reader: read the detector arm and the mounting each file states

A detector swung out on a 2theta arm was read as if it stood square on,
and a miniCBF written with a vertical spindle or a quarter-turned image
was read with the standard mounting assumed. Both are stated in the file
and both were ignored: the NXmx depends_on chain was never followed, and
Detector_2theta was parsed into a field nothing read.

Recovers three datasets that produced no usable lattice, and the
small-molecule sweeps at 30 and 55 degrees.

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

common/DetectorOrientation.cpp

@@ -46,6 +46,18 @@ RotMatrix DetectorOrientation::Matrix() const {
     return {rz_x, mirror_y ? -rz_y : rz_y, {0, 0, 1}};
 }
 
+std::optional<DetectorOrientation> DetectorOrientation::Match(const Coord &fast, const Coord &slow) {
+    for (int64_t quarter_turns = 0; quarter_turns < 4; quarter_turns++) {
+        for (const bool mirror_y: {false, true}) {
+            const DetectorOrientation orientation(mirror_y, quarter_turns);
+            const RotMatrix m = orientation.Matrix();
+            if (((m.Column(0) - fast).Length() < 1e-3f) && ((m.Column(1) - slow).Length() < 1e-3f))
+                return orientation;
+        }
+    }
+    return {};
+}
+
 bool DetectorOrientation::operator==(const DetectorOrientation &other) const {
     return (mirror_y == other.mirror_y) && (quarter_turns == other.quarter_turns);
 }

common/DetectorOrientation.h

@@ -3,6 +3,8 @@
 
 #pragma once
 
+#include <optional>
+
 #include "Coord.h"
 
 // How the stored image is laid out in the detector plane: mirrored in Y, and/or turned by a multiple
@@ -38,5 +40,11 @@ public:
     // Rz(quarter_turns * 90 deg) * diag(1,-1,1)^mirror_y. Entries are exactly 0 and +-1.
     [[nodiscard]] RotMatrix Matrix() const;
 
+    // The orientation whose fast and slow axes are the two directions given, or nothing when they are
+    // not one of the eight. Nothing means the image is turned in its own plane by something that is
+    // not a multiple of 90 degrees, which is a continuous rotation of the detector and belongs in the
+    // PONI angles - it cannot be told apart from the tilt by looking at the two directions alone.
+    [[nodiscard]] static std::optional<DetectorOrientation> Match(const Coord &fast, const Coord &slow);
+
     bool operator==(const DetectorOrientation &other) const;
 };

docs/CHANGELOG.md

@@ -1,6 +1,9 @@
 # Changelog
 ## 1.0.0
 ### 1.0.0-rc.166
+* A miniCBF sweep takes the mounting from the imgCIF axis table its header carries: which laboratory direction the image's columns and rows run along, and which the spindle turns about. Where there is no table, a `+SLOW` on the `Oscillation_axis` line still says the spindle runs along the image's slow direction. All three were previously assumed, and two instruments are not what was assumed.
+* Naming a miniCBF frame with no directory - a frame in the working directory - finds its sweep instead of reporting that no images were found.
+* 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 +59,45 @@ 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.
 
+## What a miniCBF header states about the mounting
+
+A PILATUS miniCBF gives the geometry twice. The `# ` lines every writer produces carry the distance, the
+beam centre and the angles; some beamlines then append a CBF template block holding a full **imgCIF axis
+table**, which states the laboratory direction of the image's fast and slow pixel directions, of the base
+goniometer axis, and of a 2theta arm where there is one. Where that table is present it is read, in
+preference to any assumption - it is the same information NXmx puts in `fast_pixel_direction` /
+`slow_pixel_direction` and the goniometer `vector`, in the form this format states it.
+
+imgCIF's laboratory frame has Z from the sample towards the source and Y opposite gravity, so it differs
+from the internal frame by a half turn about x - a rotation, not a mirror, so an axis carried through it
+turns the same way by the same angle.
+
+Two things a header can state that an assumption gets wrong by 90 degrees, which no refinement recovers
+and which the run's axis-sign rescue cannot reach either, a quarter turn not being a sign:
+
+* the image mounted a quarter turn round, so its columns run vertically;
+* a spindle that turns about the **vertical** rather than the horizontal.
+
+Where a header carries no axis table, a `+SLOW` on its `# Oscillation_axis` line still says the spindle
+runs along the image's slow direction rather than its fast one. The axis *name* on that line is not
+usable - one header says `X.CW +SLOW` where its own table says the axis is Y - but the direction token is,
+and on the header that states both they agree.
+
+## 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
@@ -36,18 +42,64 @@ 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]);
+    return DetectorOrientation::Match(McStasToInternal(f), McStasToInternal(s));
+}
 
