merge from formatted main

.github/workflows/build_docs.yml

@@ -2,7 +2,10 @@ name: Build the package using cmake then documentation
 
 on:
   workflow_dispatch:
-  push:
+  pull_request:
+  release:
+    types:
+      - published
     
 
 permissions:
@@ -55,7 +58,7 @@ jobs:
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
     needs: build
-    if: github.event_name == 'release' && github.event.action == 'published'
+    if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'workflow_dispatch' )
     steps:
       - name: Deploy to GitHub Pages
         id: deployment

RELEASE.md

@@ -0,0 +1,22 @@
+# Release notes
+
+
+### head
+
+Features:
+
+- Cluster finder now works with 5x5, 7x7 and 9x9 clusters
+
+
+### 2025.05.22
+
+Features:
+
+- Added scurve fitting
+
+Bugfixes:
+
+- Fixed crash when opening raw files with large number of data files
+
+
+

benchmarks/calculateeta_benchmark.cpp

@@ -41,8 +41,8 @@ BENCHMARK_F(ClusterFixture, Calculate2x2Eta)(benchmark::State &st) {
 }
 
 // almost takes double the time
-BENCHMARK_F(ClusterFixture,
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor2x2Cluster)
-            CalculateGeneralEtaFor2x2Cluster)(benchmark::State &st) {
+(benchmark::State &st) {
     for (auto _ : st) {
         // This code gets timed
         Eta2 eta = calculate_eta2<int, 2, 2>(cluster_2x2);
@@ -59,8 +59,8 @@ BENCHMARK_F(ClusterFixture, Calculate3x3Eta)(benchmark::State &st) {
 }
 
 // almost takes double the time
-BENCHMARK_F(ClusterFixture,
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor3x3Cluster)
-            CalculateGeneralEtaFor3x3Cluster)(benchmark::State &st) {
+(benchmark::State &st) {
     for (auto _ : st) {
         // This code gets timed
         Eta2 eta = calculate_eta2<int, 3, 3>(cluster_3x3);

benchmarks/ndarray_benchmark.cpp

@@ -1,6 +1,5 @@
-#include <benchmark/benchmark.h>
 #include "aare/NDArray.hpp"
-
+#include <benchmark/benchmark.h>
 
 using aare::NDArray;
 
@@ -22,9 +21,6 @@ public:
     // }
 };
 
-
-
-
 BENCHMARK_F(TwoArrays, AddWithOperator)(benchmark::State &st) {
     for (auto _ : st) {
         // This code gets timed

docs/src/Philosophy.rst

@@ -0,0 +1,47 @@
+****************
+Philosophy
+****************
+
+
+Fast code with a simple interface
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Aare should be fast and efficient, but also easy to use. We strive to keep a simple interface that feels intuitive. 
+Internally we use C++ for performance and the ability to integrate the library in other programs, but we see most 
+users using the Python interface. 
+
+Live at head
+~~~~~~~~~~~~~~~~~~
+
+As a user of the library you should be able to, and is expected to, use the latest version. Bug fixes will rarely be backported
+to older releases. By upgrading frequently you will benefit from the latest features and minimize the effort to maintain your scripts/code 
+by doing several small upgrades instead of one big upgrade.
+
+API
+~~~~~~~~~~~~~~~~~~
+
+We aim to keep the API stable and only break it for good reasons. But specially now in the early stages of development
+the API will change. On those occasions it will be clearly stated in the release notes. However, the norm should be a 
+backward compatible API.
+
+Documentation
+~~~~~~~~~~~~~~~~~~
+
+Being a library it is important to have a well documented API. We use Doxygen to generate the C++ documentation
+and Sphinx for the Python part. Breathe is used to integrate the two into one Sphinx html site. The documentation is built
+automatically on release by the CI and published to GitHub pages. In addition to the generated API documentation,
+certain classes might need more descriptions of the usage. This is then placed in the .rst files in the docs/src directory.
+
+.. attention::
+
+    The code should be well documented, but using descriptive names is more important. In the same spirit
+    if a function is called `getNumberOfFrames()` you don't need to write a comment saying that it gets the 
+    number of frames.
+
+
+Dependencies
+~~~~~~~~~~~~~~~~~~
+
+Deployment in the scientific community is often tricky. Either due to old OS versions or the lack of package managers. 
+We strive to keep the dependencies to a minimum and will vendor some libraries to simplify deployment even though it comes
+at a cost of build time.

docs/src/Requirements.rst

@@ -2,18 +2,21 @@ Requirements
 ==============================================
 
 - C++17 compiler (gcc 8/clang 7)
-- CMake 3.14+
+- CMake 3.15+
 
 **Internally used libraries**
 
 .. note ::
 
-    These can also be picked up from the system/conda environment by specifying:
+    To save compile time some of the dependencies can also be picked up from the system/conda environment by specifying:
     -DAARE_SYSTEM_LIBRARIES=ON during the cmake configuration.
 
-- pybind11
+To simplify deployment we build and statically link a few libraries.
+
 - fmt
+- lmfit - https://jugit.fz-juelich.de/mlz/lmfit
 - nlohmann_json
+- pybind11
 - ZeroMQ
 
 **Extra dependencies for building documentation**

docs/src/Workflow.rst

@@ -0,0 +1,86 @@
+****************
+Workflow
+****************
+
+This page describes how we develop aare. 
+
+GitHub centric
+~~~~~~~~~~~~~~~~~~
+
+We use GitHub for all development. Issues and pull requests provide a platform for collaboration as well
+as a record of the development process. Even if we discuss things in person, we record the outcome in an issue.
+If a particular implementation is chosen over another, the reason should be recorded in the pull request.
+
+
+Branches
+~~~~~~~~~~~~~~~~~~
+
+We aim for an as lightweight branching strategy as possible. Short-lived feature branches are merged back into main. 
+The main branch is expected to always be in a releasable state. A release is simply a tag on main which provides a
+reference and triggers the CI to build the release artifacts (conda, pypi etc.). For large features consider merging
+smaller chunks into main as they are completed, rather than waiting for the entire feature to be finished. Worst case 
+make sure your feature branch merges with main regularly to avoid large merge conflicts later on.
+
+.. note::
+
+    The main branch is expected to always work. Feel free to pull from main instead of sticking to a 
+    release
+
+
+Releases
+~~~~~~~~~~~~~~~~~~
+
+Release early, release often. As soon as "enough" new features have been implemented, a release is created.
+A release should not be a big thing, rather a routine part of development that does not require any special person or
+unfamiliar steps.
+
+
+
+Checklists for deployment
+~~~~~~~~~~~~~~~~~~
+
+**Feature:**
+
+#. Create a new issue for the feature (label feature)
+#. Create a new branch from main.
+#. Implement the feature including test and documentation
+#. Add the feature to RELEASE.md under head
+#. Create a pull request linked to the issue
+#. Code is reviewed by at least one other person
+#. Once approved, the branch is merged into main
+
+
+**BugFix:**
+
+Essentially the same as for a feature, if possible start with
+a failing test that demonstrates the bug.
+
+#. Create a new issue for the bug (label bug)
+#. Create a new branch from main.
+#. **Write a test that fails for the bug**
+#. Implement the fix
+#. **Run the test to ensure it passes**
+#. Add the bugfix to RELEASE.md under head
+#. Create a pull request linked to the issue.
+#. Code is reviewed by at least one other person
+#. Once approved, the branch is merged into main
+
+**Release:**
+
+#. Once "enough" new features have been implemented, a release is created
+#. Update RELEASE.md with the tag of the release and verify that it is complete
+#. Create the release in GitHub describing the new features and bug fixes
+#. CI makes magic
+
+
+**Update documentation only:**
+
+.. attention::
+
+    It's possible to update the documentation without changing the code, but take
+    care since the docs will reflect the code in main and not the latest release.
+
+#. Create a PR to main with the documentation changes
+#. Create a pull request linked to the issue.
+#. Code is reviewed by at least one other person
+#. Once merged you can manually trigger the CI workflow for documentation

docs/src/index.rst

@@ -67,4 +67,6 @@ AARE
     :caption: Developer
     :maxdepth: 3
     
+    Philosophy
+    Workflow
     Tests

include/aare/ArrayExpr.hpp

@@ -1,10 +1,9 @@
 #pragma once
-#include <cstdint> 
+#include "aare/defs.hpp"
-#include <cstddef> 
 #include <array>
 #include <cassert>
-#include "aare/defs.hpp"
+#include <cstddef>
-
+#include <cstdint>
 
 namespace aare {
 
@@ -15,7 +14,9 @@ template <typename E, ssize_t Ndim> class ArrayExpr {
     auto operator[](size_t i) const { return static_cast<E const &>(*this)[i]; }
     auto operator()(size_t i) const { return static_cast<E const &>(*this)[i]; }
     auto size() const { return static_cast<E const &>(*this).size(); }
-    std::array<ssize_t, Ndim> shape() const { return static_cast<E const &>(*this).shape(); }
+    std::array<ssize_t, Ndim> shape() const {
+        return static_cast<E const &>(*this).shape();
+    }
 };
 
 template <typename A, typename B, ssize_t Ndim>
@@ -74,8 +75,6 @@ class ArrayDiv : public ArrayExpr<ArrayDiv<A, B, Ndim>, Ndim> {
     std::array<ssize_t, Ndim> shape() const { return arr1_.shape(); }
 };
 
-
-
 template <typename A, typename B, ssize_t Ndim>
 auto operator+(const ArrayExpr<A, Ndim> &arr1, const ArrayExpr<B, Ndim> &arr2) {
     return ArrayAdd<ArrayExpr<A, Ndim>, ArrayExpr<B, Ndim>, Ndim>(arr1, arr2);
@@ -96,6 +95,4 @@ auto operator/(const ArrayExpr<A, Ndim> &arr1, const ArrayExpr<B, Ndim> &arr2) {
     return ArrayDiv<ArrayExpr<A, Ndim>, ArrayExpr<B, Ndim>, Ndim>(arr1, arr2);
 }
 
-
-
 } // namespace aare

include/aare/CircularFifo.hpp

@@ -17,7 +17,8 @@ template <class ItemType> class CircularFifo {
 
   public:
     CircularFifo() : CircularFifo(100){};
-    CircularFifo(uint32_t size) : fifo_size(size), free_slots(size + 1), filled_slots(size + 1) {
+    CircularFifo(uint32_t size)
+        : fifo_size(size), free_slots(size + 1), filled_slots(size + 1) {
 
         // TODO! how do we deal with alignment for writing? alignas???
         // Do we give the user a chance to provide memory locations?
@@ -55,7 +56,8 @@ template <class ItemType> class CircularFifo {
 
     bool try_pop_free(ItemType &v) { return free_slots.read(v); }
 
-    ItemType pop_value(std::chrono::nanoseconds wait, std::atomic<bool> &stopped) {
+    ItemType pop_value(std::chrono::nanoseconds wait,
+                       std::atomic<bool> &stopped) {
         ItemType v;
         while (!filled_slots.read(v) && !stopped) {
             std::this_thread::sleep_for(wait);

include/aare/ClusterFile.hpp

@@ -371,8 +371,8 @@ ClusterFile<ClusterType, Enable>::read_frame_without_cut() {
                                  "Could not read number of clusters");
     }
 
-    LOG(logDEBUG1) << "Reading " << n_clusters
+    LOG(logDEBUG1) << "Reading " << n_clusters << " clusters from frame "
-                  << " clusters from frame " << frame_number;
+                   << frame_number;
 
     ClusterVector<ClusterType> clusters(n_clusters);
     clusters.set_frame_number(frame_number);

include/aare/ClusterFinder.hpp

@@ -41,8 +41,7 @@ class ClusterFinder {
           m_pedestal(image_size[0], image_size[1]), m_clusters(capacity) {
         LOG(logDEBUG) << "ClusterFinder: "
                       << "image_size: " << image_size[0] << "x" << image_size[1]
-                       << ", nSigma: " << nSigma
+                      << ", nSigma: " << nSigma << ", capacity: " << capacity;
-                       << ", capacity: " << capacity;
     }
 
     void push_pedestal_frame(NDView<FRAME_TYPE, 2> frame) {

include/aare/ClusterFinderMT.hpp

@@ -7,8 +7,8 @@
 
 #include "aare/ClusterFinder.hpp"
 #include "aare/NDArray.hpp"
-#include "aare/logger.hpp"
 #include "aare/ProducerConsumerQueue.hpp"
+#include "aare/logger.hpp"
 
 namespace aare {
 
@@ -125,8 +125,8 @@ class ClusterFinderMT {
         : m_n_threads(n_threads) {
 
         LOG(logDEBUG1) << "ClusterFinderMT: "
-            << "image_size: " << image_size[0] << "x" << image_size[1]
+                       << "image_size: " << image_size[0] << "x"
-            << ", nSigma: " << nSigma
+                       << image_size[1] << ", nSigma: " << nSigma
                        << ", capacity: " << capacity
                        << ", n_threads: " << n_threads;
 

include/aare/CtbRawFile.hpp

@@ -1,21 +1,21 @@
 #pragma once
 
 #include "aare/FileInterface.hpp"
-#include "aare/RawMasterFile.hpp"
 #include "aare/Frame.hpp"
+#include "aare/RawMasterFile.hpp"
 
 #include <filesystem>
 #include <fstream>
 
 namespace aare {
 
-
 class CtbRawFile {
     RawMasterFile m_master;
     std::ifstream m_file;
     size_t m_current_frame{0};
     size_t m_current_subfile{0};
     size_t m_num_subfiles{0};
+
   public:
     CtbRawFile(const std::filesystem::path &fname);
 
@@ -29,13 +29,13 @@ public:
     size_t frames_in_file() const;
 
     RawMasterFile master() const;
+
   private:
     void find_subfiles();
     size_t sub_file_index(size_t frame_index) const {
         return frame_index / m_master.max_frames_per_file();
     }
     void open_data_file(size_t subfile_index);
-
 };
 
-}
+} // namespace aare

include/aare/Dtype.hpp

@@ -6,31 +6,37 @@
 
 namespace aare {
 
-// The format descriptor is a single character that specifies the type of the data
+// The format descriptor is a single character that specifies the type of the
+// data
 // - python documentation: https://docs.python.org/3/c-api/arg.html#numbers
-// - py::format_descriptor<T>::format() (in pybind11) does not return the same format as
+// - py::format_descriptor<T>::format() (in pybind11) does not return the same
+// format as
 //   written in python.org documentation.
-// - numpy also doesn't use the same format. and also numpy associates the format
+// - numpy also doesn't use the same format. and also numpy associates the
-//   with variable bitdepth types. (e.g. long is int64 on linux64 and int32 on win64)
+// format
-//   https://numpy.org/doc/stable/reference/arrays.scalars.html
+//   with variable bitdepth types. (e.g. long is int64 on linux64 and int32 on
+//   win64) https://numpy.org/doc/stable/reference/arrays.scalars.html
 //
 // github issue discussing this:
 // https://github.com/pybind/pybind11/issues/1908#issuecomment-658358767
 //
-// [IN LINUX] the difference is for int64 (long) and uint64 (unsigned long). The format
+// [IN LINUX] the difference is for int64 (long) and uint64 (unsigned long). The
-// descriptor is 'q' and 'Q' respectively and in the documentation it is 'l' and 'k'.
+// format descriptor is 'q' and 'Q' respectively and in the documentation it is
+// 'l' and 'k'.
 
 // in practice numpy doesn't seem to care when reading buffer info: the library
 // interprets 'q' or 'l' as int64 and 'Q' or 'L' as uint64.
-// for this reason we decided to use the same format descriptor as pybind to avoid
+// for this reason we decided to use the same format descriptor as pybind to
-// any further discrepancies.
+// avoid any further discrepancies.
 
 // in the following order:
 // int8, uint8, int16, uint16, int32, uint32, int64, uint64, float, double
-const char DTYPE_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i', 'I', 'q', 'Q', 'f', 'd'};
+const char DTYPE_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i',
+                                 'I', 'q', 'Q', 'f', 'd'};
 
 // on linux64 & apple
-const char NUMPY_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i', 'I', 'l', 'L', 'f', 'd'};
+const char NUMPY_FORMAT_DSC[] = {'b', 'B', 'h', 'H', 'i',
+                                 'I', 'l', 'L', 'f', 'd'};
 /**
  * @brief enum class to define the endianess of the system
  */
@@ -52,12 +58,29 @@ enum class endian {
  */
 class Dtype {
   public:
-    enum TypeIndex { INT8, UINT8, INT16, UINT16, INT32, UINT32, INT64, UINT64, FLOAT, DOUBLE, ERROR, NONE };
+    enum TypeIndex {
+        INT8,
+        UINT8,
+        INT16,
+        UINT16,
+        INT32,
+        UINT32,
+        INT64,
+        UINT64,
+        FLOAT,
+        DOUBLE,
+        ERROR,
+        NONE
+    };
 
     uint8_t bitdepth() const;
     size_t bytes() const;
-    std::string format_descr() const { return std::string(1, DTYPE_FORMAT_DSC[static_cast<int>(m_type)]); }
+    std::string format_descr() const {
-    std::string numpy_descr() const { return std::string(1, NUMPY_FORMAT_DSC[static_cast<int>(m_type)]); }
+        return std::string(1, DTYPE_FORMAT_DSC[static_cast<int>(m_type)]);
+    }
+    std::string numpy_descr() const {
+        return std::string(1, NUMPY_FORMAT_DSC[static_cast<int>(m_type)]);
+    }
 
     explicit Dtype(const std::type_info &t);
     explicit Dtype(std::string_view sv);

include/aare/File.hpp

@@ -7,7 +7,11 @@ namespace aare {
 /**
  * @brief RAII File class for reading, and in the future potentially writing
  * image files in various formats. Minimal generic interface. For specail
+<<<<<<< HEAD
  * fuctions plase use the RawFile, NumpyFile or Hdf5File classes directly. Wraps
+=======
+ * fuctions plase use the RawFile or NumpyFile classes directly. Wraps
+>>>>>>> main
  * FileInterface to abstract the underlying file format
  * @note **frame_number** refers the the frame number sent by the detector while
  * **frame_index** is the position of the frame in the file
@@ -25,9 +29,11 @@ class File {
      * @throws std::invalid_argument if the file mode is not supported
      *
      */
-    File(const std::filesystem::path &fname, const std::string &mode="r", const FileConfig &cfg = {});
+    File(const std::filesystem::path &fname, const std::string &mode = "r",
+         const FileConfig &cfg = {});
 
-     /**Since the object is responsible for managing the file we disable copy construction */
+    /**Since the object is responsible for managing the file we disable copy
+     * construction */
     File(File const &other) = delete;
 
     /**The same goes for copy assignment */
@@ -39,15 +45,19 @@ class File {
 
     // void close();                             //!< close the file
 
-    Frame read_frame();                       //!< read one frame from the file at the current position
+    Frame
-    Frame read_frame(size_t frame_index);     //!< read one frame at the position given by frame number
+    read_frame(); //!< read one frame from the file at the current position
-    std::vector<Frame> read_n(size_t n_frames); //!< read n_frames from the file at the current position
+    Frame read_frame(size_t frame_index); //!< read one frame at the position
+                                          //!< given by frame number
+    std::vector<Frame> read_n(size_t n_frames); //!< read n_frames from the file
+                                                //!< at the current position
 
     void read_into(std::byte *image_buf);
     void read_into(std::byte *image_buf, size_t n_frames);
 
     size_t frame_number(); //!< get the frame number at the current position
-    size_t frame_number(size_t frame_index);  //!< get the frame number at the given frame index
+    size_t frame_number(
+        size_t frame_index); //!< get the frame number at the given frame index
     size_t bytes_per_frame() const;
     size_t pixels_per_frame() const;
     size_t bytes_per_pixel() const;
@@ -59,8 +69,6 @@ class File {
     size_t cols() const;
 
     DetectorType detector_type() const;
-
-    
 };
 
 } // namespace aare

include/aare/FileInterface.hpp

@@ -20,8 +20,10 @@ struct FileConfig {
     uint64_t rows{};
     uint64_t cols{};
     bool operator==(const FileConfig &other) const {
-        return dtype == other.dtype && rows == other.rows && cols == other.cols && geometry == other.geometry &&
+        return dtype == other.dtype && rows == other.rows &&
-               detector_type == other.detector_type && max_frames_per_file == other.max_frames_per_file;
+               cols == other.cols && geometry == other.geometry &&
+               detector_type == other.detector_type &&
+               max_frames_per_file == other.max_frames_per_file;
     }
     bool operator!=(const FileConfig &other) const { return !(*this == other); }
 
@@ -32,8 +34,11 @@ struct FileConfig {
     int max_frames_per_file{};
     size_t total_frames{};
     std::string to_string() const {
-        return "{ dtype: " + dtype.to_string() + ", rows: " + std::to_string(rows) + ", cols: " + std::to_string(cols) +
+        return "{ dtype: " + dtype.to_string() +
-               ", geometry: " + geometry.to_string() + ", detector_type: " + ToString(detector_type) +
+               ", rows: " + std::to_string(rows) +
+               ", cols: " + std::to_string(cols) +
+               ", geometry: " + geometry.to_string() +
+               ", detector_type: " + ToString(detector_type) +
                ", max_frames_per_file: " + std::to_string(max_frames_per_file) +
                ", total_frames: " + std::to_string(total_frames) + " }";
     }
@@ -65,17 +70,20 @@ class FileInterface {
      * @param n_frames number of frames to read
      * @return vector of frames
      */
-    virtual std::vector<Frame> read_n(size_t n_frames) = 0; // Is this the right interface?
+    virtual std::vector<Frame>
+    read_n(size_t n_frames) = 0; // Is this the right interface?
 
