Merge branch 'developer' into jf_h5reader

Fix/dbitreorder should only be defined for chip and xilinx

.github/workflows/build_wheel.yml

@@ -1,64 +0,0 @@
-name: Build wheel
-
-on:
-    workflow_dispatch:
-    pull_request:
-    push:
-      branches:
-        - main
-    release:
-      types:
-        - published
-  
-
-jobs:
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest,]
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Build wheels
-        run: pipx run cibuildwheel==2.23.0
-
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: ./wheelhouse/*.whl
-    
-  build_sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Build sdist
-      run: pipx run build --sdist
-
-    - uses: actions/upload-artifact@v4
-      with:
-        name: cibw-sdist
-        path: dist/*.tar.gz
-
-  upload_pypi:
-    needs: [build_wheels, build_sdist]
-    runs-on: ubuntu-latest
-    environment: pypi
-    permissions:
-        id-token: write
-    if: github.event_name == 'release' && github.event.action == 'published'
-    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
-    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
-    steps:
-        - uses: actions/download-artifact@v4
-          with:
-            # unpacks all CIBW artifacts into dist/
-            pattern: cibw-*
-            path: dist
-            merge-multiple: true
-
-        - uses: pypa/gh-action-pypi-publish@release/v1

CMakeLists.txt

@@ -21,7 +21,6 @@ if (${CMAKE_VERSION} VERSION_GREATER "3.24")
 endif()
 include(cmake/project_version.cmake)
 include(cmake/SlsAddFlag.cmake)
-include(cmake/helpers.cmake)
 
 
 
@@ -194,9 +193,11 @@ find_package(ClangFormat)
 
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
-default_build_type("Release")
-set_std_fs_lib()
-message(STATUS "Extra linking to fs lib:${STD_FS_LIB}")
+if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "No build type selected, default to Release")
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Build type (default Release)" FORCE)
+endif()
+
 
 #Enable LTO if available
 include(CheckIPOSupported)

README.md

@@ -1,33 +1,24 @@
 ## Dependencies
-Before building from source make sure that you have the [dependencies](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing dependency packages with pip. 
+Before building from source make sure that you have the [software wiki](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing packages with pip. 
 
 ## Documentaion
 Detailed documentation including installation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html).
 
-List of releases can be found on the [official site](https://www.psi.ch/en/lxn/software-releases).
+Different releases can be found on the [official site](https://www.psi.ch/en/lxn/software-releases).
 
 Firmware compatiblity can be found in [firmware page](https://github.com/slsdetectorgroup/slsDetectorFirmware)
 
 ## Installation
 
-The slsDetectorPackage provides core detector software implemented in C++, along with Python bindings packaged as the slsdet Python extension module. Choose the option that best fits your environment and use case.
-
-1. **Install pre-built binaries using conda (Recommended)**: Install pre-built binaries for the C++ client, receiver, GUI and the Python API (`slsdet`), simplifying setup across platforms.
-
-2. **Pip**: Install only the Python extension module, either by downloading the pre-built library from PyPI or by building the extension locally from source. Available only from v9.2.0 onwards.
-
-3. **Build from source**: Compile the entire package yourself, including both the C++ core and the Python bindings, for maximum control and customization. However, make sure that you have the dependencies installed. If installing using conda, conda will manage the dependencies. Avoid installing packages with pip and conda simultaneously.
-
-### 1. Install pre-built binaries using conda (Recommended)
+### 1. Install binaries using conda
 Conda is not only useful to manage python environments but can also
 be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
 are from the developer branch. Please use released tags for stability.
 
 We have three different packages available:
-* **slsdetlib** Shared libraries and command line utilities 
+* **slsdetlib** shared libraries and command line utilities 
 * **slsdetgui** GUI
 * **slsdet** Python bindings
-* **moenchzmq** Moench
 
 ```
 #Add channels for dependencies and our library
@@ -53,26 +44,11 @@ conda search slsdetlib
 conda search slsdet
 # gui
 conda search slsdetgui
-# moench
-conda search moenchzmq
 ```
 
-## 2. Pip
-The Python extension module `slsdet` can be installed using pip. This is available from v9.2.0 onwards.
+## 2. Build from source
 
-```
-#Install the Python extension module from PyPI
-pip install slsdet
-
-# or install the python extension locally from source
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 9.2.0
-cd slsDetectorPackage
-pip install .
-```
-
-## 3. Build from source
-
-### 3.1. Download Source Code from github
+### 2.1 Download Source Code from github
 ```
 git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.0.0
 ```
@@ -80,11 +56,10 @@ git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.
 > **Note:** For v6.x.x of slsDetectorPackage and older, refer [pybind11 notes on cloning](#Pybind-and-Zeromq).
 
 
-### 3.2. Build from source
+### 2.2 Build from source
 
-One can either build using cmake or use the in-built cmk.sh script.
 
-### 3.2.1. Build using CMake
+### Build using CMake
 
 ```
 # outside slsDetecorPackage folder
@@ -124,7 +99,7 @@ ccmake ..
 
 > **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmake option to hint library location](#Pybind-and-Zeromq).
 
-### 3.2.2. Build using in-built cmk.sh script
+### Build using in-built cmk.sh script
 
 ```
 The binaries are generated in slsDetectorPackage/build/bin directory.
@@ -169,9 +144,9 @@ Usage: $0 [-b] [-c] [-d <HDF5 directory>] [-e] [-g] [-h] [-i]
 
 > **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmk script option to hint library location](#Pybind-and-Zeromq).
 
-### 3.3. Build on old distributions using conda
+### Build on old distributions
 
-If your linux distribution doesn't come with a C++17 compiler (gcc>8) then 
+If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
 it's possible to install a newer gcc using conda and build the slsDetectorPackage
 using this compiler
 
@@ -189,7 +164,7 @@ make -j12
 > **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
 
 
-### 3.4. Build slsDetectorGui (Qt5)
+### Build slsDetectorGui (Qt5)
 
