added test

.github/workflows/build_and_deploy_conda.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest] # macos-12, windows-2019]
+        platform: [ubuntu-latest, ] # macos-12, windows-2019]
         python-version: ["3.12",]
 
     runs-on: ${{ matrix.platform }}

.github/workflows/build_docs.yml

@@ -2,15 +2,11 @@ name: Build the package using cmake then documentation
 
 on:
   workflow_dispatch:
-  push:
   pull_request:
   release:
     types:
       - published
     
-env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE: Debug
 
 permissions:
   contents: read
@@ -22,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest, macos-latest] 
+        platform: [ubuntu-latest, ] 
         python-version: ["3.12",]
 
     runs-on: ${{ matrix.platform }}
@@ -43,20 +39,15 @@ jobs:
           channels: conda-forge
           conda-remove-defaults: "true"
 
-      - name: Build library and docs
+      - name: Build library 
         run: |
             mkdir build 
             cd build 
-            cmake .. -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DAARE_SYSTEM_LIBRARIES=ON -DAARE_PYTHON_BINDINGS=ON -DAARE_DOCS=ON -DAARE_TESTS=ON
-            make -j 4 
+            cmake .. -DAARE_SYSTEM_LIBRARIES=ON -DAARE_DOCS=ON 
+            make -j 2 
             make docs
 
-      - name: C++ unit tests
-        working-directory: ${{github.workspace}}/build
-        run: ctest -C ${{env.BUILD_TYPE}} -j4
-
       - name: Upload static files as artifact
-        if: matrix.platform == 'ubuntu-latest'
         id: deployment
         uses: actions/upload-pages-artifact@v3 
         with:

CMakeLists.txt

@@ -1,4 +1,3 @@
-# SPDX-License-Identifier: MPL-2.0
 cmake_minimum_required(VERSION 3.15)
 
 project(aare 
@@ -54,6 +53,7 @@ option(AARE_DOCS "Build documentation" OFF)
 option(AARE_VERBOSE "Verbose output" OFF)
 option(AARE_CUSTOM_ASSERT "Use custom assert" OFF)
 option(AARE_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/aare/" OFF)
+option(AARE_HDF5 "Hdf5 File Format" OFF)
 option(AARE_ASAN "Enable AddressSanitizer" OFF)
 
 # Configure which of the dependencies to use FetchContent for
@@ -78,6 +78,17 @@ if(AARE_SYSTEM_LIBRARIES)
     # on conda-forge
 endif()
 
+if(AARE_VERBOSE)
+    add_compile_definitions(AARE_VERBOSE)
+    add_compile_definitions(AARE_LOG_LEVEL=aare::logDEBUG5)
+else()
+    add_compile_definitions(AARE_LOG_LEVEL=aare::logINFOBLUE)
+endif()
+
+if(AARE_CUSTOM_ASSERT)
+    add_compile_definitions(AARE_CUSTOM_ASSERT)
+endif()
+
 if(AARE_BENCHMARKS)
     add_subdirectory(benchmarks)
 endif()
@@ -325,10 +336,13 @@ if(AARE_ASAN)
     )
 endif()
 
+
+
+
+
 if(AARE_TESTS)
     enable_testing()
     add_subdirectory(tests)
-    target_compile_definitions(tests PRIVATE AARE_TESTS)
 endif()
 
 ###------------------------------------------------------------------------------MAIN LIBRARY
@@ -343,6 +357,10 @@ set(PUBLICHEADERS
     include/aare/CtbRawFile.hpp
     include/aare/ClusterVector.hpp
     include/aare/decode.hpp
+    include/aare/type_traits.hpp
+    include/aare/scan_parameters.hpp
+    include/aare/to_string.hpp
+    include/aare/string_utils.hpp
     include/aare/defs.hpp
     include/aare/Dtype.hpp
     include/aare/File.hpp
@@ -351,7 +369,7 @@ set(PUBLICHEADERS
     include/aare/FilePtr.hpp
     include/aare/Frame.hpp
     include/aare/GainMap.hpp
-    include/aare/DetectorGeometry.hpp
+    include/aare/geo_helpers.hpp
     include/aare/JungfrauDataFile.hpp
     include/aare/logger.hpp
     include/aare/NDArray.hpp
@@ -369,27 +387,44 @@ set(PUBLICHEADERS
 
 
 set(SourceFiles
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/calibration.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/to_string.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/string_utils.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
     ${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/Frame.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolator.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolator.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/PixelMap.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
-) 
+)
+
+# HDF5
+if (AARE_HDF5)
+    find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
+	    add_definitions( 
+	        ${HDF5_DEFINITIONS}
+	    )
+	    list (APPEND PUBLICHEADERS 
+            include/aare/Hdf5File.hpp
+            include/aare/Hdf5MasterFile.hpp
+	    )
+	    list (APPEND SourceFiles 
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.cpp
+	    )
+endif (AARE_HDF5)
 
 add_library(aare_core STATIC ${SourceFiles})
 target_include_directories(aare_core PUBLIC 
@@ -413,20 +448,14 @@ target_link_libraries(
 
 )
 
-set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON)
-
-if(AARE_TESTS)
-    target_compile_definitions(aare_core PRIVATE AARE_TESTS)
-endif()
-if(AARE_VERBOSE)
-    target_compile_definitions(aare_core PUBLIC AARE_VERBOSE)
-    target_compile_definitions(aare_core PUBLIC AARE_LOG_LEVEL=aare::logDEBUG5)
-else()
-    target_compile_definitions(aare_core PUBLIC AARE_LOG_LEVEL=aare::logERROR)
-endif()
-
-if(AARE_CUSTOM_ASSERT)
-    target_compile_definitions(aare_core PUBLIC AARE_CUSTOM_ASSERT)
+if (AARE_HDF5 AND HDF5_FOUND)
+    add_definitions(-DHDF5_FOUND)
+    target_link_libraries(aare_core PUBLIC 
+        ${HDF5_LIBRARIES}
+    )
+    target_include_directories(aare_core PUBLIC
+        ${HDF5_INCLUDE_DIRS}
+    )
 endif()
 
 set_target_properties(aare_core PROPERTIES
@@ -434,16 +463,20 @@ set_target_properties(aare_core PROPERTIES
     PUBLIC_HEADER "${PUBLICHEADERS}"
 )
 
+if (AARE_PYTHON_BINDINGS)
+    set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON)
+endif()
+
 if(AARE_TESTS)
     set(TestSources
             ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/calibration.test.cpp
             ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/to_string.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/scan_parameters.test.cpp
             ${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/DetectorGeometry.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolation.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.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
@@ -462,10 +495,22 @@ if(AARE_TESTS)
             ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.test.cpp
 
         )
+    if(HDF5_FOUND)
+        list (APPEND TestSources 
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.test.cpp
+        )
+    endif() 
     target_sources(tests PRIVATE ${TestSources} )
 endif()
 
 
+
+
+###------------------------------------------------------------------------------------------
+###------------------------------------------------------------------------------------------
+
+
 if(AARE_MASTER_PROJECT)
     install(TARGETS aare_core aare_compiler_flags 
         EXPORT "${TARGETS_EXPORT_NAME}"
@@ -475,6 +520,7 @@ if(AARE_MASTER_PROJECT)
     )
 endif()
 
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_INSTALL_RPATH $ORIGIN)
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 

LICENSE

@@ -1,373 +0,0 @@
-Mozilla Public License Version 2.0
-==================================
-
-1. Definitions
---------------
-
-1.1. "Contributor"
-    means each individual or legal entity that creates, contributes to
-    the creation of, or owns Covered Software.
-
-1.2. "Contributor Version"
-    means the combination of the Contributions of others (if any) used
-    by a Contributor and that particular Contributor's Contribution.
-
-1.3. "Contribution"
-    means Covered Software of a particular Contributor.
-
-1.4. "Covered Software"
-    means Source Code Form to which the initial Contributor has attached
-    the notice in Exhibit A, the Executable Form of such Source Code
-    Form, and Modifications of such Source Code Form, in each case
-    including portions thereof.
-
-1.5. "Incompatible With Secondary Licenses"
-    means
-
-    (a) that the initial Contributor has attached the notice described
-        in Exhibit B to the Covered Software; or
-
-    (b) that the Covered Software was made available under the terms of
-        version 1.1 or earlier of the License, but not also under the
-        terms of a Secondary License.
-
-1.6. "Executable Form"
-    means any form of the work other than Source Code Form.
-
-1.7. "Larger Work"
-    means a work that combines Covered Software with other material, in 
-    a separate file or files, that is not Covered Software.
-
-1.8. "License"
-    means this document.
-
-1.9. "Licensable"
-    means having the right to grant, to the maximum extent possible,
-    whether at the time of the initial grant or subsequently, any and
-    all of the rights conveyed by this License.
-
-1.10. "Modifications"
-    means any of the following:
-
-    (a) any file in Source Code Form that results from an addition to,
-        deletion from, or modification of the contents of Covered
-        Software; or
-
-    (b) any new file in Source Code Form that contains any Covered
-        Software.
-
-1.11. "Patent Claims" of a Contributor
-    means any patent claim(s), including without limitation, method,
-    process, and apparatus claims, in any patent Licensable by such
-    Contributor that would be infringed, but for the grant of the
-    License, by the making, using, selling, offering for sale, having
-    made, import, or transfer of either its Contributions or its
-    Contributor Version.
-
-1.12. "Secondary License"
-    means either the GNU General Public License, Version 2.0, the GNU
-    Lesser General Public License, Version 2.1, the GNU Affero General
-    Public License, Version 3.0, or any later versions of those
-    licenses.
-
-1.13. "Source Code Form"
-    means the form of the work preferred for making modifications.
-
-1.14. "You" (or "Your")
-    means an individual or a legal entity exercising rights under this
-    License. For legal entities, "You" includes any entity that
-    controls, is controlled by, or is under common control with You. For
-    purposes of this definition, "control" means (a) the power, direct
-    or indirect, to cause the direction or management of such entity,
-    whether by contract or otherwise, or (b) ownership of more than
-    fifty percent (50%) of the outstanding shares or beneficial
-    ownership of such entity.
-
-2. License Grants and Conditions
---------------------------------
-
-2.1. Grants
-
-Each Contributor hereby grants You a world-wide, royalty-free,
-non-exclusive license:
-
-(a) under intellectual property rights (other than patent or trademark)
-    Licensable by such Contributor to use, reproduce, make available,
-    modify, display, perform, distribute, and otherwise exploit its
-    Contributions, either on an unmodified basis, with Modifications, or
-    as part of a Larger Work; and
-
-(b) under Patent Claims of such Contributor to make, use, sell, offer
-    for sale, have made, import, and otherwise transfer either its
-    Contributions or its Contributor Version.
-
-2.2. Effective Date
-
-The licenses granted in Section 2.1 with respect to any Contribution
-become effective for each Contribution on the date the Contributor first
-distributes such Contribution.
-
-2.3. Limitations on Grant Scope
-
-The licenses granted in this Section 2 are the only rights granted under
-this License. No additional rights or licenses will be implied from the
-distribution or licensing of Covered Software under this License.
-Notwithstanding Section 2.1(b) above, no patent license is granted by a
-Contributor:
-
-(a) for any code that a Contributor has removed from Covered Software;
-    or
-
-(b) for infringements caused by: (i) Your and any other third party's
-    modifications of Covered Software, or (ii) the combination of its
-    Contributions with other software (except as part of its Contributor
-    Version); or
-
-(c) under Patent Claims infringed by Covered Software in the absence of
-    its Contributions.
-
-This License does not grant any rights in the trademarks, service marks,
-or logos of any Contributor (except as may be necessary to comply with
-the notice requirements in Section 3.4).
-
-2.4. Subsequent Licenses
-
-No Contributor makes additional grants as a result of Your choice to
-distribute the Covered Software under a subsequent version of this
-License (see Section 10.2) or under the terms of a Secondary License (if
-permitted under the terms of Section 3.3).
-
-2.5. Representation
-
-Each Contributor represents that the Contributor believes its
-Contributions are its original creation(s) or it has sufficient rights
-to grant the rights to its Contributions conveyed by this License.
-
-2.6. Fair Use
-
-This License is not intended to limit any rights You have under
-applicable copyright doctrines of fair use, fair dealing, or other
-equivalents.
-
-2.7. Conditions
-
-Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
-in Section 2.1.
-
-3. Responsibilities
--------------------
-
-3.1. Distribution of Source Form
-
-All distribution of Covered Software in Source Code Form, including any
-Modifications that You create or to which You contribute, must be under
-the terms of this License. You must inform recipients that the Source
-Code Form of the Covered Software is governed by the terms of this
-License, and how they can obtain a copy of this License. You may not
-attempt to alter or restrict the recipients' rights in the Source Code
-Form.
-
-3.2. Distribution of Executable Form
-
-If You distribute Covered Software in Executable Form then:
-
-(a) such Covered Software must also be made available in Source Code
-    Form, as described in Section 3.1, and You must inform recipients of
-    the Executable Form how they can obtain a copy of such Source Code
-    Form by reasonable means in a timely manner, at a charge no more
-    than the cost of distribution to the recipient; and
-
-(b) You may distribute such Executable Form under the terms of this
-    License, or sublicense it under different terms, provided that the
-    license for the Executable Form does not attempt to limit or alter
-    the recipients' rights in the Source Code Form under this License.
-
-3.3. Distribution of a Larger Work
-
-You may create and distribute a Larger Work under terms of Your choice,
-provided that You also comply with the requirements of this License for
-the Covered Software. If the Larger Work is a combination of Covered
-Software with a work governed by one or more Secondary Licenses, and the
-Covered Software is not Incompatible With Secondary Licenses, this
-License permits You to additionally distribute such Covered Software
-under the terms of such Secondary License(s), so that the recipient of
-the Larger Work may, at their option, further distribute the Covered
-Software under the terms of either this License or such Secondary
-License(s).
-
-3.4. Notices
-
-You may not remove or alter the substance of any license notices
-(including copyright notices, patent notices, disclaimers of warranty,
-or limitations of liability) contained within the Source Code Form of
-the Covered Software, except that You may alter any license notices to
-the extent required to remedy known factual inaccuracies.
-
-3.5. Application of Additional Terms
-
-You may choose to offer, and to charge a fee for, warranty, support,
-indemnity or liability obligations to one or more recipients of Covered
-Software. However, You may do so only on Your own behalf, and not on
-behalf of any Contributor. You must make it absolutely clear that any
-such warranty, support, indemnity, or liability obligation is offered by
-You alone, and You hereby agree to indemnify every Contributor for any
-liability incurred by such Contributor as a result of warranty, support,
-indemnity or liability terms You offer. You may include additional
-disclaimers of warranty and limitations of liability specific to any
-jurisdiction.
-
-4. Inability to Comply Due to Statute or Regulation
----------------------------------------------------
-
-If it is impossible for You to comply with any of the terms of this
-License with respect to some or all of the Covered Software due to
-statute, judicial order, or regulation then You must: (a) comply with
-the terms of this License to the maximum extent possible; and (b)
-describe the limitations and the code they affect. Such description must
-be placed in a text file included with all distributions of the Covered
-Software under this License. Except to the extent prohibited by statute
-or regulation, such description must be sufficiently detailed for a
-recipient of ordinary skill to be able to understand it.
-
-5. Termination
---------------
-
-5.1. The rights granted under this License will terminate automatically
-if You fail to comply with any of its terms. However, if You become
-compliant, then the rights granted under this License from a particular
-Contributor are reinstated (a) provisionally, unless and until such
-Contributor explicitly and finally terminates Your grants, and (b) on an
-ongoing basis, if such Contributor fails to notify You of the
-non-compliance by some reasonable means prior to 60 days after You have
-come back into compliance. Moreover, Your grants from a particular
-Contributor are reinstated on an ongoing basis if such Contributor
-notifies You of the non-compliance by some reasonable means, this is the
-first time You have received notice of non-compliance with this License
-from such Contributor, and You become compliant prior to 30 days after
-Your receipt of the notice.
-
-5.2. If You initiate litigation against any entity by asserting a patent
-infringement claim (excluding declaratory judgment actions,
-counter-claims, and cross-claims) alleging that a Contributor Version
-directly or indirectly infringes any patent, then the rights granted to
-You by any and all Contributors for the Covered Software under Section
-2.1 of this License shall terminate.
-
-5.3. In the event of termination under Sections 5.1 or 5.2 above, all
-end user license agreements (excluding distributors and resellers) which
-have been validly granted by You or Your distributors under this License
-prior to termination shall survive termination.
-
-************************************************************************
-*                                                                      *
-*  6. Disclaimer of Warranty                                           *
-*  -------------------------                                           *
-*                                                                      *
-*  Covered Software is provided under this License on an "as is"       *
-*  basis, without warranty of any kind, either expressed, implied, or  *
-*  statutory, including, without limitation, warranties that the       *
-*  Covered Software is free of defects, merchantable, fit for a        *
-*  particular purpose or non-infringing. The entire risk as to the     *
-*  quality and performance of the Covered Software is with You.        *
-*  Should any Covered Software prove defective in any respect, You     *
-*  (not any Contributor) assume the cost of any necessary servicing,   *
-*  repair, or correction. This disclaimer of warranty constitutes an   *
-*  essential part of this License. No use of any Covered Software is   *
-*  authorized under this License except under this disclaimer.         *
-*                                                                      *
-************************************************************************
-
-************************************************************************
-*                                                                      *
-*  7. Limitation of Liability                                          *
-*  --------------------------                                          *
-*                                                                      *
-*  Under no circumstances and under no legal theory, whether tort      *
-*  (including negligence), contract, or otherwise, shall any           *
-*  Contributor, or anyone who distributes Covered Software as          *
-*  permitted above, be liable to You for any direct, indirect,         *
-*  special, incidental, or consequential damages of any character      *
-*  including, without limitation, damages for lost profits, loss of    *
-*  goodwill, work stoppage, computer failure or malfunction, or any    *
-*  and all other commercial damages or losses, even if such party      *
-*  shall have been informed of the possibility of such damages. This   *
-*  limitation of liability shall not apply to liability for death or   *
-*  personal injury resulting from such party's negligence to the       *
-*  extent applicable law prohibits such limitation. Some               *
-*  jurisdictions do not allow the exclusion or limitation of           *
-*  incidental or consequential damages, so this exclusion and          *
-*  limitation may not apply to You.                                    *
-*                                                                      *
-************************************************************************
-
-8. Litigation
--------------
-
-Any litigation relating to this License may be brought only in the
-courts of a jurisdiction where the defendant maintains its principal
-place of business and such litigation shall be governed by laws of that
-jurisdiction, without reference to its conflict-of-law provisions.
-Nothing in this Section shall prevent a party's ability to bring
-cross-claims or counter-claims.
-
-9. Miscellaneous
-----------------
-
-This License represents the complete agreement concerning the subject
-matter hereof. If any provision of this License is held to be
-unenforceable, such provision shall be reformed only to the extent
-necessary to make it enforceable. Any law or regulation which provides
-that the language of a contract shall be construed against the drafter
-shall not be used to construe this License against a Contributor.
-
-10. Versions of the License
----------------------------
-
-10.1. New Versions
-
-Mozilla Foundation is the license steward. Except as provided in Section
-10.3, no one other than the license steward has the right to modify or
-publish new versions of this License. Each version will be given a
-distinguishing version number.
-
-10.2. Effect of New Versions
-
-You may distribute the Covered Software under the terms of the version
-of the License under which You originally received the Covered Software,
-or under the terms of any subsequent version published by the license
-steward.
-
-10.3. Modified Versions
-
-If you create software not governed by this License, and you want to
-create a new license for such software, you may create and use a
-modified version of this License if you rename the license and remove
-any references to the name of the license steward (except to note that
-such modified license differs from this License).
-
-10.4. Distributing Source Code Form that is Incompatible With Secondary
-Licenses
-
-If You choose to distribute Source Code Form that is Incompatible With
-Secondary Licenses under the terms of this version of the License, the
-notice described in Exhibit B of this License must be attached.
-
-Exhibit A - Source Code Form License Notice
--------------------------------------------
-
-  This Source Code Form is subject to the terms of the Mozilla Public
-  License, v. 2.0. If a copy of the MPL was not distributed with this
-  file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-If it is not possible or desirable to put the notice in a particular
-file, then You may include the notice in a location (such as a LICENSE
-file in a relevant directory) where a recipient would be likely to look
-for such a notice.
-
-You may add additional accurate notices of copyright ownership.
-
-Exhibit B - "Incompatible With Secondary Licenses" Notice
----------------------------------------------------------
-
-  This Source Code Form is "Incompatible With Secondary Licenses", as
-  defined by the Mozilla Public License, v. 2.0.

README.md

@@ -1,14 +1,6 @@
 # aare
 Data analysis library for PSI hybrid detectors
 
-## Documentation 
-
-Detailed documentation including installation can be found in [Documentation](https://slsdetectorgroup.github.io/aare/)
-
-## License
-
-This project is licensed under the MPL-2.0 license.
-See the LICENSE file or https://www.mozilla.org/en-US/MPL/ for details.
 
