fatal error did not open any subfiles

Added a section on the ideas behind the library and also explaining the
branching strategy.

---------

Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>

.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.ref == 'refs/heads/main'
+    if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'workflow_dispatch' )
     steps:
       - name: Deploy to GitHub Pages
         id: deployment

CMakeLists.txt

@@ -335,13 +335,10 @@ if(AARE_ASAN)
     )
 endif()
 
-
-
-
-
 if(AARE_TESTS)
     enable_testing()
     add_subdirectory(tests)
+    target_compile_definitions(tests PRIVATE AARE_TESTS)
 endif()
 
 ###------------------------------------------------------------------------------MAIN LIBRARY
@@ -364,7 +361,7 @@ set(PUBLICHEADERS
     include/aare/FilePtr.hpp
     include/aare/Frame.hpp
     include/aare/GainMap.hpp
-    include/aare/geo_helpers.hpp
+    include/aare/DetectorGeometry.hpp
     include/aare/JungfrauDataFile.hpp
     include/aare/NDArray.hpp
     include/aare/NDView.hpp
@@ -389,7 +386,7 @@ set(SourceFiles
     ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/FilePtr.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Fit.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.cpp
@@ -424,6 +421,10 @@ target_link_libraries(
 
 )
 
+if(AARE_TESTS)
+    target_compile_definitions(aare_core PRIVATE AARE_TESTS)
+endif()
+
 set_target_properties(aare_core PROPERTIES
     ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
     PUBLIC_HEADER "${PUBLICHEADERS}"
@@ -440,7 +441,7 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp

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,
-            CalculateGeneralEtaFor2x2Cluster)(benchmark::State &st) {
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor2x2Cluster)
+(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,
-            CalculateGeneralEtaFor3x3Cluster)(benchmark::State &st) {
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor3x3Cluster)
+(benchmark::State &st) {
     for (auto _ : st) {
         // This code gets timed
         Eta2 eta = calculate_eta2<int, 3, 3>(cluster_3x3);

benchmarks/ndarray_benchmark.cpp

@@ -1,136 +1,132 @@
-#include <benchmark/benchmark.h>
 #include "aare/NDArray.hpp"
-
+#include <benchmark/benchmark.h>
 
 using aare::NDArray;
 
 constexpr ssize_t size = 1024;
 class TwoArrays : public benchmark::Fixture {
-public:
-    NDArray<int,2> a{{size,size},0};
-    NDArray<int,2> b{{size,size},0};
-  void SetUp(::benchmark::State& state) {
-    for(uint32_t i = 0; i < size; i++){
-      for(uint32_t j = 0; j < size; j++){
-        a(i, j)= i*j+1;
-        b(i, j)= i*j+1;
-      }
+  public:
+    NDArray<int, 2> a{{size, size}, 0};
+    NDArray<int, 2> b{{size, size}, 0};
+    void SetUp(::benchmark::State &state) {
+        for (uint32_t i = 0; i < size; i++) {
+            for (uint32_t j = 0; j < size; j++) {
+                a(i, j) = i * j + 1;
+                b(i, j) = i * j + 1;
+            }
+        }
     }
-  }
 
-  // void TearDown(::benchmark::State& state) {
-  // }
+    // void TearDown(::benchmark::State& state) {
+    // }
 };
 
-
-
-
-BENCHMARK_F(TwoArrays, AddWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a+b;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, AddWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) + b(i);
+BENCHMARK_F(TwoArrays, AddWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a + b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, AddWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) + b(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
-BENCHMARK_F(TwoArrays, SubtractWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a-b;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, SubtractWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) - b(i);
+BENCHMARK_F(TwoArrays, SubtractWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a - b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, SubtractWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) - b(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
-BENCHMARK_F(TwoArrays, MultiplyWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a*b;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, MultiplyWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) * b(i);
+BENCHMARK_F(TwoArrays, MultiplyWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a * b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, MultiplyWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) * b(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
-BENCHMARK_F(TwoArrays, DivideWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a/b;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, DivideWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) / b(i);
+BENCHMARK_F(TwoArrays, DivideWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a / b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, DivideWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) / b(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
-BENCHMARK_F(TwoArrays, FourAddWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a+b+a+b;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, FourAddWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) + b(i) + a(i) + b(i);
+BENCHMARK_F(TwoArrays, FourAddWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a + b + a + b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, FourAddWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) + b(i) + a(i) + b(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
-BENCHMARK_F(TwoArrays, MultiplyAddDivideWithOperator)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res = a*a+b/a;
-    benchmark::DoNotOptimize(res);
-  }
-}
-BENCHMARK_F(TwoArrays, MultiplyAddDivideWithIndex)(benchmark::State& st) {
-   for (auto _ : st) {
-    // This code gets timed
-    NDArray<int,2> res(a.shape());
-    for (uint32_t i = 0; i < a.size(); i++) {
-        res(i) = a(i) * a(i) + b(i) / a(i);
+BENCHMARK_F(TwoArrays, MultiplyAddDivideWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a * a + b / a;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, MultiplyAddDivideWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) * a(i) + b(i) / a(i);
+        }
+        benchmark::DoNotOptimize(res);
     }
-    benchmark::DoNotOptimize(res);
-  }
 }
 
 BENCHMARK_MAIN();

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

@@ -63,4 +63,6 @@ AARE
     :caption: Developer
     :maxdepth: 3
     
+    Philosophy
+    Workflow
     Tests

include/aare/ArrayExpr.hpp

@@ -1,10 +1,9 @@
 #pragma once
-#include <cstdint> 
-#include <cstddef> 
-#include <array> 
-#include <cassert>
 #include "aare/defs.hpp"
-
+#include <array>
+#include <cassert>
+#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>
@@ -47,7 +48,7 @@ class ArraySub : public ArrayExpr<ArraySub<A, B, Ndim>, Ndim> {
 };
 
 template <typename A, typename B, ssize_t Ndim>
-class ArrayMul : public ArrayExpr<ArrayMul<A, B, Ndim>,Ndim> {
+class ArrayMul : public ArrayExpr<ArrayMul<A, B, Ndim>, Ndim> {
     const A &arr1_;
     const B &arr2_;
 
@@ -74,15 +75,13 @@ 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);
 }
 
 template <typename A, typename B, ssize_t Ndim>
-auto operator-(const ArrayExpr<A,Ndim> &arr1, const ArrayExpr<B, Ndim> &arr2) {
+auto operator-(const ArrayExpr<A, Ndim> &arr1, const ArrayExpr<B, Ndim> &arr2) {
     return ArraySub<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
-                  << " clusters from frame " << frame_number;
+    LOG(logDEBUG1) << "Reading " << n_clusters << " clusters from frame "
+                   << frame_number;
 
     ClusterVector<ClusterType> clusters(n_clusters);
     clusters.set_frame_number(frame_number);

include/aare/ClusterFileSink.hpp

@@ -49,8 +49,8 @@ class ClusterFileSink {
     ClusterFileSink(ClusterFinderMT<ClusterType, uint16_t, double> *source,
                     const std::filesystem::path &fname) {
         LOG(logDEBUG) << "ClusterFileSink: "
-                       << "source: " << source->sink()
-                       << ", file: " << fname.string();
+                      << "source: " << source->sink()
+                      << ", file: " << fname.string();
         m_source = source->sink();
         m_thread = std::thread(&ClusterFileSink::process, this);
         m_file.open(fname, std::ios::binary);

include/aare/ClusterFinder.hpp

@@ -39,10 +39,9 @@ class ClusterFinder {
           c2(sqrt((ClusterSizeY + 1) / 2 * (ClusterSizeX + 1) / 2)),
           c3(sqrt(ClusterSizeX * ClusterSizeY)),
           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
-                       << ", capacity: " << capacity;
+        LOG(logDEBUG) << "ClusterFinder: "
+                      << "image_size: " << image_size[0] << "x" << image_size[1]
+                      << ", nSigma: " << nSigma << ", 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 {
 
@@ -125,10 +125,10 @@ class ClusterFinderMT {
         : m_n_threads(n_threads) {
 
         LOG(logDEBUG1) << "ClusterFinderMT: "
-            << "image_size: " << image_size[0] << "x" << image_size[1]
-            << ", nSigma: " << nSigma
-            << ", capacity: " << capacity
-            << ", n_threads: " << n_threads;
+                       << "image_size: " << image_size[0] << "x"
+                       << image_size[1] << ", nSigma: " << nSigma
+                       << ", capacity: " << capacity
+                       << ", n_threads: " << n_threads;
 
         for (size_t i = 0; i < n_threads; i++) {
             m_cluster_finders.push_back(

include/aare/CtbRawFile.hpp

@@ -1,27 +1,27 @@
 #pragma once
 
 #include "aare/FileInterface.hpp"
-#include "aare/RawMasterFile.hpp"
 #include "aare/Frame.hpp"
+#include "aare/RawMasterFile.hpp"
 
 #include <filesystem>
 #include <fstream>
 
-namespace aare{
+namespace aare {
 
-
-class CtbRawFile{
+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:
+
+  public:
     CtbRawFile(const std::filesystem::path &fname);
 
-    void read_into(std::byte *image_buf, DetectorHeader* header = nullptr);
-    void seek(size_t frame_index);          //!< seek to the given frame index
-    size_t tell() const;                    //!< get the frame index of the file pointer
+    void read_into(std::byte *image_buf, DetectorHeader *header = nullptr);
+    void seek(size_t frame_index); //!< seek to the given frame index
+    size_t tell() const;           //!< get the frame index of the file pointer
 
     // in the specific class we can expose more functionality
 
@@ -29,13 +29,13 @@ public:
     size_t frames_in_file() const;
 
     RawMasterFile master() const;
-private:
+
+  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/DetectorGeometry.hpp

@@ -0,0 +1,81 @@
+#pragma once
+#include "aare/RawMasterFile.hpp" //ROI refactor away
+#include "aare/defs.hpp"
+namespace aare {
+
+struct ModuleConfig {
+    int module_gap_row{};
+    int module_gap_col{};
+
+    bool operator==(const ModuleConfig &other) const {
+        if (module_gap_col != other.module_gap_col)
+            return false;
+        if (module_gap_row != other.module_gap_row)
+            return false;
+        return true;
+    }
+};
+
+/**
+ * @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{};
+    int origin_y{};
+    int height{};
+    int width{};
+    int row_index{};
+    int col_index{};
+};
+
+/**
+ * @brief Class to hold the geometry of a detector. Number of modules, their
+ * size and where pixel 0 for each module is located
+ */
+class DetectorGeometry {
+  public:
+    DetectorGeometry(const xy &geometry, const ssize_t module_pixels_x,
+                     const ssize_t module_pixels_y,
+                     const xy udp_interfaces_per_module = xy{1, 1},
+                     const bool quad = false);
+
+    ~DetectorGeometry() = default;
+
+    /**
+     * @brief Update the detector geometry given a region of interest
+     *
+     * @param roi
+     * @return DetectorGeometry
+     */
+    void update_geometry_with_roi(ROI roi);
+
+    size_t n_modules() const;
+
+    size_t n_modules_in_roi() const;
+
+    size_t pixels_x() const;
+    size_t pixels_y() const;
+
+    size_t modules_x() const;
+    size_t modules_y() const;
+
+    const std::vector<ssize_t> &get_modules_in_roi() const;
+
+    ssize_t get_modules_in_roi(const size_t index) const;
+
+    const std::vector<ModuleGeometry> &get_module_geometries() const;
+
+    const ModuleGeometry &get_module_geometries(const size_t index) const;
+
+  private:
+    size_t m_modules_x{};
+    size_t m_modules_y{};
+    size_t m_pixels_x{};
+    size_t m_pixels_y{};
+    static constexpr ModuleConfig cfg{0, 0};
+    std::vector<ModuleGeometry> module_geometries{};
+    std::vector<ssize_t> modules_in_roi{};
+};
+
+} // 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
-//   with variable bitdepth types. (e.g. long is int64 on linux64 and int32 on win64)
-//   https://numpy.org/doc/stable/reference/arrays.scalars.html
+// - numpy also doesn't use the same format. and also numpy associates the
+// format
+//   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
-// descriptor is 'q' and 'Q' respectively and in the documentation it is 'l' and 'k'.
+// [IN LINUX] the difference is for int64 (long) and uint64 (unsigned long). The
+// 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
-// any further discrepancies.
+// for this reason we decided to use the same format descriptor as pybind to
+// 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 numpy_descr() const { return std::string(1, NUMPY_FORMAT_DSC[static_cast<int>(m_type)]); }
+    std::string format_descr() const {
+        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

@@ -5,12 +5,12 @@
 namespace aare {
 
 /**
- * @brief RAII File class for reading, and in the future potentially writing 
- * image files in various formats. Minimal generic interface. For specail fuctions
- * plase use the RawFile or NumpyFile classes directly.
- * Wraps 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
+ * @brief RAII File class for reading, and in the future potentially writing
+ * image files in various formats. Minimal generic interface. For specail
+ * fuctions plase use the RawFile or NumpyFile classes directly. Wraps
+ * 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
  */
 class File {
     std::unique_ptr<FileInterface> file_impl;
@@ -25,42 +25,46 @@ 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 = {});
-    
-     /**Since the object is responsible for managing the file we disable copy construction */
-    File(File const &other) = delete;     
+    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 */
+    File(File const &other) = delete;
 
     /**The same goes for copy assignment */
-    File& operator=(File const &other) = delete;
+    File &operator=(File const &other) = delete;
 
     File(File &&other) noexcept;
-    File& operator=(File &&other) noexcept;
+    File &operator=(File &&other) noexcept;
     ~File() = default;
 
     // void close();                             //!< close the file
-      
-    Frame read_frame();                       //!< read one frame 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
+
+    Frame
+    read_frame(); //!< read one frame 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 bytes_per_frame() const;           
-    size_t pixels_per_frame() const;    
-    size_t bytes_per_pixel() const;  
+
+    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 bytes_per_frame() const;
+    size_t pixels_per_frame() const;
+    size_t bytes_per_pixel() const;
     size_t bitdepth() const;
-    void seek(size_t frame_index);          //!< seek to the given frame index
-    size_t tell() const;                     //!< get the frame index of the file pointer
+    void seek(size_t frame_index); //!< seek to the given frame index
+    size_t tell() const;           //!< get the frame index of the file pointer
     size_t total_frames() const;
     size_t rows() const;
     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 &&
-               detector_type == other.detector_type && max_frames_per_file == other.max_frames_per_file;
+        return dtype == other.dtype && rows == other.rows &&
+               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) +
-               ", geometry: " + geometry.to_string() + ", detector_type: " + ToString(detector_type) +
+        return "{ dtype: " + dtype.to_string() +
+               ", 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) + " }";
     }
@@ -42,7 +47,8 @@ struct FileConfig {
 /**
  * @brief FileInterface class to define the interface for file operations
  * @note parent class for NumpyFile and RawFile
- * @note all functions are pure virtual and must be implemented by the derived classes
+ * @note all functions are pure virtual and must be implemented by the derived
+ * classes
  */
 class FileInterface {
   public:
@@ -64,17 +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
@@ -134,7 +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/FilePtr.hpp

@@ -12,7 +12,7 @@ class FilePtr {
 
   public:
     FilePtr() = default;
-    FilePtr(const std::filesystem::path& fname, const std::string& mode);
+    FilePtr(const std::filesystem::path &fname, const std::string &mode);
     FilePtr(const FilePtr &) = delete;            // we don't want a copy
     FilePtr &operator=(const FilePtr &) = delete; // since we handle a resource
     FilePtr(FilePtr &&other);

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> scurve2_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> 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
@@ -67,7 +66,7 @@ NDArray<double, 3> fit_gaus(NDView<double, 1> x, NDView<double, 3> y,
  */
 void fit_gaus(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);
+              double &chi2);
 
 /**
  * @brief Fit a 1D Gaussian to each pixel with error estimates. Data layout
@@ -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,
-              int n_threads = DEFAULT_NUM_THREADS
-              );
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
+              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,
-              int n_threads = DEFAULT_NUM_THREADS);
+              NDView<double, 3> par_out, NDView<double, 3> par_err_out,
+              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); 
-void fit_scurve(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); 
-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_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);
+void fit_scurve(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);
+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); 
-void fit_scurve2(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); 
-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); 
+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);
+void fit_scurve2(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);
+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

@@ -19,7 +19,7 @@ class Frame {
     uint32_t m_cols;
     Dtype m_dtype;
     std::byte *m_data;
-    //TODO! Add frame number?
+    // TODO! Add frame number?
 
   public:
     /**
@@ -39,7 +39,7 @@ class Frame {
      * @param dtype data type of the pixels
      */
     Frame(const std::byte *bytes, uint32_t rows, uint32_t cols, Dtype dtype);
-    ~Frame(){ delete[] m_data; };
+    ~Frame() { delete[] m_data; };
 
     /** @warning Copy is disabled to ensure performance when passing
      * frames around. Can discuss enabling it.
@@ -52,7 +52,6 @@ class Frame {
     Frame &operator=(Frame &&other) noexcept;
     Frame(Frame &&other) noexcept;
 
-
     Frame clone() const; //<- Explicit copy
 
     uint32_t rows() const;
@@ -93,7 +92,7 @@ class Frame {
         if (row >= m_rows || col >= m_cols) {
             throw std::out_of_range("Invalid row or column index");
         }
-        //TODO! add tests then reimplement using pixel_ptr
+        // TODO! add tests then reimplement using pixel_ptr
         T data;
         std::memcpy(&data, m_data + (row * m_cols + col) * m_dtype.bytes(),
                     m_dtype.bytes());
@@ -102,9 +101,9 @@ class Frame {
     /**
      * @brief Return an NDView of the frame. This is the preferred way to access
      * data in the frame.
-     * 
+     *
      * @tparam T type of the pixels
-     * @return NDView<T, 2> 
+     * @return NDView<T, 2>
      */
     template <typename T> NDView<T, 2> view() {
         std::array<ssize_t, 2> shape = {static_cast<ssize_t>(m_rows),
@@ -113,7 +112,7 @@ class Frame {
         return NDView<T, 2>(data, shape);
     }
 
-    /** 
+    /**
      * @brief Copy the frame data into a new NDArray. This is a deep copy.
      */
     template <typename T> NDArray<T> image() {

include/aare/JungfrauDataFile.hpp

@@ -3,104 +3,113 @@
 #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{
+struct JungfrauDataHeader {
     uint64_t framenum;
     uint64_t bunchid;
 };
 
 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_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_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_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_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_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)
 
-    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* 
+    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 header_size = sizeof(JungfrauDataHeader);
+    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)
-    size_t bytes_per_frame() override;           
-    size_t pixels_per_frame() override;    
-    size_t bytes_per_pixel() const;  
+    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)
-    size_t tell() override;            //!< get the frame index of the file pointer
+    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;
     size_t cols() const override;
-    std::array<ssize_t,2> shape() const;
-    size_t n_files() const; //!< get the number of files in the series. 
+    std::array<ssize_t, 2> shape() const;
+    size_t n_files() const; //!< get the number of files in the series.
 
