From 93b733d5723a857519b97701b9f36fd8cc8c7c04 Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Fri, 26 Sep 2025 15:15:39 +0100
Subject: [PATCH 1/4] Define an ImageSequence, allow updating of models.

---
 dx2/detector.cxx           |  6 ++++++
 include/dx2/detector.hpp   |  1 +
 include/dx2/experiment.hpp | 30 ++++++++++++++++++++++++++++
 include/dx2/imageset.hpp   | 41 ++++++++++++++++++++++++++++++++++++++
 4 files changed, 78 insertions(+)
 create mode 100644 include/dx2/imageset.hpp

diff --git a/dx2/detector.cxx b/dx2/detector.cxx
index 732b77c..f120582 100644
--- a/dx2/detector.cxx
+++ b/dx2/detector.cxx
@@ -236,6 +236,12 @@ Detector::Detector(json detector_data) {
   }
 }
 
+Detector::Detector(std::vector<Panel> panels) {
+  for (auto it = panels.begin(); it != panels.end(); ++it) {
+    _panels.push_back(*it);
+  }
+}
+
 json Detector::to_json() const {
   json detector_data;
   std::vector<json> panels_array;
diff --git a/include/dx2/detector.hpp b/include/dx2/detector.hpp
index 5875d07..1b1af14 100644
--- a/include/dx2/detector.hpp
+++ b/include/dx2/detector.hpp
@@ -99,6 +99,7 @@ class Detector {
 public:
   Detector() = default;
   Detector(json detector_data);
+  Detector(std::vector<Panel> panels);
   json to_json() const;
   std::vector<Panel> panels() const;
   std::optional<std::pair<int, std::array<double, 2>>>
diff --git a/include/dx2/experiment.hpp b/include/dx2/experiment.hpp
index d19cc70..1ca00cd 100644
--- a/include/dx2/experiment.hpp
+++ b/include/dx2/experiment.hpp
@@ -22,6 +22,11 @@ template <class BeamType> class Experiment {
   Detector &detector();
   const Crystal &crystal() const;
   void set_crystal(Crystal crystal);
+  void set_beam(BeamType beam);
+  void set_scan(Scan scan);
+  void set_detector(Detector detector);
+  void set_goniometer(Goniometer goniometer);
+  void set_imageset_json(json imageset_json);
   void set_identifier(std::string identifier);
 
 protected:
@@ -115,10 +120,35 @@ void Experiment<BeamType>::set_crystal(Crystal crystal) {
   _crystal = crystal;
 }
 
+template <class BeamType>
+void Experiment<BeamType>::set_beam(BeamType beam) {
+  _beam = beam;
+}
+
 template <class BeamType> BeamType &Experiment<BeamType>::beam() {
   return _beam;
 }
 
+template <class BeamType>
+void Experiment<BeamType>::set_scan(Scan scan) {
+  _scan = scan;
+}
+
+template <class BeamType>
+void Experiment<BeamType>::set_detector(Detector detector) {
+  _detector = detector;
+}
+
+template <class BeamType>
+void Experiment<BeamType>::set_goniometer(Goniometer goniometer) {
+  _goniometer = goniometer;
+}
+
+template <class BeamType>
+void Experiment<BeamType>::set_imageset_json(json imageset_json) {
+  _imageset_json = imageset_json;
+}
+
 template <class BeamType>
 const std::string &Experiment<BeamType>::identifier() const {
   return _identifier;
diff --git a/include/dx2/imageset.hpp b/include/dx2/imageset.hpp
new file mode 100644
index 0000000..00cbe1e
--- /dev/null
+++ b/include/dx2/imageset.hpp
@@ -0,0 +1,41 @@
+#pragma once
+#include <nlohmann/json.hpp>
+
+using Eigen::Vector3d;
+using json = nlohmann::json;
+
+class ImageSequence {
+public:
+    ImageSequence() = default;
+    ImageSequence(std::string filename, int n_images);
+    json to_json() const;
+protected:
+    int n_images_ {};
+    std::string filename_ {};
+    std::vector<std::size_t> single_file_indices_{};
+};
+
+ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(filename), n_images_(n_images) {
+    single_file_indices_.reserve(n_images_);
+    for (std::size_t i=0;i<n_images_;++i){
+        single_file_indices_.push_back(i);
+    }
+}
+
+json ImageSequence::to_json() const {
+    json imageset_data;
+    imageset_data["__id__"] = "ImageSequence";
+    imageset_data["template"] = filename_;
+    imageset_data["single_file_indices"] = single_file_indices_;
+    // Set defaults and null for now.
+    imageset_data["mask"] = nullptr;
+    imageset_data["gain"] = nullptr;
+    imageset_data["pedestal"] =nullptr;
+    imageset_data["dx"] = nullptr;
+    imageset_data["dy"] = nullptr;
+    json params;
+    params["dynamic_shadowing"] = "Auto";
+    params["multi_panel"] = false;
+    imageset_data["params"] = params;
+    return imageset_data;
+}
\ No newline at end of file

From 23ce6a5c65027a6d204dc50af23a9d7177177372 Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Mon, 17 Nov 2025 13:44:37 +0000
Subject: [PATCH 2/4] Update name, use proper class rather than json.

