reader: place a detector swung out on a 2theta arm where the file says it stands

Chemical crystallography reaches high angle by swinging the detector out on a
2theta arm. Both readers had the number and neither used it: the miniCBF header's
Detector_2theta was parsed into a struct member nothing ever read, and on the NXmx
side the rotation was in the depends_on chain, which was not followed at all. A
sweep taken at 30 degrees was therefore processed with its detector plane 30
degrees from where it stood, and nothing indexed.

The geometry could already express it, and needed no change: the arm turns the
detector about the sample, so the distance is still measured along the detector
normal and the beam centre is still the point of normal incidence - which is
exactly the PONI convention, and a swung detector is one PONI rotation. What moves
is the direct beam, by distance*tan(2theta), off the beam centre and often off the
detector.

NXmx is the harder half, because the swing has no field of its own: it is one
rotation in the chain the detector's position depends on, and "two_theta" is only
one beamline's name for that dataset. So the chain is followed and its rotations
composed, rather than a field of one name being looked for - each transformation
states its vector in the frame of the one it depends on, which is why the product
is the whole placement. Translations are skipped; they are the distance and the
beam centre, which the file states separately in the square-on frame. Vectors come
from McStas through the same 180-degree turn about z the module directions already
use, a proper rotation, so an axis carried through it turns the same way.

The three rotations a file this system writes ARE that chain, and are also read as
the PONI angles - so those three paths are skipped, or every tilted file we have
ever written would come back tilted twice. That is the one way this change could
have broken existing data, and the test for it writes a tilted file and reads it
back.

For miniCBF the arm turns about the base spindle axis: on the four-circle geometry
those headers describe the two are one axis, and the imgCIF axis table such a
header carries states them with the same vector. Both now come from one constant,
so a later correction to the frame moves them together.

Measured. On a swung NXmx sweep the chain gives rot2 = -0.34907 rad for the 20
degrees it states, and the sweep goes from "nothing was integrated" to 25000
reflections at 82.2% completeness and CC(1/2) 0.9993, in the same space group and
the same cell to 0.03 A as the square-on sweep of that crystal; the opposite sign
indexes nothing. A miniCBF sweep at 30 degrees goes the same way, to 0.585 A, and
a second sweep of that crystal at 55 degrees reaches 0.476 A and reproduces the
cell again - with a low-resolution limit of 2.36 A rather than 13 A, which is what
a detector swung that far records. On all of them post-refinement recovers the
header's own beam centre and distance, and the beam stop shadow sits within four
pixels of where the swung geometry puts the direct beam, 417 and 537 pixels from
where the unswung one does. Seven sets whose detector is square to the beam, three
of them carrying a chain whose 2theta is zero, are byte-identical in .hkl, .mtz,
.cif and the image statistics.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01T3yNBXk4wKdMZy1ak2NY7f

docs/CHANGELOG.md

@@ -1,6 +1,7 @@
 # Changelog
 ## 1.0.0
 ### 1.0.0-rc.166
+* A detector swung out on a 2theta arm is placed where it stands, from the depends_on transformation chain of an NXmx master or the `Detector_2theta` line of a miniCBF header; both were previously read and then ignored.
 * `jfjoch_viewer` opens PILATUS miniCBF sweeps - naming any frame opens the whole sweep - and can run a processing job on one.
 * A detector whose stored image is mirrored in Y or mounted at a multiple of 90 degrees can be described as such, in the detector configuration or with `--detector-mirror-y` / `--detector-quarter-turns`, rather than having to be expressed as a detector rotation.
 * The rotation first pass refines twelve candidate lattices rather than four, so a correct cell that the pre-refinement ranking put fifth is still reached.

docs/DETECTOR_GEOMETRY.md

@@ -59,6 +59,21 @@ rot2 = asin(-slow.z)         rot1 = atan2(-fast.z, normal.z)         rot3 = atan
 with `rot2` in [-90°, 90°]. The angles are what is stored and what is written out, so a geometry
 given as angles comes back exactly as it was given.
 