 ## Build and install
 

RELEASE.md

@@ -1,76 +1,14 @@
 # Release notes
 
-## head
 
-### New Features:
-
-- Expanding 24 to 32 bit data
-- Decoding digital data from Mythen 302
-
-
-### 2025.11.21
-
-### New Features: 
-
-- Added SPDX-License-Identifier: MPL-2.0 to source files
-- Calculate Eta3 supports all cluster types 
-- interpolation class supports using cross eta3x3 and eta3x3 on full cluster as well as eta2x2 on full cluster
-- interpolation class has option to calculate the rosenblatt transform 
-- reduction operations to reduce Clusters of general size to 2x2 or 3x3 clusters 
-- `max_sum_2x2` including index of subcluster with highest energy is now available from Python API 
-- interpolation supports bilinear interpolation of eta values for more fine grained transformed uniform coordinates
-- Interpolation is documented 
-
-- Added tell to ClusterFile. Returns position in bytes for debugging
-
-### Resolved Features: 
-
-- calculate_eta coincides with theoretical definition
-
-### Bugfixes: 
-
-- eta calculation assumes correct photon center 
-- eta transformation to uniform coordinates starts at 0
-- Bug in interpolation 
-- File supports reading new master json file format (multiple ROI's not supported yet)
-
-
-### API Changes: 
-
-- ClusterFinder for 2x2 Cluster disabled 
-- eta stores corner as enum class cTopLeft, cTopRight, BottomLeft, cBottomRight indicating 2x2 subcluster with largest energy relative to cluster center 
-- max_sum_2x2 returns corner as index 
-
-### 2025.8.22
-
-Features:
-
-- Apply calibration works in G0 if passes a 2D calibration and pedestal
-- count pixels that switch
-- calculate pedestal (also g0 version)
-- NDArray::view() needs an lvalue to reduce issues with the view outliving the array
-
-
-Bugfixes:
-
-- Now using glibc 2.17 in conda builds (was using the host)
-- Fixed shifted pixels in clusters close to the edge of a frame
-
-### 2025.7.18
+### head
 
 Features:
 
 - Cluster finder now works with 5x5, 7x7 and 9x9 clusters
-- Added ClusterVector::empty() member
-- Added apply_calibration function for Jungfrau data
-
-Bugfixes:
-- Fixed reading RawFiles with ROI fully excluding some sub files. 
-- Decoding of MH02 files placed the pixels in wrong position
-- Removed unused file: ClusterFile.cpp 
 
 
-### 2025.5.22
+### 2025.05.22
 
 Features:
 
@@ -80,34 +18,5 @@ Bugfixes:
 
 - Fixed crash when opening raw files with large number of data files
 
-## Download, Documentation & Support 
-
-### Download
-
-The Source Code: 
-https://github.com/slsdetectorgroup/aare
-
-
-### Documentation 
-
-
-Documentation including installation details: 
-https://github.com/slsdetectorgroup/aare 
-
-
-### Support
-
-
-erik.frojdh@psi.ch \
-alice.mazzoleni@psi.ch \
-dhanya.thattil@psi.ch
-
-
-
-
-
-
-
-
 
 

VERSION

@@ -1 +1 @@
-2025.11.21
+2025.5.22

benchmarks/CMakeLists.txt

@@ -1,4 +1,3 @@
-# SPDX-License-Identifier: MPL-2.0
 
 include(FetchContent)
 
@@ -16,7 +15,7 @@ FetchContent_MakeAvailable(benchmark)
 
 add_executable(benchmarks)
 
-target_sources(benchmarks PRIVATE ndarray_benchmark.cpp calculateeta_benchmark.cpp reduce_benchmark.cpp)
+target_sources(benchmarks PRIVATE ndarray_benchmark.cpp calculateeta_benchmark.cpp)
 
 # Link Google Benchmark and other necessary libraries
 target_link_libraries(benchmarks PRIVATE benchmark::benchmark aare_core aare_compiler_flags)

benchmarks/calculateeta_benchmark.cpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #include "aare/CalculateEta.hpp"
 #include "aare/ClusterFile.hpp"
 #include <benchmark/benchmark.h>
@@ -9,7 +8,6 @@ class ClusterFixture : public benchmark::Fixture {
   public:
     Cluster<int, 2, 2> cluster_2x2{};
     Cluster<int, 3, 3> cluster_3x3{};
-    Cluster<int, 4, 4> cluster_4x4{};
 
   private:
     using benchmark::Fixture::SetUp;
@@ -28,13 +26,6 @@ class ClusterFixture : public benchmark::Fixture {
 
         cluster_3x3.x = 0;
         cluster_3x3.y = 0;
-
-        int temp_data3[16] = {1, 2,  3,  4,  5,  6,  7,  8,
-                              9, 10, 11, 12, 13, 14, 15, 16};
-        std::copy(std::begin(temp_data3), std::end(temp_data3),
-                  std::begin(cluster_4x4.data));
-        cluster_4x4.x = 0;
-        cluster_4x4.y = 0;
     }
 
     // void TearDown(::benchmark::State& state) {
@@ -76,29 +67,4 @@ BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor3x3Cluster)
         benchmark::DoNotOptimize(eta);
     }
 }
-
-BENCHMARK_F(ClusterFixture, Calculate2x2Etawithreduction)
-(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        auto reduced_cluster = reduce_to_2x2(cluster_4x4);
-        Eta2 eta = calculate_eta2(reduced_cluster);
-        auto reduced_cluster_from_3x3 = reduce_to_2x2(cluster_3x3);
-        Eta2 eta2 = calculate_eta2(reduced_cluster_from_3x3);
-        benchmark::DoNotOptimize(eta);
-        benchmark::DoNotOptimize(eta2);
-    }
-}
-
-BENCHMARK_F(ClusterFixture, Calculate2x2Etawithoutreduction)
-(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        Eta2 eta = calculate_eta2(cluster_4x4);
-        Eta2 eta2 = calculate_eta2(cluster_3x3);
-        benchmark::DoNotOptimize(eta);
-        benchmark::DoNotOptimize(eta2);
-    }
-}
-
 // BENCHMARK_MAIN();

benchmarks/ndarray_benchmark.cpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #include "aare/NDArray.hpp"
 #include <benchmark/benchmark.h>
 

benchmarks/reduce_benchmark.cpp

@@ -1,169 +0,0 @@
-// SPDX-License-Identifier: MPL-2.0
-#include "aare/Cluster.hpp"
-#include <benchmark/benchmark.h>
-
-using namespace aare;
-
-class ClustersForReduceFixture : public benchmark::Fixture {
-  public:
-    Cluster<int, 5, 5> cluster_5x5{};
-    Cluster<int, 3, 3> cluster_3x3{};
-
-  private:
-    using benchmark::Fixture::SetUp;
-
-    void SetUp([[maybe_unused]] const benchmark::State &state) override {
-        int temp_data[25] = {1, 1, 1, 1, 1, 1, 1, 2, 1, 1,
-                             1, 2, 3, 1, 2, 1, 1, 1, 1, 2};
-        std::copy(std::begin(temp_data), std::end(temp_data),
-                  std::begin(cluster_5x5.data));
-
-        cluster_5x5.x = 5;
-        cluster_5x5.y = 5;
-
-        int temp_data2[9] = {1, 1, 1, 2, 3, 1, 2, 2, 1};
-        std::copy(std::begin(temp_data2), std::end(temp_data2),
-                  std::begin(cluster_3x3.data));
-
-        cluster_3x3.x = 5;
-        cluster_3x3.y = 5;
-    }
-
-    // void TearDown(::benchmark::State& state) {
-    // }
-};
-
-template <typename T>
-Cluster<T, 3, 3, uint16_t> reduce_to_3x3(const Cluster<T, 5, 5, uint16_t> &c) {
-    Cluster<T, 3, 3, uint16_t> result;
-
-    // Write out the sums in the hope that the compiler can optimize this
-    std::array<T, 9> sum_3x3_subclusters;
-
-    // Write out the sums in the hope that the compiler can optimize this
-    sum_3x3_subclusters[0] = c.data[0] + c.data[1] + c.data[2] + c.data[5] +
-                             c.data[6] + c.data[7] + c.data[10] + c.data[11] +
-                             c.data[12];
-    sum_3x3_subclusters[1] = c.data[1] + c.data[2] + c.data[3] + c.data[6] +
-                             c.data[7] + c.data[8] + c.data[11] + c.data[12] +
-                             c.data[13];
-    sum_3x3_subclusters[2] = c.data[2] + c.data[3] + c.data[4] + c.data[7] +
-                             c.data[8] + c.data[9] + c.data[12] + c.data[13] +
-                             c.data[14];
-    sum_3x3_subclusters[3] = c.data[5] + c.data[6] + c.data[7] + c.data[10] +
-                             c.data[11] + c.data[12] + c.data[15] + c.data[16] +
-                             c.data[17];
-    sum_3x3_subclusters[4] = c.data[6] + c.data[7] + c.data[8] + c.data[11] +
-                             c.data[12] + c.data[13] + c.data[16] + c.data[17] +
-                             c.data[18];
-    sum_3x3_subclusters[5] = c.data[7] + c.data[8] + c.data[9] + c.data[12] +
-                             c.data[13] + c.data[14] + c.data[17] + c.data[18] +
-                             c.data[19];
-    sum_3x3_subclusters[6] = c.data[10] + c.data[11] + c.data[12] + c.data[15] +
-                             c.data[16] + c.data[17] + c.data[20] + c.data[21] +
-                             c.data[22];
-    sum_3x3_subclusters[7] = c.data[11] + c.data[12] + c.data[13] + c.data[16] +
-                             c.data[17] + c.data[18] + c.data[21] + c.data[22] +
-                             c.data[23];
-    sum_3x3_subclusters[8] = c.data[12] + c.data[13] + c.data[14] + c.data[17] +
-                             c.data[18] + c.data[19] + c.data[22] + c.data[23] +
-                             c.data[24];
-
-    auto index = std::max_element(sum_3x3_subclusters.begin(),
-                                  sum_3x3_subclusters.end()) -
-                 sum_3x3_subclusters.begin();
-
-    switch (index) {
-    case 0:
-        result.x = c.x - 1;
-        result.y = c.y + 1;
-        result.data = {c.data[0], c.data[1],  c.data[2],  c.data[5], c.data[6],
-                       c.data[7], c.data[10], c.data[11], c.data[12]};
-        break;
-    case 1:
-        result.x = c.x;
-        result.y = c.y + 1;
-        result.data = {c.data[1], c.data[2],  c.data[3],  c.data[6], c.data[7],
-                       c.data[8], c.data[11], c.data[12], c.data[13]};
-        break;
-    case 2:
-        result.x = c.x + 1;
-        result.y = c.y + 1;
-        result.data = {c.data[2], c.data[3],  c.data[4],  c.data[7], c.data[8],
-                       c.data[9], c.data[12], c.data[13], c.data[14]};
-        break;
-    case 3:
-        result.x = c.x - 1;
-        result.y = c.y;
-        result.data = {c.data[5],  c.data[6],  c.data[7],
-                       c.data[10], c.data[11], c.data[12],
-                       c.data[15], c.data[16], c.data[17]};
-        break;
-    case 4:
-        result.x = c.x + 1;
-        result.y = c.y;
-        result.data = {c.data[6],  c.data[7],  c.data[8],
-                       c.data[11], c.data[12], c.data[13],
-                       c.data[16], c.data[17], c.data[18]};
-        break;
-    case 5:
-        result.x = c.x + 1;
-        result.y = c.y;
-        result.data = {c.data[7],  c.data[8],  c.data[9],
-                       c.data[12], c.data[13], c.data[14],
-                       c.data[17], c.data[18], c.data[19]};
-        break;
-    case 6:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[10], c.data[11], c.data[12],
-                       c.data[15], c.data[16], c.data[17],
-                       c.data[20], c.data[21], c.data[22]};
-        break;
-    case 7:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[11], c.data[12], c.data[13],
-                       c.data[16], c.data[17], c.data[18],
-                       c.data[21], c.data[22], c.data[23]};
-        break;
-    case 8:
-        result.x = c.x + 1;
-        result.y = c.y - 1;
-        result.data = {c.data[12], c.data[13], c.data[14],
-                       c.data[17], c.data[18], c.data[19],
-                       c.data[22], c.data[23], c.data[24]};
-        break;
-    }
-    return result;
-}
-
-BENCHMARK_F(ClustersForReduceFixture, Reduce2x2)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_2x2<int, 3, 3, uint16_t>(
-            cluster_3x3)); // make sure compiler evaluates the expression
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, SpecificReduce2x2)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_2x2<int>(cluster_3x3));
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, Reduce3x3)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(
-            reduce_to_3x3<int, 5, 5, uint16_t>(cluster_5x5));
-    }
-}
-
-BENCHMARK_F(ClustersForReduceFixture, SpecificReduce3x3)(benchmark::State &st) {
-    for (auto _ : st) {
-        // This code gets timed
-        benchmark::DoNotOptimize(reduce_to_3x3<int>(cluster_5x5));
-    }
-}

conda-recipe/conda_build_config.yaml

@@ -3,14 +3,3 @@ python:
     - 3.12
     - 3.13
 
-c_compiler:
-  - gcc                        # [linux]
-
-c_stdlib:
-  - sysroot                    # [linux]
-
-cxx_compiler:
-  - gxx                        # [linux]
-
-c_stdlib_version:              # [linux]
-  - 2.17                       # [linux]

conda-recipe/meta.yaml

@@ -16,8 +16,6 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
-    - {{ stdlib("c") }}
     - {{ compiler('cxx') }}
     - cmake
     - ninja
@@ -49,5 +47,4 @@ test:
     - python -m pytest python/tests
 
 about:
-  license: SPDX-License-Identifier MPL-2.0
   summary: Data analysis library for hybrid pixel detectors from PSI 

docs/CMakeLists.txt

@@ -1,4 +1,3 @@
-# SPDX-License-Identifier: MPL-2.0
 find_package(Doxygen REQUIRED)
 find_package(Sphinx REQUIRED)
 
@@ -12,19 +11,14 @@ set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR})
 
 
-file(GLOB_RECURSE SPHINX_SOURCE_FILES
-     CONFIGURE_DEPENDS
-     RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}/src"
-     "${CMAKE_CURRENT_SOURCE_DIR}/src/*.rst"
-)
+file(GLOB SPHINX_SOURCE_FILES CONFIGURE_DEPENDS "src/*.rst")
 
-foreach(relpath IN LISTS SPHINX_SOURCE_FILES)
-    set(src  "${CMAKE_CURRENT_SOURCE_DIR}/src/${relpath}")
-    set(dst  "${SPHINX_BUILD}/src/${relpath}")
 
-    message(STATUS "Copying ${src} to ${dst}")
-    configure_file("${src}" "${dst}" COPYONLY)
-endforeach()
+foreach(filename ${SPHINX_SOURCE_FILES})
+    get_filename_component(fname ${filename} NAME)
+    message(STATUS "Copying ${filename} to ${SPHINX_BUILD}/src/${fname}")
+    configure_file(${filename} "${SPHINX_BUILD}/src/${fname}")  
+endforeach(filename ${SPHINX_SOURCE_FILES})
 
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in"
@@ -32,8 +26,6 @@ configure_file(
     @ONLY
 )
 
-file(COPY "${CMAKE_CURRENT_SOURCE_DIR}/figures"
-     DESTINATION "${SPHINX_BUILD}") 
 
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/static/extra.css"
@@ -52,3 +44,12 @@ add_custom_target(
     COMMENT "Generating documentation with Sphinx"
 )
 
+add_custom_target(
+    rst
+    COMMAND ${SPHINX_EXECUTABLE} -a -b html
+    -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml
+    -c "${SPHINX_BUILD}"
+    ${SPHINX_BUILD}/src 
+    ${SPHINX_BUILD}/html
+    COMMENT "Generating documentation with Sphinx"
+)

docs/Doxyfile.in

@@ -886,7 +886,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = *build* */docs/* */tests/* *.test.cpp* */python/* */manual */slsDetectorServers/* */libs/* */integrationTests *README* *_deps* *TobiSchluter*
+EXCLUDE_PATTERNS       = */docs/* */tests/* */python/* */manual */slsDetectorServers/* */libs/* */integrationTests *README* */slsDetectorGui/* */ctbGui/* */slsDetectorCalibration/* *TobiSchluter*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

docs/src/Cluster.rst

@@ -1,15 +0,0 @@
-Cluster
-========
-
-.. doxygenstruct:: aare::Cluster
-   :members:
-   :undoc-members:
-   :private-members:
-
-
-**Free Functions:** 
-
-.. doxygenfunction:: aare::reduce_to_3x3(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>&)
-   
-.. doxygenfunction:: aare::reduce_to_2x2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>&)
-   

docs/src/ClusterFile.rst

@@ -4,5 +4,4 @@ ClusterFile
 .. doxygenclass:: aare::ClusterFile
    :members:
    :undoc-members:
-   :private-members:
-
+   :private-members:

docs/src/ClusterVector.rst

@@ -3,20 +3,4 @@ ClusterVector
 
 .. doxygenclass:: aare::ClusterVector
    :members:
-   :undoc-members:
-   :private-members:
-
-
-
-.. doxygenclass:: aare::ClusterVector< Cluster< T, ClusterSizeX, ClusterSizeY, CoordType > > 
-   :members:
-   :undoc-members:
-   :private-members:
-   
-
-**Free Functions:** 
-
-.. doxygenfunction:: aare::reduce_to_3x3(const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>&)
-   
-.. doxygenfunction:: aare::reduce_to_2x2(const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>&)
-   
+   :undoc-members:

docs/src/Hdf5File.rst

@@ -0,0 +1,8 @@
+Hdf5File
+===============
+
+
+.. doxygenclass:: aare::Hdf5File
+   :members:
+   :undoc-members:
+   :private-members:

docs/src/Hdf5MasterFile.rst

@@ -0,0 +1,14 @@
+Hdf5MasterFile
+===============
+
+
+.. doxygenclass:: aare::Hdf5MasterFile
+   :members:
+   :undoc-members:
+   :private-members:
+
+
+.. doxygenclass:: aare::Hdf5FileNameComponents
+   :members:
+   :undoc-members:
+   :private-members:

docs/src/Interpolation.rst

@@ -1,102 +0,0 @@
-Interpolation
-==============
-
-Interpolation class for :math:`\eta` Interpolation. 
-
-The Interpolator class provides methods to interpolate the positions of photons based on their :math:`\eta` values. 
-
-.. warning:: 
-   The interpolation might lead to erroneous photon positions for clusters at the boarders of a frame. Make sure to filter out such cases. 
-
-:math:`\eta`-Functions: 
----------------------------
-
-.. doxygenstruct:: aare::Eta2
-    :members: 
-    :undoc-members: 
-    :private-members: 
-
-.. note::
-    The corner value ``c`` is only relevant when one uses ``calculate_eta_2`` or ``calculate_full_eta2``. Otherwise its default value is ``cTopLeft``. 
-
-Supported are the following :math:`\eta`-functions: 
-
-
-.. image:: ../figures/Eta2x2.png
-    :target: ../figures/Eta2x2.png
-    :width: 650px
-    :align: center
-    :alt: Eta2x2
-
-.. math:: 
-    \begin{equation*}
-   {\color{blue}{\eta_x}} = \frac{Q_{1,1}}{Q_{1,0} + Q_{1,1}} \quad \quad 
-   {\color{green}{\eta_y}} = \frac{Q_{1,1}}{Q_{0,1} + Q_{1,1}}
-   \end{equation*}
-
-
-.. doxygenfunction:: aare::calculate_eta2(const ClusterVector<ClusterType>&)
-
-.. doxygenfunction:: aare::calculate_eta2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>&) 
-
-.. image:: ../figures/Eta2x2Full.png
-    :target: ../figures/Eta2x2Full.png
-    :width: 650px
-    :align: center
-    :alt: Eta2x2 Full 
-
-.. math:: 
-    \begin{equation*}
-        {\color{blue}{\eta_x}}  = \frac{Q_{0,1} + Q_{1,1}}{\sum_i^{2}\sum_j^{2}Q_{i,j}} \quad \quad
-        {\textcolor{green}{\eta_y}} = \frac{Q_{1,0} + Q_{1,1}}{\sum_i^{2}\sum_j^{2}Q_{i,j}}
-    \end{equation*} 
-
-
-.. doxygenfunction:: aare::calculate_full_eta2(const ClusterVector<ClusterType>&)
-
-.. doxygenfunction:: aare::calculate_full_eta2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>&)
-
-.. image:: ../figures/Eta3x3.png
-    :target: ../figures/Eta3x3.png
-    :width: 650px
-    :align: center
-    :alt: Eta3x3
-
-.. math::
-    \begin{equation*}
-         {\color{blue}{\eta_x}} = \frac{\sum_{i}^{3} Q_{i,2} - \sum_{i}^{3} Q_{i,0}}{\sum_{i}^{3}\sum_{j}^{3} Q_{i,j}} \quad \quad
-        {\color{green}{\eta_y}} = \frac{\sum_{j}^{3} Q_{2,j} - \sum_{j}^{3} Q_{0,j}}{\sum_{i}^{3}\sum_{j}^{3} Q_{i,j}}
-    \end{equation*}
-
-.. doxygenfunction:: aare::calculate_eta3(const ClusterVector<Cluster<T, 3,3, CoordType>>&)
-
-.. doxygenfunction:: aare::calculate_eta3(const Cluster<T, 3, 3, CoordType>&)
-
-.. image:: ../figures/Eta3x3Cross.png
-    :target: ../figures/Eta3x3Cross.png
-    :width: 650px
-    :align: center
-    :alt: Cross Eta3x3
-
-.. math:: 
-    \begin{equation*}
-       {\color{blue}{\eta_x}} = \frac{Q_{1,2} - Q_{1,0}}{Q_{1,0} +  Q_{1,1} + Q_{1,0}} \quad \quad
-        {\color{green}{\eta_y}} = \frac{Q_{0,2} - Q_{0,1}}{Q_{0,1} +  Q_{1,1} + Q_{1,2}}
-    \end{equation*}
-
-.. doxygenfunction:: aare::calculate_cross_eta3(const ClusterVector<Cluster<T, 3,3, CoordType>>&)
-
-.. doxygenfunction:: aare::calculate_cross_eta3(const Cluster<T, 3, 3, CoordType>&)
-
-Interpolation class: 
----------------------
-
-.. Warning:: 
-    Make sure to use the same :math:`\eta`-function during interpolation as given by the joint :math:`\eta`-distribution passed to the constructor. 
-
-.. doxygenclass:: aare::Interpolator
-   :members:
-   :undoc-members:
-   :private-members:
-
-

docs/src/Tests.rst

@@ -2,7 +2,7 @@
 Tests
 ****************
 
-We test the code both from C++ and Python. By default only tests that does not require additional data are run.
+We test the code both from the C++ and Python API. By default only tests that does not require image data is run. 
 