---
 dx2/CMakeLists.txt            |  1 +
 dx2/imagesequence.cxx         | 56 +++++++++++++++++++++++++++++++++++
 include/dx2/experiment.hpp    | 17 ++++++-----
 include/dx2/imagesequence.hpp | 17 +++++++++++
 include/dx2/imageset.hpp      | 41 -------------------------
 5 files changed, 83 insertions(+), 49 deletions(-)
 create mode 100644 dx2/imagesequence.cxx
 create mode 100644 include/dx2/imagesequence.hpp
 delete mode 100644 include/dx2/imageset.hpp

diff --git a/dx2/CMakeLists.txt b/dx2/CMakeLists.txt
index ca7b921..877c607 100644
--- a/dx2/CMakeLists.txt
+++ b/dx2/CMakeLists.txt
@@ -9,6 +9,7 @@ add_library(
     goniometer.cxx
     scan.cxx
     detector_attenuations.cxx
+    imagesequence.cxx
 )
 target_link_libraries(
     dx2
diff --git a/dx2/imagesequence.cxx b/dx2/imagesequence.cxx
new file mode 100644
index 0000000..e15c7e4
--- /dev/null
+++ b/dx2/imagesequence.cxx
@@ -0,0 +1,56 @@
+#include "dx2/imagesequence.hpp"
+
+using json = nlohmann::json;
+
+ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(filename), n_images_(n_images) {
+    single_file_indices_.reserve(n_images_);
+    for (std::size_t i=0;i<n_images_;++i){
+        single_file_indices_.push_back(i);
+    }
+}
+
+ImageSequence::ImageSequence(json imagesequence_data) {
+    std::vector<std::string> required_keys = {"template", "single_file_indices", "__id__"};
+    for (const auto &key : required_keys) {
+        if (imagesequence_data.find(key) == imagesequence_data.end()) {
+            throw std::invalid_argument("Key " + key +
+                                       " is missing from the input imageset JSON");
+        }
+    }
+    if (imagesequence_data["__id__"] != std::string("ImageSequence")){
+        throw std::runtime_error("Only ImageSequences are supported");
+    }
+    filename_ = imagesequence_data["template"];
+    json indices = imagesequence_data["single_file_indices"];
+    single_file_indices_ = {};
+    if (*(indices.begin()) < 0){
+        throw std::runtime_error("Starting file index <0");
+    }
+    for (json::iterator it = indices.begin(); it != indices.end();
+        ++it) {
+        single_file_indices_.push_back(*it);
+    }
+    n_images_ = single_file_indices_.size();
+    imagesequence_data_ = imagesequence_data; // To propagate during serialization/deserialization.
+}
+
+json ImageSequence::to_json() const {
+    json imageset_data = imagesequence_data_;
+    imageset_data["__id__"] = "ImageSequence";
+    imageset_data["template"] = filename_;
+    imageset_data["single_file_indices"] = single_file_indices_;
+    // Set defaults and null for now.
+    std::vector<std::string> optional_keys = {"mask", "gain", "pedestal", "dx", "dy"};
+    for (const auto &key : optional_keys) {
+        if (imagesequence_data_.find(key) == imagesequence_data_.end()) {
+            imageset_data[key] = nullptr;
+        }
+    }
+    if (imagesequence_data_.find("params") == imagesequence_data_.end()) {
+        json params;
+        params["dynamic_shadowing"] = "Auto";
+        params["multi_panel"] = false;
+        imageset_data["params"] = params;
+    }
+    return imageset_data;
+}
\ No newline at end of file
diff --git a/include/dx2/experiment.hpp b/include/dx2/experiment.hpp
index 1ca00cd..a4e2345 100644
--- a/include/dx2/experiment.hpp
+++ b/include/dx2/experiment.hpp
@@ -5,6 +5,7 @@
 #include <dx2/detector.hpp>
 #include <dx2/goniometer.hpp>
 #include <dx2/scan.hpp>
+#include <dx2/imagesequence.hpp>
 #include <nlohmann/json.hpp>
 
 using Eigen::Vector3d;
@@ -26,7 +27,7 @@ template <class BeamType> class Experiment {
   void set_scan(Scan scan);
   void set_detector(Detector detector);
   void set_goniometer(Goniometer goniometer);
-  void set_imageset_json(json imageset_json);
+  void set_imagesequence(ImageSequence imagesequence);
   void set_identifier(std::string identifier);
 
 protected:
@@ -35,7 +36,7 @@ template <class BeamType> class Experiment {
   Goniometer _goniometer{};
   Detector _detector{};
   Crystal _crystal{};
-  json _imageset_json{};
+  ImageSequence _imagesequence{};
   std::string _identifier{};
 };
 