-    for (int64_t quarter_turns = 0; quarter_turns < 4; quarter_turns++) {
-        for (bool mirror_y: {false, true}) {
-            const DetectorOrientation orientation(mirror_y, quarter_turns);
-            const RotMatrix m = orientation.Matrix();
-            if (((m.Column(0) - fast).Length() < 1e-3f) && ((m.Column(1) - slow).Length() < 1e-3f))
-                return orientation;
-        }
+// 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");
     }
-    return {};
+
+    // 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;
 }
 
 
@@ -721,6 +773,21 @@ 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

@@ -7,6 +7,7 @@
 #include <cctype>
 #include <cstring>
 #include <filesystem>
+#include <array>
 #include <map>
 #include <optional>
 
@@ -57,7 +58,12 @@ std::optional<Template> TemplateOf(const std::string &filename) {
 std::vector<std::string> CollectSweep(const std::string &path) {
     std::filesystem::path p(path);
     const bool is_dir = std::filesystem::is_directory(p);
-    const std::filesystem::path dir = is_dir ? p : p.parent_path();
+    // A frame named with no directory at all is in this one - parent_path() of a bare filename is
+    // empty, and iterating an empty path finds nothing, so naming a frame from inside its own
+    // directory found no sweep.
+    std::filesystem::path dir = is_dir ? p : p.parent_path();
+    if (dir.empty())
+        dir = ".";
 
     // Naming a frame selects ITS sweep. Naming a directory selects the sweep with the most frames in
     // it, which is the one a user pointing at a data directory means.
@@ -90,14 +96,54 @@ std::vector<std::string> CollectSweep(const std::string &path) {
     return out;
 }
 