 1. Using pre-built binary on conda
 ```
@@ -240,7 +215,7 @@ cd slsDetectorPackage
 
 > **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
 
-### 3.5. Build documentation from package
+### Build documentation from package
 The documentation for the slsDetectorPackage is build using a combination 
 of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
 is to use conda 
@@ -261,7 +236,7 @@ make rst # rst only, saves time in case the API did not change
 
 
 
-## 4. Pybind and Zeromq
+## Pybind and Zeromq
 
 ### Pybind11 for Python
 **v8.0.0+**:
@@ -303,5 +278,4 @@ zeromq-devel must be installed and one can hint its location using
 
 ## Support
     dhanya.thattil@psi.ch
-    erik.frojdh@psi.ch
-    alice.mazzoleni@psi.ch
+    erik.frojdh@psi.ch

RELEASE.txt

@@ -1,272 +1,45 @@
-SLS Detector Package Major Release 10.0.0 released on 10.09.2025
-================================================================
+SLS Detector Package Major Release x.x.x released on xx.xx.202x
+===============================================================
 
-This document describes the differences between v10.0.0 and v9.2.0   
+This document describes the differences between vx.x.x and vx.0.2   
 
 
 
     CONTENTS
     --------
-    1           Changes
-    1.1         Compilation Changes
-    1.2         New or Changed Features
-        1.2.1   Breaking API
-        1.2.2   Resolved or Changed Features
-        1.2.3   New Features
-    3           On-board Detector Server Compatibility
-    4           Firmware Requirements
-    5           Kernel Requirements
-    6           Download, Documentation & Support
+    1           New, Changed or Resolved Features
+        1.1     Compilation
+        1.2     Callback
+        1.3     Python
+        1.4     Client
+        1.5     Detector Server
+        1.6     Simulator
+        1.7     Receiver
+        1.8     Gui
+    2           On-board Detector Server Compatibility
+    3           Firmware Requirements
+    4           Kernel Requirements
+    5           Download, Documentation & Support
 
 
 
 
-1 Changes
-==========
+1 New, Changed or Resolved Features
+=====================================
 
 
-
-1.1 Compilation Changes
-========================
-
-
-    *   C++ standard
-        Bumped up C++ standard from 11 (gcc4.8+) to 17 (gcc8+).
-
-
-    *   GotthardI
-        Dropped support for GotthardI from v10.0.0.
-
-
-    *   PATCH 
-        Find PATCH command required for compilation. Needed for lib zeromq patching.
-
-
-    *   pmodules support discontinued
-    
-
-1.2 New or Changed Features
-============================
-
-
-
-1.2.1 Breaking API
-===================
-
-
-    Client
-    ------
-
-
-    *   Shared Memory Version
-        Version has changed and will throw when using an earlier version of 
-        shared memory without freeing it first.
-
-
-    *   [Mythen3] patternX
-        This command has been changed back to 'pattern' as before.
-
-
-    *   TCP API Incompatibility
-        The size of the expected structure has changed when setting rx_hostname compared to previous versions. This change makes it incompatible.
-
-
-    *   User details
-        One can get user or detector details directly from shared memory without
-        creating the Detector class. It is now a free function.
-        C++ API: getUserDetails
-        python/ command line: user
-        
-
-    Receiver
-    --------
-
-    
-    *   Multiple ROIs
-        Previously, only one ROI was allowed per detector.
-        Now, multiple ROIs are allowed, but restricted to a single ROI per
-        UDP port. More details on its help.
-        
-        As before, this ROI is cut out at the receiver level before 
-        writing to file. It does not affect network load, but reduces file size.
-        
-        Please note that the signature has changed in the Detector API as it now expects a vector. getRxROI returns detector level vector of ROIs for
-        the entire detector or port level vector of ROIs for the module index
-        provided.
-        
-        Command line: rx_roi, rx_clearroi
-        C++ API: get/setRxROI, clearRxROI 
-
-  
-    *   Master File Version
-        Binary Master Version: 7.3 => 8.0
-        HDF5 Master Version: 6.7 => 7.0
-
-
-    *   Master File Attributes
-        - Fixed master file inconsistencies between binary and hdf5 format.
-            So the parameter names might differ in master file.
-        - Fixed time inconsistencies due to tolerance for gotthardII.
-        - Replaced many of the values that was simply writted usign 'toString'
-            with array-based output.
-        - JSON additional header always written.
-        - HDF5 master file reads 'Version', instead of 'version'.    
-
-
-
-1.2.2 Resolved or Changed Features
-===================================
-
-
-    Python
-    ------
-
-
-    *   Shared Memory outliving free
-        Depending on a variable’s scope, it was possible to access an invalid
-        object and its shared memory even after calling free, since resources
-        were not fully released. Shared memory structures now include a flag
-        indicating invalidity and will throw an error if accessed after being
-        freed.
-
-
-    Client
-    ------
-
-
-    *   UDP Destination List
-        CLI: udp_dstlist
-        C++ API: getDestinationUDPList
-        Was returning incorrect values. Fixed.
-        
-    
-    Receiver
-    --------
-
-
-    *   [Mythen3] Master File Attributes
-        Previously, did not create HDF5 Master file without crashing. Fixed now.
-
-
-    *   Default File Path
-        It used to be '/'. Now, changed to empty and will throw if still 
-        unchanged before an acquisition.
-
-
-    *   Command Line Arguments
-        They have been refactored for slsReceiver, slsMultiReceiver and 
-        slsFrameSynchronizer. Existing commands remain fully supported for now.
-
-        Usage: slsReceiver Options:
-            -v, --version       : Version.
-            -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-            -u, --uid           : Set effective user id if receiver started with privileges. 
-
-        Usage: slsMultiReceiver Options:
-            -v, --version       : Version.
-            -n, --num-receivers : Number of receivers.
-            -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-            -c, --callback      : Enable dummy callbacks for debugging. Disabled by default. 
-            -u, --uid           : Set effective user id if receiver started with privileges. 
-
-        Usage: slsFrameSynchronizer Options:
-            -v, --version       : Version.
-            -n, --num-receivers : Number of receivers.
-            -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-            -c, --print-headers : Print callback headers for debugging. Disabled by default.
-            -u, --uid           : Set effective user id if receiver started with privileges. 
-
-
-    *   [Moench] No intertpolation
-        Fixed no interpolation for Moench03.
-
-
-
-1.2.3 New Features
-===================
-
-
-    Compilation
-    -----------
-
-
-    *   Conda and pypi
-        Automatic release on both upon release.
-
-
-    Python
-    ------
-
-
-    *   Exposing Free Shared Memory
-        One can do either `slsdet.freeSharedMemory()` or `d.free()`
-
-
-    Client
-    ------
-
-
-    *   Port size and Port per Module Geometry in Detector class
-        C++ API: getPortSize, getPortPerModuleGeometry
-
-
-    *   ROI structure
-        Added 'overlap' function to check if it overlaps with another.
-
-
-    Receiver
-    --------
-
-
-    *   HDF5 Virtual File with ROI
-        Previously, virtual file was not created with ROI. It is now.
-
-
-    *   Readout speed added to Master File
-        
-
-    Documentation
-    -------------
-
-
-    *   Multi Detector and Multi user
-        Documentation on multi detector index and multi user considerations for
-        using the same client system.
-            https://slsdetectorgroup.github.io/devdoc/multidet.html
-
-   
-    *   10GbE PC tuning
-        Further information for permanent ethtool settings updated.
-            https://slsdetectorgroup.github.io/devdoc/troubleshooting.html#receiver-pc-tuning-options
-
-
-    *   Image Size and Output Characteristics
-        Information for different detector types and different parameters that
-        affect image size and characteristics have been added.
-            https://slsdetectorgroup.github.io/devdoc/dataformat.html
-
-
-    *   'How To' section added
-        Software Architecture
-            https://slsdetectorgroup.github.io/devdoc/softwarearchitecture.html
-
-        Set up commands most often used in the config file
-            https://slsdetectorgroup.github.io/devdoc/configcommands.html
-
-        Quick start guide has been updated
-            https://slsdetectorgroup.github.io/devdoc/quick_start_guide.html
-
+ 
 
 
 2  On-board Detector Server Compatibility
 ==========================================
 
 
-    Eiger       10.0.0
-    Jungfrau    10.0.0
-    Mythen3     10.0.0
-    Gotthard2   10.0.0
-    Moench      10.0.0
+    Eiger       9.0.0
+    Jungfrau    9.0.0
+    Mythen3     9.0.0
+    Gotthard2   9.0.0
+    Moench      9.0.0
   
 
     On-board Detector Server Upgrade
@@ -289,16 +62,17 @@ This document describes the differences between v10.0.0 and v9.2.0
 3 Firmware Requirements
 ========================
 
+
     Eiger       02.10.2023 (v32)                    (updated in 7.0.3)
     
-    Jungfrau    09.02.2025 (v1.6, HW v1.0)          (updated in 9.1.0)
-                08.02.2025 (v2.6, HW v2.0)          (updated in 9.1.0)
+    Jungfrau    20.09.2023 (v1.5, HW v1.0)          (updated in 8.0.0)
+                21.09.2023 (v2.5, HW v2.0)          (updated in 8.0.0)
 
-    Mythen3     13.11.2024 (v2.0)                   (updated in 9.0.0)
+    Mythen3     11.10.2024 (v1.5)                   (updated in 9.0.0)
 
     Gotthard2   03.10.2024 (v1.0)                   (updated in 9.0.0)
 
-    Moench      26.10.2023 (v2.0)                   (updated in 8.0.2)
+    Moench      26.10.2023 (v2.0)                   (updated in 9.0.0)
 
 
     Detector Upgrade
@@ -374,7 +148,7 @@ This document describes the differences between v10.0.0 and v9.2.0
 
     Quick Start Guide:
         https://slsdetectorgroup.github.io/devdoc/quick_start_guide.html
-
+        
     Firmware Upgrade:
         https://slsdetectorgroup.github.io/devdoc/firmware.html
 
@@ -387,15 +161,6 @@ This document describes the differences between v10.0.0 and v9.2.0
     Consuming slsDetectorPackage:
         https://slsdetectorgroup.github.io/devdoc/consuming.html
         
-    Software Architecture
-        https://slsdetectorgroup.github.io/devdoc/softwarearchitecture.html
-
-    Set up commands in config file
-        https://slsdetectorgroup.github.io/devdoc/configcommands.html
-        
-    Image Size and Output Characteristics
-        https://slsdetectorgroup.github.io/devdoc/dataformat.html
-
     API Examples:
         https://github.com/slsdetectorgroup/api-examples
 
@@ -422,14 +187,6 @@ This document describes the differences between v10.0.0 and v9.2.0
         https://slsdetectorgroup.github.io/devdoc/udpheader.html
         https://slsdetectorgroup.github.io/devdoc/udpdetspec.html
 
-    Output Data:
-        https://slsdetectorgroup.github.io/devdoc/dataformat.html
-        https://slsdetectorgroup.github.io/devdoc/fileformat.html
-        https://slsdetectorgroup.github.io/devdoc/slsreceiverheaderformat.html
-        https://slsdetectorgroup.github.io/devdoc/masterfileattributes.html
-        https://slsdetectorgroup.github.io/devdoc/binaryfileformat.html