     // Extra functions needed for FileInterface
     Frame read_frame() override;
     Frame read_frame(size_t frame_number) override;
-    std::vector<Frame> read_n(size_t n_frames=0) override;
+    std::vector<Frame> read_n(size_t n_frames = 0) override;
     void read_into(std::byte *image_buf) override;
     void read_into(std::byte *image_buf, size_t n_frames) override;
     size_t frame_number(size_t frame_index) override;
     DetectorType detector_type() const override;
 
     /**
-     * @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)
+     * @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 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)
+     * @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 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:
+  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 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;
-
-
-  };
+    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_;
@@ -34,7 +33,7 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
      * @brief Default constructor. Will construct an empty NDArray.
      *
      */
-    NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), data_(nullptr) {};
+    NDArray() : shape_(), strides_(c_strides<Ndim>(shape_)), data_(nullptr){};
 
     /**
      * @brief Construct a new NDArray object with a given 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.
      *
@@ -69,8 +67,8 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
         std::copy(v.begin(), v.end(), begin());
     }
 
-    template<size_t Size>
-    NDArray(const std::array<T, Size>& arr) : NDArray<T,1>({Size}) {
+    template <size_t Size>
+    NDArray(const std::array<T, Size> &arr) : NDArray<T, 1>({Size}) {
         std::copy(arr.begin(), arr.end(), begin());
     }
 
@@ -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
@@ -113,10 +110,10 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
     NDArray &operator-=(const NDArray &other);
     NDArray &operator*=(const NDArray &other);
 
-    //Write directly to the data array, or create a new one
-    template<size_t Size>
-    NDArray<T,1>& operator=(const std::array<T,Size> &other){
-        if(Size != size_){
+    // Write directly to the data array, or create a new one
+    template <size_t Size>
+    NDArray<T, 1> &operator=(const std::array<T, Size> &other) {
+        if (Size != size_) {
             delete[] data_;
             size_ = Size;
             data_ = new T[size_];
@@ -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)),
-    //       size_(std::accumulate(std::begin(shape), std::end(shape), 1, std::multiplies<>())) {}
+    //     : buffer_(buffer),
+    //     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) { return elemenwise(val, std::divides<T>()); }
+    NDView &operator*=(const T val) {
+        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) {
-        if(size() != static_cast<ssize_t>(arr.size()))
-            throw std::runtime_error(LOCATION + "Array and NDView size mismatch");
+    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");
         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]);
         }
@@ -170,9 +190,8 @@ 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){
+std::ostream &operator<<(std::ostream &os, const NDView<T, Ndim> &arr) {
     for (auto row = 0; row < arr.shape(0); ++row) {
         for (auto col = 0; col < arr.shape(1); ++col) {
             os << std::setw(3);
@@ -183,10 +202,8 @@ 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){
-    return NDView<T,1>(vec.data(), {static_cast<ssize_t>(vec.size())});
+template <typename T> NDView<T, 1> make_view(std::vector<T> &vec) {
+    return NDView<T, 1>(vec.data(), {static_cast<ssize_t>(vec.size())});
 }
 
 } // namespace aare

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

@@ -18,15 +18,15 @@ template <typename SUM_TYPE = double> class Pedestal {
 
     uint32_t m_samples;
     NDArray<uint32_t, 2> m_cur_samples;
-    
-    //TODO! in case of int needs to be changed to uint64_t
+
+    // TODO! in case of int needs to be changed to uint64_t
     NDArray<SUM_TYPE, 2> m_sum;
     NDArray<SUM_TYPE, 2> m_sum2;
 
-    //Cache mean since it is used over and over in the ClusterFinder
-    //This optimization is related to the access pattern of the ClusterFinder
-    //Relies on having more reads than pushes to the pedestal
-    NDArray<SUM_TYPE, 2> m_mean; 
+    // Cache mean since it is used over and over in the ClusterFinder
+    // This optimization is related to the access pattern of the ClusterFinder
+    // Relies on having more reads than pushes to the pedestal
+    NDArray<SUM_TYPE, 2> m_mean;
 
   public:
     Pedestal(uint32_t rows, uint32_t cols, uint32_t n_samples = 1000)
@@ -42,9 +42,7 @@ template <typename SUM_TYPE = double> class Pedestal {
     }
     ~Pedestal() = default;
 
-    NDArray<SUM_TYPE, 2> mean() {
-        return m_mean;
-    }
+    NDArray<SUM_TYPE, 2> 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;
@@ -92,16 +86,12 @@ 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;
         m_cur_samples(row, col) = 0;
         m_mean(row, col) = 0;
     }
-    
-
 
     template <typename T> void push(NDView<T, 2> frame) {
         assert(frame.size() == m_rows * m_cols);
@@ -122,7 +112,7 @@ template <typename SUM_TYPE = double> class Pedestal {
     /**
      * Push but don't update the cached mean. Speeds up the process
      * when initializing the pedestal.
-     * 
+     *
      */
     template <typename T> void push_no_update(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);
         }
     }
 
@@ -191,19 +180,16 @@ 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(){
-        m_mean = m_sum / m_cur_samples;
-    }
+    void update_mean() { m_mean = m_sum / m_cur_samples; }
 
-    template<typename T>
-    void push_fast(const uint32_t row, const uint32_t col, const T val_){
-        //Assume we reached the steady state where all pixels have
-        //m_samples samples
+    template <typename T>
+    void push_fast(const uint32_t row, const uint32_t col, const T val_) {
+        // Assume we reached the steady state where all pixels have
+        // m_samples samples
         SUM_TYPE val = static_cast<SUM_TYPE>(val_);
         m_sum(row, col) += val - m_sum(row, col) / m_samples;
         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 {
 
@@ -10,11 +10,11 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap();
 NDArray<ssize_t, 2> GenerateMoench05PixelMap1g();
 NDArray<ssize_t, 2> GenerateMoench05PixelMapOld();
 
-//Matterhorn02
-NDArray<ssize_t, 2>GenerateMH02SingleCounterPixelMap();
+// Matterhorn02
+NDArray<ssize_t, 2> GenerateMH02SingleCounterPixelMap();
 NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap();
 
-//Eiger 
-NDArray<ssize_t, 2>GenerateEigerFlipRowsPixelMap();
+// Eiger
+NDArray<ssize_t, 2> GenerateEigerFlipRowsPixelMap();
 
 } // 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
-// Changed extension to .hpp
-// Changed namespace to aare
+// Copied: Line 34 constexpr std::size_t hardware_destructive_interference_size
+// = 128; from folly/lang/Align.h Changed extension to .hpp Changed namespace to
+// aare
 
 #pragma once
 
@@ -45,15 +45,14 @@ template <class T> struct ProducerConsumerQueue {
     ProducerConsumerQueue(const ProducerConsumerQueue &) = delete;
     ProducerConsumerQueue &operator=(const ProducerConsumerQueue &) = delete;
 
-    
-    ProducerConsumerQueue(ProducerConsumerQueue &&other){
+    ProducerConsumerQueue(ProducerConsumerQueue &&other) {
         size_ = other.size_;
         records_ = other.records_;
         other.records_ = nullptr;
         readIndex_ = other.readIndex_.load(std::memory_order_acquire);
         writeIndex_ = other.writeIndex_.load(std::memory_order_acquire);
     }
-    ProducerConsumerQueue &operator=(ProducerConsumerQueue &&other){
+    ProducerConsumerQueue &operator=(ProducerConsumerQueue &&other) {
         size_ = other.size_;
         records_ = other.records_;
         other.records_ = nullptr;
@@ -61,16 +60,17 @@ template <class T> struct ProducerConsumerQueue {
         writeIndex_ = other.writeIndex_.load(std::memory_order_acquire);
         return *this;
     }
-    
-    
-    ProducerConsumerQueue():ProducerConsumerQueue(2){};
+
+    ProducerConsumerQueue() : ProducerConsumerQueue(2){};
     // size must be >= 2.
     //
     // Also, note that the number of usable slots in the queue at any
     // 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_;
         }
@@ -192,7 +194,7 @@ template <class T> struct ProducerConsumerQueue {
     // const uint32_t size_;
     uint32_t size_;
     // T *const records_;
-    T* records_;
+    T *records_;
 
     alignas(hardware_destructive_interference_size) AtomicIndex readIndex_;
     alignas(hardware_destructive_interference_size) AtomicIndex writeIndex_;

include/aare/RawFile.hpp

@@ -1,27 +1,23 @@
 #pragma once
+#include "aare/DetectorGeometry.hpp"
 #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"
 
+#ifdef AARE_TESTS
+#include "../tests/friend_test.hpp"
+#endif
 
 #include <optional>
 
 namespace aare {
 
-struct ModuleConfig {
-    int module_gap_row{};
-    int module_gap_col{};
-
-    bool operator==(const ModuleConfig &other) const {
-        if (module_gap_col != other.module_gap_col)
-            return false;
-        if (module_gap_row != other.module_gap_row)
-            return false;
-        return true;
-    }
-};
+#ifdef AARE_TESTS
+TEST_CASE_PRIVATE_FWD(check_find_geometry) // forward declaration
+TEST_CASE_PRIVATE_FWD(open_multi_module_file_with_roi)
+#endif
 
 /**
  * @brief Class to read .raw files. The class will parse the master file
@@ -30,11 +26,17 @@ struct ModuleConfig {
  * Consider using that unless you need raw file specific functionality.
  */
 class RawFile : public FileInterface {
+
+#ifdef AARE_TESTS
+    FRIEND_TEST(check_find_geometry)
+    FRIEND_TEST(open_multi_module_file_with_roi)
+#endif
     std::vector<std::unique_ptr<RawSubFile>> m_subfiles;
-    ModuleConfig cfg{0, 0};
+
     RawMasterFile m_master;
     size_t m_current_frame{};
     size_t m_current_subfile{};
+
     DetectorGeometry m_geometry;
 
   public:
@@ -53,10 +55,10 @@ class RawFile : public FileInterface {
     void read_into(std::byte *image_buf) override;
     void read_into(std::byte *image_buf, size_t n_frames) override;
 
-    //TODO! do we need to adapt the API? 
+    // 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;
@@ -70,33 +72,11 @@ class RawFile : public FileInterface {
     size_t bitdepth() const override;
     xy geometry();
     size_t n_modules() const;
-    
+
     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);
-
-
-    /**
-     * @brief get the frame at the given frame index
-     * @param frame_number frame number to read
-     * @return Frame
-     */
-    Frame get_frame(size_t frame_index);
-
-
-
     /**
      * @brief read the header of the file
      * @param fname path to the data subfile
@@ -104,9 +84,24 @@ class RawFile : public FileInterface {
      */
     static DetectorHeader read_header(const std::filesystem::path &fname);
 
+  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);
+
+    /**
+     * @brief get the frame at the given frame index
+     * @param frame_number frame number to read
+     * @return Frame
+     */
+    Frame get_frame(size_t frame_index);
+
     void open_subfiles();
-    void find_geometry();
 };
 
-
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -1,5 +1,6 @@
 #pragma once
 #include "aare/defs.hpp"
+#include <algorithm>
 #include <filesystem>
 #include <fmt/format.h>
 #include <fstream>
@@ -45,7 +46,7 @@ class ScanParameters {
     int m_start = 0;
     int m_stop = 0;
     int m_step = 0;
-    //TODO! add settleTime, requires string to time conversion
+    // TODO! add settleTime, requires string to time conversion
 
   public:
     ScanParameters(const std::string &par);
@@ -61,7 +62,6 @@ class ScanParameters {
     void increment_stop();
 };
 
-
 /**
  * @brief Class for parsing a master file either in our .json format or the old
  * .raw format
@@ -78,8 +78,11 @@ class RawMasterFile {
     size_t m_pixels_y{};
     size_t m_pixels_x{};
     size_t m_bitdepth{};
+    size_t m_num_udp_interfaces_per_module = 1;
+    uint8_t m_quad = 0;
 
     xy m_geometry{};
+    xy m_udp_interfaces_per_module{1, 1};
 
     size_t m_max_frames_per_file{};
     // uint32_t m_adc_mask{}; // TODO! implement reading
@@ -97,11 +100,9 @@ class RawMasterFile {
     std::optional<size_t> m_digital_samples;
     std::optional<size_t> m_transceiver_samples;
     std::optional<size_t> m_number_of_rows;
-    std::optional<uint8_t> m_quad;
 
     std::optional<ROI> m_roi;
 
-
   public:
     RawMasterFile(const std::filesystem::path &fpath);
 
@@ -117,27 +118,27 @@ class RawMasterFile {
     size_t max_frames_per_file() const;
     size_t bitdepth() const;
     size_t frame_padding() const;
+    xy udp_interfaces_per_module() const;
     const FrameDiscardPolicy &frame_discard_policy() const;
 
     size_t total_frames_expected() const;
     xy geometry() const;
     size_t n_modules() const;
+    uint8_t quad() const;
 
     std::optional<size_t> analog_samples() const;
     std::optional<size_t> digital_samples() const;
     std::optional<size_t> transceiver_samples() const;
     std::optional<size_t> number_of_rows() const;
-    std::optional<uint8_t> quad() const;
-
 
     std::optional<ROI> roi() const;
 
-
     ScanParameters scan_parameters() const;
 
   private:
     void parse_json(const std::filesystem::path &fpath);
     void parse_raw(const std::filesystem::path &fpath);
+    void retrieve_geometry();
 };
 
 } // namespace aare

include/aare/RawSubFile.hpp

@@ -10,32 +10,34 @@
 namespace aare {
 
 /**
- * @brief Class to read a singe subfile written in .raw format. Used from RawFile to read
- * the entire detector. Can be used directly to read part of the image.
+ * @brief Class to read a singe subfile written in .raw format. Used from
+ * RawFile to read the entire detector. Can be used directly to read part of the
+ * image.
  */
 class RawSubFile {
   protected:
     std::ifstream m_file;
     DetectorType m_detector_type;
     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_total_frames{};    //!< total number of frames in the series of files
+    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_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)
-    std::vector<size_t> m_last_frame_in_file{}; //!< Used for seeking to the correct 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)
+    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
      */
@@ -62,14 +66,15 @@ 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);
-    
+
     size_t rows() const;
     size_t cols() const;
-    
+
     size_t frame_number(size_t frame_index);
 
     size_t bytes_per_frame() const { return m_bytes_per_frame; }
@@ -78,15 +83,13 @@ class RawSubFile {
 
     size_t frames_in_file() const { return m_total_frames; }
 
-private:
-  template <typename T>
-  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;
+  private:
+    template <typename T> 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

@@ -38,11 +38,13 @@ 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> dj{{-1, -1, 0, 1}};               // col ### 8-neighbour by scaning from top to bottom
+    const std::array<int, 4> di{
+        {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
+    std::map<int, int> child; // heirachy: key: child; val: parent
     std::unordered_map<int, Hit> h_size;
     std::vector<Hit> hits;
     // std::vector<std::vector<int16_t>> row
@@ -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].cols[h_size[clusterIndex].size] = col;
-                //     h_size[clusterIndex].enes[h_size[clusterIndex].size] = original_(row, col);
+                //     h_size[clusterIndex].rows[h_size[clusterIndex].size] =
+                //     row; h_size[clusterIndex].cols[h_size[clusterIndex].size]
+                //     = 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
-                // (j-1 >= 0 and labeled_(i, j-1) != 0) or
+                // (i-1 >= 0 and labeled_(i-1, j) != 0) or // another circle of
+                // 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 {
 /**
@@ -15,26 +15,24 @@ namespace aare {
  * @param last iterator to the last element
  * @param val value to compare
  * @return index of the last element that is smaller than val
- * 
+ *
  */
 template <typename T>
-size_t last_smaller(const T* first, const T* last, T val) {
-    for (auto iter = first+1; iter != last; ++iter) {
+size_t last_smaller(const T *first, const T *last, T val) {
+    for (auto iter = first + 1; iter != last; ++iter) {
         if (*iter >= val) {
-            return std::distance(first, iter-1);
+            return std::distance(first, iter - 1);
         }
     }
-    return std::distance(first, last-1);
+    return std::distance(first, last - 1);
 }
 
-template <typename T>
-size_t last_smaller(const NDArray<T, 1>& arr, T val) {
+template <typename T> size_t last_smaller(const NDArray<T, 1> &arr, T val) {
     return last_smaller(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
-size_t last_smaller(const std::vector<T>& vec, T val) {
-    return last_smaller(vec.data(), vec.data()+vec.size(), val);
+template <typename T> size_t last_smaller(const std::vector<T> &vec, T val) {
+    return last_smaller(vec.data(), vec.data() + vec.size(), val);
 }
 
 /**
@@ -48,65 +46,59 @@ size_t last_smaller(const std::vector<T>& vec, T val) {
  * @return index of the first element that is larger than val
  */
 template <typename T>
-size_t first_larger(const T* first, const T* last, T val) {
+size_t first_larger(const T *first, const T *last, T val) {
     for (auto iter = first; iter != last; ++iter) {
         if (*iter > val) {
             return std::distance(first, iter);
         }
     }
-    return std::distance(first, last-1);
+    return std::distance(first, last - 1);
 }
 
-template <typename T>
-size_t first_larger(const NDArray<T, 1>& arr, T val) {
+template <typename T> size_t first_larger(const NDArray<T, 1> &arr, T val) {
     return first_larger(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
-size_t first_larger(const std::vector<T>& vec, T val) {
-    return first_larger(vec.data(), vec.data()+vec.size(), val);
+template <typename T> 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
  * @return index of the nearest element
  */
 template <typename T>
-size_t nearest_index(const T* first, const T* last, T val) {
-    auto iter = std::min_element(first, last,
-    [val](T a, T b) {
+size_t nearest_index(const T *first, const T *last, T val) {
+    auto iter = std::min_element(first, last, [val](T a, T b) {
         return std::abs(a - val) < std::abs(b - val);
     });
     return std::distance(first, iter);
 }
 
-template <typename T>
-size_t nearest_index(const NDArray<T, 1>& arr, T val) {
+template <typename T> size_t nearest_index(const NDArray<T, 1> &arr, T val) {
     return nearest_index(arr.begin(), arr.end(), val);
 }
 
-template <typename T>
-size_t nearest_index(const std::vector<T>& vec, T val) {
-    return nearest_index(vec.data(), vec.data()+vec.size(), val);
+template <typename T> size_t nearest_index(const std::vector<T> &vec, T val) {
+    return nearest_index(vec.data(), vec.data() + vec.size(), val);
 }
 
 template <typename T, size_t N>
-size_t nearest_index(const std::array<T,N>& arr, T val) {
-    return nearest_index(arr.data(), arr.data()+arr.size(), val);
+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>
-std::vector<T> cumsum(const std::vector<T>& vec) {
+template <typename T> 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_04_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);
+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
- * for each bit i that is set in the input value.
+ * @brief Apply custom weights to a 16-bit input value. Will sum up
+ * 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

@@ -3,16 +3,15 @@
 #include "aare/Dtype.hpp"
 
 #include <array>
-#include <stdexcept>
 #include <cassert>
 #include <cstdint>
 #include <cstring>
+#include <stdexcept>
 #include <string>
 #include <string_view>
 #include <variant>
 #include <vector>
 
-
 /**
  * @brief LOCATION macro to get the current location in the code
  */
@@ -20,28 +19,24 @@
     std::string(__FILE__) + std::string(":") + std::to_string(__LINE__) +      \
         ":" + std::string(__func__) + ":"
 
-
-
 #ifdef AARE_CUSTOM_ASSERT
-#define AARE_ASSERT(expr)\
-    if (expr)\
-        {}\
-    else\
+#define AARE_ASSERT(expr)                                                      \
+    if (expr) {                                                                \
+    } else                                                                     \
         aare::assert_failed(LOCATION + " Assertion failed: " + #expr + "\n");
 #else
-#define AARE_ASSERT(cond)\
-    do { (void)sizeof(cond); } while(0)
+#define AARE_ASSERT(cond)                                                      \
+    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;
@@ -55,7 +50,7 @@ class DynamicCluster {
 
   public:
     DynamicCluster(int cluster_sizeX_, int cluster_sizeY_,
-            Dtype dt_ = Dtype(typeid(int32_t)))
+                   Dtype dt_ = Dtype(typeid(int32_t)))
         : cluster_sizeX(cluster_sizeX_), cluster_sizeY(cluster_sizeY_),
           dt(dt_) {
         m_data = new std::byte[cluster_sizeX * cluster_sizeY * dt.bytes()]{};
@@ -179,60 +174,30 @@ 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
- */
-struct ModuleGeometry{
-    int origin_x{};
-    int origin_y{};
-    int height{};
-    int width{};
-    int row_index{};
-    int col_index{}; 
-};
-
-/**
- * @brief Class to hold the geometry of a detector. Number of modules, their size and where pixel 0 
- * for each module is located
- */
-struct DetectorGeometry{
-    int modules_x{};
-    int modules_y{};
-    int pixels_x{};
-    int pixels_y{};
-    int module_gap_row{};
-    int module_gap_col{};
-    std::vector<ModuleGeometry> module_pixel_0;
-    
-    auto size() const { return module_pixel_0.size(); }
-};
-
-struct ROI{
+struct ROI {
     ssize_t xmin{};
     ssize_t xmax{};
     ssize_t ymin{};
     ssize_t ymax{};
-  
+
     ssize_t height() const { return ymax - ymin; }
     ssize_t width() const { return xmax - xmin; }
     bool contains(ssize_t x, ssize_t y) const {
         return x >= xmin && x < xmax && y >= ymin && y < ymax;
     }
-  };
-
+};
 
 using dynamic_shape = std::vector<ssize_t>;
 
-//TODO! Can we uniform enums between the libraries?
+// TODO! Can we uniform enums between the libraries?
 