+## A detector swung out on a 2theta arm
+
+Chemical crystallography reaches high angle by swinging the detector out on a 2theta arm rather than by
+moving it closer. The arm turns the detector about the sample, so it changes nothing else: the distance
+is still measured along the detector normal, and the beam centre is still the point of normal incidence,
+which is where the arm's own axis meets the detector and does not move. The swing is therefore exactly a
+PONI rotation, and the direct beam is what moves - by `distance * tan(2theta)`, off the beam centre and
+often off the detector altogether.
+
+Nothing has to be given for this: rugnux takes it from the file. An NXmx master states the detector's
+position as a `depends_on` chain of transformations, and the arm is one rotation in that chain - so the
+chain is followed, rather than a field of one particular name being looked for. A PILATUS miniCBF states
+it as `# Detector_2theta`, which turns about the same axis as the base spindle, the two being one axis on
+the four-circle geometry those headers describe.
+
 ## Mirrored and quarter-turned detectors
 
 On top of the continuous tilt the detector setup carries a **discrete image orientation**: whether the

reader/HDF5MetadataSource.cpp

@@ -14,8 +14,14 @@
 #include "../common/Logger.h"
 #include "../common/ROIDefinition.h"
 
+// A McStas direction in the internal frame. The two differ by a 180 degree turn about z, which is a
+// rotation and not a mirror - so an axis carried through it turns the same way by the same angle.
+static Coord McStasToInternal(const std::vector<double> &v) {
+    return {static_cast<float>(-v[0]), static_cast<float>(-v[1]), static_cast<float>(v[2])};
+}
+
 // The image orientation the file itself states, in its NXdetector_module pixel directions. NXmx gives
-// those in the McStas frame, which is the internal frame turned 180 degrees about z.
+// those in the McStas frame.
 //
 // Only an exact match against one of the eight discrete orientations is taken. Anything else is a
 // continuous rotation of the detector in its own plane, which belongs in rot1/rot2/rot3 and cannot be
@@ -36,8 +42,8 @@ static std::optional<DetectorOrientation> ReadModuleOrientation(HDF5Object *file
     if ((f.size() != 3) || (s.size() != 3))
         return {};
 
-    const Coord fast(-f[0], -f[1], f[2]);
-    const Coord slow(-s[0], -s[1], s[2]);
+    const Coord fast = McStasToInternal(f);
+    const Coord slow = McStasToInternal(s);
 
     for (int64_t quarter_turns = 0; quarter_turns < 4; quarter_turns++) {
         for (bool mirror_y: {false, true}) {
@@ -50,6 +56,63 @@ static std::optional<DetectorOrientation> ReadModuleOrientation(HDF5Object *file
     return {};
 }
 