+// An imgCIF laboratory direction in the internal frame. imgCIF puts Z from the sample towards the
+// source and Y opposite gravity, while the internal frame has z along the beam and y along increasing
+// row, so the two differ by a half turn about x - a rotation and not a mirror, so an axis carried
+// through it turns the same way by the same angle. (writer/HDF5NXmx.cpp states the same relation from
+// the other side, where it separates this from the McStas one, which is a half turn about z.)
+Coord ImgCIFToInternal(const std::array<double, 3> &v) {
+    return {static_cast<float>(v[0]), static_cast<float>(-v[1]), static_cast<float>(-v[2])};
+}
+
+// The base rotation axis where a header states nothing about it, in the internal frame (x along
+// increasing detector column, y along increasing row, z along the beam). It is a convention: such a
+// header names its rotation axis but gives no direction, so this is the sign an NXmx master writes
+// for the same instruments, and a file that needs the other one is settled from the data by the run's
+// axis-sign rescue.
+const Coord ASSUMED_BASE_AXIS(-1.0f, 0.0f, 0.0f);
+
+// The base rotation axis of the instrument, in the internal frame.
+//
+// Two headers in every corpus examined here state it and were being overruled by the assumption. One
+// beamline's PILATUS turns about the VERTICAL: its axis table says so outright, and its "# Oscillation
+// _axis" line says so a second way, by naming the image direction the spindle runs along rather than a
+// vector. Assuming the horizontal axis put the spindle 90 degrees out - which no amount of refinement
+// recovers, and which a sign rescue cannot reach either, since it is not a sign - and the run indexed
+// nothing. The sign is still the rescue's business; the DIRECTION is the file's.
+Coord BaseAxis(const minicbf::Header &h) {
+    if (h.spindle_axis.has_value())
+        return ImgCIFToInternal(*h.spindle_axis);
+    if (h.spindle_along_slow)
+        return {0.0f, -1.0f, 0.0f};     // minus the slow direction, as the default is minus the fast
+    return ASSUMED_BASE_AXIS;
+}
+
+// How the stored image sits in the detector plane, where the header's axis table states it - the same
+// thing the NXmx module directions say, in the form this format says it. Nothing comes back when the
+// header carries no table, or when what it states is not one of the eight discrete orientations.
+std::optional<DetectorOrientation> ImageOrientation(const minicbf::Header &h) {
+    if (!h.fast_direction.has_value() || !h.slow_direction.has_value())
+        return {};
+    return DetectorOrientation::Match(ImgCIFToInternal(*h.fast_direction),
+                                      ImgCIFToInternal(*h.slow_direction));
+}
+
 // The axis a miniCBF sweep turns about, in the internal frame (x along increasing detector column,
 // y along increasing row, z along the beam).
 //
-// The base axis is a convention: a miniCBF names its rotation axis but never states a direction, so
-// this is the sign an NXmx master writes for the same instruments, and a file that needs the other
-// one is settled from the data by the run's axis-sign rescue. The sense of the omega rotation below
-// follows that same convention, so a sweep parked at a non-zero omega inherits whichever sign the
-// base axis turns out to have.
+// The base axis comes from the header where it states one (BaseAxis above) and is otherwise assumed.
+// The sense of the omega rotation below follows the base axis, so a sweep parked at a non-zero omega
+// inherits whichever direction it turns out to have.
 //
 // The head is base -> chi -> phi, so only the axes OUTSIDE the scanned one can tilt it. An omega
 // scan turns about the base axis however the cradle is set - which is why a header carrying a large
@@ -106,7 +152,7 @@ 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 = BaseAxis(h);
     if (!minicbf::ScansPhi(h))
         return base;
 
@@ -153,6 +199,8 @@ void JFJochCBFReader::ReadFiles(const std::string &path) {
     // Images are handed out as signed 32-bit whatever the file stored, so that is the depth the rest
     // of the code must see; the real overflow is the header's Count_cutoff, set above.
     detector.BitDepthImage(32);
+    if (const auto orientation = ImageOrientation(header0_))
+        detector.ImageOrientation(orientation.value());
     detector.MinFrameTime(std::chrono::microseconds(0));
     detector.MinCountTime(std::chrono::microseconds(0));
     detector.ReadOutTime(std::chrono::nanoseconds(0));
@@ -161,6 +209,24 @@ 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 axis the header's table gives the arm, and otherwise about the base spindle axis: on the
+    // four-circle geometry these headers describe the arm and the spindle are one axis, and the one
+    // header here that states both states them with the same vector.
+    if (header0_.two_theta_deg != 0.0) {
+        const Coord axis = header0_.detector_axis.has_value()
+                               ? ImgCIFToInternal(*header0_.detector_axis) : BaseAxis(header0_);
+        float rot1 = 0, rot2 = 0, rot3 = 0;
+        PoniAnglesFromMatrix(RotMatrix(static_cast<float>(header0_.two_theta_deg * PI / 180.0), 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>(

reader/MiniCBF.cpp

@@ -8,7 +8,9 @@
 #include <cstring>
 #include <fstream>
 #include <limits>
+#include <map>
 #include <regex>
+#include <stdexcept>
 
 #include "../common/JFJochException.h"
 
@@ -48,6 +50,133 @@ std::optional<double> Angle(const std::string &text, const char *pattern) {
     return v;
 }
 