 /**
- * @brief Enum class to identify different detectors. 
+ * @brief Enum class to identify different detectors.
  * The values are the same as in slsDetectorPackage
  * Different spelling to avoid confusion with the slsDetectorPackage
  */
 enum class DetectorType {
-    //Standard detectors match the enum values from slsDetectorPackage
+    // Standard detectors match the enum values from slsDetectorPackage
     Generic,
     Eiger,
     Gotthard,
@@ -243,8 +208,9 @@ enum class DetectorType {
     Gotthard2,
     Xilinx_ChipTestBoard,
 
-    //Additional detectors used for defining processing. Variants of the standard ones.
-    Moench03=100,
+    // Additional detectors used for defining processing. Variants of the
+    // standard ones.
+    Moench03 = 100,
     Moench03_old,
     Unknown
 };

include/aare/geo_helpers.hpp

@@ -1,16 +0,0 @@
-#pragma once
-#include "aare/defs.hpp"
-#include "aare/RawMasterFile.hpp" //ROI refactor away
-namespace aare{
-
-/**
- * @brief Update the detector geometry given a region of interest
- * 
- * @param geo 
- * @param roi 
- * @return DetectorGeometry 
- */
-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/ifstream_helpers.hpp

@@ -4,9 +4,9 @@
 #include <string>
 namespace aare {
 
-/** 
+/**
  * @brief Get the error message from an ifstream object
-*/
+ */
 std::string ifstream_error_msg(std::ifstream &ifs);
 
 } // namespace aare

include/aare/utils/par.hpp

@@ -1,18 +1,18 @@
 #include <thread>
-#include <vector>
 #include <utility>
+#include <vector>
 
 namespace aare {
 
-    template<typename F>
-    void RunInParallel(F func, const std::vector<std::pair<int, int>>& tasks) {
-        // auto tasks = split_task(0, y.shape(0), n_threads);
-        std::vector<std::thread> threads;
-        for (auto &task : tasks) {
-            threads.push_back(std::thread(func, task.first, task.second));
-        }
-        for (auto &thread : threads) {
-            thread.join();
-        }
+template <typename F>
+void RunInParallel(F func, const std::vector<std::pair<int, int>> &tasks) {
+    // auto tasks = split_task(0, y.shape(0), n_threads);
+    std::vector<std::thread> threads;
+    for (auto &task : tasks) {
+        threads.push_back(std::thread(func, task.first, task.second));
     }
+    for (auto &thread : threads) {
+        thread.join();
+    }
+}
 } // 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,
-                                       const std::string &typestr) {
+void define_ClusterCollector(py::module &m, 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,
-                                     const std::string &typestr) {
+void define_ClusterFile(py::module &m, 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,
-                                       const std::string &typestr) {
+void define_ClusterFileSink(py::module &m, 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,
-                                       const std::string &typestr) {
+void define_ClusterFinderMT(py::module &m, const std::string &typestr) {
     auto class_name = fmt::format("ClusterFinderMT_{}", typestr);
 
     using ClusterType = Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>;
@@ -49,9 +48,11 @@ 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){
-            return py::make_tuple(ClusterSizeX, ClusterSizeY);
-        })
+        .def_property_readonly(
+            "cluster_size",
+            [](ClusterFinderMT<ClusterType, uint16_t, pd_type> &self) {
+                return py::make_tuple(ClusterSizeX, ClusterSizeY);
+            })
         .def("clear_pedestal",
              &ClusterFinderMT<ClusterType, uint16_t, pd_type>::clear_pedestal)
         .def("sync", &ClusterFinderMT<ClusterType, uint16_t, pd_type>::sync)
@@ -77,5 +78,4 @@ void define_ClusterFinderMT(py::module &m,
             py::arg("thread_index") = 0);
 }
 
-
 #pragma GCC diagnostic pop

python/src/bind_ClusterVector.hpp

@@ -44,10 +44,11 @@ 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){
-            auto *vec = new std::vector<Type>(self.sum_2x2());
-            return return_vector(vec);
-        })
+        .def("sum_2x2",
+             [](ClusterVector<ClusterType> &self) {
+                 auto *vec = new std::vector<Type>(self.sum_2x2());
+                 return return_vector(vec);
+             })
         .def_property_readonly("size", &ClusterVector<ClusterType>::size)
         .def("item_size", &ClusterVector<ClusterType>::item_size)
         .def_property_readonly("fmt",

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"
@@ -26,95 +26,103 @@ 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) {
+    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");
+        }
 
-    
-    if(input.ndim() != 2){
-        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)};
+        py::array_t<uint16_t> output(shape);
 
-    //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)};
-    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<uint16_t, 2> output_view(output.mutable_data(),
+                                        {output.shape(0), output.shape(1)});
 
-    //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<uint16_t, 2> output_view(output.mutable_data(), {output.shape(0), output.shape(1)});
+        adc_sar_05_decode64to16(input_view, output_view);
 
-    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"); 
-    }
-
-    //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)};
-    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<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(
-    "apply_custom_weights",
-    [](py::array_t<uint16_t, py::array::c_style | py::array::forcecast> &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)
-        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<double, 1> output_view(output.mutable_data(), {output.size()});
-
-        apply_custom_weights(input_view, output_view, weights_view);
         return output;
     });
 
-py::class_<CtbRawFile>(m, "CtbRawFile")
-    .def(py::init<const std::filesystem::path &>())
-    .def("read_frame",
-         [](CtbRawFile &self) {
-             size_t image_size = self.image_size_in_bytes();
-             py::array image;
-             std::vector<ssize_t> shape;
-             shape.reserve(2);
-             shape.push_back(1);
-             shape.push_back(image_size);
+    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");
+        }
 
-             py::array_t<DetectorHeader> header(1);
+        // 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)};
+        py::array_t<uint16_t> output(shape);
 
-             // always read bytes
-             image = py::array_t<uint8_t>(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<uint16_t, 2> output_view(output.mutable_data(),
+                                        {output.shape(0), output.shape(1)});
 
-             self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
-                            header.mutable_data());
+        adc_sar_04_decode64to16(input_view, output_view);
 
-             return py::make_tuple(header, image);
-         })
-    .def("seek", &CtbRawFile::seek)
-    .def("tell", &CtbRawFile::tell)
-    .def("master", &CtbRawFile::master)
+        return output;
+    });
 
-    .def_property_readonly("image_size_in_bytes",
-                           &CtbRawFile::image_size_in_bytes)
+    m.def("apply_custom_weights",
+          [](py::array_t<uint16_t, py::array::c_style | py::array::forcecast>
+                 &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)
+              py::buffer_info buf = input.request();
+              py::array_t<double> output(buf.shape);
 
-    .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
+              // 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<double, 1> output_view(output.mutable_data(),
+                                            {output.size()});
 
+              apply_custom_weights(input_view, output_view, weights_view);
+              return output;
+          });
+
+    py::class_<CtbRawFile>(m, "CtbRawFile")
+        .def(py::init<const std::filesystem::path &>())
+        .def("read_frame",
+             [](CtbRawFile &self) {
+                 size_t image_size = self.image_size_in_bytes();
+                 py::array image;
+                 std::vector<ssize_t> shape;
+                 shape.reserve(2);
+                 shape.push_back(1);
+                 shape.push_back(image_size);
+
+                 py::array_t<DetectorHeader> header(1);
+
+                 // always read bytes
+                 image = py::array_t<uint8_t>(shape);
+
+                 self.read_into(
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
+                     header.mutable_data());
+
+                 return py::make_tuple(header, image);
+             })
+        .def("seek", &CtbRawFile::seek)
+        .def("tell", &CtbRawFile::tell)
+        .def("master", &CtbRawFile::master)
+
+        .def_property_readonly("image_size_in_bytes",
+                               &CtbRawFile::image_size_in_bytes)
+
+        .def_property_readonly("frames_in_file", &CtbRawFile::frames_in_file);
 }

python/src/file.hpp

@@ -20,17 +20,13 @@
 namespace py = pybind11;
 using namespace ::aare;
 
-
-
-
-//Disable warnings for unused parameters, as we ignore some
-//in the __exit__ method
+// Disable warnings for unused parameters, as we ignore some
+// in the __exit__ method
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 
 void define_file_io_bindings(py::module &m) {
 
-
     py::enum_<DetectorType>(m, "DetectorType")
         .value("Jungfrau", DetectorType::Jungfrau)
         .value("Eiger", DetectorType::Eiger)
@@ -41,13 +37,10 @@ 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", {});
@@ -112,45 +105,18 @@ 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) {
-            //adjust for actual frames left in the file
-            n_frames = std::min(n_frames, self.total_frames()-self.tell());
-            if(n_frames == 0){
-                throw std::runtime_error("No frames left in file");
-            }
-            std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
-            
-            py::array image;
-            const uint8_t item_size = self.bytes_per_pixel();
-            if (item_size == 1) {
-                image = py::array_t<uint8_t>(shape);
-            } else if (item_size == 2) {
-                image = py::array_t<uint16_t>(shape);
-            } else if (item_size == 4) {
-                image = py::array_t<uint32_t>(shape);
-            }
-            self.read_into(reinterpret_cast<std::byte *>(image.mutable_data()),
-                           n_frames);
-            return image;
-        })
-        .def("__enter__", [](File &self) { return &self; })
-        .def("__exit__",
-             [](File &self,
-                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) {
+        .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());
+                 if (n_frames == 0) {
+                     throw std::runtime_error("No frames left in file");
+                 }
+                 std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
 
-            try{
-                const uint8_t item_size = self.bytes_per_pixel();
                  py::array image;
-                 std::vector<ssize_t> shape;
-                 shape.reserve(2);
-                 shape.push_back(self.rows());
-                 shape.push_back(self.cols());
+                 const uint8_t item_size = self.bytes_per_pixel();
                  if (item_size == 1) {
                      image = py::array_t<uint8_t>(shape);
                  } else if (item_size == 2) {
@@ -159,14 +125,41 @@ void define_file_io_bindings(py::module &m) {
                      image = py::array_t<uint32_t>(shape);
                  }
                  self.read_into(
-                     reinterpret_cast<std::byte *>(image.mutable_data()));
+                     reinterpret_cast<std::byte *>(image.mutable_data()),
+                     n_frames);
                  return image;
-            }catch(std::runtime_error &e){
+             })
+        .def("__enter__", [](File &self) { return &self; })
+        .def("__exit__",
+             [](File &self, 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;
+                std::vector<ssize_t> shape;
+                shape.reserve(2);
+                shape.push_back(self.rows());
+                shape.push_back(self.cols());
+                if (item_size == 1) {
+                    image = py::array_t<uint8_t>(shape);
+                } else if (item_size == 2) {
+                    image = py::array_t<uint16_t>(shape);
+                } else if (item_size == 4) {
+                    image = py::array_t<uint32_t>(shape);
+                }
+                self.read_into(
+                    reinterpret_cast<std::byte *>(image.mutable_data()));
+                return image;
+            } catch (std::runtime_error &e) {
                 throw py::stop_iteration();
             }
         });
 
-
     py::class_<FileConfig>(m, "FileConfig")
         .def(py::init<>())
         .def_readwrite("rows", &FileConfig::rows)
@@ -183,8 +176,6 @@ 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 &>())
@@ -195,7 +186,6 @@ 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"),
@@ -204,23 +194,21 @@ 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){
-            return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}", self.xmin, self.xmax, self.ymin, self.ymax);
-        })
-        .def("__repr__", [](const ROI& self){
-            return fmt::format("<ROI: xmin: {} xmax: {} ymin: {} ymax: {}>", self.xmin, self.xmax, self.ymin, self.ymax);
-        })
+        .def("__str__",
+             [](const ROI &self) {
+                 return fmt::format("ROI: xmin: {} xmax: {} ymin: {} ymax: {}",
+                                    self.xmin, self.xmax, self.ymin, self.ymax);
+             })
+        .def("__repr__",
+             [](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
+            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);
@@ -248,11 +247,10 @@ n_threads : int, optional
                 aare::fit_pol1(x_view, y_view, y_view_err, par->view(),
                                par_err->view(), chi2->view(), n_threads);
                 return py::dict("par"_a = return_image_data(par),
-                                "par_err"_a = return_image_data(par_err), 
+                                "par_err"_a = return_image_data(par_err),
                                 "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});
@@ -289,7 +287,7 @@ n_threads : int, optional
 )",
         py::arg("x"), py::arg("y"), py::arg("y_err"), py::arg("n_threads") = 4);
 
-//=========
+    //=========
     m.def(
         "fit_scurve",
         [](py::array_t<double, py::array::c_style | py::array::forcecast> x,
@@ -333,13 +331,12 @@ n_threads : int, optional
                 auto chi2 = new NDArray<double, 2>({y.shape(0), y.shape(1)});
 
                 aare::fit_scurve(x_view, y_view, y_view_err, par->view(),
-                               par_err->view(), chi2->view(), n_threads);
+                                 par_err->view(), chi2->view(), n_threads);
                 return py::dict("par"_a = return_image_data(par),
-                                "par_err"_a = return_image_data(par_err), 
+                                "par_err"_a = return_image_data(par_err),
                                 "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});
@@ -351,7 +348,7 @@ n_threads : int, optional
                 double chi2 = 0;
 
                 aare::fit_scurve(x_view, y_view, y_view_err, par->view(),
-                               par_err->view(), chi2);
+                                 par_err->view(), chi2);
                 return py::dict("par"_a = return_image_data(par),
                                 "par_err"_a = return_image_data(par_err),
                                 "chi2"_a = chi2, "Ndf"_a = y.size() - 2);
@@ -375,7 +372,6 @@ n_threads : int, optional
     The number of threads to use. Default is 4.
 )",
         py::arg("x"), py::arg("y"), py::arg("y_err"), py::arg("n_threads") = 4);
-    
 
     m.def(
         "fit_scurve2",
@@ -420,13 +416,12 @@ n_threads : int, optional
                 auto chi2 = new NDArray<double, 2>({y.shape(0), y.shape(1)});
 
                 aare::fit_scurve2(x_view, y_view, y_view_err, par->view(),
-                               par_err->view(), chi2->view(), n_threads);
+                                  par_err->view(), chi2->view(), n_threads);
                 return py::dict("par"_a = return_image_data(par),
-                                "par_err"_a = return_image_data(par_err), 
+                                "par_err"_a = return_image_data(par_err),
                                 "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});
@@ -438,7 +433,7 @@ n_threads : int, optional
                 double chi2 = 0;
 
                 aare::fit_scurve2(x_view, y_view, y_view_err, par->view(),
-                               par_err->view(), chi2);
+                                  par_err->view(), chi2);
                 return py::dict("par"_a = return_image_data(par),
                                 "par_err"_a = return_image_data(par_err),
                                 "chi2"_a = chi2, "Ndf"_a = y.size() - 2);

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({
-        self.rows(), 
-        self.cols() 
-    });
+    py::array_t<uint16_t> image({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({
-        n_frames, self.rows(), 
-        self.cols()});
+    py::array_t<uint16_t> image({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

@@ -1,26 +1,26 @@
 // Files with bindings to the different classes
 
-//New style file naming
+// 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
+// TODO! migrate the other names
 #include "ctb_raw_file.hpp"
 #include "file.hpp"
 #include "fit.hpp"
 #include "interpolation.hpp"
-#include "raw_sub_file.hpp"
-#include "raw_master_file.hpp"
-#include "raw_file.hpp"
-#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>
@@ -34,17 +34,18 @@ 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) \
-    define_ClusterFile<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_ClusterVector<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_ClusterFinder<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_ClusterFinderMT<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_ClusterFileSink<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_ClusterCollector<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE); \
-    define_Cluster<T, N, M, U>(m, #N "x" #M #TYPE_CODE); \
+#define DEFINE_CLUSTER_BINDINGS(T, N, M, U, TYPE_CODE)                         \
+    define_ClusterFile<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);         \
+    define_ClusterVector<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);       \
+    define_ClusterFinder<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);       \
+    define_ClusterFinderMT<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);     \
+    define_ClusterFileSink<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);     \
+    define_ClusterCollector<T, N, M, U>(m, "Cluster" #N "x" #M #TYPE_CODE);    \
+    define_Cluster<T, N, M, U>(m, #N "x" #M #TYPE_CODE);                       \
     register_calculate_eta<T, N, M, U>(m);
 
 PYBIND11_MODULE(_aare, m) {

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>())
@@ -19,16 +20,18 @@ 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) {
-            auto var = new NDArray<SUM_TYPE, 2>{};
-            *var = self.variance();
-            return return_image_data(var);
-        })
-        .def("std", [](Pedestal<SUM_TYPE> &self) {
-            auto std = new NDArray<SUM_TYPE, 2>{};
-            *std = self.std();
-            return return_image_data(std);
-        })
+        .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) {
+                 auto std = new NDArray<SUM_TYPE, 2>{};
+                 *std = self.std();
+                 return return_image_data(std);
+             })
         .def("clear", py::overload_cast<>(&Pedestal<SUM_TYPE>::clear))
         .def_property_readonly("rows", &Pedestal<SUM_TYPE>::rows)
         .def_property_readonly("cols", &Pedestal<SUM_TYPE>::cols)
@@ -39,14 +42,19 @@ template <typename SUM_TYPE> void define_pedestal_bindings(py::module &m, const
              [&](Pedestal<SUM_TYPE> &pedestal) {
                  return Pedestal<SUM_TYPE>(pedestal);
              })
-        //TODO! add push for other data types
-        .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) {
-            auto v = make_view_2d(f);
-            pedestal.push_no_update(v);
-        }, py::arg().noconvert())
+        // TODO! add push for other data types
+        .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) {
+                auto v = make_view_2d(f);
+                pedestal.push_no_update(v);
+            },
+            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;
-
+using namespace ::aare;
 
 void define_pixel_map_bindings(py::module &m) {
-    m.def("GenerateMoench03PixelMap", []() {
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench03PixelMap());
-        return return_image_data(ptr);
-    })
-    .def("GenerateMoench05PixelMap", []() {
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap());
-        return return_image_data(ptr);
-    })
-        .def("GenerateMoench05PixelMap1g", []() {
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMap1g());
-        return return_image_data(ptr);
-    })
-    .def("GenerateMoench05PixelMapOld", []() {
-        auto ptr = new NDArray<ssize_t,2>(GenerateMoench05PixelMapOld());
-        return return_image_data(ptr);
-    })
-    .def("GenerateMH02SingleCounterPixelMap", []() {
-        auto ptr = new NDArray<ssize_t,2>(GenerateMH02SingleCounterPixelMap());
-        return return_image_data(ptr);
-    })
-    .def("GenerateMH02FourCounterPixelMap", []() {
-        auto ptr = new NDArray<ssize_t,3>(GenerateMH02FourCounterPixelMap());
-        return return_image_data(ptr);
-    });
-
+    m.def("GenerateMoench03PixelMap",
+          []() {
+              auto ptr = new NDArray<ssize_t, 2>(GenerateMoench03PixelMap());
+              return return_image_data(ptr);
+          })
+        .def("GenerateMoench05PixelMap",
+             []() {
+                 auto ptr = new NDArray<ssize_t, 2>(GenerateMoench05PixelMap());
+                 return return_image_data(ptr);
+             })
+        .def("GenerateMoench05PixelMap1g",
+             []() {
+                 auto ptr =
+                     new NDArray<ssize_t, 2>(GenerateMoench05PixelMap1g());
+                 return return_image_data(ptr);
+             })
+        .def("GenerateMoench05PixelMapOld",
+             []() {
+                 auto ptr =
+                     new NDArray<ssize_t, 2>(GenerateMoench05PixelMapOld());
+                 return return_image_data(ptr);
+             })
+        .def("GenerateMH02SingleCounterPixelMap",
+             []() {
+                 auto ptr = new NDArray<ssize_t, 2>(
+                     GenerateMH02SingleCounterPixelMap());
+                 return return_image_data(ptr);
+             })
+        .def("GenerateMH02FourCounterPixelMap", []() {
+            auto ptr =
+                new NDArray<ssize_t, 3>(GenerateMH02FourCounterPixelMap());
+            return return_image_data(ptr);
+        });
 }

python/src/raw_file.hpp

@@ -58,13 +58,14 @@ void define_raw_file_io_bindings(py::module &m) {
                     throw std::runtime_error("No frames left in file");
                 }
                 std::vector<size_t> shape{n_frames, self.rows(), self.cols()};
-            
+
                 // return headers from all subfiles
                 py::array_t<DetectorHeader> header;
                 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});
 
@@ -100,7 +101,7 @@ void define_raw_file_io_bindings(py::module &m) {
         .def_property_readonly("cols", &RawFile::cols)
         .def_property_readonly("bitdepth", &RawFile::bitdepth)
         .def_property_readonly("geometry", &RawFile::geometry)
-        .def_property_readonly("n_modules", &RawFile::n_modules)
         .def_property_readonly("detector_type", &RawFile::detector_type)
-        .def_property_readonly("master", &RawFile::master);
+        .def_property_readonly("master", &RawFile::master)
+        .def_property_readonly("n_modules", &RawFile::n_modules);
 }

python/src/raw_master_file.hpp

@@ -57,7 +57,10 @@ 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("udp_interfaces_per_module",
+                               &RawMasterFile::udp_interfaces_per_module)
+        .def_property_readonly("analog_samples", &RawMasterFile::analog_samples,
+                               R"(
             Number of analog samples
 
             Returns
@@ -66,7 +69,7 @@ void define_raw_master_file_bindings(py::module &m) {
                     The number of analog samples in the file (or None if not enabled)
             )")
         .def_property_readonly("digital_samples",
-                               &RawMasterFile::digital_samples,  R"(
+                               &RawMasterFile::digital_samples, R"(
             Number of digital samples
 
             Returns

python/src/raw_sub_file.hpp

@@ -24,8 +24,8 @@ auto read_frame_from_RawSubFile(RawSubFile &self) {
     py::array_t<DetectorHeader> header(1);
     const uint8_t item_size = self.bytes_per_pixel();
     std::vector<ssize_t> shape{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) {
         image = py::array_t<uint8_t>(shape);
@@ -43,12 +43,10 @@ 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{
-        static_cast<ssize_t>(n_frames), 
-        static_cast<ssize_t>(self.rows()),
-        static_cast<ssize_t>(self.cols())
-    };
-    
+    std::vector<ssize_t> shape{static_cast<ssize_t>(n_frames),
+                               static_cast<ssize_t>(self.rows()),
+                               static_cast<ssize_t>(self.cols())};
+
     py::array image;
     if (item_size == 1) {
         image = py::array_t<uint8_t>(shape);
@@ -57,15 +55,14 @@ 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,
-                   header.mutable_data());
+    self.read_into(reinterpret_cast<std::byte *>(image.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
+// Disable warnings for unused parameters, as we ignore some
+// in the __exit__ method
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 
@@ -76,7 +73,7 @@ void define_raw_sub_file_io_bindings(py::module &m) {
         .def_property_readonly("bytes_per_frame", &RawSubFile::bytes_per_frame)
         .def_property_readonly("pixels_per_frame",
                                &RawSubFile::pixels_per_frame)
-        .def_property_readonly("bytes_per_pixel", &RawSubFile::bytes_per_pixel)                    
+        .def_property_readonly("bytes_per_pixel", &RawSubFile::bytes_per_pixel)
         .def("seek", &RawSubFile::seek)
         .def("tell", &RawSubFile::tell)
         .def_property_readonly("rows", &RawSubFile::rows)
@@ -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){
-            self.seek(0);
-            auto n_frames = self.frames_in_file();
-            return read_n_frames_from_RawSubFile(self, n_frames);
-        })
+        .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,
-                const std::optional<pybind11::type> &exc_type,
+             [](RawSubFile &self, 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

@@ -12,10 +12,8 @@
 // #include <pybind11/stl/filesystem.h>
 // #include <string>
 