+// Where the detector stands, from the chain of transformations the file says it depends on.
+//
+// NXmx has no field for a detector swung out on a 2theta arm. It states the detector's position as a
+// depends_on chain and the arm is one rotation in that chain, so following the chain is the only way
+// to find it: "two_theta" is one beamline's name for that dataset and the next spells it otherwise.
+//
+// Only the rotations are taken, composed from the detector outwards. Each transformation states its
+// vector in the frame of the one it depends on, so the product is the rotation that carries a
+// detector square to the beam to where this one stands. The translations in the chain are the
+// detector distance and the beam centre, which the file states separately in that square-on frame -
+// the arm turns the detector about the sample and moves neither, and a Diamond master writes the same
+// beam_center_x/y for a swung sweep as for the square-on one beside it. Nothing comes back when no
+// rotation in the chain turns, which is every detector square to the beam.
+static std::optional<RotMatrix> ReadDetectorRotationChain(HDF5Object *file) {
+    std::string node = file->GetString("/entry/instrument/detector/depends_on");
+    if (node.empty() && file->IsDataSet("/entry/instrument/detector/module/module_offset")) {
+        HDF5DataSet module_offset(*file, "/entry/instrument/detector/module/module_offset");
+        if (module_offset.AttrExists("depends_on"))
+            node = module_offset.ReadAttrStr("depends_on");
+    }
+
+    // A file this system wrote states its PONI angles in the chain as well, and they are read from
+    // these three paths just before this is called. Taking them here too would apply the tilt twice.
+    static const std::set<std::string> poni_angles = {"/entry/instrument/detector/transformations/rot1",
+                                                      "/entry/instrument/detector/transformations/rot2",
+                                                      "/entry/instrument/detector/transformations/rot3"};
+
+    RotMatrix chain;
+    bool turns = false;
+    std::set<std::string> seen;
+    while ((node != ".") && !node.empty() && file->IsDataSet(node) && seen.insert(node).second) {
+        HDF5DataSet axis(*file, node);
+        const std::string current = node;
+        node = axis.AttrExists("depends_on") ? axis.ReadAttrStr("depends_on") : ".";
+
+        if (poni_angles.contains(current) || !axis.AttrExists("transformation_type") || !axis.AttrExists("vector")
+                || (axis.ReadAttrStr("transformation_type") != "rotation"))
+            continue;
+
+        std::vector<double> value;
+        axis.ReadVector(value);
+        const auto vec = axis.ReadAttrVec("vector");
+        if (value.empty() || (value[0] == 0.0) || (vec.size() != 3))
+            continue;
+
+        // NXmx states a rotation in degrees unless it says otherwise.
+        const bool radians = axis.AttrExists("units") && (axis.ReadAttrStr("units") == "rad");
+        const auto angle_rad = static_cast<float>(radians ? value[0] : value[0] * PI / 180.0);
+        chain = RotMatrix(angle_rad, McStasToInternal(vec)) * chain;
+        turns = true;
+    }
+
+    if (!turns)
+        return {};
+    return chain;
+}
+
 
 inline std::pair<gemmi::CrystalSystem, char> parse_bravais_lattice(const std::string &val) {
     if (val.empty())
@@ -721,6 +784,21 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
             master_file->GetOptFloat("/entry/instrument/detector/transformations/rot2").value_or(0.0));
         dataset->experiment.PoniRot3_rad(
             master_file->GetOptFloat("/entry/instrument/detector/transformations/rot3").value_or(0.0));
+        // A detector swung out on a 2theta arm - routine in chemical crystallography - and any other
+        // rotation the file puts in the detector's chain. It turns the detector about the sample, so
+        // it carries the whole square-on geometry with it and composes on the left of the PONI
+        // rotation the file states directly.
+        if (const auto chain = ReadDetectorRotationChain(master_file.get())) {
+            float rot1 = 0, rot2 = 0, rot3 = 0;
+            PoniAnglesFromMatrix(chain.value()
+                                     * PoniRotMatrix(dataset->experiment.GetPoniRot1_rad(),
+                                                     dataset->experiment.GetPoniRot2_rad(),
+                                                     dataset->experiment.GetPoniRot3_rad()),
+                                 rot1, rot2, rot3);
+            dataset->experiment.PoniRot1_rad(rot1).PoniRot2_rad(rot2).PoniRot3_rad(rot3);
+            Logger("HDF5Reader").Info("Detector placed by its NXmx transformation chain: "
+                                      "rot1 {:.5f} rot2 {:.5f} rot3 {:.5f} rad", rot1, rot2, rot3);
+        }
         dataset->experiment.SampleTemperature_K(master_file->GetOptFloat("/entry/sample/temperature"));
 
         dataset->experiment.BeamX_pxl(master_file->GetFloat("/entry/instrument/detector/beam_center_x"));

reader/JFJochCBFReader.cpp

@@ -90,6 +90,11 @@ std::vector<std::string> CollectSweep(const std::string &path) {
     return out;
 }
 
+// The base rotation axis of the instrument, in the internal frame (x along increasing detector
+// column, y along increasing row, z along the beam). Both the spindle and the detector arm turn
+// about it: the spindle in RotationAxis below, and the 2theta arm in ReadFiles.
+const Coord BASE_AXIS(-1.0f, 0.0f, 0.0f);
+
 // The axis a miniCBF sweep turns about, in the internal frame (x along increasing detector column,
 // y along increasing row, z along the beam).
 //
@@ -106,7 +111,7 @@ std::vector<std::string> CollectSweep(const std::string &path) {
 // source; internal z points the other way, hence the minus. A kappa arm cannot be expressed at all:
 // its inclination is a property of the hardware that no miniCBF header states.
 Coord RotationAxis(const minicbf::Header &h) {
-    const Coord base(-1.0f, 0.0f, 0.0f);
+    const Coord base = BASE_AXIS;
     if (!minicbf::ScansPhi(h))
         return base;
 