     /**
-     * @brief read one frame from the file at the current position and store it in the provided buffer
+     * @brief read one frame from the file at the current position and store it
+     * in the provided buffer
      * @param image_buf buffer to store the frame
      * @return void
      */
     virtual void read_into(std::byte *image_buf) = 0;
 
     /**
-     * @brief read n_frames from the file at the current position and store them in the provided buffer
+     * @brief read n_frames from the file at the current position and store them
+     * in the provided buffer
      * @param image_buf buffer to store the frames
      * @param n_frames number of frames to read
      * @return void
@@ -135,7 +143,6 @@ class FileInterface {
      */
     virtual size_t bitdepth() const = 0;
 
-
     virtual DetectorType detector_type() const = 0;
 
     // function to query the data type of the file

include/aare/Fit.hpp

@@ -23,16 +23,19 @@ NDArray<double, 1> scurve2(NDView<double, 1> x, NDView<double, 1> par);
 
 } // namespace func
 
-
 /**
  * @brief Estimate the initial parameters for a Gaussian fit
  */
-std::array<double, 3> gaus_init_par(const NDView<double, 1> x, const NDView<double, 1> y);
+std::array<double, 3> gaus_init_par(const NDView<double, 1> x,
+                                    const NDView<double, 1> y);
 
-std::array<double, 2> pol1_init_par(const NDView<double, 1> x, const NDView<double, 1> y);
+std::array<double, 2> pol1_init_par(const NDView<double, 1> x,
+                                    const NDView<double, 1> y);
 
-std::array<double, 6> scurve_init_par(const NDView<double, 1> x, const NDView<double, 1> y); 
+std::array<double, 6> scurve_init_par(const NDView<double, 1> x,
-std::array<double, 6> scurve2_init_par(const NDView<double, 1> x, const NDView<double, 1> y);
+                                      const NDView<double, 1> y);
+std::array<double, 6> scurve2_init_par(const NDView<double, 1> x,
+                                       const NDView<double, 1> y);
 
 static constexpr int DEFAULT_NUM_THREADS = 4;
 
@@ -43,7 +46,6 @@ static constexpr int DEFAULT_NUM_THREADS = 4;
  */
 NDArray<double, 1> fit_gaus(NDView<double, 1> x, NDView<double, 1> y);
 
-
 /**
  * @brief Fit a 1D Gaussian to each pixel. Data layout [row, col, values]
  * @param x x values
@@ -54,9 +56,6 @@ NDArray<double, 1> fit_gaus(NDView<double, 1> x, NDView<double, 1> y);
 NDArray<double, 3> fit_gaus(NDView<double, 1> x, NDView<double, 3> y,
                             int n_threads = DEFAULT_NUM_THREADS);
 
-
-
-
 /**
  * @brief Fit a 1D Gaussian with error estimates
  * @param x x values
@@ -80,9 +79,8 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
  * @param n_threads number of threads to use
  */
 void fit_gaus(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
-              int n_threads = DEFAULT_NUM_THREADS
+              NDView<double, 2> chi2_out, int n_threads = DEFAULT_NUM_THREADS);
-              );
 
 NDArray<double, 1> fit_pol1(NDView<double, 1> x, NDView<double, 1> y);
 
@@ -90,26 +88,33 @@ NDArray<double, 3> fit_pol1(NDView<double, 1> x, NDView<double, 3> y,
                             int n_threads = DEFAULT_NUM_THREADS);
 
 void fit_pol1(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2);
+              NDView<double, 1> par_out, NDView<double, 1> par_err_out,
+              double &chi2);
 
 // TODO! not sure we need to offer the different version in C++
 void fit_pol1(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out,NDView<double, 2> chi2_out,
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
-              int n_threads = DEFAULT_NUM_THREADS);
+              NDView<double, 2> chi2_out, int n_threads = DEFAULT_NUM_THREADS);
 
 NDArray<double, 1> fit_scurve(NDView<double, 1> x, NDView<double, 1> y);
-NDArray<double, 3> fit_scurve(NDView<double, 1> x, NDView<double, 3> y, int n_threads); 
+NDArray<double, 3> fit_scurve(NDView<double, 1> x, NDView<double, 3> y,
-void fit_scurve(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
+                              int n_threads);
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2); 
+void fit_scurve(NDView<double, 1> x, NDView<double, 1> y,
-void fit_scurve(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
+                NDView<double, 1> y_err, NDView<double, 1> par_out,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+                NDView<double, 1> par_err_out, double &chi2);
+void fit_scurve(NDView<double, 1> x, NDView<double, 3> y,
+                NDView<double, 3> y_err, NDView<double, 3> par_out,
+                NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
                 int n_threads);
 
 NDArray<double, 1> fit_scurve2(NDView<double, 1> x, NDView<double, 1> y);
-NDArray<double, 3> fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, int n_threads); 
+NDArray<double, 3> fit_scurve2(NDView<double, 1> x, NDView<double, 3> y,
-void fit_scurve2(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
+                               int n_threads);
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2); 
+void fit_scurve2(NDView<double, 1> x, NDView<double, 1> y,
-void fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
+                 NDView<double, 1> y_err, NDView<double, 1> par_out,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+                 NDView<double, 1> par_err_out, double &chi2);
+void fit_scurve2(NDView<double, 1> x, NDView<double, 3> y,
+                 NDView<double, 3> y_err, NDView<double, 3> par_out,
+                 NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
                  int n_threads);
 } // namespace aare

include/aare/Frame.hpp

@@ -52,7 +52,6 @@ class Frame {
     Frame &operator=(Frame &&other) noexcept;
     Frame(Frame &&other) noexcept;
 
-
     Frame clone() const; //<- Explicit copy
 
     uint32_t rows() const;

include/aare/JungfrauDataFile.hpp

@@ -3,13 +3,12 @@
 #include <filesystem>
 #include <vector>
 
-#include "aare/FilePtr.hpp"
-#include "aare/defs.hpp"
-#include "aare/NDArray.hpp"
 #include "aare/FileInterface.hpp"
+#include "aare/FilePtr.hpp"
+#include "aare/NDArray.hpp"
+#include "aare/defs.hpp"
 namespace aare {
 
-
 struct JungfrauDataHeader {
     uint64_t framenum;
     uint64_t bunchid;
@@ -18,33 +17,39 @@ struct JungfrauDataHeader{
 class JungfrauDataFile : public FileInterface {
 
     size_t m_rows{}; //!< number of rows in the image, from find_frame_size();
-    size_t m_cols{};     //!< number of columns in the image, from find_frame_size();
+    size_t
+        m_cols{}; //!< number of columns in the image, from find_frame_size();
     size_t m_bytes_per_frame{}; //!< number of bytes per frame excluding header
     size_t m_total_frames{}; //!< total number of frames in the series of files
-    size_t m_offset{}; //!< file index of the first file, allow starting at non zero file
+    size_t m_offset{}; //!< file index of the first file, allow starting at non
+                       //!< zero file
     size_t m_current_file_index{};  //!< The index of the open file
-    size_t m_current_frame_index{};  //!< The index of the current frame (with reference to all files)
+    size_t m_current_frame_index{}; //!< The index of the current frame (with
+                                    //!< reference to all files)
 
-    std::vector<size_t> m_last_frame_in_file{}; //!< Used for seeking to the correct file
+    std::vector<size_t>
+        m_last_frame_in_file{};   //!< Used for seeking to the correct file
     std::filesystem::path m_path; //!< path to the files
     std::string m_base_name;      //!< base name used for formatting file names
 
     FilePtr m_fp; //!< RAII wrapper for a FILE*
 
-    
     using pixel_type = uint16_t;
     static constexpr size_t header_size = sizeof(JungfrauDataHeader);
-    static constexpr size_t n_digits_in_file_index = 6; //!< to format file names
+    static constexpr size_t n_digits_in_file_index =
+        6; //!< to format file names
 
   public:
     JungfrauDataFile(const std::filesystem::path &fname);
 
-    std::string base_name() const;      //!< get the base name of the file (without path and extension)
+    std::string base_name()
+        const; //!< get the base name of the file (without path and extension)
     size_t bytes_per_frame() override;
     size_t pixels_per_frame() override;
     size_t bytes_per_pixel() const;
     size_t bitdepth() const override;
-    void seek(size_t frame_index) override;  //!< seek to the given frame index (note not byte offset)
+    void seek(size_t frame_index)
+        override; //!< seek to the given frame index (note not byte offset)
     size_t tell() override; //!< get the frame index of the file pointer
     size_t total_frames() const override;
     size_t rows() const override;
@@ -63,44 +68,48 @@ class JungfrauDataFile : public FileInterface {
 
     /**
      * @brief Read a single frame from the file into the given buffer.
-     * @param image_buf buffer to read the frame into. (Note the caller is responsible for allocating the buffer)
+     * @param image_buf buffer to read the frame into. (Note the caller is
+     * responsible for allocating the buffer)
      * @param header pointer to a JungfrauDataHeader or nullptr to skip header)
      */
     void read_into(std::byte *image_buf, JungfrauDataHeader *header = nullptr);
 
     /**
      * @brief Read a multiple frames from the file into the given buffer.
-     * @param image_buf buffer to read the frame into. (Note the caller is responsible for allocating the buffer)
+     * @param image_buf buffer to read the frame into. (Note the caller is
+     * responsible for allocating the buffer)
      * @param n_frames number of frames to read
      * @param header pointer to a JungfrauDataHeader or nullptr to skip header)
      */
-    void read_into(std::byte *image_buf, size_t n_frames, JungfrauDataHeader *header = nullptr);
+    void read_into(std::byte *image_buf, size_t n_frames,
+                   JungfrauDataHeader *header = nullptr);
 
     /**
      * @brief Read a single frame from the file into the given NDArray
      * @param image NDArray to read the frame into.
      */
-    void read_into(NDArray<uint16_t>* image, JungfrauDataHeader* header = nullptr);
+    void read_into(NDArray<uint16_t> *image,
+                   JungfrauDataHeader *header = nullptr);
 
     JungfrauDataHeader read_header();
-    std::filesystem::path current_file() const { return fpath(m_current_file_index+m_offset); }
+    std::filesystem::path current_file() const {
-
+        return fpath(m_current_file_index + m_offset);
+    }
 
   private:
     /**
-     * @brief Find the size of the frame in the file. (256x256, 256x1024, 512x1024)
+     * @brief Find the size of the frame in the file. (256x256, 256x1024,
+     * 512x1024)
      * @param fname path to the file
-     * @throws std::runtime_error if the file is empty or the size cannot be determined
+     * @throws std::runtime_error if the file is empty or the size cannot be
+     * determined
      */
     void find_frame_size(const std::filesystem::path &fname);
 
-
     void parse_fname(const std::filesystem::path &fname);
     void scan_files();
     void open_file(size_t file_index);
     std::filesystem::path fpath(size_t frame_index) const;
-
-
 };
 
 } // namespace aare

include/aare/NDArray.hpp

@@ -21,7 +21,6 @@ TODO! Add expression templates for operators
 
 namespace aare {
 
-
 template <typename T, ssize_t Ndim = 2>
 class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
     std::array<ssize_t, Ndim> shape_;
@@ -48,7 +47,6 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
                                 std::multiplies<>())),
           data_(new T[size_]) {}
 
-
     /**
      * @brief Construct a new NDArray object with a shape and value.
      *
@@ -79,7 +77,6 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
         : shape_(other.shape_), strides_(c_strides<Ndim>(shape_)),
           size_(other.size_), data_(other.data_) {
         other.reset(); // TODO! is this necessary?
-
     }
 
     // Copy constructor
@@ -157,11 +154,6 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
 
     NDArray &operator&=(const T & /*mask*/);
 
-  
-
-
-    
-
     void sqrt() {
         for (int i = 0; i < size_; ++i) {
             data_[i] = std::sqrt(data_[i]);
@@ -345,9 +337,6 @@ NDArray<T, Ndim> &NDArray<T, Ndim>::operator+=(const T &value) {
     return *this;
 }
 
-
-
-
 template <typename T, ssize_t Ndim>
 NDArray<T, Ndim> NDArray<T, Ndim>::operator+(const T &value) {
     NDArray result = *this;
@@ -448,6 +437,4 @@ NDArray<T, Ndim> load(const std::string &pathname,
     return img;
 }
 
-
-
 } // namespace aare

include/aare/NDView.hpp

@@ -1,6 +1,6 @@
 #pragma once
-#include "aare/defs.hpp"
 #include "aare/ArrayExpr.hpp"
+#include "aare/defs.hpp"
 
 #include <algorithm>
 #include <array>
@@ -17,7 +17,8 @@ namespace aare {
 template <ssize_t Ndim> using Shape = std::array<ssize_t, Ndim>;
 
 // TODO! fix mismatch between signed and unsigned
-template <ssize_t Ndim> Shape<Ndim> make_shape(const std::vector<size_t> &shape) {
+template <ssize_t Ndim>
+Shape<Ndim> make_shape(const std::vector<size_t> &shape) {
     if (shape.size() != Ndim)
         throw std::runtime_error("Shape size mismatch");
     Shape<Ndim> arr;
@@ -25,14 +26,18 @@ template <ssize_t Ndim> Shape<Ndim> make_shape(const std::vector<size_t> &shape)
     return arr;
 }
 
-template <ssize_t Dim = 0, typename Strides> ssize_t element_offset(const Strides & /*unused*/) { return 0; }
+template <ssize_t Dim = 0, typename Strides>
+ssize_t element_offset(const Strides & /*unused*/) {
+    return 0;
+}
 
 template <ssize_t Dim = 0, typename Strides, typename... Ix>
 ssize_t element_offset(const Strides &strides, ssize_t i, Ix... index) {
     return i * strides[Dim] + element_offset<Dim + 1>(strides, index...);
 }
 
-template <ssize_t Ndim> std::array<ssize_t, Ndim> c_strides(const std::array<ssize_t, Ndim> &shape) {
+template <ssize_t Ndim>
+std::array<ssize_t, Ndim> c_strides(const std::array<ssize_t, Ndim> &shape) {
     std::array<ssize_t, Ndim> strides{};
     std::fill(strides.begin(), strides.end(), 1);
     for (ssize_t i = Ndim - 1; i > 0; --i) {
@@ -41,14 +46,16 @@ template <ssize_t Ndim> std::array<ssize_t, Ndim> c_strides(const std::array<ssi
     return strides;
 }
 
-template <ssize_t Ndim> std::array<ssize_t, Ndim> make_array(const std::vector<ssize_t> &vec) {
+template <ssize_t Ndim>
+std::array<ssize_t, Ndim> make_array(const std::vector<ssize_t> &vec) {
     assert(vec.size() == Ndim);
     std::array<ssize_t, Ndim> arr{};
     std::copy_n(vec.begin(), Ndim, arr.begin());
     return arr;
 }
 
-template <typename T, ssize_t Ndim = 2> class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
+template <typename T, ssize_t Ndim = 2>
+class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
   public:
     NDView() = default;
     ~NDView() = default;
@@ -57,17 +64,23 @@ template <typename T, ssize_t Ndim = 2> class NDView : public ArrayExpr<NDView<T
 
     NDView(T *buffer, std::array<ssize_t, Ndim> shape)
         : buffer_(buffer), strides_(c_strides<Ndim>(shape)), shape_(shape),
-          size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {}
+          size_(std::accumulate(std::begin(shape), std::end(shape), 1,
+                                std::multiplies<>())) {}
 
     // NDView(T *buffer, const std::vector<ssize_t> &shape)
-    //     : buffer_(buffer), strides_(c_strides<Ndim>(make_array<Ndim>(shape))), shape_(make_array<Ndim>(shape)),
+    //     : buffer_(buffer),
-    //       size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {}
+    //     strides_(c_strides<Ndim>(make_array<Ndim>(shape))),
+    //     shape_(make_array<Ndim>(shape)),
+    //       size_(std::accumulate(std::begin(shape), std::end(shape), 1,
+    //       std::multiplies<>())) {}
 
-    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) {
+    template <typename... Ix>
+    std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) {
         return buffer_[element_offset(strides_, index...)];
     }
 
-    template <typename... Ix> std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) const {
+    template <typename... Ix>
+    std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) const {
         return buffer_[element_offset(strides_, index...)];
     }
 
@@ -94,16 +107,21 @@ template <typename T, ssize_t Ndim = 2> class NDView : public ArrayExpr<NDView<T
 
     NDView &operator+=(const T val) { return elemenwise(val, std::plus<T>()); }
     NDView &operator-=(const T val) { return elemenwise(val, std::minus<T>()); }
-    NDView &operator*=(const T val) { return elemenwise(val, std::multiplies<T>()); }
+    NDView &operator*=(const T val) {
-    NDView &operator/=(const T val) { return elemenwise(val, std::divides<T>()); }
+        return elemenwise(val, std::multiplies<T>());
+    }
+    NDView &operator/=(const T val) {
+        return elemenwise(val, std::divides<T>());
+    }
 
-    NDView &operator/=(const NDView &other) { return elemenwise(other, std::divides<T>()); }
+    NDView &operator/=(const NDView &other) {
+        return elemenwise(other, std::divides<T>());
+    }
 
-
+    template <size_t Size> NDView &operator=(const std::array<T, Size> &arr) {
-    template<size_t Size>
-    NDView& operator=(const std::array<T, Size> &arr) {
         if (size() != static_cast<ssize_t>(arr.size()))
-            throw std::runtime_error(LOCATION + "Array and NDView size mismatch");
+            throw std::runtime_error(LOCATION +
+                                     "Array and NDView size mismatch");
         std::copy(arr.begin(), arr.end(), begin());
         return *this;
     }
@@ -147,13 +165,15 @@ template <typename T, ssize_t Ndim = 2> class NDView : public ArrayExpr<NDView<T
     std::array<ssize_t, Ndim> shape_{};
     uint64_t size_{};
 
-    template <class BinaryOperation> NDView &elemenwise(T val, BinaryOperation op) {
+    template <class BinaryOperation>
+    NDView &elemenwise(T val, BinaryOperation op) {
         for (uint64_t i = 0; i != size_; ++i) {
             buffer_[i] = op(buffer_[i], val);
         }
         return *this;
     }
-    template <class BinaryOperation> NDView &elemenwise(const NDView &other, BinaryOperation op) {
+    template <class BinaryOperation>
+    NDView &elemenwise(const NDView &other, BinaryOperation op) {
         for (uint64_t i = 0; i != size_; ++i) {
             buffer_[i] = op(buffer_[i], other.buffer_[i]);
         }
@@ -170,7 +190,6 @@ template <typename T, ssize_t Ndim> void NDView<T, Ndim>::print_all() const {
     }
 }
 
-
 template <typename T, ssize_t Ndim>
 std::ostream &operator<<(std::ostream &os, const NDView<T, Ndim> &arr) {
     for (auto row = 0; row < arr.shape(0); ++row) {
@@ -183,9 +202,7 @@ std::ostream& operator <<(std::ostream& os, const NDView<T, Ndim>& arr){
     return os;
 }
 
-
+template <typename T> NDView<T, 1> make_view(std::vector<T> &vec) {
-template <typename T>
-NDView<T,1> make_view(std::vector<T>& vec){
     return NDView<T, 1>(vec.data(), {static_cast<ssize_t>(vec.size())});
 }
 

include/aare/NumpyFile.hpp

@@ -1,9 +1,8 @@
 #pragma once
 #include "aare/Dtype.hpp"
-#include "aare/defs.hpp"
 #include "aare/FileInterface.hpp"
 #include "aare/NumpyHelpers.hpp"
-
+#include "aare/defs.hpp"
 
 #include <filesystem>
 #include <iostream>
@@ -11,13 +10,12 @@
 
 namespace aare {
 
-
-
 /**
  * @brief NumpyFile class to read and write numpy files
  * @note derived from FileInterface
  * @note implements all the pure virtual functions from FileInterface
- * @note documentation for the functions can also be found in the FileInterface class
+ * @note documentation for the functions can also be found in the FileInterface
+ * class
  */
 class NumpyFile : public FileInterface {
 
@@ -28,26 +26,35 @@ class NumpyFile : public FileInterface {
      * @param mode file mode (r, w)
      * @param cfg file configuration
      */
-    explicit NumpyFile(const std::filesystem::path &fname, const std::string &mode = "r", FileConfig cfg = {});
+    explicit NumpyFile(const std::filesystem::path &fname,
+                       const std::string &mode = "r", FileConfig cfg = {});
 
     void write(Frame &frame);
     Frame read_frame() override { return get_frame(this->current_frame++); }
-    Frame read_frame(size_t frame_number) override { return get_frame(frame_number); }
+    Frame read_frame(size_t frame_number) override {
+        return get_frame(frame_number);
+    }
 
     std::vector<Frame> read_n(size_t n_frames) override;
-    void read_into(std::byte *image_buf) override { return get_frame_into(this->current_frame++, image_buf); }
+    void read_into(std::byte *image_buf) override {
+        return get_frame_into(this->current_frame++, image_buf);
+    }
     void read_into(std::byte *image_buf, size_t n_frames) override;
     size_t frame_number(size_t frame_index) override { return frame_index; };
     size_t bytes_per_frame() override;
     size_t pixels_per_frame() override;
-    void seek(size_t frame_number) override { this->current_frame = frame_number; }
+    void seek(size_t frame_number) override {
+        this->current_frame = frame_number;
+    }
     size_t tell() override { return this->current_frame; }
     size_t total_frames() const override { return m_header.shape[0]; }
     size_t rows() const override { return m_header.shape[1]; }
     size_t cols() const override { return m_header.shape[2]; }
     size_t bitdepth() const override { return m_header.dtype.bitdepth(); }
 
-    DetectorType detector_type() const override { return DetectorType::Unknown; }
+    DetectorType detector_type() const override {
+        return DetectorType::Unknown;
+    }
 
     /**
      * @brief get the data type of the numpy file
@@ -70,7 +77,8 @@ class NumpyFile : public FileInterface {
     template <typename T, size_t NDim> NDArray<T, NDim> load() {
         NDArray<T, NDim> arr(make_shape<NDim>(m_header.shape));
         if (fseek(fp, static_cast<long>(header_size), SEEK_SET)) {
-            throw std::runtime_error(LOCATION + "Error seeking to the start of the data");
+            throw std::runtime_error(LOCATION +
+                                     "Error seeking to the start of the data");
         }
         size_t rc = fread(arr.data(), sizeof(T), arr.size(), fp);
         if (rc != static_cast<size_t>(arr.size())) {
@@ -78,16 +86,20 @@ class NumpyFile : public FileInterface {
         }
         return arr;
     }
-    template <typename A, typename TYPENAME, A Ndim> void write(NDView<TYPENAME, Ndim> &frame) {
+    template <typename A, typename TYPENAME, A Ndim>
+    void write(NDView<TYPENAME, Ndim> &frame) {
         write_impl(frame.data(), frame.total_bytes());
     }
-    template <typename A, typename TYPENAME, A Ndim> void write(NDArray<TYPENAME, Ndim> &frame) {
+    template <typename A, typename TYPENAME, A Ndim>
+    void write(NDArray<TYPENAME, Ndim> &frame) {
         write_impl(frame.data(), frame.total_bytes());
     }
-    template <typename A, typename TYPENAME, A Ndim> void write(NDView<TYPENAME, Ndim> &&frame) {
+    template <typename A, typename TYPENAME, A Ndim>
+    void write(NDView<TYPENAME, Ndim> &&frame) {
         write_impl(frame.data(), frame.total_bytes());
     }
-    template <typename A, typename TYPENAME, A Ndim> void write(NDArray<TYPENAME, Ndim> &&frame) {
+    template <typename A, typename TYPENAME, A Ndim>
+    void write(NDArray<TYPENAME, Ndim> &&frame) {
         write_impl(frame.data(), frame.total_bytes());
     }
 

include/aare/NumpyHelpers.hpp

@@ -40,15 +40,18 @@ bool parse_bool(const std::string &in);
 
 std::string get_value_from_map(const std::string &mapstr);
 
-std::unordered_map<std::string, std::string> parse_dict(std::string in, const std::vector<std::string> &keys);
+std::unordered_map<std::string, std::string>
+parse_dict(std::string in, const std::vector<std::string> &keys);
 
-template <typename T, size_t N> bool in_array(T val, const std::array<T, N> &arr) {
+template <typename T, size_t N>
+bool in_array(T val, const std::array<T, N> &arr) {
     return std::find(std::begin(arr), std::end(arr), val) != std::end(arr);
 }
 bool is_digits(const std::string &str);
 
 aare::Dtype parse_descr(std::string typestring);
-size_t write_header(const std::filesystem::path &fname, const NumpyHeader &header);
+size_t write_header(const std::filesystem::path &fname,
+                    const NumpyHeader &header);
 size_t write_header(std::ostream &out, const NumpyHeader &header);
 
 } // namespace NumpyHelpers

include/aare/Pedestal.hpp

@@ -42,9 +42,7 @@ template <typename SUM_TYPE = double> class Pedestal {
     }
     ~Pedestal() = default;
 
-    NDArray<SUM_TYPE, 2> mean() {
+    NDArray<SUM_TYPE, 2> mean() { return m_mean; }
-        return m_mean;
-    }
 
     SUM_TYPE mean(const uint32_t row, const uint32_t col) const {
         return m_mean(row, col);
@@ -71,8 +69,6 @@ template <typename SUM_TYPE = double> class Pedestal {
         return variance_array;
     }
 
-    
-
     NDArray<SUM_TYPE, 2> std() {
         NDArray<SUM_TYPE, 2> standard_deviation_array({m_rows, m_cols});
         for (uint32_t i = 0; i < m_rows * m_cols; i++) {
@@ -83,8 +79,6 @@ template <typename SUM_TYPE = double> class Pedestal {
         return standard_deviation_array;
     }
 
-    
-
     void clear() {
         m_sum = 0;
         m_sum2 = 0;
@@ -92,8 +86,6 @@ template <typename SUM_TYPE = double> class Pedestal {
         m_mean = 0;
     }
 
-    
-
     void clear(const uint32_t row, const uint32_t col) {
         m_sum(row, col) = 0;
         m_sum2(row, col) = 0;
@@ -101,8 +93,6 @@ template <typename SUM_TYPE = double> class Pedestal {
         m_mean(row, col) = 0;
     }
 
-
-
     template <typename T> void push(NDView<T, 2> frame) {
         assert(frame.size() == m_rows * m_cols);
 
@@ -140,9 +130,6 @@ template <typename SUM_TYPE = double> class Pedestal {
         }
     }
 
-
-
-
     template <typename T> void push(Frame &frame) {
         assert(frame.rows() == static_cast<size_t>(m_rows) &&
                frame.cols() == static_cast<size_t>(m_cols));
@@ -170,7 +157,8 @@ template <typename SUM_TYPE = double> class Pedestal {
             m_sum(row, col) += val - m_sum(row, col) / m_samples;
             m_sum2(row, col) += val * val - m_sum2(row, col) / m_samples;
         }
-        //Since we just did a push we know that m_cur_samples(row, col) is at least 1
+        // Since we just did a push we know that m_cur_samples(row, col) is at
+        // least 1
         m_mean(row, col) = m_sum(row, col) / m_cur_samples(row, col);
     }
 