 C++
 ~~~~~~~~~~~~~~~~~~
@@ -15,7 +15,7 @@ C++
     make -j 4
 
     export AARE_TEST_DATA=/path/to/test/data
-    ./run_test [.with-data] #or using ctest, [.with-data] is the option to include tests needing data
+    ./run_test [.files] #or using ctest, [.files] is the option to include tests needing data
 
 
 
@@ -25,7 +25,7 @@ Python
 .. code-block:: bash
 
     #From the root dir of the library
-    python -m pytest python/tests --with-data # passing --with-data will run the tests needing data
+    python -m pytest python/tests --files # passing --files will run the tests needing data
 
 
 
@@ -35,7 +35,7 @@ Getting the test data
 .. attention ::
 
     The tests needing the test data are not run by default. To make the data available, you need to set the environment variable
-    AARE_TEST_DATA to the path of the test data directory. Then pass either [.with-data] for the C++ tests or --files for Python
+    AARE_TEST_DATA to the path of the test data directory. Then pass either [.files] for the C++ tests or --files for Python
 
 The image files needed for the test are large and are not included in the repository. They are stored
 using GIT LFS in a separate repository. To get the test data, you need to clone the repository.

docs/src/Workflow.rst

@@ -37,7 +37,7 @@ unfamiliar steps.
 
 
 Checklists for deployment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~
 
 **Feature:**
 

docs/src/index.rst

@@ -22,14 +22,20 @@ AARE
 
 .. toctree::
     :caption: Python API
-    :maxdepth: 3
-    :hidden:
-
-    pycalibration
-    python/cluster/index
-    python/file/index
-    pyFit
+    :maxdepth: 1
     
+    pyFile
+    pyCtbRawFile
+    pyClusterFile
+    pyClusterVector
+    pyJungfrauDataFile
+    pyRawFile
+    pyRawMasterFile
+    pyHdf5File
+    pyHdf5MasterFile
+    pyVarClusterFinder
+
+    pyFit
 
 
 .. toctree::
@@ -42,17 +48,17 @@ AARE
     Frame
     File
     Dtype
-    Cluster
     ClusterFinder
     ClusterFinderMT
     ClusterFile
     ClusterVector
-    Interpolation
     JungfrauDataFile
     Pedestal
     RawFile
     RawSubFile
     RawMasterFile
+    Hdf5File
+    Hdf5MasterFile
     VarClusterFinder
 
 

docs/src/pyClusterFile.rst

@@ -0,0 +1,11 @@
+
+ClusterFile
+============
+
+.. py:currentmodule:: aare
+
+.. autoclass:: ClusterFile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/pyClusterVector.rst

@@ -1,13 +1,9 @@
-.. _py_clustervector:
-    
 ClusterVector
 ================
 
 The ClusterVector, holds clusters from the ClusterFinder. Since it is templated
-in C++  we use a suffix indicating the type of cluster it holds. The suffix follows
-the same pattern as for ClusterFile i.e. ``ClusterVector_Cluster3x3i``
-for a vector holding 3x3 integer clusters.
-
+in C++  we use a suffix indicating the data type in python. The suffix is
+``_i`` for integer, ``_f`` for float, and ``_d`` for double.
 
 At the moment the functionality from python is limited and it is not supported
 to push_back clusters to the vector. The intended use case is to pass it to 
@@ -30,29 +26,8 @@ C++ functions that support the ClusterVector or to view it as a numpy array.
 
 .. py:currentmodule:: aare
 
-.. autoclass:: ClusterVector
-    :members:
-    :undoc-members:
-    :inherited-members:
-
-Below is the API of the ClusterVector_Cluster3x3i but all variants share the same API.
-
-.. autoclass::  aare._aare.ClusterVector_Cluster3x3i
-    :special-members: __init__
+.. autoclass:: ClusterVector_i
     :members:
     :undoc-members:
     :show-inheritance:
-    :inherited-members:
-
-
-**Free Functions:** 
-
-.. autofunction:: reduce_to_3x3
-   :noindex:
-
-   Reduce a single Cluster to 3x3 by taking the 3x3 subcluster with highest photon energy.
-
-.. autofunction:: reduce_to_2x2
-   :noindex:
-
-   Reduce a single Cluster to 2x2 by taking the 2x2 subcluster with highest photon energy.
+    :inherited-members:

docs/src/pyCtbRawFile.rst

@@ -0,0 +1,11 @@
+
+CtbRawFile
+============
+
+.. py:currentmodule:: aare
+
+.. autoclass:: CtbRawFile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/pyHdf5File.rst

@@ -0,0 +1,10 @@
+Hdf5File
+===================
+
+.. py:currentmodule:: aare
+
+.. autoclass:: Hdf5File
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/pyHdf5MasterFile.rst

@@ -0,0 +1,10 @@
+Hdf5MasterFile
+===================
+
+.. py:currentmodule:: aare
+
+.. autoclass:: Hdf5MasterFile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/pycalibration.rst

@@ -1,40 +0,0 @@
-
-Calibration
-==============
-
-Functions for applying calibration to data.
-
-.. code-block:: python
-
-    import aare
-
-    # Load calibration data for a single JF module (512x1024 pixels)
-    calibration = aare.load_calibration('path/to/calibration/file.bin')
-
-    raw_data = ...  # Load your raw data here
-    pedestal = ...  # Load your pedestal data here
-
-    # Apply calibration to raw data to convert from raw ADC values to keV
-    data = aare.apply_calibration(raw_data, pd=pedestal, cal=calibration)
-
-    # If you pass a 2D pedestal and calibration only G0 will be used for the conversion
-    # Pixels that switched to G1 or G2 will be set to 0
-    data = aare.apply_calibration(raw_data, pd=pedestal[0], cal=calibration[0])
-
-    
-
-.. py:currentmodule:: aare
-
-.. autofunction:: apply_calibration
-
-.. autofunction:: load_calibration
-
-.. autofunction:: calculate_pedestal
-
-.. autofunction:: calculate_pedestal_float
-
-.. autofunction:: calculate_pedestal_g0
-
-.. autofunction:: calculate_pedestal_g0_float
-
-.. autofunction:: count_switching_pixels

docs/src/python/cluster/index.rst

@@ -1,11 +0,0 @@
-Cluster & Interpolation
-==========================
-
-.. toctree::
-   :caption: Cluster & Interpolation
-   :maxdepth: 1
-
-   pyCluster
-   pyClusterVector
-   pyInterpolation
-   pyVarClusterFinder

docs/src/python/cluster/pyCluster.rst

@@ -1,23 +0,0 @@
-Cluster
-========
-
-.. py:currentmodule:: aare
-
-.. autoclass:: Cluster
-    :members:
-    :undoc-members:
-    :inherited-members:
-
-
-Below is the API of a cluster of size :math:`3\times 3` and type ``int`` but all variants share the same API.
-
-    .. autoclass::  aare._aare.Cluster3x3i
-        :special-members: __init__
-        :members:
-        :undoc-members:
-        :show-inheritance:
-        :inherited-members:
-
-.. note:: 
-    More functions can be found in the :ref:`ClusterVector <py_clustervector>` documentation. Generally apply functions directly on the ``ClusterVector`` instead of looping over individual clusters.
-

docs/src/python/cluster/pyInterpolation.rst

@@ -1,94 +0,0 @@
-Interpolation 
-==============
-
-Interpolation class for :math:`\eta` Interpolation. 
-
-The Interpolator class provides methods to interpolate the positions of photons based on their :math:`\eta` values. 
-
-.. warning:: 
-   The interpolation might lead to erroneous photon positions for clusters at the boarders of a frame. Make sure to filter out such cases. 
-
-Below is an example of the Eta class of type ``double``. Supported are ``Etaf`` of type ``float`` and ``Etai`` of type ``int``. 
-
-.. autoclass:: aare._aare.Etad
-    :members:
-    :private-members:
-
-.. note::
-    The corner value ``c`` is only relevant when one uses ``calculate_eta_2`` or ``calculate_full_eta2``. Otherwise its default value is ``cTopLeft``. 
-
-Supported are the following :math:`\eta`-functions: 
-
-.. py:currentmodule:: aare
-
-.. image:: ../../../figures/Eta2x2.png
-    :target: ../../../figures/Eta2x2.png
-    :width: 650px
-    :align: center
-    :alt: Eta2x2
-
-.. math:: 
-    \begin{equation*}
-   {\color{blue}{\eta_x}} = \frac{Q_{1,1}}{Q_{1,0} + Q_{1,1}} \quad \quad 
-   {\color{green}{\eta_y}} = \frac{Q_{1,1}}{Q_{0,1} + Q_{1,1}}
-   \end{equation*}    
-
-.. autofunction:: calculate_eta2
-
-.. image:: ../../../figures/Eta2x2Full.png
-    :target: ../../../figures/Eta2x2Full.png
-    :width: 650px
-    :align: center
-    :alt: Eta2x2 Full 
-
-.. math:: 
-    \begin{equation*}
-        {\color{blue}{\eta_x}}  = \frac{Q_{0,1} + Q_{1,1}}{\sum_i^{2}\sum_j^{2}Q_{i,j}} \quad \quad
-        {\textcolor{green}{\eta_y}} = \frac{Q_{1,0} + Q_{1,1}}{\sum_i^{2}\sum_j^{2}Q_{i,j}}
-    \end{equation*} 
-
-.. autofunction:: calculate_full_eta2
-
-.. image:: ../../../figures/Eta3x3.png
-    :target: ../../../figures/Eta3x3.png
-    :width: 650px
-    :align: center
-    :alt: Eta3x3
-
-.. math::
-    \begin{equation*}
-         {\color{blue}{\eta_x}} = \frac{\sum_{i}^{3} Q_{i,2} - \sum_{i}^{3} Q_{i,0}}{\sum_{i}^{3}\sum_{j}^{3} Q_{i,j}} \quad \quad
-        {\color{green}{\eta_y}} = \frac{\sum_{j}^{3} Q_{2,j} - \sum_{j}^{3} Q_{0,j}}{\sum_{i}^{3}\sum_{j}^{3} Q_{i,j}}
-    \end{equation*}
-
-.. autofunction:: calculate_eta3
-
-.. image:: ../../../figures/Eta3x3Cross.png
-    :target: ../../../figures/Eta3x3Cross.png
-    :width: 650px
-    :align: center
-    :alt: Cross Eta3x3
-
-.. math:: 
-    \begin{equation*}
-       {\color{blue}{\eta_x}} = \frac{Q_{1,2} - Q_{1,0}}{Q_{1,0} +  Q_{1,1} + Q_{1,0}} \quad \quad
-        {\color{green}{\eta_y}} = \frac{Q_{0,2} - Q_{0,1}}{Q_{0,1} +  Q_{1,1} + Q_{1,2}}
-    \end{equation*}
-
-.. autofunction:: calculate_cross_eta3
-
-
-Interpolation class for :math:`\eta`-Interpolation 
-----------------------------------------------------
-
-.. Warning:: 
-    Make sure to use the same :math:`\eta`-function during interpolation as given by the joint :math:`\eta`-distribution passed to the constructor. 
-
-.. py:currentmodule:: aare
-
-.. autoclass:: Interpolator
-    :special-members: __init__
-    :members:
-    :undoc-members:
-    :inherited-members:
-

docs/src/python/file/index.rst

@@ -1,14 +0,0 @@
-File I/O
-===================
-
-.. toctree::
-   :caption: File I/O
-   :maxdepth: 1
-
-   pyClusterFile
-   pyCtbRawFile
-   pyFile
-   pyJungfrauDataFile
-   pyRawFile
-   pyRawMasterFile
-   pyTransform

docs/src/python/file/pyClusterFile.rst

@@ -1,26 +0,0 @@
-
-ClusterFile
-============
-
-
-The :class:`ClusterFile` class is the main interface to read and write clusters in aare. Unfortunately the
-old file format does not include metadata like the cluster size and the data type. This means that the
-user has to know this information from other sources. Specifying the wrong cluster size or data type
-will lead to garbage data being read. 
-
-.. py:currentmodule:: aare
-
-.. autoclass:: ClusterFile
-    :members:
-    :undoc-members:
-    :inherited-members:
-
-
-Below is the API of the ClusterFile_Cluster3x3i but all variants share the same API.
-
-.. autoclass:: aare._aare.ClusterFile_Cluster3x3i
-    :special-members: __init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :inherited-members:

docs/src/python/file/pyCtbRawFile.rst

@@ -1,25 +0,0 @@
-
-CtbRawFile
-============
-
-Read analog, digital and transceiver samples from a raw file containing
-data from the Chip Test Board. Uses :mod:`aare.transform` to decode the 
-data into a format that the user can work with. 
-
-.. code:: python
-
-    import aare
-    from aare.transform import Mythen302Transform
-    my302 = Mythen302Transform(offset = 4)
-
-    with aare.CtbRawFile(fname, transform = my302) as f:
-    for header, data in f:
-       #do something with the data
-
-.. py:currentmodule:: aare
-
-.. autoclass:: CtbRawFile
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :inherited-members:

docs/src/python/file/pyTransform.rst

@@ -1,27 +0,0 @@
-Transform
-===================
-
-The transform module takes data read by :class:`aare.CtbRawFile` and decodes it
-to a useful image format. Depending on detector it supports both analog
-and digital samples. 
-
-For convenience the following transform objects are defined with a short name
-
-.. code:: python
-
-    moench05 = Moench05Transform()
-    moench05_1g = Moench05Transform1g()
-    moench05_old = Moench05TransformOld()
-    matterhorn02 = Matterhorn02Transform()
-    adc_sar_04_64to16 = AdcSar04Transform64to16()
-    adc_sar_05_64to16 = AdcSar05Transform64to16()
-
-.. py:currentmodule:: aare
-
-.. automodule:: aare.transform
-    :members:
-    :undoc-members:
-    :private-members:
-    :special-members: __call__
-    :show-inheritance:
-    :inherited-members:

etc/add_license.py

@@ -1,103 +0,0 @@
-#!/usr/bin/env python3
-import argparse
-import fnmatch
-import os
-from pathlib import Path
-
-CPP_PATTERNS = ["*.h", "*.hpp", "*.cpp"]
-PY_PATTERNS = ["*.py"]
-CMAKE_PATTERNS = ["CMakeLists.txt"]
-
-FILE_PATTERNS = CPP_PATTERNS + PY_PATTERNS + CMAKE_PATTERNS
-LICENSE_TEXT = "SPDX-License-Identifier: MPL-2.0"
-
-
-def get_comment_prefix(filename: str) -> str | None:
-    if any(fnmatch.fnmatch(filename, p) for p in CPP_PATTERNS):
-        return "// "
-    if any(fnmatch.fnmatch(filename, p) for p in (PY_PATTERNS + CMAKE_PATTERNS)):
-        return "# "
-    return None
-
-
-def matches_pattern(filename: str) -> bool:
-    return any(fnmatch.fnmatch(filename, p) for p in FILE_PATTERNS)
-
-
-def process_file(filepath: Path) -> bool:
-    filename = filepath.name
-    prefix = get_comment_prefix(filename)
-    if not prefix:
-        return False
-
-    license_line = f"{prefix}{LICENSE_TEXT}\n"
-
-    try:
-        with filepath.open("r", encoding="utf-8") as f:
-            lines = f.readlines()
-    except Exception as e:
-        print(f"⚠️ Error reading {filepath}: {e}")
-        return False
-
-    # Skip if SPDX already present anywhere in the file
-    if any("SPDX-License-Identifier" in line for line in lines):
-        return False
-
-    insert_index = 0
-
-    # For Python, keep shebang on the very first line
-    if filename.endswith(".py") and lines:
-        if lines[0].startswith("#!"):
-            insert_index = 1
-
-    lines.insert(insert_index, license_line)
-
-    try:
-        with filepath.open("w", encoding="utf-8") as f:
-            f.writelines(lines)
-    except Exception as e:
-        print(f"⚠️ Error writing {filepath}: {e}")
-        return False
-
-    return True
-
-
-def main() -> None:
-    parser = argparse.ArgumentParser(
-        description="Add SPDX-License-Identifier: MPL-2.0 to source files."
-    )
-    parser.add_argument(
-        "path",
-        help="Root directory to recursively process "
-             "(*.h, *.cpp, *.py, and CMakeLists.txt).",
-    )
-
-    args = parser.parse_args()
-
-    root_path = Path(args.path).expanduser().resolve()
-
-    if not root_path.exists():
-        print(f"Error: Path does not exist: {root_path}")
-        raise SystemExit(1)
-
-    if not root_path.is_dir():
-        print(f"Error: Path is not a directory: {root_path}")
-        raise SystemExit(1)
-
-    print(f"Processing directory: {root_path}")
-    modified = 0
-
-    for dirpath, _, files in os.walk(root_path):
-        dirpath = Path(dirpath)
-        for name in files:
-            if matches_pattern(name):
-                fullpath = dirpath / name
-                if process_file(fullpath):
-                    print(f"✔ Added SPDX: {fullpath}")
-                    modified += 1
-
-    print(f"\nDone. Updated {modified} file(s).")
-
-
-if __name__ == "__main__":
-    main()

etc/dev-env.yml

@@ -3,16 +3,11 @@ channels:
   - conda-forge
 dependencies:
   - anaconda-client
-  - catch2
   - conda-build
   - doxygen 
-  - sphinx
+  - sphinx=7.1.2 
   - breathe 
   - sphinx_rtd_theme 
   - furo 
   - zeromq 
-  - pybind11
-  - numpy
-  - matplotlib
-  - nlohmann_json
 

include/aare/ArrayExpr.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/defs.hpp"
 #include <array>

include/aare/CalculateEta.hpp

@@ -1,13 +1,18 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/Cluster.hpp"
 #include "aare/ClusterVector.hpp"
 #include "aare/NDArray.hpp"
-#include "aare/defs.hpp"
 
 namespace aare {
 
+enum class corner : int {
+    cBottomLeft = 0,
+    cBottomRight = 1,
+    cTopLeft = 2,
+    cTopRight = 3
+};
+
 enum class pixel : int {
     pBottomLeft = 0,
     pBottom = 1,
@@ -20,427 +25,146 @@ enum class pixel : int {
     pTopRight = 8
 };
 
-// TODO: better to have sum after x,y
-/**
- * eta struct
- */
 template <typename T> struct Eta2 {
-    /// @brief eta in x direction
-    double x{};
-    /// @brief eta in y direction
-    double y{};
-    /// @brief index of subcluster given as corner relative to cluster center
-    corner c{0};
-    /// @brief photon energy (cluster sum)
-    T sum{};
+    double x;
+    double y;
+    int c;
+    T sum;
 };
 
 /**
- * @brief Calculate the eta2 values for all clusters in a ClusterVector
+ * @brief Calculate the eta2 values for all clusters in a Clustervector
  */
 template <typename ClusterType,
           typename = std::enable_if_t<is_cluster_v<ClusterType>>>
-std::vector<Eta2<typename ClusterType::value_type>>
-calculate_eta2(const ClusterVector<ClusterType> &clusters) {
-
-    std::vector<Eta2<typename ClusterType::value_type>> eta2{};
-    eta2.reserve(clusters.size());
+NDArray<double, 2> calculate_eta2(const ClusterVector<ClusterType> &clusters) {
+    NDArray<double, 2> eta2({static_cast<int64_t>(clusters.size()), 2});
 
     for (size_t i = 0; i < clusters.size(); i++) {
         auto e = calculate_eta2(clusters[i]);
-        eta2.push_back(e);
+        eta2(i, 0) = e.x;
+        eta2(i, 1) = e.y;
     }
 
     return eta2;
 }
 
-/**
- * @brief Calculate the full eta2 values for all clusters in a ClusterVector
- */
-template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
-std::vector<Eta2<typename ClusterType::value_type>>
-calculate_full_eta2(const ClusterVector<ClusterType> &clusters) {
-    std::vector<Eta2<typename ClusterType::value_type>> eta2{};
-    eta2.reserve(clusters.size());
-
-    for (size_t i = 0; i < clusters.size(); i++) {
-        auto e = calculate_full_eta2(clusters[i]);
-        eta2.push_back(e);
-    }
-
-    return eta2;
-}
-
-/**
- * @brief Calculate eta3 for all 3x3 clusters in a ClusterVector
- */
-template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
-std::vector<Eta2<typename ClusterType::value_type>>
-calculate_eta3(const ClusterVector<ClusterType> &clusters) {
-    std::vector<Eta2<typename ClusterType::value_type>> eta2{};
-    eta2.reserve(clusters.size());
-
-    for (size_t i = 0; i < clusters.size(); i++) {
-        auto e = calculate_eta3(clusters[i]);
-        eta2.push_back(e);
-    }
-
-    return eta2;
-}
-
-/**
- * @brief Calculate cross eta3 for all 3x3 clusters in a ClusterVector
- */
-template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
-std::vector<Eta2<typename ClusterType::value_type>>
-calculate_cross_eta3(const ClusterVector<ClusterType> &clusters) {
-    std::vector<Eta2<typename ClusterType::value_type>> eta2{};
-    eta2.reserve(clusters.size());
-
-    for (size_t i = 0; i < clusters.size(); i++) {
-        auto e = calculate_cross_eta3(clusters[i]);
-        eta2.push_back(e);
-    }
-
-    return eta2;
-}
-
-/**
- * @brief helper function to calculate eta2 x and y values
- * @param eta reference to the Eta2 object to update
- * @param left_x value of the left pixel
- * @param right_x value of the right pixel
- * @param bottom_y value of the bottom pixel
- * @param top_y value of the top pixel
- */
-template <typename T>
-inline void calculate_eta2(Eta2<T> &eta, const T left_x, const T right_x,
-                           const T bottom_y, const T top_y) {
-    if ((right_x + left_x) != 0)
-        eta.x = static_cast<double>(right_x) /
-                static_cast<double>(right_x + left_x); // between (0,1) the
-                                                       // closer to zero left
-                                                       // value probably larger
-    if ((top_y + bottom_y) != 0)
-        eta.y = static_cast<double>(top_y) /
-                static_cast<double>(top_y + bottom_y); // between (0,1) the
-                                                       // closer to zero bottom
-                                                       // value probably larger
-}
-
 /**
  * @brief Calculate the eta2 values for a generic sized cluster and return them
- * in a Eta2 struct containing etay, etax and the index (as corner) of the