@@ -161,6 +166,22 @@ void JFJochCBFReader::ReadFiles(const std::string &path) {
     dataset_->experiment.BeamX_pxl(static_cast<float>(header0_.beam_x_px));
     dataset_->experiment.BeamY_pxl(static_cast<float>(header0_.beam_y_px));
     dataset_->experiment.DetectorDistance_mm(static_cast<float>(header0_.distance_m * 1000.0));
+
+    // A detector swung out on a 2theta arm, which small-molecule collection uses routinely. The arm
+    // turns the detector about the sample, so it carries the square-on geometry with it: the header's
+    // Detector_distance stays the distance along the detector normal and Beam_xy stays the point of
+    // normal incidence, neither of which the swing moves - which is exactly what the PONI convention
+    // wants, so the swing is a PONI rotation and nothing else in the header changes. It turns about
+    // the base spindle axis, the four-circle geometry these headers describe having the arm and the
+    // spindle on one axis; the imgCIF axis table such a header carries states the two with the same
+    // vector.
+    if (header0_.two_theta_deg != 0.0) {
+        float rot1 = 0, rot2 = 0, rot3 = 0;
+        PoniAnglesFromMatrix(RotMatrix(static_cast<float>(header0_.two_theta_deg * PI / 180.0), BASE_AXIS),
+                             rot1, rot2, rot3);
+        dataset_->experiment.PoniRot1_rad(rot1).PoniRot2_rad(rot2).PoniRot3_rad(rot3);
+    }
+
     dataset_->experiment.IncidentEnergy_keV(WVL_1A_IN_KEV / static_cast<float>(header0_.wavelength_A));
     dataset_->experiment.FrameTime(
         std::chrono::duration_cast<std::chrono::nanoseconds>(

tests/DiffractionGeometryTest.cpp

@@ -831,3 +831,48 @@ TEST_CASE("DetectorOrientation_recip_roundtrip") {
             }
         }
 }
+
+// A detector swung out on a 2theta arm, which is how chemical crystallography reaches high angle.
+// The arm turns the detector about the sample, so the geometry that describes it is the PONI rotation
+// and nothing else moves: the distance stays the distance along the detector normal and the beam
+// centre stays the point of normal incidence. What DOES move is the direct beam, which is no longer
+// at the beam centre - the two coincide only on a detector square to the beam.
+TEST_CASE("DiffractionGeometry_TwoThetaArm", "[LinearAlgebra][Coord]") {
+    const float two_theta = 30.0f * PI / 180.0f;
+    const float distance_mm = 160.0f, pixel_mm = 0.172f, wavelength = 0.6889f;
+    const float bx = 740.0f, by = 866.0f;
+
+    DiffractionGeometry geom;
+    geom.BeamX_pxl(bx).BeamY_pxl(by).DetectorDistance_mm(distance_mm)
+        .PixelSize_mm(pixel_mm).Wavelength_A(wavelength);
+    // The arm turns about the internal x axis; a rotation of +2theta about it is rot2 = -2theta.
+    geom.PoniRot2_rad(-two_theta);
+
+    // The beam centre pixel is the PONI: still on the detector normal through the sample, and now
+    // 2theta away from the beam.
+    CHECK(geom.TwoTheta_rad(bx, by) == Catch::Approx(two_theta));
+    CHECK(geom.LabCoord(bx, by).Length() == Catch::Approx(distance_mm));
+    CHECK(geom.GetNormalAxis() * Coord(0, 0, 1) == Catch::Approx(cosf(two_theta)));
+    // The plane turned about x, so the fast axis - along +x - did not move, and the slow one tipped
+    // out of the detector plane by the full 2theta.
+    CHECK((geom.GetFastAxis() - Coord(1, 0, 0)).Length() < 1e-6f);
+    CHECK(geom.GetSlowAxis() * Coord(0, 0, 1) == Catch::Approx(sinf(two_theta)));
+
+    // The direct beam is off the PONI by D*tan(2theta), along the direction the arm swung.
+    auto [direct_x, direct_y] = geom.GetDirectBeam_pxl();
+    CHECK(direct_x == Catch::Approx(bx));
+    CHECK(direct_y == Catch::Approx(by + distance_mm * tanf(two_theta) / pixel_mm));
+
+    // Resolution at the PONI is the Bragg spacing of 2theta, not of a pixel at zero distance from
+    // the beam centre - the reason a swung detector reaches so much further than a square-on one.
+    CHECK(geom.PxlToRes(bx, by) == Catch::Approx(wavelength / (2.0f * sinf(two_theta / 2.0f))));
+
+    // Round trip through reciprocal space, at the PONI and away from it in both directions.
+    const std::vector<std::pair<float, float>> probes =
+            {{bx, by}, {bx + 300.0f, by - 500.0f}, {bx - 700.0f, by + 200.0f}};
+    for (const auto &[x, y]: probes) {
+        auto [back_x, back_y] = geom.RecipToDetector(geom.DetectorToRecip(x, y));
+        CHECK(back_x == Catch::Approx(x));
+        CHECK(back_y == Catch::Approx(y));
+    }
+}

