v1.0.0-rc.169 (#79)

* Building Jungfraujoch no longer needs zlib or Eigen installed on the machine, and the dependencies the build fetches are pinned and updated to current releases.
* rugnux: improvements in indexing, lattice selection and geometry post-refinement, which index crystals that previously returned no lattice and keep the better of the two geometries a run measures.
* rugnux: improvements in beam-centre measurement, beam-stop detection and space-group determination.
* rugnux: the unit cell reported with a determined space group now obeys that group - a cell whose symmetry was confirmed from the intensities is re-refined under it, and a cell the group cannot describe is reported with a warning rather than as it stands.
* rugnux drops the stretches of a rotation sweep whose removal measurably improves the merged intensities and reports what became of every frame, and decides the resolution cut on the crystal's own diffraction rather than on its ice rings.
* The rugnux results report is machine-readable - every line that is not `KEY= value` data starts with `#` - and states the build it was written by, its authorship and its terms of use (`REPORT_VERSION= 8`).
* `jfjoch_viewer`: improvements in the file manager (CBF frames beside HDF5 datasets, a remembered root), the dataset plots, the inspector and the image statistics, plus a settable font size, a view of the rugnux results report, usable performance over a remote display (`ssh -X`) and a reset of all settings to defaults; the reciprocal-space window is removed.
* Broker fixes around DECTRIS collections and dark-mask calibration: re-initialising after a run that never started no longer freezes the broker, a cancelled calibration is abandoned instead of reported as done, and a collection whose start message never arrives ends by itself.

Reviewed-on: #79
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

image_analysis/WriteReflections.cpp

@@ -733,7 +733,7 @@ void WriteUnmergedMtzReflections(const std::vector<IntegrationOutcome> &outcomes
     ds.wavelength = experiment.GetWavelength_A();
 
     // Every data column belongs to HKL_base and only the batches carry a dataset id, as in a
-    // POINTLESS file. Down to FLAG this is POINTLESS's own column set, plus QE; the four after it
+    // POINTLESS file. Down to FLAG this is POINTLESS's own column set, plus QE and FLIGHT; the four after it
     // are what rugnux measures beyond it - the offset of the reflection from the centre of its
     // rocking curve, the Lorentz geometry of that curve, and the background that was subtracted.
     //
@@ -787,10 +787,11 @@ void WriteUnmergedMtzReflections(const std::vector<IntegrationOutcome> &outcomes
     // crystal-frame information careless scales on, and what makes the file unmerged rather than a
     // merge waiting to happen.
     // I and SIGI are the integrated intensity with every deterministic per-reflection correction
-    // applied and nothing else, which is what IOBS means in every unmerged format. Two columns
-    // record what was applied, so the raw count sum is recoverable exactly as I / LP * QE:
-    // LP is Lorentz x polarization and QE the sensor efficiency (a divisor, hence the multiply).
-    // Neither is a scale, and a program that reads this file has no way to recompute them. The
+    // applied and nothing else, which is what IOBS means in every unmerged format. Three columns
+    // record what was applied, so the raw count sum is recoverable exactly as I / LP * QE * FLIGHT:
+    // LP is Lorentz x polarization, QE the sensor efficiency and FLIGHT the attenuation of the
+    // flight-path medium (both divisors, hence the multiplies).
+    // None of the three is a scale, and a program that reads this file has no way to recompute them. The
     // partiality is NOT divided out - that IS a scale, FRACTIONCALC carries it, and every program
     // this file is for wants to handle it its own way.
     gemmi::UnmergedHklMover hkl_mover(mtz.spacegroup);