- * respective 2x2 subcluster relative to the cluster center.
+ * in a Eta2 struct containing etay, etax and the index of the respective 2x2
+ * subcluster.
  */
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
+          typename CoordType>
 Eta2<T>
 calculate_eta2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-
-    static_assert(ClusterSizeX > 1 && ClusterSizeY > 1);
     Eta2<T> eta{};
 
+    auto max_sum = cl.max_sum_2x2();
+    eta.sum = max_sum.first;
+    auto c = max_sum.second;
+
     size_t cluster_center_index =
         (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
 
-    auto max_sum = cl.max_sum_2x2();
-    eta.sum = max_sum.sum;
-    corner c = max_sum.index;
+    size_t index_bottom_left_max_2x2_subcluster =
+        (int(c / (ClusterSizeX - 1))) * ClusterSizeX + c % (ClusterSizeX - 1);
 
-    // subcluster top right from center
-    switch (c) {
-    case (corner::cTopLeft):
-        calculate_eta2(eta, cl.data[cluster_center_index - 1],
-                       cl.data[cluster_center_index],
-                       cl.data[cluster_center_index - ClusterSizeX],
-                       cl.data[cluster_center_index]);
-        // dx = -1
-        // dy = -1
-        break;
-    case (corner::cTopRight):
-        calculate_eta2(eta, cl.data[cluster_center_index],
-                       cl.data[cluster_center_index + 1],
-                       cl.data[cluster_center_index - ClusterSizeX],
-                       cl.data[cluster_center_index]);
-        // dx = 0
-        // dy = -1
-        break;
-    case (corner::cBottomLeft):
-        calculate_eta2(eta, cl.data[cluster_center_index - 1],
-                       cl.data[cluster_center_index],
-                       cl.data[cluster_center_index],
-                       cl.data[cluster_center_index + ClusterSizeX]);
-        // dx = -1
-        // dy = 0
-        break;
-    case (corner::cBottomRight):
-        calculate_eta2(eta, cl.data[cluster_center_index],
-                       cl.data[cluster_center_index + 1],
-                       cl.data[cluster_center_index],
-                       cl.data[cluster_center_index + ClusterSizeX]);
-        // dx = 0
-        // dy = 0
-        break;
+    // check that cluster center is in max subcluster
+    if (cluster_center_index != index_bottom_left_max_2x2_subcluster &&
+        cluster_center_index != index_bottom_left_max_2x2_subcluster + 1 &&
+        cluster_center_index !=
+            index_bottom_left_max_2x2_subcluster + ClusterSizeX &&
+        cluster_center_index !=
+            index_bottom_left_max_2x2_subcluster + ClusterSizeX + 1)
+        throw std::runtime_error("Photon center is not in max 2x2_subcluster");
+
+    if ((cluster_center_index - index_bottom_left_max_2x2_subcluster) %
+            ClusterSizeX ==
+        0) {
+        if ((cl.data[cluster_center_index + 1] +
+             cl.data[cluster_center_index]) != 0)
+
+            eta.x = static_cast<double>(cl.data[cluster_center_index + 1]) /
+                    static_cast<double>((cl.data[cluster_center_index + 1] +
+                                         cl.data[cluster_center_index]));
+    } else {
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index - 1]) != 0)
+
+            eta.x = static_cast<double>(cl.data[cluster_center_index]) /
+                    static_cast<double>((cl.data[cluster_center_index - 1] +
+                                         cl.data[cluster_center_index]));
     }
-
-    eta.c = c;
-
-    return eta;
-}
-
-/**
- * @brief Calculate the eta2 values for a generic sized cluster and return them
- * in a Eta2 struct containing etay, etax and the index (as corner) of the
- * respective 2x2 subcluster relative to the cluster center.
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType>
-Eta2<T> calculate_full_eta2(
-    const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-
-    static_assert(ClusterSizeX > 1 && ClusterSizeY > 1);
-    Eta2<T> eta{};
-
-    constexpr size_t cluster_center_index =
-        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
-
-    auto max_sum = cl.max_sum_2x2();
-    eta.sum = max_sum.sum;
-    corner c = max_sum.index;
-
-    // subcluster top right from center
-    switch (c) {
-    case (corner::cTopLeft):
-        if (eta.sum != 0) {
-            eta.x = static_cast<double>(
-                        cl.data[cluster_center_index] +
-                        cl.data[cluster_center_index - ClusterSizeX]) /
-                    static_cast<double>(eta.sum);
-
-            eta.y = static_cast<double>(cl.data[cluster_center_index - 1] +
-                                        cl.data[cluster_center_index]) /
-                    static_cast<double>(eta.sum);
-        }
-        // dx = -1
-        // dy = -1
-        break;
-    case (corner::cTopRight):
-        if (eta.sum != 0) {
-            eta.x = static_cast<double>(
-                        cl.data[cluster_center_index + 1] +
-                        cl.data[cluster_center_index - ClusterSizeX + 1]) /
-                    static_cast<double>(eta.sum);
-            eta.y = static_cast<double>(cl.data[cluster_center_index] +
-                                        cl.data[cluster_center_index + 1]) /
-                    static_cast<double>(eta.sum);
-        }
-        // dx = 0
-        // dy = -1
-        break;
-    case (corner::cBottomLeft):
-        if (eta.sum != 0) {
-            eta.x = static_cast<double>(
-                        cl.data[cluster_center_index] +
+    if ((cluster_center_index - index_bottom_left_max_2x2_subcluster) /
+            ClusterSizeX <
+        1) {
+        assert(cluster_center_index + ClusterSizeX <
+               ClusterSizeX * ClusterSizeY); // suppress warning
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index + ClusterSizeX]) != 0)
+            eta.y = static_cast<double>(
                         cl.data[cluster_center_index + ClusterSizeX]) /
-                    static_cast<double>(eta.sum);
-            eta.y = static_cast<double>(
-                        cl.data[cluster_center_index + ClusterSizeX] +
-                        cl.data[cluster_center_index + ClusterSizeX - 1]) /
-                    static_cast<double>(eta.sum);
-        }
-        // dx = -1
-        // dy = 0
-        break;
-    case (corner::cBottomRight):
-        if (eta.sum != 0) {
-            eta.x = static_cast<double>(
-                        cl.data[cluster_center_index + 1] +
-                        cl.data[cluster_center_index + ClusterSizeX + 1]) /
-                    static_cast<double>(eta.sum);
-            eta.y = static_cast<double>(
-                        cl.data[cluster_center_index + ClusterSizeX] +
-                        cl.data[cluster_center_index + ClusterSizeX + 1]) /
-                    static_cast<double>(eta.sum);
-        }
-        // dx = 0
-        // dy = 0
-        break;
+                    static_cast<double>(
+                        (cl.data[cluster_center_index] +
+                         cl.data[cluster_center_index + ClusterSizeX]));
+    } else {
+        if ((cl.data[cluster_center_index] +
+             cl.data[cluster_center_index - ClusterSizeX]) != 0)
+            eta.y = static_cast<double>(cl.data[cluster_center_index]) /
+                    static_cast<double>(
+                        (cl.data[cluster_center_index] +
+                         cl.data[cluster_center_index - ClusterSizeX]));
     }
 
-    eta.c = c;
-
+    eta.c = c; // TODO only supported for 2x2 and 3x3 clusters -> at least no
+               // underyling enum class
     return eta;
 }
 
+// TODO! Look up eta2 calculation - photon center should be top right corner
 template <typename T>
-Eta2<T> calculate_eta2(const Cluster<T, 2, 2, uint16_t> &cl) {
+Eta2<T> calculate_eta2(const Cluster<T, 2, 2, int16_t> &cl) {
     Eta2<T> eta{};
 
-    // TODO: maybe have as member function of cluster
-    const uint8_t photon_hit_index =
-        std::max_element(cl.data.begin(), cl.data.end()) - cl.data.begin();
-
-    eta.c = static_cast<corner>(3 - photon_hit_index);
-
-    switch (eta.c) {
-    case corner::cTopLeft:
-        calculate_eta2(eta, cl.data[2], cl.data[3], cl.data[1], cl.data[3]);
-        break;
-    case corner::cTopRight:
-        calculate_eta2(eta, cl.data[2], cl.data[3], cl.data[0], cl.data[2]);
-        break;
-    case corner::cBottomLeft:
-        calculate_eta2(eta, cl.data[0], cl.data[1], cl.data[1], cl.data[3]);
-        break;
-    case corner::cBottomRight:
-        calculate_eta2(eta, cl.data[0], cl.data[1], cl.data[0], cl.data[2]);
-        break;
-    }
-
+    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.sum();
-
+    eta.c = static_cast<int>(corner::cBottomLeft); // TODO! This is not correct,
+                                                   // but need to put something
     return eta;
 }
 
-template <typename T>
-Eta2<T> calculate_full_eta2(const Cluster<T, 2, 2, uint16_t> &cl) {
+// calculates Eta3 for 3x3 cluster based on code from analyze_cluster
+// TODO only supported for 3x3 Clusters
+template <typename T> Eta2<T> calculate_eta3(const Cluster<T, 3, 3> &cl) {
 
     Eta2<T> eta{};
 
-    eta.sum = cl.sum();
+    T sum = 0;
 
-    const uint8_t photon_hit_index =
-        std::max_element(cl.data.begin(), cl.data.end()) - cl.data.begin();
+    std::for_each(std::begin(cl.data), std::end(cl.data),
+                  [&sum](T x) { sum += x; });
 
-    eta.c = static_cast<corner>(3 - photon_hit_index);
+    eta.sum = sum;
 
-    if (eta.sum != 0) {
-        eta.x = static_cast<double>(cl.data[1] + cl.data[3]) /
-                static_cast<double>(eta.sum);
-        eta.y = static_cast<double>(cl.data[2] + cl.data[3]) /
-                static_cast<double>(eta.sum);
-    }
-
-    return eta;
-}
-
-// TODO generalize
-template <typename T>
-Eta2<T> calculate_eta2(const Cluster<T, 1, 2, uint16_t> &cl) {
-    Eta2<T> eta{};
-
-    eta.x = 0;
-    eta.y = static_cast<double>(cl.data[1]) / cl.data[0];
-    eta.sum = cl.sum();
-}
-
-template <typename T>
-Eta2<T> calculate_eta2(const Cluster<T, 2, 1, uint16_t> &cl) {
-    Eta2<T> eta{};
-
-    eta.x = static_cast<double>(cl.data[1]) / cl.data[0];
-    eta.y = 0;
-    eta.sum = cl.sum();
-}
-
-/**
- * @brief calculates cross Eta3 for 3x3 cluster
- * cross Eta3 calculates the eta by taking into account only the cross pixels
- * {top, bottom, left, right, center}
- */
-template <typename T, typename CoordType = uint16_t>
-Eta2<T> calculate_cross_eta3(const Cluster<T, 3, 3, CoordType> &cl) {
-
-    Eta2<T> eta{};
-
-    T photon_energy = cl.sum();
-
-    eta.sum = photon_energy;
+    eta.c = corner::cBottomLeft;
 
     if ((cl.data[3] + cl.data[4] + cl.data[5]) != 0)
 
-        eta.x =
-            static_cast<double>(-cl.data[3] + cl.data[3 + 2]) /
+        eta.x = static_cast<double>(-cl.data[3] + cl.data[3 + 2]) /
 
-            static_cast<double>(cl.data[3] + cl.data[4] + cl.data[5]); // (-1,1)
+                (cl.data[3] + cl.data[4] + cl.data[5]);
 
     if ((cl.data[1] + cl.data[4] + cl.data[7]) != 0)
 
         eta.y = static_cast<double>(-cl.data[1] + cl.data[2 * 3 + 1]) /
 
-                static_cast<double>(cl.data[1] + cl.data[4] + cl.data[7]);
+                (cl.data[1] + cl.data[4] + cl.data[7]);
 
     return eta;
 }
 
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-Eta2<T> calculate_cross_eta3(
-    const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-
-    static_assert(ClusterSizeX > 2 && ClusterSizeY > 2,
-                  "calculate_eta3 only defined for clusters larger than 2x2");
-
-    if constexpr (ClusterSizeX != 3 || ClusterSizeY != 3) {
-        auto reduced_cluster = reduce_cluster_to_3x3(cl);
-        return calculate_cross_eta3(reduced_cluster);
-    } else {
-        return calculate_cross_eta3(cl);
-    }
-}
-
-/**
- * @brief calculates Eta3 for 3x3 cluster
- * It calculates the eta by taking into account all pixels in the 3x3 cluster
- */
-template <typename T, typename CoordType = uint16_t>
-Eta2<T> calculate_eta3(const Cluster<T, 3, 3, CoordType> &cl) {
-
-    Eta2<T> eta{};
-
-    T photon_energy = cl.sum();
-
-    eta.sum = photon_energy;
-
-    // TODO: how do we handle potential arithmetic overflows? - T could be
-    // uint16
-    if (photon_energy != 0) {
-        std::array<T, 2> column_sums{
-            static_cast<T>(cl.data[0] + cl.data[3] + cl.data[6]),
-            static_cast<T>(cl.data[2] + cl.data[5] + cl.data[8])};
-
-        eta.x = static_cast<double>(-column_sums[0] + column_sums[1]) /
-                static_cast<double>(photon_energy);
-
-        std::array<T, 2> row_sums{
-            static_cast<T>(cl.data[0] + cl.data[1] + cl.data[2]),
-            static_cast<T>(cl.data[6] + cl.data[7] + cl.data[8])};
-
-        eta.y = static_cast<double>(-row_sums[0] + row_sums[1]) /
-                static_cast<double>(photon_energy);
-    }
-
-    return eta;
-}
-
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-Eta2<T>
-calculate_eta3(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &cl) {
-
-    static_assert(ClusterSizeX > 2 && ClusterSizeY > 2,
-                  "calculate_eta3 only defined for clusters larger than 2x2");
-
-    if constexpr (ClusterSizeX != 3 || ClusterSizeY != 3) {
-        auto reduced_cluster = reduce_cluster_to_3x3(cl);
-        return calculate_eta3(reduced_cluster);
-    } else {
-        return calculate_eta3(cl);
-    }
-}
-
 } // namespace aare

include/aare/CircularFifo.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include <chrono>

include/aare/Cluster.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 
 /************************************************
  * @file Cluster.hpp
@@ -9,7 +8,6 @@
 
 #pragma once
 
-#include "defs.hpp"
 #include <algorithm>
 #include <array>
 #include <cstdint>
@@ -19,12 +17,8 @@
 namespace aare {
 
 // requires clause c++20 maybe update
-
-/**
- * @brief Cluster struct
- */
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
+          typename CoordType = int16_t>
 struct Cluster {
 
     static_assert(std::is_arithmetic_v<T>, "T needs to be an arithmetic type");
@@ -33,11 +27,8 @@ struct Cluster {
     static_assert(ClusterSizeX > 0 && ClusterSizeY > 0,
                   "Cluster sizes must be bigger than zero");
 
-    /// @brief Cluster center x coordinate (in pixel coordinates)
     CoordType x;
-    /// @brief Cluster center y coordinate (in pixel coordinates)
     CoordType y;
-    /// @brief Cluster data stored in row-major order starting from top-left
     std::array<T, ClusterSizeX * ClusterSizeY> data;
 
     static constexpr uint8_t cluster_size_x = ClusterSizeX;
@@ -45,18 +36,9 @@ struct Cluster {
     using value_type = T;
     using coord_type = CoordType;
 
-    /**
-     * @brief Sum of all elements in the cluster
-     */
     T sum() const { return std::accumulate(data.begin(), data.end(), T{}); }
 
-    // TODO: handle 1 dimensional clusters
-    /**
-     * @brief sum of 2x2 subcluster with highest energy
-     * @return photon energy of subcluster, 2x2 subcluster index relative to
-     * cluster center
-     */
-    Sum_index_pair<T, corner> max_sum_2x2() const {
+    std::pair<T, int> max_sum_2x2() const {
 
         if constexpr (cluster_size_x == 3 && cluster_size_y == 3) {
             std::array<T, 4> sum_2x2_subclusters;
@@ -67,166 +49,31 @@ struct Cluster {
             int index = std::max_element(sum_2x2_subclusters.begin(),
                                          sum_2x2_subclusters.end()) -
                         sum_2x2_subclusters.begin();
-            return Sum_index_pair<T, corner>{sum_2x2_subclusters[index],
-                                             corner{index}};
+            return std::make_pair(sum_2x2_subclusters[index], index);
         } else if constexpr (cluster_size_x == 2 && cluster_size_y == 2) {
-            return Sum_index_pair<T, corner>{
-                data[0] + data[1] + data[2] + data[3], corner{0}};
+            return std::make_pair(data[0] + data[1] + data[2] + data[3], 0);
         } else {
-            constexpr size_t cluster_center_index =
-                (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
+            constexpr size_t num_2x2_subclusters =
+                (ClusterSizeX - 1) * (ClusterSizeY - 1);
 
-            std::array<T, 4> sum_2x2_subcluster{0};
-            // subcluster top left from center
-            sum_2x2_subcluster[0] =
-                data[cluster_center_index] + data[cluster_center_index - 1] +
-                data[cluster_center_index - ClusterSizeX] +
-                data[cluster_center_index - 1 - ClusterSizeX];
-            // subcluster top right from center
-            if (ClusterSizeX > 2) {
-                sum_2x2_subcluster[1] =
-                    data[cluster_center_index] +
-                    data[cluster_center_index + 1] +
-                    data[cluster_center_index - ClusterSizeX] +
-                    data[cluster_center_index - ClusterSizeX + 1];
-            }
-            // subcluster bottom left from center
-            if (ClusterSizeY > 2) {
-                sum_2x2_subcluster[2] =
-                    data[cluster_center_index] +
-                    data[cluster_center_index - 1] +
-                    data[cluster_center_index + ClusterSizeX] +
-                    data[cluster_center_index + ClusterSizeX - 1];
-            }
-            // subcluster bottom right from center
-            if (ClusterSizeX > 2 && ClusterSizeY > 2) {
-                sum_2x2_subcluster[3] =
-                    data[cluster_center_index] +
-                    data[cluster_center_index + 1] +
-                    data[cluster_center_index + ClusterSizeX] +
-                    data[cluster_center_index + ClusterSizeX + 1];
+            std::array<T, num_2x2_subclusters> sum_2x2_subcluster;
+            for (size_t i = 0; i < ClusterSizeY - 1; ++i) {
+                for (size_t j = 0; j < ClusterSizeX - 1; ++j)
+                    sum_2x2_subcluster[i * (ClusterSizeX - 1) + j] =
+                        data[i * ClusterSizeX + j] +
+                        data[i * ClusterSizeX + j + 1] +
+                        data[(i + 1) * ClusterSizeX + j] +
+                        data[(i + 1) * ClusterSizeX + j + 1];
             }
 
             int index = std::max_element(sum_2x2_subcluster.begin(),
                                          sum_2x2_subcluster.end()) -
                         sum_2x2_subcluster.begin();
-            return Sum_index_pair<T, corner>{sum_2x2_subcluster[index],
-                                             corner{index}};
+            return std::make_pair(sum_2x2_subcluster[index], index);
         }
     }
 };
 
-/**
- * @brief Reduce a cluster to a 2x2 cluster by selecting the 2x2 block with the
- * highest sum.
- * @param c Cluster to reduce
- * @return reduced cluster
- * @note The cluster is filled using row major ordering starting at the top-left
- * (thus for a max subcluster in the top left cornern the photon hit is at
- * the fourth position)
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = uint16_t>
-Cluster<T, 2, 2, CoordType>
-reduce_to_2x2(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &c) {
-
-    static_assert(ClusterSizeX >= 2 && ClusterSizeY >= 2,
-                  "Cluster sizes must be at least 2x2 for reduction to 2x2");
-
-    Cluster<T, 2, 2, CoordType> result{};
-
-    auto [sum, index] = c.max_sum_2x2();
-
-    constexpr int16_t cluster_center_index =
-        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
-
-    int16_t index_top_left_max_2x2_subcluster = cluster_center_index;
-    switch (index) {
-    case corner::cTopLeft:
-        index_top_left_max_2x2_subcluster -= (ClusterSizeX + 1);
-        break;
-    case corner::cTopRight:
-        index_top_left_max_2x2_subcluster -= ClusterSizeX;
-        break;
-    case corner::cBottomLeft:
-        index_top_left_max_2x2_subcluster -= 1;
-        break;
-    case corner::cBottomRight:
-        // no change needed
-        break;
-    }
-
-    result.x = c.x;
-    result.y = c.y;
-
-    result.data = {
-        c.data[index_top_left_max_2x2_subcluster],
-        c.data[index_top_left_max_2x2_subcluster + 1],
-        c.data[index_top_left_max_2x2_subcluster + ClusterSizeX],
-        c.data[index_top_left_max_2x2_subcluster + ClusterSizeX + 1]};
-
-    return result;
-}
-
-template <typename T>
-Cluster<T, 2, 2, uint16_t> reduce_to_2x2(const Cluster<T, 3, 3, uint16_t> &c) {
-    Cluster<T, 2, 2, uint16_t> result{};
-
-    auto [s, i] = c.max_sum_2x2();
-    result.x = c.x;
-    result.y = c.y;
-    switch (i) {
-    case corner::cTopLeft:
-        result.data = {c.data[0], c.data[1], c.data[3], c.data[4]};
-        break;
-    case corner::cTopRight:
-        result.data = {c.data[1], c.data[2], c.data[4], c.data[5]};
-        break;
-    case corner::cBottomLeft:
-        result.data = {c.data[3], c.data[4], c.data[6], c.data[7]};
-        break;
-    case corner::cBottomRight:
-        result.data = {c.data[4], c.data[5], c.data[7], c.data[8]};
-        break;
-    }
-
-    return result;
-}
-
-/**
- * @brief Reduce a cluster to a 3x3 cluster
- * @param c Cluster to reduce
- * @return reduced cluster
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType = int16_t>
-Cluster<T, 3, 3, CoordType>
-reduce_to_3x3(const Cluster<T, ClusterSizeX, ClusterSizeY, CoordType> &c) {
-
-    static_assert(ClusterSizeX >= 3 && ClusterSizeY >= 3,
-                  "Cluster sizes must be at least 3x3 for reduction to 3x3");
-
-    Cluster<T, 3, 3, CoordType> result{};
-
-    int16_t cluster_center_index =
-        (ClusterSizeX / 2) + (ClusterSizeY / 2) * ClusterSizeX;
-
-    result.x = c.x;
-    result.y = c.y;
-
-    result.data = {c.data[cluster_center_index - ClusterSizeX - 1],
-                   c.data[cluster_center_index - ClusterSizeX],
-                   c.data[cluster_center_index - ClusterSizeX + 1],
-                   c.data[cluster_center_index - 1],
-                   c.data[cluster_center_index],
-                   c.data[cluster_center_index + 1],
-                   c.data[cluster_center_index + ClusterSizeX - 1],
-                   c.data[cluster_center_index + ClusterSizeX],
-                   c.data[cluster_center_index + ClusterSizeX + 1]};
-
-    return result;
-}
-
 // Type Traits for is_cluster_type
 template <typename T>
 struct is_cluster : std::false_type {}; // Default case: Not a Cluster

include/aare/ClusterCollector.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <atomic>
 #include <thread>
@@ -6,7 +5,6 @@
 #include "aare/ClusterFinderMT.hpp"
 #include "aare/ClusterVector.hpp"
 #include "aare/ProducerConsumerQueue.hpp"
-#include "aare/defs.hpp"
 
 namespace aare {
 

include/aare/ClusterFile.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/Cluster.hpp"
@@ -15,7 +14,7 @@
 namespace aare {
 
 /*
-Binary cluster file. Expects data to be laid out as:
+Binary cluster file. Expects data to be layed out as:
 int32_t frame_number
 uint32_t number_of_clusters
 int16_t x, int16_t y, int32_t data[9] x number_of_clusters
@@ -190,16 +189,6 @@ class ClusterFile {
         }
     }
 
-    /**
-     * @brief Return the current position in the file (bytes)
-     */
-    int64_t tell() {
-        if (!fp) {
-            throw std::runtime_error(LOCATION + "File not opened");
-        }
-        return ftell(fp);
-    }
-
     /** @brief Open the file in specific mode
      *
      */
@@ -365,20 +354,15 @@ template <typename ClusterType, typename Enable>
 ClusterVector<ClusterType>
 ClusterFile<ClusterType, Enable>::read_frame_without_cut() {
     if (m_mode != "r") {
-        throw std::runtime_error(LOCATION + "File not opened for reading");
+        throw std::runtime_error("File not opened for reading");
     }
     if (m_num_left) {
         throw std::runtime_error(
-            LOCATION + "There are still photons left in the last frame");
+            "There are still photons left in the last frame");
     }
     int32_t frame_number;
     if (fread(&frame_number, sizeof(frame_number), 1, fp) != 1) {
-        if (feof(fp))
-            throw std::runtime_error(LOCATION + "Unexpected end of file");
-        else if (ferror(fp))
-            throw std::runtime_error(LOCATION + "Error reading from file");
-
-        throw std::runtime_error(LOCATION + "Unexpected error (not feof or ferror) when reading frame number");
+        throw std::runtime_error(LOCATION + "Could not read frame number");
     }
 
     int32_t n_clusters; // Saved as 32bit integer in the cluster file
@@ -454,8 +438,8 @@ bool ClusterFile<ClusterType, Enable>::is_selected(ClusterType &cl) {
 
     if (m_noise_map) {
         auto sum_1x1 = cl.data[cluster_center_index]; // central pixel
-        auto sum_2x2 = cl.max_sum_2x2().sum; // highest sum of 2x2 subclusters
-        auto total_sum = cl.sum();           // sum of all pixels
+        auto sum_2x2 = cl.max_sum_2x2().first; // highest sum of 2x2 subclusters
+        auto total_sum = cl.sum();             // sum of all pixels
 
         auto noise =
             (*m_noise_map)(cl.y, cl.x); // TODO! check if this is correct

include/aare/ClusterFileSink.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <atomic>
 #include <filesystem>
@@ -11,8 +10,7 @@
 namespace aare {
 
 template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>,
-          typename = std::enable_if_t<no_2x2_cluster<ClusterType>::value>>
+          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
 class ClusterFileSink {
     ProducerConsumerQueue<ClusterVector<ClusterType>> *m_source;
     std::atomic<bool> m_stop_requested{false};

include/aare/ClusterFinder.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/ClusterFile.hpp"
 #include "aare/ClusterVector.hpp"
@@ -11,16 +10,8 @@
 
 namespace aare {
 
-template <typename ClusterType,
-          typename = std::enable_if_t<is_cluster_v<ClusterType>>>
-struct no_2x2_cluster {
-    constexpr static bool value =
-        ClusterType::cluster_size_x > 2 && ClusterType::cluster_size_y > 2;
-};
-
 template <typename ClusterType = Cluster<int32_t, 3, 3>,
-          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double,
-          typename = std::enable_if_t<no_2x2_cluster<ClusterType>::value>>
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinder {
     Shape<2> m_image_size;
     const PEDESTAL_TYPE m_nSigma;
@@ -145,7 +136,7 @@ class ClusterFinder {
                     // don't have a photon
                     int i = 0;
                     for (int ir = -dy; ir < dy + has_center_pixel_y; ir++) {
-                        for (int ic = -dx; ic < dx + has_center_pixel_x; ic++) {
+                        for (int ic = -dx; ic < dx + has_center_pixel_y; ic++) {
                             if (ix + ic >= 0 && ix + ic < frame.shape(1) &&
                                 iy + ir >= 0 && iy + ir < frame.shape(0)) {
                                 CT tmp =
@@ -154,8 +145,8 @@ class ClusterFinder {
                                         m_pedestal.mean(iy + ir, ix + ic));
                                 cluster.data[i] =
                                     tmp; // Watch for out of bounds access
+                                i++;
                             }
-                            i++;
                         }
                     }
 

include/aare/ClusterFinderMT.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <atomic>
 #include <cstdint>
@@ -33,8 +32,7 @@ struct FrameWrapper {
  * @tparam CT type of the cluster data
  */
 template <typename ClusterType = Cluster<int32_t, 3, 3>,
-          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double,
-          typename = std::enable_if_t<no_2x2_cluster<ClusterType>::value>>
+          typename FRAME_TYPE = uint16_t, typename PEDESTAL_TYPE = double>
 class ClusterFinderMT {
 
   protected:

include/aare/ClusterVector.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Cluster.hpp" //TODO maybe store in seperate file !!!
 #include <algorithm>
@@ -29,7 +28,7 @@ class ClusterVector; // Forward declaration
  * needed.
  * @tparam T data type of the pixels in the cluster
  * @tparam CoordType data type of the x and y coordinates of the cluster
- * (normally uint16_t)
+ * (normally int16_t)
  */
 template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
           typename CoordType>
@@ -87,14 +86,15 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
     /**
      * @brief Sum the pixels in the 2x2 subcluster with the biggest pixel sum in
      * each cluster
-     * @return vector of sums index pairs for each cluster
+     * @return std::vector<T> vector of sums for each cluster
      */
-    std::vector<Sum_index_pair<T, corner>> sum_2x2() {
-        std::vector<Sum_index_pair<T, corner>> sums_2x2(m_data.size());
+    std::vector<T> sum_2x2() {
+        std::vector<T> sums_2x2(m_data.size());
 
-        std::transform(
-            m_data.begin(), m_data.end(), sums_2x2.begin(),
-            [](const ClusterType &cluster) { return cluster.max_sum_2x2(); });
+        std::transform(m_data.begin(), m_data.end(), sums_2x2.begin(),
+                       [](const ClusterType &cluster) {
+                           return cluster.max_sum_2x2().first;
+                       });
 
         return sums_2x2;
     }
@@ -122,11 +122,6 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
      */
     size_t size() const { return m_data.size(); }
 
-    /**
-     * @brief Check if the vector is empty
-     */
-    bool empty() const { return m_data.empty(); }
-
     uint8_t cluster_size_x() const { return ClusterSizeX; }
 
     uint8_t cluster_size_y() const { return ClusterSizeY; }
@@ -172,42 +167,4 @@ class ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>> {
     }
 };
 
-/**
- * @brief Reduce a cluster to a 2x2 cluster by selecting the 2x2 block with the
- * highest sum.
- * @param cv Clustervector containing clusters to reduce
- * @return Clustervector with reduced clusters
- * @note The cluster is filled using row major ordering starting at the top-left
- * (thus for a max subcluster in the top left cornern the photon hit is at
- * the fourth position)
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType>
-ClusterVector<Cluster<T, 2, 2, CoordType>> reduce_to_2x2(
-    const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>
-        &cv) {
-    ClusterVector<Cluster<T, 2, 2, CoordType>> result;
-    for (const auto &c : cv) {
-        result.push_back(reduce_to_2x2(c));
-    }
-    return result;
-}
-
-/**
- * @brief Reduce a cluster to a 3x3 cluster
- * @param cv Clustervector containing clusters to reduce
- * @return Clustervector with reduced clusters
- */
-template <typename T, uint8_t ClusterSizeX, uint8_t ClusterSizeY,
-          typename CoordType>
-ClusterVector<Cluster<T, 3, 3, CoordType>> reduce_to_3x3(
-    const ClusterVector<Cluster<T, ClusterSizeX, ClusterSizeY, CoordType>>
-        &cv) {
-    ClusterVector<Cluster<T, 3, 3, CoordType>> result;
-    for (const auto &c : cv) {
-        result.push_back(reduce_to_3x3(c));
-    }
-    return result;
-}
-
 } // namespace aare

include/aare/CtbRawFile.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/FileInterface.hpp"

include/aare/DetectorGeometry.hpp

@@ -1,82 +0,0 @@
-// SPDX-License-Identifier: MPL-2.0
-#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

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <cstdint>
 #include <map>

include/aare/File.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/FileInterface.hpp"
 #include <memory>
@@ -8,7 +7,7 @@ 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
+ * fuctions plase use the RawFile, NumpyFile or Hdf5File 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

include/aare/FileInterface.hpp

@@ -1,8 +1,7 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Dtype.hpp"
 #include "aare/Frame.hpp"
-#include "aare/defs.hpp"
+#include "aare/to_string.hpp"
 
 #include <filesystem>
 #include <vector>
@@ -47,7 +46,7 @@ struct FileConfig {
 
 /**
  * @brief FileInterface class to define the interface for file operations
- * @note parent class for NumpyFile and RawFile
+ * @note parent class for NumpyFile, RawFile and Hdf5File
  * @note all functions are pure virtual and must be implemented by the derived
  * classes
  */

include/aare/FilePtr.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <cstdio>
 #include <filesystem>

include/aare/Fit.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include <cmath>

include/aare/Frame.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Dtype.hpp"
 #include "aare/NDArray.hpp"
@@ -106,7 +105,7 @@ class Frame {
      * @tparam T type of the pixels
      * @return NDView<T, 2>
      */
-    template <typename T> NDView<T, 2> view() & {
+    template <typename T> NDView<T, 2> view() {
         std::array<ssize_t, 2> shape = {static_cast<ssize_t>(m_rows),
                                         static_cast<ssize_t>(m_cols)};
         T *data = reinterpret_cast<T *>(m_data);

include/aare/GainMap.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 /************************************************
  * @file GainMap.hpp
  * @short function to apply gain map of image size to a vector of clusters -

include/aare/Hdf5File.hpp

@@ -0,0 +1,211 @@
+#pragma once
+#include "aare/FileInterface.hpp"
+#include "aare/Frame.hpp"
+#include "aare/Hdf5MasterFile.hpp"
+#include "aare/NDArray.hpp" //for pixel map
+
+#include <optional>
+
+namespace aare {
+
+class H5Handles {
+    std::string file_name;
+    std::string dataset_name;
+    H5::H5File file;
+    H5::DataSet dataset;
+    H5::DataSpace dataspace;
+    H5::DataType datatype;
+    std::unique_ptr<H5::DataSpace> memspace;
+    std::vector<hsize_t> dims;
+    std::vector<hsize_t> count;
+    std::vector<hsize_t> offset;
+
+  public:
+    H5Handles(const std::string &fname, const std::string &dname)
+        : file_name(fname), dataset_name(dname), file(fname, H5F_ACC_RDONLY),
+          dataset(file.openDataSet(dname)), dataspace(dataset.getSpace()),
+          datatype(dataset.getDataType()) {
+        intialize_dimensions();
+        initialize_memspace();
+    }
+
+    std::vector<hsize_t> get_dims() const { return dims; }
+
+    void seek(size_t frame_index) {
+        if (frame_index >= dims[0]) {
+            throw std::runtime_error(LOCATION + "Invalid frame number");
+        }
+        offset[0] = static_cast<hsize_t>(frame_index);
+    }
+
+    void get_data_into(size_t frame_index, std::byte *frame_buffer,
+                       size_t n_frames = 1) {
+        seek(frame_index);
+        count[0] = static_cast<hsize_t>(n_frames);
+        // std::cout << "offset:" << ToString(offset) << " count:" <<
+        // ToString(count) << std::endl;
+        dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
+        dataset.read(frame_buffer, datatype, *memspace, dataspace);
+    }
+
+    void get_header_into(size_t frame_index, int part_index,
+                         std::byte *header_buffer) {
+        seek(frame_index);
+        offset[1] = static_cast<hsize_t>(part_index);
+        // std::cout << "offset:" << ToString(offset) << " count:" <<
+        // ToString(count) << std::endl;
+        dataspace.selectHyperslab(H5S_SELECT_SET, count.data(), offset.data());
+        dataset.read(header_buffer, datatype, *memspace, dataspace);
+    }
+
+  private:
+    void intialize_dimensions() {
+        int rank = dataspace.getSimpleExtentNdims();
+        dims.resize(rank);
+        dataspace.getSimpleExtentDims(dims.data(), nullptr);
+    }
+
+    void initialize_memspace() {
+        int rank = dataspace.getSimpleExtentNdims();
+        count.clear();
+        offset.clear();
+
+        // header datasets or header virtual datasets
+        if (rank == 1 || rank == 2) {
+            count = std::vector<hsize_t>(rank, 1); // slice 1 value
+            offset = std::vector<hsize_t>(rank, 0);
+            memspace = std::make_unique<H5::DataSpace>(H5S_SCALAR);
+        } else if (rank >= 3) {
+            // data dataset (frame x height x width)
+            count = {1, dims[1], dims[2]};
+            offset = {0, 0, 0};
+            hsize_t dims_image[2] = {dims[1], dims[2]};
+            memspace = std::make_unique<H5::DataSpace>(2, dims_image);
+        } else {
+            throw std::runtime_error(
+                LOCATION + "Invalid rank for dataset: " + std::to_string(rank));
+        }
+    }
+};
+
+template <typename Fn>
+void read_hdf5_header_fields(DetectorHeader *header, Fn &&fn_read_field) {
+    fn_read_field(0, reinterpret_cast<std::byte *>(&(header->frameNumber)));
+    fn_read_field(1, reinterpret_cast<std::byte *>(&(header->expLength)));
+    fn_read_field(2, reinterpret_cast<std::byte *>(&(header->packetNumber)));
+    fn_read_field(3, reinterpret_cast<std::byte *>(&(header->bunchId)));
+    fn_read_field(4, reinterpret_cast<std::byte *>(&(header->timestamp)));
+    fn_read_field(5, reinterpret_cast<std::byte *>(&(header->modId)));
+    fn_read_field(6, reinterpret_cast<std::byte *>(&(header->row)));
+    fn_read_field(7, reinterpret_cast<std::byte *>(&(header->column)));
+    fn_read_field(8, reinterpret_cast<std::byte *>(&(header->reserved)));
+    fn_read_field(9, reinterpret_cast<std::byte *>(&(header->debug)));
+    fn_read_field(10, reinterpret_cast<std::byte *>(&(header->roundRNumber)));
+    fn_read_field(11, reinterpret_cast<std::byte *>(&(header->detType)));
+    fn_read_field(12, reinterpret_cast<std::byte *>(&(header->version)));
+    fn_read_field(13, reinterpret_cast<std::byte *>(&(header->packetMask)));
+}
+
+/**
+ * @brief Class to read .h5 files. The class will parse the master file
+ * to find the correct geometry for the frames.
+ * @note A more generic interface is available in the aare::File class.
+ * Consider using that unless you need hdf5 file specific functionality.
+ */
+class Hdf5File : public FileInterface {
+    Hdf5MasterFile m_master;
+
+    size_t m_current_frame{};
+    size_t m_total_frames{};
+    size_t m_rows{};
+    size_t m_cols{};
+
+    static const std::string metadata_group_name;
+    static const std::vector<std::string> header_dataset_names;
+    std::unique_ptr<H5Handles> m_data_dataset{nullptr};
+    std::vector<std::unique_ptr<H5Handles>> m_header_datasets{};
+
+  public:
+    /**
+     * @brief Hdf5File constructor
+     * @param fname path to the master file (.json)
+     * @param mode file mode (only "r" is supported at the moment)
+
+     */
+    Hdf5File(const std::filesystem::path &fname, const std::string &mode = "r");
+    virtual ~Hdf5File() override;
+
+    Frame read_frame() override;
+    Frame read_frame(size_t frame_number) override;
+    std::vector<Frame> read_n(size_t n_frames) override;
+    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?
+    void read_into(std::byte *image_buf, 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;
+    size_t pixels_per_frame() override;
+    size_t bytes_per_pixel() const;
+    void seek(size_t frame_index) override;
+    size_t tell() override;
+    size_t total_frames() const override;
+    size_t rows() const override;
+    size_t cols() const override;
+    size_t bitdepth() const override;
+    xy geometry();
+    size_t n_modules() const;
+    Hdf5MasterFile master() const;
+
+    DetectorType detector_type() const override;
+
+  private:
+    /**
+     * @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 frame at the given frame index into the image buffer
+     * @param frame_number frame number to read
+     * @param n_frames number of frames to read (default is 1)
+     * @param image_buf buffer to store the frame
+     */
+    void get_frame_into(size_t frame_index, std::byte *frame_buffer,
+                        size_t n_frames = 1, DetectorHeader *header = nullptr);
+
+    /**
+     * @brief read the frame at the given frame index into the image buffer
+     * @param frame_index frame number to read
+     * @param n_frames number of frames to read (default is 1)