@@ -183,7 +171,8 @@ template <typename SUM_TYPE = double> class Pedestal {
             m_cur_samples(row, col)++;
         } else {
             m_sum(row, col) += val - m_sum(row, col) / m_cur_samples(row, col);
-            m_sum2(row, col) += val * val - m_sum2(row, col) / m_cur_samples(row, col);
+            m_sum2(row, col) +=
+                val * val - m_sum2(row, col) / m_cur_samples(row, col);
         }
     }
 
@@ -191,9 +180,7 @@ template <typename SUM_TYPE = double> class Pedestal {
      * @brief Update the mean of the pedestal. This is used after having done
      * push_no_update. It is not necessary to call this function after push.
      */
-    void update_mean(){
+    void update_mean() { m_mean = m_sum / m_cur_samples; }
-        m_mean = m_sum / m_cur_samples;
-    }
 
     template <typename T>
     void push_fast(const uint32_t row, const uint32_t col, const T val_) {
@@ -204,6 +191,5 @@ template <typename SUM_TYPE = double> class Pedestal {
         m_sum2(row, col) += val * val - m_sum2(row, col) / m_samples;
         m_mean(row, col) = m_sum(row, col) / m_samples;
     }
-
 };
 } // namespace aare

include/aare/PixelMap.hpp

@@ -1,7 +1,7 @@
 #pragma once
 
-#include "aare/defs.hpp"
 #include "aare/NDArray.hpp"
+#include "aare/defs.hpp"
 
 namespace aare {
 

include/aare/ProducerConsumerQueue.hpp

@@ -18,9 +18,9 @@
 // @author Jordan DeLong (delong.j@fb.com)
 
 // Changes made by PSD Detector Group:
-// Copied: Line 34 constexpr std::size_t hardware_destructive_interference_size = 128; from folly/lang/Align.h
+// Copied: Line 34 constexpr std::size_t hardware_destructive_interference_size
-// Changed extension to .hpp
+// = 128; from folly/lang/Align.h Changed extension to .hpp Changed namespace to
-// Changed namespace to aare
+// aare
 
 #pragma once
 
@@ -45,7 +45,6 @@ template <class T> struct ProducerConsumerQueue {
     ProducerConsumerQueue(const ProducerConsumerQueue &) = delete;
     ProducerConsumerQueue &operator=(const ProducerConsumerQueue &) = delete;
 
-    
     ProducerConsumerQueue(ProducerConsumerQueue &&other) {
         size_ = other.size_;
         records_ = other.records_;
@@ -62,7 +61,6 @@ template <class T> struct ProducerConsumerQueue {
         return *this;
     }
 
-    
     ProducerConsumerQueue() : ProducerConsumerQueue(2){};
     // size must be >= 2.
     //
@@ -70,7 +68,9 @@ template <class T> struct ProducerConsumerQueue {
     // given time is actually (size-1), so if you start with an empty queue,
     // isFull() will return true after size-1 insertions.
     explicit ProducerConsumerQueue(uint32_t size)
-        : size_(size), records_(static_cast<T *>(std::malloc(sizeof(T) * size))), readIndex_(0), writeIndex_(0) {
+        : size_(size),
+          records_(static_cast<T *>(std::malloc(sizeof(T) * size))),
+          readIndex_(0), writeIndex_(0) {
         assert(size >= 2);
         if (!records_) {
             throw std::bad_alloc();
@@ -154,7 +154,8 @@ template <class T> struct ProducerConsumerQueue {
     }
 
     bool isEmpty() const {
-        return readIndex_.load(std::memory_order_acquire) == writeIndex_.load(std::memory_order_acquire);
+        return readIndex_.load(std::memory_order_acquire) ==
+               writeIndex_.load(std::memory_order_acquire);
     }
 
     bool isFull() const {
@@ -175,7 +176,8 @@ template <class T> struct ProducerConsumerQueue {
     //   be removing items concurrently).
     // * It is undefined to call this from any other thread.
     size_t sizeGuess() const {
-        int ret = writeIndex_.load(std::memory_order_acquire) - readIndex_.load(std::memory_order_acquire);
+        int ret = writeIndex_.load(std::memory_order_acquire) -
+                  readIndex_.load(std::memory_order_acquire);
         if (ret < 0) {
             ret += size_;
         }

include/aare/RawFile.hpp

@@ -1,11 +1,10 @@
 #pragma once
 #include "aare/FileInterface.hpp"
-#include "aare/RawMasterFile.hpp"
 #include "aare/Frame.hpp"
 #include "aare/NDArray.hpp" //for pixel map
+#include "aare/RawMasterFile.hpp"
 #include "aare/RawSubFile.hpp"
 
-
 #include <optional>
 
 namespace aare {
@@ -55,8 +54,8 @@ class RawFile : public FileInterface {
 
     // TODO! do we need to adapt the API?
     void read_into(std::byte *image_buf, DetectorHeader *header);
-    void read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header);
+    void read_into(std::byte *image_buf, size_t n_frames,
-
+                   DetectorHeader *header);
 
     size_t frame_number(size_t frame_index) override;
     size_t bytes_per_frame() override;
@@ -73,20 +72,17 @@ class RawFile : public FileInterface {
 
     RawMasterFile master() const;
 
-
-
     DetectorType detector_type() const override;
 
   private:
-
     /**
      * @brief read the frame at the given frame index into the image buffer
      * @param frame_number frame number to read
      * @param image_buf buffer to store the frame
      */
 
-    void get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header = nullptr);
+    void get_frame_into(size_t frame_index, std::byte *frame_buffer,
-
+                        DetectorHeader *header = nullptr);
 
     /**
      * @brief get the frame at the given frame index
@@ -95,8 +91,6 @@ class RawFile : public FileInterface {
      */
     Frame get_frame(size_t frame_index);
 
-
-
     /**
      * @brief read the header of the file
      * @param fname path to the data subfile
@@ -108,5 +102,4 @@ class RawFile : public FileInterface {
     void find_geometry();
 };
 
-
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -79,7 +79,6 @@ class RawMasterFile {
 
     std::optional<ROI> m_roi;
 
-
   public:
     RawMasterFile(const std::filesystem::path &fpath);
 
@@ -107,7 +106,6 @@ class RawMasterFile {
     std::optional<size_t> number_of_rows() const;
     std::optional<uint8_t> quad() const;
 
-
     std::optional<ROI> roi() const;
 
     ScanParameters scan_parameters() const;

include/aare/RawSubFile.hpp

@@ -10,8 +10,9 @@
 namespace aare {
 
 /**
- * @brief Class to read a singe subfile written in .raw format. Used from RawFile to read
+ * @brief Class to read a singe subfile written in .raw format. Used from
- * the entire detector. Can be used directly to read part of the image.
+ * RawFile to read the entire detector. Can be used directly to read part of the
+ * image.
  */
 class RawSubFile {
   protected:
@@ -20,22 +21,23 @@ class RawSubFile {
     size_t m_bitdepth;
     std::filesystem::path m_path; //!< path to the subfile
     std::string m_base_name;      //!< base name used for formatting file names
-    size_t m_offset{}; //!< file index of the first file, allow starting at non zero file
+    size_t m_offset{}; //!< file index of the first file, allow starting at non
+                       //!< zero file
     size_t m_total_frames{}; //!< total number of frames in the series of files
     size_t m_rows{};
     size_t m_cols{};
     size_t m_bytes_per_frame{};
 
-
     int m_module_index{};
     size_t m_current_file_index{};  //!< The index of the open file
-    size_t m_current_frame_index{};  //!< The index of the current frame (with reference to all files)
+    size_t m_current_frame_index{}; //!< The index of the current frame (with
-    std::vector<size_t> m_last_frame_in_file{}; //!< Used for seeking to the correct file
+                                    //!< reference to all files)
+    std::vector<size_t>
+        m_last_frame_in_file{}; //!< Used for seeking to the correct file
 
     uint32_t m_pos_row{};
     uint32_t m_pos_col{};
 
-    
     std::optional<NDArray<ssize_t, 2>> m_pixel_map;
 
   public:
@@ -49,12 +51,14 @@ class RawSubFile {
      * @throws std::invalid_argument if the detector,type pair is not supported
      */
     RawSubFile(const std::filesystem::path &fname, DetectorType detector,
-               size_t rows, size_t cols, size_t bitdepth, uint32_t pos_row = 0, uint32_t pos_col = 0);
+               size_t rows, size_t cols, size_t bitdepth, uint32_t pos_row = 0,
+               uint32_t pos_col = 0);
 
     ~RawSubFile() = default;
     /**
      * @brief Seek to the given frame number
-     * @note Puts the file pointer at the start of the header, not the start of the data
+     * @note Puts the file pointer at the start of the header, not the start of
+     * the data
      * @param frame_index frame position in file to seek to
      * @throws std::runtime_error if the frame number is out of range
      */
@@ -62,7 +66,8 @@ class RawSubFile {
     size_t tell();
 
     void read_into(std::byte *image_buf, DetectorHeader *header = nullptr);
-    void read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header= nullptr);
+    void read_into(std::byte *image_buf, size_t n_frames,
+                   DetectorHeader *header = nullptr);
     void get_part(std::byte *buffer, size_t frame_index);
 
     void read_header(DetectorHeader *header);
@@ -79,14 +84,12 @@ class RawSubFile {
     size_t frames_in_file() const { return m_total_frames; }
 
   private:
-  template <typename T>
+    template <typename T> void read_with_map(std::byte *image_buf);
-  void read_with_map(std::byte *image_buf);
 
     void parse_fname(const std::filesystem::path &fname);
     void scan_files();
     void open_file(size_t file_index);
     std::filesystem::path fpath(size_t file_index) const;
-
 };
 
 } // namespace aare

include/aare/VarClusterFinder.hpp

@@ -38,8 +38,10 @@ template <typename T> class VarClusterFinder {
     bool use_noise_map = false;
     int peripheralThresholdFactor_ = 5;
     int current_label;
-    const std::array<int, 4> di{{0, -1, -1, -1}};              // row ### 8-neighbour by scaning from left to right
+    const std::array<int, 4> di{
-    const std::array<int, 4> dj{{-1, -1, 0, 1}};               // col ### 8-neighbour by scaning from top to bottom
+        {0, -1, -1, -1}}; // row ### 8-neighbour by scaning from left to right
+    const std::array<int, 4> dj{
+        {-1, -1, 0, 1}}; // col ### 8-neighbour by scaning from top to bottom
     const std::array<int, 8> di_{{0, 0, -1, 1, -1, 1, -1, 1}}; // row
     const std::array<int, 8> dj_{{-1, 1, 0, 0, 1, -1, -1, 1}}; // col
     std::map<int, int> child; // heirachy: key: child; val: parent
@@ -50,7 +52,8 @@ template <typename T> class VarClusterFinder {
 
   public:
     VarClusterFinder(Shape<2> shape, T threshold)
-        : shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0), binary_(shape), threshold_(threshold) {
+        : shape_(shape), labeled_(shape, 0), peripheral_labeled_(shape, 0),
+          binary_(shape), threshold_(threshold) {
         hits.reserve(2000);
     }
 
@@ -60,7 +63,9 @@ template <typename T> class VarClusterFinder {
         noiseMap = noise_map;
         use_noise_map = true;
     }
-    void set_peripheralThresholdFactor(int factor) { peripheralThresholdFactor_ = factor; }
+    void set_peripheralThresholdFactor(int factor) {
+        peripheralThresholdFactor_ = factor;
+    }
     void find_clusters(NDView<T, 2> img);
     void find_clusters_X(NDView<T, 2> img);
     void rec_FillHit(int clusterIndex, int i, int j);
@@ -144,7 +149,8 @@ template <typename T> int VarClusterFinder<T>::check_neighbours(int i, int j) {
     }
 }
 
-template <typename T> void VarClusterFinder<T>::find_clusters(NDView<T, 2> img) {
+template <typename T>
+void VarClusterFinder<T>::find_clusters(NDView<T, 2> img) {
     original_ = img;
     labeled_ = 0;
     peripheral_labeled_ = 0;
@@ -156,7 +162,8 @@ template <typename T> void VarClusterFinder<T>::find_clusters(NDView<T, 2> img)
     store_clusters();
 }
 
-template <typename T> void VarClusterFinder<T>::find_clusters_X(NDView<T, 2> img) {
+template <typename T>
+void VarClusterFinder<T>::find_clusters_X(NDView<T, 2> img) {
     original_ = img;
     int clusterIndex = 0;
     for (int i = 0; i < shape_[0]; ++i) {
@@ -175,7 +182,8 @@ template <typename T> void VarClusterFinder<T>::find_clusters_X(NDView<T, 2> img
     h_size.clear();
 }
 
-template <typename T> void VarClusterFinder<T>::rec_FillHit(int clusterIndex, int i, int j) {
+template <typename T>
+void VarClusterFinder<T>::rec_FillHit(int clusterIndex, int i, int j) {
     // printf("original_(%d, %d)=%f\n", i, j, original_(i,j));
     // printf("h_size[%d].size=%d\n", clusterIndex, h_size[clusterIndex].size);
     if (h_size[clusterIndex].size < MAX_CLUSTER_SIZE) {
@@ -203,11 +211,15 @@ template <typename T> void VarClusterFinder<T>::rec_FillHit(int clusterIndex, in
             } else {
                 // if (h_size[clusterIndex].size < MAX_CLUSTER_SIZE){
                 //     h_size[clusterIndex].size += 1;
-                //     h_size[clusterIndex].rows[h_size[clusterIndex].size] = row;
+                //     h_size[clusterIndex].rows[h_size[clusterIndex].size] =
-                //     h_size[clusterIndex].cols[h_size[clusterIndex].size] = col;
+                //     row; h_size[clusterIndex].cols[h_size[clusterIndex].size]
-                //     h_size[clusterIndex].enes[h_size[clusterIndex].size] = original_(row, col);
+                //     = col;
+                //     h_size[clusterIndex].enes[h_size[clusterIndex].size] =
+                //     original_(row, col);
                 // }// ? weather to include peripheral pixels
-                original_(row, col) = 0; // remove peripheral pixels, to avoid potential influence for pedestal updating
+                original_(row, col) =
+                    0; // remove peripheral pixels, to avoid potential influence
+                       // for pedestal updating
             }
         }
     }
@@ -275,8 +287,8 @@ template <typename T> void VarClusterFinder<T>::store_clusters() {
     for (int i = 0; i < shape_[0]; ++i) {
         for (int j = 0; j < shape_[1]; ++j) {
             if (labeled_(i, j) != 0 || false
-                // (i-1 >= 0 and labeled_(i-1, j) != 0) or // another circle of peripheral pixels
+                // (i-1 >= 0 and labeled_(i-1, j) != 0) or // another circle of
-                // (j-1 >= 0 and labeled_(i, j-1) != 0) or
+                // peripheral pixels (j-1 >= 0 and labeled_(i, j-1) != 0) or
                 // (i+1 < shape_[0] and labeled_(i+1, j) != 0) or
                 // (j+1 < shape_[1] and labeled_(i, j+1) != 0)
             ) {

include/aare/algorithm.hpp

@@ -1,9 +1,9 @@
 
 #pragma once
+#include <aare/NDArray.hpp>
 #include <algorithm>
 #include <array>
 #include <vector>
-#include <aare/NDArray.hpp>
 
 namespace aare {
 /**
@@ -27,13 +27,11 @@ size_t last_smaller(const T* first, const T* last, T val) {
     return std::distance(first, last - 1);
 }
 
-template <typename T>
+template <typename T> size_t last_smaller(const NDArray<T, 1> &arr, T val) {
-size_t last_smaller(const NDArray<T, 1>& arr, T val) {
     return last_smaller(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
+template <typename T> size_t last_smaller(const std::vector<T> &vec, T val) {
-size_t last_smaller(const std::vector<T>& vec, T val) {
     return last_smaller(vec.data(), vec.data() + vec.size(), val);
 }
 
@@ -57,19 +55,18 @@ size_t first_larger(const T* first, const T* last, T val) {
     return std::distance(first, last - 1);
 }
 
-template <typename T>
+template <typename T> size_t first_larger(const NDArray<T, 1> &arr, T val) {
-size_t first_larger(const NDArray<T, 1>& arr, T val) {
     return first_larger(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
+template <typename T> size_t first_larger(const std::vector<T> &vec, T val) {
-size_t first_larger(const std::vector<T>& vec, T val) {
     return first_larger(vec.data(), vec.data() + vec.size(), val);
 }
 
 /**
  * @brief Index of the nearest element to val.
- * Requires a sorted array. If there is no difference it takes the first element.
+ * Requires a sorted array. If there is no difference it takes the first
+ * element.
  * @param first iterator to the first element
  * @param last iterator to the last element
  * @param val value to compare
@@ -77,20 +74,17 @@ size_t first_larger(const std::vector<T>& vec, T val) {
  */
 template <typename T>
 size_t nearest_index(const T *first, const T *last, T val) {
-    auto iter = std::min_element(first, last,
+    auto iter = std::min_element(first, last, [val](T a, T b) {
-    [val](T a, T b) {
         return std::abs(a - val) < std::abs(b - val);
     });
     return std::distance(first, iter);
 }
 
-template <typename T>
+template <typename T> size_t nearest_index(const NDArray<T, 1> &arr, T val) {
-size_t nearest_index(const NDArray<T, 1>& arr, T val) {
     return nearest_index(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
+template <typename T> size_t nearest_index(const std::vector<T> &vec, T val) {
-size_t nearest_index(const std::vector<T>& vec, T val) {
     return nearest_index(vec.data(), vec.data() + vec.size(), val);
 }
 
@@ -99,14 +93,12 @@ size_t nearest_index(const std::array<T,N>& arr, T val) {
     return nearest_index(arr.data(), arr.data() + arr.size(), val);
 }
 
-template <typename T>
+template <typename T> std::vector<T> cumsum(const std::vector<T> &vec) {
-std::vector<T> cumsum(const std::vector<T>& vec) {
     std::vector<T> result(vec.size());
     std::partial_sum(vec.begin(), vec.end(), result.begin());
     return result;
 }
 
-
 template <typename Container> bool all_equal(const Container &c) {
     if (!c.empty() &&
         std::all_of(begin(c), end(c),
@@ -117,6 +109,4 @@ template <typename Container> bool all_equal(const Container &c) {
     return false;
 }
 
-
-
 } // namespace aare

include/aare/decode.hpp

@@ -1,26 +1,27 @@
 #pragma once
 
+#include <aare/NDView.hpp>
 #include <cstdint>
 #include <vector>
-#include <aare/NDView.hpp>
 namespace aare {
 
-
 uint16_t adc_sar_05_decode64to16(uint64_t input);
 uint16_t adc_sar_04_decode64to16(uint64_t input);
-void adc_sar_05_decode64to16(NDView<uint64_t, 2> input, NDView<uint16_t,2> output);
+void adc_sar_05_decode64to16(NDView<uint64_t, 2> input,
-void adc_sar_04_decode64to16(NDView<uint64_t, 2> input, NDView<uint16_t,2> output);
+                             NDView<uint16_t, 2> output);
-
+void adc_sar_04_decode64to16(NDView<uint64_t, 2> input,
+                             NDView<uint16_t, 2> output);
 
 /**
- * @brief Apply custom weights to a 16-bit input value. Will sum up weights[i]**i
+ * @brief Apply custom weights to a 16-bit input value. Will sum up
- * for each bit i that is set in the input value.
+ * weights[i]**i for each bit i that is set in the input value.
  * @throws std::out_of_range if weights.size() < 16
  * @param input 16-bit input value
  * @param weights vector of weights, size must be less than or equal to 16
  */
 double apply_custom_weights(uint16_t input, const NDView<double, 1> weights);
 
-void apply_custom_weights(NDView<uint16_t, 1> input, NDView<double, 1> output, const NDView<double, 1> weights);
+void apply_custom_weights(NDView<uint16_t, 1> input, NDView<double, 1> output,
+                          const NDView<double, 1> weights);
 
 } // namespace aare

include/aare/defs.hpp

@@ -25,28 +25,24 @@
     std::string(__FILE__) + std::string(":") + std::to_string(__LINE__) +      \
         ":" + std::string(__func__) + ":"
 
-
-
 #ifdef AARE_CUSTOM_ASSERT
 #define AARE_ASSERT(expr)                                                      \
-    if (expr)\
+    if (expr) {                                                                \
-        {}\
+    } else                                                                     \
-    else\
         aare::assert_failed(LOCATION + " Assertion failed: " + #expr + "\n");
 #else
 #define AARE_ASSERT(cond)                                                      \
-    do { (void)sizeof(cond); } while(0)
+    do {                                                                       \
+        (void)sizeof(cond);                                                    \
+    } while (0)
 #endif
 
-
 namespace aare {
 
 inline constexpr size_t bits_per_byte = 8;
 
 void assert_failed(const std::string &msg);
 
-
-
 class DynamicCluster {
   public:
     int cluster_sizeX;
@@ -184,9 +180,9 @@ template <typename T> struct t_xy {
 };
 using xy = t_xy<uint32_t>;
 
-
 /**
- * @brief Class to hold the geometry of a module. Where pixel 0 is located and the size of the module
+ * @brief Class to hold the geometry of a module. Where pixel 0 is located and
+ * the size of the module
  */
 struct ModuleGeometry {
     int origin_x{};
@@ -198,8 +194,8 @@ struct ModuleGeometry{
 };
 
 /**
- * @brief Class to hold the geometry of a detector. Number of modules, their size and where pixel 0 
+ * @brief Class to hold the geometry of a detector. Number of modules, their
- * for each module is located
+ * size and where pixel 0 for each module is located
  */
 struct DetectorGeometry {
     int modules_x{};
@@ -226,7 +222,6 @@ struct ROI{
     }
 };
 
-
 using dynamic_shape = std::vector<ssize_t>;
 
 
@@ -288,7 +283,8 @@ enum class DetectorType {
     Gotthard2,
     Xilinx_ChipTestBoard,
 
-    //Additional detectors used for defining processing. Variants of the standard ones.
+    // Additional detectors used for defining processing. Variants of the
+    // standard ones.
     Moench03 = 100,
     Moench03_old,
     Unknown

include/aare/geo_helpers.hpp

@@ -1,6 +1,6 @@
 #pragma once
-#include "aare/defs.hpp"
 #include "aare/RawMasterFile.hpp" //ROI refactor away
+#include "aare/defs.hpp"
 namespace aare {
 
 /**
@@ -12,5 +12,4 @@ namespace aare{
  */
 DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, ROI roi);
 
-
 } // namespace aare

include/aare/logger.hpp

@@ -1,7 +1,6 @@
 #pragma once
 /*Utility to log to console*/
 
-
 #include <iostream>
 #include <sstream>
 #include <sys/time.h>
@@ -27,7 +26,6 @@ namespace aare {
 #define RESET      "\x1b[0m"
 #define BOLD       "\x1b[1m"
 
-
 enum TLogLevel {
     logERROR,
     logWARNING,
@@ -37,7 +35,8 @@ enum TLogLevel {
     logINFOCYAN,
     logINFOMAGENTA,
     logINFO,
-    logDEBUG,  // constructors, destructors etc. should still give too much output
+    logDEBUG, // constructors, destructors etc. should still give too much
+              // output
     logDEBUG1,
     logDEBUG2,
     logDEBUG3,
@@ -47,7 +46,9 @@ enum TLogLevel {
 
 // Compiler should optimize away anything below this value
 #ifndef AARE_LOG_LEVEL
-#define AARE_LOG_LEVEL "LOG LEVEL NOT SET IN CMAKE" //This is configured in the main CMakeLists.txt
+#define AARE_LOG_LEVEL                                                         \
+    "LOG LEVEL NOT SET IN CMAKE" // This is configured in the main
+                                 // CMakeLists.txt
 #endif
 
 #define __AT__                                                                 \
@@ -72,7 +73,8 @@ class Logger {
         std::clog << os.str() << std::flush; // Single write
     }
 
-    static TLogLevel &ReportingLevel() { // singelton eeh TODO! Do we need a runtime option?
+    static TLogLevel &
+    ReportingLevel() { // singelton eeh TODO! Do we need a runtime option?
         static TLogLevel reportingLevel = logDEBUG5;
         return reportingLevel;
     }

include/aare/utils/par.hpp

@@ -1,6 +1,6 @@
 #include <thread>
-#include <vector>
 #include <utility>
+#include <vector>
 
 namespace aare {
 

python/src/bind_Cluster.hpp

@@ -1,10 +1,10 @@
 #include "aare/Cluster.hpp"
 