+// One "loop_" of the imgCIF template block these headers carry, as rows keyed by tag. Tags and values
+// are both read as whitespace-separated tokens rather than by line, because a template packs several
+// tags onto one line ("_axis.vector[1] _axis.vector[2] _axis.vector[3]") and the rows that follow are
+// laid out to match the tags, not the lines.
+std::vector<std::map<std::string, std::string>> ParseLoop(const std::string &text, const std::string &tag) {
+    // The loop_ that introduces the tag, not the tag's own position: everything before it is another
+    // loop's data.
+    const size_t tag_at = text.find("\n" + tag);
+    if (tag_at == std::string::npos)
+        return {};
+    const size_t loop_at = text.rfind("loop_", tag_at);
+    if (loop_at == std::string::npos)
+        return {};
+
+    // Bare tokens, and the quoted ones a CIF value may be - a quoted value holding spaces would
+    // otherwise be counted as several columns and shift every row after it.
+    std::vector<std::string> tokens;
+    for (size_t i = loop_at + 5; i < text.size();) {
+        while ((i < text.size()) && std::isspace(static_cast<unsigned char>(text[i])))
+            i++;
+        if (i >= text.size())
+            break;
+        size_t end;
+        if ((text[i] == '\'') || (text[i] == '"')) {
+            end = text.find(text[i], i + 1);
+            if (end == std::string::npos)
+                break;
+            tokens.push_back(text.substr(i + 1, end - i - 1));
+            end++;
+        } else {
+            end = i;
+            while ((end < text.size()) && !std::isspace(static_cast<unsigned char>(text[end])))
+                end++;
+            tokens.push_back(text.substr(i, end - i));
+        }
+        // A second loop_, or a tag belonging to another category, ends this one.
+        if ((tokens.back() == "loop_")
+                || (tokens.back().starts_with("_") && !tokens.back().starts_with(tag.substr(0, tag.find('.') + 1)))) {
+            tokens.pop_back();
+            break;
+        }
+        i = end;
+    }
+
+    std::vector<std::string> names;
+    size_t first_value = 0;
+    while ((first_value < tokens.size()) && tokens[first_value].starts_with("_"))
+        names.push_back(tokens[first_value++]);
+    if (names.empty())
+        return {};
+
+    std::vector<std::map<std::string, std::string>> rows;
+    for (size_t i = first_value; i + names.size() <= tokens.size(); i += names.size()) {
+        std::map<std::string, std::string> row;
+        for (size_t j = 0; j < names.size(); j++)
+            row[names[j]] = tokens[i + j];
+        rows.push_back(std::move(row));
+    }
+    return rows;
+}
+
+std::string Field(const std::map<std::string, std::string> &row, const std::string &name) {
+    const auto it = row.find(name);
+    return (it == row.end()) ? std::string() : it->second;
+}
+
+// The imgCIF axis table: which axis turns or translates in which laboratory direction, and which two
+// axes the image's columns and rows run along. Absent from most headers, which say nothing about any
+// of this and are left exactly as they were read before.
+//
+// The element vectors are stated in the frame of the axis they depend on. Between them and the
+// detector's own rotation every header seen has translations only, so they describe the image in the
+// unswung detector frame - which is where the image orientation belongs, with the arm applied on top.
+void ParseAxisTable(const std::string &text, Header &h) {
+    const auto axes = ParseLoop(text, "_axis.id");
+    if (axes.empty())
+        return;
+
+    std::map<std::string, std::array<double, 3>> vector_of;
+    for (const auto &row: axes) {
+        const std::string id = Field(row, "_axis.id");
+        const std::string type = Field(row, "_axis.type");
+        const std::string equipment = Field(row, "_axis.equipment");
+        const std::string depends_on = Field(row, "_axis.depends_on");
+        std::array<double, 3> v{};
+        try {
+            for (int i = 0; i < 3; i++)
+                v[i] = std::stod(Field(row, "_axis.vector[" + std::to_string(i + 1) + "]"));
+        } catch (const std::exception &) {
+            continue;   // "." for a vector: the table states no direction for this axis
+        }
+        vector_of[id] = v;
+
+        // The base spindle and the detector arm are the rotations that hang off nothing: everything
+        // further in is carried by them. Naming neither, so a beamline is free to call them anything.
+        if ((type == "rotation") && (depends_on == ".")) {
+            if (equipment == "goniometer")
+                h.spindle_axis = v;
+            else if (equipment == "detector")
+                h.detector_axis = v;
+        }
+    }
+
+    // Which axis the fast index runs along, and which the slow, through the two tables that say so.
+    std::map<std::string, std::string> axis_of_set;
+    for (const auto &row: ParseLoop(text, "_array_structure_list_axis.axis_set_id"))
+        axis_of_set[Field(row, "_array_structure_list_axis.axis_set_id")]
+                = Field(row, "_array_structure_list_axis.axis_id");
+
+    for (const auto &row: ParseLoop(text, "_array_structure_list.array_id")) {
+        const std::string set = Field(row, "_array_structure_list.axis_set_id");
+        const auto id = axis_of_set.contains(set) ? axis_of_set[set] : set;
+        const auto it = vector_of.find(id);
+        if (it == vector_of.end())
+            continue;
+        std::array<double, 3> v = it->second;
+        if (Field(row, "_array_structure_list.direction") == "decreasing")
+            for (double &c: v)
+                c = -c;
+        const std::string index = Field(row, "_array_structure_list.index");
+        if (index == "1")
+            h.fast_direction = v;
+        else if (index == "2")
+            h.slow_direction = v;
+    }
+}
+
 int16_t ReadI16(const uint8_t *p) { int16_t v; std::memcpy(&v, p, 2); return v; }
 int32_t ReadI32(const uint8_t *p) { int32_t v; std::memcpy(&v, p, 4); return v; }
 int64_t ReadI64(const uint8_t *p) { int64_t v; std::memcpy(&v, p, 8); return v; }
@@ -99,6 +228,11 @@ Header ParseHeader(const char *data, size_t size) {
     h.period_s       = Num(t, R"(#\s*Exposure_period\s+([\d.eE+-]+))");
     h.count_cutoff   = Int(t, R"(#\s*Count_cutoff\s+(\d+))");
     h.axis_name      = Match(t, R"(#\s*Oscillation_axis\s+(\S+))").value_or("omega");
+    // "+SLOW" / "+FAST" on that same line: which of the image's two directions the spindle runs
+    // along. Some writers state that instead of an axis name, and it is the only thing a header with
+    // no axis table says about the spindle's direction at all.
+    h.spindle_along_slow = Match(t, R"(#\s*Oscillation_axis[^\r\n]*\+(SLOW|slow))").has_value();
+    ParseAxisTable(t, h);
 