@@ -56,8 +57,9 @@ Experiment<BeamType>::Experiment(json experiment_data) {
   this->_goniometer = gonio;
   this->_detector = detector;
   // Save the imageset json to propagate when saving to file.
-  json imageset_data = experiment_data["imageset"][0];
-  this->_imageset_json = imageset_data;
+  json imagesequence_data = experiment_data["imageset"][0];
+  ImageSequence imagesequence(imagesequence_data);
+  this->_imagesequence = imagesequence;
   try { // We don't always have a crystal model e.g. before indexing.
     json crystal_data = experiment_data["crystal"][0];
     Crystal crystal(crystal_data);
@@ -72,7 +74,6 @@ template <class BeamType> json Experiment<BeamType>::to_json() const {
   json elist_out; // a list of potentially multiple experiments
   elist_out["__id__"] = "ExperimentList";
   json expt_out; // our single experiment
-  // no imageset (for now?).
   expt_out["__id__"] = "Experiment";
   expt_out["identifier"] = _identifier;
   expt_out["beam"] =
@@ -87,7 +88,7 @@ template <class BeamType> json Experiment<BeamType>::to_json() const {
   elist_out["goniometer"] = std::array<json, 1>{_goniometer.to_json()};
   elist_out["beam"] = std::array<json, 1>{_beam.to_json()};
   elist_out["detector"] = std::array<json, 1>{_detector.to_json()};
-  elist_out["imageset"] = std::array<json, 1>{_imageset_json};
+  elist_out["imageset"] = std::array<json, 1>{_imagesequence.to_json()};
 
   if (_crystal.get_U_matrix().determinant()) {
     expt_out["crystal"] = 0;
@@ -145,8 +146,8 @@ void Experiment<BeamType>::set_goniometer(Goniometer goniometer) {
 }
 
 template <class BeamType>
-void Experiment<BeamType>::set_imageset_json(json imageset_json) {
-  _imageset_json = imageset_json;
+void Experiment<BeamType>::set_imagesequence(ImageSequence imagesequence) {
+  _imagesequence = imagesequence;
 }
 
 template <class BeamType>
diff --git a/include/dx2/imagesequence.hpp b/include/dx2/imagesequence.hpp
new file mode 100644
index 0000000..b3935df
--- /dev/null
+++ b/include/dx2/imagesequence.hpp
@@ -0,0 +1,17 @@
+#pragma once
+#include <nlohmann/json.hpp>
+
+using json = nlohmann::json;
+
+class ImageSequence {
+public:
+    ImageSequence() = default;
+    ImageSequence(std::string filename, int n_images);
+    ImageSequence(json imagesequence_data);
+    json to_json() const;
+protected:
+    int n_images_ {};
+    std::string filename_ {};
+    std::vector<std::size_t> single_file_indices_{};
+    json imagesequence_data_ {}; // For propagating additional metadata during serialization/deserialization.
+};
\ No newline at end of file
diff --git a/include/dx2/imageset.hpp b/include/dx2/imageset.hpp
deleted file mode 100644
index 00cbe1e..0000000
--- a/include/dx2/imageset.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#pragma once
-#include <nlohmann/json.hpp>
-
-using Eigen::Vector3d;
-using json = nlohmann::json;
-
-class ImageSequence {
-public:
-    ImageSequence() = default;
-    ImageSequence(std::string filename, int n_images);
-    json to_json() const;
-protected:
-    int n_images_ {};
-    std::string filename_ {};
-    std::vector<std::size_t> single_file_indices_{};
-};
-
-ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(filename), n_images_(n_images) {
-    single_file_indices_.reserve(n_images_);
-    for (std::size_t i=0;i<n_images_;++i){
-        single_file_indices_.push_back(i);
-    }
-}
-
-json ImageSequence::to_json() const {
-    json imageset_data;
-    imageset_data["__id__"] = "ImageSequence";
-    imageset_data["template"] = filename_;
-    imageset_data["single_file_indices"] = single_file_indices_;
-    // Set defaults and null for now.
-    imageset_data["mask"] = nullptr;
-    imageset_data["gain"] = nullptr;
-    imageset_data["pedestal"] =nullptr;
-    imageset_data["dx"] = nullptr;
-    imageset_data["dy"] = nullptr;
-    json params;
-    params["dynamic_shadowing"] = "Auto";
-    params["multi_panel"] = false;
-    imageset_data["params"] = params;
-    return imageset_data;
-}
\ No newline at end of file

From 35238776e5b6866967eedd3770fd00691f13a458 Mon Sep 17 00:00:00 2001
From: James Beilsten-Edmands
 <30625594+jbeilstenedmands@users.noreply.github.com>
Date: Mon, 17 Nov 2025 14:32:35 +0000
Subject: [PATCH 3/4] Move ersatz_uuid function into utils, split into header
 and implementation.