tests/JFJochReaderTest.cpp

@@ -3594,3 +3594,182 @@ TEST_CASE("JFJochReader_ThirdPartyNXmxMaster", "[HDF5][Full]") {
     // No leftover HDF5 objects
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
+
+// A detector swung out on a 2theta arm. NXmx has no field for it: the swing is one rotation in the
+// depends_on chain the detector's position is stated as, and "two_theta" is only one beamline's name
+// for that dataset. So the chain is what the reader follows, and the chain here carries two rotations
+// about different axes, outboard of the translation that sets the distance - a file that stated only
+// the innermost one, or composed them the other way round, gives a different plane.
+//
+// Both axes are stated in McStas, which is the internal frame turned half a turn about z: a reader
+// that takes the vector as it stands swings the detector the wrong way, which is twice the error of
+// not reading it at all.
+TEST_CASE("JFJochReader_DetectorTwoThetaArm", "[HDF5][Full]") {
+    const hsize_t nx = 8, ny = 6;
+    const double two_theta_deg = 20.0, tilt_deg = 7.0;
+    std::vector<uint16_t> image(nx * ny, 5);
+    WriteThirdPartyDataFile("two_theta_000001.h5", image, 2, ny, nx);
+
+    {
+        HDF5File master("two_theta_master.h5");
+        HDF5Group entry(master, "entry");
+        entry.SaveScalar("definition", "NXmx");
+        HDF5Group instrument(entry, "instrument");
+        HDF5Group beam(instrument, "beam");
+        beam.SaveScalar("incident_wavelength", 0.6889)->Units("angstrom");
+        HDF5Group transformations(instrument, "transformations");
+        // Outermost first in the file, innermost first along the chain: det_z -> two_theta -> tilt
+        transformations.SaveVector("tilt", std::vector<double>{tilt_deg})
+                ->Transformation("deg", ".", "detector", "", "rotation", {0, 1, 0});
+        transformations.SaveVector("two_theta", std::vector<double>{two_theta_deg})
+                ->Transformation("deg", "/entry/instrument/transformations/tilt",
+                                 "detector", "", "rotation", {-1, 0, 0});
+        transformations.SaveVector("det_z", std::vector<double>{160.0})
+                ->Transformation("mm", "/entry/instrument/transformations/two_theta",
+                                 "detector", "", "translation", {0, 0, 1});
+        HDF5Group detector(instrument, "detector");
+        detector.SaveScalar("depends_on", "/entry/instrument/transformations/det_z");
+        detector.SaveScalar("description", "PILATUS 2M");
+        detector.SaveScalar("beam_center_x", 4.0)->Units("pixels");
+        detector.SaveScalar("beam_center_y", 3.0)->Units("pixels");
+        detector.SaveScalar("distance", 0.160)->Units("m");
+        detector.SaveScalar("x_pixel_size", 0.172)->Units("mm");
+        detector.SaveScalar("y_pixel_size", 0.172)->Units("mm");
+        detector.SaveScalar("sensor_thickness", 0.32)->Units("mm");
+        detector.SaveScalar("count_time", 0.2);
+        detector.SaveScalar("saturation_value", static_cast<int64_t>(65535));
+        HDF5Group data(entry, "data");
+        data.ExternalLink("two_theta_000001.h5", "/data", "data_000001");
+    }
+
+    DiffractionGeometry geom;