 #include <cstdint>
-#include <fmt/format.h>
 #include <filesystem>
-#include <pybind11/pybind11.h>
+#include <fmt/format.h>
 #include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 #include <pybind11/stl_bind.h>
 

python/src/bind_ClusterCollector.hpp

@@ -21,11 +21,9 @@ using namespace aare;
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 
-
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType = uint16_t>
-void define_ClusterCollector(py::module &m,
+void define_ClusterCollector(py::module &m, const std::string &typestr) {
-                                       const std::string &typestr) {
     auto class_name = fmt::format("ClusterCollector_{}", typestr);
 
     using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;

python/src/bind_ClusterFile.hpp

@@ -21,8 +21,7 @@ using namespace ::aare;
 
 template <typename Type, uint8_t CoordSizeX, uint8_t CoordSizeY,
           typename CoordType = uint16_t>
-void define_ClusterFile(py::module &m,
+void define_ClusterFile(py::module &m, const std::string &typestr) {
-                                     const std::string &typestr) {
 
     using ClusterType = Cluster<Type, CoordSizeX, CoordSizeY, CoordType>;
 

python/src/bind_ClusterFileSink.hpp

@@ -21,15 +21,9 @@ using namespace aare;
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 
-
-
-
-
-
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType = uint16_t>
-void define_ClusterFileSink(py::module &m,
+void define_ClusterFileSink(py::module &m, const std::string &typestr) {
-                                       const std::string &typestr) {
     auto class_name = fmt::format("ClusterFileSink_{}", typestr);
 
     using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
@@ -40,5 +34,4 @@ void define_ClusterFileSink(py::module &m,
         .def("stop", &ClusterFileSink<ClusterType>::stop);
 }
 
-
 #pragma GCC diagnostic pop

python/src/bind_ClusterFinderMT.hpp

@@ -23,8 +23,7 @@ using namespace aare;
 
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType = uint16_t>
-void define_ClusterFinderMT(py::module &m,
+void define_ClusterFinderMT(py::module &m, const std::string &typestr) {
-                                       const std::string &typestr) {
     auto class_name = fmt::format("ClusterFinderMT_{}", typestr);
 
     using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
@@ -49,7 +48,9 @@ void define_ClusterFinderMT(py::module &m,
                 return;
             },
             py::arg(), py::arg("frame_number") = 0)
-        .def_property_readonly("cluster_size", [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self){
+        .def_property_readonly(
+            "cluster_size",
+            [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self) {
                 return py::make_tuple(ClusterSizeX, ClusterSizeY);
             })
         .def("clear_pedestal",
@@ -77,5 +78,4 @@ void define_ClusterFinderMT(py::module &m,
             py::arg("thread_index") = 0);
 }
 
-
 #pragma GCC diagnostic pop

python/src/bind_ClusterVector.hpp

@@ -44,7 +44,8 @@ void define_ClusterVector(py::module &m, const std::string &typestr) {
                  auto *vec = new std::vector<Type>(self.sum());
                  return return_vector(vec);
              })
-        .def("sum_2x2", [](ClusterVector<ClusterType> &self){
+        .def("sum_2x2",
+             [](ClusterVector<ClusterType> &self) {
                  auto *vec = new std::vector<Type>(self.sum_2x2());
                  return return_vector(vec);
              })

python/src/ctb_raw_file.hpp

@@ -6,8 +6,8 @@
 #include "aare/RawMasterFile.hpp"
 #include "aare/RawSubFile.hpp"
 
-#include "aare/defs.hpp"
 #include "aare/decode.hpp"
+#include "aare/defs.hpp"
 // #include "aare/fClusterFileV2.hpp"
 
 #include "np_helper.hpp"
@@ -27,61 +27,69 @@ using namespace ::aare;
 void define_ctb_raw_file_io_bindings(py::module &m) {
 
     m.def("adc_sar_05_decode64to16", [](py::array_t<uint8_t> input) {
-
-    
         if (input.ndim() != 2) {
-        throw std::runtime_error("Only 2D arrays are supported at this moment"); 
+            throw std::runtime_error(
+                "Only 2D arrays are supported at this moment");
         }
 
         // Create a 2D output array with the same shape as the input
-    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/static_cast<ssize_t>(bits_per_byte)};
+        std::vector<ssize_t> shape{input.shape(0),
+                                   input.shape(1) /
+                                       static_cast<ssize_t>(bits_per_byte)};
         py::array_t<uint16_t> output(shape);
 
         // Create a view of the input and output arrays
-    NDView<uint64_t, 2> input_view(reinterpret_cast<uint64_t*>(input.mutable_data()), {output.shape(0), output.shape(1)});
+        NDView<uint64_t, 2> input_view(
-    NDView<uint16_t, 2> output_view(output.mutable_data(), {output.shape(0), output.shape(1)});
+            reinterpret_cast<uint64_t *>(input.mutable_data()),
+            {output.shape(0), output.shape(1)});
+        NDView<uint16_t, 2> output_view(output.mutable_data(),
+                                        {output.shape(0), output.shape(1)});
 
         adc_sar_05_decode64to16(input_view, output_view);
 
         return output;
     });
 
-
     m.def("adc_sar_04_decode64to16", [](py::array_t<uint8_t> input) {
-
-    
         if (input.ndim() != 2) {
-        throw std::runtime_error("Only 2D arrays are supported at this moment"); 
+            throw std::runtime_error(
+                "Only 2D arrays are supported at this moment");
         }
 
         // Create a 2D output array with the same shape as the input
-    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/static_cast<ssize_t>(bits_per_byte)};
+        std::vector<ssize_t> shape{input.shape(0),
+                                   input.shape(1) /
+                                       static_cast<ssize_t>(bits_per_byte)};
         py::array_t<uint16_t> output(shape);
 
         // Create a view of the input and output arrays
-    NDView<uint64_t, 2> input_view(reinterpret_cast<uint64_t*>(input.mutable_data()), {output.shape(0), output.shape(1)});
+        NDView<uint64_t, 2> input_view(
-    NDView<uint16_t, 2> output_view(output.mutable_data(), {output.shape(0), output.shape(1)});
+            reinterpret_cast<uint64_t *>(input.mutable_data()),
+            {output.shape(0), output.shape(1)});
+        NDView<uint16_t, 2> output_view(output.mutable_data(),
+                                        {output.shape(0), output.shape(1)});
 
         adc_sar_04_decode64to16(input_view, output_view);
 
         return output;
     });
 
-m.def(
+    m.def("apply_custom_weights",
-    "apply_custom_weights",
+          [](py::array_t<uint16_t, py::array::c_style | py::array::forcecast>
-    [](py::array_t<uint16_t, py::array::c_style | py::array::forcecast> &input,
+                 &input,
              py::array_t<double, py::array::c_style | py::array::forcecast>
                  &weights) {
-        
+              // Create new array with same shape as the input array
-
+              // (uninitialized values)
-        // Create new array with same shape as the input array (uninitialized values)
               py::buffer_info buf = input.request();
               py::array_t<double> output(buf.shape);
 
               // Use NDViews to call into the C++ library
               auto weights_view = make_view_1d(weights);
-        NDView<uint16_t, 1> input_view(input.mutable_data(), {input.size()});
+              NDView<uint16_t, 1> input_view(input.mutable_data(),
-        NDView<double, 1> output_view(output.mutable_data(), {output.size()});
+                                             {input.size()});
+              NDView<double, 1> output_view(output.mutable_data(),
+                                            {output.size()});
 
               apply_custom_weights(input_view, output_view, weights_view);
               return output;
@@ -103,7 +111,8 @@ py::class_<CtbRawFile>(m, "CtbRawFile")
                  // always read bytes
                  image = py::array_t<uint8_t>(shape);
 
-             self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
+                 self.read_into(
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
                      header.mutable_data());
 
                  return py::make_tuple(header, image);
@@ -116,5 +125,4 @@ py::class_<CtbRawFile>(m, "CtbRawFile")
                                &CtbRawFile::image_size_in_bytes)
 
         .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
-
 }

python/src/file.hpp

@@ -25,9 +25,6 @@
 namespace py = pybind11;
 using namespace ::aare;
 
-
-
-
 // Disable warnings for unused parameters, as we ignore some
 // in the __exit__ method
 #pragma GCC diagnostic push
@@ -35,7 +32,6 @@ using namespace ::aare;
 
 void define_file_io_bindings(py::module &m) {
 
-
     py::enum_<DetectorType>(m, "DetectorType")
         .value("Jungfrau", DetectorType::Jungfrau)
         .value("Eiger", DetectorType::Eiger)
@@ -46,13 +42,10 @@ void define_file_io_bindings(py::module &m) {
         .value("ChipTestBoard", DetectorType::ChipTestBoard)
         .value("Unknown", DetectorType::Unknown);
 
-
     PYBIND11_NUMPY_DTYPE(DetectorHeader, frameNumber, expLength, packetNumber,
                          bunchId, timestamp, modId, row, column, reserved,
                          debug, roundRNumber, detType, version, packetMask);
 
-   
-
     py::class_<File>(m, "File")
         .def(py::init([](const std::filesystem::path &fname) {
             return File(fname, "r", {});
@@ -117,9 +110,11 @@ void define_file_io_bindings(py::module &m) {
                      reinterpret_cast<std::byte *>(image.mutable_data()));
                  return image;
              })
-        .def("read_n", [](File &self, size_t n_frames) {
+        .def("read_n",
+             [](File &self, size_t n_frames) {
                  // adjust for actual frames left in the file
-            n_frames = std::min(n_frames, self.total_frames()-self.tell());
+                 n_frames =
+                     std::min(n_frames, self.total_frames() - self.tell());
                  if (n_frames == 0) {
                      throw std::runtime_error("No frames left in file");
                  }
@@ -134,21 +129,20 @@ void define_file_io_bindings(py::module &m) {
                  } else if (item_size == 4) {
                      image = py::array_t<uint32_t>(shape);
                  }
-            self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
+                 self.read_into(
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
                      n_frames);
                  return image;
              })
         .def("__enter__", [](File &self) { return &self; })
         .def("__exit__",
-             [](File &self,
+             [](File &self, const std::optional<pybind11::type> &exc_type,
-                const std::optional<pybind11::type> &exc_type,
                 const std::optional<pybind11::object> &exc_value,
                 const std::optional<pybind11::object> &traceback) {
                  //  self.close();
              })
         .def("__iter__", [](File &self) { return &self; })
         .def("__next__", [](File &self) {
-
             try {
                 const uint8_t item_size = self.bytes_per_pixel();
                 py::array image;
@@ -171,7 +165,6 @@ void define_file_io_bindings(py::module &m) {
             }
         });
 
-
     py::class_<FileConfig>(m, "FileConfig")
         .def(py::init<>())
         .def_readwrite("rows", &FileConfig::rows)
@@ -188,8 +181,6 @@ void define_file_io_bindings(py::module &m) {
             return "<FileConfig: " + a.to_string() + ">";
         });
 
-
-
     py::class_<ScanParameters>(m, "ScanParameters")
         .def(py::init<const std::string &>())
         .def(py::init<const ScanParameters &>())
@@ -200,7 +191,6 @@ void define_file_io_bindings(py::module &m) {
         .def_property_readonly("stop", &ScanParameters::stop)
         .def_property_readonly("step", &ScanParameters::step);
 
-
     py::class_<ROI>(m, "ROI")
         .def(py::init<>())
         .def(py::init<ssize_t, ssize_t, ssize_t, ssize_t>(), py::arg("xmin"),
@@ -209,23 +199,21 @@ void define_file_io_bindings(py::module &m) {
         .def_readwrite("xmax", &ROI::xmax)
         .def_readwrite("ymin", &ROI::ymin)
         .def_readwrite("ymax", &ROI::ymax)
-        .def("__str__", [](const ROI& self){
+        .def("__str__",
-            return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}", self.xmin, self.xmax, self.ymin, self.ymax);
+             [](const ROI &self) {
+                 return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}",
+                                    self.xmin, self.xmax, self.ymin, self.ymax);
              })
-        .def("__repr__", [](const ROI& self){
+        .def("__repr__",
-            return fmt::format("<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin, self.xmax, self.ymin, self.ymax);
+             [](const ROI &self) {
+                 return fmt::format(
+                     "<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin,
+                     self.xmax, self.ymin, self.ymax);
              })
         .def("__iter__", [](const ROI &self) {
             return py::make_iterator(&self.xmin, &self.ymax + 1); // NOLINT
         });
 
-    
-
-
-
-
-
-
 #pragma GCC diagnostic pop
     // py::class_<ClusterHeader>(m, "ClusterHeader")
     //     .def(py::init<>())

python/src/fit.hpp

@@ -9,7 +9,6 @@
 namespace py = pybind11;
 using namespace pybind11::literals;
 
-
 void define_fit_bindings(py::module &m) {
 
     // TODO! Evaluate without converting to double
@@ -61,7 +60,8 @@ void define_fit_bindings(py::module &m) {
            py::array_t<double, py::array::c_style | py::array::forcecast> par) {
             auto x_view = make_view_1d(x);
             auto par_view = make_view_1d(par);
-            auto y = new NDArray<double, 1>{aare::func::scurve(x_view, par_view)};
+            auto y =
+                new NDArray<double, 1>{aare::func::scurve(x_view, par_view)};
             return return_image_data(y);
         },
         R"(
@@ -82,7 +82,8 @@ void define_fit_bindings(py::module &m) {
            py::array_t<double, py::array::c_style | py::array::forcecast> par) {
             auto x_view = make_view_1d(x);
             auto par_view = make_view_1d(par);
-            auto y = new NDArray<double, 1>{aare::func::scurve2(x_view, par_view)};
+            auto y =
+                new NDArray<double, 1>{aare::func::scurve2(x_view, par_view)};
             return return_image_data(y);
         },
         R"(
@@ -139,7 +140,6 @@ n_threads : int, optional
            py::array_t<double, py::array::c_style | py::array::forcecast> y,
            py::array_t<double, py::array::c_style | py::array::forcecast> y_err,
            int n_threads) {
-
             if (y.ndim() == 3) {
                 // Allocate memory for the output
                 // Need to have pointers to allow python to manage
@@ -173,7 +173,6 @@ n_threads : int, optional
                 auto y_view_err = make_view_1d(y_err);
                 auto x_view = make_view_1d(x);
 
-
                 double chi2 = 0;
                 aare::fit_gaus(x_view, y_view, y_view_err, par->view(),
                                par_err->view(), chi2);
@@ -252,7 +251,6 @@ n_threads : int, optional
                                 "chi2"_a = return_image_data(chi2),
                                 "Ndf"_a = y.shape(2) - 2);
 
-
             } else if (y.ndim() == 1) {
                 auto par = new NDArray<double, 1>({2});
                 auto par_err = new NDArray<double, 1>({2});
@@ -339,7 +337,6 @@ n_threads : int, optional
                                 "chi2"_a = return_image_data(chi2),
                                 "Ndf"_a = y.shape(2) - 2);
 
-
             } else if (y.ndim() == 1) {
                 auto par = new NDArray<double, 1>({2});
                 auto par_err = new NDArray<double, 1>({2});
@@ -376,7 +373,6 @@ n_threads : int, optional
 )",
         py::arg("x"), py::arg("y"), py::arg("y_err"), py::arg("n_threads") = 4);
 
-
     m.def(
         "fit_scurve2",
         [](py::array_t<double, py::array::c_style | py::array::forcecast> x,
@@ -426,7 +422,6 @@ n_threads : int, optional
                                 "chi2"_a = return_image_data(chi2),
                                 "Ndf"_a = y.shape(2) - 2);
 
-
             } else if (y.ndim() == 1) {
                 auto par = new NDArray<double, 1>({6});
                 auto par_err = new NDArray<double, 1>({6});

python/src/jungfrau_data_file.hpp

@@ -21,10 +21,7 @@ using namespace ::aare;
 
 auto read_dat_frame(JungfrauDataFile &self) {
     py::array_t<JungfrauDataHeader> header(1);
-    py::array_t<uint16_t> image({
+    py::array_t<uint16_t> image({self.rows(), self.cols()});
-        self.rows(), 
-        self.cols() 
-    });
 
     self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
                    header.mutable_data());
@@ -40,9 +37,7 @@ auto read_n_dat_frames(JungfrauDataFile &self, size_t n_frames) {
     }
 
     py::array_t<JungfrauDataHeader> header(n_frames);
-    py::array_t<uint16_t> image({
+    py::array_t<uint16_t> image({n_frames, self.rows(), self.cols()});
-        n_frames, self.rows(), 
-        self.cols()});
 
     self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
                    n_frames, header.mutable_data());

python/src/module.cpp

@@ -3,10 +3,10 @@
 // New style file naming
 #include "bind_Cluster.hpp"
 #include "bind_ClusterCollector.hpp"
-#include "bind_ClusterFinder.hpp"
-#include "bind_ClusterFinderMT.hpp"
 #include "bind_ClusterFile.hpp"
 #include "bind_ClusterFileSink.hpp"
+#include "bind_ClusterFinder.hpp"
+#include "bind_ClusterFinderMT.hpp"
 #include "bind_ClusterVector.hpp"
 
 // TODO! migrate the other names
@@ -14,17 +14,17 @@
 #include "file.hpp"
 #include "fit.hpp"
 #include "interpolation.hpp"
-#include "raw_sub_file.hpp"
-#include "raw_master_file.hpp"
-#include "raw_file.hpp"
 #ifdef HDF5_FOUND
 #include "hdf5_file.hpp"
 #include "hdf5_master_file.hpp"
 #endif
-#include "pixel_map.hpp"
-#include "var_cluster.hpp"
-#include "pedestal.hpp"
 #include "jungfrau_data_file.hpp"
+#include "pedestal.hpp"
+#include "pixel_map.hpp"
+#include "raw_file.hpp"
+#include "raw_master_file.hpp"
+#include "raw_sub_file.hpp"
+#include "var_cluster.hpp"
 
 // Pybind stuff
 #include <pybind11/pybind11.h>
@@ -38,7 +38,8 @@ T - Storage type of the cluster data (int, float, double)
 N - Number of rows in the cluster
 M - Number of columns in the cluster
 U - Type of the pixel data (e.g., uint16_t)
-TYPE_CODE - A character representing the type code (e.g., 'i' for int, 'd' for double, 'f' for float)
+TYPE_CODE - A character representing the type code (e.g., 'i' for int, 'd' for
+double, 'f' for float)
 
 */
 #define DEFINE_CLUSTER_BINDINGS(T, N, M, U, TYPE_CODE)                         \

python/src/pedestal.hpp

@@ -9,7 +9,8 @@
 
 namespace py = pybind11;
 
-template <typename SUM_TYPE> void define_pedestal_bindings(py::module &m, const std::string &name) {
+template <typename SUM_TYPE>
+void define_pedestal_bindings(py::module &m, const std::string &name) {
     py::class_<Pedestal<SUM_TYPE>>(m, name.c_str())
         .def(py::init<int, int, int>())
         .def(py::init<int, int>())
@@ -19,12 +20,14 @@ template <typename SUM_TYPE> void define_pedestal_bindings(py::module &m, const
                  *mea = self.mean();
                  return return_image_data(mea);
              })
-        .def("variance", [](Pedestal<SUM_TYPE> &self) {
+        .def("variance",
+             [](Pedestal<SUM_TYPE> &self) {
                  auto var = new NDArray<SUM_TYPE, 2>{};
                  *var = self.variance();
                  return return_image_data(var);
              })
-        .def("std", [](Pedestal<SUM_TYPE> &self) {
+        .def("std",
+             [](Pedestal<SUM_TYPE> &self) {
                  auto std = new NDArray<SUM_TYPE, 2>{};
                  *std = self.std();
                  return return_image_data(std);
@@ -40,13 +43,18 @@ template <typename SUM_TYPE> void define_pedestal_bindings(py::module &m, const
                  return Pedestal<SUM_TYPE>(pedestal);
              })
         // TODO! add push for other data types
-        .def("push", [](Pedestal<SUM_TYPE> &pedestal, py::array_t<uint16_t> &f) {
+        .def("push",
+             [](Pedestal<SUM_TYPE> &pedestal, py::array_t<uint16_t> &f) {
                  auto v = make_view_2d(f);
                  pedestal.push(v);
              })
-        .def("push_no_update", [](Pedestal<SUM_TYPE> &pedestal, py::array_t<uint16_t, py::array::c_style> &f) {
+        .def(
+            "push_no_update",
+            [](Pedestal<SUM_TYPE> &pedestal,
+               py::array_t<uint16_t, py::array::c_style> &f) {
                 auto v = make_view_2d(f);
                 pedestal.push_no_update(v);
-        }, py::arg().noconvert())
+            },
+            py::arg().noconvert())
         .def("update_mean", &Pedestal<SUM_TYPE>::update_mean);
 }

python/src/pixel_map.hpp

@@ -1,41 +1,46 @@
 #include "aare/PixelMap.hpp"
 #include "np_helper.hpp"
 
-
 #include <cstdint>
 #include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
-
 namespace py = pybind11;
 using namespace ::aare;
 
-
 void define_pixel_map_bindings(py::module &m) {
-    m.def("GenerateMoench03PixelMap", []() {
+    m.def("GenerateMoench03PixelMap",
+          []() {
               auto ptr = new NDArray<ssize_t, 2>(GenerateMoench03PixelMap());
               return return_image_data(ptr);
           })
-    .def("GenerateMoench05PixelMap", []() {
+        .def("GenerateMoench05PixelMap",
+             []() {
                  auto ptr = new NDArray<ssize_t, 2>(GenerateMoench05PixelMap());
                  return return_image_data(ptr);
              })
-        .def("GenerateMoench05PixelMap1g", []() {
+        .def("GenerateMoench05PixelMap1g",
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap1g());
+             []() {
+                 auto ptr =
+                     new NDArray<ssize_t, 2>(GenerateMoench05PixelMap1g());
                  return return_image_data(ptr);
              })
-    .def("GenerateMoench05PixelMapOld", []() {
+        .def("GenerateMoench05PixelMapOld",
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMapOld());
+             []() {
+                 auto ptr =
+                     new NDArray<ssize_t, 2>(GenerateMoench05PixelMapOld());
                  return return_image_data(ptr);
              })
-    .def("GenerateMH02SingleCounterPixelMap", []() {
+        .def("GenerateMH02SingleCounterPixelMap",
-        auto ptr = new NDArray<ssize_t,2>(GenerateMH02SingleCounterPixelMap());
+             []() {
+                 auto ptr = new NDArray<ssize_t, 2>(
+                     GenerateMH02SingleCounterPixelMap());
                  return return_image_data(ptr);
              })
         .def("GenerateMH02FourCounterPixelMap", []() {
-        auto ptr = new NDArray<ssize_t,3>(GenerateMH02FourCounterPixelMap());
+            auto ptr =
+                new NDArray<ssize_t, 3>(GenerateMH02FourCounterPixelMap());
             return return_image_data(ptr);
         });
-
 }

python/src/raw_file.hpp

@@ -64,7 +64,8 @@ void define_raw_file_io_bindings(py::module &m) {
                 if (self.n_modules() == 1) {
                     header = py::array_t<DetectorHeader>(n_frames);
                 } else {
-                    header = py::array_t<DetectorHeader>({self.n_modules(), n_frames});
+                    header = py::array_t<DetectorHeader>(
+                        {self.n_modules(), n_frames});
                 }
                 // py::array_t<DetectorHeader> header({self.n_mod(), n_frames});
 

python/src/raw_master_file.hpp

@@ -57,7 +57,8 @@ void define_raw_master_file_bindings(py::module &m) {
         .def_property_readonly("total_frames_expected",
                                &RawMasterFile::total_frames_expected)
         .def_property_readonly("geometry", &RawMasterFile::geometry)
-        .def_property_readonly("analog_samples", &RawMasterFile::analog_samples, R"(
+        .def_property_readonly("analog_samples", &RawMasterFile::analog_samples,
+                               R"(
             Number of analog samples
 