---
 dx2/CMakeLists.txt            |  1 +
 dx2/imagesequence.cxx         | 31 ++++++++++------
 dx2/reflection.cxx            | 27 +-------------
 dx2/utils.cxx                 | 68 +++++++++++++++++++++++++++++++++++
 include/dx2/experiment.hpp    |  7 ++++
 include/dx2/imagesequence.hpp |  3 +-
 include/dx2/reflection.hpp    | 21 -----------
 include/dx2/utils.hpp         | 18 ++--------
 8 files changed, 102 insertions(+), 74 deletions(-)
 create mode 100644 dx2/utils.cxx

diff --git a/dx2/CMakeLists.txt b/dx2/CMakeLists.txt
index 877c607..bf28b2e 100644
--- a/dx2/CMakeLists.txt
+++ b/dx2/CMakeLists.txt
@@ -1,5 +1,6 @@
 add_library(
     dx2
+    utils.cxx
     reflection.cxx
     h5/h5read_processed.cxx
     h5/h5write.cxx
diff --git a/dx2/imagesequence.cxx b/dx2/imagesequence.cxx
index e15c7e4..33455ca 100644
--- a/dx2/imagesequence.cxx
+++ b/dx2/imagesequence.cxx
@@ -2,6 +2,7 @@
 
 using json = nlohmann::json;
 
+// Constructor for MultiImage formats e.g. h5.
 ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(filename), n_images_(n_images) {
     single_file_indices_.reserve(n_images_);
     for (std::size_t i=0;i<n_images_;++i){
@@ -9,8 +10,11 @@ ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(fil
     }
 }
 
+// Constructor for non-MultiImage formats e.g. cbf.
+ImageSequence::ImageSequence(std::string filename) : filename_(filename) {}
+
 ImageSequence::ImageSequence(json imagesequence_data) {
-    std::vector<std::string> required_keys = {"template", "single_file_indices", "__id__"};
+    std::vector<std::string> required_keys = {"template", "__id__"};
     for (const auto &key : required_keys) {
         if (imagesequence_data.find(key) == imagesequence_data.end()) {
             throw std::invalid_argument("Key " + key +
@@ -21,16 +25,19 @@ ImageSequence::ImageSequence(json imagesequence_data) {
         throw std::runtime_error("Only ImageSequences are supported");
     }
     filename_ = imagesequence_data["template"];
-    json indices = imagesequence_data["single_file_indices"];
-    single_file_indices_ = {};
-    if (*(indices.begin()) < 0){
-        throw std::runtime_error("Starting file index <0");
-    }
-    for (json::iterator it = indices.begin(); it != indices.end();
-        ++it) {
-        single_file_indices_.push_back(*it);
+    if (imagesequence_data.find("single_file_indices") != imagesequence_data.end()) {
+        // for non-multimage formats (e.g. non-h5), allow parsing.
+        json indices = imagesequence_data["single_file_indices"];
+        single_file_indices_ = {};
+        if (*(indices.begin()) < 0){
+            throw std::runtime_error("Starting file index <0");
+        }
+        for (json::iterator it = indices.begin(); it != indices.end();
+            ++it) {
+            single_file_indices_.push_back(*it);
+        }
+        n_images_ = single_file_indices_.size();
     }
-    n_images_ = single_file_indices_.size();
     imagesequence_data_ = imagesequence_data; // To propagate during serialization/deserialization.
 }
 
@@ -38,7 +45,9 @@ json ImageSequence::to_json() const {
     json imageset_data = imagesequence_data_;
     imageset_data["__id__"] = "ImageSequence";
     imageset_data["template"] = filename_;
-    imageset_data["single_file_indices"] = single_file_indices_;
+    if (single_file_indices_.size() > 0){ // i.e. MultiImage formats (h5).
+        imageset_data["single_file_indices"] = single_file_indices_;
+    }
     // Set defaults and null for now.
     std::vector<std::string> optional_keys = {"mask", "gain", "pedestal", "dx", "dy"};
     for (const auto &key : optional_keys) {
diff --git a/dx2/reflection.cxx b/dx2/reflection.cxx
index df0cc01..369efcc 100644
--- a/dx2/reflection.cxx
+++ b/dx2/reflection.cxx
@@ -4,6 +4,7 @@
  */
 