-        https://slsdetectorgroup.github.io/devdoc/hdf5fileformat.html
-
     slsReceiver Zmq Format:
         https://slsdetectorgroup.github.io/devdoc/slsreceiver.html#zmq-json-header-format
 
@@ -449,4 +206,3 @@ This document describes the differences between v10.0.0 and v9.2.0
 
         dhanya.thattil@psi.ch
         erik.frojdh@psi.ch
-        alice.mazzoleni@psi.ch

VERSION

@@ -1 +1 @@
-10.0.0
+0.0.0

cmake/FindClangFormat.cmake

@@ -25,9 +25,7 @@ mark_as_advanced(
     ClangFormat_BIN)
 
 if(ClangFormat_FOUND)
-    execute_process(COMMAND ${ClangFormat_BIN} --version
-                 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-                 OUTPUT_VARIABLE CLANG_VERSION_TEXT)
+    exec_program(${ClangFormat_BIN} ${CMAKE_CURRENT_SOURCE_DIR} ARGS --version OUTPUT_VARIABLE CLANG_VERSION_TEXT)
     string(REGEX MATCH "([0-9]+)\\.[0-9]+\\.[0-9]+" CLANG_VERSION ${CLANG_VERSION_TEXT})
     if((${CLANG_VERSION} GREATER "9") OR (${CLANG_VERSION} EQUAL "9"))
         # A CMake script to find all source files and setup clang-format targets for them

cmake/helpers.cmake

@@ -1,46 +0,0 @@
-function(default_build_type val)
-if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
-  message(STATUS "No build type selected, default to Release")
-  set(CMAKE_BUILD_TYPE ${val} CACHE STRING "Build type (default ${val})" FORCE)
-endif()
-endfunction()
-
-function(set_std_fs_lib)
-# from pybind11
-# Check if we need to add -lstdc++fs or -lc++fs or nothing
-if(DEFINED CMAKE_CXX_STANDARD AND CMAKE_CXX_STANDARD LESS 17)
-  set(STD_FS_NO_LIB_NEEDED TRUE)
-elseif(MSVC)
-  set(STD_FS_NO_LIB_NEEDED TRUE)
-else()
-  file(
-    WRITE ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
-    "#include <filesystem>\nint main(int argc, char ** argv) {\n  std::filesystem::path p(argv[0]);\n  return p.string().length();\n}"
-  )
-  try_compile(
-    STD_FS_NO_LIB_NEEDED ${CMAKE_CURRENT_BINARY_DIR}
-    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
-    COMPILE_DEFINITIONS -std=c++17)
-  try_compile(
-    STD_FS_NEEDS_STDCXXFS ${CMAKE_CURRENT_BINARY_DIR}
-    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
-    COMPILE_DEFINITIONS -std=c++17
-    LINK_LIBRARIES stdc++fs)
-  try_compile(
-    STD_FS_NEEDS_CXXFS ${CMAKE_CURRENT_BINARY_DIR}
-    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
-    COMPILE_DEFINITIONS -std=c++17
-    LINK_LIBRARIES c++fs)
-endif()
-
-if(${STD_FS_NEEDS_STDCXXFS})
-  set(STD_FS_LIB stdc++fs PARENT_SCOPE)
-elseif(${STD_FS_NEEDS_CXXFS})
-  set(STD_FS_LIB c++fs PARENT_SCOPE)
-elseif(${STD_FS_NO_LIB_NEEDED})
-  set(STD_FS_LIB "" PARENT_SCOPE)
-else()
-  message(WARNING "Unknown C++17 compiler - not passing -lstdc++fs")
-  set(STD_FS_LIB "")
-endif()
-endfunction()

conda-recipes/main-library/meta.yaml

@@ -28,8 +28,7 @@ requirements:
     - libgl-devel  # [linux]
     - libtiff
     - zlib
-    - expat
-  
+
   run:
     - libstdcxx-ng
     - libgcc-ng 
@@ -58,7 +57,6 @@ outputs:
         - {{ compiler('c') }}
         - {{compiler('cxx')}}
         - {{ pin_subpackage('slsdetlib', exact=True) }}
-        
 
       run:
         - {{ pin_subpackage('slsdetlib', exact=True) }}

docs/CMakeLists.txt

@@ -42,7 +42,6 @@ set(SPHINX_SOURCE_FILES
   src/pyexamples.rst
   src/pyPatternGenerator.rst
   src/servers.rst
-  src/multidet.rst
   src/receiver_api.rst
   src/result.rst
   src/type_traits.rst
@@ -67,9 +66,6 @@ set(SPHINX_SOURCE_FILES
   src/binaryfileformat.rst
   src/hdf5fileformat.rst
   src/zmqjsonheaderformat.rst
-  src/dataformat.rst
-  src/softwarearchitecture.rst
-  src/configcommands.rst
 )
 
 foreach(filename ${SPHINX_SOURCE_FILES})
@@ -87,16 +83,11 @@ configure_file(
   "${SPHINX_BUILD}/gen_server_doc.py"
   @ONLY)
 
-configure_file(
+  configure_file(
   "${CMAKE_CURRENT_SOURCE_DIR}/static/extra.css"
   "${SPHINX_BUILD}/static/css/extra.css"
   @ONLY)
 
-
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/src/images
-     DESTINATION ${SPHINX_BUILD}/src)
-     
-
 add_custom_target(server_rst python gen_server_doc.py)  
 
 add_custom_target(docs

docs/images_src/system_communication_architecture.drawio

@@ -1,787 +0,0 @@
-<mxfile host="app.diagrams.net" agent="Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/139.0.0.0 Safari/537.36" version="28.1.0">
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docs/src/binaryfileformat.rst

@@ -1,5 +1,3 @@
-.. _binary file format:
-
 Binary File Format
 ====================
 
@@ -33,7 +31,6 @@ Data File
 
 * Each frame includes a :ref:`**sls_receiver_header** <sls receiver header format>` structure, followed by the actual frame data.
 
-* More details on :ref:`slsReceiverHeader<sls receiver header format>` and the actual image data is described in the :ref:`Detector Image Size and Format <data format>` section.
 
 
 .. _json master file examples:

docs/src/commandline.rst

@@ -6,8 +6,6 @@ Usage
 
 The syntax is *'[detector index]-[module index]:[command]'*, where the indices are by default '0', when not specified.
 
-.. _cl-module-index-label:
-
 Module index
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Modules are indexed based on their order in the hostname command. They are used to configure a specific module within a detector and are followed by a ':' in syntax.

docs/src/configcommands.rst

@@ -1,242 +0,0 @@
-.. _setup commands:
-
-Setup Commands
-================================
-
-
-Introduction
--------------
-
-To connect to any device, one needs a unique combination of **IP address** (which identifies the device) and **port number** (which specifies the service). 
-
-This package typically deals with two types of network interfaces:
-
-* **1 GbE public interface** - Accessible from anywhere on the network. Connectivity can be verified by pinging this interface from any PC.
-
-* **10 GbE private interface** - Dedicated to high-speed data transfer with a specific PC. In addition to the 1 GbE public interface (MTU 1500), the device may include one or more private 10 GbE interfaces (MTU 9000), which are not accessible from other machines.
-
-Client to Module
------------------
-
-.. figure:: images/Client_module_commands.png
-   :target: _images/Client_module_commands.png
-   :width: 700px
-   :align: center
-   :alt: Client Module Commands
-
-   Client Module TCP Commands
-
-The client configures and controls modules via the 1 GbE public TCP interface.
-
-* Should be able to ping the module's hostname from any PC on the network.
-* If one cannot ping, ensure that it is powered on.
-* If the command cannot connect to the port (`hostname command <commandline.html#term-hostname>`_ failed), the onboard servers may not have started yet.
-
-Each physical module has its own unique IP address. As the IPs are already different, all modules can share the same default ports:
-
-* 1952 - Default Module TCP Control Port
-* 1953 - Default Module TCP Stop port
-
-.. code-block:: bash  
-
-    # Therefore, one can use 
-    hostname bchip100+bchip101+
-    # instead of 
-    hostname bchip100:1952+bchip101:1954+
-
-
-**Simulators**, however, usually run on the same PC. See `virtual servers <https://slsdetectorgroup.github.io/devdoc/virtualserver.html>`_ for more details. In that case, each instance must use a different port. By incrementing port numbers, you can also use the virtual command for convenience.
-
-.. code-block:: bash  
-
-    # Therefore, one can use 
-    virtual 2 1952
-    # instead of 
-    hostname localhost:1952+localhost:1954+
-
-
-
-
-Client to Receiver
---------------------
-
-.. figure:: images/Client_receiver_commands.png
-   :target: _images/Client_receiver_commands.png
-   :align: center
-   :alt: Client Receiver Commands
-
-   Client Receiver TCP Commands
-
-Each module has a receiver, which can be either local or remote.
-
-The client can configure and control receivers via the 1 GbE public TCP interface:
-
-* Should be able to ping the receiver's hostname from any PC on the network.
-* If one cannot ping, ensure that it is powered on.
-* If the command cannot connect to the port (`rx_hostname command <commandline.html#term-rx_hostname-hostname-or-ip-address>`_ failed), the receivers may not have started yet.
-
-
-Since multiple receiver processes typically run on the same PC, they share the same IP. Here, each receiver process must use a different TCP port for a unique connection. 
-
-* 1954 - Default Receiver TCP port
-
-Configuring the receiver with the command `rx_hostname command <commandline.html#term-rx_hostname-hostname-or-ip-address>`_, sets up a receiver for every module in shared memory automatically ie. every module's receiver TCP port will automatically increment in shared memory. The starting port is defined by the command `rx_tcpport <commandline.html#term-rx_tcpport-port>`_ with the default being 1954.
-
-
-A multi-module command (without colon or module index) sets incremental ports starting from the specified port number.
-
-.. code-block:: bash  
-
-    hostname bchip100+bchip101+bchip102+bchip103+
-    rx_tcport 2000 # sets the receiver port to 2000, 2001, 2002, 2003
-
-
-For example, using default TCP ports (1954, 1955):
-
-.. code-block:: bash  
-
-    hostname bchip100+bchip101+
-    rx_hostname localhost
-    # Equivalent to:
-    rx_hostname localhost:1954+localhost:1955+
-    
-    # or set to another set of ports (automatically incremented)
-    rx_tcpport 1984
-    rx_hostname localhost
-    # instead of
-    rx_hostname localhost:1984+localhost:1985+
-
-
-
-
-Module to Receiver
--------------------
-
-.. figure:: images/Module_receiver_commands.png
-   :target: _images/Module_receiver_commands.png
-   :align: center
-   :alt: Module Receiver Commands
-
-   Module Receiver UDP Commands
-
-**10GbE Interface**
-
-The module typically sends images to the receiver via a 10 GbE private interface on the receiver PC, which has an MTU of 9000 to support jumbo packets. The private interface is not reachable from other machines, so it cannot be pinged from anywhere. 
-
-**Multiple UDP Packets**
-
-Images are split into UDP packets for transmission. Unlike TCP, UDP is connectionless and does not guarantee delivery. Therefore, the receiver PC must be tuned for reliable reception. See `Troubleshooting <https://slsdetectorgroup.github.io/devdoc/troubleshooting.html>`_.
-
-**UDP Configuration**
-
-Unlike TCP, the module (hardware) requires explicit configuration for sending images via UDP, including:
-
-* Source and destination IPs
-* Source and destination MAC addresses
-* Source and destination ports
-
-**UDP Destination**
-
-Info on where to send the image from the module to.
-
-**UDP Desination IP** - The IP of the receiver PC's 10 GbE interface, usually found via ``ifconfig``. Command: `udp_dstip <commandline.html#term-udp_dstip-x.x.x.x-or-auto>`_. For 1GbE interface and for this command, one can use 'auto' as an argument, which will pick up the IP from the `rx_hostname command <commandline.html#term-rx_hostname-hostname-or-ip-address>`_.
-
-**UDP desintation MAC** - Also obtained from the interface using ``ifconfig``. For built-in receivers, the module configures this automatically from the ``UDP destination IP``. For custom receivers, it must be explicitly provided. Command: `udp_dstmac <commandline.html#term-udp_dstmac-x-x-x-x-x-x>`_
-
-**UDP destination port** - Ensure uniqueness if multiple users share the interface. Command: `udp_dstport <commandline.html#term-udp_dstport-n>`_
-
-* 50001 - Default Receiver UDP port
-
-
-**UDP Source**
-
-As it is a one-way communication (module to receiver with no reply or acknowledgements), info on the source of the image is more for debugging purposes and prevent packet rejection.
-