     // "# Silicon sensor, ..." / "# CdTe sensor, ...". The rest of the code compares the material
     // against "CdTe" (BraggIntegrationEngine), so an unnormalised "Silicon" would silently give a

reader/MiniCBF.h

@@ -3,6 +3,7 @@
 
 #pragma once
 
+#include <array>
 #include <cstdint>
 #include <optional>
 #include <string>
@@ -44,6 +45,21 @@ struct Header {
     int64_t count_cutoff = 0;      // saturation
     std::string axis_name = "omega";
     bool byte_offset = false;      // the only conversion supported
+
+    // The imgCIF axis table the CBF template block carries after the "# " lines, as the file states
+    // it: vectors in the imgCIF laboratory frame (Z from the sample towards the source, Y opposite
+    // gravity, X completing a right-handed set). Turning them into any other frame is the caller's
+    // business, not this format reader's. Most headers carry no such table and leave all of these
+    // empty, which is not the same as their stating the usual mounting.
+    std::optional<std::array<double, 3>> fast_direction;   // laboratory direction of a +1 column step
+    std::optional<std::array<double, 3>> slow_direction;   // ... of a +1 row step
+    std::optional<std::array<double, 3>> spindle_axis;     // the base goniometer rotation axis
+    std::optional<std::array<double, 3>> detector_axis;    // the detector's own rotation axis: a 2theta arm
+    // "# Oscillation_axis X.CW +SLOW". Some writers say which of the two image directions the spindle
+    // runs along instead of stating a vector. The axis NAME on that line is a poor discriminator (see
+    // ScansPhi, and note that the one header carrying both a name and a table says "X" where its table
+    // says Y) but this token is not: where both are present they agree.
+    bool spindle_along_slow = false;
 };
 