 #include "dx2/reflection.hpp"
+#include "dx2/utils.hpp"
 #include <algorithm>
 #include <chrono>
 #include <unordered_set>
@@ -142,32 +143,6 @@ void ReflectionTable::merge_into_set(std::unordered_set<size_t> &set,
                                      const std::vector<size_t> &rows) const {
   set.insert(rows.begin(), rows.end());
 }
-
-std::string ReflectionTable::ersatz_uuid4() const {
-  // Generate 16 random bytes
-  std::array<unsigned char, 16> bytes;
-  std::random_device rd;
-  std::uniform_int_distribution<int> dist(0, 255);
-  for (auto &b : bytes) {
-    b = static_cast<unsigned char>(dist(rd));
-  }
-
-  // Convert bytes to a single 128-bit hex string (little endian)
-  std::ostringstream oss;
-  for (auto it = bytes.rbegin(); it != bytes.rend(); ++it) {
-    oss << std::hex << std::setw(2) << std::setfill('0')
-        << static_cast<int>(*it);
-  }
-  std::string hex = oss.str();
-
-  // Format as UUID: 8-4-4-4-12
-  std::ostringstream uuid;
-  uuid << hex.substr(0, 8) << "-" << hex.substr(8, 4) << "-"
-       << hex.substr(12, 4) << "-" << hex.substr(16, 4) << "-"
-       << hex.substr(20, 12);
-
-  return uuid.str();
-}
 #pragma endregion
 
 #pragma region Selection Methods
diff --git a/dx2/utils.cxx b/dx2/utils.cxx
new file mode 100644
index 0000000..37adb67
--- /dev/null
+++ b/dx2/utils.cxx
@@ -0,0 +1,68 @@
+#include "dx2/utils.hpp"
+#include <Eigen/Dense>
+#include <math.h>
+#include <random>
+#include <sstream>
+#include <iomanip>
+
+using Eigen::Vector3d;
+
+double angle_between_vectors_degrees(Vector3d v1, Vector3d v2) {
+  double l1 = v1.norm();
+  double l2 = v2.norm();
+  double dot = v1.dot(v2);
+  double normdot = dot / (l1 * l2);
+  if (std::abs(normdot - 1.0) < 1E-6) {
+    return 0.0;
+  }
+  if (std::abs(normdot + 1.0) < 1E-6) {
+    return 180.0;
+  }
+  double angle = std::acos(normdot) * 180.0 / M_PI;
+  return angle;
+}
+
+/**
+   * @brief Generate a pseudo-random UUID-like identifier.
+   *
+   * This function replicates the behaviour of the Python function
+   * `ersatz_uuid4` from the dxtbx library. It generates a 128-bit
+   * random value and formats it as a UUID-style string using
+   * little-endian byte order, without enforcing RFC 4122 compliance.
+   *
+   * The output is a 36-character string in the format:
+   * `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx`, where each `x` is a
+   * hexadecimal digit.
+   *
+   * @return A string representing the generated UUID-like identifier.
+   *
+   * @note This function does not set the version or variant bits as
+   *       specified in RFC 4122. It is intended for internal use where
+   *       uniqueness is sufficient, and compliance with UUID standards
+   *       is unnecessary.
+   */
+std::string ersatz_uuid4() {
+  // Generate 16 random bytes
+  std::array<unsigned char, 16> bytes;
+  std::random_device rd;
+  std::uniform_int_distribution<int> dist(0, 255);
+  for (auto &b : bytes) {
+    b = static_cast<unsigned char>(dist(rd));
+  }
+
+  // Convert bytes to a single 128-bit hex string (little endian)
+  std::ostringstream oss;
+  for (auto it = bytes.rbegin(); it != bytes.rend(); ++it) {
+    oss << std::hex << std::setw(2) << std::setfill('0')
+        << static_cast<int>(*it);
+  }
+  std::string hex = oss.str();
+
+  // Format as UUID: 8-4-4-4-12
+  std::ostringstream uuid;
+  uuid << hex.substr(0, 8) << "-" << hex.substr(8, 4) << "-"
+       << hex.substr(12, 4) << "-" << hex.substr(16, 4) << "-"
+       << hex.substr(20, 12);
+
+  return uuid.str();
+}
\ No newline at end of file
diff --git a/include/dx2/experiment.hpp b/include/dx2/experiment.hpp
index a4e2345..70fc361 100644
--- a/include/dx2/experiment.hpp
+++ b/include/dx2/experiment.hpp
@@ -5,6 +5,7 @@
 #include <dx2/detector.hpp>
 #include <dx2/goniometer.hpp>
 #include <dx2/scan.hpp>
+#include <dx2/utils.hpp>
 #include <dx2/imagesequence.hpp>
 #include <nlohmann/json.hpp>
 