             Returns

python/src/raw_sub_file.hpp

@@ -43,11 +43,9 @@ auto read_frame_from_RawSubFile(RawSubFile &self) {
 auto read_n_frames_from_RawSubFile(RawSubFile &self, size_t n_frames) {
     py::array_t<DetectorHeader> header(n_frames);
     const uint8_t item_size = self.bytes_per_pixel();
-    std::vector<ssize_t> shape{
+    std::vector<ssize_t> shape{static_cast<ssize_t>(n_frames),
-        static_cast<ssize_t>(n_frames), 
                                static_cast<ssize_t>(self.rows()),
-        static_cast<ssize_t>(self.cols())
+                               static_cast<ssize_t>(self.cols())};
-    };
 
     py::array image;
     if (item_size == 1) {
@@ -57,13 +55,12 @@ auto read_n_frames_from_RawSubFile(RawSubFile &self, size_t n_frames) {
     } else if (item_size == 4) {
         image = py::array_t<uint32_t>(shape);
     }
-    self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()), n_frames,
+    self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
-                   header.mutable_data());
+                   n_frames, header.mutable_data());
 
     return py::make_tuple(header, image);
 }
 
-
 // Disable warnings for unused parameters, as we ignore some
 // in the __exit__ method
 #pragma GCC diagnostic push
@@ -84,18 +81,17 @@ void define_raw_sub_file_io_bindings(py::module &m) {
         .def_property_readonly("frames_in_file", &RawSubFile::frames_in_file)
         .def("read_frame", &read_frame_from_RawSubFile)
         .def("read_n", &read_n_frames_from_RawSubFile)
-        .def("read", [](RawSubFile &self){
+        .def("read",
+             [](RawSubFile &self) {
                  self.seek(0);
                  auto n_frames = self.frames_in_file();
                  return read_n_frames_from_RawSubFile(self, n_frames);
              })
         .def("__enter__", [](RawSubFile &self) { return &self; })
         .def("__exit__",
-             [](RawSubFile &self,
+             [](RawSubFile &self, const std::optional<pybind11::type> &exc_type,
-                const std::optional<pybind11::type> &exc_type,
                 const std::optional<pybind11::object> &exc_value,
-                const std::optional<pybind11::object> &traceback) {
+                const std::optional<pybind11::object> &traceback) {})
-             })
         .def("__iter__", [](RawSubFile &self) { return &self; })
         .def("__next__", [](RawSubFile &self) {
             try {
@@ -104,7 +100,6 @@ void define_raw_sub_file_io_bindings(py::module &m) {
                 throw py::stop_iteration();
             }
         });
-
 }
 
 #pragma GCC diagnostic pop

python/src/var_cluster.hpp

@@ -12,11 +12,9 @@
 // #include <pybind11/stl/filesystem.h>
 // #include <string>
 
-
 namespace py = pybind11;
 using namespace ::aare;
 
-
 void define_var_cluster_finder_bindings(py::module &m) {
     PYBIND11_NUMPY_DTYPE(VarClusterFinder<double>::Hit, size, row, col,
                          reserved, energy, max, rows, cols, enes);
@@ -65,9 +63,7 @@ void define_var_cluster_finder_bindings(py::module &m) {
                  return return_vector(ptr);
              })
         .def("clear_hits",
-             [](VarClusterFinder<double> &self) {
+             [](VarClusterFinder<double> &self) { self.clear_hits(); })
-                 self.clear_hits();
-             })
         .def("steal_hits",
              [](VarClusterFinder<double> &self) {
                  auto ptr = new std::vector<VarClusterFinder<double>::Hit>(
@@ -75,5 +71,4 @@ void define_var_cluster_finder_bindings(py::module &m) {
                  return return_vector(ptr);
              })
         .def("total_clusters", &VarClusterFinder<double>::total_clusters);
-
 }

src/ClusterFile.cpp

@@ -31,9 +31,7 @@ ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
     }
 }
 
-void ClusterFile::set_roi(ROI roi){
+void ClusterFile::set_roi(ROI roi) { m_roi = roi; }
-    m_roi = roi;
-}
 
 void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map) {
     m_noise_map = NDArray<int32_t, 2>(noise_map);
@@ -75,16 +73,17 @@ void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
     // Then write the number of clusters - 4 bytes
     uint32_t n_clusters = clusters.size();
     if (fwrite(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not write number of clusters");
+        throw std::runtime_error(LOCATION +
+                                 "Could not write number of clusters");
     }
 
     // Now write the clusters in the frame
-    if(fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp)!=clusters.size()){
+    if (fwrite(clusters.data(), clusters.item_size(), clusters.size(), fp) !=
+        clusters.size()) {
         throw std::runtime_error(LOCATION + "Could not write clusters");
     }
 }
 
-
 ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters) {
     if (m_mode != "r") {
         throw std::runtime_error("File not opened for reading");
@@ -96,7 +95,8 @@ ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters){
     }
 }
 
-ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters) {
+ClusterVector<int32_t>
+ClusterFile::read_clusters_without_cut(size_t n_clusters) {
     if (m_mode != "r") {
         throw std::runtime_error("File not opened for reading");
     }
@@ -152,7 +152,6 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
     return clusters;
 }
 
-
 ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
     ClusterVector<int32_t> clusters(3, 3);
     clusters.reserve(n_clusters);
@@ -162,7 +161,8 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
         while (m_num_left && clusters.size() < n_clusters) {
             Cluster3x3 c = read_one_cluster();
             if (is_selected(c)) {
-                clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
+                clusters.push_back(c.x, c.y,
+                                   reinterpret_cast<std::byte *>(c.data));
             }
         }
     }
@@ -172,17 +172,21 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
     if (clusters.size() < n_clusters) {
         // sanity check
         if (m_num_left) {
-            throw std::runtime_error(LOCATION + "Entered second loop with clusters left\n");
+            throw std::runtime_error(
+                LOCATION + "Entered second loop with clusters left\n");
         }
 
         int32_t frame_number = 0; // frame number needs to be 4 bytes!
         while (fread(&frame_number, sizeof(frame_number), 1, fp)) {
             if (fread(&m_num_left, sizeof(m_num_left), 1, fp)) {
-                clusters.set_frame_number(frame_number); //cluster vector will hold the last frame number
+                clusters.set_frame_number(
+                    frame_number); // cluster vector will hold the last frame
+                                   // number
                 while (m_num_left && clusters.size() < n_clusters) {
                     Cluster3x3 c = read_one_cluster();
                     if (is_selected(c)) {
-                        clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
+                        clusters.push_back(
+                            c.x, c.y, reinterpret_cast<std::byte *>(c.data));
                     }
                 }
             }
@@ -191,7 +195,6 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
             if (clusters.size() >= n_clusters)
                 break;
         }
-
     }
     if (m_gain_map)
         clusters.apply_gain_map(m_gain_map->view());
@@ -235,7 +238,8 @@ ClusterVector<int32_t> ClusterFile::read_frame_without_cut() {
 
     int32_t n_clusters; // Saved as 32bit integer in the cluster file
     if (fread(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
-        throw std::runtime_error(LOCATION + "Could not read number of clusters");
+        throw std::runtime_error(LOCATION +
+                                 "Could not read number of clusters");
     }
 
     ClusterVector<int32_t> clusters(3, 3, n_clusters);
@@ -264,7 +268,6 @@ ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
         throw std::runtime_error("Could not read frame number");
     }
 
-
     if (fread(&m_num_left, sizeof(m_num_left), 1, fp) != 1) {
         throw std::runtime_error("Could not read number of clusters");
     }
@@ -283,8 +286,6 @@ ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
     return clusters;
 }
 
-
-
 bool ClusterFile::is_selected(Cluster3x3 &cl) {
     // Should fail fast
     if (m_roi) {
@@ -297,7 +298,8 @@ bool ClusterFile::is_selected(Cluster3x3 &cl) {
         int32_t sum_2x2 = cl.sum_2x2(); // highest sum of 2x2 subclusters
         int32_t sum_3x3 = cl.sum();     // sum of all pixels
 
-        auto noise = (*m_noise_map)(cl.y, cl.x); //TODO! check if this is correct
+        auto noise =
+            (*m_noise_map)(cl.y, cl.x); // TODO! check if this is correct
         if (sum_1x1 <= noise || sum_2x2 <= 2 * noise || sum_3x3 <= 3 * noise) {
             return false;
         }
@@ -316,7 +318,8 @@ NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
             eta2(i, 0) = e.x;
             eta2(i, 1) = e.y;
         }
-    }else if(clusters.cluster_size_x() == 2 || clusters.cluster_size_y() == 2){
+    } else if (clusters.cluster_size_x() == 2 ||
+               clusters.cluster_size_y() == 2) {
         for (size_t i = 0; i < clusters.size(); i++) {
             auto e = calculate_eta2(clusters.at<Cluster2x2>(i));
             eta2(i, 0) = e.x;
@@ -330,8 +333,8 @@ NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
 }
 
 /**
- * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2 struct
+ * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2
- * containing etay, etax and the corner of the cluster. 
+ * struct containing etay, etax and the corner of the cluster.
  */
 Eta2 calculate_eta2(Cluster3x3 &cl) {
     Eta2 eta{};
@@ -347,38 +350,30 @@ Eta2 calculate_eta2(Cluster3x3 &cl) {
     switch (c) {
     case cBottomLeft:
         if ((cl.data[3] + cl.data[4]) != 0)
-            eta.x =
+            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
         if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
+            eta.y = static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
         eta.c = cBottomLeft;
         break;
     case cBottomRight:
         if ((cl.data[2] + cl.data[5]) != 0)
-            eta.x =
+            eta.x = static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
-                static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
         if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
+            eta.y = static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
         eta.c = cBottomRight;
         break;
     case cTopLeft:
         if ((cl.data[7] + cl.data[4]) != 0)
-            eta.x =
+            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
         if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
+            eta.y = static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
         eta.c = cTopLeft;
         break;
     case cTopRight:
         if ((cl.data[5] + cl.data[4]) != 0)
-            eta.x =
+            eta.x = static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
-                static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
         if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
+            eta.y = static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
         eta.c = cTopRight;
         break;
         // no default to allow compiler to warn about missing cases
@@ -386,7 +381,6 @@ Eta2 calculate_eta2(Cluster3x3 &cl) {
     return eta;
 }
 
-
 Eta2 calculate_eta2(Cluster2x2 &cl) {
     Eta2 eta{};
     if ((cl.data[0] + cl.data[1]) != 0)
@@ -398,5 +392,4 @@ Eta2 calculate_eta2(Cluster2x2 &cl) {
     return eta;
 }
 
-
 } // namespace aare

src/ClusterFile.test.cpp

@@ -10,7 +10,6 @@ using aare::Cluster;
 using aare::ClusterFile;
 using aare::ClusterVector;
 
-
 TEST_CASE("Read one frame from a cluster file", "[.files]") {
     // We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
@@ -27,7 +26,6 @@ TEST_CASE("Read one frame from a cluster file", "[.files]") {
                      std::begin(expected_cluster_data)));
 }
 
-
 TEST_CASE("Read one frame using ROI", "[.files]") {
     // We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
@@ -60,8 +58,6 @@ TEST_CASE("Read one frame using ROI", "[.files]") {
                      std::begin(expected_cluster_data)));
 }
 
-
-
 TEST_CASE("Read clusters from single frame file", "[.files]") {
 
     //  frame_number, num_clusters   [135] 97

src/CtbRawFile.cpp

@@ -19,7 +19,8 @@ void CtbRawFile::read_into(std::byte *image_buf, DetectorHeader* header) {
         throw std::runtime_error(LOCATION + " End of file reached");
     }
 
-    if(m_current_frame != 0 && m_current_frame % m_master.max_frames_per_file() == 0){
+    if (m_current_frame != 0 &&
+        m_current_frame % m_master.max_frames_per_file() == 0) {
         open_data_file(m_current_subfile + 1);
     }
 
@@ -29,7 +30,8 @@ void CtbRawFile::read_into(std::byte *image_buf, DetectorHeader* header) {
         m_file.seekg(sizeof(DetectorHeader), std::ios::cur);
     }
 
-    m_file.read(reinterpret_cast<char *>(image_buf), m_master.image_size_in_bytes());
+    m_file.read(reinterpret_cast<char *>(image_buf),
+                m_master.image_size_in_bytes());
     m_current_frame++;
 }
 
@@ -38,13 +40,16 @@ void CtbRawFile::seek(size_t frame_number) {
         open_data_file(index);
     }
     size_t frame_number_in_file = frame_number % m_master.max_frames_per_file();
-    m_file.seekg((sizeof(DetectorHeader)+m_master.image_size_in_bytes()) * frame_number_in_file);
+    m_file.seekg((sizeof(DetectorHeader) + m_master.image_size_in_bytes()) *
+                 frame_number_in_file);
     m_current_frame = frame_number;
 }
 
 size_t CtbRawFile::tell() const { return m_current_frame; }
 
-size_t CtbRawFile::image_size_in_bytes() const { return m_master.image_size_in_bytes(); }
+size_t CtbRawFile::image_size_in_bytes() const {
+    return m_master.image_size_in_bytes();
+}
 
 size_t CtbRawFile::frames_in_file() const { return m_master.frames_in_file(); }
 
@@ -63,12 +68,11 @@ void CtbRawFile::open_data_file(size_t subfile_index) {
         throw std::runtime_error(LOCATION + "Subfile index out of range");
     }
     m_current_subfile = subfile_index;
-    m_file = std::ifstream(m_master.data_fname(0, subfile_index), std::ios::binary); // only one module for CTB
+    m_file = std::ifstream(m_master.data_fname(0, subfile_index),
+                           std::ios::binary); // only one module for CTB
     if (!m_file.is_open()) {
         throw std::runtime_error(LOCATION + "Could not open data file");
     }
 }
 
-
-
 } // namespace aare

src/Dtype.cpp

@@ -10,7 +10,8 @@ namespace aare {
  * @brief Construct a DType object from a type_info object
  * @param t type_info object
  * @throw runtime_error if the type is not supported
- * @note supported types are: int8_t, uint8_t, int16_t, uint16_t, int32_t, uint32_t, int64_t, uint64_t, float, double
+ * @note supported types are: int8_t, uint8_t, int16_t, uint16_t, int32_t,
+ * uint32_t, int64_t, uint64_t, float, double
  * @note the type_info object is obtained using typeid (e.g. typeid(int))
  */
 Dtype::Dtype(const std::type_info &t) {
@@ -35,7 +36,8 @@ Dtype::Dtype(const std::type_info &t) {
     else if (t == typeid(double))
         m_type = TypeIndex::DOUBLE;
     else
-        throw std::runtime_error("Could not construct data type. Type not supported.");
+        throw std::runtime_error(
+            "Could not construct data type. Type not supported.");
 }
 
 /**
@@ -63,7 +65,8 @@ uint8_t Dtype::bitdepth() const {
     case TypeIndex::NONE:
         return 0;
     default:
-        throw std::runtime_error(LOCATION + "Could not get bitdepth. Type not supported.");
+        throw std::runtime_error(LOCATION +
+                                 "Could not get bitdepth. Type not supported.");
     }
 }
 
@@ -138,7 +141,8 @@ Dtype Dtype::from_bitdepth(uint8_t bitdepth) {
     case 64:
         return Dtype(TypeIndex::UINT64);
     default:
-        throw std::runtime_error("Could not construct data type from bitdepth.");
+        throw std::runtime_error(
+            "Could not construct data type from bitdepth.");
     }
 }
 /**
@@ -175,17 +179,27 @@ std::string Dtype::to_string() const {
     case TypeIndex::DOUBLE:
         return "f8";
     case TypeIndex::ERROR:
-        throw std::runtime_error("Could not get string representation. Type not supported.");
+        throw std::runtime_error(
+            "Could not get string representation. Type not supported.");
     case TypeIndex::NONE:
-        throw std::runtime_error("Could not get string representation. Type not supported.");
+        throw std::runtime_error(
+            "Could not get string representation. Type not supported.");
     }
     return {};
 }
 
-bool Dtype::operator==(const Dtype &other) const noexcept { return m_type == other.m_type; }
+bool Dtype::operator==(const Dtype &other) const noexcept {
-bool Dtype::operator!=(const Dtype &other) const noexcept { return !(*this == other); }
+    return m_type == other.m_type;
+}
+bool Dtype::operator!=(const Dtype &other) const noexcept {
+    return !(*this == other);
+}
 
-bool Dtype::operator==(const std::type_info &t) const { return Dtype(t) == *this; }
+bool Dtype::operator==(const std::type_info &t) const {
-bool Dtype::operator!=(const std::type_info &t) const { return Dtype(t) != *this; }
+    return Dtype(t) == *this;
+}
+bool Dtype::operator!=(const std::type_info &t) const {
+    return Dtype(t) != *this;
+}
 
 } // namespace aare

src/Dtype.test.cpp

@@ -51,4 +51,6 @@ TEST_CASE("Construct from string with endianess") {
     REQUIRE_THROWS(Dtype(">i4") == typeid(int32_t));
 }
 
-TEST_CASE("Convert to string") { REQUIRE(Dtype(typeid(int)).to_string() == "<i4"); }
+TEST_CASE("Convert to string") {
+    REQUIRE(Dtype(typeid(int)).to_string() == "<i4");
+}

src/File.cpp

@@ -27,8 +27,7 @@ File::File(const std::filesystem::path &fname, const std::string &mode,
     if (fname.extension() == ".raw" || fname.extension() == ".json") {
         // file_impl = new RawFile(fname, mode, cfg);
         file_impl = std::make_unique<RawFile>(fname, mode);
-    }
+    } else if (fname.extension() == ".npy") {
-    else if (fname.extension() == ".npy") {
         // file_impl = new NumpyFile(fname, mode, cfg);
         file_impl = std::make_unique<NumpyFile>(fname, mode, cfg);
     }
@@ -48,10 +47,7 @@ File::File(const std::filesystem::path &fname, const std::string &mode,
     }
 }
 
-
+File::File(File &&other) noexcept { std::swap(file_impl, other.file_impl); }
-File::File(File &&other) noexcept{
-    std::swap(file_impl, other.file_impl);
-}
 
 File &File::operator=(File &&other) noexcept {
     if (this != &other) {
@@ -89,9 +85,10 @@ size_t File::tell() const { return file_impl->tell(); }
 size_t File::rows() const { return file_impl->rows(); }
 size_t File::cols() const { return file_impl->cols(); }
 size_t File::bitdepth() const { return file_impl->bitdepth(); }
-size_t File::bytes_per_pixel() const { return file_impl->bitdepth() / bits_per_byte; }
+size_t File::bytes_per_pixel() const {
+    return file_impl->bitdepth() / bits_per_byte;
+}
 
 DetectorType File::detector_type() const { return file_impl->detector_type(); }
 
-
 } // namespace aare

src/FilePtr.cpp

@@ -6,10 +6,12 @@
 
 namespace aare {
 
-FilePtr::FilePtr(const std::filesystem::path& fname, const std::string& mode = "rb") {
+FilePtr::FilePtr(const std::filesystem::path &fname,
+                 const std::string &mode = "rb") {
     fp_ = fopen(fname.c_str(), mode.c_str());
     if (!fp_)
-        throw std::runtime_error(fmt::format("Could not open: {}", fname.c_str()));
+        throw std::runtime_error(
+            fmt::format("Could not open: {}", fname.c_str()));
 }
 
 FilePtr::FilePtr(FilePtr &&other) { std::swap(fp_, other.fp_); }
@@ -24,7 +26,8 @@ FILE *FilePtr::get() { return fp_; }
 ssize_t FilePtr::tell() {
     auto pos = ftell(fp_);
     if (pos == -1)
-        throw std::runtime_error(fmt::format("Error getting file position: {}", error_msg()));
+        throw std::runtime_error(
+            fmt::format("Error getting file position: {}", error_msg()));
     return pos;
 }
 FilePtr::~FilePtr() {

src/Fit.cpp

@@ -1,13 +1,12 @@
 #include "aare/Fit.hpp"
-#include "aare/utils/task.hpp"
 #include "aare/utils/par.hpp"
+#include "aare/utils/task.hpp"
 #include <lmcurve2.h>
 #include <lmfit.hpp>
 #include <thread>
 
 #include <array>
 
-
 namespace aare {
 
 namespace func {
@@ -35,7 +34,9 @@ NDArray<double, 1> pol1(NDView<double, 1> x, NDView<double, 1> par) {
 }
 
 double scurve(const double x, const double *par) {
-    return (par[0] + par[1] * x) + 0.5 * (1 + erf((x - par[2]) / (sqrt(2) * par[3]))) * (par[4] + par[5] * (x - par[2]));
+    return (par[0] + par[1] * x) +
+           0.5 * (1 + erf((x - par[2]) / (sqrt(2) * par[3]))) *
+               (par[4] + par[5] * (x - par[2]));
 }
 
 NDArray<double, 1> scurve(NDView<double, 1> x, NDView<double, 1> par) {
@@ -47,7 +48,9 @@ NDArray<double, 1> scurve(NDView<double, 1> x, NDView<double, 1> par) {
 }
 
 double scurve2(const double x, const double *par) {
-    return (par[0] + par[1] * x) + 0.5 * (1 - erf((x - par[2]) / (sqrt(2) * par[3]))) * (par[4] + par[5] * (x - par[2]));
+    return (par[0] + par[1] * x) +
+           0.5 * (1 - erf((x - par[2]) / (sqrt(2) * par[3]))) *
+               (par[4] + par[5] * (x - par[2]));
 }
 
 NDArray<double, 1> scurve2(NDView<double, 1> x, NDView<double, 1> par) {
@@ -91,7 +94,8 @@ NDArray<double, 3> fit_gaus(NDView<double, 1> x, NDView<double, 3> y,
     return result;
 }
 
-std::array<double, 3> gaus_init_par(const NDView<double, 1> x, const NDView<double, 1> y) {
+std::array<double, 3> gaus_init_par(const NDView<double, 1> x,
+                                    const NDView<double, 1> y) {
     std::array<double, 3> start_par{0, 0, 0};
     auto e = std::max_element(y.begin(), y.end());
     auto idx = std::distance(y.begin(), e);
@@ -103,20 +107,18 @@ std::array<double, 3> gaus_init_par(const NDView<double, 1> x, const NDView<doub
     // For sigma we estimate the fwhm and divide by 2.35
     // assuming equally spaced x values
     auto delta = x[1] - x[0];
-    start_par[2] =
+    start_par[2] = std::count_if(y.begin(), y.end(),
-        std::count_if(y.begin(), y.end(),
                                  [e](double val) { return val > *e / 2; }) *
                    delta / 2.35;
 
     return start_par;
 }
 
-
+std::array<double, 2> pol1_init_par(const NDView<double, 1> x,
-std::array<double, 2> pol1_init_par(const NDView<double, 1> x, const NDView<double, 1> y){
+                                    const NDView<double, 1> y) {
     // Estimate the initial parameters for the fit
     std::array<double, 2> start_par{0, 0};
 
-    
     auto y2 = std::max_element(y.begin(), y.end());
     auto x2 = x[std::distance(y.begin(), y2)];
     auto y1 = std::min_element(y.begin(), y.end());
@@ -141,7 +143,6 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
                                  "and par_out, par_err_out must have size 3");
     }
 
-
     // /* Collection of output parameters for status info. */
     // typedef struct {
     //     double fnorm;  /* norm of the residue vector fvec. */
@@ -153,23 +154,32 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
     //     */
     // } lm_status_struct;
 
-
     lm_status_struct status;
     par_out = gaus_init_par(x, y);
     std::array<double, 9> cov{0, 0, 0, 0, 0, 0, 0, 0, 0};
 
-    // void lmcurve2( const int n_par, double *par, double *parerr, double *covar, const int m_dat, const double *t, const double *y, const double *dy, double (*f)( const double ti, const double *par ), const lm_control_struct *control, lm_status_struct *status);
+    // void lmcurve2( const int n_par, double *par, double *parerr, double
-    // n_par - Number of free variables. Length of parameter vector par.
+    // *covar, const int m_dat, const double *t, const double *y, const double
-    // par - Parameter vector. On input, it must contain a reasonable guess. On output, it contains the solution found to minimize ||r||.
+    // *dy, double (*f)( const double ti, const double *par ), const
-    // parerr - Parameter uncertainties vector. Array of length n_par or NULL. On output, unless it or covar is NULL, it contains the weighted parameter uncertainties for the found parameters.
+    // lm_control_struct *control, lm_status_struct *status); n_par - Number of
-    // covar - Covariance matrix. Array of length n_par * n_par or NULL. On output, unless it is NULL, it contains the covariance matrix.
+    // free variables. Length of parameter vector par. par - Parameter vector.
-    // m_dat - Number of data points. Length of vectors t, y, dy. Must statisfy n_par <= m_dat.
+    // On input, it must contain a reasonable guess. On output, it contains the
-    // t - Array of length m_dat. Contains the abcissae (time, or "x") for which function f will be evaluated.
+    // solution found to minimize ||r||. parerr - Parameter uncertainties
-    // y - Array of length m_dat. Contains the ordinate values that shall be fitted.
+    // vector. Array of length n_par or NULL. On output, unless it or covar is
-    // dy - Array of length m_dat. Contains the standard deviations of the values y.
+    // NULL, it contains the weighted parameter uncertainties for the found
-    // f - A user-supplied parametric function f(ti;par).
+    // parameters. covar - Covariance matrix. Array of length n_par * n_par or
-    // control - Parameter collection for tuning the fit procedure. In most cases, the default &lm_control_double is adequate. If f is only computed with single-precision accuracy, &lm_control_float should be used. Parameters are explained in lmmin2(3).
+    // NULL. On output, unless it is NULL, it contains the covariance matrix.
-    // status - A record used to return information about the minimization process: For details, see lmmin2(3).
+    // m_dat - Number of data points. Length of vectors t, y, dy. Must statisfy
+    // n_par <= m_dat. t - Array of length m_dat. Contains the abcissae (time,
+    // or "x") for which function f will be evaluated. y - Array of length
+    // m_dat. Contains the ordinate values that shall be fitted. dy - Array of
+    // length m_dat. Contains the standard deviations of the values y. f - A
+    // user-supplied parametric function f(ti;par). control - Parameter
+    // collection for tuning the fit procedure. In most cases, the default
+    // &lm_control_double is adequate. If f is only computed with
+    // single-precision accuracy, &lm_control_float should be used. Parameters
+    // are explained in lmmin2(3). status - A record used to return information
+    // about the minimization process: For details, see lmmin2(3).
 