 // Whether the sweep turns PHI rather than the base (omega) axis. What moved is the axis with a

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

@@ -7,9 +7,14 @@
 #include "../common/ScanResultGenerator.h"
 #include "../writer/FileWriter.h"
 #include "../reader/JFJochHDF5Reader.h"
+#include "../reader/JFJochCBFReader.h"
+#include "../reader/MiniCBF.h"
 #include "../compression/JFJochCompressor.h"
 
+#include <fstream>
 #include <future>
+#include <iomanip>
+#include <sstream>
 
 TEST_CASE("HDF5DataType_Sign","[HDF5]") {
     HDF5DataType type_u8((uint8_t)0), type_fl(0.0f), type_i32((int32_t) 0), type_u32((uint32_t) 0);
@@ -3594,3 +3599,339 @@ 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);
+}
+
+// A miniCBF header states more about the instrument than the "# " lines do: the CBF template block
+// some beamlines write carries a full imgCIF axis table, saying which laboratory direction the image's
+// columns and rows run along and which the spindle turns about. The reader assumed all three, and two
+// instruments in the corpus are not what it assumed - one stores its image a quarter turn round, the
+// other turns about the VERTICAL. Either way the spindle ends up 90 degrees from the image, which is
+// not a sign and so is beyond the axis-sign rescue; both indexed nothing at all.
+namespace {
+    // Two frames of a sweep whose pixels are all zero. Every delta of a zero image is zero, so the
+    // byte-offset stream is one 0x00 per pixel - which is a valid stream and enough to open a sweep.
+    void WriteMiniCBFSweep(const std::string &prefix, const std::string &header_body,
+                           int64_t nx, int64_t ny) {
+        for (int frame = 1; frame <= 2; frame++) {
+            std::ostringstream head;
+            head << "###CBF: VERSION 1.5\n_array_data.header_convention \"PILATUS_1.2\"\n"
+                 << "_array_data.header_contents\n"
+                 << "# Detector: PILATUS3 6M, S/N 60-0119\n"
+                 << "# Pixel_size 172e-6 m x 172e-6 m\n"
+                 << "# Silicon sensor, thickness 0.000450 m\n"
+                 << "# Exposure_time 0.1 s\n# Exposure_period 0.1 s\n# Count_cutoff 768595 counts\n"
+                 << "# Wavelength 0.96864 A\n# Detector_distance 0.33161 m\n"
+                 << "# Beam_xy (12.00, 8.00) pixels\n"
+                 << "# Start_angle " << (frame - 1) * 0.1 << " deg.\n# Angle_increment 0.1000 deg.\n"
+                 << "# Omega " << (frame - 1) * 0.1 << " deg.\n# Omega_increment 0.1000 deg.\n"
+                 << "# Phi 0.0000 deg.\n# Phi_increment 0.0000 deg.\n"
+                 << "# Chi 0.0000 deg.\n# Chi_increment 0.0000 deg.\n"
+                 << header_body
+                 << "_array_data.data\n--CIF-BINARY-FORMAT-SECTION--\n"
+                 << "Content-Type: application/octet-stream;\n"
+                 << "     conversions=\"x-CBF_BYTE_OFFSET\"\n"
+                 << "Content-Transfer-Encoding: BINARY\n"
+                 << "X-Binary-Size: " << nx * ny << "\n"
+                 << "X-Binary-Element-Type: \"signed 32-bit integer\"\n"
+                 << "X-Binary-Number-of-Elements: " << nx * ny << "\n"
+                 << "X-Binary-Size-Fastest-Dimension: " << nx << "\n"
+                 << "X-Binary-Size-Second-Dimension: " << ny << "\n\n";
+
+            std::ostringstream name;
+            name << prefix << "_" << std::setfill('0') << std::setw(4) << frame << ".cbf";
+            std::ofstream f(name.str(), std::ios::binary);