+     * @param frame_buffer buffer to store the frame
+     */
+    void get_data_into(size_t frame_index, std::byte *frame_buffer,
+                       size_t n_frames = 1);
+
+    /**
+     * @brief read the header at the given frame index into the header buffer
+     * @param frame_index frame number to read
+     * @param part_index part index to read (for virtual datasets)
+     * @param header buffer to store the header
+     */
+    void get_header_into(size_t frame_index, int part_index,
+                         DetectorHeader *header);
+
+    /**
+     * @brief read the header of the file
+     * @param fname path to the data subfile
+     * @return DetectorHeader
+     */
+    static DetectorHeader read_header(const std::filesystem::path &fname);
+
+    void open_data_file();
+    void open_header_files();
+};
+
+} // namespace aare

include/aare/Hdf5MasterFile.hpp

@@ -0,0 +1,135 @@
+#pragma once
+#include "aare/defs.hpp"
+#include "aare/scan_parameters.hpp"
+
+#include "H5Cpp.h"
+#include <filesystem>
+#include <fmt/format.h>
+#include <fstream>
+#include <optional>
+
+namespace aare {
+
+using ns = std::chrono::nanoseconds;
+
+/**
+ * @brief Class for parsing a master file either in our .json format or the old
+ * .Hdf5 format
+ */
+class Hdf5MasterFile {
+    std::filesystem::path m_file_name{};
+    std::string m_version;
+    DetectorType m_type;
+    TimingMode m_timing_mode;
+    xy m_geometry{};
+    int m_image_size_in_bytes{};
+    int m_pixels_y{};
+    int m_pixels_x{};
+    int m_max_frames_per_file{};
+    FrameDiscardPolicy m_frame_discard_policy{};
+    int m_frame_padding{};
+    std::optional<ScanParameters> m_scan_parameters{};
+    size_t m_total_frames_expected{};
+    std::optional<ns> m_exptime{};
+    std::optional<ns> m_period{};
+    std::optional<BurstMode> m_burst_mode{};
+    std::optional<int> m_number_of_udp_interfaces{};
+    int m_bitdepth{};
+    std::optional<bool> m_ten_giga{};
+    std::optional<int> m_threshold_energy{};
+    std::optional<std::vector<int>> m_threshold_energy_all{};
+    std::optional<ns> m_subexptime{};
+    std::optional<ns> m_subperiod{};
+    std::optional<bool> m_quad{};
+    std::optional<int> m_number_of_rows{};
+    std::optional<std::vector<size_t>> m_rate_corrections{};
+    std::optional<uint32_t> m_adc_mask{};
+    bool m_analog_flag{};
+    std::optional<int> m_analog_samples{};
+    bool m_digital_flag{};
+    std::optional<int> m_digital_samples{};
+    std::optional<int> m_dbit_offset{};
+    std::optional<size_t> m_dbit_list{};
+    std::optional<int> m_transceiver_mask{};
+    bool m_transceiver_flag{};
+    std::optional<int> m_transceiver_samples{};
+    // g1 roi - will not be implemented?
+    std::optional<ROI> m_roi{};
+    std::optional<int> m_counter_mask{};
+    std::optional<std::vector<ns>> m_exptime_array{};
+    std::optional<std::vector<ns>> m_gate_delay_array{};
+    std::optional<int> m_gates{};
+    std::optional<std::map<std::string, std::string>>
+        m_additional_json_header{};
+    size_t m_frames_in_file{};
+
+    // TODO! should these be bool?
+
+  public:
+    Hdf5MasterFile(const std::filesystem::path &fpath);
+
+    std::filesystem::path file_name() const;
+
+    const std::string &version() const; //!< For example "7.2"
+    const DetectorType &detector_type() const;
+    const TimingMode &timing_mode() const;
+    xy geometry() const;
+    int image_size_in_bytes() const;
+    int pixels_y() const;
+    int pixels_x() const;
+    int max_frames_per_file() const;
+    const FrameDiscardPolicy &frame_discard_policy() const;
+    int frame_padding() const;
+    std::optional<ScanParameters> scan_parameters() const;
+    size_t total_frames_expected() const;
+    std::optional<ns> exptime() const;
+    std::optional<ns> period() const;
+    std::optional<BurstMode> burst_mode() const;
+    std::optional<int> number_of_udp_interfaces() const;
+    int bitdepth() const;
+    std::optional<bool> ten_giga() const;
+    std::optional<int> threshold_energy() const;
+    std::optional<std::vector<int>> threshold_energy_all() const;
+    std::optional<ns> subexptime() const;
+    std::optional<ns> subperiod() const;
+    std::optional<bool> quad() const;
+    std::optional<int> number_of_rows() const;
+    std::optional<std::vector<size_t>> rate_corrections() const;
+    std::optional<uint32_t> adc_mask() const;
+    bool analog_flag() const;
+    std::optional<int> analog_samples() const;
+    bool digital_flag() const;
+    std::optional<int> digital_samples() const;
+    std::optional<int> dbit_offset() const;
+    std::optional<size_t> dbit_list() const;
+    std::optional<int> transceiver_mask() const;
+    bool transceiver_flag() const;
+    std::optional<int> transceiver_samples() const;
+    // g1 roi - will not be implemented?
+    std::optional<ROI> roi() const;
+    std::optional<int> counter_mask() const;
+    std::optional<std::vector<ns>> exptime_array() const;
+    std::optional<std::vector<ns>> gate_delay_array() const;
+    std::optional<int> gates() const;
+    std::optional<std::map<std::string, std::string>>
+    additional_json_header() const;
+    size_t frames_in_file() const;
+    size_t n_modules() const;
+
+  private:
+    static const std::string metadata_group_name;
+    void parse_acquisition_metadata(const std::filesystem::path &fpath);
+
+    template <typename T>
+    T h5_read_scalar_dataset(const H5::DataSet &dataset,
+                             const H5::DataType &data_type);
+
+    template <typename T>
+    T h5_get_scalar_dataset(const H5::H5File &file,
+                            const std::string &dataset_name);
+};
+
+template <>
+std::string Hdf5MasterFile::h5_read_scalar_dataset<std::string>(
+    const H5::DataSet &dataset, const H5::DataType &data_type);
+} // namespace aare

include/aare/Interpolator.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/CalculateEta.hpp"
@@ -18,10 +17,7 @@ struct Photon {
 };
 
 class Interpolator {
-    // marginal CDF of eta_x (if rosenblatt applied), conditional
-    // CDF of eta_x conditioned on eta_y
     NDArray<double, 3> m_ietax;
-    // conditional CDF of eta_y conditioned on eta_x
     NDArray<double, 3> m_ietay;
 
     NDArray<double, 1> m_etabinsx;
@@ -29,210 +25,106 @@ class Interpolator {
     NDArray<double, 1> m_energy_bins;
 
   public:
-    /**
-     * @brief Constructor for the Interpolator class
-     * @param etacube joint distribution of etaX, etaY and photon energy
-     * @param xbins bin edges for etaX
-     * @param ybins bin edges for etaY
-     * @param ebins bin edges for photon energy
-     * @note note first dimension is etaX, second etaY, third photon energy
-     */
     Interpolator(NDView<double, 3> etacube, NDView<double, 1> xbins,
                  NDView<double, 1> ybins, NDView<double, 1> ebins);
-
-    /**
-     * @brief Constructor for the Interpolator class
-     * @param xbins bin edges for etaX
-     * @param ybins bin edges for etaY
-     * @param ebins bin edges for photon energy
-     */
-    Interpolator(NDView<double, 1> xbins, NDView<double, 1> ybins,
-                 NDView<double, 1> ebins);
-
-    /**
-     * @brief transforms the joint eta distribution of etaX and etaY to the two
-     * independant uniform distributions based on the Roseblatt transform for
-     * each energy level
-     * @param etacube joint distribution of etaX, etaY and photon energy
-     * @note note first dimension is etaX, second etaY, third photon energy
-     */
-    void rosenblatttransform(NDView<double, 3> etacube);
-
     NDArray<double, 3> get_ietax() { return m_ietax; }
     NDArray<double, 3> get_ietay() { return m_ietay; }
 
-    /**
-     * @brief interpolates the cluster centers for all clusters to a better
-     * precision
-     * @tparam ClusterType Type of Clusters to interpolate
-     * @tparam Etafunction Function object that calculates desired eta default:
-     * calculate_eta2
-     * @return interpolated photons (photon positions are given as double but
-     * following row column format e.g. x=0, y=0 means top row and first column
-     * of frame)
-     */
-    template <auto EtaFunction = calculate_eta2, typename ClusterType,
+    template <typename ClusterType,
               typename Eanble = std::enable_if_t<is_cluster_v<ClusterType>>>
     std::vector<Photon> interpolate(const ClusterVector<ClusterType> &clusters);
-
-  private:
-    /**
-     * @brief implements underlying interpolation logic based on EtaFunction
-     * Type
-     * @tparam EtaFunction Function object that calculates desired eta default:
-     * @param u: transformed photon position in x between [0,1]
-     * @param v: transformed photon position in y between [0,1]
-     * @param c: corner of eta
-     */
-    template <auto EtaFunction, typename ClusterType>
-    void interpolation_logic(Photon &photon, const double u, const double v,
-                             const corner c = corner::cTopLeft);
-
-    /**
-     *  @brief bilinear interpolation of the transformed eta values
-     * @param ix index of etaX bin
-     * @param iy index of etaY bin
-     * @param ie index of energy bin
-     * @return pair of interpolated transformed eta values (ietax, ietay)
-     */
-    template <typename T>
-    std::pair<double, double>
-    bilinear_interpolation(const size_t ix, const size_t iy, const size_t ie,
-                           const Eta2<T> &eta);
 };
 
-template <typename T>
-std::pair<double, double>
-Interpolator::bilinear_interpolation(const size_t ix, const size_t iy,
-                                     const size_t ie, const Eta2<T> &eta) {
-    auto next_index_y = static_cast<ssize_t>(iy + 1) >= m_ietax.shape(1)
-                            ? m_ietax.shape(1) - 1
-                            : iy + 1;
-    auto next_index_x = static_cast<ssize_t>(ix + 1) >= m_ietax.shape(0)
-                            ? m_ietax.shape(0) - 1
-                            : ix + 1;
-
-    // bilinear interpolation
-    double ietax_interp_left = linear_interpolation(
-        {m_etabinsy(iy), m_etabinsy(iy + 1)},
-        {m_ietax(ix, iy, ie), m_ietax(ix, next_index_y, ie)}, eta.y);
-    double ietax_interp_right =
-        linear_interpolation({m_etabinsy(iy), m_etabinsy(iy + 1)},
-                             {m_ietax(next_index_x, iy, ie),
-                              m_ietax(next_index_x, next_index_y, ie)},
-                             eta.y);
-
-    // transformed photon position x between [0,1]
-    double ietax_interpolated =
-        linear_interpolation({m_etabinsx(ix), m_etabinsx(ix + 1)},
-                             {ietax_interp_left, ietax_interp_right}, eta.x);
-
-    double ietay_interp_left = linear_interpolation(
-        {m_etabinsx(ix), m_etabinsx(ix + 1)},
-        {m_ietay(ix, iy, ie), m_ietay(next_index_x, iy, ie)}, eta.x);
-    double ietay_interp_right =
-        linear_interpolation({m_etabinsx(ix), m_etabinsx(ix + 1)},
-                             {m_ietay(ix, next_index_y, ie),
-                              m_ietay(next_index_x, next_index_y, ie)},
-                             eta.x);
-
-    // transformed photon position y between [0,1]
-    double ietay_interpolated =
-        linear_interpolation({m_etabinsy(iy), m_etabinsy(iy + 1)},
-                             {ietay_interp_left, ietay_interp_right}, eta.y);
-
-    return {ietax_interpolated, ietay_interpolated};
-}
-
-template <auto EtaFunction, typename ClusterType, typename Enable>
+// TODO: generalize to support any clustertype!!! otherwise add std::enable_if_t
+// to only take Cluster2x2 and Cluster3x3
+template <typename ClusterType, typename Enable>
 std::vector<Photon>
 Interpolator::interpolate(const ClusterVector<ClusterType> &clusters) {
     std::vector<Photon> photons;
     photons.reserve(clusters.size());
 
-    for (const ClusterType &cluster : clusters) {
+    if (clusters.cluster_size_x() == 3 || clusters.cluster_size_y() == 3) {
+        for (const ClusterType &cluster : clusters) {
 
-        auto eta = EtaFunction(cluster);
+            auto eta = calculate_eta2(cluster);
 
-        Photon photon;
-        photon.x = cluster.x;
-        photon.y = cluster.y;
-        photon.energy = static_cast<decltype(photon.energy)>(eta.sum);
+            Photon photon;
+            photon.x = cluster.x;
+            photon.y = cluster.y;
+            photon.energy = static_cast<decltype(photon.energy)>(eta.sum);
 
-        // std::cout << "eta.x: " << eta.x << " eta.y: " << eta.y << std::endl;
+            // auto ie = nearest_index(m_energy_bins, photon.energy)-1;
+            // auto ix = nearest_index(m_etabinsx, eta.x)-1;
+            // auto iy = nearest_index(m_etabinsy, eta.y)-1;
+            // Finding the index of the last element that is smaller
+            // should work fine as long as we have many bins
+            auto ie = last_smaller(m_energy_bins, photon.energy);
+            auto ix = last_smaller(m_etabinsx, eta.x);
+            auto iy = last_smaller(m_etabinsy, eta.y);
 
-        // Finding the index of the last element that is smaller
-        // should work fine as long as we have many bins
-        auto ie = last_smaller(m_energy_bins, photon.energy);
-        auto ix = last_smaller(m_etabinsx, eta.x);
-        auto iy = last_smaller(m_etabinsy, eta.y);
+            // fmt::print("ex: {}, ix: {}, iy: {}\n", ie, ix, iy);
 
-        // std::cout << "ix: " << ix << " iy: " << iy << std::endl;
+            double dX, dY;
+            // cBottomLeft = 0,
+            // cBottomRight = 1,
+            // cTopLeft = 2,
+            // cTopRight = 3
+            switch (static_cast<corner>(eta.c)) {
+            case corner::cTopLeft:
+                dX = -1.;
+                dY = 0;
+                break;
+            case corner::cTopRight:;
+                dX = 0;
+                dY = 0;
+                break;
+            case corner::cBottomLeft:
+                dX = -1.;
+                dY = -1.;
+                break;
+            case corner::cBottomRight:
+                dX = 0.;
+                dY = -1.;
+                break;
+            }
+            photon.x += m_ietax(ix, iy, ie) * 2 + dX;
+            photon.y += m_ietay(ix, iy, ie) * 2 + dY;
+            photons.push_back(photon);
+        }
+    } else if (clusters.cluster_size_x() == 2 ||
+               clusters.cluster_size_y() == 2) {
+        for (const ClusterType &cluster : clusters) {
+            auto eta = calculate_eta2(cluster);
 
-        // TODO: bilinear interpolation only works if all bins have a size > 1 -
-        // otherwise bilinear interpolation with zero values which skew the
-        // results
-        // TODO: maybe trim the bins at the edges with zero values beforehand
-        // auto [ietax_interpolated, ietay_interpolated] =
-        // bilinear_interpolation(ix, iy, ie, eta);
+            Photon photon;
+            photon.x = cluster.x;
+            photon.y = cluster.y;
+            photon.energy = static_cast<decltype(photon.energy)>(eta.sum);
 
-        double ietax_interpolated = m_ietax(ix, iy, ie);
-        double ietay_interpolated = m_ietay(ix, iy, ie);
+            // Now do some actual interpolation.
+            // Find which energy bin the cluster is in
+            //  auto ie = nearest_index(m_energy_bins, photon.energy)-1;
+            //  auto ix = nearest_index(m_etabinsx, eta.x)-1;
+            //  auto iy = nearest_index(m_etabinsy, eta.y)-1;
+            // Finding the index of the last element that is smaller
+            // should work fine as long as we have many bins
+            auto ie = last_smaller(m_energy_bins, photon.energy);
+            auto ix = last_smaller(m_etabinsx, eta.x);
+            auto iy = last_smaller(m_etabinsy, eta.y);
 
-        interpolation_logic<EtaFunction, ClusterType>(
-            photon, ietax_interpolated, ietay_interpolated, eta.c);
+            photon.x += m_ietax(ix, iy, ie) *
+                        2; // eta goes between 0 and 1 but we could move the hit
+                           // anywhere in the 2x2
+            photon.y += m_ietay(ix, iy, ie) * 2;
+            photons.push_back(photon);
+        }
 
-        photons.push_back(photon);
+    } else {
+        throw std::runtime_error(
+            "Only 3x3 and 2x2 clusters are supported for interpolation");
     }
 
     return photons;
 }
 
-template <auto EtaFunction, typename ClusterType>
-void Interpolator::interpolation_logic(Photon &photon, const double u,
-                                       const double v, const corner c) {
-
-    // std::cout << "u: " << u << " v: " << v << std::endl;
-
-    // TODO: try to call this with std::is_same_v and have it constexpr if
-    // possible
-    if (EtaFunction == &calculate_eta2<typename ClusterType::value_type,
-                                       ClusterType::cluster_size_x,
-                                       ClusterType::cluster_size_y,
-                                       typename ClusterType::coord_type> ||
-        EtaFunction == &calculate_full_eta2<typename ClusterType::value_type,
-                                            ClusterType::cluster_size_x,
-                                            ClusterType::cluster_size_y,
-                                            typename ClusterType::coord_type>) {
-        double dX{}, dY{};
-
-        // TODO: could also chaneg the sign of the eta calculation
-        switch (c) {
-        case corner::cTopLeft:
-            dX = -1.0;
-            dY = -1.0;
-            break;
-        case corner::cTopRight:;
-            dX = 0.0;
-            dY = -1.0;
-            break;
-        case corner::cBottomLeft:
-            dX = -1.0;
-            dY = 0.0;
-            break;
-        case corner::cBottomRight:
-            dX = 0.0;
-            dY = 0.0;
-            break;
-        }
-        photon.x = photon.x + 0.5 + u + dX; // use pixel center + 0.5
-        photon.y = photon.y + 0.5 + v +
-                   dY; // eta2 calculates the ratio between bottom and sum of
-                       // bottom and top  shift by 1 add eta value correctly
-    } else {
-        photon.x += u;
-        photon.y += v;
-    }
-}
-
 } // namespace aare

include/aare/JungfrauDataFile.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include <cstdint>
 #include <filesystem>

include/aare/NDArray.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 /*
 Container holding image data, or a time series of image data in contigious
@@ -26,7 +25,7 @@ template <typename T, ssize_t Ndim = 2>
 class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
     std::array<ssize_t, Ndim> shape_;
     std::array<ssize_t, Ndim> strides_;
-    size_t size_{}; //TODO! do we need to store size when we have shape?
+    size_t size_{};
     T *data_;
 
   public:
@@ -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.
@@ -44,7 +43,8 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
      */
     explicit NDArray(std::array<ssize_t, Ndim> shape)
         : shape_(shape), strides_(c_strides<Ndim>(shape_)),
-          size_(num_elements(shape_)),
+          size_(std::accumulate(shape_.begin(), shape_.end(), 1,
+                                std::multiplies<>())),
           data_(new T[size_]) {}
 
     /**
@@ -79,24 +79,6 @@ class NDArray : public ArrayExpr<NDArray<T, Ndim>, Ndim> {
         other.reset(); // TODO! is this necessary?
     }
 
-
-    //Move constructor from an an array with Ndim + 1
-    template <ssize_t M, typename = std::enable_if_t<(M == Ndim + 1)>>
-    NDArray(NDArray<T, M> &&other) 
-        : shape_(drop_first_dim(other.shape())),
-          strides_(c_strides<Ndim>(shape_)), size_(num_elements(shape_)),
-          data_(other.data()) {
-
-            // For now only allow move if the size matches, to avoid unreachable data
-            // if the use case arises we can remove this check
-            if(size() != other.size()) {
-                data_ = nullptr; // avoid double free, other will clean up the memory in it's destructor