-**UDP source IP** - Must be on the same subnet as the destination IP (same first three octets) to prevent packet rejection by the receiver interface. For 1GbE interface and for this command (except for Eiger), one can use ``auto`` as an argument, which will pick up the IP from the `hostname command <commandline.html#term-hostname>`_. Command: `udp_srcip <commandline.html#term-udp_srcip-x.x.x.x-or-auto>`_
-
-.. code-block:: bash  
-
-    # 10 GbE interface
-    hostname bchip100
-    udp_dstip 10.0.2.1
-    udp_srcip 10.0.2.19
-    rx_hostname localhost
-
-    # 1 GbE interface
-    hostname bchip100
-    rx_hostname localhost
-    udp_dstip auto # this command uses IP from rx_hostname. So, it comes after.
-    udp_srcip auto # this command uses IP from hostname
-
-**UDP source MAC** - By default, it is set to ``aa:bb:cc:dd:xx:yy`` where ``xx`` and ``yy`` are module row and column indices to differentiate the modules while debugging. Command: `udp_srcmac <commandline.html#term-udp_srcmac-x-x-x-x-x-x>`_
-
-
-**UDP source port** - This is hardcoded in every module to the same value in the detector server and cannot be changed.
-
-Note: If there is a second UDP port on the module, use 'udp_dstport2' or 'udp_dstip2'etc. See `here <https://slsdetectorgroup.github.io/devdoc/dataformat.html>`_ for more detector specific info. 
-
-Receiver to GUI
------------------
-
-.. figure:: images/Receiver_gui_commands.png
-   :target: _images/Receiver_gui_commands.png
-   :align: center
-   :alt: Receiver GUI Commands
-
-   Receiver GUI Commands
-
-
-Enabling the GUI automatically streams images from the receiver via ZMQ sockets. Even without the GUI, streaming can be activated explicitly using the command `rx_zmqstream <commandline.html#term-rx_zmqstream-0-1>`_. ZMQ streaming uses TCP/IP, so the ports must be configured appropriately.
-
-**Receiver ZMQ Port** - Port from which the receiver streams ZMQ packets. Command: `rx_zmqport <commandline.html#term-rx_zmqport-port>`_
-
-* 30001 - Default Receiver ZMQ Port (stream out from)
-
-**Client ZMQ Port** - Port that the client ZMQ socket listens to. Command: `zmqport <commandline.html#term-zmqport-port>`_
-
-* 30001 - Default Client ZMQ Port (listens to)
-
-**Client ZMQ IP** - IP address the client ZMQ socket listens to. Command: `zmqip <commandline.html#term-zmqip-x.x.x.x>`_. By default, this is set to the IP of ``rx_hostname``, but can be set to any IP address that the client can reach.
-
-* Default: Receiver’s hostname (rx_hostname)
-
-
-.. note ::   
-
-    ``zmqport`` and ``zmqip`` need to be set up in shared memory before starting up the Gui. If the Gui is already running, change it in the Advanced Tab directly in the Gui.
-    
-    ``rx_zmqstream`` is set to 1 when the GUI is started, but has to be manually set back to 0 to disable zmq streaming in the receiver for better performance when not using the Gui.
-    
-    The GUI hwm (high water mark, which is like a measurement of the number of enqueued zmq packets) values are set to a low number (from library default of possibly 1000 to 2) to reduce the zmq buffer to display only some of the images. Resetting it back to -1 or 1000 should only matter if one plans to not use the Gui and still zmq stream without wanting to drop zmq images (eg. for external processing chain). 
-
-
-
-
-
-Receiver to External Processing
---------------------------------
-
-.. figure:: images/Receiver_external_process_commands.png
-   :target: _images/Receiver_external_process_commands.png
-   :align: center
-   :alt: Click to zoom
-
-   Receiver External Process Commands
-
-Images from the receiver can also be streamed to an external processing chain for further processing or storage. In this setup:
-
-* The external processor listens to the ZMQ ports and IPs that the receiver streams from.
-
-* The client ZMQ sockets now listen to the ports and IPs that the external processor streams from instead of the receiver.
-
-**Receiver ZMQ Port** - Port from which the receiver streams ZMQ packets. Command: `rx_zmqport <commandline.html#term-rx_zmqport-port>`_
-
-* 30001 - Default Receiver ZMQ Port (stream out from)
-
-**Client ZMQ Port** - Port that the client ZMQ socket listens to. Command: `zmqport <commandline.html#term-zmqport-port>`_. In this set up, it should listen to the zmq port that the external process is streaming out from.
-
-* 30001 - Default Client ZMQ Port (listens to)
-
-**Client ZMQ IP** - IP address the client ZMQ socket listens to. Command: `zmqip <commandline.html#term-zmqip-x.x.x.x>`_. By default, this is set to the IP of ``rx_hostname``, but in this set up, it should listen to the zmq IP that the external process is streaming out from.
-
-* Default: Receiver’s hostname (rx_hostname)

docs/src/dataformat.rst

@@ -1,330 +0,0 @@
-.. _data format:
-
-Detector Image Size and Format
-================================
-
-Each UDP port creates its own output file, which contains the data of the image transmitted over that port. More on number of files and naming for each file in the `File format <fileformat.html>`_ section.
-
-Jungfrau
--------------
-
-Single Port Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Jungfrau_module.png
-   :target: _images/Jungfrau_module.png
-   :width: 650px
-   :align: center
-   :alt: Jungfrau Module Single Port Configuration
-
-By default, only the outer 10GbE interface is enabled, transmitting the full image over a single UDP port. This results in one file per module containing the complete image.
-
-Total image size = 524,288 bytes 
-   - 8 chips (2 x 4 grid)
-   - 256 x 256 pixels (chip size)
-   - 2 bytes (pixel width)
-
-
-
-Double Port Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Jungfrau_two_port.png
-   :target: _images/Jungfrau_two_port.png
-   :width: 500px
-   :align: center
-   :alt: Jungfrau Module Two Port Configuration
-
-If both interfaces are enabled using the `numinterfaces <commandline.html#term-numinterfaces-1-2>`_ command on compatible hardware and firmware, the image splits into top and bottom halves sent over two UDP ports:
-
-   - The top half transmits via the inner interface (`udp_dstport2 <commandline.html#term-udp_dstport2-n>`_ and `udp_dstip2 <commandline.html#term-udp_dstip2-x.x.x.x-or-auto>`_).
-
-   - The bottom half uses the outer interface(`udp_dstport <commandline.html#term-udp_dstport-n>`_ and `udp_dstip <commandline.html#term-udp_dstip-x.x.x.x-or-auto>`_).
-
-The number of files per module equals the active UDP ports—two files per module when both interfaces are used.
-
-Image size per UDP port or File = 262,144 bytes
-    - **Complete Image size / 2**
-
-
-
-Read Partial Rows
-^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Jungfrau_read_rows.png
-   :target: _images/Jungfrau_read_rows.png
-   :width: 550px
-   :align: center
-   :alt: Jungfrau Module Read Partial Rows Configuration
-
-
-The number of image rows per port can be adjusted using the `readnrows <commandline.html#term-readnrows>`_ command. By default, 512 rows are read, but a smaller value centers the readout vertically (e.g., 8 rows reads 4 above and 4 below the center). Increasing the value symmetrically expands the region toward the top and bottom. Permissible values are multiples of 8.
-
-
-Total image size = 32,768 bytes 
-   - 8 chips (2 x 4 grid)
-   - **8** x 256 pixels (chip size: **8 rows**)
-   - 2 bytes (pixel width)
-
-Note: Still in prototype stage, writes complete image (padded or not depending on `rx_padding <commandline.html#term-rx_padding-0-1>`_ parameter) to file. Only the summary written to console in the receiver handles the `readnrows <commandline.html#term-readnrows>`_ to calculate to calculate complete images received. Only reduces network load, not file size. Use `rx_roi <commandline.html#term-rx_roi-xmin-xmax-ymin-ymax>`_ for file size.
-
-Moench
--------------
-
-Single Port Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Moench_module.png
-   :target: _images/Moench_module.png
-   :width: 550px
-   :align: center
-   :alt: Moench Module Single Port Configuration
-
-By default, only the outer 10GbE interface is enabled, transmitting the full image over a single UDP port. This results in one file per module containing the complete image.
-
-Total image size = 320,000 bytes 
-   - 400 x 400 pixels (chip size)
-   - 2 bytes (pixel width)
-
-
-
-Double Port Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Moench_two_port.png
-   :target: _images/Moench_two_port.png
-   :width: 400px
-   :align: center
-   :alt: Moench Module Two Port Configuration
-
-If both interfaces are enabled using the `numinterfaces <commandline.html#term-numinterfaces-1-2>`_ command on compatible hardware and firmware, the image splits into top and bottom halves sent over two UDP ports:
-
-   - The top half transmits via the inner interface (`udp_dstport2 <commandline.html#term-udp_dstport2-n>`_ and `udp_dstip2 <commandline.html#term-udp_dstip2-x.x.x.x-or-auto>`_).
-
-   - The bottom half uses the outer interface(`udp_dstport <commandline.html#term-udp_dstport-n>`_ and `udp_dstip <commandline.html#term-udp_dstip-x.x.x.x-or-auto>`_).
-
-The number of files per module equals the active UDP ports—two files per module when both interfaces are used.
-
-Image size per UDP port or File = 160,000 bytes
-    - **Complete Image size / 2**
-
-
-
-Read Partial Rows
-^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Moench_read_rows.png
-   :target: _images/Moench_read_rows.png
-   :width: 400px
-   :align: center
-   :alt: Moench Module Read Partial Rows Configuration
-
-
-The number of image rows per port can be adjusted using the `readnrows <commandline.html#term-readnrows>`_ command. By default, 400 rows are read, but a smaller value centers the readout vertically (e.g., 16 rows reads 8 above and 8 below the center). Increasing the value symmetrically expands the region toward the top and bottom. Permissible values are multiples of 16.
-
-
-Total image size = 12,800 bytes 
-   - **16** x 400 pixels (chip size: **16 rows**)
-   - 2 bytes (pixel width)
-
-Note: Still in prototype stage, writes complete image (padded or not depending on `rx_padding <commandline.html#term-rx_padding-0-1>`_ parameter) to file. Only the summary written to console in the receiver handles the read n rows to calculate complete images received. Only reduces network load, not file size. Use `rx_roi <commandline.html#term-rx_roi-xmin-xmax-ymin-ymax>`_ for file size.
-
-Eiger
--------------
-
-Default Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Eiger_module.png
-   :target: _images/Eiger_module.png
-   :width: 350px
-   :align: center
-   :alt: Eiger Module Default Configuration
-
-
-Each Eiger module has two independent identical readout systems (other than firmware), each with its own control port and `hostname <commandline.html#term-hostname>`_ to be configured with. They are referred to as the 'top' and 'bottom' half modules. The bottom half module is flipped vertically.
-
-Each half module has 2 parallel UDP ports for 2 chips each. The left UDP port is configured with `udp_dstport <commandline.html#term-udp_dstport-n>`_, while the right UDP port is configured with `udp_dstport2 <commandline.html#term-udp_dstport2-n>`_. This is vice versa for the bottom half module.
-
-
-Image size per UDP port or File = 262,144 bytes 
-   - 2 chips (1 x 2 grid)
-   - 256 x 256 pixels (chip size)
-   - 2 bytes (default pixel width)
-
-
-The myth, the legend, the bottom ports: Demystifying them
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-.. figure:: images/Eiger_bottom_1.png
-   :target: _images/Eiger_bottom_1.png
-   :width: 350px
-   :align: center
-   :alt: Eiger Bottom as Firmware gets it
-
-   How the firmware gets the images
-
-
-.. figure:: images/Eiger_bottom_2.png