     lmcurve2(par_out.size(), par_out.data(), par_err_out.data(), cov.data(),
              x.size(), x.data(), y.data(), y_err.data(), aare::func::gaus,
@@ -178,12 +188,14 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
     // Calculate chi2
     chi2 = 0;
     for (ssize_t i = 0; i < y.size(); i++) {
-        chi2 += std::pow((y(i) - func::gaus(x(i), par_out.data())) / y_err(i), 2);
+        chi2 +=
+            std::pow((y(i) - func::gaus(x(i), par_out.data())) / y_err(i), 2);
     }
 }
 
 void fit_gaus(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out,  NDView<double, 2> chi2_out,
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
+              NDView<double, 2> chi2_out,
 
               int n_threads) {
 
@@ -200,7 +212,6 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
 
                 fit_gaus(x, y_view, y_err_view, par_out_view, par_err_out_view,
                          chi2_out(row, col));
-
             }
         }
     };
@@ -210,7 +221,8 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
 }
 
 void fit_pol1(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2) {
+              NDView<double, 1> par_out, NDView<double, 1> par_err_out,
+              double &chi2) {
 
     // Check that we have the correct sizes
     if (y.size() != x.size() || y.size() != y_err.size() ||
@@ -230,13 +242,14 @@ void fit_pol1(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
     // Calculate chi2
     chi2 = 0;
     for (ssize_t i = 0; i < y.size(); i++) {
-        chi2 += std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
+        chi2 +=
+            std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
     }
 }
 
 void fit_pol1(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
-              int n_threads) {
+              NDView<double, 2> chi2_out, int n_threads) {
 
     auto process = [&](ssize_t first_row, ssize_t last_row) {
         for (ssize_t row = first_row; row < last_row; row++) {
@@ -249,15 +262,14 @@ void fit_pol1(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
                 NDView<double, 1> par_err_out_view(&par_err_out(row, col, 0),
                                                    {par_err_out.shape(2)});
 
-                fit_pol1(x, y_view, y_err_view, par_out_view, par_err_out_view, chi2_out(row, col));
+                fit_pol1(x, y_view, y_err_view, par_out_view, par_err_out_view,
-
+                         chi2_out(row, col));
             }
         }
     };
 
     auto tasks = split_task(0, y.shape(0), n_threads);
     RunInParallel(process, tasks);
-
 }
 
 NDArray<double, 1> fit_pol1(NDView<double, 1> x, NDView<double, 1> y) {
@@ -300,7 +312,8 @@ NDArray<double, 3> fit_pol1(NDView<double, 1> x, NDView<double, 3> y,
 // ~~ S-CURVES ~~
 
 // SCURVE --
-std::array<double, 6> scurve_init_par(const NDView<double, 1> x, const NDView<double, 1> y){
+std::array<double, 6> scurve_init_par(const NDView<double, 1> x,
+                                      const NDView<double, 1> y) {
     // Estimate the initial parameters for the fit
     std::array<double, 6> start_par{0, 0, 0, 0, 0, 0};
 
@@ -308,7 +321,8 @@ std::array<double, 6> scurve_init_par(const NDView<double, 1> x, const NDView<do
     auto ymin = std::min_element(y.begin(), y.end());
     start_par[4] = *ymin + (*ymax - *ymin) / 2;
 
-        // Find the first x where the corresponding y value is above the threshold (start_par[4])
+    // Find the first x where the corresponding y value is above the threshold
+    // (start_par[4])
     for (ssize_t i = 0; i < y.size(); ++i) {
         if (y[i] >= start_par[4]) {
             start_par[2] = x[i];
@@ -334,7 +348,8 @@ NDArray<double, 1> fit_scurve(NDView<double, 1> x, NDView<double, 1> y) {
     return result;
 }
 
-NDArray<double, 3> fit_scurve(NDView<double, 1> x, NDView<double, 3> y, int n_threads) {
+NDArray<double, 3> fit_scurve(NDView<double, 1> x, NDView<double, 3> y,
+                              int n_threads) {
     NDArray<double, 3> result({y.shape(0), y.shape(1), 6}, 0);
 
     auto process = [&x, &y, &result](ssize_t first_row, ssize_t last_row) {
@@ -358,8 +373,9 @@ NDArray<double, 3> fit_scurve(NDView<double, 1> x, NDView<double, 3> y, int n_th
 }
 
 // - Error
-void fit_scurve(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
+void fit_scurve(NDView<double, 1> x, NDView<double, 1> y,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2) {
+                NDView<double, 1> y_err, NDView<double, 1> par_out,
+                NDView<double, 1> par_err_out, double &chi2) {
 
     // Check that we have the correct sizes
     if (y.size() != x.size() || y.size() != y_err.size() ||
@@ -380,12 +396,14 @@ void fit_scurve(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_er
     // Calculate chi2
     chi2 = 0;
     for (ssize_t i = 0; i < y.size(); i++) {
-        chi2 += std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
+        chi2 +=
+            std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
     }
 }
 
-void fit_scurve(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
+void fit_scurve(NDView<double, 1> x, NDView<double, 3> y,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+                NDView<double, 3> y_err, NDView<double, 3> par_out,
+                NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
                 int n_threads) {
 
     auto process = [&](ssize_t first_row, ssize_t last_row) {
@@ -399,20 +417,20 @@ void fit_scurve(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_er
                 NDView<double, 1> par_err_out_view(&par_err_out(row, col, 0),
                                                    {par_err_out.shape(2)});
 
-                fit_scurve(x, y_view, y_err_view, par_out_view, par_err_out_view, chi2_out(row, col));
+                fit_scurve(x, y_view, y_err_view, par_out_view,
-
+                           par_err_out_view, chi2_out(row, col));
             }
         }
     };
 
     auto tasks = split_task(0, y.shape(0), n_threads);
     RunInParallel(process, tasks);
-
 }
 
 // SCURVE2 ---
 
-std::array<double, 6> scurve2_init_par(const NDView<double, 1> x, const NDView<double, 1> y){
+std::array<double, 6> scurve2_init_par(const NDView<double, 1> x,
+                                       const NDView<double, 1> y) {
     // Estimate the initial parameters for the fit
     std::array<double, 6> start_par{0, 0, 0, 0, 0, 0};
 
@@ -420,7 +438,8 @@ std::array<double, 6> scurve2_init_par(const NDView<double, 1> x, const NDView<d
     auto ymin = std::min_element(y.begin(), y.end());
     start_par[4] = *ymin + (*ymax - *ymin) / 2;
 
-        // Find the first x where the corresponding y value is above the threshold (start_par[4])
+    // Find the first x where the corresponding y value is above the threshold
+    // (start_par[4])
     for (ssize_t i = 0; i < y.size(); ++i) {
         if (y[i] <= start_par[4]) {
             start_par[2] = x[i];
@@ -446,7 +465,8 @@ NDArray<double, 1> fit_scurve2(NDView<double, 1> x, NDView<double, 1> y) {
     return result;
 }
 
-NDArray<double, 3> fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, int n_threads) {
+NDArray<double, 3> fit_scurve2(NDView<double, 1> x, NDView<double, 3> y,
+                               int n_threads) {
     NDArray<double, 3> result({y.shape(0), y.shape(1), 6}, 0);
 
     auto process = [&x, &y, &result](ssize_t first_row, ssize_t last_row) {
@@ -470,8 +490,9 @@ NDArray<double, 3> fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, int n_t
 }
 
 // - Error
-void fit_scurve2(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
+void fit_scurve2(NDView<double, 1> x, NDView<double, 1> y,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2) {
+                 NDView<double, 1> y_err, NDView<double, 1> par_out,
+                 NDView<double, 1> par_err_out, double &chi2) {
 
     // Check that we have the correct sizes
     if (y.size() != x.size() || y.size() != y_err.size() ||
@@ -492,12 +513,14 @@ void fit_scurve2(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_e
     // Calculate chi2
     chi2 = 0;
     for (ssize_t i = 0; i < y.size(); i++) {
-        chi2 += std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
+        chi2 +=
+            std::pow((y(i) - func::pol1(x(i), par_out.data())) / y_err(i), 2);
     }
 }
 
-void fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
+void fit_scurve2(NDView<double, 1> x, NDView<double, 3> y,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
+                 NDView<double, 3> y_err, NDView<double, 3> par_out,
+                 NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
                  int n_threads) {
 
     auto process = [&](ssize_t first_row, ssize_t last_row) {
@@ -511,15 +534,14 @@ void fit_scurve2(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_e
                 NDView<double, 1> par_err_out_view(&par_err_out(row, col, 0),
                                                    {par_err_out.shape(2)});
 
-                fit_scurve2(x, y_view, y_err_view, par_out_view, par_err_out_view, chi2_out(row, col));
+                fit_scurve2(x, y_view, y_err_view, par_out_view,
-
+                            par_err_out_view, chi2_out(row, col));
             }
         }
     };
 
     auto tasks = split_task(0, y.shape(0), n_threads);
     RunInParallel(process, tasks);
-
 }
 
 } // namespace aare

src/Frame.cpp

@@ -29,7 +29,6 @@ uint64_t Frame::size() const { return m_rows * m_cols; }
 size_t Frame::bytes() const { return m_rows * m_cols * m_dtype.bytes(); }
 std::byte *Frame::data() const { return m_data; }
 
-
 std::byte *Frame::pixel_ptr(uint32_t row, uint32_t col) const {
     if ((row >= m_rows) || (col >= m_cols)) {
         std::cerr << "Invalid row or column index" << '\n';
@@ -38,7 +37,6 @@ std::byte *Frame::pixel_ptr(uint32_t row, uint32_t col) const{
     return m_data + (row * m_cols + col) * (m_dtype.bytes());
 }
 
-
 Frame &Frame::operator=(Frame &&other) noexcept {
     if (this == &other) {
         return *this;
@@ -70,5 +68,4 @@ Frame Frame::clone() const {
     return frame;
 }
 
-
 } // namespace aare

src/Frame.test.cpp

@@ -65,7 +65,8 @@ TEST_CASE("Set a value in a 64 bit frame") {
     // only the value we did set should be non-zero
     for (size_t i = 0; i < rows; i++) {
         for (size_t j = 0; j < cols; j++) {
-            uint64_t *data = reinterpret_cast<uint64_t *>(frame.pixel_ptr(i, j));
+            uint64_t *data =
+                reinterpret_cast<uint64_t *>(frame.pixel_ptr(i, j));
             REQUIRE(data != nullptr);
             if (i == 5 && j == 7) {
                 REQUIRE(*data == value);
@@ -150,4 +151,3 @@ TEST_CASE("test explicit copy constructor") {
     REQUIRE(frame2.bytes() == rows * cols * bitdepth / 8);
     REQUIRE(frame2.data() != data);
 }
-

src/JungfrauDataFile.cpp

@@ -19,7 +19,6 @@ JungfrauDataFile::JungfrauDataFile(const std::filesystem::path &fname) {
     open_file(m_current_file_index);
 }
 
-
 // FileInterface
 
 Frame JungfrauDataFile::read_frame() {
@@ -59,7 +58,9 @@ std::array<ssize_t, 2> JungfrauDataFile::shape() const {
     return {static_cast<ssize_t>(rows()), static_cast<ssize_t>(cols())};
 }
 
-DetectorType JungfrauDataFile::detector_type() const { return DetectorType::Jungfrau; }
+DetectorType JungfrauDataFile::detector_type() const {
+    return DetectorType::Jungfrau;
+}
 
 std::string JungfrauDataFile::base_name() const { return m_base_name; }
 
@@ -202,15 +203,16 @@ void JungfrauDataFile::read_into(std::byte *image_buf, size_t n_frames,
     }
 }
 
-void JungfrauDataFile::read_into(NDArray<uint16_t>* image, JungfrauDataHeader* header) {
+void JungfrauDataFile::read_into(NDArray<uint16_t> *image,
+                                 JungfrauDataHeader *header) {
     if (image->shape() != shape()) {
-        throw std::runtime_error(LOCATION +
+        throw std::runtime_error(
-            "Image shape does not match file size: " + std::to_string(rows()) + "x" + std::to_string(cols()));
+            LOCATION + "Image shape does not match file size: " +
+            std::to_string(rows()) + "x" + std::to_string(cols()));
     }
     read_into(reinterpret_cast<std::byte *>(image->data()), header);
 }
 
-
 JungfrauDataHeader JungfrauDataFile::read_header() {
     JungfrauDataHeader header;
     if (auto rc = fread(&header, 1, sizeof(header), m_fp.get());

src/JungfrauDataFile.test.cpp

@@ -1,7 +1,7 @@
 #include "aare/JungfrauDataFile.hpp"
 
-#include <catch2/catch_test_macros.hpp>
 #include "test_config.hpp"
+#include <catch2/catch_test_macros.hpp>
 
 using aare::JungfrauDataFile;
 using aare::JungfrauDataHeader;
@@ -92,7 +92,6 @@ TEST_CASE("Open a Jungfrau data file with non zero file index", "[.files]"){
     REQUIRE(f.n_files() == 4);
 
     REQUIRE(f.current_file().stem() == "AldoJF65k_000003");
-
 }
 
 TEST_CASE("Read into throws if size doesn't match", "[.files]") {
@@ -109,6 +108,4 @@ TEST_CASE("Read into throws if size doesn't match", "[.files]"){
     REQUIRE_THROWS(f.read_into(&image));
 
     REQUIRE(f.tell() == 0);
-
-
 }

src/NDArray.test.cpp

@@ -162,7 +162,6 @@ NDArray<int> AddNDArrayUsingIndex(NDArray<int> &a, NDArray<int> &b) {
     return res;
 }
 
-
 TEST_CASE("Compare two images") {
     NDArray<int> a;
     NDArray<int> b;
@@ -222,7 +221,6 @@ TEST_CASE("Bitwise and on data") {
     REQUIRE(a(2) == 384);
 }
 
-
 TEST_CASE("Elementwise operations on images") {
     std::array<ssize_t, 2> shape{5, 5};
     double a_val = 3.0;
@@ -258,7 +256,8 @@ TEST_CASE("Elementwise operations on images") {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
         NDArray<double> C = A - B;
-        // auto C = A - B; // This works but the result is a lazy ArraySub object
+        // auto C = A - B; // This works but the result is a lazy ArraySub
+        // object
 
         // Value of C matches
         for (uint32_t i = 0; i < C.size(); ++i) {
@@ -282,7 +281,8 @@ TEST_CASE("Elementwise operations on images") {
     SECTION("Multiply two images") {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
-        // auto C = A * B; // This works but the result is a lazy ArrayMul object
+        // auto C = A * B; // This works but the result is a lazy ArrayMul
+        // object
         NDArray<double> C = A * B;
 
         // Value of C matches
@@ -307,7 +307,8 @@ TEST_CASE("Elementwise operations on images") {
     SECTION("Divide two images") {
         NDArray<double> A(shape, a_val);
         NDArray<double> B(shape, b_val);
-        // auto C = A / B; // This works but the result is a lazy ArrayDiv object
+        // auto C = A / B; // This works but the result is a lazy ArrayDiv
+        // object
         NDArray<double> C = A / B;
 
         // Value of C matches

src/NDView.test.cpp

@@ -2,8 +2,8 @@
 #include <catch2/catch_test_macros.hpp>
 
 #include <iostream>
-#include <vector>
 #include <numeric>
+#include <vector>
 
 using aare::NDView;
 using aare::Shape;
@@ -151,8 +151,10 @@ TEST_CASE("divide with another span") {
     std::vector<int> vec1{3, 2, 1};
     std::vector<int> result{3, 6, 3};
 
-    NDView<int, 1> data0(vec0.data(), Shape<1>{static_cast<ssize_t>(vec0.size())});
+    NDView<int, 1> data0(vec0.data(),
-    NDView<int, 1> data1(vec1.data(), Shape<1>{static_cast<ssize_t>(vec1.size())});
+                         Shape<1>{static_cast<ssize_t>(vec0.size())});
+    NDView<int, 1> data1(vec1.data(),
+                         Shape<1>{static_cast<ssize_t>(vec1.size())});
 
     data0 /= data1;
 
@@ -181,7 +183,6 @@ TEST_CASE("compare two views") {
     REQUIRE((view1 == view2));
 }
 
-
 TEST_CASE("Create a view over a vector") {
     std::vector<int> vec(12);
     std::iota(vec.begin(), vec.end(), 0);

src/NumpyFile.cpp

@@ -4,16 +4,16 @@
 
 namespace aare {
 
-
+NumpyFile::NumpyFile(const std::filesystem::path &fname,
-
+                     const std::string &mode, FileConfig cfg) {
-NumpyFile::NumpyFile(const std::filesystem::path &fname, const std::string &mode, FileConfig cfg) {
     // TODO! add opts to constructor
 
     m_mode = mode;
     if (mode == "r") {
         fp = fopen(fname.string().c_str(), "rb");
         if (!fp) {
-            throw std::runtime_error(fmt::format("Could not open: {} for reading", fname.string()));
+            throw std::runtime_error(
+                fmt::format("Could not open: {} for reading", fname.string()));
         }
         load_metadata();
     } else if (mode == "w") {
@@ -24,11 +24,15 @@ NumpyFile::NumpyFile(const std::filesystem::path &fname, const std::string &mode
         m_header.shape = {0, cfg.rows, cfg.cols};
         fp = fopen(fname.string().c_str(), "wb");
         if (!fp) {
-            throw std::runtime_error(fmt::format("Could not open: {} for reading", fname.string()));
+            throw std::runtime_error(
+                fmt::format("Could not open: {} for reading", fname.string()));
         }
-        initial_header_len = aare::NumpyHelpers::write_header(std::filesystem::path(fname.c_str()), m_header);
+        initial_header_len = aare::NumpyHelpers::write_header(
+            std::filesystem::path(fname.c_str()), m_header);
     }
-    m_pixels_per_frame = std::accumulate(m_header.shape.begin() + 1, m_header.shape.end(), 1, std::multiplies<>());
+    m_pixels_per_frame =
+        std::accumulate(m_header.shape.begin() + 1, m_header.shape.end(), 1,
+                        std::multiplies<>());
 
     m_bytes_per_frame = m_header.dtype.bitdepth() / 8 * m_pixels_per_frame;
 }
@@ -63,7 +67,8 @@ void NumpyFile::get_frame_into(size_t frame_number, std::byte *image_buf) {
     if (frame_number > m_header.shape[0]) {
         throw std::invalid_argument("Frame number out of range");
     }
-    if (fseek(fp, header_size + frame_number * m_bytes_per_frame, SEEK_SET)) // NOLINT
+    if (fseek(fp, header_size + frame_number * m_bytes_per_frame,
+              SEEK_SET)) // NOLINT
         throw std::runtime_error("Could not seek to frame");
 
     size_t const rc = fread(image_buf, m_bytes_per_frame, 1, fp);
@@ -113,7 +118,8 @@ NumpyFile::~NumpyFile() noexcept {
         // write header
         size_t const rc = fwrite(header_str.c_str(), header_str.size(), 1, fp);
         if (rc != 1) {
-            std::cout << "Error writing header to numpy file in destructor" << std::endl;
+            std::cout << "Error writing header to numpy file in destructor"
+                      << std::endl;
         }
     }
 
@@ -140,8 +146,10 @@ void NumpyFile::load_metadata() {
     }
 
     // read version
-    rc = fread(reinterpret_cast<char *>(&major_ver_), sizeof(major_ver_), 1, fp);
+    rc =
-    rc += fread(reinterpret_cast<char *>(&minor_ver_), sizeof(minor_ver_), 1, fp);
+        fread(reinterpret_cast<char *>(&major_ver_), sizeof(major_ver_), 1, fp);
+    rc +=
+        fread(reinterpret_cast<char *>(&minor_ver_), sizeof(minor_ver_), 1, fp);
     if (rc != 2) {
         throw std::runtime_error("Error reading numpy version");
     }
@@ -159,7 +167,8 @@ void NumpyFile::load_metadata() {
     if (rc != 1) {
         throw std::runtime_error("Error reading header length");
     }
-    header_size = aare::NumpyHelpers::magic_string_length + 2 + header_len_size + header_len;
+    header_size = aare::NumpyHelpers::magic_string_length + 2 +
+                  header_len_size + header_len;
     if (header_size % 16 != 0) {
         fmt::print("Warning: header length is not a multiple of 16\n");
     }

src/NumpyFile.test.cpp

@@ -1,8 +1,8 @@
 #include "aare/NumpyFile.hpp"
 #include "aare/NDArray.hpp"
 
-#include <catch2/catch_test_macros.hpp>
 #include "test_config.hpp"
+#include <catch2/catch_test_macros.hpp>
 
 using aare::Dtype;
 using aare::NumpyFile;

src/NumpyHelpers.cpp

@@ -29,7 +29,8 @@ namespace aare {
 
 std::string NumpyHeader::to_string() const {
     std::stringstream sstm;
-    sstm << "dtype: " << dtype.to_string() << ", fortran_order: " << fortran_order << ' ';
+    sstm << "dtype: " << dtype.to_string()
+         << ", fortran_order: " << fortran_order << ' ';
     sstm << "shape: (";
     for (auto item : shape)
         sstm << item << ',';
@@ -37,10 +38,10 @@ std::string NumpyHeader::to_string() const {
     return sstm.str();
 }
 
-
 namespace NumpyHelpers {
 
-std::unordered_map<std::string, std::string> parse_dict(std::string in, const std::vector<std::string> &keys) {
+std::unordered_map<std::string, std::string>
+parse_dict(std::string in, const std::vector<std::string> &keys) {
     std::unordered_map<std::string, std::string> map;
     if (keys.empty())
         return map;
@@ -100,7 +101,8 @@ aare::Dtype parse_descr(std::string typestring) {
     constexpr char little_endian_char = '<';
     constexpr char big_endian_char = '>';
     constexpr char no_endian_char = '|';
-    constexpr std::array<char, 3> endian_chars = {little_endian_char, big_endian_char, no_endian_char};
+    constexpr std::array<char, 3> endian_chars = {
+        little_endian_char, big_endian_char, no_endian_char};
     constexpr std::array<char, 4> numtype_chars = {'f', 'i', 'u', 'c'};
 
     const char byteorder_c = typestring[0];
@@ -139,7 +141,9 @@ std::string get_value_from_map(const std::string &mapstr) {
     return trim(tmp);
 }
 
-bool is_digits(const std::string &str) { return std::all_of(str.begin(), str.end(), ::isdigit); }
+bool is_digits(const std::string &str) {
+    return std::all_of(str.begin(), str.end(), ::isdigit);
+}
 
 std::vector<std::string> parse_tuple(std::string in) {
     std::vector<std::string> v;
@@ -215,20 +219,25 @@ inline std::string write_boolean(bool b) {
     return "False";
 }
 
-inline std::string write_header_dict(const std::string &descr, bool fortran_order, const std::vector<size_t> &shape) {
+inline std::string write_header_dict(const std::string &descr,
+                                     bool fortran_order,
+                                     const std::vector<size_t> &shape) {
     std::string const s_fortran_order = write_boolean(fortran_order);
     std::string const shape_s = write_tuple(shape);
 