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("two_theta_master.h5"));
+        geom = reader.GetDataset()->experiment.GetDiffractionGeometry();
+    }
+
+    // The chain as it stands in the internal frame: McStas (-1,0,0) is internal (1,0,0) and McStas
+    // (0,1,0) is internal (0,-1,0), and the outer rotation multiplies on the left.
+    const auto to_rad = [](double deg) { return static_cast<float>(deg * PI / 180.0); };
+    const RotMatrix expected = RotMatrix(to_rad(tilt_deg), {0, -1, 0})
+                             * RotMatrix(to_rad(two_theta_deg), {1, 0, 0});
+    for (int64_t column = 0; column < 3; column++)
+        CHECK((geom.GetDetectorMatrix().Column(column) - expected.Column(column)).Length() < 1e-5f);
+
+    // Distance and beam centre are the ones the file states: the arm turns the detector about the
+    // sample and moves neither.
+    CHECK(geom.GetDetectorDistance_mm() == Catch::Approx(160.0));
+    CHECK(geom.GetBeamX_pxl() == Catch::Approx(4.0));
+    CHECK(geom.GetBeamY_pxl() == Catch::Approx(3.0));
+    // And the beam centre pixel is now that far from the beam - the whole point of a 2theta arm.
+    CHECK(geom.TwoTheta_rad(4.0f, 3.0f) * 180.0f / PI
+              == Catch::Approx(angle_deg(expected * Coord(0, 0, 1), Coord(0, 0, 1))));
+    CHECK(geom.TwoTheta_rad(4.0f, 3.0f) * 180.0f / PI > two_theta_deg);
+
+    remove("two_theta_000001.h5");
+    remove("two_theta_master.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+// The same file with the arm parked at zero: the chain is there, nothing in it turns, and the
+// geometry must be exactly the square-on one. This is nearly every file, so it has to cost nothing.
+TEST_CASE("JFJochReader_DetectorTwoThetaZeroIsSquareOn", "[HDF5][Full]") {
+    const hsize_t nx = 8, ny = 6;
+    std::vector<uint16_t> image(nx * ny, 5);
+    WriteThirdPartyDataFile("two_theta_zero_000001.h5", image, 2, ny, nx);
+
+    {
+        HDF5File master("two_theta_zero_master.h5");
+        HDF5Group entry(master, "entry");
+        entry.SaveScalar("definition", "NXmx");
+        HDF5Group instrument(entry, "instrument");
+        HDF5Group beam(instrument, "beam");
+        beam.SaveScalar("incident_wavelength", 0.6889)->Units("angstrom");
+        HDF5Group transformations(instrument, "transformations");
+        transformations.SaveVector("two_theta", std::vector<double>{0.0})
+                ->Transformation("deg", ".", "detector", "", "rotation", {-1, 0, 0});
+        transformations.SaveVector("det_z", std::vector<double>{160.0})
+                ->Transformation("mm", "/entry/instrument/transformations/two_theta",
+                                 "detector", "", "translation", {0, 0, 1});
+        HDF5Group detector(instrument, "detector");
+        detector.SaveScalar("depends_on", "/entry/instrument/transformations/det_z");
+        detector.SaveScalar("description", "PILATUS 2M");
+        detector.SaveScalar("beam_center_x", 4.0)->Units("pixels");
+        detector.SaveScalar("beam_center_y", 3.0)->Units("pixels");
+        detector.SaveScalar("distance", 0.160)->Units("m");
+        detector.SaveScalar("x_pixel_size", 0.172)->Units("mm");
+        detector.SaveScalar("y_pixel_size", 0.172)->Units("mm");