@@ -29,6 +30,7 @@ template <class BeamType> class Experiment {
   void set_goniometer(Goniometer goniometer);
   void set_imagesequence(ImageSequence imagesequence);
   void set_identifier(std::string identifier);
+  void generate_identifier();
 
 protected:
   BeamType _beam{};
@@ -157,4 +159,9 @@ const std::string &Experiment<BeamType>::identifier() const {
 template <class BeamType>
 void Experiment<BeamType>::set_identifier(std::string identifier) {
   _identifier = identifier;
+}
+
+template <class BeamType>
+void Experiment<BeamType>::generate_identifier() {
+  _identifier = ersatz_uuid4();
 }
\ No newline at end of file
diff --git a/include/dx2/imagesequence.hpp b/include/dx2/imagesequence.hpp
index b3935df..6eea2fa 100644
--- a/include/dx2/imagesequence.hpp
+++ b/include/dx2/imagesequence.hpp
@@ -6,7 +6,8 @@ using json = nlohmann::json;
 class ImageSequence {
 public:
     ImageSequence() = default;
-    ImageSequence(std::string filename, int n_images);
+    ImageSequence(std::string filename, int n_images); // Constructor for MultiImage formats e.g. h5.
+    ImageSequence(std::string filename); // Constructor for non-MultiImage formats e.g. cbf.
     ImageSequence(json imagesequence_data);
     json to_json() const;
 protected:
diff --git a/include/dx2/reflection.hpp b/include/dx2/reflection.hpp
index 5563f76..4a9c468 100644
--- a/include/dx2/reflection.hpp
+++ b/include/dx2/reflection.hpp
@@ -316,27 +316,6 @@ class ReflectionTable {
   template <typename T>
   struct is_column_predicate<ColumnPredicate<T>> : std::true_type {};
 
-  /**
-   * @brief Generate a pseudo-random UUID-like identifier.
-   *
-   * This function replicates the behaviour of the Python function
-   * `ersatz_uuid4` from the dxtbx library. It generates a 128-bit
-   * random value and formats it as a UUID-style string using
-   * little-endian byte order, without enforcing RFC 4122 compliance.
-   *
-   * The output is a 36-character string in the format:
-   * `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx`, where each `x` is a
-   * hexadecimal digit.
-   *
-   * @return A string representing the generated UUID-like identifier.
-   *
-   * @note This function does not set the version or variant bits as
-   *       specified in RFC 4122. It is intended for internal use where
-   *       uniqueness is sufficient, and compliance with UUID standards
-   *       is unnecessary.
-   */
-  std::string ersatz_uuid4() const;
-
 public:
 #pragma region Constructors
   /// Re-exported type aliase for convenience
diff --git a/include/dx2/utils.hpp b/include/dx2/utils.hpp
index 65079b4..a0ea002 100644
--- a/include/dx2/utils.hpp
+++ b/include/dx2/utils.hpp
@@ -1,20 +1,8 @@
 #pragma once
 #include <Eigen/Dense>
-#include <math.h>
 
 using Eigen::Vector3d;
 
-double angle_between_vectors_degrees(Vector3d v1, Vector3d v2) {
-  double l1 = v1.norm();
-  double l2 = v2.norm();
-  double dot = v1.dot(v2);
-  double normdot = dot / (l1 * l2);
-  if (std::abs(normdot - 1.0) < 1E-6) {
-    return 0.0;
-  }
-  if (std::abs(normdot + 1.0) < 1E-6) {
-    return 180.0;
-  }
-  double angle = std::acos(normdot) * 180.0 / M_PI;
-  return angle;
-}
+double angle_between_vectors_degrees(Vector3d v1, Vector3d v2);
+
+std::string ersatz_uuid4();
\ No newline at end of file

From 076d42565f7833ba3f34275d655bf5ec0a4a0638 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 18 Nov 2025 09:31:18 +0000
Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dx2/imagesequence.cxx         | 95 ++++++++++++++++++-----------------
 dx2/utils.cxx                 | 38 +++++++-------
 include/dx2/experiment.hpp    | 11 ++--
 include/dx2/imagesequence.hpp | 22 ++++----
 4 files changed, 85 insertions(+), 81 deletions(-)

diff --git a/dx2/imagesequence.cxx b/dx2/imagesequence.cxx
index 33455ca..3205a56 100644
--- a/dx2/imagesequence.cxx
+++ b/dx2/imagesequence.cxx
@@ -3,63 +3,66 @@
 using json = nlohmann::json;
 
 // Constructor for MultiImage formats e.g. h5.
-ImageSequence::ImageSequence(std::string filename, int n_images) : filename_(filename), n_images_(n_images) {
-    single_file_indices_.reserve(n_images_);
-    for (std::size_t i=0;i<n_images_;++i){
-        single_file_indices_.push_back(i);
-    }
+ImageSequence::ImageSequence(std::string filename, int n_images)
+    : filename_(filename), n_images_(n_images) {
+  single_file_indices_.reserve(n_images_);
+  for (std::size_t i = 0; i < n_images_; ++i) {
+    single_file_indices_.push_back(i);
+  }
 }
 
 // Constructor for non-MultiImage formats e.g. cbf.
 ImageSequence::ImageSequence(std::string filename) : filename_(filename) {}
 