-    return "{'descr': '" + descr + "', 'fortran_order': " + s_fortran_order + ", 'shape': " + shape_s + ", }";
+    return "{'descr': '" + descr + "', 'fortran_order': " + s_fortran_order +
+           ", 'shape': " + shape_s + ", }";
 }
 
-size_t write_header(const std::filesystem::path &fname, const NumpyHeader &header) {
+size_t write_header(const std::filesystem::path &fname,
+                    const NumpyHeader &header) {
     std::ofstream out(fname, std::ios::binary | std::ios::out);
     return write_header(out, header);
 }
 
 size_t write_header(std::ostream &out, const NumpyHeader &header) {
-    std::string const header_dict = write_header_dict(header.dtype.to_string(), header.fortran_order, header.shape);
+    std::string const header_dict = write_header_dict(
+        header.dtype.to_string(), header.fortran_order, header.shape);
 
     size_t length = magic_string_length + 2 + 2 + header_dict.length() + 1;
 
@@ -247,17 +256,22 @@ size_t write_header(std::ostream &out, const NumpyHeader &header) {
 
     // write header length
     if (version_major == 1 && version_minor == 0) {
-        auto header_len = static_cast<uint16_t>(header_dict.length() + padding.length() + 1);
+        auto header_len =
+            static_cast<uint16_t>(header_dict.length() + padding.length() + 1);
 
-        std::array<uint8_t, 2> header_len_le16{static_cast<uint8_t>((header_len >> 0) & 0xff),
+        std::array<uint8_t, 2> header_len_le16{
+            static_cast<uint8_t>((header_len >> 0) & 0xff),
             static_cast<uint8_t>((header_len >> 8) & 0xff)};
         out.write(reinterpret_cast<char *>(header_len_le16.data()), 2);
     } else {
-        auto header_len = static_cast<uint32_t>(header_dict.length() + padding.length() + 1);
+        auto header_len =
+            static_cast<uint32_t>(header_dict.length() + padding.length() + 1);
 
         std::array<uint8_t, 4> header_len_le32{
-            static_cast<uint8_t>((header_len >> 0) & 0xff), static_cast<uint8_t>((header_len >> 8) & 0xff),
+            static_cast<uint8_t>((header_len >> 0) & 0xff),
-            static_cast<uint8_t>((header_len >> 16) & 0xff), static_cast<uint8_t>((header_len >> 24) & 0xff)};
+            static_cast<uint8_t>((header_len >> 8) & 0xff),
+            static_cast<uint8_t>((header_len >> 16) & 0xff),
+            static_cast<uint8_t>((header_len >> 24) & 0xff)};
         out.write(reinterpret_cast<char *>(header_len_le32.data()), 4);
     }
 

src/NumpyHelpers.test.cpp

@@ -19,7 +19,9 @@ TEST_CASE("Check for quotes and return stripped string") {
     REQUIRE(parse_str("''") == "");
 }
 
-TEST_CASE("parsing a string without quotes throws") { REQUIRE_THROWS(parse_str("hej")); }
+TEST_CASE("parsing a string without quotes throws") {
+    REQUIRE_THROWS(parse_str("hej"));
+}
 
 TEST_CASE("trim whitespace") {
     REQUIRE(trim(" hej ") == "hej");
@@ -53,7 +55,8 @@ TEST_CASE("is element in array") {
 }
 
 TEST_CASE("Parse numpy dict") {
-    std::string in = "{'descr': '<f4', 'fortran_order': False, 'shape': (3, 4)}";
+    std::string in =
+        "{'descr': '<f4', 'fortran_order': False, 'shape': (3, 4)}";
     std::vector<std::string> keys{"descr", "fortran_order", "shape"};
     auto map = parse_dict(in, keys);
     REQUIRE(map["descr"] == "'<f4'");

src/Pedestal.test.cpp

@@ -1,8 +1,7 @@
 #include "aare/Pedestal.hpp"
 
-
-#include <catch2/matchers/catch_matchers_floating_point.hpp>
 #include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
 #include <chrono>
 #include <random>
 
@@ -58,7 +57,8 @@ TEST_CASE("test pedestal push") {
                 if (k < 5) {
                     REQUIRE(pedestal.cur_samples()(i, j) == k + 1);
                     REQUIRE(pedestal.get_sum()(i, j) == (k + 1) * (i + j));
-                    REQUIRE(pedestal.get_sum2()(i, j) == (k + 1) * (i + j) * (i + j));
+                    REQUIRE(pedestal.get_sum2()(i, j) ==
+                            (k + 1) * (i + j) * (i + j));
                 } else {
                     REQUIRE(pedestal.cur_samples()(i, j) == 5);
                     REQUIRE(pedestal.get_sum()(i, j) == 5 * (i + j));
@@ -95,9 +95,12 @@ TEST_CASE("test pedestal with normal distribution") {
 
     for (int i = 0; i < 3; i++) {
         for (int j = 0; j < 5; j++) {
-            REQUIRE_THAT(mean(i, j), Catch::Matchers::WithinAbs(MEAN, MEAN * TOLERANCE));
+            REQUIRE_THAT(mean(i, j),
-            REQUIRE_THAT(variance(i, j), Catch::Matchers::WithinAbs(VAR, VAR * TOLERANCE));
+                         Catch::Matchers::WithinAbs(MEAN, MEAN * TOLERANCE));
-            REQUIRE_THAT(standard_deviation(i, j), Catch::Matchers::WithinAbs(STD, STD * TOLERANCE));
+            REQUIRE_THAT(variance(i, j),
+                         Catch::Matchers::WithinAbs(VAR, VAR * TOLERANCE));
+            REQUIRE_THAT(standard_deviation(i, j),
+                         Catch::Matchers::WithinAbs(STD, STD * TOLERANCE));
         }
     }
 }

src/PixelMap.cpp

@@ -42,9 +42,9 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
                 int adc_nr = adc_numbers[i_sc];
                 int i_analog = n_pixel * 12 + adc_nr;
 
-                // analog_frame[row * 150 + col] = analog_data[i_analog] & 0x3FFF;
+                // analog_frame[row * 150 + col] = analog_data[i_analog] &
+                // 0x3FFF;
                 order_map(row, col) = i_analog;
-                
             }
         }
     }
@@ -63,10 +63,9 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap1g() {
                 int adc_nr = adc_numbers[i_sc];
                 int i_analog = n_pixel * 3 + adc_nr;
 
-
+                // analog_frame[row * 150 + col] = analog_data[i_analog] &
-                // analog_frame[row * 150 + col] = analog_data[i_analog] & 0x3FFF;
+                // 0x3FFF;
                 order_map(row, col) = i_analog;
-                
             }
         }
     }
@@ -85,10 +84,9 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMapOld() {
                 int adc_nr = adc_numbers[i_sc];
                 int i_analog = n_pixel * 32 + adc_nr;
 
-
+                // analog_frame[row * 150 + col] = analog_data[i_analog] &
-                // analog_frame[row * 150 + col] = analog_data[i_analog] & 0x3FFF;
+                // 0x3FFF;
                 order_map(row, col) = i_analog;
-                
             }
         }
     }
@@ -120,7 +118,8 @@ NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap(){
     for (int counter = 0; counter < 4; counter++) {
         for (int row = 0; row < 48; row++) {
             for (int col = 0; col < 48; col++) {
-                order_map(counter, row, col) = counter*48*48 + row*48 + col;
+                order_map(counter, row, col) =
+                    counter * 48 * 48 + row * 48 + col;
             }
         }
     }

src/RawFile.cpp

@@ -1,9 +1,9 @@
 #include "aare/RawFile.hpp"
-#include "aare/algorithm.hpp"
 #include "aare/PixelMap.hpp"
+#include "aare/algorithm.hpp"
 #include "aare/defs.hpp"
-#include "aare/logger.hpp"
 #include "aare/geo_helpers.hpp"
+#include "aare/logger.hpp"
 
 #include <fmt/format.h>
 #include <nlohmann/json.hpp>
@@ -18,7 +18,8 @@ RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
     if (mode == "r") {
         find_geometry();
         if (m_master.roi()) {
-            m_geometry = update_geometry_with_roi(m_geometry, m_master.roi().value());
+            m_geometry =
+                update_geometry_with_roi(m_geometry, m_master.roi().value());
         }
         open_subfiles();
     } else {
@@ -47,13 +48,13 @@ void RawFile::read_into(std::byte *image_buf) {
     return get_frame_into(m_current_frame++, image_buf);
 }
 
-
 void RawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
 
     return get_frame_into(m_current_frame++, image_buf, header);
 }
 
-void RawFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header) {
+void RawFile::read_into(std::byte *image_buf, size_t n_frames,
+                        DetectorHeader *header) {
     // return get_frame_into(m_current_frame++, image_buf, header);
 
     for (size_t i = 0; i < n_frames; i++) {
@@ -62,14 +63,13 @@ void RawFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *h
         if (header)
             header += n_modules();
     }
-
 }
 
 size_t RawFile::n_modules() const { return m_master.n_modules(); }
 
-
 size_t RawFile::bytes_per_frame() {
-    return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() / bits_per_byte;
+    return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() /
+           bits_per_byte;
 }
 size_t RawFile::pixels_per_frame() {
     // return m_rows * m_cols;
@@ -128,7 +128,6 @@ DetectorHeader RawFile::read_header(const std::filesystem::path &fname) {
     return h;
 }
 
-
 RawMasterFile RawFile::master() const { return m_master; }
 
 /**
@@ -142,7 +141,6 @@ void RawFile::find_geometry() {
     uint16_t r{};
     uint16_t c{};
 
-
     for (size_t i = 0; i < n_modules(); i++) {
         auto h = read_header(m_master.data_fname(i, 0));
         r = std::max(r, h.row);
@@ -157,7 +155,6 @@ void RawFile::find_geometry() {
         g.width = m_master.pixels_x();
         g.height = m_master.pixels_y();
         m_geometry.module_pixel_0.push_back(g);
-
     }
 
     r++;
@@ -168,23 +165,20 @@ void RawFile::find_geometry() {
     m_geometry.modules_x = c;
     m_geometry.modules_y = r;
     m_geometry.pixels_y += static_cast<size_t>((r - 1) * cfg.module_gap_row);
-
 }
 
-
 Frame RawFile::get_frame(size_t frame_index) {
-    auto f = Frame(m_geometry.pixels_y, m_geometry.pixels_x, Dtype::from_bitdepth(m_master.bitdepth()));
+    auto f = Frame(m_geometry.pixels_y, m_geometry.pixels_x,
+                   Dtype::from_bitdepth(m_master.bitdepth()));
     std::byte *frame_buffer = f.data();
     get_frame_into(frame_index, frame_buffer);
     return f;
 }
 
+size_t RawFile::bytes_per_pixel() const { return m_master.bitdepth() / 8; }
 
-size_t RawFile::bytes_per_pixel() const {
+void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer,
-    return m_master.bitdepth() / 8;
+                             DetectorHeader *header) {
-}
-
-void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, DetectorHeader *header) {
     LOG(logDEBUG) << "RawFile::get_frame_into(" << frame_index << ")";
     if (frame_index >= total_frames()) {
         throw std::runtime_error(LOCATION + "Frame number out of range");
@@ -192,12 +186,12 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
     std::vector<size_t> frame_numbers(n_modules());
     std::vector<size_t> frame_indices(n_modules(), frame_index);
 
-
     // sync the frame numbers
 
     if (n_modules() != 1) { // if we have more than one module
         for (size_t part_idx = 0; part_idx != n_modules(); ++part_idx) {
-            frame_numbers[part_idx] = m_subfiles[part_idx]->frame_number(frame_index); 
+            frame_numbers[part_idx] =
+                m_subfiles[part_idx]->frame_number(frame_index);
         }
 
         // 1. if frame number vector is the same break
@@ -218,7 +212,8 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
             }
 
             frame_numbers[min_frame_idx] =
-                m_subfiles[min_frame_idx]->frame_number(frame_indices[min_frame_idx]);
+                m_subfiles[min_frame_idx]->frame_number(
+                    frame_indices[min_frame_idx]);
         }
     }
 
@@ -228,11 +223,14 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
             auto corrected_idx = frame_indices[part_idx];
 
             // This is where we start writing
-            auto offset = (m_geometry.module_pixel_0[part_idx].origin_y * m_geometry.pixels_x +
+            auto offset = (m_geometry.module_pixel_0[part_idx].origin_y *
-                m_geometry.module_pixel_0[part_idx].origin_x)*m_master.bitdepth()/8;
+                               m_geometry.pixels_x +
+                           m_geometry.module_pixel_0[part_idx].origin_x) *
+                          m_master.bitdepth() / 8;
 
             if (m_geometry.module_pixel_0[part_idx].origin_x != 0)
-                throw std::runtime_error(LOCATION + " Implementation error. x pos not 0.");
+                throw std::runtime_error(LOCATION +
+                                         " Implementation error. x pos not 0.");
 
             // TODO! What if the files don't match?
             m_subfiles[part_idx]->seek(corrected_idx);
@@ -271,15 +269,13 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
                 auto dest = (irow * this->m_geometry.pixels_x + icol);
                 dest = dest * m_master.bitdepth() / 8;
                 memcpy(frame_buffer + dest,
-                       part_buffer + cur_row * pos.width *
+                       part_buffer +
-                                         m_master.bitdepth() / 8,
+                           cur_row * pos.width * m_master.bitdepth() / 8,
                        pos.width * m_master.bitdepth() / 8);
-
             }
         }
         delete[] part_buffer;
     }
-        
 }
 
 std::vector<Frame> RawFile::read_n(size_t n_frames) {
@@ -299,5 +295,4 @@ size_t RawFile::frame_number(size_t frame_index) {
     return m_subfiles[0]->frame_number(frame_index);
 }
 
-
 } // namespace aare

src/RawFile.test.cpp

@@ -1,18 +1,18 @@
+#include "aare/RawFile.hpp"
 #include "aare/File.hpp"
 #include "aare/RawMasterFile.hpp" //needed for ROI
-#include "aare/RawFile.hpp"
 
 #include <catch2/catch_test_macros.hpp>
 #include <filesystem>
 
 #include "test_config.hpp"
 
-
 using aare::File;
 
 TEST_CASE("Read number of frames from a jungfrau raw file", "[.integration]") {
 
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
@@ -20,7 +20,8 @@ TEST_CASE("Read number of frames from a jungfrau raw file", "[.integration]") {
 }
 
 TEST_CASE("Read frame numbers from a jungfrau raw file", "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
@@ -36,7 +37,8 @@ TEST_CASE("Read frame numbers from a jungfrau raw file", "[.integration]") {
 }
 
 TEST_CASE("Read a frame number too high throws", "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
@@ -49,8 +51,10 @@ TEST_CASE("Read a frame number too high throws", "[.integration]") {
     REQUIRE_THROWS(f.frame_number(10));
 }
 
-TEST_CASE("Read a frame numbers where the subfile is missing throws", "[.integration]") {
+TEST_CASE("Read a frame numbers where the subfile is missing throws",
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_missing_subfile_master_0.json";
+          "[.integration]") {
+    auto fpath = test_data_path() / "jungfrau" /
+                 "jungfrau_missing_subfile_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
@@ -69,15 +73,18 @@ TEST_CASE("Read a frame numbers where the subfile is missing throws", "[.integra
     REQUIRE_THROWS(f.frame_number(10));
 }
 
-
+TEST_CASE("Read data from a jungfrau 500k single port raw file",
-TEST_CASE("Read data from a jungfrau 500k single port raw file", "[.integration]") {
+          "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
 
-    // we know this file has 10 frames with pixel 0,0 being: 2123, 2051, 2109, 2117, 2089, 2095, 2072, 2126, 2097, 2102
+    // we know this file has 10 frames with pixel 0,0 being: 2123, 2051, 2109,
-    std::vector<uint16_t> pixel_0_0 = {2123, 2051, 2109, 2117, 2089, 2095, 2072, 2126, 2097, 2102};
+    // 2117, 2089, 2095, 2072, 2126, 2097, 2102
+    std::vector<uint16_t> pixel_0_0 = {2123, 2051, 2109, 2117, 2089,
+                                       2095, 2072, 2126, 2097, 2102};
     for (size_t i = 0; i < 10; i++) {
         auto frame = f.read_frame();
         CHECK(frame.rows() == 512);
@@ -100,10 +107,12 @@ TEST_CASE("Read frame numbers from a raw file", "[.integration]") {
 }
 
 TEST_CASE("Compare reading from a numpy file with a raw file", "[.files]") {
-    auto fpath_raw = test_data_path() / "raw/jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath_raw =
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath_raw));
 
-    auto fpath_npy = test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
+    auto fpath_npy =
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
     REQUIRE(std::filesystem::exists(fpath_npy));
 
     File raw(fpath_raw, "r");
@@ -121,17 +130,23 @@ TEST_CASE("Compare reading from a numpy file with a raw file", "[.files]") {
 }
 
 TEST_CASE("Read multipart files", "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_double_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_double_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
 
     // we know this file has 10 frames check read_multiport.py for the values
-    std::vector<uint16_t> pixel_0_0 = {2099, 2121, 2108, 2084, 2084, 2118, 2066, 2108, 2112, 2116};
+    std::vector<uint16_t> pixel_0_0 = {2099, 2121, 2108, 2084, 2084,
-    std::vector<uint16_t> pixel_0_1 = {2842, 2796, 2865, 2798, 2805, 2817, 2852, 2789, 2792, 2833};
+                                       2118, 2066, 2108, 2112, 2116};
-    std::vector<uint16_t> pixel_255_1023 = {2149, 2037, 2115, 2102, 2118, 2090, 2036, 2071, 2073, 2142};
+    std::vector<uint16_t> pixel_0_1 = {2842, 2796, 2865, 2798, 2805,
-    std::vector<uint16_t> pixel_511_1023 = {3231, 3169, 3167, 3162, 3168, 3160, 3171, 3171, 3169, 3171};
+                                       2817, 2852, 2789, 2792, 2833};
-    std::vector<uint16_t> pixel_1_0 = {2748, 2614, 2665, 2629, 2618, 2630, 2631, 2634, 2577, 2598};
+    std::vector<uint16_t> pixel_255_1023 = {2149, 2037, 2115, 2102, 2118,
+                                            2090, 2036, 2071, 2073, 2142};
+    std::vector<uint16_t> pixel_511_1023 = {3231, 3169, 3167, 3162, 3168,
+                                            3160, 3171, 3171, 3169, 3171};
+    std::vector<uint16_t> pixel_1_0 = {2748, 2614, 2665, 2629, 2618,
+                                       2630, 2631, 2634, 2577, 2598};
 
     for (size_t i = 0; i < 10; i++) {
         auto frame = f.read_frame();
@@ -152,5 +167,3 @@ TEST_CASE("Read file with unordered frames", "[.integration]") {
     File f(fpath);
     REQUIRE_THROWS((f.read_frame()));
 }
-
-

src/RawMasterFile.cpp

@@ -37,18 +37,15 @@ std::filesystem::path RawFileNameComponents::master_fname() const {
 }
 
 std::filesystem::path RawFileNameComponents::data_fname(size_t mod_id,
-                                                        size_t file_id
+                                                        size_t file_id) const {
-                                                        ) const {
-    
-    
 
     std::string fmt = "{}_d{}_f{}_{}.raw";
     // Before version X we used to name the data files f000000000000
     if (m_old_scheme) {
         fmt = "{}_d{}_f{:012}_{}.raw";
     }
-    return m_base_path / fmt::format(fmt, m_base_name, mod_id,
+    return m_base_path /
-                                     file_id, m_file_index);
+           fmt::format(fmt, m_base_name, mod_id, file_id, m_file_index);
 }
 
 void RawFileNameComponents::set_old_scheme(bool old_scheme) {
@@ -135,10 +132,8 @@ ScanParameters RawMasterFile::scan_parameters() const {
     return m_scan_parameters;
 }
 
-
 std::optional<ROI> RawMasterFile::roi() const { return m_roi; }
 
-
 void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     std::ifstream ifs(fpath);
     json j;
@@ -177,7 +172,6 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // keep the optional empty
     }
 
-
     // ----------------------------------------------------------------
     // Special treatment of analog flag because of Moench03
     try {
@@ -233,13 +227,13 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         std::string scan_parameters = j.at("Scan Parameters");
         m_scan_parameters = ScanParameters(scan_parameters);
         if (v < 7.21) {
-                m_scan_parameters.increment_stop(); //adjust for endpoint being included
+            m_scan_parameters
+                .increment_stop(); // adjust for endpoint being included
         }
     } catch (const json::out_of_range &e) {
         // not a scan
     }
 
-
     try {
         ROI tmp_roi;
         auto obj = j.at("Receiver Roi");
@@ -260,19 +254,14 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
             m_roi = tmp_roi;
         }
 
-
     } catch (const json::out_of_range &e) {
         // leave the optional empty
     }
 
     // if we have an roi we need to update the geometry for the subfiles
     if (m_roi) {
-
     }
 
-
-
-
 // Update detector type for Moench
 // TODO! How does this work with old .raw master files?
 #ifdef AARE_VERBOSE
@@ -382,7 +371,6 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
         m_type = DetectorType::Moench03_old;
     }
 
-
     // TODO! Look for d0, d1...dn and update geometry
     if (m_geometry.col == 0 && m_geometry.row == 0) {
         m_geometry = {1, 1};

src/RawMasterFile.test.cpp

@@ -1,11 +1,10 @@
 #include "aare/RawMasterFile.hpp"
 
-#include <catch2/catch_test_macros.hpp>
 #include "test_config.hpp"
+#include <catch2/catch_test_macros.hpp>
 
 using namespace aare;
 
-
 TEST_CASE("Parse a master file fname") {
     RawFileNameComponents m("test_master_1.json");
     REQUIRE(m.base_name() == "test");
@@ -47,10 +46,9 @@ TEST_CASE("Master file name does not fit pattern"){
     REQUIRE_THROWS(RawFileNameComponents("test_master_1.txt"));
 }
 
-
-
 TEST_CASE("Parse scan parameters") {
-    ScanParameters s("[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]");
+    ScanParameters s("[enabled\ndac dac 4\nstart 500\nstop 2200\nstep "
+                     "5\nsettleTime 100us\n]");
     REQUIRE(s.enabled());
     REQUIRE(s.dac() == "dac 4");
     REQUIRE(s.start() == 500);
@@ -67,9 +65,9 @@ TEST_CASE("A disabled scan"){
     REQUIRE(s.step() == 0);
 }
 
-
 TEST_CASE("Parse a master file in .json format", "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
 
@@ -103,7 +101,6 @@ TEST_CASE("Parse a master file in .json format", "[.integration]"){
     // Jungfrau doesn't write but it is 16
     REQUIRE(f.bitdepth() == 16);
 
-
     // "Frame Discard Policy": "nodiscard",
 
     // "Frame Padding": 1,
@@ -146,12 +143,14 @@ TEST_CASE("Parse a master file in .json format", "[.integration]"){
 
     REQUIRE_FALSE(f.analog_samples());
     REQUIRE_FALSE(f.digital_samples());
-
 }
 
 TEST_CASE("Parse a master file in .raw format", "[.integration]") {
 
-    auto fpath = test_data_path() / "moench/moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw";
+    auto fpath =
+        test_data_path() /
+        "moench/"
+        "moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
 
@@ -209,11 +208,8 @@ TEST_CASE("Parse a master file in .raw format", "[.integration]"){
     // Detector Type              : 1 byte
     // Header Version             : 1 byte
     // Packets Caught Mask        : 64 bytes
-
-
 }
 
-
 TEST_CASE("Read eiger master file", "[.integration]") {
     auto fpath = test_data_path() / "eiger" / "eiger_500k_32bit_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
@@ -282,7 +278,4 @@ REQUIRE(f.frame_padding() == 1);
     //         "Packets Caught Mask": "64 bytes"
     //     }
     // }
-
-
-
 }

src/RawSubFile.cpp

@@ -1,27 +1,22 @@
 #include "aare/RawSubFile.hpp"
 #include "aare/PixelMap.hpp"
 #include "aare/algorithm.hpp"
-#include "aare/utils/ifstream_helpers.hpp"
 #include "aare/logger.hpp"
-
+#include "aare/utils/ifstream_helpers.hpp"
 
 #include <cstring> // memcpy
 #include <fmt/core.h>
 #include <iostream>
 #include <regex>
 