-
 namespace py = pybind11;
-using namespace::aare;
-
+using namespace ::aare;
 
 void define_var_cluster_finder_bindings(py::module &m) {
     PYBIND11_NUMPY_DTYPE(VarClusterFinder<double>::Hit, size, row, col,
@@ -29,12 +27,12 @@ void define_var_cluster_finder_bindings(py::module &m) {
                  return return_image_data(ptr);
              })
         .def("set_noiseMap",
-            [](VarClusterFinder<double> &self,
+             [](VarClusterFinder<double> &self,
                 py::array_t<double, py::array::c_style | py::array::forcecast>
                     noise_map) {
-                auto noise_map_span = make_view_2d(noise_map);
-                self.set_noiseMap(noise_map_span);
-            })
+                 auto noise_map_span = make_view_2d(noise_map);
+                 self.set_noiseMap(noise_map_span);
+             })
         .def("set_peripheralThresholdFactor",
              &VarClusterFinder<double>::set_peripheralThresholdFactor)
         .def("find_clusters",
@@ -65,9 +63,7 @@ void define_var_cluster_finder_bindings(py::module &m) {
                  return return_vector(ptr);
              })
         .def("clear_hits",
-             [](VarClusterFinder<double> &self) {
-                 self.clear_hits();
-             })
+             [](VarClusterFinder<double> &self) { 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

@@ -31,17 +31,15 @@ ClusterFile::ClusterFile(const std::filesystem::path &fname, size_t chunk_size,
     }
 }
 
-void ClusterFile::set_roi(ROI roi){
-    m_roi = roi;
-}
+void ClusterFile::set_roi(ROI roi) { m_roi = roi; }
 
-void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map){
+void ClusterFile::set_noise_map(const NDView<int32_t, 2> noise_map) {
     m_noise_map = NDArray<int32_t, 2>(noise_map);
 }
 
-void ClusterFile::set_gain_map(const NDView<double, 2> gain_map){
+void ClusterFile::set_gain_map(const NDView<double, 2> gain_map) {
     m_gain_map = NDArray<double, 2>(gain_map);
-    
+
     // Gain map is passed as ADU/keV to avoid dividing in when applying the gain
     // map we invert it here
     for (auto &item : m_gain_map->view()) {
@@ -66,42 +64,44 @@ void ClusterFile::write_frame(const ClusterVector<int32_t> &clusters) {
         !(clusters.cluster_size_y() == 3)) {
         throw std::runtime_error("Only 3x3 clusters are supported");
     }
-    //First write the frame number - 4 bytes
+    // First write the frame number - 4 bytes
     int32_t frame_number = clusters.frame_number();
-    if(fwrite(&frame_number, sizeof(frame_number), 1, fp)!=1){
+    if (fwrite(&frame_number, sizeof(frame_number), 1, fp) != 1) {
         throw std::runtime_error(LOCATION + "Could not write frame number");
     }
 
-    //Then write the number of clusters - 4 bytes
+    // 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");
+    if (fwrite(&n_clusters, sizeof(n_clusters), 1, fp) != 1) {
+        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()){
+    // Now write the clusters in the frame
+    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){
+ClusterVector<int32_t> ClusterFile::read_clusters(size_t n_clusters) {
     if (m_mode != "r") {
         throw std::runtime_error("File not opened for reading");
     }
-    if (m_noise_map || m_roi){
+    if (m_noise_map || m_roi) {
         return read_clusters_with_cut(n_clusters);
-    }else{
+    } else {
         return read_clusters_without_cut(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");
     }
-    
-    ClusterVector<int32_t> clusters(3,3, n_clusters);
+
+    ClusterVector<int32_t> clusters(3, 3, n_clusters);
 
     int32_t iframe = 0; // frame number needs to be 4 bytes!
     size_t nph_read = 0;
@@ -119,7 +119,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
         } else {
             nn = nph;
         }
-        nph_read += fread((buf + nph_read*clusters.item_size()),
+        nph_read += fread((buf + nph_read * clusters.item_size()),
                           clusters.item_size(), nn, fp);
         m_num_left = nph - nn; // write back the number of photons left
     }
@@ -135,7 +135,7 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
                 else
                     nn = nph;
 
-                nph_read += fread((buf + nph_read*clusters.item_size()),
+                nph_read += fread((buf + nph_read * clusters.item_size()),
                                   clusters.item_size(), nn, fp);
                 m_num_left = nph - nn;
             }
@@ -147,22 +147,22 @@ ClusterVector<int32_t> ClusterFile::read_clusters_without_cut(size_t n_clusters)
     // Resize the vector to the number of clusters.
     // No new allocation, only change bounds.
     clusters.resize(nph_read);
-    if(m_gain_map)
+    if (m_gain_map)
         clusters.apply_gain_map(m_gain_map->view());
     return clusters;
 }
 
-
 ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
-    ClusterVector<int32_t> clusters(3,3);
+    ClusterVector<int32_t> clusters(3, 3);
     clusters.reserve(n_clusters);
 
     // if there are photons left from previous frame read them first
     if (m_num_left) {
-        while(m_num_left && clusters.size() < 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));
+            if (is_selected(c)) {
+                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
-                while(m_num_left && clusters.size() < n_clusters){
+                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));
+                    if (is_selected(c)) {
+                        clusters.push_back(
+                            c.x, c.y, reinterpret_cast<std::byte *>(c.data));
                     }
                 }
             }
@@ -191,15 +195,14 @@ ClusterVector<int32_t> ClusterFile::read_clusters_with_cut(size_t n_clusters) {
             if (clusters.size() >= n_clusters)
                 break;
         }
-
     }
-    if(m_gain_map)
+    if (m_gain_map)
         clusters.apply_gain_map(m_gain_map->view());
 
     return clusters;
 }
 
-Cluster3x3 ClusterFile::read_one_cluster(){
+Cluster3x3 ClusterFile::read_one_cluster() {
     Cluster3x3 c;
     auto rc = fread(&c, sizeof(c), 1, fp);
     if (rc != 1) {
@@ -209,13 +212,13 @@ Cluster3x3 ClusterFile::read_one_cluster(){
     return c;
 }
 
-ClusterVector<int32_t> ClusterFile::read_frame(){
+ClusterVector<int32_t> ClusterFile::read_frame() {
     if (m_mode != "r") {
         throw std::runtime_error(LOCATION + "File not opened for reading");
     }
-    if (m_noise_map || m_roi){
+    if (m_noise_map || m_roi) {
         return read_frame_with_cut();
-    }else{
+    } else {
         return read_frame_without_cut();
     }
 }
@@ -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);
@@ -264,18 +268,17 @@ 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");
     }
-    
+
     ClusterVector<int32_t> clusters(3, 3);
     clusters.reserve(m_num_left);
     clusters.set_frame_number(frame_number);
-    while(m_num_left){
+    while (m_num_left) {
         Cluster3x3 c = read_one_cluster();
-        if(is_selected(c)){
-            clusters.push_back(c.x, c.y, reinterpret_cast<std::byte*>(c.data));
+        if (is_selected(c)) {
+            clusters.push_back(c.x, c.y, reinterpret_cast<std::byte *>(c.data));
         }
     }
     if (m_gain_map)
@@ -283,56 +286,56 @@ ClusterVector<int32_t> ClusterFile::read_frame_with_cut() {
     return clusters;
 }
 
-
-
 bool ClusterFile::is_selected(Cluster3x3 &cl) {
-    //Should fail fast
+    // Should fail fast
     if (m_roi) {
         if (!(m_roi->contains(cl.x, cl.y))) {
             return false;
         }
     }
-    if (m_noise_map){
-        int32_t sum_1x1 = cl.data[4]; // central pixel
+    if (m_noise_map) {
+        int32_t sum_1x1 = cl.data[4];   // central pixel
         int32_t sum_2x2 = cl.sum_2x2(); // highest sum of 2x2 subclusters
-        int32_t sum_3x3 = cl.sum(); // sum of all pixels
+        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;
         }
     }
-    //we passed all checks
+    // we passed all checks
     return true;
 }
 
 NDArray<double, 2> calculate_eta2(ClusterVector<int> &clusters) {
-    //TOTO! make work with 2x2 clusters
+    // TOTO! make work with 2x2 clusters
     NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
-    
+
     if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
         for (size_t i = 0; i < clusters.size(); i++) {
             auto e = calculate_eta2(clusters.at<Cluster3x3>(i));
             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;
             eta2(i, 1) = e.y;
         }
-    }else{
+    } else {
         throw std::runtime_error("Only 3x3 and 2x2 clusters are supported");
     }
-    
+
     return eta2;
 }
 
-/** 
- * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2 struct
- * containing etay, etax and the corner of the cluster. 
-*/
+/**
+ * @brief Calculate the eta2 values for a 3x3 cluster and return them in a Eta2
+ * struct containing etay, etax and the corner of the cluster.
+ */
 Eta2 calculate_eta2(Cluster3x3 &cl) {
     Eta2 eta{};
 
@@ -347,56 +350,46 @@ Eta2 calculate_eta2(Cluster3x3 &cl) {
     switch (c) {
     case cBottomLeft:
         if ((cl.data[3] + cl.data[4]) != 0)
-            eta.x =
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
+            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
         if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
+            eta.y = 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 =
-                static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
+            eta.x = static_cast<double>(cl.data[5]) / (cl.data[4] + cl.data[5]);
         if ((cl.data[1] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[4]) / (cl.data[1] + cl.data[4]);
+            eta.y = 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 =
-                static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
+            eta.x = static_cast<double>(cl.data[4]) / (cl.data[3] + cl.data[4]);
         if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
+            eta.y = 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 =
-                static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
+            eta.x = static_cast<double>(cl.data[5]) / (cl.data[5] + cl.data[4]);
         if ((cl.data[7] + cl.data[4]) != 0)
-            eta.y =
-                static_cast<double>(cl.data[7]) / (cl.data[7] + cl.data[4]);
+            eta.y = 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
+        // no default to allow compiler to warn about missing cases
     }
     return eta;
 }
 
-
 Eta2 calculate_eta2(Cluster2x2 &cl) {
     Eta2 eta{};
     if ((cl.data[0] + cl.data[1]) != 0)
         eta.x = static_cast<double>(cl.data[1]) / (cl.data[0] + cl.data[1]);
     if ((cl.data[0] + cl.data[2]) != 0)
         eta.y = static_cast<double>(cl.data[2]) / (cl.data[0] + cl.data[2]);
-    eta.sum = cl.data[0] + cl.data[1] + cl.data[2]+ cl.data[3];
-    eta.c = cBottomLeft; //TODO! This is not correct, but need to put something
+    eta.sum = cl.data[0] + cl.data[1] + cl.data[2] + cl.data[3];
+    eta.c = cBottomLeft; // TODO! This is not correct, but need to put something
     return eta;
 }
 
-
 } // namespace aare

src/ClusterFile.test.cpp

@@ -10,9 +10,8 @@ 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
+    // We know that the frame has 97 clusters
     auto fpath = test_data_path() / "clust" / "single_frame_97_clustrers.clust";
     REQUIRE(std::filesystem::exists(fpath));
 
@@ -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/ClusterFinderMT.test.cpp

@@ -58,8 +58,10 @@ class ClusterFinderMTWrapper
 };
 
 TEST_CASE("multithreaded cluster finder", "[.files][.ClusterFinder]") {
-    auto fpath = "/mnt/sls_det_storage/matterhorn_data/aare_test_data/"
-                 "Moench03new/cu_half_speed_master_4.json";
+    auto fpath =
+        test_data_path() / "clust/Moench03new/cu_half_speed_master_4.json";
+
+    REQUIRE(std::filesystem::exists(fpath));
 
     File file(fpath);
 

src/CtbRawFile.cpp

@@ -14,22 +14,24 @@ CtbRawFile::CtbRawFile(const std::filesystem::path &fname) : m_master(fname) {
     m_file.open(m_master.data_fname(0, 0), std::ios::binary);
 }
 
-void CtbRawFile::read_into(std::byte *image_buf, DetectorHeader* header) {
-    if(m_current_frame >= m_master.frames_in_file()){
+void CtbRawFile::read_into(std::byte *image_buf, DetectorHeader *header) {
+    if (m_current_frame >= m_master.frames_in_file()) {
         throw std::runtime_error(LOCATION + " End of file reached");
     }
 
-    if(m_current_frame != 0 && m_current_frame % m_master.max_frames_per_file() == 0){
-        open_data_file(m_current_subfile+1);
+    if (m_current_frame != 0 &&
+        m_current_frame % m_master.max_frames_per_file() == 0) {
+        open_data_file(m_current_subfile + 1);
     }
-    
-    if(header){
+
+    if (header) {
         m_file.read(reinterpret_cast<char *>(header), sizeof(DetectorHeader));
-    }else{
+    } else {
         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/DetectorGeometry.cpp

@@ -0,0 +1,152 @@
+
+#include "aare/DetectorGeometry.hpp"
+#include "fmt/core.h"
+#include <iostream>
+#include <vector>
+
+namespace aare {
+
+DetectorGeometry::DetectorGeometry(const xy &geometry,
+                                   const ssize_t module_pixels_x,
+                                   const ssize_t module_pixels_y,
+                                   const xy udp_interfaces_per_module,
+                                   const bool quad) {
+
+    size_t num_modules = geometry.col * geometry.row;
+    module_geometries.reserve(num_modules);
+    for (size_t col = 0; col < geometry.col;
+         col += udp_interfaces_per_module.col)
+        for (size_t row = 0; row < geometry.row;
+             row += udp_interfaces_per_module.row) {
+            for (size_t port_row = 0; port_row < udp_interfaces_per_module.row;
+                 ++port_row)
+                for (size_t port_col = 0;
+                     port_col < udp_interfaces_per_module.col; ++port_col) {
+                    ModuleGeometry g;
+                    g.origin_x = (col + port_col) * module_pixels_x;
+                    g.origin_y = (row + port_row) *
+                                 module_pixels_y; // TODO: quad doesnt seem
+                                                  // to have an effect
+                    g.row_index =
+                        quad ? (row + port_row + 1) % 2 : (row + port_row);
+                    g.col_index = col + port_col;
+                    g.width = module_pixels_x;
+                    g.height = module_pixels_y;
+                    module_geometries.push_back(g);
+                }
+        }
+
+    m_pixels_y = (geometry.row * module_pixels_y);
+    m_pixels_x = (geometry.col * module_pixels_x);
+    m_modules_x = geometry.col;
+    m_modules_y = geometry.row;
+    m_pixels_y += static_cast<size_t>((geometry.row - 1) * cfg.module_gap_row);
+
+    modules_in_roi.resize(num_modules);
+    std::iota(modules_in_roi.begin(), modules_in_roi.end(), 0);
+}
+
+size_t DetectorGeometry::n_modules() const { return m_modules_x * m_modules_y; }
+
+size_t DetectorGeometry::n_modules_in_roi() const {
+    return modules_in_roi.size();
+};
+
+size_t DetectorGeometry::pixels_x() const { return m_pixels_x; }
+size_t DetectorGeometry::pixels_y() const { return m_pixels_y; }
+
+size_t DetectorGeometry::modules_x() const { return m_modules_x; };
+size_t DetectorGeometry::modules_y() const { return m_modules_y; };
+
+const std::vector<ssize_t> &DetectorGeometry::get_modules_in_roi() const {
+    return modules_in_roi;
+}
+
+ssize_t DetectorGeometry::get_modules_in_roi(const size_t index) const {
+    return modules_in_roi[index];
+}
+
+const std::vector<ModuleGeometry> &
+DetectorGeometry::get_module_geometries() const {
+    return module_geometries;
+}
+
+const ModuleGeometry &
+DetectorGeometry::get_module_geometries(const size_t index) const {
+    return module_geometries[index];
+}
+
+void DetectorGeometry::update_geometry_with_roi(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: {} {} {} {} {} {}", m_modules_x, m_modules_y,
+                 m_pixels_x, m_pixels_y, cfg.module_gap_row,
+                 cfg.module_gap_col);
+
+#endif
+
+    modules_in_roi.clear();
+    modules_in_roi.reserve(m_modules_x * m_modules_y);
+    int pos_y = 0;
+    int pos_y_increment = 0;
+    for (size_t row = 0; row < m_modules_y; row++) {
+        int pos_x = 0;
+        for (size_t col = 0; col < m_modules_x; col++) {
+            auto &m = module_geometries[row * m_modules_x + col];
+
+            auto original_height = m.height;
+            auto original_width = m.width;
+
+            // module is to the left of the roi
+            if (m.origin_x + m.width < roi.xmin) {
+                m.width = 0;
+
+                // roi is in module
+            } else {
+                // here we only arrive when the roi is in or to the left of
+                // the module
+                if (roi.xmin > m.origin_x) {
+                    m.width -= roi.xmin - m.origin_x;
+                }
+                if (roi.xmax < m.origin_x + original_width) {
+                    m.width -= m.origin_x + original_width - roi.xmax;
+                }
+                m.origin_x = pos_x;
+                pos_x += m.width;
+            }
+
+            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)) {
+                    m.height -= roi.ymin - m.origin_y;
+                }
+                if (roi.ymax < m.origin_y + original_height) {
+                    m.height -= m.origin_y + original_height - roi.ymax;
+                }
+                m.origin_y = pos_y;
+                pos_y_increment = m.height;
+            }
+
+            if (m.height != 0 && m.width != 0) {
+                modules_in_roi.push_back(row * m_modules_x + col);
+            }
+
+#ifdef AARE_VERBOSE
+            fmt::println("Module {} {} {} {}", m.origin_x, m.origin_y, m.width,
+                         m.height);
+#endif
+        }
+        // increment pos_y
+        pos_y += pos_y_increment;
+    }
+
+    // m_rows = roi.height();
+    // m_cols = roi.width();
+    m_pixels_x = roi.width();
+    m_pixels_y = roi.height();
+}
+
+} // namespace aare

src/DetectorGeometry.test.cpp

@@ -0,0 +1,194 @@
+#include "aare/File.hpp"
+#include "aare/RawFile.hpp"
+#include "aare/RawMasterFile.hpp" //needed for ROI
+
+#include <catch2/catch_test_macros.hpp>
+#include <filesystem>
+
+#include "aare/DetectorGeometry.hpp"
+#include "test_config.hpp"
+
+TEST_CASE("Simple ROIs on one module") {
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
+    aare::DetectorGeometry geo(aare::xy{1, 1}, 1024, 512);
+
+    REQUIRE(geo.get_module_geometries(0).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(0).origin_y == 0);
+    REQUIRE(geo.get_module_geometries(0).width == 1024);
+    REQUIRE(geo.get_module_geometries(0).height == 512);
+
+    SECTION("ROI is the whole module") {
+        aare::ROI roi;
+        roi.xmin = 0;
+        roi.xmax = 1024;
+        roi.ymin = 0;
+        roi.ymax = 512;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 1024);
+        REQUIRE(geo.pixels_y() == 512);
+        REQUIRE(geo.modules_x() == 1);
+        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(geo.get_module_geometries(0).height == 512);
+        REQUIRE(geo.get_module_geometries(0).width == 1024);
+    }
+    SECTION("ROI is the top left corner of the module") {
+        aare::ROI roi;
+        roi.xmin = 100;
+        roi.xmax = 200;
+        roi.ymin = 150;
+        roi.ymax = 200;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 100);
+        REQUIRE(geo.pixels_y() == 50);
+        REQUIRE(geo.modules_x() == 1);
+        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(geo.get_module_geometries(0).height == 50);
+        REQUIRE(geo.get_module_geometries(0).width == 100);
+    }
+
+    SECTION("ROI is a small square") {
+        aare::ROI roi;
+        roi.xmin = 1000;
+        roi.xmax = 1010;
+        roi.ymin = 500;
+        roi.ymax = 510;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 10);
+        REQUIRE(geo.pixels_y() == 10);
+        REQUIRE(geo.modules_x() == 1);
+        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(geo.get_module_geometries(0).height == 10);
+        REQUIRE(geo.get_module_geometries(0).width == 10);
+    }
+    SECTION("ROI is a few columns") {
+        aare::ROI roi;
+        roi.xmin = 750;
+        roi.xmax = 800;
+        roi.ymin = 0;
+        roi.ymax = 512;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 50);
+        REQUIRE(geo.pixels_y() == 512);
+        REQUIRE(geo.modules_x() == 1);
+        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(geo.get_module_geometries(0).height == 512);
+        REQUIRE(geo.get_module_geometries(0).width == 50);
+    }
+}
+
+TEST_CASE("Two modules side by side") {
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
+    aare::DetectorGeometry geo(aare::xy{1, 2}, 1024, 512);
+
+    REQUIRE(geo.get_module_geometries(0).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(0).origin_y == 0);
+    REQUIRE(geo.get_module_geometries(0).width == 1024);
+    REQUIRE(geo.get_module_geometries(0).height == 512);
+    REQUIRE(geo.get_module_geometries(1).origin_x == 1024);
+    REQUIRE(geo.get_module_geometries(1).origin_y == 0);
+
+    SECTION("ROI is the whole image") {
+        aare::ROI roi;
+        roi.xmin = 0;
+        roi.xmax = 2048;
+        roi.ymin = 0;
+        roi.ymax = 512;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 2048);
+        REQUIRE(geo.pixels_y() == 512);
+        REQUIRE(geo.modules_x() == 2);
+        REQUIRE(geo.modules_y() == 1);
+    }
+    SECTION("rectangle on both modules") {
+        aare::ROI roi;
+        roi.xmin = 800;
+        roi.xmax = 1300;
+        roi.ymin = 200;
+        roi.ymax = 499;
+        geo.update_geometry_with_roi(roi);
+
+        REQUIRE(geo.pixels_x() == 500);
+        REQUIRE(geo.pixels_y() == 299);
+        REQUIRE(geo.modules_x() == 2);
+        REQUIRE(geo.modules_y() == 1);
+        REQUIRE(geo.get_module_geometries(0).height == 299);
+        REQUIRE(geo.get_module_geometries(0).width == 224);
+        REQUIRE(geo.get_module_geometries(1).height == 299);
+        REQUIRE(geo.get_module_geometries(1).width == 276);
+    }
+}
+
+TEST_CASE("Three modules side by side") {
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
+    aare::DetectorGeometry geo(aare::xy{1, 3}, 1024, 512);
+    aare::ROI roi;
+    roi.xmin = 700;
+    roi.xmax = 2500;
+    roi.ymin = 0;
+    roi.ymax = 123;
+
+    REQUIRE(geo.get_module_geometries(0).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(0).origin_y == 0);
+    REQUIRE(geo.get_module_geometries(0).width == 1024);
+    REQUIRE(geo.get_module_geometries(0).height == 512);
+    REQUIRE(geo.get_module_geometries(1).origin_x == 1024);
+    REQUIRE(geo.get_module_geometries(2).origin_x == 2048);
+
+    geo.update_geometry_with_roi(roi);
+
+    REQUIRE(geo.pixels_x() == 1800);
+    REQUIRE(geo.pixels_y() == 123);
+    REQUIRE(geo.modules_x() == 3);
+    REQUIRE(geo.modules_y() == 1);
+    REQUIRE(geo.get_module_geometries(0).height == 123);
+    REQUIRE(geo.get_module_geometries(0).width == 324);
+    REQUIRE(geo.get_module_geometries(1).height == 123);
+    REQUIRE(geo.get_module_geometries(1).width == 1024);
+    REQUIRE(geo.get_module_geometries(2).height == 123);
+    REQUIRE(geo.get_module_geometries(2).width == 452);
+}
+
+TEST_CASE("Four modules as a square") {
+    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI
+    // roi)
+    aare::DetectorGeometry geo(aare::xy{2, 2}, 1024, 512, aare::xy{1, 2});
+    aare::ROI roi;
+    roi.xmin = 500;
+    roi.xmax = 2000;
+    roi.ymin = 500;
+    roi.ymax = 600;
+
+    REQUIRE(geo.get_module_geometries(0).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(0).origin_y == 0);
+    REQUIRE(geo.get_module_geometries(0).width == 1024);
+    REQUIRE(geo.get_module_geometries(0).height == 512);
+    REQUIRE(geo.get_module_geometries(1).origin_x == 1024);
+    REQUIRE(geo.get_module_geometries(1).origin_y == 0);
+    REQUIRE(geo.get_module_geometries(2).origin_x == 0);
+    REQUIRE(geo.get_module_geometries(2).origin_y == 512);
+    REQUIRE(geo.get_module_geometries(3).origin_x == 1024);
+    REQUIRE(geo.get_module_geometries(3).origin_y == 512);
+
+    geo.update_geometry_with_roi(roi);
+
+    REQUIRE(geo.pixels_x() == 1500);
+    REQUIRE(geo.pixels_y() == 100);
+    REQUIRE(geo.modules_x() == 2);
+    REQUIRE(geo.modules_y() == 2);
+    REQUIRE(geo.get_module_geometries(0).height == 12);
+    REQUIRE(geo.get_module_geometries(0).width == 524);
+    REQUIRE(geo.get_module_geometries(1).height == 12);
+    REQUIRE(geo.get_module_geometries(1).width == 976);
+    REQUIRE(geo.get_module_geometries(2).height == 88);
+    REQUIRE(geo.get_module_geometries(2).width == 524);
+    REQUIRE(geo.get_module_geometries(3).height == 88);
+    REQUIRE(geo.get_module_geometries(3).width == 976);
+}

