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/HDF5WritingTest.cpp

@@ -98,6 +98,25 @@ TEST_CASE("HDF5DataSet_scalar", "[HDF5][Unit]") {
     REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+// NXmx puts no rank on distance, saturation_value or an axis setting, and a writer outside the
+// DECTRIS toolchain may store any of them as a length-1 array. That is the same one number.
+TEST_CASE("HDF5DataSet_scalar_stored_rank1", "[HDF5][Unit]") {
+    {
+        HDF5File file("scratch1b.h5");
+        file.SaveVector("one", std::vector<double>{85.5});
+        file.SaveVector("two", std::vector<double>{85.5, 90.0});
+    }
+    {
+        HDF5ReadOnlyFile file("scratch1b.h5");
+        HDF5DataSet one(file, "one");
+        CHECK(HDF5DataSpace(one).GetNumOfDimensions() == 1);
+        CHECK(one.ReadScalar<double>() == 85.5);
+        REQUIRE_THROWS(HDF5DataSet(file, "two").ReadScalar<double>());
+    }
+    remove("scratch1b.h5");
+    REQUIRE (H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
 TEST_CASE("HDF5DataSet_string", "[HDF5][Unit]") {
     std::string tmp_string = "HDF5Content";
 
@@ -1432,3 +1451,92 @@ TEST_CASE("HDF5FilePusher_finalize_failure_recovers", "[HDF5FilePusher][Repro]")
             std::filesystem::remove(e.path());
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
+
+// A link that is written in the file and points at something not there is NOT an existing dataset.
+// Every DECTRIS Eiger master links saturation_value, pixel_mask, bit_depth_readout and
+// serial_number into a companion <prefix>_meta.h5, and that file is routinely not kept when a
+// dataset is archived or deposited. Asking only whether the LINK exists then answers yes and the
+// read that follows throws, which turns every optional-field guard in the reader into a hard
+// failure - measured on a deposited Eiger 16M set that could not be opened at all.
+TEST_CASE("HDF5Objects_dangling_external_link_does_not_exist", "[HDF5][Unit]") {
+    const std::string fname = "test_dangling_link.h5";
+    remove(fname.c_str());
+    {
+        HDF5File file(fname);
+        HDF5Group group(file, "/entry");
+        group.SaveScalar("present", static_cast<int64_t>(7));
+        // ...and a link into a file that does not exist, exactly as an orphaned Eiger master has.
+        REQUIRE(H5Lcreate_external("no_such_meta.h5", "/_dectris/whatever",
+                                   group.GetID(), "absent", H5P_DEFAULT, H5P_DEFAULT) >= 0);
+    }
+    {
+        HDF5ReadOnlyFile file(fname);
+        CHECK(file.Exists("/entry/present"));
+        CHECK(file.GetInt("/entry/present") == 7);
+        // The link is there, the object is not.
+        CHECK(H5Lexists(file.GetID(), "/entry/absent", H5P_DEFAULT) > 0);
+        CHECK_FALSE(file.Exists("/entry/absent"));
+        // ...so an optional read of it falls back instead of throwing.
+        CHECK(file.GetString("/entry/absent", "fallback") == "fallback");
+    }
+    remove(fname.c_str());
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+// The direct beam - where the undeflected beam lands - is not the PONI stored as beam_center_x/y:
+// on a tilted detector the two are D*tan(rot)/pixel apart, which is what a downstream program (XDS,
+// say) needs and cannot read out of beam_center_x/y. Written into detectorSpecific for all three
+// NXmx layouts, so check the value in all three and check it is really the tilted point.
+TEST_CASE("HDF5Writer_DirectBeamInDetectorSpecific", "[HDF5][Full]") {
+    const std::array formats{FileWriterFormat::NXmxLegacy, FileWriterFormat::NXmxVDS,
+                             FileWriterFormat::NXmxIntegrated};
+    for (const auto format : formats) {
+        const std::string prefix = "direct_beam_" + std::to_string(static_cast<int>(format));
+        DiffractionExperiment x(DetJF(1));
+        x.ImagesPerTrigger(2).ImagesPerFile(2).Compression(CompressionAlgorithm::NO_COMPRESSION)
+         .FilePrefix(prefix);
+        x.SetFileWriterFormat(format).OverwriteExistingFiles(true);
+        x.BeamX_pxl(500).BeamY_pxl(400).DetectorDistance_mm(150)
+         .PoniRot1_rad(0.031f).PoniRot2_rad(-0.047f).PoniRot3_rad(0.019f);
+
+        const auto expected = x.GetDiffractionGeometry().GetDirectBeam_pxl();
+        // The tilt must actually move the point, or the test would pass on a writer that stored the PONI.
+        REQUIRE(std::abs(expected.first - x.GetBeamX_pxl()) > 1.0f);
+        REQUIRE(std::abs(expected.second - x.GetBeamY_pxl()) > 1.0f);
+
+        {
+            RegisterHDF5Filter();
+            StartMessage start_message;
+            x.FillMessage(start_message);
+            REQUIRE(start_message.direct_beam_x);
+            REQUIRE(start_message.direct_beam_y);
+            CHECK(start_message.direct_beam_x.value() == Catch::Approx(expected.first));
+            CHECK(start_message.direct_beam_y.value() == Catch::Approx(expected.second));
+
+            EndMessage end_message;
+            end_message.max_image_number = x.GetImageNum();
+
+            FileWriter writer(start_message);
+            std::vector<int16_t> image(x.GetPixelsNum(), 42);
+            for (int i = 0; i < x.GetImageNum(); i++) {
+                DataMessage message{};
+                message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+                message.number = i;
+                REQUIRE_NOTHROW(writer.Write(message));
+            }
+            writer.WriteHDF5(end_message);
+            writer.Finalize();
+        }
+        {
+            HDF5ReadOnlyFile file(prefix + "_master.h5");
+            CHECK(file.GetFloat("/entry/instrument/detector/beam_center_x") == Catch::Approx(500));
+            CHECK(file.GetFloat("/entry/instrument/detector/detectorSpecific/direct_beam_x")
+                  == Catch::Approx(expected.first));
+            CHECK(file.GetFloat("/entry/instrument/detector/detectorSpecific/direct_beam_y")
+                  == Catch::Approx(expected.second));
+        }
+        remove((prefix + "_master.h5").c_str());
+        remove((prefix + "_data_000001.h5").c_str());
+        REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+    }
+}