-
-
-
 namespace aare {
 
 RawSubFile::RawSubFile(const std::filesystem::path &fname,
                        DetectorType detector, size_t rows, size_t cols,
                        size_t bitdepth, uint32_t pos_row, uint32_t pos_col)
-    : m_detector_type(detector), m_bitdepth(bitdepth),
+    : m_detector_type(detector), m_bitdepth(bitdepth), m_rows(rows),
-      m_rows(rows), m_cols(cols),
+      m_cols(cols), m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols),
-      m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols), m_pos_row(pos_row),
+      m_pos_row(pos_row), m_pos_col(pos_col) {
-      m_pos_col(pos_col) {
 
     LOG(logDEBUG) << "RawSubFile::RawSubFile()";
     if (m_detector_type == DetectorType::Moench03_old) {
@@ -30,7 +25,6 @@ RawSubFile::RawSubFile(const std::filesystem::path &fname,
         m_pixel_map = GenerateEigerFlipRowsPixelMap();
     }
 
-
     parse_fname(fname);
     scan_files();
     open_file(m_current_file_index); // open the first file
@@ -51,7 +45,8 @@ void RawSubFile::seek(size_t frame_index) {
     auto frame_offset = (file_index)
                             ? frame_index - m_last_frame_in_file[file_index - 1]
                             : frame_index;
-    auto byte_offset = frame_offset * (m_bytes_per_frame + sizeof(DetectorHeader));
+    auto byte_offset =
+        frame_offset * (m_bytes_per_frame + sizeof(DetectorHeader));
     m_file.seekg(byte_offset);
 }
 
@@ -85,7 +80,8 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
         } else if (m_bitdepth == 32) {
             read_with_map<uint32_t>(image_buf);
         } else {
-            throw std::runtime_error("Unsupported bitdepth for read with pixel map");
+            throw std::runtime_error(
+                "Unsupported bitdepth for read with pixel map");
         }
 
     } else {
@@ -105,7 +101,8 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
     }
 }
 
-void RawSubFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader *header) {
+void RawSubFile::read_into(std::byte *image_buf, size_t n_frames,
+                           DetectorHeader *header) {
     for (size_t i = 0; i < n_frames; i++) {
         read_into(image_buf, header);
         image_buf += bytes_per_frame();
@@ -115,10 +112,7 @@ void RawSubFile::read_into(std::byte *image_buf, size_t n_frames, DetectorHeader
     }
 }
 
-
+template <typename T> void RawSubFile::read_with_map(std::byte *image_buf) {
-
-template <typename T>
-void RawSubFile::read_with_map(std::byte *image_buf) {
     auto part_buffer = new std::byte[bytes_per_frame()];
     m_file.read(reinterpret_cast<char *>(part_buffer), bytes_per_frame());
     auto *data = reinterpret_cast<T *>(image_buf);
@@ -157,14 +151,17 @@ void RawSubFile::parse_fname(const std::filesystem::path &fname) {
     std::smatch match;
 
     if (std::regex_match(m_base_name, match, pattern)) {
-        m_offset = std::stoi(match[4].str()); // find the first file index in case of a truncated series
+        m_offset = std::stoi(match[4].str()); // find the first file index in
-        m_base_name = match[1].str() + match[2].str() + match[3].str() + "{}" + match[5].str();
+                                              // case of a truncated series
+        m_base_name = match[1].str() + match[2].str() + match[3].str() + "{}" +
+                      match[5].str();
         LOG(logDEBUG) << "Base name: " << m_base_name;
         LOG(logDEBUG) << "Offset: " << m_offset;
         LOG(logDEBUG) << "Path: " << m_path.string();
     } else {
         throw std::runtime_error(
-            LOCATION + fmt::format("Could not parse file name {}", fname.string()));
+            LOCATION +
+            fmt::format("Could not parse file name {}", fname.string()));
     }
 }
 
@@ -180,7 +177,8 @@ void RawSubFile::open_file(size_t file_index) {
     m_file.open(fname, std::ios::binary);
     if (!m_file.is_open()) {
         throw std::runtime_error(
-            LOCATION + fmt::format("Could not open file {}", fpath(file_index).string()));
+            LOCATION +
+            fmt::format("Could not open file {}", fpath(file_index).string()));
     }
     m_current_file_index = file_index;
 }
@@ -195,7 +193,8 @@ void RawSubFile::scan_files() {
         auto n_frames = std::filesystem::file_size(fpath(file_index)) /
                         (m_bytes_per_frame + sizeof(DetectorHeader));
         m_last_frame_in_file.push_back(n_frames);
-        LOG(logDEBUG) << "Found: " << n_frames << " frames in file: " << fpath(file_index).string();
+        LOG(logDEBUG) << "Found: " << n_frames
+                      << " frames in file: " << fpath(file_index).string();
         ++file_index;
     }
 

src/RawSubFile.test.cpp

@@ -1,13 +1,14 @@
 #include "aare/RawSubFile.hpp"
 #include "aare/File.hpp"
 #include "aare/NDArray.hpp"
-#include <catch2/catch_test_macros.hpp>
 #include "test_config.hpp"
+#include <catch2/catch_test_macros.hpp>
 
 using namespace aare;
 
 TEST_CASE("Read frames directly from a RawSubFile", "[.files]") {
-    auto fpath_raw = test_data_path() / "raw/jungfrau" / "jungfrau_single_d0_f0_0.raw";
+    auto fpath_raw =
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_d0_f0_0.raw";
     REQUIRE(std::filesystem::exists(fpath_raw));
 
     RawSubFile f(fpath_raw, DetectorType::Jungfrau, 512, 1024, 16);
@@ -17,8 +18,8 @@ TEST_CASE("Read frames directly from a RawSubFile", "[.files]"){
     REQUIRE(f.bytes_per_frame() == 512 * 1024 * 2);
     REQUIRE(f.bytes_per_pixel() == 2);
 
-
+    auto fpath_npy =
-    auto fpath_npy = test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
     REQUIRE(std::filesystem::exists(fpath_npy));
 
     // Numpy file with the same data to use as reference
@@ -27,9 +28,9 @@ TEST_CASE("Read frames directly from a RawSubFile", "[.files]"){
     CHECK(f.frames_in_file() == 10);
     CHECK(npy.total_frames() == 10);
 
-
     DetectorHeader header{};
-    NDArray<uint16_t, 2> image({static_cast<ssize_t>(f.rows()), static_cast<ssize_t>(f.cols())});
+    NDArray<uint16_t, 2> image(
+        {static_cast<ssize_t>(f.rows()), static_cast<ssize_t>(f.cols())});
     for (size_t i = 0; i < 10; ++i) {
         CHECK(f.tell() == i);
         f.read_into(image.buffer(), &header);
@@ -38,20 +39,22 @@ TEST_CASE("Read frames directly from a RawSubFile", "[.files]"){
     }
 }
 
-TEST_CASE("Read frames directly from a RawSubFile starting at the second file", "[.files]"){
+TEST_CASE("Read frames directly from a RawSubFile starting at the second file",
+          "[.files]") {
     // we know this file has 10 frames with frame numbers 1 to 10
     // f0 1,2,3
     // f1 4,5,6 <-- starting here
     // f2 7,8,9
     // f3 10
 
-    auto fpath_raw = test_data_path() / "raw/jungfrau" / "jungfrau_single_d0_f1_0.raw";
+    auto fpath_raw =
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_d0_f1_0.raw";
     REQUIRE(std::filesystem::exists(fpath_raw));
 
     RawSubFile f(fpath_raw, DetectorType::Jungfrau, 512, 1024, 16);
 
-
+    auto fpath_npy =
-    auto fpath_npy = test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
+        test_data_path() / "raw/jungfrau" / "jungfrau_single_0.npy";
     REQUIRE(std::filesystem::exists(fpath_npy));
 
     // Numpy file with the same data to use as reference
@@ -61,9 +64,9 @@ TEST_CASE("Read frames directly from a RawSubFile starting at the second file",
     CHECK(f.frames_in_file() == 7);
     CHECK(npy.total_frames() == 10);
 
-
     DetectorHeader header{};
-    NDArray<uint16_t, 2> image({static_cast<ssize_t>(f.rows()), static_cast<ssize_t>(f.cols())});
+    NDArray<uint16_t, 2> image(
+        {static_cast<ssize_t>(f.rows()), static_cast<ssize_t>(f.cols())});
     for (size_t i = 0; i < 7; ++i) {
         CHECK(f.tell() == i);
         f.read_into(image.buffer(), &header);

src/algorithm.test.cpp

@@ -161,12 +161,10 @@ TEST_CASE("cumsum works with negative numbers", "[algorithm]") {
     REQUIRE(result[4] == -10);
 }
 
-
 TEST_CASE("cumsum on an empty vector", "[algorithm]") {
     std::vector<double> vec = {};
     auto result = aare::cumsum(vec);
     REQUIRE(result.size() == 0);
-
 }
 
 TEST_CASE("All equal on an empty vector is false", "[algorithm]") {
@@ -184,7 +182,8 @@ TEST_CASE("All equal on a vector with 2 elements is true", "[algorithm]") {
     REQUIRE(aare::all_equal(vec) == true);
 }
 
-TEST_CASE("All equal on a vector with two different  elements is false", "[algorithm]") {
+TEST_CASE("All equal on a vector with two different  elements is false",
+          "[algorithm]") {
     std::vector<int> vec = {1, 2};
     REQUIRE(aare::all_equal(vec) == false);
 }

src/decode.cpp

@@ -21,9 +21,11 @@ uint16_t adc_sar_05_decode64to16(uint64_t input){
     return output;
 }
 
-void adc_sar_05_decode64to16(NDView<uint64_t, 2> input, NDView<uint16_t,2> output){
+void adc_sar_05_decode64to16(NDView<uint64_t, 2> input,
+                             NDView<uint16_t, 2> output) {
     if (input.shape() != output.shape()) {
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+        throw std::invalid_argument(LOCATION +
+                                    " input and output shapes must match");
     }
 
     for (ssize_t i = 0; i < input.shape(0); i++) {
@@ -52,9 +54,11 @@ uint16_t adc_sar_04_decode64to16(uint64_t input){
     return output;
 }
 
-void adc_sar_04_decode64to16(NDView<uint64_t, 2> input, NDView<uint16_t,2> output){
+void adc_sar_04_decode64to16(NDView<uint64_t, 2> input,
+                             NDView<uint16_t, 2> output) {
     if (input.shape() != output.shape()) {
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+        throw std::invalid_argument(LOCATION +
+                                    " input and output shapes must match");
     }
     for (ssize_t i = 0; i < input.shape(0); i++) {
         for (ssize_t j = 0; j < input.shape(1); j++) {
@@ -65,7 +69,8 @@ void adc_sar_04_decode64to16(NDView<uint64_t, 2> input, NDView<uint16_t,2> outpu
 
 double apply_custom_weights(uint16_t input, const NDView<double, 1> weights) {
     if (weights.size() > 16) {
-        throw std::invalid_argument("weights size must be less than or equal to 16");
+        throw std::invalid_argument(
+            "weights size must be less than or equal to 16");
     }
 
     double result = 0.0;
@@ -73,12 +78,13 @@ double apply_custom_weights(uint16_t input, const NDView<double, 1> weights) {
         result += ((input >> i) & 1) * std::pow(weights[i], i);
     }
     return result;
-
 }
 
-void apply_custom_weights(NDView<uint16_t, 1> input, NDView<double, 1> output, const NDView<double,1> weights) {
+void apply_custom_weights(NDView<uint16_t, 1> input, NDView<double, 1> output,
+                          const NDView<double, 1> weights) {
     if (input.shape() != output.shape()) {
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+        throw std::invalid_argument(LOCATION +
+                                    " input and output shapes must match");
     }
 
     // Calculate weights to avoid repeatedly calling std::pow
@@ -90,13 +96,12 @@ void apply_custom_weights(NDView<uint16_t, 1> input, NDView<double, 1> output, c
     // Apply custom weights to each element in the input array
     for (ssize_t i = 0; i < input.shape(0); i++) {
         double result = 0.0;
-        for (size_t bit_index = 0; bit_index < weights_powers.size(); ++bit_index) {
+        for (size_t bit_index = 0; bit_index < weights_powers.size();
+             ++bit_index) {
             result += ((input(i) >> bit_index) & 1) * weights_powers[bit_index];
         }
         output(i) = result;
     }
 }
 
-
-
 } // namespace aare

src/decode.test.cpp

@@ -1,8 +1,8 @@
 #include "aare/decode.hpp"
 
-#include <catch2/matchers/catch_matchers_floating_point.hpp>
-#include <catch2/catch_test_macros.hpp>
 #include "aare/NDArray.hpp"
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
 using Catch::Matchers::WithinAbs;
 #include <vector>
 
@@ -11,7 +11,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     uint16_t output = aare::adc_sar_05_decode64to16(input);
     CHECK(output == 0);
 
-
     // bit 29 on th input is bit 0 on the output
     input = 1UL << 29;
     output = aare::adc_sar_05_decode64to16(input);
@@ -25,7 +24,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
         CHECK(output == (1 << i));
     }
 
-    
     // test a few "random" values
     input = 0;
     input |= (1UL << 29);
@@ -34,7 +32,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     output = aare::adc_sar_05_decode64to16(input);
     CHECK(output == 7UL);
 
-
     input = 0;
     input |= (1UL << 18);
     input |= (1UL << 27);
@@ -49,7 +46,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     CHECK(output == 3072UL);
 }
 
-
 TEST_CASE("test_apply_custom_weights") {
 
     uint16_t input = 1;
@@ -60,7 +56,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
 
     auto weights = weights_data.view();
 
-
     double output = aare::apply_custom_weights(input, weights);
     CHECK_THAT(output, WithinAbs(1.0, 0.001));
 
@@ -68,7 +63,6 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     output = aare::apply_custom_weights(input, weights);
     CHECK_THAT(output, WithinAbs(2.1, 0.001));
 
-
     input = 1 << 2;
     output = aare::apply_custom_weights(input, weights);
     CHECK_THAT(output, WithinAbs(3.24, 0.001));
@@ -76,5 +70,4 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     input = 0b111;
     output = aare::apply_custom_weights(input, weights);
     CHECK_THAT(output, WithinAbs(6.34, 0.001));
-
 }

src/defs.cpp

@@ -6,15 +6,11 @@
 #include <fmt/core.h>
 namespace aare {
 
-
+void assert_failed(const std::string &msg) {
-void assert_failed(const std::string &msg)
- {
     fmt::print(msg);
     exit(1);
 }
 
-
-
 /**
  * @brief Convert a DetectorType to a string
  * @param type DetectorType
@@ -121,7 +117,8 @@ template <> TimingMode StringTo(const std::string &arg) {
         return TimingMode::Auto;
     if (arg == "trigger")
         return TimingMode::Trigger;
-    throw std::runtime_error("Could not decode timing mode from: \"" + arg + "\"");
+    throw std::runtime_error("Could not decode timing mode from: \"" + arg +
+                             "\"");
 }
 
 /**
@@ -151,7 +148,8 @@ template <> FrameDiscardPolicy StringTo(const std::string &arg) {
         return FrameDiscardPolicy::Discard;
     if (arg == "discardpartial")
         return FrameDiscardPolicy::DiscardPartial;
-    throw std::runtime_error("Could not decode frame discard policy from: \"" + arg + "\"");
+    throw std::runtime_error("Could not decode frame discard policy from: \"" +
+                             arg + "\"");
 }
 
 /**

src/defs.test.cpp

@@ -3,12 +3,12 @@
 #include <catch2/catch_test_macros.hpp>
 #include <string>
 
-using aare::ToString;
 using aare::StringTo;
+using aare::ToString;
 
 TEST_CASE("Enum to string conversion") {
-    // TODO! By the way I don't think the enum string conversions should be in the defs.hpp file
+    // TODO! By the way I don't think the enum string conversions should be in
-    // but let's use this to show a test
+    // the defs.hpp file but let's use this to show a test
     REQUIRE(ToString(aare::DetectorType::Generic) == "Generic");
     REQUIRE(ToString(aare::DetectorType::Eiger) == "Eiger");
     REQUIRE(ToString(aare::DetectorType::Gotthard) == "Gotthard");
@@ -17,25 +17,37 @@ TEST_CASE("Enum to string conversion") {
     REQUIRE(ToString(aare::DetectorType::Moench) == "Moench");
     REQUIRE(ToString(aare::DetectorType::Mythen3) == "Mythen3");
     REQUIRE(ToString(aare::DetectorType::Gotthard2) == "Gotthard2");
-    REQUIRE(ToString(aare::DetectorType::Xilinx_ChipTestBoard) == "Xilinx_ChipTestBoard");
+    REQUIRE(ToString(aare::DetectorType::Xilinx_ChipTestBoard) ==
+            "Xilinx_ChipTestBoard");
     REQUIRE(ToString(aare::DetectorType::Moench03) == "Moench03");
     REQUIRE(ToString(aare::DetectorType::Moench03_old) == "Moench03_old");
     REQUIRE(ToString(aare::DetectorType::Unknown) == "Unknown");
 }
 
 TEST_CASE("String to enum") {
-    REQUIRE(StringTo<aare::DetectorType>("Generic") == aare::DetectorType::Generic);
+    REQUIRE(StringTo<aare::DetectorType>("Generic") ==
+            aare::DetectorType::Generic);
     REQUIRE(StringTo<aare::DetectorType>("Eiger") == aare::DetectorType::Eiger);
-    REQUIRE(StringTo<aare::DetectorType>("Gotthard") == aare::DetectorType::Gotthard);
+    REQUIRE(StringTo<aare::DetectorType>("Gotthard") ==
-    REQUIRE(StringTo<aare::DetectorType>("Jungfrau") == aare::DetectorType::Jungfrau);
+            aare::DetectorType::Gotthard);
-    REQUIRE(StringTo<aare::DetectorType>("ChipTestBoard") == aare::DetectorType::ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Jungfrau") ==
-    REQUIRE(StringTo<aare::DetectorType>("Moench") == aare::DetectorType::Moench);
+            aare::DetectorType::Jungfrau);
-    REQUIRE(StringTo<aare::DetectorType>("Mythen3") == aare::DetectorType::Mythen3);
+    REQUIRE(StringTo<aare::DetectorType>("ChipTestBoard") ==
-    REQUIRE(StringTo<aare::DetectorType>("Gotthard2") == aare::DetectorType::Gotthard2);
+            aare::DetectorType::ChipTestBoard);
-    REQUIRE(StringTo<aare::DetectorType>("Xilinx_ChipTestBoard") == aare::DetectorType::Xilinx_ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Moench") ==
-    REQUIRE(StringTo<aare::DetectorType>("Moench03") == aare::DetectorType::Moench03);
+            aare::DetectorType::Moench);
-    REQUIRE(StringTo<aare::DetectorType>("Moench03_old") == aare::DetectorType::Moench03_old);
+    REQUIRE(StringTo<aare::DetectorType>("Mythen3") ==
-    REQUIRE(StringTo<aare::DetectorType>("Unknown") == aare::DetectorType::Unknown);
+            aare::DetectorType::Mythen3);
+    REQUIRE(StringTo<aare::DetectorType>("Gotthard2") ==
+            aare::DetectorType::Gotthard2);
+    REQUIRE(StringTo<aare::DetectorType>("Xilinx_ChipTestBoard") ==
+            aare::DetectorType::Xilinx_ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Moench03") ==
+            aare::DetectorType::Moench03);
+    REQUIRE(StringTo<aare::DetectorType>("Moench03_old") ==
+            aare::DetectorType::Moench03_old);
+    REQUIRE(StringTo<aare::DetectorType>("Unknown") ==
+            aare::DetectorType::Unknown);
 }
 
 TEST_CASE("Enum values") {
@@ -85,5 +97,6 @@ TEST_CASE("DynamicCluster creation") {
 //     double v3 = c2.get<double>(33 * 44 - 1);
 //     REQUIRE(aare::compare_floats<double>(123.11, v3));
 
-//     REQUIRE_THROWS_AS(c2.set(0, 1), std::invalid_argument); // set int to double
+//     REQUIRE_THROWS_AS(c2.set(0, 1), std::invalid_argument); // set int to
+//     double
 // }

src/geo_helpers.cpp

@@ -8,8 +8,9 @@ DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi) {
 #ifdef AARE_VERBOSE
     fmt::println("update_geometry_with_roi() called with ROI: {} {} {} {}",
                  roi.xmin, roi.xmax, roi.ymin, roi.ymax);
-    fmt::println("Geometry: {} {} {} {} {} {}",
+    fmt::println("Geometry: {} {} {} {} {} {}", geo.modules_x, geo.modules_y,
-                 geo.modules_x, geo.modules_y, geo.pixels_x, geo.pixels_y, geo.module_gap_row, geo.module_gap_col);
+                 geo.pixels_x, geo.pixels_y, geo.module_gap_row,
+                 geo.module_gap_col);
 #endif
     int pos_y = 0;
     int pos_y_increment = 0;
@@ -41,9 +42,9 @@ DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi) {
             if (m.origin_y + m.height < roi.ymin) {
                 m.height = 0;
             } else {
-                if ((roi.ymin > m.origin_y) && (roi.ymin < m.origin_y + m.height)) {
+                if ((roi.ymin > m.origin_y) &&
+                    (roi.ymin < m.origin_y + m.height)) {
                     m.height -= roi.ymin - m.origin_y;
-
                 }
                 if (roi.ymax < m.origin_y + original_height) {
                     m.height -= m.origin_y + original_height - roi.ymax;
@@ -52,7 +53,8 @@ DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi) {
                 pos_y_increment = m.height;
             }
 #ifdef AARE_VERBOSE
-    fmt::println("Module {} {} {} {}", m.origin_x, m.origin_y, m.width, m.height);
+            fmt::println("Module {} {} {} {}", m.origin_x, m.origin_y, m.width,
+                         m.height);
 #endif
         }
         // increment pos_y
@@ -65,7 +67,6 @@ DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi) {
     geo.pixels_y = roi.height();
 
     return geo;
-
 }
 
 } // namespace aare

src/geo_helpers.test.cpp

@@ -1,6 +1,6 @@
 #include "aare/File.hpp"
-#include "aare/RawMasterFile.hpp" //needed for ROI
 #include "aare/RawFile.hpp"
+#include "aare/RawMasterFile.hpp" //needed for ROI
 
 #include <catch2/catch_test_macros.hpp>
 #include <filesystem>
@@ -9,18 +9,16 @@
 #include "test_config.hpp"
 
 TEST_CASE("Simple ROIs on one module") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
     aare::DetectorGeometry geo;
 
-
     aare::ModuleGeometry mod;
     mod.origin_x = 0;
     mod.origin_y = 0;
     mod.width = 1024;
     mod.height = 512;
 
-
-    
     geo.pixels_x = 1024;
     geo.pixels_y = 512;
     geo.modules_x = 1;
@@ -90,13 +88,11 @@ TEST_CASE("Simple ROIs on one module"){
     }
 }
 
-
-
 TEST_CASE("Two modules side by side") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
     aare::DetectorGeometry geo;
 
-
     aare::ModuleGeometry mod;
     mod.origin_x = 0;
     mod.origin_y = 0;
@@ -145,7 +141,8 @@ TEST_CASE("Two modules side by side"){
 }
 
 TEST_CASE("Three modules side by side") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
     aare::DetectorGeometry geo;
     aare::ROI roi;
     roi.xmin = 700;
@@ -185,7 +182,8 @@ TEST_CASE("Three modules side by side"){
 }
 
 TEST_CASE("Four modules as a square") {
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
     aare::DetectorGeometry geo;
     aare::ROI roi;
     roi.xmin = 500;

src/utils/task.test.cpp

@@ -1,8 +1,7 @@
 #include "aare/utils/task.hpp"
 
-#include <catch2/matchers/catch_matchers_floating_point.hpp>
 #include <catch2/catch_test_macros.hpp>
-
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
 
 TEST_CASE("Split a range into multiple tasks") {
 
@@ -26,7 +25,4 @@ TEST_CASE("Split a range into multiple tasks"){
         REQUIRE(tasks[i].first == i);
         REQUIRE(tasks[i].second == i + 1);
     }
-    
-
-
 }

tests/test.cpp

@@ -2,8 +2,8 @@
 #include <catch2/catch_test_macros.hpp>
 #include <climits>
 #include <filesystem>
-#include <fstream>
 #include <fmt/core.h>
+#include <fstream>
 
 TEST_CASE("Test suite can find data assets", "[.integration]") {
     auto fpath = test_data_path() / "numpy" / "test_numpy_file.npy";