v1.0.0-rc.166 (#76)

* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.

Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

common/DiffractionExperiment.cpp

@@ -198,6 +198,11 @@ DiffractionExperiment &DiffractionExperiment::SpaceGroupNumber(std::optional<int
     return *this;
 }
 
+DiffractionExperiment &DiffractionExperiment::SetSpaceGroup(const std::optional<gemmi::SpaceGroup> &input) {
+    dataset.SetSpaceGroup(input);
+    return *this;
+}
+
 DiffractionExperiment &DiffractionExperiment::StorageCells(int64_t input) {
     detector_settings.StorageCells(input);
     return *this;
@@ -649,6 +654,9 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
     message.images_per_file = GetImagesPerFile();
     message.beam_center_x = GetBeamX_pxl();
     message.beam_center_y = GetBeamY_pxl();
+    const auto direct_beam = GetDiffractionGeometry().GetDirectBeam_pxl();
+    message.direct_beam_x = direct_beam.first;
+    message.direct_beam_y = direct_beam.second;
     message.detector_distance = GetDetectorDistance_mm() * 1e-3f;
     message.incident_wavelength = GetWavelength_A();
     // NXmx incident_wavelength_spread is the FWHM of the wavelength distribution,
@@ -657,9 +665,17 @@ void DiffractionExperiment::FillMessage(StartMessage &message) const {
     if (const auto bw = GetBandwidthFWHM())
         message.incident_wavelength_spread = bw.value() * GetWavelength_A();
     message.incident_energy = GetIncidentEnergy_keV() * 1e3f;
+    // NXmx incident_beam_size is a length like every other in this message, so micrometres in
+    // the settings become metres here.
+    if (const auto beam_size_x = GetBeamSizeX_um())
+        message.beam_size_x = beam_size_x.value() * 1e-6f;
+    if (const auto beam_size_y = GetBeamSizeY_um())
+        message.beam_size_y = beam_size_y.value() * 1e-6f;
     message.image_size_x = GetXPixelsNum();
     message.image_size_y = GetYPixelsNum();
     message.mirror_y = IsDetectorMirroredY();
+    message.detector_orientation_mirror_y = detector.GetImageOrientation().IsMirrorY();
+    message.detector_orientation_quarter_turns = detector.GetImageOrientation().GetQuarterTurns();
     message.saturation_value = SaturationValueFromLimit(GetSaturationLimit());
     // The marker actually stored in the pixels: UINTx_MAX unsigned, INTx_MIN signed. GetUnderflow()
     // was written here, which is -1 for an unsigned image and so matches no pixel it can contain.
@@ -910,6 +926,16 @@ DiffractionExperiment &DiffractionExperiment::TotalFlux(const std::optional<floa
     return *this;
 }
 
+DiffractionExperiment &DiffractionExperiment::BeamSizeX_um(const std::optional<float> &input) {
+    dataset.BeamSizeX_um(input);
+    return *this;
+}
+
+DiffractionExperiment &DiffractionExperiment::BeamSizeY_um(const std::optional<float> &input) {
+    dataset.BeamSizeY_um(input);
+    return *this;
+}
+
 std::optional<float> DiffractionExperiment::GetAttenuatorTransmission() const {
     return dataset.GetAttenuatorTransmission();
 }
@@ -918,6 +944,14 @@ std::optional<float> DiffractionExperiment::GetTotalFlux() const {
     return dataset.GetTotalFlux();
 }
 
+std::optional<float> DiffractionExperiment::GetBeamSizeX_um() const {
+    return dataset.GetBeamSizeX_um();
+}
+
+std::optional<float> DiffractionExperiment::GetBeamSizeY_um() const {
+    return dataset.GetBeamSizeY_um();
+}
+
 DiffractionExperiment &DiffractionExperiment::Goniometer(const std::optional<GoniometerAxis> &input) {
     dataset.Goniometer(input);
     return *this;
@@ -1501,8 +1535,10 @@ std::vector<DetectorTransformation> DiffractionExperiment::BuildTransformationCh
             axis.Value(goniometer->GetStart_deg());
         add(std::move(axis));
     } else if (GetGridScan().has_value()) {
-        // A grid scan still sits on a spindle that simply does not turn. NXmx cannot say "there is no
-        // rotation", and a sample chain of translations alone is not something readers accept.
+        // A grid scan still sits on a spindle that simply does not turn, and 0 is a placeholder for
+        // an angle nobody told us: send the axis with step 0 and the position it really stood at is
+        // written instead. NXmx does allow a sample with no goniometer at all (depends_on "."), but
+        // a sample chain of translations alone is not something readers accept - dxtbx raises on it.
         add(DetectorTransformation("omega", TransformationType::Rotation, {-1, 0, 0}).Value(0.0f));
     }
 
@@ -1598,6 +1634,7 @@ DiffractionGeometry DiffractionExperiment::GetDiffractionGeometry() const {
             .PoniRot1_rad(dataset.GetPoniRot1_rad())
             .PoniRot2_rad(dataset.GetPoniRot2_rad())
             .PoniRot3_rad(dataset.GetPoniRot3_rad())
+            .Orientation(detector.GetImageOrientation())
             .Rotation(dataset.GetGoniometer());
     return g;
 }
@@ -1789,14 +1826,13 @@ std::string DiffractionExperiment::GetSpaceGroupName() const {
     return sg->short_name();
 }
 
-std::optional<gemmi::SpaceGroup> DiffractionExperiment::GetGemmiSpaceGroup() const {
-    auto sg = GetSpaceGroupNumber();
-    if (!sg)
-        return std::nullopt;
-    const gemmi::SpaceGroup *g = gemmi::find_spacegroup_by_number(sg.value());
-    if (g == nullptr)
-        return std::nullopt;
-    return *g;
+const std::optional<gemmi::SpaceGroup> &DiffractionExperiment::GetGemmiSpaceGroup() const {
+    return dataset.GetSpaceGroup();
+}
+
+const gemmi::SpaceGroup &DiffractionExperiment::GetSpaceGroupOrP1() const {
+    const auto &sg = dataset.GetSpaceGroup();
+    return sg ? *sg : *gemmi::find_spacegroup_by_number(1);
 }
 
 char DiffractionExperiment::GetCentering() const {