+            const std::string text = head.str();
+            f.write(text.data(), static_cast<std::streamsize>(text.size()));
+            f.write(reinterpret_cast<const char *>(minicbf::BINARY_SEPARATOR),
+                    sizeof(minicbf::BINARY_SEPARATOR));
+            const std::vector<char> zeros(static_cast<size_t>(nx * ny), 0);
+            f.write(zeros.data(), static_cast<std::streamsize>(zeros.size()));
+        }
+    }
+
+    void RemoveMiniCBFSweep(const std::string &prefix) {
+        for (int frame = 1; frame <= 2; frame++) {
+            std::ostringstream name;
+            name << prefix << "_" << std::setfill('0') << std::setw(4) << frame << ".cbf";
+            remove(name.str().c_str());
+        }
+    }
+
+    // The axis table in the form these headers write it, several tags to a line.
+    std::string AxisTable(const std::string &rows, int64_t nx, int64_t ny) {
+        return "loop_\n_axis.id\n_axis.type\n_axis.equipment\n_axis.depends_on\n"
+               "_axis.vector[1] _axis.vector[2] _axis.vector[3]\n"
+               "_axis.offset[1] _axis.offset[2] _axis.offset[3]\n"
+             + rows +
+               "loop_\n_array_structure_list.array_id\n_array_structure_list.index\n"
+               "_array_structure_list.dimension\n_array_structure_list.precedence\n"
+               "_array_structure_list.direction\n_array_structure_list.axis_set_id\n"
+               "ARRAY1 1 " + std::to_string(nx) + " 1 increasing ELEMENT_X\n"
+               "ARRAY1 2 " + std::to_string(ny) + " 2 increasing ELEMENT_Y\n"
+               "loop_\n_array_structure_list_axis.axis_set_id\n_array_structure_list_axis.axis_id\n"
+               "_array_structure_list_axis.displacement\n_array_structure_list_axis.displacement_increment\n"
+               "ELEMENT_X ELEMENT_X 0.0 0.1720\nELEMENT_Y ELEMENT_Y 0.0 0.1720\n";
+    }
+}
+
+TEST_CASE("JFJochCBFReader_AxisTableStatesTheMounting", "[HDF5][Full]") {
+    const int64_t nx = 24, ny = 16;
+
+    // A header that states nothing: the assumption, and the behaviour of nearly every file there is.
+    SECTION("no table, no hint - the assumption stands") {
+        WriteMiniCBFSweep("cbfaxis_plain", "# Detector_2theta 0.0000 deg.\n# Oscillation_axis OMEGA\n",
+                          nx, ny);
+        JFJochCBFReader reader;
+        REQUIRE_NOTHROW(reader.ReadFiles("cbfaxis_plain_0001.cbf"));
+        const auto x = reader.GetDataset()->experiment;
+        REQUIRE(x.GetGoniometer().has_value());
+        CHECK((x.GetGoniometer()->GetAxis() - Coord(-1, 0, 0)).Length() < 1e-6f);
+        CHECK(x.GetDetectorSetup().GetImageOrientation().IsIdentity());
+        CHECK(x.GetDiffractionGeometry().GetPoniRot2_rad() == 0.0f);
+        reader.Close();
+        RemoveMiniCBFSweep("cbfaxis_plain");
+    }
+
+    // A spindle that turns about the VERTICAL, with the image mounted the usual way round. imgCIF Y is
+    // up and the internal frame's y is down, so the stated (0,1,0) is internal (0,-1,0) - and NOT the
+    // (-1,0,0) that was assumed, which is 90 degrees away and indexes nothing.
+    SECTION("vertical spindle, standard image") {
+        WriteMiniCBFSweep("cbfaxis_vert",
+                          "# Detector_2theta 0.0000 deg.\n# Oscillation_axis X.CW +SLOW\n"
+                          + AxisTable("GON_OMEGA rotation goniometer . 0 1 0 . . .\n"
+                                      "DET_Z translation detector . 0 0 -1 0 0 0\n"