 ImageSequence::ImageSequence(json imagesequence_data) {
-    std::vector<std::string> required_keys = {"template", "__id__"};
-    for (const auto &key : required_keys) {
-        if (imagesequence_data.find(key) == imagesequence_data.end()) {
-            throw std::invalid_argument("Key " + key +
-                                       " is missing from the input imageset JSON");
-        }
+  std::vector<std::string> required_keys = {"template", "__id__"};
+  for (const auto &key : required_keys) {
+    if (imagesequence_data.find(key) == imagesequence_data.end()) {
+      throw std::invalid_argument("Key " + key +
+                                  " is missing from the input imageset JSON");
     }
-    if (imagesequence_data["__id__"] != std::string("ImageSequence")){
-        throw std::runtime_error("Only ImageSequences are supported");
+  }
+  if (imagesequence_data["__id__"] != std::string("ImageSequence")) {
+    throw std::runtime_error("Only ImageSequences are supported");
+  }
+  filename_ = imagesequence_data["template"];
+  if (imagesequence_data.find("single_file_indices") !=
+      imagesequence_data.end()) {
+    // for non-multimage formats (e.g. non-h5), allow parsing.
+    json indices = imagesequence_data["single_file_indices"];
+    single_file_indices_ = {};
+    if (*(indices.begin()) < 0) {
+      throw std::runtime_error("Starting file index <0");
     }
-    filename_ = imagesequence_data["template"];
-    if (imagesequence_data.find("single_file_indices") != imagesequence_data.end()) {
-        // for non-multimage formats (e.g. non-h5), allow parsing.
-        json indices = imagesequence_data["single_file_indices"];
-        single_file_indices_ = {};
-        if (*(indices.begin()) < 0){
-            throw std::runtime_error("Starting file index <0");
-        }
-        for (json::iterator it = indices.begin(); it != indices.end();
-            ++it) {
-            single_file_indices_.push_back(*it);
-        }
-        n_images_ = single_file_indices_.size();
+    for (json::iterator it = indices.begin(); it != indices.end(); ++it) {
+      single_file_indices_.push_back(*it);
     }
-    imagesequence_data_ = imagesequence_data; // To propagate during serialization/deserialization.
+    n_images_ = single_file_indices_.size();
+  }
+  imagesequence_data_ =
+      imagesequence_data; // To propagate during serialization/deserialization.
 }
 
 json ImageSequence::to_json() const {
-    json imageset_data = imagesequence_data_;
-    imageset_data["__id__"] = "ImageSequence";
-    imageset_data["template"] = filename_;
-    if (single_file_indices_.size() > 0){ // i.e. MultiImage formats (h5).
-        imageset_data["single_file_indices"] = single_file_indices_;
-    }
-    // Set defaults and null for now.
-    std::vector<std::string> optional_keys = {"mask", "gain", "pedestal", "dx", "dy"};
-    for (const auto &key : optional_keys) {
-        if (imagesequence_data_.find(key) == imagesequence_data_.end()) {
-            imageset_data[key] = nullptr;
-        }
-    }
-    if (imagesequence_data_.find("params") == imagesequence_data_.end()) {
-        json params;
-        params["dynamic_shadowing"] = "Auto";
-        params["multi_panel"] = false;
-        imageset_data["params"] = params;
+  json imageset_data = imagesequence_data_;
+  imageset_data["__id__"] = "ImageSequence";
+  imageset_data["template"] = filename_;
+  if (single_file_indices_.size() > 0) { // i.e. MultiImage formats (h5).
+    imageset_data["single_file_indices"] = single_file_indices_;
+  }
+  // Set defaults and null for now.
+  std::vector<std::string> optional_keys = {"mask", "gain", "pedestal", "dx",
+                                            "dy"};
+  for (const auto &key : optional_keys) {
+    if (imagesequence_data_.find(key) == imagesequence_data_.end()) {
+      imageset_data[key] = nullptr;
     }
-    return imageset_data;
+  }
+  if (imagesequence_data_.find("params") == imagesequence_data_.end()) {
+    json params;
+    params["dynamic_shadowing"] = "Auto";
+    params["multi_panel"] = false;
+    imageset_data["params"] = params;
+  }
+  return imageset_data;
 }
\ No newline at end of file
diff --git a/dx2/utils.cxx b/dx2/utils.cxx
index 37adb67..48c12f0 100644
--- a/dx2/utils.cxx
+++ b/dx2/utils.cxx
@@ -1,9 +1,9 @@
 #include "dx2/utils.hpp"
 #include <Eigen/Dense>
+#include <iomanip>
 #include <math.h>
 #include <random>
 #include <sstream>
-#include <iomanip>
 
 using Eigen::Vector3d;
 
@@ -23,24 +23,24 @@ double angle_between_vectors_degrees(Vector3d v1, Vector3d v2) {
 }
 