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 { return !(*this == other); }
+bool Dtype::operator==(const Dtype &other) const noexcept {
+    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 { return Dtype(t) != *this; }
+bool Dtype::operator==(const std::type_info &t) const {
+    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

@@ -19,28 +19,24 @@ File::File(const std::filesystem::path &fname, const std::string &mode,
             fmt::format("File does not exist: {}", fname.string()));
     }
 
-    // Assuming we are pointing at a master file? 
+    // Assuming we are pointing at a master file?
     // TODO! How do we read raw files directly?
     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);
-    }else if(fname.extension() == ".dat"){
+    } else if (fname.extension() == ".dat") {
         file_impl = std::make_unique<JungfrauDataFile>(fname);
     } else {
         throw std::runtime_error("Unsupported file type");
     }
 }
 
+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 {
+File &File::operator=(File &&other) noexcept {
     if (this != &other) {
         File tmp(std::move(other));
         std::swap(file_impl, tmp.file_impl);
@@ -70,15 +66,16 @@ size_t File::frame_number(size_t frame_index) {
 }
 
 size_t File::bytes_per_frame() const { return file_impl->bytes_per_frame(); }
-size_t File::pixels_per_frame() const{ return file_impl->pixels_per_frame(); }
+size_t File::pixels_per_frame() const { return file_impl->pixels_per_frame(); }
 void File::seek(size_t frame_index) { file_impl->seek(frame_index); }
 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_); }
@@ -24,15 +26,16 @@ 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() {
     if (fp_)
         fclose(fp_); // check?
 }
 
-std::string FilePtr::error_msg(){
+std::string FilePtr::error_msg() {
     if (feof(fp_)) {
         return "End of file reached";
     }

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 {
@@ -34,8 +33,10 @@ NDArray<double, 1> pol1(NDView<double, 1> x, NDView<double, 1> par) {
     return y;
 }
 
-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]));
+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]));
 }
 
 NDArray<double, 1> scurve(NDView<double, 1> x, NDView<double, 1> par) {
@@ -46,8 +47,10 @@ NDArray<double, 1> scurve(NDView<double, 1> x, NDView<double, 1> par) {
     return y;
 }
 
-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]));
+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]));
 }
 
 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);
@@ -103,31 +107,29 @@ 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] =
-        std::count_if(y.begin(), y.end(),
-                      [e](double val) { return val > *e / 2; }) *
-        delta / 2.35;
+    start_par[2] = 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,
+                                    const NDView<double, 1> y) {
+    // Estimate the initial parameters for the fit
+    std::array<double, 2> start_par{0, 0};
 
-std::array<double, 2> pol1_init_par(const NDView<double, 1> x, 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());
+    auto x1 = x[std::distance(y.begin(), y1)];
 
-    
-        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());
-        auto x1 = x[std::distance(y.begin(), y1)];
-    
-        start_par[0] =
-            (*y2 - *y1) / (x2 - x1); // For amplitude we use the maximum value
-        start_par[1] =
-            *y1 - ((*y2 - *y1) / (x2 - x1)) *
-                      x1; // For the mean we use the x value of the maximum value
-        return start_par;
+    start_par[0] =
+        (*y2 - *y1) / (x2 - x1); // For amplitude we use the maximum value
+    start_par[1] =
+        *y1 - ((*y2 - *y1) / (x2 - x1)) *
+                  x1; // For the mean we use the x value of the maximum value
+    return start_par;
 }
 
 void fit_gaus(NDView<double, 1> x, NDView<double, 1> y, NDView<double, 1> y_err,
@@ -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};
+    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);
-    // n_par - Number of free variables. Length of parameter vector par.
-    // par - Parameter vector. On input, it must contain a reasonable guess. On output, it contains the solution found to minimize ||r||.
-    // 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.
-    // covar - Covariance matrix. Array of length n_par * n_par or NULL. On output, unless it is NULL, it contains the covariance matrix.
-    // 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).
+    // 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); n_par - Number of
+    // free variables. Length of parameter vector par. par - Parameter vector.
+    // On input, it must contain a reasonable guess. On output, it contains the
+    // solution found to minimize ||r||. 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. covar - Covariance matrix. Array of length n_par * n_par or
+    // NULL. On output, unless it is NULL, it contains the covariance matrix.
+    // 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) {
 
@@ -197,10 +209,9 @@ void fit_gaus(NDView<double, 1> x, NDView<double, 3> y, NDView<double, 3> y_err,
                                                {par_out.shape(2)});
                 NDView<double, 1> par_err_out_view(&par_err_out(row, col, 0),
                                                    {par_err_out.shape(2)});
- 
+
                 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,
-              int n_threads) {
+              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) {
         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) {
@@ -300,27 +312,29 @@ 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){
-        // Estimate the initial parameters for the fit
-        std::array<double, 6> start_par{0, 0, 0, 0, 0, 0};
+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};
 
-        auto ymax = std::max_element(y.begin(), y.end());
-        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])
-        for (ssize_t i = 0; i < y.size(); ++i) {
-            if (y[i] >= start_par[4]) {
-                start_par[2] = x[i];
-                break; // Exit the loop after finding the first valid x
-            }
+    auto ymax = std::max_element(y.begin(), y.end());
+    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])
+    for (ssize_t i = 0; i < y.size(); ++i) {
+        if (y[i] >= start_par[4]) {
+            start_par[2] = x[i];
+            break; // Exit the loop after finding the first valid x
         }
+    }
 
-        start_par[3] = 2 * sqrt(start_par[2]); 
-        start_par[0] = 100; 
-        start_par[1] = 0.25;
-        start_par[5] = 1;
-        return start_par;
+    start_par[3] = 2 * sqrt(start_par[2]);
+    start_par[0] = 100;
+    start_par[1] = 0.25;
+    start_par[5] = 1;
+    return start_par;
 }
 
 // - No error
@@ -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,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2) {
+void fit_scurve(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) {
 
     // Check that we have the correct sizes
     if (y.size() != x.size() || y.size() != y_err.size() ||
@@ -380,13 +396,15 @@ 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,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
-              int n_threads) {
+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) {
 
     auto process = [&](ssize_t first_row, ssize_t last_row) {
         for (ssize_t row = first_row; row < last_row; row++) {
@@ -399,40 +417,41 @@ 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){
-        // Estimate the initial parameters for the fit
-        std::array<double, 6> start_par{0, 0, 0, 0, 0, 0};
+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};
 
-        auto ymax = std::max_element(y.begin(), y.end());
-        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])
-        for (ssize_t i = 0; i < y.size(); ++i) {
-            if (y[i] <= start_par[4]) {
-                start_par[2] = x[i];
-                break; // Exit the loop after finding the first valid x
-            }
+    auto ymax = std::max_element(y.begin(), y.end());
+    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])
+    for (ssize_t i = 0; i < y.size(); ++i) {
+        if (y[i] <= start_par[4]) {
+            start_par[2] = x[i];
+            break; // Exit the loop after finding the first valid x
         }
+    }
 
-        start_par[3] = 2 * sqrt(start_par[2]); 
-        start_par[0] = 100; 
-        start_par[1] = 0.25;
-        start_par[5] = -1;
-        return start_par;
+    start_par[3] = 2 * sqrt(start_par[2]);
+    start_par[0] = 100;
+    start_par[1] = 0.25;
+    start_par[5] = -1;
+    return start_par;
 }
 
 // - No error
@@ -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,
-              NDView<double, 1> par_out, NDView<double, 1> par_err_out, double& chi2) {
+void fit_scurve2(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) {
 
     // Check that we have the correct sizes
     if (y.size() != x.size() || y.size() != y_err.size() ||
@@ -492,13 +513,15 @@ 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,
-              NDView<double, 3> par_out, NDView<double, 3> par_err_out, NDView<double, 2> chi2_out,
-              int n_threads) {
+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) {
 
     auto process = [&](ssize_t first_row, ssize_t last_row) {
         for (ssize_t row = first_row; row < last_row; 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

@@ -29,8 +29,7 @@ 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{
+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';
         return nullptr;
@@ -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

@@ -19,16 +19,15 @@ JungfrauDataFile::JungfrauDataFile(const std::filesystem::path &fname) {
     open_file(m_current_file_index);
 }
 
-
 // FileInterface
 
-Frame JungfrauDataFile::read_frame(){
+Frame JungfrauDataFile::read_frame() {
     Frame f(rows(), cols(), Dtype::UINT16);
     read_into(reinterpret_cast<std::byte *>(f.data()), nullptr);
     return f;
 }
 
-Frame JungfrauDataFile::read_frame(size_t frame_number){
+Frame JungfrauDataFile::read_frame(size_t frame_number) {
     seek(frame_number);
     Frame f(rows(), cols(), Dtype::UINT16);
     read_into(reinterpret_cast<std::byte *>(f.data()), nullptr);
@@ -37,7 +36,7 @@ Frame JungfrauDataFile::read_frame(size_t frame_number){
 
 std::vector<Frame> JungfrauDataFile::read_n(size_t n_frames) {
     std::vector<Frame> frames;
-    for(size_t i = 0; i < n_frames; ++i){
+    for (size_t i = 0; i < n_frames; ++i) {
         frames.push_back(read_frame());
     }
     return frames;
@@ -48,7 +47,7 @@ void JungfrauDataFile::read_into(std::byte *image_buf) {
 }
 void JungfrauDataFile::read_into(std::byte *image_buf, size_t n_frames) {
     read_into(image_buf, n_frames, nullptr);
-}   
+}
 
 size_t JungfrauDataFile::frame_number(size_t frame_index) {
     seek(frame_index);
@@ -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; }
 
@@ -195,22 +196,23 @@ void JungfrauDataFile::read_into(std::byte *image_buf, size_t n_frames,
                                  JungfrauDataHeader *header) {
     if (header) {
         for (size_t i = 0; i < n_frames; ++i)
-            read_into(image_buf + i * m_bytes_per_frame, header + i); 
-    }else{
+            read_into(image_buf + i * m_bytes_per_frame, header + i);
+    } else {
         for (size_t i = 0; i < n_frames; ++i)
             read_into(image_buf + i * m_bytes_per_frame, nullptr);
     }
 }
 
-void JungfrauDataFile::read_into(NDArray<uint16_t>* image, JungfrauDataHeader* header) {
-    if(image->shape()!=shape()){
-        throw std::runtime_error(LOCATION +
-            "Image shape does not match file size: " + std::to_string(rows()) + "x" + std::to_string(cols()));
+void JungfrauDataFile::read_into(NDArray<uint16_t> *image,
+                                 JungfrauDataHeader *header) {
+    if (image->shape() != shape()) {
+        throw std::runtime_error(
+            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

@@ -1,21 +1,21 @@
 #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;
 TEST_CASE("Open a Jungfrau data file", "[.files]") {
-    //we know we have 4 files with 7, 7, 7, and 3 frames
-    //firs frame number if 1 and the bunch id is frame_number**2
-    //so we can check the header
+    // we know we have 4 files with 7, 7, 7, and 3 frames
+    // firs frame number if 1 and the bunch id is frame_number**2
+    // so we can check the header
     auto fpath = test_data_path() / "dat" / "AldoJF500k_000000.dat";
     REQUIRE(std::filesystem::exists(fpath));
 
     JungfrauDataFile f(fpath);
     REQUIRE(f.rows() == 512);
     REQUIRE(f.cols() == 1024);
-    REQUIRE(f.bytes_per_frame() == 1048576);    
+    REQUIRE(f.bytes_per_frame() == 1048576);
     REQUIRE(f.pixels_per_frame() == 524288);
     REQUIRE(f.bytes_per_pixel() == 2);
     REQUIRE(f.bitdepth() == 16);
@@ -25,7 +25,7 @@ TEST_CASE("Open a Jungfrau data file", "[.files]") {
     REQUIRE(f.total_frames() == 24);
     REQUIRE(f.current_file() == fpath);
 
-    //Check that the frame number and buch id is read correctly
+    // Check that the frame number and buch id is read correctly
     for (size_t i = 0; i < 24; ++i) {
         JungfrauDataHeader header;
         aare::NDArray<uint16_t> image(f.shape());
@@ -37,65 +37,64 @@ TEST_CASE("Open a Jungfrau data file", "[.files]") {
     }
 }
 
-TEST_CASE("Seek in a JungfrauDataFile", "[.files]"){
+TEST_CASE("Seek in a JungfrauDataFile", "[.files]") {
     auto fpath = test_data_path() / "dat" / "AldoJF65k_000000.dat";
     REQUIRE(std::filesystem::exists(fpath));
 
     JungfrauDataFile f(fpath);
 
-    //The file should have 113 frames
+    // The file should have 113 frames
     f.seek(19);
     REQUIRE(f.tell() == 19);
     auto h = f.read_header();
-    REQUIRE(h.framenum == 19+1);
+    REQUIRE(h.framenum == 19 + 1);
 
-    //Reading again does not change the file pointer
+    // Reading again does not change the file pointer
     auto h2 = f.read_header();
-    REQUIRE(h2.framenum == 19+1);
+    REQUIRE(h2.framenum == 19 + 1);
 
     f.seek(59);
     REQUIRE(f.tell() == 59);
     auto h3 = f.read_header();
-    REQUIRE(h3.framenum == 59+1);
+    REQUIRE(h3.framenum == 59 + 1);
 
     JungfrauDataHeader h4;
     aare::NDArray<uint16_t> image(f.shape());
     f.read_into(&image, &h4);
-    REQUIRE(h4.framenum == 59+1);
+    REQUIRE(h4.framenum == 59 + 1);
 
-    //now we should be on the next frame
+    // now we should be on the next frame
     REQUIRE(f.tell() == 60);
-    REQUIRE(f.read_header().framenum == 60+1);
+    REQUIRE(f.read_header().framenum == 60 + 1);
 
-    REQUIRE_THROWS(f.seek(86356)); //out of range
+    REQUIRE_THROWS(f.seek(86356)); // out of range
 }
 
-TEST_CASE("Open a Jungfrau data file with non zero file index", "[.files]"){
+TEST_CASE("Open a Jungfrau data file with non zero file index", "[.files]") {
 
     auto fpath = test_data_path() / "dat" / "AldoJF65k_000003.dat";
     REQUIRE(std::filesystem::exists(fpath));
 
     JungfrauDataFile f(fpath);
 
-    //18 files per data file, opening the 3rd file we ignore the first 3
-    REQUIRE(f.total_frames() == 113-18*3);
+    // 18 files per data file, opening the 3rd file we ignore the first 3
+    REQUIRE(f.total_frames() == 113 - 18 * 3);
     REQUIRE(f.tell() == 0);
 
-    //Frame numbers start at 1 in the first file
-    REQUIRE(f.read_header().framenum == 18*3+1);
+    // Frame numbers start at 1 in the first file
+    REQUIRE(f.read_header().framenum == 18 * 3 + 1);
 
     // moving relative to the third file
     f.seek(5);
-    REQUIRE(f.read_header().framenum == 18*3+1+5);
+    REQUIRE(f.read_header().framenum == 18 * 3 + 1 + 5);
 
     // ignoring the first 3 files
     REQUIRE(f.n_files() == 4);
 
     REQUIRE(f.current_file().stem() == "AldoJF65k_000003");
-
 }
 
-TEST_CASE("Read into throws if size doesn't match", "[.files]"){
+TEST_CASE("Read into throws if size doesn't match", "[.files]") {
     auto fpath = test_data_path() / "dat" / "AldoJF65k_000000.dat";
     REQUIRE(std::filesystem::exists(fpath));
 
@@ -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

@@ -35,7 +35,7 @@ TEST_CASE("Construct from an NDView") {
     }
 }
 
-TEST_CASE("3D NDArray from NDView"){
+TEST_CASE("3D NDArray from NDView") {
     std::vector<int> data(27);
     std::iota(data.begin(), data.end(), 0);
     NDView<int, 3> view(data.data(), Shape<3>{3, 3, 3});
@@ -44,9 +44,9 @@ TEST_CASE("3D NDArray from NDView"){
     REQUIRE(image.size() == view.size());
     REQUIRE(image.data() != view.data());
 
-    for(ssize_t i=0; i<image.shape(0); i++){
-        for(ssize_t j=0; j<image.shape(1); j++){
-            for(ssize_t k=0; k<image.shape(2); k++){
+    for (ssize_t i = 0; i < image.shape(0); i++) {
+        for (ssize_t j = 0; j < image.shape(1); j++) {
+            for (ssize_t k = 0; k < image.shape(2); k++) {
                 REQUIRE(image(i, j, k) == view(i, j, k));
             }
         }
@@ -132,7 +132,7 @@ TEST_CASE("Elementwise multiplication of 3D image") {
 
 NDArray<int> MultiplyNDArrayUsingOperator(NDArray<int> &a, NDArray<int> &b) {
     // return a * a * b * b;
-    NDArray<int>c =  a*b;
+    NDArray<int> c = a * b;
     return c;
 }
 
@@ -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> data1(vec1.data(), Shape<1>{static_cast<ssize_t>(vec1.size())});
+    NDView<int, 1> data0(vec0.data(),
+                         Shape<1>{static_cast<ssize_t>(vec0.size())});
+    NDView<int, 1> data1(vec1.data(),
+                         Shape<1>{static_cast<ssize_t>(vec1.size())});
 
     data0 /= data1;
 
@@ -181,8 +183,7 @@ TEST_CASE("compare two views") {
     REQUIRE((view1 == view2));
 }
 
-
-TEST_CASE("Create a view over a vector"){
+TEST_CASE("Create a view over a vector") {
     std::vector<int> vec(12);
     std::iota(vec.begin(), vec.end(), 0);
     auto v = aare::make_view(vec);

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 += fread(reinterpret_cast<char *>(&minor_ver_), sizeof(minor_ver_), 1, fp);
+    rc =
+        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;
@@ -23,7 +23,7 @@ TEST_CASE("Read a 1D numpy file with int32 data type", "[.integration]") {
         REQUIRE(data(i) == i);
     }
 }
- 
+
 TEST_CASE("Read a 3D numpy file with np.double data type", "[.integration]") {
 
     auto fpath = test_data_path() / "numpy" / "test_3d_double.npy";