-   :target: _images/Eiger_bottom_2.png
-   :width: 350px
-   :align: center
-   :alt: Eiger Bottom after the firmware flips it horizontally
-
-   After the firmware flips it horizontally
-
-
-.. figure:: images/Eiger_bottom_3.png
-   :target: _images/Eiger_bottom_3.png
-   :width: 350px
-   :align: center
-   :alt: After the software swaps the udp ports
-
-   After the software swaps the udp ports
-
-
-.. figure:: images/Eiger_bottom_4.png
-   :target: _images/Eiger_bottom_4.png
-   :width: 400px
-   :align: center
-   :alt: After the gui has flipped the bottom vertically
-
-   After the gui has flipped the bottom vertically
-
-
-Note: The same process happens for the bottom 2 udp ports of the quad.
-
-
-Pixel width
-^^^^^^^^^^^^^
-
-The pixel width can be configured to 4, 8, 16 (default) or 32 bits using the command `dr <commandline.html#term-dr-value>`_. This affects image size per UDP port or file.
-
-Flip rows
-^^^^^^^^^^
-
-One can use the command `fliprows <commandline.html#term-fliprows-0-1>`_ to flip the rows vertically for the bottom or top half module. It is sent out to the reciever, but does not flip rows in the output file itself, but rather streams out this info via the json header and thus instructs the GUI to display them correctly.
-
-1GbE/ 10GbE Interfaces
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Both UDP ports `udp_dstport <commandline.html#term-udp_dstport-n>`_ and `udp_dstport2 <commandline.html#term-udp_dstport2-n>`_ are used in Eiger as shows in the figure. Both of them can be set to use either the 1GbE or the 10GbE interface for data. The 1GbE interface is used also for control and configuration. For data, the 1GbE interface is enabled by default. It can be disabled by enabling the `tengiga <commandline.html#term-tengiga-0-1>`_ command and updating both the `udp_dstport <commandline.html#term-udp_dstport-n>`_ , `udp_dstport2 <commandline.html#term-udp_dstport2-n>`_ , `udp_dstip <commandline.html#term-udp_dstip-x.x.x.x-or-auto>`_ commands to match the 1GbE or 10GbE interface. This setting only affects packetsize and number of packets, but does not affect the total image size. 
-
-Reducing network load
-^^^^^^^^^^^^^^^^^^^^^^
-
-**Activate**: By default, the `hostname <commandline.html#term-hostname>`_ command activates the respective half module it connects to, enabling all UDP ports. To deactivate an entire half module (i.e., both UDP ports), use the `activate <commandline.html#term-activate-0-1>`_ command. This disables both UDP ports for that half module, so no data is transmitted from it — only half of the module is read out. To specify which half module to activate or deactivate, use the module index (for Eiger, each half module has its own module index).
-
-
-**Datastream**: The `datastream <commandline.html#term-datastream-left-right-0-1>`_ command with arguments to specify which port can be used to disable the data streaming from one or both the two UDP ports in a half module. This allows for more flexible configurations, such as reading only two chips or one UDP port of a half module. To specify which half module to activate or deactivate, use the module index (for Eiger, each half module has its own module index).
-
-Note: Only the activated ports will write data as it does not make sense to write an empty file.
-
-**Read Partial Rows**: The number of image rows per port can be adjusted using the `readnrows <commandline.html#term-readnrows>`_ command. By default, 256 rows are read, but a smaller value centers the readout vertically (e.g., 8 rows reads 4 above and 4 below the center). Increasing the value symmetrically expands the region toward the top and bottom. Permissible values depend on dynamic range and 10GbE enable.
-
-.. image:: images/Eiger_read_rows.png
-   :target: _images/Eiger_read_rows.png
-   :width: 400px
-   :align: center
-   :alt: Eiger Module Read Partial Rows Configuration
-
-
-
-Total image size per UDP Port = 8,192 bytes 
-   - 2 chips (1 x 2 grid)
-   - **8** x 256 pixels (chip size: **8 rows**)
-   - 2 bytes (default pixel width)
-
-Note: Still in prototype stage, writes complete image (padded or not depending on `rx_padding <commandline.html#term-rx_padding-0-1>`_ parameter) to file. Only the summary written to console in the receiver handles the `readnrows <commandline.html#term-readnrows>`_ to calculate complete images received. Only reduces network load, not file size. Use `rx_roi <commandline.html#term-rx_roi-xmin-xmax-ymin-ymax>`_ for file size.
-
-Quad
-^^^^^^
-
-The Eiger quad is a special hardware configuration that uses only the top half-module to create a quad layout. In this setup, the second half of the top module—normally associated with the right-side UDP port—is used to represent the inverted bottom half of the quad.
-
-As with any standard half-module, it includes one control TCP port (with a hostname) and two UDP data ports (top and bottom). When the quad option is enabled, the firmware automatically flips the second UDP port vertically.
-
-In this configuration, the fliprows command cannot be used to flip the entire half-module. Instead, the receiver automatically includes row-flipping information only for the second UDP port in the JSON header, so the GUI can apply the correct orientation during display
-
-.. image:: images/Eiger_quad.png
-   :target: _images/Eiger_quad.png
-   :width: 300px
-   :align: center
-   :alt: Eiger Quad Configuration
-
-Image size per UDP port = same as a normal Eiger UDP port
-
-Mythen3 
--------------
-
-
-
-Default Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Mythen3_module.png
-   :target: _images/Mythen3_module.png
-   :align: center
-   :alt: Mythen3 Module Default Configuration
-
-Each Mythen3 module is a 1D detector with 10 chips, each with 128 channels. Each channel has 3 counters that are enabled by default.
-
-Image size = 15,360 bytes 
-   - 10 chips (1 x 10 grid)
-   - 128 channels
-   - 3 counters
-   - 4 bytes (default pixel width)
-
-Counters
-^^^^^^^^^^^
-
-If all 3 counters are enabeld, the frame size for each channel is multiplied by 3. The counters are stored consecutively per channel. One can disable one or more of the counters using the `counters <commandline.html#term-counters-i0-i1-i2-...>`_ command. The frame size will then be reduced accordingly.
-
-Image size = 10,240 bytes 
-   - 10 chips (1 x 10 grid)
-   - 128 channels
-   - 2 counters (0, 1 enabled)
-   - 4 bytes (default pixel width)
-
-Pixel width
-^^^^^^^^^^^^^
-
-The pixel width can be configured to 8, 16 or 32 (default) bits using the command `dr <commandline.html#term-dr-value>`_. 32 bits is actually 24 bits in the chip. This setting does affect image size.
-
-1GbE/ 10GbE Interfaces
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-The UDP port can be set to use either the 1GbE or the 10GbE interface for data. The 1GbE interface is used also for control and configuration. For data, the 10GbE interface is enabled by default. It can be disabled by using the `tengiga <commandline.html#term-tengiga-0-1>`_ command and updating the `udp_dstport <commandline.html#term-udp_dstport-n>`_ and `udp_dstip <commandline.html#term-udp_dstip-x.x.x.x-or-auto>`_ commands to match the 1GbE or 10GbE interface. This setting only affects packetsize and number of packets, but does not affect the total image size. 
-
-
-Gotthard2
--------------
-
-
-Default Configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. image:: images/Gotthard2_module.png
-   :target: _images/Gotthard2_module.png
-   :align: center
-   :alt: Gotthard2 Module Default Configuration
-
-Each Gotthard2 module is a 1D detector with 10 chips, each with 128 channels. 
-
-Image size = 2,560 bytes 
-   - 10 chips (1 x 10 grid)
-   - 128 channels
-   - 2 bytes (pixel width)
-
-Veto Info
-^^^^^^^^^^^
-
-One can enable veto data in the chip of the Gotthard2 module using the `veto <commandline.html#term-veto-0-1>`_ command. By default, this is disabled. This does not affect the image size as veto information is not sent out through the same 10GbE interface.
-
-One can either stream out the veto info through the low latency link (2.5 gbps) or for debugging purposes through another 10GbE interface.
-
-For debugging purposes, the veto info can be enabled using the `numinterfaces <commandline.html#term-numinterfaces-1-2>`_ command and the following parameters are updated: `udp_dstport2 <commandline.html#term-udp_dstport2-n>`_ and `udp_dstip2 <commandline.html#term-udp_dstip2-x.x.x.x-or-auto>`_. The veto data from this port is of course written to a separate file and is not combined in the virtual HDF5 file mapping (complete image mapped).
-
-

docs/src/dependencies.rst

@@ -14,12 +14,7 @@ the shared libraries these are needed:
 
  * Linux, preferably recent kernel (currently no cross platform support)
  * CMake >= 3.14 
- * C++17 compatible compiler. (We test with gcc and clang)
-
-.. note ::  
-    
-    For v9.x.x of slsDetectorPackage and older, C++11 compatible compiler.
-
+ * C++11 compatible compiler. (We test with gcc and clang)
 
 -----------------------
 Python bindings

docs/src/fileformat.rst

@@ -1,5 +1,3 @@
-.. _file format:
-
 File format
 ================================
 
@@ -62,14 +60,3 @@ There are 2 file formats supported by the receiver:
 
 The default is binary. HDF5 can be enabled by compiling the package with HDF5 option enabled. The file format is set using the command `fformat <commandline.html#term-fformat-binary-hdf5>`_.
 
-
-Content
---------
-
-| `Master File`: Contains the metadata of the acquisition. The content is described in :ref:`master file attributes <master file attributes>`.
-
-
-| `Data File`: Contains the metadata for each image (:ref:`slsReceiverHeader<sls receiver header format>`) and the `data of the image` transmitted over that port. The image data is described in :ref:`Detector Image Size and Format <data format>` section.
-
-
-| More content and examples are found in the :ref:`HDF5 file format <hdf5 file format>` and :ref:`Binary file format <binary file format>` sections.

docs/src/firmware.rst

@@ -1,5 +1,3 @@
-.. _firmware upgrade:
-
 Firmware Upgrade
 =================
 

docs/src/hdf5fileformat.rst

@@ -1,4 +1,4 @@
-.. _hdf5 file format:
+
 
 HDF5 File Format
 ================================
@@ -76,8 +76,6 @@ Data File
 
 * File Name: [fpath]/[fname]_dx_fy_[findex].h5 :ref:`Details here<file name format>`
 
-* More details on :ref:`slsReceiverHeader<sls receiver header format>` and the actual image data is described in the :ref:`Detector Image Size and Format <data format>` section.
-
 
 Virtual Data File
 ------------------

docs/src/index.rst

@@ -18,17 +18,6 @@ Welcome to slsDetectorPackage's documentation!
     installation
     dependencies
     consuming
-
-
-.. toctree::
-    :caption: how to
-    :maxdepth: 2
-
-    softwarearchitecture
-    configcommands
-    quick_start_guide
-    dataformat
-    multidet
    
 .. toctree::
     :caption: C++ API
@@ -39,9 +28,6 @@ Welcome to slsDetectorPackage's documentation!
     receiver_api
     examples
 
-
-
-    
 .. toctree::
     :caption: Python API
     :maxdepth: 2
@@ -58,7 +44,7 @@ Welcome to slsDetectorPackage's documentation!
     :maxdepth: 1
 
     commandline  
-
+    quick_start_guide
 
 .. toctree::
     :caption: Developer
@@ -95,9 +81,8 @@ Welcome to slsDetectorPackage's documentation!
     :caption: Receiver
     :maxdepth: 2
 
-    slsreceiver
     receivers
-    
+    slsreceiver
 
 .. toctree::
     :caption: Receiver Files
@@ -105,7 +90,6 @@ Welcome to slsDetectorPackage's documentation!
 
     fileformat
     slsreceiverheaderformat
-    dataformat
     masterfileattributes
     binaryfileformat
     hdf5fileformat