 /**
-   * @brief Generate a pseudo-random UUID-like identifier.
-   *
-   * This function replicates the behaviour of the Python function
-   * `ersatz_uuid4` from the dxtbx library. It generates a 128-bit
-   * random value and formats it as a UUID-style string using
-   * little-endian byte order, without enforcing RFC 4122 compliance.
-   *
-   * The output is a 36-character string in the format:
-   * `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx`, where each `x` is a
-   * hexadecimal digit.
-   *
-   * @return A string representing the generated UUID-like identifier.
-   *
-   * @note This function does not set the version or variant bits as
-   *       specified in RFC 4122. It is intended for internal use where
-   *       uniqueness is sufficient, and compliance with UUID standards
-   *       is unnecessary.
-   */
+ * @brief Generate a pseudo-random UUID-like identifier.
+ *
+ * This function replicates the behaviour of the Python function
+ * `ersatz_uuid4` from the dxtbx library. It generates a 128-bit
+ * random value and formats it as a UUID-style string using
+ * little-endian byte order, without enforcing RFC 4122 compliance.
+ *
+ * The output is a 36-character string in the format:
+ * `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx`, where each `x` is a
+ * hexadecimal digit.
+ *
+ * @return A string representing the generated UUID-like identifier.
+ *
+ * @note This function does not set the version or variant bits as
+ *       specified in RFC 4122. It is intended for internal use where
+ *       uniqueness is sufficient, and compliance with UUID standards
+ *       is unnecessary.
+ */
 std::string ersatz_uuid4() {
   // Generate 16 random bytes
   std::array<unsigned char, 16> bytes;
diff --git a/include/dx2/experiment.hpp b/include/dx2/experiment.hpp
index 70fc361..8d9bd91 100644
--- a/include/dx2/experiment.hpp
+++ b/include/dx2/experiment.hpp
@@ -4,9 +4,9 @@
 #include <dx2/crystal.hpp>
 #include <dx2/detector.hpp>
 #include <dx2/goniometer.hpp>
+#include <dx2/imagesequence.hpp>
 #include <dx2/scan.hpp>
 #include <dx2/utils.hpp>
-#include <dx2/imagesequence.hpp>
 #include <nlohmann/json.hpp>
 
 using Eigen::Vector3d;
@@ -123,8 +123,7 @@ void Experiment<BeamType>::set_crystal(Crystal crystal) {
   _crystal = crystal;
 }
 
-template <class BeamType>
-void Experiment<BeamType>::set_beam(BeamType beam) {
+template <class BeamType> void Experiment<BeamType>::set_beam(BeamType beam) {
   _beam = beam;
 }
 
@@ -132,8 +131,7 @@ template <class BeamType> BeamType &Experiment<BeamType>::beam() {
   return _beam;
 }
 
-template <class BeamType>
-void Experiment<BeamType>::set_scan(Scan scan) {
+template <class BeamType> void Experiment<BeamType>::set_scan(Scan scan) {
   _scan = scan;
 }
 
@@ -161,7 +159,6 @@ void Experiment<BeamType>::set_identifier(std::string identifier) {
   _identifier = identifier;
 }
 
-template <class BeamType>
-void Experiment<BeamType>::generate_identifier() {
+template <class BeamType> void Experiment<BeamType>::generate_identifier() {
   _identifier = ersatz_uuid4();
 }
\ No newline at end of file
diff --git a/include/dx2/imagesequence.hpp b/include/dx2/imagesequence.hpp
index 6eea2fa..a386472 100644
--- a/include/dx2/imagesequence.hpp
+++ b/include/dx2/imagesequence.hpp
@@ -5,14 +5,18 @@ using json = nlohmann::json;
 
 class ImageSequence {
 public:
-    ImageSequence() = default;
-    ImageSequence(std::string filename, int n_images); // Constructor for MultiImage formats e.g. h5.
-    ImageSequence(std::string filename); // Constructor for non-MultiImage formats e.g. cbf.
-    ImageSequence(json imagesequence_data);
-    json to_json() const;
+  ImageSequence() = default;
+  ImageSequence(std::string filename,
+                int n_images); // Constructor for MultiImage formats e.g. h5.
+  ImageSequence(
+      std::string filename); // Constructor for non-MultiImage formats e.g. cbf.
+  ImageSequence(json imagesequence_data);
+  json to_json() const;
+
 protected:
-    int n_images_ {};
-    std::string filename_ {};
-    std::vector<std::size_t> single_file_indices_{};
-    json imagesequence_data_ {}; // For propagating additional metadata during serialization/deserialization.
+  int n_images_{};
+  std::string filename_{};
+  std::vector<std::size_t> single_file_indices_{};
+  json imagesequence_data_{}; // For propagating additional metadata during
+                              // serialization/deserialization.
 };
\ No newline at end of file