+                                      "ELEMENT_X translation detector DET_Z 1 0 0 -1 1 0\n"
+                                      "ELEMENT_Y translation detector ELEMENT_X 0 -1 0 0 0 0\n", nx, ny),
+                          nx, ny);
+        JFJochCBFReader reader;
+        REQUIRE_NOTHROW(reader.ReadFiles("cbfaxis_vert_0001.cbf"));
+        const auto x = reader.GetDataset()->experiment;
+        REQUIRE(x.GetGoniometer().has_value());
+        CHECK((x.GetGoniometer()->GetAxis() - Coord(0, -1, 0)).Length() < 1e-6f);
+        // The image itself is standard, so nothing about it is turned - the axis was the whole error.
+        CHECK(x.GetDetectorSetup().GetImageOrientation().IsIdentity());
+        reader.Close();
+        RemoveMiniCBFSweep("cbfaxis_vert");
+    }
+
+    // The same vertical spindle, stated only by the "+SLOW" token, which is all a header with no axis
+    // table says. Two datasets from that instrument are in this state.
+    SECTION("vertical spindle from the +SLOW token alone") {
+        WriteMiniCBFSweep("cbfaxis_slow", "# Detector_2theta 0.0000 deg.\n# Oscillation_axis X.CW +SLOW\n",
+                          nx, ny);
+        JFJochCBFReader reader;
+        REQUIRE_NOTHROW(reader.ReadFiles("cbfaxis_slow_0001.cbf"));
+        const auto x = reader.GetDataset()->experiment;
+        REQUIRE(x.GetGoniometer().has_value());
+        CHECK((x.GetGoniometer()->GetAxis() - Coord(0, -1, 0)).Length() < 1e-6f);
+        reader.Close();
+        RemoveMiniCBFSweep("cbfaxis_slow");
+    }
+
+    // An image stored a quarter turn round, on a detector swung out to 30 degrees. The two are read
+    // together or not at all: the arm turns about a laboratory axis, and which way that runs across
+    // the stored image is exactly what the mounting says.
+    SECTION("quarter-turned image on a swung arm") {
+        WriteMiniCBFSweep("cbfaxis_turn",
+                          "# Detector_2theta 30.0000 deg.\n# Oscillation_axis OMEGA\n"
+                          + AxisTable("GON_OMEGA rotation goniometer . 1 0 0 . . .\n"
+                                      "DET_2THETA rotation detector . 1 0 0 . . .\n"
+                                      "DET_Z translation detector DET_2THETA 0 0 -1 0 0 0\n"
+                                      "ELEMENT_X translation detector DET_Z 0 1 0 -1 1 0\n"
+                                      "ELEMENT_Y translation detector ELEMENT_X 1 0 0 0 0 0\n", nx, ny),
+                          nx, ny);
+        JFJochCBFReader reader;
+        REQUIRE_NOTHROW(reader.ReadFiles("cbfaxis_turn_0001.cbf"));
+        const auto x = reader.GetDataset()->experiment;
+        REQUIRE(x.GetGoniometer().has_value());
+        CHECK((x.GetGoniometer()->GetAxis() - Coord(1, 0, 0)).Length() < 1e-6f);
+        // fast = imgCIF (0,1,0) = internal (0,-1,0), slow = imgCIF (1,0,0) = internal (1,0,0)
+        CHECK(x.GetDetectorSetup().GetImageOrientation() == DetectorOrientation(false, 3));
+        // and the arm turns about its own stated axis, internal +x, by the stated 30 degrees
+        const auto geom = x.GetDiffractionGeometry();
+        const RotMatrix expected = RotMatrix(static_cast<float>(30.0 * PI / 180.0), {1, 0, 0})
+                                 * DetectorOrientation(false, 3).Matrix();
+        for (int64_t column = 0; column < 3; column++)
+            CHECK((geom.GetDetectorMatrix().Column(column) - expected.Column(column)).Length() < 1e-5f);
+        reader.Close();
+        RemoveMiniCBFSweep("cbfaxis_turn");
+    }
+}