docs/src/installation.rst

@@ -6,33 +6,18 @@
 Installation
 ===============
 
-.. contents::
-   :local:
-   :depth: 2
-   :backlinks: top
-
-
-Overview
---------------
-
-The ``slsDetectorPackage`` provides core detector software implemented in C++, along with Python bindings packaged as the ``slsdet`` Python extension module. Choose the option that best fits your environment and use case.
-
-:ref:`conda pre-built binaries`: 
-Install pre-built binaries for the C++ client, receiver, GUI and the Python API (``slsdet``), simplifying setup across platforms.
-
-:ref:`pip`:
-Install only the Python extension module, either by downloading the pre-built library from PyPI or by building the extension locally from source. Available only from v9.2.0 onwards.
-
-:ref:`build from source`: 
-Compile the entire package yourself, including both the C++ core and the Python bindings, for maximum control and customization. However, make sure that you have the :doc:`dependencies <../dependencies>` installed. If installing using conda, conda will manage the dependencies. Avoid installing packages with pip and conda simultaneously.
-
-
+One can either install pre-built binaries using conda or build from source.
 
+.. warning ::
+    
+    Before building from source make sure that you have the 
+    :doc:`dependencies <../dependencies>` installed. If installing using conda, conda will 
+    manage the dependencies. Avoid also installing packages with pip. 
    
-.. _conda pre-built binaries:
 
-1. Install pre-built binaries using conda (Recommended)
---------------------------------------------------------
+
+Install binaries using conda
+----------------------------------
 
 Conda is not only useful to manage python environments but can also
 be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
@@ -78,29 +63,12 @@ We have four different packages available:
     conda search moenchzmq
 
 
-.. _pip:
-
-2. Pip
--------
-The Python extension module ``slsdet`` can be installed using pip. This is available from v9.2.0 onwards.
-
-.. code-block:: bash
-    
-    #Install the Python extension module from PyPI
-    pip install slsdet
-
-    # or install the python extension locally from source
-    git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 9.2.0
-    cd slsDetectorPackage
-    pip install .
 
 
-.. _build from source:
+Build from source
+----------------------
 
-3. Build from source
--------------------------
-
-3.1. Download Source Code from github
+1. Download Source Code from github
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
@@ -115,53 +83,30 @@ The Python extension module ``slsdet`` can be installed using pip. This is avail
 
 
 
-3.2. Build from Source
+2. Build from Source
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 One can either build using cmake or use the in-built cmk.sh script.
 
-3.2.1. Build using CMake
+Build using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-
 .. code-block:: bash
 
     # outside slsDetecorPackage folder
     mkdir build && cd build
 
-    # configure & generate Makefiles using cmake by listing all your options 
-    # (alternately use ccmake described below)
-    # cmake3 instead of cmake for some systems
-    
-    # eg. enable gui option (without conda)
-    cmake ../slsDetectorPacakge -DSLS_USE_GUI=ON
-    # eg. enable python from virtual env, hdf5 and simulator options
-    cmake ../slsDetectorPackage -DSLS_USE_PYTHON=ON -DPython_FIND_VIRTUALENV=ONLY -DSLS_USE_HDF5=ON -DSLS_USE_SIMULATOR=ON
+    # configure & generate Makefiles using cmake
+    # by listing all your options (alternately use ccmake described below)
+    # cmake3 for some systems
+    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
 
     # compiled to the build/bin directory
     make -j12 #or whatever number of cores you are using to build
 
-
-To install in a clean custom directory and to use the slsDetectorPackage 
-libraries and headers in your project, specify the install directory 
-(eg. /your/install/path). 
-
-.. code-block:: bash
-
-    # outside slsDetecorPackage folder
-    mkdir build && cd build
-    # configure & generate Makefiles
-    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-    # compile
-    make -j12
     # install headers and libs in /your/install/path directory
     make install
 
-.. note ::   
-
-    Please refer to `api examples <https://github.com/slsdetectorgroup/api-examples>`__ 
-    on how to compile your project using the installed headers and libs.
-    
 
 Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.
 
@@ -190,7 +135,7 @@ Example cmake options               Comment
     For v7.x.x of slsDetectorPackage and older, refer :ref:`zeromq notes for cmake option to hint library location. <zeromq for different slsDetectorPackage versions>` 
 
 
-3.2.2. Build using in-built cmk.sh script
+Build using in-built cmk.sh script
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 
@@ -240,10 +185,10 @@ Example cmake options               Comment
     For v7.x.x of slsDetectorPackage and older, refer :ref:`zeromq notes for cmk script option to hint library location. <zeromq for different slsDetectorPackage versions>` 
 
 
-3.3. Build on old distributions using conda
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Build on old distributions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-If your linux distribution doesn't come with a C++17 compiler (gcc>8) then 
+If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
 it's possible to install a newer gcc using conda and build the slsDetectorPackage
 using this compiler
 
@@ -265,7 +210,7 @@ using this compiler
 
 
 
-3.4. Build slsDetectorGui (Qt5)
+Build slsDetectorGui (Qt5)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 1. Using pre-built binary on conda
@@ -326,7 +271,7 @@ using this compiler
 
 
 
-3.5. Build this documentation
+Build this documentation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The documentation for the slsDetectorPackage is build using a combination 
@@ -349,8 +294,8 @@ is to use conda
     make rst # rst only, saves time in case the API did not change
 
 
-4. Pybind and Zeromq
--------------------------
+Pybind and Zeromq
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. _pybind for different slsDetectorPackage versions:
 

docs/src/multidet.rst

@@ -1,230 +0,0 @@
-.. _using multiple detectors:
-
-Using multiple detectors
-==========================
-
-The slsDetectorPackage supports using several detectors on the same computer.
-This can either be two users, that need to use the same computer without interfering
-with each other, or the same user that wants to use multiple detectors at the same time.
-The detectors in turn can consist of multiple modules. For example, a 9M Jungfrau detector
-consists of 18 modules which typically are addressed at once as a single detector.
-
-.. note ::
-
-    To address a single module of a multi-module detector you can use the module index. 
-    
-    - Command line: :ref:`cl-module-index-label`
-    - Python: :ref:`py-module-index-label`
-
-
-Coming back to multiple detectors we have two tools to our disposal:
-
-#. Detector index 
-#. The SLSDETNAME environment variable
-
-They can be used together or separately depending on the use case.
-
-Detector index
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-When configuring a detector you can specify a detector index. The default is 0. 
-
-**Command line**
-
-.. code-block:: bash
-
-    # Given that we have two detectors (my-det and my-det2) that we want to use,
-    # we can configure them with different indices.
-
-    # Configure the first detector with index 0
-    $ sls_detector_put hostname my-det
-    
-    # Set number of frames for detector 0 to 10
-    $ sls_detector_put frames 10
-
-
-    # 
-    #Configure the second detector with index 1 (notice the 1- before hostname)
-    $ sls_detector_put 1-hostname my-det2
-    
-
-    # Further configuration
-    ...
-
-    # Set number of frames for detector 1 to 19
-    $ sls_detector_put 1-frames 19
-
-    # Note that if we call sls_detector_get without specifying the index,
-    # it will return the configuration of detector 0
-    $ sls_detector_get frames
-    10
-
-The detector index is added to the name of the shared memory segment, so in this case
-the shared memory segments would be:
-
-.. code-block:: bash
-
-
-    #First detector
-    /dev/shm/slsDetectorPackage_detector_0
-    /dev/shm/slsDetectorPackage_detector_0_module_0
-
-    #Second detector
-    /dev/shm/slsDetectorPackage_detector_1
-    /dev/shm/slsDetectorPackage_detector_1_module_0
-
-
-**Python**
-
-The main difference between the command line and the Python API is that you set the index
-when you create the detector object and you don't have to repeat it for every call.
-
-The C++ API works int the same way. 
-
-.. code-block:: python
-
-    from slsdet import Detector
-    
-
-    # The same can be achieved in Python by creating a detector object with an index.
-    # Again we have two detectors (my-det and my-det2) that we want to use:
-
-    # Configure detector with index 0
-    d = Detector()
-
-    # If the detector has already been configured and has a shared memory
-    # segment, you can omit setting the hostname again
-    d.hostname = 'my-det'
-
-    #Further configuration
-    ...
-
-    # Configure a second detector with index 1
-    d2 = Detector(1)
-    d2.hostname = 'my-det2'
-   
-    d.frames = 10
-    d2.frames = 19
- 
-
-$SLSDETNAME
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-To avoid interfering with other users on shared PCs it is best to always set the SLSDETNAME environmental variable.
-Imagining a fictive user: Anna, we can set SLSDETNAME from the shell before configuring the detector:
-
-**Command line**
-
-.. code-block:: bash
-
-    # Set the SLSDETNAME variable
-    $ export SLSDETNAME=Anna
-
-    # You can check that it is set
-    $ echo $SLSDETNAME
-    Anna
-
-    # Now configures a detector with index 0 and prefixed with the name Anna
-    # /dev/shm/slsDetectorPackage_detector_0_Anna
-    $ sls_detector_put hostname my-det
-
-
-.. tip ::
-
-    Set SLSDETNAME in your .bashrc in order to not forget it when opening a new terminal.
-
-
-**Python**
-
-With python the best way is to set the SLSDETNAME from the command line before starting the python interpreter.
-
-Bash:
-
-.. code-block:: bash
-
-    $ export SLSDETNAME=Anna
-
-Python:
-
-.. code-block:: python
-
-    from slsdet import Detector
-    
-    # Now configures a detector with index 0 and prefixed with the name Anna
-    # /dev/shm/slsDetectorPackage_detector_0_Anna
-    d = Detector()
-    d.hostname = 'my-det'
-
-You can also set SLSDETNAME from within the Python interpreter, but you have to be aware that it will only
-affect the current process and not the whole shell session.
-
-.. code-block:: python
-
-    import os
-    os.environ['SLSDETNAME'] = 'Anna'
-
-    # You can check that it is set
-    print(os.environ['SLSDETNAME'])  # Output: Anna
-
-    #Now SLSDETNAME is set to Anna but as soon as you exit the python interpreter
-    # it will not be set anymore
-
-.. note ::
-
-    Python has two ways of reading environment variables: `**os.environ**` as shown above which throws a
-    KeyError if the variable is not set and `os.getenv('SLSDETNAME')` which returns None if the variable is not set.
-
-    For more details see the official python documentation on: https://docs.python.org/3/library/os.html#os.environ
-
-
-Checking for other detectors
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If using shared accounts on a shared computer (which you anyway should not do), it is good practice to check
