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>

viewer/widgets/PowderCalibrationWidget.cpp

@@ -25,6 +25,16 @@ PowderCalibrationWidget::PowderCalibrationWidget(QWidget *parent) : QWidget(pare
                             "(q x azimuth) azimuthal profile over every image and fits the ring arcs in it; "
                             "spots pools the found spots and fits those.");
 
+    // The detector tilt is a free parameter of every one of these fits. Unticking it holds rot1/rot2
+    // where the geometry already has them - what a calibration handed to a program with no way to
+    // express a tilted detector (XDS) needs. It applies to the two buttons and to "Analyze dataset".
+    refineTiltCheck = new QCheckBox("Refine detector tilt", this);
+    refineTiltCheck->setChecked(true);
+    refineTiltCheck->setToolTip("Fit the detector tilt (PONI rot1/rot2) together with the beam centre "
+                                "and the distance. Untick to hold the tilt where it is and fit only the "
+                                "beam centre and the distance - for a calibration that will be given to "
+                                "a program which cannot express a tilted detector, such as XDS.");
+
     auto findBeamCenterButton = new QPushButton("Guess detector calibration", this);
     connect(findBeamCenterButton, &QPushButton::clicked,this, &PowderCalibrationWidget::findBeamCenterClicked);
 
@@ -48,6 +58,8 @@ PowderCalibrationWidget::PowderCalibrationWidget(QWidget *parent) : QWidget(pare
 
     refine_row->addWidget(calibrantRingsButton,2, 0);
 
+    refine_row->addWidget(refineTiltCheck,2, 1);
+
     refine_row->addWidget(new QLabel("Dataset method:"),3,0);
     refine_row->addWidget(methodCombo,3,1);
 
@@ -68,14 +80,22 @@ std::vector<float> PowderCalibrationWidget::GetCalibrantRings() const {
     const auto &table = Calibrants();
     if (idx >= 0 && idx < static_cast<int>(table.size()))
         return CalibrantRings(table[idx].name);
-    if (sample_cell)
+    if (sample_cell) {
+        // With the group where the dataset has one: the absences then come from the symmetry rather
+        // than from a bare P-lattice assumption, and a centred cell's list no longer opens with a
+        // reflection that is not there - which would scale the whole calibration by the ratio between
+        // that ring and the first real one. Same call the CLI makes.
+        if (sample_sg)
+            return CalculateXtalRings(sample_cell.value(), *sample_sg);
         return CalculateXtalRings(sample_cell.value());
+    }
     return CalibrantRings(table.front().name);
 }
 
 CalibrationSelection PowderCalibrationWidget::Selection() const {
     return {calibrantCombo->currentText(), GetCalibrantRings(),
-            static_cast<CalibrationMethod>(methodCombo->currentData().toInt())};
+            static_cast<CalibrationMethod>(methodCombo->currentData().toInt()),
+            refineTiltCheck->isChecked()};
 }
 
 void PowderCalibrationWidget::updateCalibrantList() {
@@ -95,17 +115,19 @@ void PowderCalibrationWidget::updateCalibrantList() {
 }
 
 void PowderCalibrationWidget::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
-    if (image)
+    if (image) {
         sample_cell = image->Dataset().experiment.GetUnitCell();
+        sample_sg = image->Dataset().experiment.GetGemmiSpaceGroup();
+    }
     updateCalibrantList();
 }
 
 void PowderCalibrationWidget::findBeamCenterClicked() {
     const std::vector<float> rings = GetCalibrantRings();
-    emit findBeamCenter(QVector<float>(rings.begin(), rings.end()), true);
+    emit findBeamCenter(QVector<float>(rings.begin(), rings.end()), true, refineTiltCheck->isChecked());
 }
 
 void PowderCalibrationWidget::optimizeBeamCenterClicked() {
     const std::vector<float> rings = GetCalibrantRings();
-    emit findBeamCenter(QVector<float>(rings.begin(), rings.end()), false);
+    emit findBeamCenter(QVector<float>(rings.begin(), rings.end()), false, refineTiltCheck->isChecked());
 }