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),
-                                               static_cast<uint8_t>((header_len >> 8) & 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 >> 16) & 0xff), static_cast<uint8_t>((header_len >> 24) & 0xff)};
+            static_cast<uint8_t>((header_len >> 0) & 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(variance(i, j), Catch::Matchers::WithinAbs(VAR, VAR * TOLERANCE));
-            REQUIRE_THAT(standard_deviation(i, j), Catch::Matchers::WithinAbs(STD, STD * TOLERANCE));
+            REQUIRE_THAT(mean(i, j),
+                         Catch::Matchers::WithinAbs(MEAN, MEAN * 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

@@ -31,7 +31,7 @@ NDArray<ssize_t, 2> GenerateMoench03PixelMap() {
 }
 
 NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
-    std::array<int, 3> adc_numbers = {5, 9, 1};  
+    std::array<int, 3> adc_numbers = {5, 9, 1};
     NDArray<ssize_t, 2> order_map({160, 150});
     int n_pixel = 0;
     for (int row = 0; row < 160; row++) {
@@ -40,11 +40,11 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
             for (int i_sc = 0; i_sc < 3; i_sc++) {
                 int col = 50 * i_sc + i_col;
                 int adc_nr = adc_numbers[i_sc];
-                int i_analog = n_pixel * 12 + adc_nr;  
+                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;
-                
             }
         }
     }
@@ -52,7 +52,7 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap() {
 }
 
 NDArray<ssize_t, 2> GenerateMoench05PixelMap1g() {
-    std::array<int, 3> adc_numbers = {1, 2, 0}; 
+    std::array<int, 3> adc_numbers = {1, 2, 0};
     NDArray<ssize_t, 2> order_map({160, 150});
     int n_pixel = 0;
     for (int row = 0; row < 160; row++) {
@@ -61,12 +61,11 @@ NDArray<ssize_t, 2> GenerateMoench05PixelMap1g() {
             for (int i_sc = 0; i_sc < 3; i_sc++) {
                 int col = 50 * i_sc + i_col;
                 int adc_nr = adc_numbers[i_sc];
-                int i_analog = n_pixel * 3 + adc_nr;  
+                int i_analog = n_pixel * 3 + 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;
-                
             }
         }
     }
@@ -85,42 +84,42 @@ 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] & 0x3FFF;
+                // analog_frame[row * 150 + col] = analog_data[i_analog] &
+                // 0x3FFF;
                 order_map(row, col) = i_analog;
-                
             }
         }
     }
     return order_map;
 }
 
-NDArray<ssize_t, 2>GenerateEigerFlipRowsPixelMap(){
+NDArray<ssize_t, 2> GenerateEigerFlipRowsPixelMap() {
     NDArray<ssize_t, 2> order_map({256, 512});
-    for(int row = 0; row < 256; row++){
-        for(int col = 0; col < 512; col++){
-            order_map(row, col) = 255*512-row*512 + col;
+    for (int row = 0; row < 256; row++) {
+        for (int col = 0; col < 512; col++) {
+            order_map(row, col) = 255 * 512 - row * 512 + col;
         }
     }
     return order_map;
 }
 
-NDArray<ssize_t, 2>GenerateMH02SingleCounterPixelMap(){
+NDArray<ssize_t, 2> GenerateMH02SingleCounterPixelMap() {
     NDArray<ssize_t, 2> order_map({48, 48});
-    for(int row = 0; row < 48; row++){
-        for(int col = 0; col < 48; col++){
-            order_map(row, col) = row*48 + col;
+    for (int row = 0; row < 48; row++) {
+        for (int col = 0; col < 48; col++) {
+            order_map(row, col) = row * 48 + col;
         }
     }
     return order_map;
 }
 
-NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap(){
+NDArray<ssize_t, 3> GenerateMH02FourCounterPixelMap() {
     NDArray<ssize_t, 3> order_map({4, 48, 48});
-    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;
+    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;
             }
         }
     }

src/RawFile.cpp

@@ -1,9 +1,9 @@
 #include "aare/RawFile.hpp"
-#include "aare/algorithm.hpp"
+#include "aare/DetectorGeometry.hpp"
 #include "aare/PixelMap.hpp"
+#include "aare/algorithm.hpp"
 #include "aare/defs.hpp"
 #include "aare/logger.hpp"
-#include "aare/geo_helpers.hpp"
 
 #include <fmt/format.h>
 #include <nlohmann/json.hpp>
@@ -13,12 +13,14 @@ using json = nlohmann::json;
 namespace aare {
 
 RawFile::RawFile(const std::filesystem::path &fname, const std::string &mode)
-    : m_master(fname) {
+    : m_master(fname),
+      m_geometry(m_master.geometry(), m_master.pixels_x(), m_master.pixels_y(),
+                 m_master.udp_interfaces_per_module(), m_master.quad()) {
     m_mode = mode;
+
     if (mode == "r") {
-        find_geometry();
-        if (m_master.roi()){
-            m_geometry = update_geometry_with_roi(m_geometry, m_master.roi().value());
+        if (m_master.roi()) {
+            m_geometry.update_geometry_with_roi(m_master.roi().value());
         }
         open_subfiles();
     } else {
@@ -47,40 +49,38 @@ 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++) {
         this->get_frame_into(m_current_frame++, image_buf, header);
         image_buf += bytes_per_frame();
-        if(header) 
-            header+=n_modules();
+        if (header)
+            header += m_geometry.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; 
-    return m_geometry.pixels_x * m_geometry.pixels_y;
+size_t RawFile::pixels_per_frame() {
+    // return m_rows * m_cols;
+    return m_geometry.pixels_x() * m_geometry.pixels_y();
 }
 
 DetectorType RawFile::detector_type() const { return m_master.detector_type(); }
 
 void RawFile::seek(size_t frame_index) {
     // check if the frame number is greater than the total frames
-    // if frame_number == total_frames, then the next read will throw an error
+    // if frame_number == total_frames, then the next read will throw an
+    // error
     if (frame_index > total_frames()) {
         throw std::runtime_error(
             fmt::format("frame number {} is greater than total frames {}",
@@ -92,15 +92,17 @@ void RawFile::seek(size_t frame_index) {
 size_t RawFile::tell() { return m_current_frame; }
 
 size_t RawFile::total_frames() const { return m_master.frames_in_file(); }
-size_t RawFile::rows() const { return m_geometry.pixels_y; }
-size_t RawFile::cols() const { return m_geometry.pixels_x; }
+size_t RawFile::rows() const { return m_geometry.pixels_y(); }
+size_t RawFile::cols() const { return m_geometry.pixels_x(); }
 size_t RawFile::bitdepth() const { return m_master.bitdepth(); }
 xy RawFile::geometry() { return m_master.geometry(); }
 
+size_t RawFile::n_modules() const { return m_geometry.n_modules(); };
+
 void RawFile::open_subfiles() {
     if (m_mode == "r")
-        for (size_t i = 0; i != n_modules(); ++i) {
-            auto pos = m_geometry.module_pixel_0[i];
+        for (size_t i : m_geometry.get_modules_in_roi()) {
+            auto pos = m_geometry.get_module_geometries(i);
             m_subfiles.emplace_back(std::make_unique<RawSubFile>(
                 m_master.data_fname(i, 0), m_master.detector_type(), pos.height,
                 pos.width, m_master.bitdepth(), pos.row_index, pos.col_index));
@@ -128,76 +130,35 @@ DetectorHeader RawFile::read_header(const std::filesystem::path &fname) {
     return h;
 }
 
-
 RawMasterFile RawFile::master() const { return m_master; }
 
-/**
- * @brief Find the geometry of the detector by opening all the subfiles and
- * reading the headers. 
- */
-void RawFile::find_geometry() {
-    
-    //Hold the maximal row and column number found
-    //Later used for calculating the total number of rows and columns
-    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);
-        c = std::max(c, h.column);
-        // positions.push_back({h.row, h.column});
-       
-        ModuleGeometry g;
-        g.origin_x = h.column * m_master.pixels_x();
-        g.origin_y = h.row * m_master.pixels_y();
-        g.row_index = h.row;
-        g.col_index = h.column;
-        g.width = m_master.pixels_x();
-        g.height = m_master.pixels_y();
-        m_geometry.module_pixel_0.push_back(g);
-
-    }
-
-    r++;
-    c++;
-
-    m_geometry.pixels_y = (r * m_master.pixels_y());
-    m_geometry.pixels_x  = (c * m_master.pixels_x());
-    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 {
-    return m_master.bitdepth() / 8;
-}
-
-void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, 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");
     }
-    std::vector<size_t> frame_numbers(n_modules());
-    std::vector<size_t> frame_indices(n_modules(), frame_index);
-
+    std::vector<size_t> frame_numbers(m_geometry.n_modules_in_roi());
+    std::vector<size_t> frame_indices(m_geometry.n_modules_in_roi(),
+                                      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); 
+    if (m_geometry.n_modules() != 1) { // if we have more than one module
+        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+             ++part_idx) {
+            frame_numbers[part_idx] =
+                m_subfiles[part_idx]->frame_number(frame_index);
         }
 
         // 1. if frame number vector is the same break
@@ -218,23 +179,40 @@ 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]);
         }
     }
 
     if (m_master.geometry().col == 1) {
         // get the part from each subfile and copy it to the frame
-        for (size_t part_idx = 0; part_idx != n_modules(); ++part_idx) {
+        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+             ++part_idx) {
             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 +
-                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.");
-            
-            //TODO! What if the files don't match?
+            // This is where we start writing
+            auto offset = (m_geometry
+                                   .get_module_geometries(
+                                       m_geometry.get_modules_in_roi(part_idx))
+                                   .origin_y *
+                               m_geometry.pixels_x() +
+                           m_geometry
+                               .get_module_geometries(
+                                   m_geometry.get_modules_in_roi(part_idx))
+                               .origin_x) *
+                          m_master.bitdepth() / 8;
+
+            if (m_geometry
+                    .get_module_geometries(
+                        m_geometry.get_modules_in_roi(part_idx))
+                    .origin_x != 0)
+                throw std::runtime_error(
+                    LOCATION +
+                    " Implementation error. x pos not 0."); // TODO: origin
+                                                            // can still
+                                                            // change if roi
+                                                            // changes
+            // TODO! What if the files don't match?
             m_subfiles[part_idx]->seek(corrected_idx);
             m_subfiles[part_idx]->read_into(frame_buffer + offset, header);
             if (header)
@@ -242,7 +220,7 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
         }
 
     } else {
-        //TODO! should we read row by row?
+        // TODO! should we read row by row?
 
         // create a buffer large enough to hold a full module
         auto bytes_per_part = m_master.pixels_y() * m_master.pixels_x() *
@@ -251,16 +229,18 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
 
         auto *part_buffer = new std::byte[bytes_per_part];
 
-        // TODO! if we have many submodules we should reorder them on the module
-        // level
+        // TODO! if we have many submodules we should reorder them on the
+        // module level
 
-        for (size_t part_idx = 0; part_idx != n_modules(); ++part_idx) {
-            auto pos = m_geometry.module_pixel_0[part_idx];
+        for (size_t part_idx = 0; part_idx != m_geometry.n_modules_in_roi();
+             ++part_idx) {
+            auto pos = m_geometry.get_module_geometries(
+                m_geometry.get_modules_in_roi(part_idx));
             auto corrected_idx = frame_indices[part_idx];
 
             m_subfiles[part_idx]->seek(corrected_idx);
             m_subfiles[part_idx]->read_into(part_buffer, header);
-            if(header)
+            if (header)
                 ++header;
 
             for (size_t cur_row = 0; cur_row < static_cast<size_t>(pos.height);
@@ -268,18 +248,16 @@ void RawFile::get_frame_into(size_t frame_index, std::byte *frame_buffer, Detect
 
                 auto irow = (pos.origin_y + cur_row);
                 auto icol = pos.origin_x;
-                auto dest = (irow * this->m_geometry.pixels_x + icol);
+                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 *
-                                         m_master.bitdepth() / 8,
+                       part_buffer +
+                           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 +277,4 @@ 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 +1,22 @@
+#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 <catch2/generators/catch_generators.hpp>
 #include <filesystem>
 
 #include "test_config.hpp"
-
+#include "test_macros.hpp"
 
 using aare::File;
+using aare::RawFile;
+using namespace aare;
 
 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 +24,8 @@ 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 +41,8 @@ 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 +55,10 @@ 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]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_missing_subfile_master_0.json";
+TEST_CASE("Read a frame numbers where the subfile is missing throws",
+          "[.integration]") {
+    auto fpath = test_data_path() / "jungfrau" /
+                 "jungfrau_missing_subfile_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
 
     File f(fpath, "r");
@@ -58,7 +66,7 @@ TEST_CASE("Read a frame numbers where the subfile is missing throws", "[.integra
     // we know this file has 10 frames with frame numbers 1 to 10
     // f0 1,2,3
     // f1 4,5,6 - but files f1-f3 are missing
-    // f2 7,8,9 - gone  
+    // f2 7,8,9 - gone
     // f3 10    - gone
     REQUIRE(f.frame_number(0) == 1);
     REQUIRE(f.frame_number(1) == 2);
@@ -69,15 +77,18 @@ 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", "[.integration]") {
-    auto fpath = test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
+TEST_CASE("Read data from a jungfrau 500k single port raw file",
+          "[.integration]") {
+    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
-    std::vector<uint16_t> pixel_0_0 = {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,
+    // 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 +111,12 @@ 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 +134,23 @@ 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_1 = {2842, 2796, 2865, 2798, 2805, 2817, 2852, 2789, 2792, 2833};
-    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};
+    std::vector<uint16_t> pixel_0_0 = {2099, 2121, 2108, 2084, 2084,
+                                       2118, 2066, 2108, 2112, 2116};
+    std::vector<uint16_t> pixel_0_1 = {2842, 2796, 2865, 2798, 2805,
+                                       2817, 2852, 2789, 2792, 2833};
+    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();
@@ -145,12 +164,112 @@ TEST_CASE("Read multipart files", "[.integration]") {
     }
 }
 
+struct TestParameters {
+    const std::string master_filename{};
+    const uint8_t num_ports{};
+    const size_t modules_x{};
+    const size_t modules_y{};
+    const size_t pixels_x{};
+    const size_t pixels_y{};
+    std::vector<ModuleGeometry> module_geometries{};
+};
+
+TEST_CASE_PRIVATE(aare, check_find_geometry, "check find_geometry",
+                  "[.integration][.files][.rawfile]") {
+
+    auto test_parameters = GENERATE(
+        TestParameters{"raw/jungfrau_2modules_version6.1.2/run_master_0.raw", 2,
+                       1, 2, 1024, 1024,
+                       std::vector<ModuleGeometry>{
+                           ModuleGeometry{0, 0, 512, 1024, 0, 0},
+                           ModuleGeometry{0, 512, 512, 1024, 0, 1}}},
+        TestParameters{
+            "raw/eiger_1_module_version7.0.0/eiger_1mod_master_7.json", 4, 2, 2,
+            1024, 512,
+            std::vector<ModuleGeometry>{
+                ModuleGeometry{0, 0, 256, 512, 0, 0},
+                ModuleGeometry{512, 0, 256, 512, 0, 1},
+                ModuleGeometry{0, 256, 256, 512, 1, 0},
+                ModuleGeometry{512, 256, 256, 512, 1, 1}}},
+
+        TestParameters{"raw/jungfrau_2modules_2interfaces/run_master_0.json", 4,
+                       1, 4, 1024, 1024,
+                       std::vector<ModuleGeometry>{
+                           ModuleGeometry{0, 0, 256, 1024, 0, 0},
+                           ModuleGeometry{0, 256, 256, 1024, 1, 0},
+                           ModuleGeometry{0, 512, 256, 1024, 2, 0},
+                           ModuleGeometry{0, 768, 256, 1024, 3, 0}}},
+        TestParameters{
+            "raw/eiger_quad_data/"
+            "W13_vthreshscan_m21C_300V_800eV_vrpre3400_master_0.json",
+            2, 1, 2, 512, 512,
+            std::vector<ModuleGeometry>{
+                ModuleGeometry{0, 0, 256, 512, 0, 0},
+                ModuleGeometry{0, 256, 256, 512, 1, 0}}});
+
+    auto fpath = test_data_path() / test_parameters.master_filename;
+
+    REQUIRE(std::filesystem::exists(fpath));
+
+    RawFile f(fpath, "r");
+
+    auto geometry = f.m_geometry;
+
+    CHECK(geometry.modules_x() == test_parameters.modules_x);
+    CHECK(geometry.modules_y() == test_parameters.modules_y);
+    CHECK(geometry.pixels_x() == test_parameters.pixels_x);
+    CHECK(geometry.pixels_y() == test_parameters.pixels_y);
+
+    REQUIRE(geometry.get_module_geometries().size() ==
+            test_parameters.num_ports);
+
+    // compare to data stored in header
+    for (size_t i = 0; i < test_parameters.num_ports; ++i) {
+
+        auto subfile1_path = f.master().data_fname(i, 0);
+        REQUIRE(std::filesystem::exists(subfile1_path));
+
+        auto header = RawFile::read_header(subfile1_path);
+
+        CHECK(header.column == geometry.get_module_geometries(i).col_index);
+        CHECK(header.row == geometry.get_module_geometries(i).row_index);
+
+        CHECK(geometry.get_module_geometries(i).height ==
+              test_parameters.module_geometries[i].height);
+        CHECK(geometry.get_module_geometries(i).width ==
+              test_parameters.module_geometries[i].width);
+
+        CHECK(geometry.get_module_geometries(i).origin_x ==
+              test_parameters.module_geometries[i].origin_x);
+        CHECK(geometry.get_module_geometries(i).origin_y ==
+              test_parameters.module_geometries[i].origin_y);
+    }
+}
+
+} // close the namespace
+
+TEST_CASE_PRIVATE(aare, open_multi_module_file_with_roi,
+                  "Open multi module file with ROI",
+                  "[.integration][.files][.rawfile]") {
+
+    auto fpath = test_data_path() / "raw/SingleChipROI/Data_master_0.json";
+    REQUIRE(std::filesystem::exists(fpath));
+
+    RawFile f(fpath, "r");
+
+    REQUIRE(f.master().roi().value().width() == 256);
+    REQUIRE(f.master().roi().value().height() == 256);
+
+    CHECK(f.m_geometry.n_modules() == 2);
+
+    CHECK(f.m_geometry.n_modules_in_roi() == 1);
+}
+} // close namespace aare
+
 TEST_CASE("Read file with unordered frames", "[.integration]") {
-    //TODO! Better explanation and error message
+    // TODO! Better explanation and error message
     auto fpath = test_data_path() / "mythen" / "scan242_master_3.raw";
     REQUIRE(std::filesystem::exists(fpath));
     File f(fpath);
     REQUIRE_THROWS((f.read_frame()));
 }
-
-

src/RawMasterFile.cpp

@@ -1,5 +1,6 @@
 #include "aare/RawMasterFile.hpp"
-#include <sstream>  
+#include "aare/RawFile.hpp"
+#include <sstream>
 namespace aare {
 
 RawFileNameComponents::RawFileNameComponents(
@@ -37,18 +38,15 @@ std::filesystem::path RawFileNameComponents::master_fname() const {
 }
 
 std::filesystem::path RawFileNameComponents::data_fname(size_t mod_id,
-                                                        size_t file_id
-                                                        ) const {
-    
-    
-    
+                                                        size_t file_id) const {
+
     std::string fmt = "{}_d{}_f{}_{}.raw";
-    //Before version X we used to name the data files f000000000000
+    // 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,
-                                     file_id, m_file_index);
+    return m_base_path /
+           fmt::format(fmt, m_base_name, mod_id, file_id, m_file_index);
 }
 
 void RawFileNameComponents::set_old_scheme(bool old_scheme) {
@@ -65,19 +63,19 @@ const std::string &RawFileNameComponents::ext() const { return m_ext; }
 int RawFileNameComponents::file_index() const { return m_file_index; }
 
 // "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
-ScanParameters::ScanParameters(const std::string& par){
-    std::istringstream iss(par.substr(1, par.size()-2));
+ScanParameters::ScanParameters(const std::string &par) {
+    std::istringstream iss(par.substr(1, par.size() - 2));
     std::string line;
-    while(std::getline(iss, line)){
-        if(line == "enabled"){
+    while (std::getline(iss, line)) {
+        if (line == "enabled") {
             m_enabled = true;
-        }else if(line.find("dac") != std::string::npos){
+        } else if (line.find("dac") != std::string::npos) {
             m_dac = line.substr(4);
-        }else if(line.find("start") != std::string::npos){
+        } else if (line.find("start") != std::string::npos) {
             m_start = std::stoi(line.substr(6));
-        }else if(line.find("stop") != std::string::npos){
+        } else if (line.find("stop") != std::string::npos) {
             m_stop = std::stoi(line.substr(5));
-        }else if(line.find("step") != std::string::npos){
+        } else if (line.find("step") != std::string::npos) {
             m_step = std::stoi(line.substr(5));
         }
     }
@@ -85,14 +83,11 @@ ScanParameters::ScanParameters(const std::string& par){
 
 int ScanParameters::start() const { return m_start; }
 int ScanParameters::stop() const { return m_stop; }
-void ScanParameters::increment_stop(){
-    m_stop += 1;
-}
+void ScanParameters::increment_stop() { m_stop += 1; }
 int ScanParameters::step() const { return m_step; }
 const std::string &ScanParameters::dac() const { return m_dac; }
 bool ScanParameters::enabled() const { return m_enabled; }
 