+        detector.SaveScalar("sensor_thickness", 0.32)->Units("mm");
+        detector.SaveScalar("count_time", 0.2);
+        detector.SaveScalar("saturation_value", static_cast<int64_t>(65535));
+        HDF5Group data(entry, "data");
+        data.ExternalLink("two_theta_zero_000001.h5", "/data", "data_000001");
+    }
+
+    DiffractionGeometry geom;
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("two_theta_zero_master.h5"));
+        geom = reader.GetDataset()->experiment.GetDiffractionGeometry();
+    }
+
+    CHECK(geom.GetPoniRot1_rad() == 0.0f);
+    CHECK(geom.GetPoniRot2_rad() == 0.0f);
+    CHECK(geom.GetPoniRot3_rad() == 0.0f);
+    CHECK(geom.TwoTheta_rad(4.0f, 3.0f) == 0.0f);
+
+    remove("two_theta_zero_000001.h5");
+    remove("two_theta_zero_master.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+// A file this system wrote states its own PONI angles twice: as the three scalars the reader takes
+// them from, and as three rotations in the detector's depends_on chain. Following the chain must
+// therefore skip them - applied on top of the scalars they would tilt the detector twice, which is
+// how a correct 2theta reader breaks every tilted file this system has ever written. A test that only
+// wrote an untilted detector could not see it.
+TEST_CASE("JFJochReader_DetectorChainDoesNotDoubleTheTilt", "[HDF5][Full]") {
+    const float rot1 = 0.031f, rot2 = -0.047f, rot3 = 0.019f;
+
+    DiffractionExperiment x(DetJF(1));
+    x.ImagesPerTrigger(2).OverwriteExistingFiles(true).FilePrefix("test_ponichain");
+    x.BeamX_pxl(100).BeamY_pxl(200).DetectorDistance_mm(150)
+            .IncidentEnergy_keV(WVL_1A_IN_KEV).PixelSigned(false).BitDepthImage(16)
+            .FrameTime(std::chrono::microseconds(500), std::chrono::microseconds(10));
+    x.PoniRot1_rad(rot1).PoniRot2_rad(rot2).PoniRot3_rad(rot3);
+
+    RegisterHDF5Filter();
+    std::vector<uint16_t> image(x.GetPixelsNum(), 0);
+
+    StartMessage start_message;
+    x.FillMessage(start_message);
+    FileWriter file_set(start_message);
+    DataMessage message{};
+    for (int i = 0; i < x.GetImageNum(); i++) {
+        message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+        message.number = i;
+        REQUIRE_NOTHROW(file_set.WriteHDF5(message));
+    }
+    EndMessage end_message;
+    end_message.max_image_number = x.GetImageNum();
+    file_set.WriteHDF5(end_message);
+    file_set.Finalize();
+
+    DiffractionGeometry geom;
+    {
+        JFJochHDF5Reader reader;
+        REQUIRE_NOTHROW(reader.ReadFile("test_ponichain_master.h5"));
+        geom = reader.GetDataset()->experiment.GetDiffractionGeometry();
+    }
+    CHECK(geom.GetPoniRot1_rad() == Catch::Approx(rot1).margin(1e-6));
+    CHECK(geom.GetPoniRot2_rad() == Catch::Approx(rot2).margin(1e-6));
+    CHECK(geom.GetPoniRot3_rad() == Catch::Approx(rot3).margin(1e-6));
+    for (int64_t column = 0; column < 3; column++)
+        CHECK((geom.GetDetectorMatrix().Column(column)
+                   - PoniRotMatrix(rot1, rot2, rot3).Column(column)).Length() < 1e-5f);
+
+    remove("test_ponichain_master.h5");
+    remove("test_ponichain_data_000001.h5");
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}