-                throw std::runtime_error(LOCATION +
-                                         "Size mismatch in move constructor of NDArray<T, Ndim-1>");
-            }
-        other.reset();
-    }
-
     // Copy constructor
     NDArray(const NDArray &other)
         : shape_(other.shape_), strides_(c_strides<Ndim>(shape_)),
@@ -398,6 +380,12 @@ NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
     result *= value;
     return result;
 }
+// template <typename T, ssize_t Ndim> void NDArray<T, Ndim>::Print() {
+//     if (shape_[0] < 20 && shape_[1] < 20)
+//         Print_all();
+//     else
+//         Print_some();
+// }
 
 template <typename T, ssize_t Ndim>
 std::ostream &operator<<(std::ostream &os, const NDArray<T, Ndim> &arr) {
@@ -449,23 +437,4 @@ NDArray<T, Ndim> load(const std::string &pathname,
     return img;
 }
 
-template <typename RT, typename NT, typename DT, ssize_t Ndim>
-NDArray<RT, Ndim> safe_divide(const NDArray<NT, Ndim> &numerator,
-                              const NDArray<DT, Ndim> &denominator) {
-    if (numerator.shape() != denominator.shape()) {
-        throw std::runtime_error(
-            "Shapes of numerator and denominator must match");
-    }
-    NDArray<RT, Ndim> result(numerator.shape());
-    for (ssize_t i = 0; i < numerator.size(); ++i) {
-        if (denominator[i] != 0) {
-            result[i] =
-                static_cast<RT>(numerator[i]) / static_cast<RT>(denominator[i]);
-        } else {
-            result[i] = RT{0}; // or handle division by zero as needed
-        }
-    }
-    return result;
-}
-
 } // namespace aare

include/aare/NDView.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/ArrayExpr.hpp"
 #include "aare/defs.hpp"
@@ -27,33 +26,6 @@ Shape<Ndim> make_shape(const std::vector<size_t> &shape) {
     return arr;
 }
 
-
-/**
- * @brief Helper function to drop the first dimension of a shape.
- * This is useful when you want to create a 2D view from a 3D array.
- * @param shape The shape to drop the first dimension from.
- * @return A new shape with the first dimension dropped.
- */
-template<size_t Ndim>
-Shape<Ndim-1> drop_first_dim(const Shape<Ndim> &shape) {
-    static_assert(Ndim > 1, "Cannot drop first dimension from a 1D shape");
-    Shape<Ndim - 1> new_shape;
-    std::copy(shape.begin() + 1, shape.end(), new_shape.begin());
-    return new_shape;
-}
-
-/**
- * @brief Helper function when constructing NDArray/NDView. Calculates the number
- * of elements in the resulting array from a shape.
- * @param shape The shape to calculate the number of elements for.
- * @return The number of elements in and NDArray/NDView of that shape.
- */
-template <size_t Ndim>
-size_t num_elements(const Shape<Ndim> &shape) {
-    return std::accumulate(shape.begin(), shape.end(), 1,
-                           std::multiplies<size_t>());
-}
-
 template <ssize_t Dim = 0, typename Strides>
 ssize_t element_offset(const Strides & /*unused*/) {
     return 0;
@@ -94,28 +66,24 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
         : buffer_(buffer), strides_(c_strides<Ndim>(shape)), shape_(shape),
           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<>())) {}
+
     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) == 1 && (Ndim > 1), NDView<T, Ndim - 1>> operator()(Ix... index) {
-        // return a view of the next dimension
-        std::array<ssize_t, Ndim - 1> new_shape{};
-        std::copy_n(shape_.begin() + 1, Ndim - 1, new_shape.begin());
-        return NDView<T, Ndim - 1>(&buffer_[element_offset(strides_, index...)],
-                                   new_shape);
-        
-    }
-
-    template <typename... Ix>
-    std::enable_if_t<sizeof...(Ix) == Ndim, const T &> operator()(Ix... index) const {
+    std::enable_if_t<sizeof...(Ix) == Ndim, T &> operator()(Ix... index) const {
         return buffer_[element_offset(strides_, index...)];
     }
 
-
     ssize_t size() const { return static_cast<ssize_t>(size_); }
     size_t total_bytes() const { return size_ * sizeof(T); }
     std::array<ssize_t, Ndim> strides() const noexcept { return strides_; }
@@ -124,27 +92,13 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
     T *end() { return buffer_ + size_; }
     T const *begin() const { return buffer_; }
     T const *end() const { return buffer_ + size_; }
-    
-    
-
-
-
-    /**
-     * @brief Access element at index i.
-     */
-    T &operator[](ssize_t i)  { return buffer_[i]; }
-
-    /**
-     * @brief Access element at index i.
-     */
-    const T &operator[](ssize_t i) const { return buffer_[i]; }
+    T &operator()(ssize_t i) const { return buffer_[i]; }
+    T &operator[](ssize_t i) const { return buffer_[i]; }
 
     bool operator==(const NDView &other) const {
         if (size_ != other.size_)
             return false;
-        if (shape_ != other.shape_)
-            return false;
-        for (size_t i = 0; i != size_; ++i) {
+        for (uint64_t i = 0; i != size_; ++i) {
             if (buffer_[i] != other.buffer_[i])
                 return false;
         }
@@ -203,25 +157,8 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
     auto shape(ssize_t i) const { return shape_[i]; }
 
     T *data() { return buffer_; }
-    const T *data() const { return buffer_; }
     void print_all() const;
 
-    /**
-     * @brief Create a subview of a range of the first dimension. 
-     * This is useful for splitting a batches of frames in parallel processing.
-     * @param first The first index of the subview (inclusive).
-     * @param last The last index of the subview (exclusive).
-     * @return A new NDView that is a subview of the current view.
-     * @throws std::runtime_error if the range is invalid.
-     */
-    NDView sub_view(ssize_t first, ssize_t last) const {
-        if (first < 0 || last > shape_[0] || first >= last)
-            throw std::runtime_error(LOCATION + "Invalid sub_view range");
-        auto new_shape = shape_;
-        new_shape[0] = last - first;
-        return NDView(buffer_ + first * strides_[0], new_shape);
-    }
-
   private:
     T *buffer_{nullptr};
     std::array<ssize_t, Ndim> strides_{};
@@ -243,7 +180,6 @@ class NDView : public ArrayExpr<NDView<T, Ndim>, Ndim> {
         return *this;
     }
 };
-
 template <typename T, ssize_t Ndim> void NDView<T, Ndim>::print_all() const {
     for (auto row = 0; row < shape_[0]; ++row) {
         for (auto col = 0; col < shape_[1]; ++col) {

include/aare/NumpyFile.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Dtype.hpp"
 #include "aare/FileInterface.hpp"

include/aare/NumpyHelpers.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 
 #pragma once
 #include <algorithm>

include/aare/Pedestal.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Frame.hpp"
 #include "aare/NDArray.hpp"

include/aare/PixelMap.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/NDArray.hpp"

include/aare/ProducerConsumerQueue.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 /*
  * Copyright (c) Meta Platforms, Inc. and affiliates.
  *

include/aare/RawFile.hpp

@@ -1,20 +1,27 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
-#include "aare/DetectorGeometry.hpp"
 #include "aare/FileInterface.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;
+    }
+};
+
 /**
  * @brief Class to read .raw files. The class will parse the master file
  * to find the correct geometry for the frames.
@@ -22,12 +29,11 @@ namespace aare {
  * Consider using that unless you need raw file specific functionality.
  */
 class RawFile : public FileInterface {
-
     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:
@@ -61,21 +67,13 @@ class RawFile : public FileInterface {
     size_t rows() const override;
     size_t cols() const override;
     size_t bitdepth() const override;
+    xy geometry();
     size_t n_modules() const;
-    size_t n_modules_in_roi() const;
-    xy geometry() const;
 
     RawMasterFile master() const;
 
     DetectorType detector_type() const override;
 
-    /**
-     * @brief read the header of the file
-     * @param fname path to the data subfile
-     * @return DetectorHeader
-     */
-    static DetectorHeader read_header(const std::filesystem::path &fname);
-
   private:
     /**
      * @brief read the frame at the given frame index into the image buffer
@@ -93,7 +91,15 @@ class RawFile : public FileInterface {
      */
     Frame get_frame(size_t frame_index);
 
+    /**
+     * @brief read the header of the file
+     * @param fname path to the data subfile
+     * @return DetectorHeader
+     */
+    static DetectorHeader read_header(const std::filesystem::path &fname);
+
     void open_subfiles();
+    void find_geometry();
 };
 
 } // namespace aare

include/aare/RawMasterFile.hpp

@@ -1,7 +1,7 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/defs.hpp"
-#include <algorithm>
+#include "aare/scan_parameters.hpp"
+
 #include <filesystem>
 #include <fmt/format.h>
 #include <fstream>
@@ -41,31 +41,6 @@ class RawFileNameComponents {
     void set_old_scheme(bool old_scheme);
 };
 
-class ScanParameters {
-    bool m_enabled = false;
-    DACIndex m_dac{};
-    int m_start = 0;
-    int m_stop = 0;
-    int m_step = 0;
-    int64_t m_settleTime = 0; // [ns]
-
-  public:
-    ScanParameters(const std::string &par);
-    ScanParameters(const bool enabled, const DACIndex dac, const int start,
-                   const int stop, const int step, const int64_t settleTime);
-    ScanParameters() = default;
-    ScanParameters(const ScanParameters &) = default;
-    ScanParameters &operator=(const ScanParameters &) = default;
-    ScanParameters(ScanParameters &&) = default;
-    int start() const;
-    int stop() const;
-    int step() const;
-    DACIndex dac() const;
-    bool enabled() const;
-    int64_t settleTime() const;
-    void increment_stop();
-};
-
 /**
  * @brief Class for parsing a master file either in our .json format or the old
  * .raw format
@@ -82,10 +57,8 @@ class RawMasterFile {
     size_t m_pixels_y{};
     size_t m_pixels_x{};
     size_t m_bitdepth{};
-    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
@@ -103,7 +76,7 @@ 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_counter_mask;
+    std::optional<uint8_t> m_quad;
 
     std::optional<ROI> m_roi;
 
@@ -122,19 +95,17 @@ 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> counter_mask() const;
+    std::optional<uint8_t> quad() const;
 
     std::optional<ROI> roi() const;
 
@@ -143,7 +114,6 @@ class RawMasterFile {
   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

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 #include "aare/Frame.hpp"
 #include "aare/defs.hpp"

include/aare/VarClusterFinder.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include <algorithm>
@@ -241,14 +240,14 @@ template <typename T> void VarClusterFinder<T>::first_pass() {
 
     for (ssize_t i = 0; i < original_.size(); ++i) {
         if (use_noise_map)
-            threshold_ = 5 * noiseMap[i];
-        binary_[i] = (original_[i] > threshold_);
+            threshold_ = 5 * noiseMap(i);
+        binary_(i) = (original_(i) > threshold_);
     }
 
     for (int i = 0; i < shape_[0]; ++i) {
         for (int j = 0; j < shape_[1]; ++j) {
 
-            // do we have something to process?
+            // do we have someting to process?
             if (binary_(i, j)) {
                 auto tmp = check_neighbours(i, j);
                 if (tmp != 0) {

include/aare/algorithm.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 
 #pragma once
 #include <aare/NDArray.hpp>
@@ -110,19 +109,4 @@ template <typename Container> bool all_equal(const Container &c) {
     return false;
 }
 
-/**
- * linear interpolation
- * @param bin_edge left and right bin edges
- * @param bin_values function values at bin edges
- * @param coord coordinate to interpolate at
- * @return interpolated value at coord
- */
-inline double linear_interpolation(const std::pair<double, double> &bin_edge,
-                                   const std::pair<double, double> &bin_values,
-                                   const double coord) {
-    const double bin_width = bin_edge.second - bin_edge.first;
-    return bin_values.first * (1 - (coord - bin_edge.first) / bin_width) +
-           bin_values.second * (coord - bin_edge.first) / bin_width;
-}
-
 } // namespace aare

include/aare/calibration.hpp

@@ -1,210 +0,0 @@
-// SPDX-License-Identifier: MPL-2.0
-#pragma once
-
-#include "aare/NDArray.hpp"
-#include "aare/NDView.hpp"
-#include "aare/defs.hpp"
-#include "aare/utils/par.hpp"
-#include "aare/utils/task.hpp"
-#include <cstdint>
-#include <future>
-
-namespace aare {
-
-// Really try to convince the compile to inline this function
-// TODO! Clang?
-#if (defined(_MSC_VER) || defined(__INTEL_COMPILER))
-#define STRONG_INLINE __forceinline
-#else
-#define STRONG_INLINE inline
-#endif
-
-#if defined(__GNUC__)
-#define ALWAYS_INLINE __attribute__((always_inline)) inline
-#else
-#define ALWAYS_INLINE STRONG_INLINE
-#endif
-
-/**
- * @brief Get the gain from the raw ADC value. In Jungfrau the gain is
- * encoded in the left most 2 bits of the raw value.
- * 00 -> gain 0
- * 01 -> gain 1
- * 11 -> gain 2
- * @param raw the raw ADC value
- * @return the gain as an integer
- */
-ALWAYS_INLINE int get_gain(uint16_t raw) {
-    switch (raw >> 14) {
-    case 0:
-        return 0;
-    case 1:
-        return 1;
-    case 3:
-        return 2;
-    default:
-        return 0;
-    }
-}
-
-ALWAYS_INLINE uint16_t get_value(uint16_t raw) { return raw & ADC_MASK; }
-
-ALWAYS_INLINE std::pair<uint16_t, int16_t> get_value_and_gain(uint16_t raw) {
-    static_assert(
-        sizeof(std::pair<uint16_t, int16_t>) ==
-            sizeof(uint16_t) + sizeof(int16_t),
-        "Size of pair<uint16_t, int16_t> does not match expected size");
-    return {get_value(raw), get_gain(raw)};
-}
-
-template <class T>
-void apply_calibration_impl(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
-                            NDView<T, 3> ped, NDView<T, 3> cal, int start,
-                            int stop) {
-
-    for (int frame_nr = start; frame_nr != stop; ++frame_nr) {
-        for (int row = 0; row != raw_data.shape(1); ++row) {
-            for (int col = 0; col != raw_data.shape(2); ++col) {
-                auto [value, gain] =
-                    get_value_and_gain(raw_data(frame_nr, row, col));
-
-                // Using multiplication does not seem to speed up the code here
-                // ADU/keV is the standard unit for the calibration which
-                // means rewriting the formula is not worth it.
-                res(frame_nr, row, col) =
-                    (value - ped(gain, row, col)) / cal(gain, row, col);
-            }
-        }
-    }
-}
-
-template <class T>
-void apply_calibration_impl(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
-                            NDView<T, 2> ped, NDView<T, 2> cal, int start,
-                            int stop) {
-
-    for (int frame_nr = start; frame_nr != stop; ++frame_nr) {
-        for (int row = 0; row != raw_data.shape(1); ++row) {
-            for (int col = 0; col != raw_data.shape(2); ++col) {
-                auto [value, gain] =
-                    get_value_and_gain(raw_data(frame_nr, row, col));
-
-                // Using multiplication does not seem to speed up the code here
-                // ADU/keV is the standard unit for the calibration which
-                // means rewriting the formula is not worth it.
-
-                // Set the value to 0 if the gain is not 0
-                if (gain == 0)
-                    res(frame_nr, row, col) =
-                        (value - ped(row, col)) / cal(row, col);
-                else
-                    res(frame_nr, row, col) = 0;
-            }
-        }
-    }
-}
-
-template <class T, ssize_t Ndim = 3>
-void apply_calibration(NDView<T, 3> res, NDView<uint16_t, 3> raw_data,
-                       NDView<T, Ndim> ped, NDView<T, Ndim> cal,
-                       ssize_t n_threads = 4) {
-    std::vector<std::future<void>> futures;
-    futures.reserve(n_threads);
-    auto limits = split_task(0, raw_data.shape(0), n_threads);
-    for (const auto &lim : limits)
-        futures.push_back(std::async(
-            static_cast<void (*)(NDView<T, 3>, NDView<uint16_t, 3>,
-                                 NDView<T, Ndim>, NDView<T, Ndim>, int, int)>(
-                apply_calibration_impl),
-            res, raw_data, ped, cal, lim.first, lim.second));
-    for (auto &f : futures)
-        f.get();
-}
-
-template <bool only_gain0>
-std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>>
-sum_and_count_per_gain(NDView<uint16_t, 3> raw_data) {
-    constexpr ssize_t num_gains = only_gain0 ? 1 : 3;
-    NDArray<size_t, 3> accumulator(
-        std::array<ssize_t, 3>{num_gains, raw_data.shape(1), raw_data.shape(2)},
-        0);
-    NDArray<size_t, 3> count(
-        std::array<ssize_t, 3>{num_gains, raw_data.shape(1), raw_data.shape(2)},
-        0);
-    for (int frame_nr = 0; frame_nr != raw_data.shape(0); ++frame_nr) {
-        for (int row = 0; row != raw_data.shape(1); ++row) {
-            for (int col = 0; col != raw_data.shape(2); ++col) {
-                auto [value, gain] =
-                    get_value_and_gain(raw_data(frame_nr, row, col));
-                if (gain != 0 && only_gain0)
-                    continue;
-                accumulator(gain, row, col) += value;
-                count(gain, row, col) += 1;
-            }
-        }
-    }
-
-    return {std::move(accumulator), std::move(count)};
-}
-
-template <typename T, bool only_gain0 = false>
-NDArray<T, 3 - static_cast<ssize_t>(only_gain0)>
-calculate_pedestal(NDView<uint16_t, 3> raw_data, ssize_t n_threads) {
-
-    constexpr ssize_t num_gains = only_gain0 ? 1 : 3;
-    std::vector<std::future<std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>>>>
-        futures;
-    futures.reserve(n_threads);
-
-    auto subviews = make_subviews(raw_data, n_threads);
-
-    for (auto view : subviews) {
-        futures.push_back(std::async(
-            static_cast<std::pair<NDArray<size_t, 3>, NDArray<size_t, 3>> (*)(
-                NDView<uint16_t, 3>)>(&sum_and_count_per_gain<only_gain0>),
-            view));
-    }
-    Shape<3> shape{num_gains, raw_data.shape(1), raw_data.shape(2)};
-    NDArray<size_t, 3> accumulator(shape, 0);
-    NDArray<size_t, 3> count(shape, 0);
-
-    // Combine the results from the futures
-    for (auto &f : futures) {
-        auto [acc, cnt] = f.get();
-        accumulator += acc;
-        count += cnt;
-    }
-
-
-    // Will move to a NDArray<T, 3 - static_cast<ssize_t>(only_gain0)>
-    // if only_gain0 is true
-    return safe_divide<T>(accumulator, count);
-
-}
-
-/**
- * @brief Count the number of switching pixels in the raw data.
- * This function counts the number of pixels that switch between G1 and G2 gain.
- * It returns an NDArray with the number of switching pixels per pixel.
- * @param raw_data The NDView containing the raw data
- * @return An NDArray with the number of switching pixels per pixel
- */
-NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data);
-
-/**
- * @brief Count the number of switching pixels in the raw data.
- * This function counts the number of pixels that switch between G1 and G2 gain.
- * It returns an NDArray with the number of switching pixels per pixel.
- * @param raw_data The NDView containing the raw data
- * @param n_threads The number of threads to use for parallel processing
- * @return An NDArray with the number of switching pixels per pixel
- */
-NDArray<int, 2> count_switching_pixels(NDView<uint16_t, 3> raw_data,
-                                       ssize_t n_threads);
-
-template <typename T>
-auto calculate_pedestal_g0(NDView<uint16_t, 3> raw_data, ssize_t n_threads) {
-    return calculate_pedestal<T, true>(raw_data, n_threads);
-}
-
-} // namespace aare

include/aare/decode.hpp

@@ -1,12 +1,10 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