-if there are other detectors configured by other users before configuring your own detector.
-
-You can do this by listing the files in the shared memory directory `/dev/shm/` that start with `sls`. In this
-example we can see that two single module detectors are configured one with index 0 and one with index 1.
-SLSDETNAME is set to `Anna` so it makes sense to assume that she is the user that configured these detectors.
-
-
-.. code-block:: bash
-
-    # List the files in /dev/shm that starts with sls
-    $ ls /dev/shm/sls*
-    /dev/shm/slsDetectorPackage_detector_0_Anna
-    /dev/shm/slsDetectorPackage_detector_0_module_0_Anna
-    /dev/shm/slsDetectorPackage_detector_1_Anna
-    /dev/shm/slsDetectorPackage_detector_1_module_0_Anna
-
-We also provide a command: user, which gets information about the shared memory segment that
-the client points to without doing any changes. 
-
-.. code-block:: bash
-
-    #in this case 3 simulated Mythen3 modules
-    $ sls_detector_get user
-    user 
-    Hostname: localhost+localhost+localhost+
-    Type: Mythen3
-    PID: 1226078
-    User: l_msdetect
-    Date: Mon Jun  2 05:46:20 PM CEST 2025
-
-
-Other considerations
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The shared memory is not the only way to interfere with other users. You also need to make sure that you are not
-using the same:
-
-* rx_tcpport
-* Unique combination of udp_dstip and udp_dstport
-* rx_zmqport
-* zmqport
-
-.. attention ::
-
-    The computer that you are using need to have enough resources to run multiple detectors at the same time.
-    This includes CPU and network bandwidth. Please coordinate with the other users!
-

docs/src/pygettingstarted.rst

@@ -123,47 +123,6 @@ in a large detector.
     # Set exposure time for module 1, 5 and 7
     d.setExptime(0.1, [1,5,7])
 
-
-
-.. _py-module-index-label:
-
-----------------------------------
-Accessing individual modules
-----------------------------------
-
-Using the C++ like API you can access individual modules in a large detector
-by passing in the module index as an argument to the function.
-
-::
-    
-    # Read the UDP destination port for all modules
-    >>> d.getDestinationUDPPort()
-    [50001, 50002, 50003]
-
-
-    # Read it for module 0 and 1
-    >>> d.getDestinationUDPPort([0, 1])
-    [50001, 50002]
-
-    >>> d.setDestinationUDPPort(50010, 1)
-    >>> d.getDestinationUDPPort()
-    [50001, 50010, 50003]
-
-From the more pythonic API there is no way to read from only one module but you can read 
-and then use list slicing to get the values for the modules you are interested in.
-
-::
-
-    >>> d.udp_dstport
-    [50001, 50010, 50003]
-    >>> d.udp_dstport[0]
-    50001
-
-    #For some but not all properties you can also pass in a dictionary with module index as key
-    >>> ip = IpAddr('127.0.0.1')
-    >>> d.udp_dstip = {1:ip}
-
-
 --------------------
 Finding functions 
 --------------------

docs/src/quick_start_guide.rst

@@ -19,14 +19,14 @@ For a Single Module
         slsReceiver
 
         # custom port 2012
-        slsReceiver -p 2012
+        slsReceiver -t2012
 
 
 For Multiple Modules
     .. code-block:: bash  
 
-        # slsMultiReceiver [-p: starting port, -n: number of receivers]
-        slsMultiReceiver -p 2012 -n 2 
+        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
+        slsMultiReceiver 2012 2 0 
 
 
 Client
@@ -131,27 +131,6 @@ For Multiple Modules
 .. note ::   
     The **hostname** and **detsize** command in a multi module system can affect the row and column values in the udp/zmq header. The modules are stacked row by row until they reach the y-axis limit set by detsize (if specified). Then, stacking continues in the next column and so on. 
 
-
-
-
-
-Data
------
-
-Check out the :ref:`UDP header section<detector udp header>` for details on output UDP header data format.`
-
-Check out the :ref:`Detector image size and format section<data format>`  for details on output data format.
-
-
-Receiver
----------
-
-When using `slsReceiver`, `slsMultiReceiver` or `slsFrameSynchronizer`, check out the following sections:
-
- - :ref:`File format<file format>`
- - :ref:`slsReceiver header format<sls receiver header format>`
- - :ref:`Master file attributes<master file attributes>`
-
     
 Gui
 ----

docs/src/receivers.rst

@@ -1,25 +1,25 @@
-Custom Receiver
+Receivers
 =================
 
-The receiver essentially listens to UDP data packets sent out by the detector.
-
-To know more about detector receiver setup in the config file, please check out :ref:`the detector-receiver UDP configuration in the config file<detector udp header config>` and the :ref:`detector udp format<detector udp header>`.
+Receiver processes can be run on same or different machines as the client, receives the data from the detector (via UDP packets).
+When using the slsReceiver/ slsMultiReceiver, they can be further configured by the client control software (via TCP/IP) to set file name, file path, progress of acquisition etc.
 
 
-| Please note the following when using a custom receiver:
+To know more about detector receiver configuration, please check out :ref:`detector udp header and udp commands in the config file <detector udp header>`
 
-* **udp_dstmac** must be configured in the config file. This parameter is not required when using an in-built receiver.
+Custom Receiver
+----------------
 
-* Cannot use "auto" for **udp_dstip**.
+| When using  custom receiver with our package, ensure that **udp_dstmac** is also configured in the config file. This parameter is not required when using slsReceiver.
 
-* No **rx_** commands in the config file. These commands are for configuring the slsReceiver.
+| Cannot use "auto" for **udp_dstip**.
 
-
-
-The main difference is the lack of **rx_** commands or file commands (eg. **f**write, **f**path) and the **udp_dstmac** is required in config file.
+| Also ensure that there are no **rx_** commands in the config file. These commands are for configuring the slsReceiver.
 
 Example of a custom receiver config file
 
+* The main difference is the lack of **rx_** commands or file commands (eg. fwrite, fpath) and the udp_dstmac is required in config file.
+
 .. code-block:: bash
 
     # detector hostname

docs/src/servers.rst

@@ -1,5 +1,3 @@
-.. _detector_servers:
-
 Getting Started
 ===============
 

docs/src/serverupgrade.rst

@@ -1,5 +1,4 @@
 .. _Detector Server Upgrade:
-
 Upgrade
 ========
 

docs/src/slsreceiver.rst

@@ -1,78 +1,16 @@
-In-built Receiver   
+slsReceiver/ slsMultiReceiver
 ================================
 
-
-
-The receiver essentially listens to UDP data packets sent out by the detector. It's main features are:
-
-- **Listening**: Receives UDP data from the detector.
-- **Writing to File**: Optionally writes received data to disk.
-- **Streaming via ZMQ**: Optionally streams out the data using ZeroMQ.
-
-Each of these operations runs asynchronously and in parallel for each UDP port.
-
-
-.. note ::   
-
-    * Can be run on the same or different machine as the client.
-    * Can be configured by the client. (set file name/ discard policy, get progress etc.)
-    * Has to be started before the client runs any receiver specific command.
-
-
-Receiver Variants
------------------
-There are three main receiver types. How to start them is described :ref:`below<Starting up the Receiver>`.
-
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-| Receiver Type        | slsReceiver        | slsMultiReceiver                        |slsFrameSynchronizer            | 
-+======================+====================+=========================================+================================+
-| Modules Supported    | 1                  | Multiple                                | Multiple                       |
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-| Internal Architecture| Threads per porttt | Multiple child processes of slsReceiver | Multi-threading of slsReceiver |
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-| ZMQ Streaming        | Disabled by default| Disabled by default                     | Enabled, not optional          |
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-| ZMQ Synchronization  | No                 | No                                      | Yes, across ports              |
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-| Image Reconstruction | No                 | No                                      | No                             |
-+----------------------+--------------------+-----------------------------------------+--------------------------------+
-
-
-.. _Starting up the Receiver:
-
-Starting up the Receiver
--------------------------
-
-.. code-block:: bash  
-
-    Usage: slsReceiver Options:
-        -v, --version       : Version.
-        -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-        -u, --uid           : Set effective user id if receiver started with privileges. 
-
-    Usage: slsMultiReceiver Options:
-        -v, --version       : Version.
-        -n, --num-receivers : Number of receivers.
-        -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-        -c, --callback      : Enable dummy callbacks for debugging. Disabled by default. 
-        -u, --uid           : Set effective user id if receiver started with privileges. 
-
-    Usage: slsFrameSynchronizer Options:
-        -v, --version       : Version.
-        -n, --num-receivers : Number of receivers.
-        -p, --port          : TCP port to communicate with client for configuration. Non-zero and 16 bit.
-        -c, --print-headers : Print callback headers for debugging. Disabled by default.
-        -u, --uid           : Set effective user id if receiver started with privileges. 
-
-
-
+| One has to start the slsReceiver before loading config file or using any receiver commands (prefix: **rx_** )
 
 For a Single Module
     .. code-block:: bash  
-        
-        slsReceiver # default port 1954
 
-        slsReceiver -p 2012 # custom port 2012
+        # default port 1954
+        slsReceiver
+
+        # custom port 2012
+        slsReceiver -t2012
 
 
 For Multiple Modules
@@ -80,66 +18,57 @@ For Multiple Modules
 
         # each receiver (for each module) requires a unique tcp port (if all on same machine)
 
-        # option 1 (one for each module)
+        # using slsReceiver in multiple consoles
         slsReceiver
-        slsReceiver -p 1955
+        slsReceiver -t1955
 
-        # option 2
-        slsMultiReceiver -p 2012 -n 2
-
-        # option 3
-        slsFrameSynchronizer -p 2012 -n 2
+        # slsMultiReceiver [starting port] [number of receivers]
+        slsMultiReceiver 2012 2
 
+        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
+        slsMultiReceiver 2012 2 1
 
 
 Client Commands 
 -----------------
 
-* Client commands to the receiver begin with **rx_** or **f_** (file commands).
+| One can remove **udp_dstmac** from the config file, as the slsReceiver fetches this from the **udp_ip**.
 
-* **rx_hostname** has to be the first command to the receiver so the client knows which receiver process to communicate with.
+| One can use "auto" for **udp_dstip** if one wants to use default ip of **rx_hostname**.
 
-* Can use 'auto' for **udp_dstip** if using 1GbE interface or the :ref:`virtual simulators<Virtual Detector Servers>`.
-
-
-To know more about detector receiver setup in the config file, please check out :ref:`the detector-receiver UDP configuration in the config file<detector udp header config>` and the :ref:`detector udp format<detector udp header>`.
-
-
-The following are the different ways to establish contact using **rx_hostname** command.
