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>

tests/StrongPixelSetTest.cpp

@@ -29,17 +29,12 @@ TEST_CASE("StrongPixelSet_BuildSpots","[StrongPixelSet]") {
     settings.min_pix_per_spot = 3;
     settings.max_pix_per_spot = 200;
 
+    // In raster order, which is what AddStrongPixel requires and what both callers produce.
     std::vector<DiffractionSpot> spots;
     StrongPixelSet strong_pixel_set;
-    strong_pixel_set.AddStrongPixel(7,105);
-    strong_pixel_set.AddStrongPixel(7,106);
-    strong_pixel_set.AddStrongPixel(7,104);
-    strong_pixel_set.AddStrongPixel(6,106);
-    strong_pixel_set.AddStrongPixel(6,105);
-    strong_pixel_set.AddStrongPixel(6,104);
-    strong_pixel_set.AddStrongPixel(8,106);
-    strong_pixel_set.AddStrongPixel(8,105);
-    strong_pixel_set.AddStrongPixel(8,104);
+    for (uint16_t line = 104; line <= 106; line++)
+        for (uint16_t col = 6; col <= 8; col++)
+            strong_pixel_set.AddStrongPixel(col, line);
     strong_pixel_set.FindSpots(experiment, settings, spots, 0);
     REQUIRE(spots.size() == 1);
 
@@ -49,6 +44,40 @@ TEST_CASE("StrongPixelSet_BuildSpots","[StrongPixelSet]") {
     REQUIRE(spots[0].RawCoord().y == Catch::Approx(105.0));
 }
 
+TEST_CASE("StrongPixelSet_LargeSpotMustBeCompact","[StrongPixelSet]") {
+    SpotFindingSettings settings;   // max_pix_per_spot 200, so all three pass on size alone
+
+    // A filled 9x9 square: 81 pixels in a 9-wide box, so it fills all of it. A Bragg reflection is
+    // this shape however bright it is, and this is what a raised size bound is meant to admit.
+    StrongPixelSet square;
+    for (uint16_t line = 100; line < 109; line++)
+        for (uint16_t col = 200; col < 209; col++)
+            square.AddStrongPixel(col, line);
+    std::vector<DiffractionSpot> spots;
+    square.FindComponentsImage(settings, spots);
+    REQUIRE(spots.size() == 1);
+    CHECK(spots[0].PixelCount() == 81);
+
+    // The same 81 pixels drawn as a line: an ice arc, a cosmic-ray track or a lit detector row. It
+    // fills 1/81 of its bounding square, so it is refused however many pixels it has.
+    StrongPixelSet streak;
+    for (uint16_t col = 200; col < 281; col++)
+        streak.AddStrongPixel(col, 100);
+    spots.clear();
+    streak.FindComponentsImage(settings, spots);
+    CHECK(spots.empty());
+
+    // Shape is asked of large components only. A short line of the same one-pixel width is below
+    // SPOT_SHAPE_FREE_PIXELS and is kept, exactly as it was before the bound was raised.
+    StrongPixelSet short_streak;
+    for (uint16_t col = 200; col < 210; col++)
+        short_streak.AddStrongPixel(col, 100);
+    spots.clear();
+    short_streak.FindComponentsImage(settings, spots);
+    REQUIRE(spots.size() == 1);
+    CHECK(spots[0].PixelCount() == 10);
+}
+
 /*
 TEST_CASE("StrongPixelSet_ReadFPGAOutput_1","[StrongPixelSet]") {
     DiffractionExperiment experiment(DetectorGeometry(8, 2, 8, 36, true));