-#include "aare/defs.hpp"
+
 #include <aare/NDView.hpp>
 #include <cstdint>
 #include <vector>
 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,
@@ -14,25 +12,6 @@ void adc_sar_05_decode64to16(NDView<uint64_t, 2> input,
 void adc_sar_04_decode64to16(NDView<uint64_t, 2> input,
                              NDView<uint16_t, 2> output);
 
-/**
- * @brief Called with a 32 bit unsigned integer, shift by offset
- * and then return the lower 24 bits as an 32 bit integer
- * @param input 32-ibt input value
- * @param offset (should be in range 0-7 to allow for full 24 bits)
- * @return uint32_t 
- */
-uint32_t mask32to24bits(uint32_t input, BitOffset offset={});
-
-/**
- * @brief Expand 24 bit values in a 8bit buffer to 32bit unsigned integers
- * Used for detectors with 24bit counters in combination with CTB
- * 
- * @param input View of the 24 bit data as uint8_t (no 24bit native data type exists)
- * @param output Destination of the expanded data (32bit, unsigned) 
- * @param offset Offset within the first byte to where the data starts (0-7 bits)
- */
-void expand24to32bit(NDView<uint8_t,1> input, NDView<uint32_t,1> output, BitOffset offset={});
-
 /**
  * @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.

include/aare/defs.hpp

@@ -1,12 +1,15 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include "aare/Dtype.hpp"
+#include "aare/type_traits.hpp"
 
+#include <algorithm>
 #include <array>
 #include <cassert>
 #include <cstdint>
 #include <cstring>
+#include <iostream>
+#include <sstream>
 #include <stdexcept>
 #include <string>
 #include <string_view>
@@ -175,6 +178,35 @@ 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 {
     ssize_t xmin{};
     ssize_t xmax{};
@@ -216,171 +248,15 @@ enum class DetectorType {
     Unknown
 };
 
-/**
- * @brief Enum class to define the Digital to Analog converter
- * The values are the same as in slsDetectorPackage
- */
-enum DACIndex {
-    DAC_0,
-    DAC_1,
-    DAC_2,
-    DAC_3,
-    DAC_4,
-    DAC_5,
-    DAC_6,
-    DAC_7,
-    DAC_8,
-    DAC_9,
-    DAC_10,
-    DAC_11,
-    DAC_12,
-    DAC_13,
-    DAC_14,
-    DAC_15,
-    DAC_16,
-    DAC_17,
-    VSVP,
-    VTRIM,
-    VRPREAMP,
-    VRSHAPER,
-    VSVN,
-    VTGSTV,
-    VCMP_LL,
-    VCMP_LR,
-    VCAL,
-    VCMP_RL,
-    RXB_RB,
-    RXB_LB,
-    VCMP_RR,
-    VCP,
-    VCN,
-    VISHAPER,
-    VTHRESHOLD,
-    IO_DELAY,
-    VREF_DS,
-    VOUT_CM,
-    VIN_CM,
-    VREF_COMP,
-    VB_COMP,
-    VDD_PROT,
-    VIN_COM,
-    VREF_PRECH,
-    VB_PIXBUF,
-    VB_DS,
-    VREF_H_ADC,
-    VB_COMP_FE,
-    VB_COMP_ADC,
-    VCOM_CDS,
-    VREF_RSTORE,
-    VB_OPA_1ST,
-    VREF_COMP_FE,
-    VCOM_ADC1,
-    VREF_L_ADC,
-    VREF_CDS,
-    VB_CS,
-    VB_OPA_FD,
-    VCOM_ADC2,
-    VCASSH,
-    VTH2,
-    VRSHAPER_N,
-    VIPRE_OUT,
-    VTH3,
-    VTH1,
-    VICIN,
-    VCAS,
-    VCAL_N,
-    VIPRE,
-    VCAL_P,
-    VDCSH,
-    VBP_COLBUF,
-    VB_SDA,
-    VCASC_SFP,
-    VIPRE_CDS,
-    IBIAS_SFP,
-    ADC_VPP,
-    HIGH_VOLTAGE,
-    TEMPERATURE_ADC,
-    TEMPERATURE_FPGA,
-    TEMPERATURE_FPGAEXT,
-    TEMPERATURE_10GE,
-    TEMPERATURE_DCDC,
-    TEMPERATURE_SODL,
-    TEMPERATURE_SODR,
-    TEMPERATURE_FPGA2,
-    TEMPERATURE_FPGA3,
-    TRIMBIT_SCAN,
-    V_POWER_A = 100,
-    V_POWER_B = 101,
-    V_POWER_C = 102,
-    V_POWER_D = 103,
-    V_POWER_IO = 104,
-    V_POWER_CHIP = 105,
-    I_POWER_A = 106,
-    I_POWER_B = 107,
-    I_POWER_C = 108,
-    I_POWER_D = 109,
-    I_POWER_IO = 110,
-    V_LIMIT = 111,
-    SLOW_ADC0 = 1000,
-    SLOW_ADC1,
-    SLOW_ADC2,
-    SLOW_ADC3,
-    SLOW_ADC4,
-    SLOW_ADC5,
-    SLOW_ADC6,
-    SLOW_ADC7,
-    SLOW_ADC_TEMP
-};
-
-// helper pair class to easily expose in python
-template <typename T1, typename T2> struct Sum_index_pair {
-    T1 sum;
-    T2 index;
-};
-
-enum class corner : int {
-    cTopLeft = 0,
-    cTopRight = 1,
-    cBottomLeft = 2,
-    cBottomRight = 3
-};
-
 enum class TimingMode { Auto, Trigger };
 enum class FrameDiscardPolicy { NoDiscard, Discard, DiscardPartial };
-
-template <class T> T StringTo(const std::string &arg) { return T(arg); }
-
-template <class T> std::string ToString(T arg) { return T(arg); }
-
-template <> DetectorType StringTo(const std::string & /*name*/);
-template <> std::string ToString(DetectorType arg);
-
-template <> TimingMode StringTo(const std::string & /*mode*/);
-
-template <> FrameDiscardPolicy StringTo(const std::string & /*mode*/);
+enum class BurstMode {
+    Burst_Interal,
+    Burst_External,
+    Continuous_Internal,
+    Continuous_External
+};
 
 using DataTypeVariants = std::variant<uint16_t, uint32_t>;
 
-constexpr uint16_t ADC_MASK =
-    0x3FFF; // used to mask out the gain bits in Jungfrau
-
-/**
- * @brief Convert a string to a DACIndex
- * @param arg string representation of the dacIndex
- * @return DACIndex
- * @throw invalid argument error if the string does not match any DACIndex
- */
-template <> DACIndex StringTo(const std::string &arg);
-
-class BitOffset{
-    uint8_t m_offset{};
-    public:
-    BitOffset() = default;
-    explicit BitOffset(uint32_t offset);
-    uint8_t value() const {return m_offset;}
-    bool operator==(const BitOffset& other) const;
-    bool operator<(const BitOffset& other) const;
-
-};
-
 } // namespace aare

include/aare/geo_helpers.hpp

@@ -0,0 +1,15 @@
+#pragma once
+#include "aare/RawMasterFile.hpp" //ROI refactor away
+#include "aare/defs.hpp"
+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

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 /*Utility to log to console*/
 

include/aare/scan_parameters.hpp

@@ -0,0 +1,51 @@
+#pragma once
+
+#include <string>
+#include <sstream>
+
+namespace aare {
+
+class ScanParameters {
+    bool m_enabled = false;
+    std::string m_dac;
+    int m_start = 0;
+    int m_stop = 0;
+    int m_step = 0;
+    // ns m_dac_settle_time{0};
+    //  TODO! add settleTime, requires string to time conversion
+
+  public:
+    // "[enabled\ndac dac 4\nstart 500\nstop 2200\nstep 5\nsettleTime 100us\n]"
+    // TODO: use StringTo<ScanParameters> and move this to to_string
+    // add ways of setting the members of the class
+
+    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") {
+                m_enabled = true;
+            } else if (line.find("dac") != std::string::npos) {
+                m_dac = line.substr(4);
+            } else if (line.find("start") != std::string::npos) {
+                m_start = std::stoi(line.substr(6));
+            } else if (line.find("stop") != std::string::npos) {
+                m_stop = std::stoi(line.substr(5));
+            } else if (line.find("step") != std::string::npos) {
+                m_step = std::stoi(line.substr(5));
+            }
+        }
+    };
+    ScanParameters() = default;
+    ScanParameters(const ScanParameters &) = default;
+    ScanParameters &operator=(const ScanParameters &) = default;
+    ScanParameters(ScanParameters &&) = default;
+    int start() const { return m_start; };
+    int stop() const { return m_stop; };
+    int step() const { return m_step; };
+    const std::string &dac() const { return m_dac; };
+    bool enabled() const { return m_enabled; };
+    void increment_stop() { m_stop += 1; };
+};
+
+} // namespace aare

include/aare/string_utils.hpp

@@ -0,0 +1,11 @@
+#pragma once
+
+#include <string>
+
+namespace aare {
+
+std::string RemoveUnit(std::string &str);
+
+void TrimWhiteSpaces(std::string &s);
+
+} // namespace aare

include/aare/to_string.hpp

@@ -0,0 +1,288 @@
+#pragma once
+
+#include "aare/defs.hpp"
+#include "aare/scan_parameters.hpp"
+#include "aare/string_utils.hpp"
+
+#include <optional>
+#include <chrono>
+
+
+namespace aare {
+
+// generic
+template <class T, typename = std::enable_if_t<!is_duration<T>::value>>
+std::string ToString(T arg) {
+    return T(arg);
+}
+
+template <typename T,
+          std::enable_if_t<!is_duration<T>::value && !is_container<T>::value,
+                           int> = 0>
+T StringTo(const std::string &arg) {
+    return T(arg);
+}
+
+// time
+
+/** Convert std::chrono::duration with specified output unit */
+template <typename T, typename Rep = double>
+typename std::enable_if<is_duration<T>::value, std::string>::type
+ToString(T t, const std::string &unit) {
+    using std::chrono::duration;
+    using std::chrono::duration_cast;
+    std::ostringstream os;
+    if (unit == "ns")
+        os << duration_cast<duration<Rep, std::nano>>(t).count() << unit;
+    else if (unit == "us")
+        os << duration_cast<duration<Rep, std::micro>>(t).count() << unit;
+    else if (unit == "ms")
+        os << duration_cast<duration<Rep, std::milli>>(t).count() << unit;
+    else if (unit == "s")
+        os << duration_cast<duration<Rep>>(t).count() << unit;
+    else
+        throw std::runtime_error("Unknown unit: " + unit);
+    return os.str();
+}
+
+/** Convert std::chrono::duration automatically selecting the unit */
+template <typename From>
+typename std::enable_if<is_duration<From>::value, std::string>::type
+ToString(From t) {
+
+    using std::chrono::abs;
+    using std::chrono::duration_cast;
+    using std::chrono::microseconds;
+    using std::chrono::milliseconds;
+    using std::chrono::nanoseconds;
+    auto tns = duration_cast<nanoseconds>(t);
+    if (abs(tns) < microseconds(1)) {
+        return ToString(tns, "ns");
+    } else if (abs(tns) < milliseconds(1)) {
+        return ToString(tns, "us");
+    } else if (abs(tns) < milliseconds(99)) {
+        return ToString(tns, "ms");
+    } else {
+        return ToString(tns, "s");
+    }
+}
+template <class Rep, class Period>
+std::ostream &operator<<(std::ostream &os,
+                         const std::chrono::duration<Rep, Period> &d) {
+    return os << ToString(d);
+}
+
+template <typename T>
+T StringTo(const std::string &t, const std::string &unit) {
+    double tval{0};
+    try {
+        tval = std::stod(t);
+    } catch (const std::invalid_argument &e) {
+        throw std::invalid_argument("[ERROR] Could not convert string to time");
+    }
+
+    using std::chrono::duration;
+    using std::chrono::duration_cast;
+    if (unit == "ns") {
+        return duration_cast<T>(duration<double, std::nano>(tval));
+    } else if (unit == "us") {
+        return duration_cast<T>(duration<double, std::micro>(tval));
+    } else if (unit == "ms") {
+        return duration_cast<T>(duration<double, std::milli>(tval));
+    } else if (unit == "s" || unit.empty()) {
+        return duration_cast<T>(std::chrono::duration<double>(tval));
+    } else {
+        throw std::invalid_argument("[ERROR] Invalid unit in conversion from "
+                                    "string to std::chrono::duration");
+    }
+}
+
+template <typename T, std::enable_if_t<is_duration<T>::value, int> = 0>
+T StringTo(const std::string &t) {
+    std::string tmp{t};
+    auto unit = RemoveUnit(tmp);
+    return StringTo<T>(tmp, unit);
+}
+
+template <> inline bool StringTo(const std::string &s) {
+    int i = std::stoi(s, nullptr, 10);
+    switch (i) {
+    case 0:
+        return false;
+    case 1:
+        return true;
+    default:
+        throw std::runtime_error("Unknown boolean. Expecting be 0 or 1.");
+    }
+}
+
+template <> inline uint8_t StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    int value = std::stoi(s, nullptr, base);
+    if (value < std::numeric_limits<uint8_t>::min() ||
+        value > std::numeric_limits<uint8_t>::max()) {
+        throw std::runtime_error("Cannot scan uint8_t from string '" + s +
+                                 "'. Value must be in range 0 - 255.");
+    }
+    return static_cast<uint8_t>(value);
+}
+
+template <> inline uint16_t StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    int value = std::stoi(s, nullptr, base);
+    if (value < std::numeric_limits<uint16_t>::min() ||
+        value > std::numeric_limits<uint16_t>::max()) {
+        throw std::runtime_error("Cannot scan uint16_t from string '" + s +
+                                 "'. Value must be in range 0 - 65535.");
+    }
+    return static_cast<uint16_t>(value);
+}
+
+template <> inline uint32_t StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    return std::stoul(s, nullptr, base);
+}
+
+template <> inline uint64_t StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    return std::stoull(s, nullptr, base);
+}
+
+template <> inline int StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    return std::stoi(s, nullptr, base);
+}
+
+/*template <> inline size_t StringTo(const std::string &s) {
+    int base = s.find("0x") != std::string::npos ? 16 : 10;
+    return std::stoull(s, nullptr, base);
+}*/
+
+// vector
+template <typename T> std::string ToString(const std::vector<T> &vec) {
+    std::ostringstream oss;
+    oss << "[";
+    for (size_t i = 0; i < vec.size(); ++i) {
+        oss << vec[i];
+        if (i != vec.size() - 1)
+            oss << ", ";
+    }
+    oss << "]";
+    return oss.str();
+}
+
+template <typename T>
+std::ostream &operator<<(std::ostream &os, const std::vector<T> &v) {
+    return os << ToString(v);
+}
+
+template <typename Container,
+          std::enable_if_t<is_container<Container>::value &&
+                               !is_std_string_v<Container> /*&&
+                               !is_map_v<Container>*/
+                           ,
+                           int> = 0>
+Container StringTo(const std::string &s) {
+    using Value = typename Container::value_type;
+
+    // strip outer brackets
+    std::string str = s;
+    str.erase(
+        std::remove_if(str.begin(), str.end(),
+                       [](unsigned char c) { return c == '[' || c == ']'; }),
+        str.end());
+
+    std::stringstream ss(str);
+    std::string item;
+    Container result;
+
+    while (std::getline(ss, item, ',')) {
+        TrimWhiteSpaces(item);
+        if (!item.empty()) {
+            result.push_back(StringTo<Value>(item));
+        }
+    }
+    return result;
+}
+
+// map
+template <typename KeyType, typename ValueType>
+std::string ToString(const std::map<KeyType, ValueType> &m) {
+    std::ostringstream os;
+    os << '{';
+    if (!m.empty()) {
+        auto it = m.cbegin();
+        os << ToString(it->first) << ": " << ToString(it->second);
+        it++;
+        while (it != m.cend()) {
+            os << ", " << ToString(it->first) << ": " << ToString(it->second);
+            it++;
+        }
+    }
+    os << '}';
+    return os.str();
+}
+
+template <>
+inline std::map<std::string, std::string> StringTo(const std::string &s) {
+    std::map<std::string, std::string> result;
+    std::string str = s;
+
+    // Remove outer braces if present
+    if (!str.empty() && str.front() == '{' && str.back() == '}') {
+        str = str.substr(1, str.size() - 2);
+    }
+
+    std::stringstream ss(str);
+    std::string item;
+
+    while (std::getline(ss, item, ',')) {
+        auto colon_pos = item.find(':');
+        if (colon_pos == std::string::npos)
+            throw std::runtime_error("Missing ':' in item: " + item);
+
+        std::string key = item.substr(0, colon_pos);
+        std::string value = item.substr(colon_pos + 1);
+
+        TrimWhiteSpaces(key);
+        TrimWhiteSpaces(value);
+
+        result[key] = value;
+    }
+    return result;
+}
+
+// optional
+template <class T> std::string ToString(const std::optional<T> &opt) {
+    return opt ? ToString(*opt) : "nullopt";
+}
+
+template <typename T>
+std::ostream &operator<<(std::ostream &os, const std::optional<T> &opt) {
+    if (opt)
+        os << *opt;
+    else
+        os << "nullopt";
+    return os;
+}
+
+// enums
+template <> std::string ToString(DetectorType arg);
+template <> DetectorType StringTo(const std::string & /*name*/);
+
+template <> std::string ToString(TimingMode arg);
+template <> TimingMode StringTo(const std::string & /*mode*/);
+
+template <> std::string ToString(FrameDiscardPolicy arg);
+template <> FrameDiscardPolicy StringTo(const std::string & /*mode*/);
+
+template <> std::string ToString(BurstMode arg);
+template <> BurstMode StringTo(const std::string & /*mode*/);
+
+template <> std::string ToString(ROI arg);
+std::ostream &operator<<(std::ostream &os, const ROI &roi);
+
+template <> std::string ToString(ScanParameters arg);
+std::ostream &operator<<(std::ostream &os, const ScanParameters &r);
+
+} // namespace aare

include/aare/type_traits.hpp

@@ -0,0 +1,72 @@
+#pragma once
+
+#include <type_traits>
+
+namespace aare {
+
+/**
+ * Type trait to check if a template parameter is a std::chrono::duration
+ */
+
+template <typename T, typename _ = void>
+struct is_duration : std::false_type {};
+
+template <typename... Ts> struct is_duration_helper {};
+
+template <typename T>
+struct is_duration<T,
+                   typename std::conditional<
+                       false,
+                       is_duration_helper<typename T::rep, typename T::period,
+                                          decltype(std::declval<T>().min()),
+                                          decltype(std::declval<T>().max()),
+                                          decltype(std::declval<T>().zero())>,
+                       void>::type> : public std::true_type {};
+
+/**
+ * Type trait to evaluate if template parameter is
+ * complying with a standard container
+ */
+template <typename T, typename _ = void>
+struct is_container : std::false_type {};
+
+template <typename... Ts> struct is_container_helper {};
+
+template <typename T>
+struct is_container<
+    T, typename std::conditional<
+           false,
+           is_container_helper<
+               typename std::remove_reference<T>::type::value_type,
+               typename std::remove_reference<T>::type::size_type,
+               typename std::remove_reference<T>::type::iterator,
+               typename std::remove_reference<T>::type::const_iterator,
+               decltype(std::declval<T>().size()),
+               decltype(std::declval<T>().begin()),
+               decltype(std::declval<T>().end()),
+               decltype(std::declval<T>().cbegin()),
+               decltype(std::declval<T>().cend()),
+               decltype(std::declval<T>().empty())>,
+           void>::type> : public std::true_type {};
+
+/**
+ * Type trait to evaluate if template parameter is
+ * complying with a std::string
+ */
+template <typename T>
+inline constexpr bool is_std_string_v =
+    std::is_same_v<std::decay_t<T>, std::string>;
+
+/**
+ * Type trait to evaluate if template parameter is
+ * complying with std::map
+ */
+template <typename T> struct is_map : std::false_type {};
+
+template <typename K, typename V, typename... Args>
+struct is_map<std::map<K, V, Args...>> : std::true_type {};
+
+template <typename T>
+inline constexpr bool is_map_v = is_map<std::decay_t<T>>::value;
+
+} // namespace aare

include/aare/utils/ifstream_helpers.hpp

@@ -1,4 +1,3 @@
-// SPDX-License-Identifier: MPL-2.0
 #pragma once
 
 #include <fstream>

include/aare/utils/par.hpp

@@ -1,11 +1,7 @@
-// SPDX-License-Identifier: MPL-2.0
-#pragma once
 #include <thread>
 #include <utility>
 #include <vector>
 
-#include "aare/utils/task.hpp"
-
 namespace aare {
 
 template <typename F>
@@ -19,17 +15,4 @@ void RunInParallel(F func, const std::vector<std::pair<int, int>> &tasks) {
         thread.join();
     }
 }
-
-
-template <typename T>
-std::vector<NDView<T,3>> make_subviews(NDView<T, 3> &data, ssize_t n_threads) {
-    std::vector<NDView<T, 3>> subviews;
-    subviews.reserve(n_threads);
-    auto limits = split_task(0, data.shape(0), n_threads);
-    for (const auto &lim : limits) {
-        subviews.push_back(data.sub_view(lim.first, lim.second));
-    }
-    return subviews;
-}
-
 } // namespace aare

include/aare/utils/task.hpp

@@ -1,5 +1,4 @@
-// SPDX-License-Identifier: MPL-2.0
-#pragma once
+
 #include <utility>
 #include <vector>
 

pyproject.toml

@@ -16,7 +16,6 @@ dependencies = [
     "numpy",
     "matplotlib",
 ]
-license = { file = "LICENSE" }
 
 
 [tool.cibuildwheel]