-
 RawMasterFile::RawMasterFile(const std::filesystem::path &fpath)
     : m_fnc(fpath) {
     if (!std::filesystem::exists(fpath)) {
@@ -144,7 +139,11 @@ size_t RawMasterFile::n_modules() const {
     return m_geometry.row * m_geometry.col;
 }
 
-std::optional<uint8_t> RawMasterFile::quad() const { return m_quad; }
+xy RawMasterFile::udp_interfaces_per_module() const {
+    return m_udp_interfaces_per_module;
+}
+
+uint8_t RawMasterFile::quad() const { return m_quad; }
 
 // optional values, these may or may not be present in the master file
 // and are therefore modeled as std::optional
@@ -163,10 +162,8 @@ 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 +174,10 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
     m_type = StringTo<DetectorType>(j["Detector Type"].get<std::string>());
     m_timing_mode = StringTo<TimingMode>(j["Timing Mode"].get<std::string>());
 
-    m_geometry = {j["Geometry"]["y"], j["Geometry"]["x"]};
+    m_geometry = {
+        j["Geometry"]["y"],
+        j["Geometry"]["x"]}; // TODO: isnt it only available for version > 7.1?
+                             // - try block default should be 1x1
 
     m_image_size_in_bytes = j["Image Size in bytes"];
     m_frames_in_file = j["Frames in File"];
@@ -205,17 +205,16 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // keep the optional empty
     }
 
-
     // ----------------------------------------------------------------
     // Special treatment of analog flag because of Moench03
-    try{
+    try {
         m_analog_flag = j.at("Analog Flag");
-    }catch (const json::out_of_range &e) {
+    } catch (const json::out_of_range &e) {
         // if it doesn't work still set it to one
         // to try to decode analog samples (Old Moench03)
         m_analog_flag = 1;
     }
-    try {        
+    try {
         if (m_analog_flag) {
             m_analog_samples = j.at("Analog Samples");
         }
@@ -248,27 +247,36 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         // keep the optional empty
     }
 
-    try{
+    try {
         m_transceiver_flag = j.at("Transceiver Flag");
-        if(m_transceiver_flag){
+        if (m_transceiver_flag) {
             m_transceiver_samples = j.at("Transceiver Samples");
         }
-    }catch (const json::out_of_range &e) {
+    } catch (const json::out_of_range &e) {
         // keep the optional empty
     }
 
-    try{
+    try {
         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
-            }
-    }catch (const json::out_of_range &e) {
+        if (v < 7.21) {
+            m_scan_parameters
+                .increment_stop(); // adjust for endpoint being included
+        }
+    } catch (const json::out_of_range &e) {
         // not a scan
     }
+    try {
+        m_udp_interfaces_per_module = {j.at("Number of UDP Interfaces"), 1};
+    } catch (const json::out_of_range &e) {
+        if (m_type == DetectorType::Eiger && m_quad == 1)
+            m_udp_interfaces_per_module = {2, 1};
+        else if (m_type == DetectorType::Eiger) {
+            m_udp_interfaces_per_module = {1, 2};
+        }
+    }
 
-
-    try{
+    try {
         ROI tmp_roi;
         auto obj = j.at("Receiver Roi");
         tmp_roi.xmin = obj.at("xmin");
@@ -276,37 +284,32 @@ void RawMasterFile::parse_json(const std::filesystem::path &fpath) {
         tmp_roi.ymin = obj.at("ymin");
         tmp_roi.ymax = obj.at("ymax");
 
-        //if any of the values are set update the roi
+        // if any of the values are set update the roi
         if (tmp_roi.xmin != 4294967295 || tmp_roi.xmax != 4294967295 ||
             tmp_roi.ymin != 4294967295 || tmp_roi.ymax != 4294967295) {
-            
-            if(v<7.21){
-                tmp_roi.xmax++;
+
+            if (v < 7.21) {
+                tmp_roi.xmax++; // why is it updated
                 tmp_roi.ymax++;
             }
-            
             m_roi = tmp_roi;
         }
 
-
-    }catch (const json::out_of_range &e) {
+    } catch (const json::out_of_range &e) {
+        std::cout << e.what() << std::endl;
         // leave the optional empty
     }
 
-    //if we have an roi we need to update the geometry for the subfiles
-    if (m_roi){
-
+    // 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
+// Update detector type for Moench
+// TODO! How does this work with old .raw master files?
+#ifdef AARE_VERBOSE
     fmt::print("Detecting Moench03: m_pixels_y: {}, m_analog_samples: {}\n",
                m_pixels_y, m_analog_samples.value_or(0));
-    #endif
+#endif
     if (m_type == DetectorType::Moench && !m_analog_samples &&
         m_pixels_y == 400) {
         m_type = DetectorType::Moench03;
@@ -332,19 +335,19 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
             if (key == "Version") {
                 m_version = value;
 
-                //TODO!: How old versions can we handle?
+                // TODO!: How old versions can we handle?
                 auto v = std::stod(value);
 
-                //TODO! figure out exactly when we did the change
-                //This enables padding of f to 12 digits
-                if (v<4.0)
+                // TODO! figure out exactly when we did the change
+                // This enables padding of f to 12 digits
+                if (v < 4.0)
                     m_fnc.set_old_scheme(true);
 
             } else if (key == "TimeStamp") {
 
             } else if (key == "Detector Type") {
                 m_type = StringTo<DetectorType>(value);
-                if(m_type==DetectorType::Moench){
+                if (m_type == DetectorType::Moench) {
                     m_type = DetectorType::Moench03_old;
                 }
             } else if (key == "Timing Mode") {
@@ -381,10 +384,10 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
                 pos = value.find(',');
                 m_pixels_x = std::stoi(value.substr(1, pos));
                 m_pixels_y = std::stoi(value.substr(pos + 1));
-            }else if(key == "row"){
+            } else if (key == "row") {
                 pos = value.find('p');
                 m_pixels_y = std::stoi(value.substr(0, pos));
-            }else if(key == "col"){
+            } else if (key == "col") {
                 pos = value.find('p');
                 m_pixels_x = std::stoi(value.substr(0, pos));
             } else if (key == "Total Frames") {
@@ -395,30 +398,62 @@ void RawMasterFile::parse_raw(const std::filesystem::path &fpath) {
                 m_quad = std::stoi(value);
             } else if (key == "Max Frames Per File") {
                 m_max_frames_per_file = std::stoi(value);
-            }else if(key == "Max. Frames Per File"){
-                //Version 3.0 way of writing it
+            } else if (key == "Max. Frames Per File") {
+                // Version 3.0 way of writing it
                 m_max_frames_per_file = std::stoi(value);
             } else if (key == "Geometry") {
                 pos = value.find(',');
                 m_geometry = {
                     static_cast<uint32_t>(std::stoi(value.substr(1, pos))),
                     static_cast<uint32_t>(std::stoi(value.substr(pos + 1)))};
+            } else if (key == "Number of UDP Interfaces") {
+                m_udp_interfaces_per_module = {
+                    static_cast<uint32_t>(std::stoi(value)), 1};
             }
         }
     }
+
+    if (m_type == DetectorType::Eiger && m_quad == 1) {
+        m_udp_interfaces_per_module = {2, 1};
+    } else if (m_type == DetectorType::Eiger) {
+        m_udp_interfaces_per_module = {1, 2};
+    }
+
     if (m_pixels_x == 400 && m_pixels_y == 400) {
         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};
-        fmt::print("Warning: No geometry found in master file. Assuming 1x1\n");
+    if (m_geometry.col == 0 && m_geometry.row == 0) {
+        retrieve_geometry();
+        fmt::print("Warning: No geometry found in master file. Retrieved "
+                   "geometry of {}x{}\n",
+                   m_geometry.row, m_geometry.col);
     }
 
-    //TODO! Read files and find actual frames
-    if(m_frames_in_file==0)
+    // TODO! Read files and find actual frames
+    if (m_frames_in_file == 0)
         m_frames_in_file = m_total_frames_expected;
 }
+
+void RawMasterFile::retrieve_geometry() {
+    uint32_t module_index = 0;
+    uint16_t rows = 0;
+    uint16_t cols = 0;
+    // TODO use case for Eiger
+
+    while (std::filesystem::exists(data_fname(module_index, 0))) {
+
+        auto header = RawFile::read_header(data_fname(module_index, 0));
+
+        rows = std::max(rows, header.row);
+        cols = std::max(cols, header.column);
+
+        ++module_index;
+    }
+    ++rows;
+    ++cols;
+
+    m_geometry = {rows, cols};
+}
+
 } // namespace aare

src/RawMasterFile.test.cpp

@@ -1,12 +1,12 @@
 #include "aare/RawMasterFile.hpp"
 
-#include <catch2/catch_test_macros.hpp>
 #include "test_config.hpp"
+#include <catch2/catch_test_macros.hpp>
+#include <iostream>
 
 using namespace aare;
 
-
-TEST_CASE("Parse a master file fname"){
+TEST_CASE("Parse a master file fname") {
     RawFileNameComponents m("test_master_1.json");
     REQUIRE(m.base_name() == "test");
     REQUIRE(m.ext() == ".json");
@@ -14,7 +14,7 @@ TEST_CASE("Parse a master file fname"){
     REQUIRE(m.base_path() == "");
 }
 
-TEST_CASE("Extraction of base path works"){
+TEST_CASE("Extraction of base path works") {
     RawFileNameComponents m("some/path/test_master_73.json");
     REQUIRE(m.base_name() == "test");
     REQUIRE(m.ext() == ".json");
@@ -22,7 +22,7 @@ TEST_CASE("Extraction of base path works"){
     REQUIRE(m.base_path() == "some/path");
 }
 
-TEST_CASE("Construction of master file name and data files"){
+TEST_CASE("Construction of master file name and data files") {
     RawFileNameComponents m("test_master_1.json");
     REQUIRE(m.master_fname() == "test_master_1.json");
     REQUIRE(m.data_fname(0, 0) == "test_d0_f0_1.raw");
@@ -31,7 +31,7 @@ TEST_CASE("Construction of master file name and data files"){
     REQUIRE(m.data_fname(1, 1) == "test_d1_f1_1.raw");
 }
 
-TEST_CASE("Construction of master file name and data files using old scheme"){
+TEST_CASE("Construction of master file name and data files using old scheme") {
     RawFileNameComponents m("test_master_1.raw");
     m.set_old_scheme(true);
     REQUIRE(m.master_fname() == "test_master_1.raw");
@@ -41,16 +41,15 @@ TEST_CASE("Construction of master file name and data files using old scheme"){
     REQUIRE(m.data_fname(1, 1) == "test_d1_f000000000001_1.raw");
 }
 
-TEST_CASE("Master file name does not fit pattern"){
+TEST_CASE("Master file name does not fit pattern") {
     REQUIRE_THROWS(RawFileNameComponents("somefile.json"));
     REQUIRE_THROWS(RawFileNameComponents("another_test_d0_f0_1.raw"));
     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]");
+TEST_CASE("Parse scan parameters") {
+    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);
@@ -58,7 +57,7 @@ TEST_CASE("Parse scan parameters"){
     REQUIRE(s.step() == 5);
 }
 
-TEST_CASE("A disabled scan"){
+TEST_CASE("A disabled scan") {
     ScanParameters s("[disabled]");
     REQUIRE_FALSE(s.enabled());
     REQUIRE(s.dac() == "");
@@ -67,9 +66,9 @@ 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";
+TEST_CASE("Parse a master file in .json format", "[.integration]") {
+    auto fpath =
+        test_data_path() / "jungfrau" / "jungfrau_single_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
 
@@ -80,7 +79,7 @@ TEST_CASE("Parse a master file in .json format", "[.integration]"){
     REQUIRE(f.detector_type() == DetectorType::Jungfrau);
     // "Timing Mode": "auto",
     REQUIRE(f.timing_mode() == TimingMode::Auto);
-    
+
     // "Geometry": {
     //     "x": 1,
     //     "y": 1
@@ -100,10 +99,9 @@ TEST_CASE("Parse a master file in .json format", "[.integration]"){
     // "Max Frames Per File": 3,
     REQUIRE(f.max_frames_per_file() == 3);
 
-    //Jungfrau doesn't write but it is 16
+    // Jungfrau doesn't write but it is 16
     REQUIRE(f.bitdepth() == 16);
 
-
     // "Frame Discard Policy": "nodiscard",
 
     // "Frame Padding": 1,
@@ -125,33 +123,48 @@ TEST_CASE("Parse a master file in .json format", "[.integration]"){
     // "Frames in File": 10,
     REQUIRE(f.frames_in_file() == 10);
 
-    //TODO! Should we parse this? 
-    // "Frame Header Format": {
-    //     "Frame Number": "8 bytes",
-    //     "SubFrame Number/ExpLength": "4 bytes",
-    //     "Packet Number": "4 bytes",
-    //     "Bunch ID": "8 bytes",
-    //     "Timestamp": "8 bytes",
-    //     "Module Id": "2 bytes",
-    //     "Row": "2 bytes",
-    //     "Column": "2 bytes",
-    //     "Reserved": "2 bytes",
-    //     "Debug": "4 bytes",
-    //     "Round Robin Number": "2 bytes",
-    //     "Detector Type": "1 byte",
-    //     "Header Version": "1 byte",
-    //     "Packets Caught Mask": "64 bytes"
-    // }
-    // }         
+    // TODO! Should we parse this?
+    //  "Frame Header Format": {
+    //      "Frame Number": "8 bytes",
+    //      "SubFrame Number/ExpLength": "4 bytes",
+    //      "Packet Number": "4 bytes",
+    //      "Bunch ID": "8 bytes",
+    //      "Timestamp": "8 bytes",
+    //      "Module Id": "2 bytes",
+    //      "Row": "2 bytes",
+    //      "Column": "2 bytes",
+    //      "Reserved": "2 bytes",
+    //      "Debug": "4 bytes",
+    //      "Round Robin Number": "2 bytes",
+    //      "Detector Type": "1 byte",
+    //      "Header Version": "1 byte",
+    //      "Packets Caught Mask": "64 bytes"
+    //  }
+    //  }
 
     REQUIRE_FALSE(f.analog_samples());
-    REQUIRE_FALSE(f.digital_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";
+TEST_CASE("Parse a master file in old .raw format",
+          "[.integration][.files][.rawmasterfile]") {
+    auto fpath = test_data_path() /
+                 "raw/jungfrau_2modules_version6.1.2/run_master_0.raw";
+    REQUIRE(std::filesystem::exists(fpath));
+    RawMasterFile f(fpath);
+
+    CHECK(f.udp_interfaces_per_module() == xy{1, 1});
+    CHECK(f.n_modules() == 2);
+    CHECK(f.geometry().row == 2);
+    CHECK(f.geometry().col == 1);
+}
+
+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";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
 
@@ -209,80 +222,74 @@ 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";
+TEST_CASE("Read eiger master file", "[.integration]") {
+    auto fpath = test_data_path() / "eiger" / "eiger_500k_32bit_master_0.json";
     REQUIRE(std::filesystem::exists(fpath));
     RawMasterFile f(fpath);
-    
-// {
-//     "Version": 7.2,
-REQUIRE(f.version() == "7.2");
-//     "Timestamp": "Tue Mar 26 17:24:34 2024",
-//     "Detector Type": "Eiger",
-REQUIRE(f.detector_type() == DetectorType::Eiger);
-//     "Timing Mode": "auto",
-REQUIRE(f.timing_mode() == TimingMode::Auto);
-//     "Geometry": {
-//         "x": 2,
-//         "y": 2
-//     },
-//     "Image Size in bytes": 524288,
-REQUIRE(f.image_size_in_bytes() == 524288);
-//     "Pixels": {
-//         "x": 512,
-REQUIRE(f.pixels_x() == 512);
-//         "y": 256
-REQUIRE(f.pixels_y() == 256);
-//     },
-//     "Max Frames Per File": 10000,
-REQUIRE(f.max_frames_per_file() == 10000);
-//     "Frame Discard Policy": "nodiscard",
-REQUIRE(f.frame_discard_policy() == FrameDiscardPolicy::NoDiscard);
-//     "Frame Padding": 1,
-REQUIRE(f.frame_padding() == 1);
-
-//     "Scan Parameters": "[disabled]",
-//     "Total Frames": 3,
-//     "Receiver Roi": {
-//         "xmin": 4294967295,
-//         "xmax": 4294967295,
-//         "ymin": 4294967295,
-//         "ymax": 4294967295
-//     },
-//     "Dynamic Range": 32,
-//     "Ten Giga": 0,
-//     "Exptime": "5s",
-//     "Period": "1s",
-//     "Threshold Energy": -1,
-//     "Sub Exptime": "2.62144ms",
-//     "Sub Period": "2.62144ms",
-//     "Quad": 0,
-//     "Number of rows": 256,
-//     "Rate Corrections": "[0, 0]",
-//     "Frames in File": 3,
-//     "Frame Header Format": {
-//         "Frame Number": "8 bytes",
-//         "SubFrame Number/ExpLength": "4 bytes",
-//         "Packet Number": "4 bytes",
-//         "Bunch ID": "8 bytes",
-//         "Timestamp": "8 bytes",
-//         "Module Id": "2 bytes",
-//         "Row": "2 bytes",
-//         "Column": "2 bytes",
-//         "Reserved": "2 bytes",
-//         "Debug": "4 bytes",
-//         "Round Robin Number": "2 bytes",
-//         "Detector Type": "1 byte",
-//         "Header Version": "1 byte",
-//         "Packets Caught Mask": "64 bytes"
-//     }
-// }            
-
 
+    // {
+    //     "Version": 7.2,
+    REQUIRE(f.version() == "7.2");
+    //     "Timestamp": "Tue Mar 26 17:24:34 2024",
+    //     "Detector Type": "Eiger",
+    REQUIRE(f.detector_type() == DetectorType::Eiger);
+    //     "Timing Mode": "auto",
+    REQUIRE(f.timing_mode() == TimingMode::Auto);
+    //     "Geometry": {
+    //         "x": 2,
+    //         "y": 2
+    //     },
+    //     "Image Size in bytes": 524288,
+    REQUIRE(f.image_size_in_bytes() == 524288);
+    //     "Pixels": {
+    //         "x": 512,
+    REQUIRE(f.pixels_x() == 512);
+    //         "y": 256
+    REQUIRE(f.pixels_y() == 256);
+    //     },
+    //     "Max Frames Per File": 10000,
+    REQUIRE(f.max_frames_per_file() == 10000);
+    //     "Frame Discard Policy": "nodiscard",
+    REQUIRE(f.frame_discard_policy() == FrameDiscardPolicy::NoDiscard);
+    //     "Frame Padding": 1,
+    REQUIRE(f.frame_padding() == 1);
 
+    //     "Scan Parameters": "[disabled]",
+    //     "Total Frames": 3,
+    //     "Receiver Roi": {
+    //         "xmin": 4294967295,
+    //         "xmax": 4294967295,
+    //         "ymin": 4294967295,
+    //         "ymax": 4294967295
+    //     },
+    //     "Dynamic Range": 32,
+    //     "Ten Giga": 0,
+    //     "Exptime": "5s",
+    //     "Period": "1s",
+    //     "Threshold Energy": -1,
+    //     "Sub Exptime": "2.62144ms",
+    //     "Sub Period": "2.62144ms",
+    //     "Quad": 0,
+    //     "Number of rows": 256,
+    //     "Rate Corrections": "[0, 0]",
+    //     "Frames in File": 3,
+    //     "Frame Header Format": {
+    //         "Frame Number": "8 bytes",
+    //         "SubFrame Number/ExpLength": "4 bytes",
+    //         "Packet Number": "4 bytes",
+    //         "Bunch ID": "8 bytes",
+    //         "Timestamp": "8 bytes",
+    //         "Module Id": "2 bytes",
+    //         "Row": "2 bytes",
+    //         "Column": "2 bytes",
+    //         "Reserved": "2 bytes",
+    //         "Debug": "4 bytes",
+    //         "Round Robin Number": "2 bytes",
+    //         "Detector Type": "1 byte",
+    //         "Header Version": "1 byte",
+    //         "Packets Caught Mask": "64 bytes"
+    //     }
+    // }
 }

src/RawSubFile.cpp

@@ -1,36 +1,30 @@
 #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_rows(rows), m_cols(cols),
-      m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols), m_pos_row(pos_row),
-      m_pos_col(pos_col) {
+    : m_detector_type(detector), m_bitdepth(bitdepth), m_rows(rows),
+      m_cols(cols), m_bytes_per_frame((m_bitdepth / 8) * m_rows * m_cols),
+      m_pos_row(pos_row), m_pos_col(pos_col) {
 
-    LOG(logDEBUG) << "RawSubFile::RawSubFile()";  
+    LOG(logDEBUG) << "RawSubFile::RawSubFile()";
     if (m_detector_type == DetectorType::Moench03_old) {
         m_pixel_map = GenerateMoench03PixelMap();
     } else if (m_detector_type == DetectorType::Eiger && m_pos_row % 2 == 0) {
         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);
 }
 
@@ -69,7 +64,7 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
         m_file.seekg(sizeof(DetectorHeader), std::ios::cur);
     }
 
-    if (m_file.fail()){
+    if (m_file.fail()) {
         throw std::runtime_error(LOCATION + ifstream_error_msg(m_file));
     }
 
