnux); the broker leaves it empty
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// and the user-provided goniometer axis stands.
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const std::vector<double> axis_vector = end.refined_rotation_axis
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? std::vector<double>{end.refined_rotation_axis->x, end.refined_rotation_axis->y,
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end.refined_rotation_axis->z}
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: start.goniometer->GetAxisVector();
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SaveVector(transformations, start.goniometer->GetName(),
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start.goniometer->GetAngleContainer(end.max_image_number))->
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Transformation("deg", depends_on, "", "",
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"rotation", axis_vector, {0,0,0}, "");
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SaveVector(transformations, start.goniometer->GetName() + "_end",
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start.goniometer->GetAngleContainerEnd(end.max_image_number))
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->Units("deg");
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SaveScalar(transformations, start.goniometer->GetName() + "_range_average",
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start.goniometer->GetIncrement_deg())
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->Units("deg");
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SaveScalar(transformations, start.goniometer->GetName() + "_range_total",
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start.goniometer->GetIncrement_deg() * end.max_image_number)
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->Units("deg");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName();
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} else if (write_grid_scan) {
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// No axis was given, but the sample still sits on a spindle - it simply does not turn.
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// Say so: NXmx cannot express "no rotation", and a chain of translations alone is not
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// something readers accept (dxtbx raises on it outright). At 0 degrees the rotation is
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// the identity whatever the axis points along, so the conventional vector below carries
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// no geometric claim.
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SaveScalar(transformations, "omega", 0.0f)->
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Transformation("deg", depends_on, "", "",
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"rotation", {-1, 0, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/omega";
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}
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// Smargon chi/phi sit between the spindle and the sample.
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write_smargon(transformations, depends_on);
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if (write_goniometer) {
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auto helical = start.goniometer->GetHelicalStep();
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if (helical.has_value()) {
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_x",
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start.goniometer->GetXContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {1, 0, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_x";
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_y",
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start.goniometer->GetYContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {0, 1, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_y";
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SaveVector(transformations,
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start.goniometer->GetName() + "_helical_z",
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start.goniometer->GetZContainer_m(end.max_image_number))->
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Transformation("m", depends_on, "", "",
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"translation", {0, 0, 1}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/" + start.goniometer->GetName() + "_helical_z";
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}
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}
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// The grid stage is mounted on the head, so its translations are innermost. The position
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// containers hold one entry per image and are empty if the scan stopped at the first image.
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if (write_grid_scan && (end.max_image_number > 0)) {
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SaveVector(transformations,"grid_scan_x", start.grid_scan->GetXContainer_m(end.max_image_number))
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->Transformation("m", depends_on, "", "",
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"translation", {1, 0, 0}, {0,0,0}, "");
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@@ -842,8 +862,6 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
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"translation", {0, 1, 0}, {0,0,0}, "");
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depends_on = "/entry/sample/transformations/grid_scan_y";
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}
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write_smargon(transformations, depends_on);
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}
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group.SaveScalar("depends_on", depends_on);
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