@@ -78,14 +73,15 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
         // read into a temporary buffer and then copy the data to the buffer
         // in the correct order
         // TODO! add 4 bit support
-        if(m_bitdepth == 8){
+        if (m_bitdepth == 8) {
             read_with_map<uint8_t>(image_buf);
-        }else if (m_bitdepth == 16) {
+        } else if (m_bitdepth == 16) {
             read_with_map<uint16_t>(image_buf);
         } else if (m_bitdepth == 32) {
             read_with_map<uint32_t>(image_buf);
-        }else{
-            throw std::runtime_error("Unsupported bitdepth for read with pixel map");
+        } else {
+            throw std::runtime_error(
+                "Unsupported bitdepth for read with pixel map");
         }
 
     } else {
@@ -93,11 +89,11 @@ void RawSubFile::read_into(std::byte *image_buf, DetectorHeader *header) {
         m_file.read(reinterpret_cast<char *>(image_buf), bytes_per_frame());
     }
 
-    if (m_file.fail()){
+    if (m_file.fail()) {
         throw std::runtime_error(LOCATION + ifstream_error_msg(m_file));
     }
 
-    ++ m_current_frame_index;
+    ++m_current_frame_index;
     if (m_current_frame_index >= m_last_frame_in_file[m_current_file_index] &&
         (m_current_frame_index < m_total_frames)) {
         ++m_current_file_index;
@@ -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_base_name = match[1].str() + match[2].str() + match[3].str() + "{}" + match[5].str();
+        m_offset = std::stoi(match[4].str()); // find the first file index in
+                                              // 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()));
     }
 }
 
@@ -175,12 +172,13 @@ std::filesystem::path RawSubFile::fpath(size_t file_index) const {
 
 void RawSubFile::open_file(size_t file_index) {
     m_file.close();
-    auto fname = fpath(file_index+m_offset);
+    auto fname = fpath(file_index + m_offset);
     LOG(logDEBUG) << "RawSubFile::open_file():  " << fname.string();
     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;
 }
@@ -190,20 +188,21 @@ void RawSubFile::scan_files() {
     // find how many files we have and the number of frames in each file
     m_last_frame_in_file.clear();
     size_t file_index = m_offset;
-    
+
     while (std::filesystem::exists(fpath(file_index))) {
         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;
     }
 
     // find where we need to open the next file and total number of frames
     m_last_frame_in_file = cumsum(m_last_frame_in_file);
-    if(m_last_frame_in_file.empty()){
+    if (m_last_frame_in_file.empty()) {
         m_total_frames = 0;
-    }else{
+    } else {
         m_total_frames = m_last_frame_in_file.back();
     }
 }

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";
+TEST_CASE("Read frames directly from a RawSubFile", "[.files]") {
+    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);
@@ -17,19 +18,19 @@ 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 = 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));
 
-    //Numpy file with the same data to use as reference
+    // Numpy file with the same data to use as reference
     File npy(fpath_npy, "r");
 
     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);
@@ -38,38 +39,40 @@ 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 = 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));
 
-    //Numpy file with the same data to use as reference
+    // Numpy file with the same data to use as reference
     File npy(fpath_npy, "r");
     npy.seek(3);
 
     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);
-        // frame numbers start at 1 frame index at 0 
+        // frame numbers start at 1 frame index at 0
         // adding 3 + 1 to verify the frame number
-        CHECK(header.frameNumber == i + 4); 
+        CHECK(header.frameNumber == i + 4);
         auto npy_frame = npy.read_frame();
         CHECK((image.view() == npy_frame.view<uint16_t>()));
     }

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

@@ -2,9 +2,9 @@
 #include <cmath>
 namespace aare {
 
-uint16_t adc_sar_05_decode64to16(uint64_t input){
+uint16_t adc_sar_05_decode64to16(uint64_t input) {
 
-    //we want bits 29,19,28,18,31,21,27,20,24,23,25,22 and then pad to 16
+    // we want bits 29,19,28,18,31,21,27,20,24,23,25,22 and then pad to 16
     uint16_t output = 0;
     output |= ((input >> 22) & 1) << 11;
     output |= ((input >> 25) & 1) << 10;
@@ -21,19 +21,21 @@ 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){
-    if(input.shape() != output.shape()){
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+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");
     }
 
-    for(ssize_t i = 0; i < input.shape(0); i++){
-        for(ssize_t j = 0; j < input.shape(1); j++){
-            output(i,j) = adc_sar_05_decode64to16(input(i,j));
+    for (ssize_t i = 0; i < input.shape(0); i++) {
+        for (ssize_t j = 0; j < input.shape(1); j++) {
+            output(i, j) = adc_sar_05_decode64to16(input(i, j));
         }
     }
 }
 
-uint16_t adc_sar_04_decode64to16(uint64_t input){
+uint16_t adc_sar_04_decode64to16(uint64_t input) {
 
     // bit_map = array([15,17,19,21,23,4,6,8,10,12,14,16] LSB->MSB
     uint16_t output = 0;
@@ -52,20 +54,23 @@ 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){
-    if(input.shape() != output.shape()){
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+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");
     }
-    for(ssize_t i = 0; i < input.shape(0); i++){
-        for(ssize_t j = 0; j < input.shape(1); j++){
-            output(i,j) = adc_sar_04_decode64to16(input(i,j));
+    for (ssize_t i = 0; i < input.shape(0); i++) {
+        for (ssize_t j = 0; j < input.shape(1); j++) {
+            output(i, j) = adc_sar_04_decode64to16(input(i, j));
         }
     }
 }
 
 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");
+    if (weights.size() > 16) {
+        throw std::invalid_argument(
+            "weights size must be less than or equal to 16");
     }
 
     double result = 0.0;
@@ -73,30 +78,30 @@ 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) {
-    if(input.shape() != output.shape()){
-        throw std::invalid_argument(LOCATION + " input and output shapes must match");
+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");
     }
 
-    //Calculate weights to avoid repeatedly calling std::pow
+    // Calculate weights to avoid repeatedly calling std::pow
     std::vector<double> weights_powers(weights.size());
     for (ssize_t i = 0; i < weights.size(); ++i) {
         weights_powers[i] = std::pow(weights[i], i);
     }
 
     // Apply custom weights to each element in the input array
-    for (ssize_t i = 0; i < input.shape(0); i++) {            
+    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

@@ -1,17 +1,16 @@
 #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>
 
-TEST_CASE("test_adc_sar_05_decode64to16"){
+TEST_CASE("test_adc_sar_05_decode64to16") {
     uint64_t input = 0;
     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);
@@ -47,10 +44,9 @@ TEST_CASE("test_adc_sar_05_decode64to16"){
     input |= (1UL << 22);
     output = aare::adc_sar_05_decode64to16(input);
     CHECK(output == 3072UL);
- }
+}
 
-
- TEST_CASE("test_apply_custom_weights") {
+TEST_CASE("test_apply_custom_weights") {
 
     uint16_t input = 1;
     aare::NDArray<double, 1> weights_data({3}, 0.0);
@@ -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

@@ -5,15 +5,11 @@
 #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
@@ -40,7 +36,7 @@ template <> std::string ToString(DetectorType arg) {
     case DetectorType::Xilinx_ChipTestBoard:
         return "Xilinx_ChipTestBoard";
 
-    //Custom ones
+    // Custom ones
     case DetectorType::Moench03:
         return "Moench03";
     case DetectorType::Moench03_old:
@@ -48,8 +44,8 @@ template <> std::string ToString(DetectorType arg) {
     case DetectorType::Unknown:
         return "Unknown";
 
-    //no default case to trigger compiler warning if not all 
-    //enum values are handled
+        // no default case to trigger compiler warning if not all
+        // enum values are handled
     }
     throw std::runtime_error("Could not decode detector to string");
 }
@@ -80,14 +76,14 @@ template <> DetectorType StringTo(const std::string &arg) {
     if (arg == "Xilinx_ChipTestBoard")
         return DetectorType::Xilinx_ChipTestBoard;
 
-    //Custom ones
+    // Custom ones
     if (arg == "Moench03")
         return DetectorType::Moench03;
     if (arg == "Moench03_old")
         return DetectorType::Moench03_old;
     if (arg == "Unknown")
         return DetectorType::Unknown;
-    
+
     throw std::runtime_error("Could not decode detector from: \"" + arg + "\"");
 }
 
@@ -102,7 +98,8 @@ 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 +
+                             "\"");
 }
 
 template <> FrameDiscardPolicy StringTo(const std::string &arg) {
@@ -112,7 +109,8 @@ 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 + "\"");
 }
 
 // template <> TimingMode StringTo<TimingMode>(std::string mode);

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
-    // but let's use this to show a test
+    // TODO! By the way I don't think the enum string conversions should be in
+    // 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");
@@ -17,30 +17,42 @@ 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);
+TEST_CASE("String to enum") {
+    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>("Jungfrau") == aare::DetectorType::Jungfrau);
-    REQUIRE(StringTo<aare::DetectorType>("ChipTestBoard") == aare::DetectorType::ChipTestBoard);
-    REQUIRE(StringTo<aare::DetectorType>("Moench") == aare::DetectorType::Moench);
-    REQUIRE(StringTo<aare::DetectorType>("Mythen3") == 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);
+    REQUIRE(StringTo<aare::DetectorType>("Gotthard") ==
+            aare::DetectorType::Gotthard);
+    REQUIRE(StringTo<aare::DetectorType>("Jungfrau") ==
+            aare::DetectorType::Jungfrau);
+    REQUIRE(StringTo<aare::DetectorType>("ChipTestBoard") ==
+            aare::DetectorType::ChipTestBoard);
+    REQUIRE(StringTo<aare::DetectorType>("Moench") ==
+            aare::DetectorType::Moench);
+    REQUIRE(StringTo<aare::DetectorType>("Mythen3") ==
+            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"){
-    //Since some of the enums are written to file we need to make sure 
-    //they match the value in the slsDetectorPackage
+TEST_CASE("Enum values") {
+    // Since some of the enums are written to file we need to make sure
+    // they match the value in the slsDetectorPackage
 
     REQUIRE(static_cast<int>(aare::DetectorType::Generic) == 0);
     REQUIRE(static_cast<int>(aare::DetectorType::Eiger) == 1);
@@ -52,7 +64,7 @@ TEST_CASE("Enum values"){
     REQUIRE(static_cast<int>(aare::DetectorType::Gotthard2) == 7);
     REQUIRE(static_cast<int>(aare::DetectorType::Xilinx_ChipTestBoard) == 8);
 
-    //Not included
+    // Not included
     REQUIRE(static_cast<int>(aare::DetectorType::Moench03) == 100);
 }
 
@@ -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

@@ -1,71 +0,0 @@
-
-#include "aare/geo_helpers.hpp"
-#include "fmt/core.h"
-
-namespace aare{
-
-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: {} {} {} {} {} {}",
-                 geo.modules_x, geo.modules_y, geo.pixels_x, geo.pixels_y, geo.module_gap_row, geo.module_gap_col);
-    #endif
-    int pos_y = 0;
-    int pos_y_increment = 0;
-    for (int row = 0; row < geo.modules_y; row++) {
-        int pos_x = 0;
-        for (int col = 0; col < geo.modules_x; col++) {
-            auto &m = geo.module_pixel_0[row * geo.modules_x + col];
-            auto original_height = m.height;
-            auto original_width = m.width;
-
-            // module is to the left of the roi
-            if (m.origin_x + m.width < roi.xmin) {
-                m.width = 0;
-
-                // roi is in module
-            } else {
-                // here we only arrive when the roi is in or to the left of
-                // the module
-                if (roi.xmin > m.origin_x) {
-                    m.width -= roi.xmin - m.origin_x;
-                }
-                if (roi.xmax < m.origin_x + original_width) {
-                    m.width -= m.origin_x + original_width - roi.xmax;
-                }
-                m.origin_x = pos_x;
-                pos_x += m.width;
-            }
-
-            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)) {
-                    m.height -= roi.ymin - m.origin_y;
-
-                }
-                if (roi.ymax < m.origin_y + original_height) {
-                    m.height -= m.origin_y + original_height - roi.ymax;
-                }
-                m.origin_y = pos_y;
-                pos_y_increment = m.height;
-            }
-            #ifdef AARE_VERBOSE
-    fmt::println("Module {} {} {} {}", m.origin_x, m.origin_y, m.width, m.height);
-    #endif
-        }
-        // increment pos_y
-        pos_y += pos_y_increment;
-    }
-
-    // m_rows = roi.height();
-    // m_cols = roi.width();
-    geo.pixels_x = roi.width();
-    geo.pixels_y = roi.height();
-
-    return geo;
-
-}
-
-} // namespace aare

src/geo_helpers.test.cpp

@@ -1,230 +0,0 @@
-#include "aare/File.hpp"
-#include "aare/RawMasterFile.hpp" //needed for ROI
-#include "aare/RawFile.hpp"
-
-#include <catch2/catch_test_macros.hpp>
-#include <filesystem>
-
-#include "aare/geo_helpers.hpp"
-#include "test_config.hpp"
-
-TEST_CASE("Simple ROIs on one module"){
-    // 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;
-    geo.modules_y = 1;
-    geo.module_pixel_0.push_back(mod);
-
-    SECTION("ROI is the whole module"){
-        aare::ROI roi;
-        roi.xmin = 0;
-        roi.xmax = 1024;
-        roi.ymin = 0;
-        roi.ymax = 512;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 1024);
-        REQUIRE(updated_geo.pixels_y == 512);
-        REQUIRE(updated_geo.modules_x == 1);
-        REQUIRE(updated_geo.modules_y == 1);
-        REQUIRE(updated_geo.module_pixel_0[0].height == 512);
-        REQUIRE(updated_geo.module_pixel_0[0].width == 1024);
-    }
-    SECTION("ROI is the top left corner of the module"){
-        aare::ROI roi;
-        roi.xmin = 100;
-        roi.xmax = 200;
-        roi.ymin = 150;
-        roi.ymax = 200;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 100);
-        REQUIRE(updated_geo.pixels_y == 50);
-        REQUIRE(updated_geo.modules_x == 1);
-        REQUIRE(updated_geo.modules_y == 1);
-        REQUIRE(updated_geo.module_pixel_0[0].height == 50);
-        REQUIRE(updated_geo.module_pixel_0[0].width == 100);
-    }
-
-    SECTION("ROI is a small square"){
-        aare::ROI roi;
-        roi.xmin = 1000;
-        roi.xmax = 1010;
-        roi.ymin = 500;
-        roi.ymax = 510;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 10);
-        REQUIRE(updated_geo.pixels_y == 10);
-        REQUIRE(updated_geo.modules_x == 1);
-        REQUIRE(updated_geo.modules_y == 1);
-        REQUIRE(updated_geo.module_pixel_0[0].height == 10);
-        REQUIRE(updated_geo.module_pixel_0[0].width == 10);
-    }
-    SECTION("ROI is a few columns"){
-        aare::ROI roi;
-        roi.xmin = 750;
-        roi.xmax = 800;
-        roi.ymin = 0;
-        roi.ymax = 512;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 50);
-        REQUIRE(updated_geo.pixels_y == 512);
-        REQUIRE(updated_geo.modules_x == 1);
-        REQUIRE(updated_geo.modules_y == 1);
-        REQUIRE(updated_geo.module_pixel_0[0].height == 512);
-        REQUIRE(updated_geo.module_pixel_0[0].width == 50);
-    }
-}
-
-
-
-TEST_CASE("Two modules side by side"){
-    // 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 = 2048;
-    geo.pixels_y = 512;
-    geo.modules_x = 2;
-    geo.modules_y = 1;
-
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 1024;
-    geo.module_pixel_0.push_back(mod);
-
-    SECTION("ROI is the whole image"){
-        aare::ROI roi;
-        roi.xmin = 0;
-        roi.xmax = 2048;
-        roi.ymin = 0;
-        roi.ymax = 512;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 2048);
-        REQUIRE(updated_geo.pixels_y == 512);
-        REQUIRE(updated_geo.modules_x == 2);
-        REQUIRE(updated_geo.modules_y == 1);
-    }
-    SECTION("rectangle on both modules"){
-        aare::ROI roi;
-        roi.xmin = 800;
-        roi.xmax = 1300;
-        roi.ymin = 200;
-        roi.ymax = 499;
-        auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-        REQUIRE(updated_geo.pixels_x == 500);
-        REQUIRE(updated_geo.pixels_y == 299);
-        REQUIRE(updated_geo.modules_x == 2);
-        REQUIRE(updated_geo.modules_y == 1);
-        REQUIRE(updated_geo.module_pixel_0[0].height == 299);
-        REQUIRE(updated_geo.module_pixel_0[0].width == 224);
-        REQUIRE(updated_geo.module_pixel_0[1].height == 299);
-        REQUIRE(updated_geo.module_pixel_0[1].width == 276);
-    }   
-}
-
-TEST_CASE("Three modules side by side"){
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
-    aare::DetectorGeometry geo;
-    aare::ROI roi;
-    roi.xmin = 700;
-    roi.xmax = 2500;
-    roi.ymin = 0;
-    roi.ymax = 123;
-
-    aare::ModuleGeometry mod; 
-    mod.origin_x = 0;
-    mod.origin_y = 0;
-    mod.width = 1024;
-    mod.height = 512;
-
-    geo.pixels_x = 3072;
-    geo.pixels_y = 512;
-    geo.modules_x = 3;
-    geo.modules_y = 1;
-
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 1024;
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 2048;
-    geo.module_pixel_0.push_back(mod);
-
-    auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-    REQUIRE(updated_geo.pixels_x == 1800);
-    REQUIRE(updated_geo.pixels_y == 123);
-    REQUIRE(updated_geo.modules_x == 3);
-    REQUIRE(updated_geo.modules_y == 1);
-    REQUIRE(updated_geo.module_pixel_0[0].height == 123);
-    REQUIRE(updated_geo.module_pixel_0[0].width == 324);
-    REQUIRE(updated_geo.module_pixel_0[1].height == 123);
-    REQUIRE(updated_geo.module_pixel_0[1].width == 1024);
-    REQUIRE(updated_geo.module_pixel_0[2].height == 123);
-    REQUIRE(updated_geo.module_pixel_0[2].width == 452);
-}
-
-TEST_CASE("Four modules as a square"){
-    // DetectorGeometry update_geometry_with_roi(DetectorGeometry geo, aare::ROI roi)
-    aare::DetectorGeometry geo;
-    aare::ROI roi;
-    roi.xmin = 500;
-    roi.xmax = 2000;
-    roi.ymin = 500;
-    roi.ymax = 600;
-
-    aare::ModuleGeometry mod; 
-    mod.origin_x = 0;
-    mod.origin_y = 0;
-    mod.width = 1024;
-    mod.height = 512;
-
-    geo.pixels_x = 2048;
-    geo.pixels_y = 1024;
-    geo.modules_x = 2;
-    geo.modules_y = 2;
-
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 1024;
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 0;
-    mod.origin_y = 512;
-    geo.module_pixel_0.push_back(mod);
-    mod.origin_x = 1024;
-    geo.module_pixel_0.push_back(mod);
-
-    auto updated_geo = aare::update_geometry_with_roi(geo, roi);
-
-    REQUIRE(updated_geo.pixels_x == 1500);
-    REQUIRE(updated_geo.pixels_y == 100);
-    REQUIRE(updated_geo.modules_x == 2);
-    REQUIRE(updated_geo.modules_y == 2);
-    REQUIRE(updated_geo.module_pixel_0[0].height == 12);
-    REQUIRE(updated_geo.module_pixel_0[0].width == 524);
-    REQUIRE(updated_geo.module_pixel_0[1].height == 12);
-    REQUIRE(updated_geo.module_pixel_0[1].width == 976);
-    REQUIRE(updated_geo.module_pixel_0[2].height == 88);
-    REQUIRE(updated_geo.module_pixel_0[2].width == 524);
-    REQUIRE(updated_geo.module_pixel_0[3].height == 88);
-    REQUIRE(updated_geo.module_pixel_0[3].width == 976);
-}

src/utils/ifstream_helpers.cpp

@@ -10,7 +10,7 @@ std::string ifstream_error_msg(std::ifstream &ifs) {
         return " Bad file stream";
     } else if (state & std::ios_base::failbit) {
         return " File read failed";
-    }else{
+    } else {
         return " Unknown/no error";
     }
 }

src/utils/task.test.cpp

@@ -1,10 +1,9 @@
 #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"){    
+TEST_CASE("Split a range into multiple tasks") {
 
     auto tasks = aare::split_task(0, 10, 3);
     REQUIRE(tasks.size() == 3);
@@ -22,11 +21,8 @@ TEST_CASE("Split a range into multiple tasks"){
 
     tasks = aare::split_task(0, 10, 10);
     REQUIRE(tasks.size() == 10);
-    for (int i = 0; i < 10; i++){
+    for (int i = 0; i < 10; i++) {
         REQUIRE(tasks[i].first == i);
-        REQUIRE(tasks[i].second == i+1);
+        REQUIRE(tasks[i].second == i + 1);
     }
-    
-
-
 }

tests/CMakeLists.txt

@@ -40,5 +40,8 @@ target_sources(tests PRIVATE ${TestSources} )
 #configure a header to pass test file paths
 get_filename_component(TEST_FILE_PATH ${PROJECT_SOURCE_DIR}/data ABSOLUTE)
 configure_file(test_config.hpp.in test_config.hpp)
-target_include_directories(tests PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+target_include_directories(tests PRIVATE ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
+
+
+
 

tests/friend_test.hpp

@@ -0,0 +1,4 @@
+#define FRIEND_TEST(test_name) friend void test_name##_impl();
+
+#define TEST_CASE_PRIVATE_FWD(test_name)                                       \
+    void test_name##_impl(); // foward declaration

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";