+| The first command to the receiver (**rx_** commands) should be **rx_hostname**. The following are the different ways to establish contact.
 
     .. code-block:: bash  
 
-        # ---single module---
-
-        # default receiver port at 1954
+        # default receiver tcp port (1954)
         rx_hostname xxx
-       
+
         # custom receiver port
-        rx_hostname xxx:1957 # option 1
-       
-        rx_tcpport 1957  # option 2
+        rx_hostname xxx:1957
+
+        # custom receiver port
+        rx_tcpport 1954
         rx_hostname xxx
 
-
-        # ---multi module---
-
-        # using increasing tcp ports
+        # multi modules with custom ports
+        rx_hostname xxx:1955+xxx:1956+
+        
+        
+        # multi modules using increasing tcp ports when using multi detector command
         rx_tcpport 1955
         rx_hostname xxx
 
-        # custom ports
-        rx_hostname xxx:1955+xxx:1958+ # option 1
-
-        0:rx_tcpport 1954 # option 2
+        # or specify multi modules with custom ports on same rxr pc
+        0:rx_tcpport 1954
         1:rx_tcpport 1955
         2:rx_tcpport 1956
         rx_hostname xxx
 
-        # custom ports on different receiver machines
+        # multi modules with custom ports on different rxr pc
         0:rx_tcpport 1954
         0:rx_hostname xxx
         1:rx_tcpport 1955
-        1:rx_hostname yyyrxr
+        1:rx_hostname yyy
 
 
 | Example commands:
@@ -162,32 +91,6 @@ The following are the different ways to establish contact using **rx_hostname**
         sls_detector_get -h rx_framescaught
 
 
-Example of a config file using in-built receiver
-
-.. code-block:: bash
-
-    # detector hostname
-    hostname bchip052+bchip053+
-
-    # udp destination port (receiver)
-    # sets increasing destination udp ports starting at 50004
-    udp_dstport 50004
-
-    # udp destination ip (receiver)
-    0:udp_dstip 10.0.1.100
-    1:udp_dstip 10.0.2.100
-
-    # udp source ip (same subnet as udp_dstip)
-    0:udp_srcip 10.0.1.184
-    1:udp_srcip 10.0.2.184
-
-    # udp destination mac - not required (picked up from udp_dstip)
-    #udp_dstmac 22:47:d5:48:ad:ef
-
-    # connects to receivers at increasing tcp port starting at 1954
-    rx_hostname mpc3434
-    # same as rx_hostname mpc3434:1954+mpc3434:1955+
-
 
 
 Performance 

docs/src/softwarearchitecture.rst

@@ -1,147 +0,0 @@
-.. _software architecture:
-
-Software Architecture
-================================
-
-
-Introduction
-------------------------------------
-
-.. figure:: images/System_communication_architecture.png
-   :target: _images/System_communication_architecture.png
-   :width: 700px
-   :align: center
-   :alt: System communication architecture
-
-   Software Communication Architecture
-
-
-**Detector** 
-
-A detector can consist of a single module or multiple modules combined.
-
-**Module** 
-
-Each module sends its data via UDP over distinct ports. Since UDP does not provide acknowledgements, data is transmitted as fast as possible, which can lead to packet loss if the network is not properly configured, among other causes. A single image streamed out could be split into multiple UDP packets and each module can have one or two UDP ports to transmit in parallel different physical sections of the image.
-
-**Receiver** 
-
-UDP data is received by one or more receivers—either built-in or custom. In the diagram above, there is one built-in receiver per module (1:1). For example, a detector with two modules (two hostnames) will have two built-in receivers. Each receiver could listen to one or two UDP ports (depending on the module it listens to). For each UDP port, the receiver reassembles these packets into sub-images and optionally saved to file.
-
-**ZMQ** 
-
-Each UDP port in the receiver can also stream out independently sub-images via ZMQ (core: TCP/IP).
-    
-* Directly to the GUI for display.
-* To an external processing chain for post-processing and optional storage, which can in turn stream the processed data back to the GUI.
-
-**Client** 
-
-A single client can configure and control individual modules and receivers, or multiple of them in parallel. This communication is handled over TCP/IP, ensuring acknowledgements. 
-
-It can also listen to multiple ZMQ sockets from the Receiver(s) or the external processing chain to assemble the full image for GUI display or Client call backs.
-
-Next, each component is examined in detail.
-
-Module
--------
-
-.. figure:: images/Module_architecture.png
-   :target: _images/Module_architecture.png
-   :width: 700px
-   :align: center
-   :alt: Module architecture
-
-   Module Architecture
-
-
-**Detector Server**
-
-The module contains an onboard CPU (type depends on the detector — e.g., Nios for Mythen3, Blackfin for Jungfrau). The detector server and detector configuration files are stored here, with the server compiled in C using the CPU-specific compiler. Running the binary starts a Control Server and a Stop Server. Client control/configuration requests go to the Control Server via the TCP control port, while stop/status requests go to the Stop Server via the TCP stop port as the Control Server may be busy with an acquisition. For more details see :ref:`detector server <detector_servers>` and :ref:`detector simulators<Virtual Detector Servers>` to play around with.
-
-**Firmware**
-
-The module also includes an FPGA with VHDL firmware (file format depends on the detector — e.g., Mythen3 uses .rbf, Jungfrau uses .pof). Client requests trigger register read/write operations in the FPGA, which manages chip readout and processing. Data from the chips is sent through a UDP generator in the FPGA and output as UDP packets via the UDP port. A single image may be split across multiple packets. A module could have 1 or 2 UDP ports to transmit in parallel different physical sections of the image.
-
-Upgrade
-^^^^^^^^
-
-.. figure:: images/Soft_upgrade_components.png
-   :target: _images/Soft_upgrade_components.png
-   :width: 700px
-   :align: center
-   :alt: Software Upgrade Components
-
-   Software Upgrade Components
-
-There are mainly three components to the soft upgrade:
-
-* Detector Server upgrade: The server running on the module.
-* Firmware upgrade: The VHDL code running on the FPGA.
-* slsDetectorPackage upgrade: The client code running on the host PC to control the module(s) and receiver(s) if any.
-
-Please use the `update command <commandline.html#term-update>`_ when updating both the server and firmware simulataneously and `programfpga command <commandline.html#term-programfpga-fname.pof-fname.rbf-full-path-opitonal-force-delete-normal-file>`_ when only updating the firmware. See :ref:`firmware upgrade <firmware upgrade>` for details.
-
-When only updating the detector server, use the `updatedetectorserver command <commandline.html#term-updatedetectorserver-server_name-with-full-path>`_ command. See :ref:`detector server upgrade <Detector Server Upgrade>` for details.
-
-.. note::
-   
-   **Compatibility**
-
-   When updating anything on the module via the client (server or firmware), the server and client will have to be compatible (same major version). If not, the client and server will not communicate properly.
-
-   Since they are ideally compatible before the upgrade, upgrade the server and firmware first, then the slsDetectorPackage.
-
-
-
-Receiver
---------
-
-.. figure:: images/Receiver_architecture.png
-   :target: _images/Receiver_architecture.png
-   :align: center
-   :alt: Receiver Architecture
-
-   Receiver Architecture
-
-The receiver mainly consists of:
-
-* A TCP server that listens to client TCP requests for configuration and control.
-* One or 2 listeners that listen to a UDP port each, reassembling the UDP packets into sub-images in memory.
-* One or 2 data processors that processes the sub-images with optional callbacks for online processing and file writing.
-* One or 2 data streamers that stream the processed sub-images to the GUI or external processing chain via ZMQ.
-
-Few characteristics of the receiver:
-
-* It can be run on the same host as the client or on a different host.
-* There is a receiver process for every module and a file for every UDP port. 
-* Each receiver process is independent and asynchronized for performance. So are the UDP ports.
-
-
-Client
---------
-
-.. figure:: images/Client_architecture.png
-   :target: _images/Client_architecture.png
-   :align: center
-   :alt: Client Architecture
-
-   Client Architecture
-
-Users can control the detector and receivers through four interfaces: 
-
-* their C++ API, 
-* their Python API, 
-* the command-line interface, or 
-* the Qt-based GUI. 
-
-Regardless of the interface, each ultimately invokes our Detector class—either directly (CLI and GUI) or through our C++/Python libraries (when using their APIs). The Detector class then calls the appropriate module functions, either for a specific module or in parallel for all modules. Each module object sends requests over TCP to its corresponding module and, if needed, to the receiver.
-
-**Shared Memory**
-
-As the command-line interface is supported, shared memory is used to store essential information such as the module hostname and TCP port, or the receiver hostname and TCP port. This ensures the system knows which components to communicate with, without requiring the user to re-enter this information for every command-line call.
-
-.. note::
-   
-   Only the client maintains shared memory. Care must be taken when multiple users operate from the same PC. See :ref:`multi detector and user section <using multiple detectors>` for more details.
-

docs/src/troubleshooting.rst

@@ -202,56 +202,6 @@ Receiver PC Tuning Options
             ethtool -K xth1 gro
         
 
-    * **permanent ethtool settings**
-
-        There are two main methods.
-
-        1. ``systemd service`` (recommended for Fedora and modern RHEL)
-
-            This is the preferred method on systems using systemd and NetworkManager, such as Fedora and RHEL 8+.
-
-            Create a systemd service template:
-                .. code-block:: ini
-
-                    # /etc/systemd/system/ethtool@.service
-
-                    [Unit]
-                    Description=Set RX buffer size with ethtool
-                    After=network-online.target
-                    Wants=network-online.target
-
-                    [Service]
-                    ExecStart=/usr/sbin/ethtool -G %i rx 8192
-                    Type=oneshot
-
-                    [Install]
-                    WantedBy=multi-user.target
-
-
-            Enable the service for a specific interface:
-                .. code-block:: bash
-
-                    sudo systemctl enable ethtool@xth1.service
-
-            This ensures the setting is applied at every boot once the network is online.
-
-
-        2. ``ETHTOOL_OPTS in ifcfg scripts`` (legacy method for RHEL 7 and earlier)
-
-            This method applies only to systems using the legacy network-scripts backend, typically RHEL 7 and earlier. 
-
-            .. code-block:: bash
-
-                # edit the corresponding ``ifcfg-*`` file
-                # file: /etc/sysconfig/network-scripts/ifcfg-eth0
-
-                # add or modify the following line:
-                ETHTOOL_OPTS="-K ${DEVICE} gro on; -G ${DEVICE} rx 4096; -L ${DEVICE} combined 4; -C ${DEVICE} rx-usecs 100; -C ${DEVICE} adaptive-rx on"
-
-                # restart the interface
-                ifdown eth0 && ifup eth0
-
-
 #. Disable power saving in CPU frequency scaling and set system to performance 
     * Check current policy (default might be powersave or schedutil)
         .. code-block:: bash

docs/src/udpconfig.rst

@@ -1,4 +1,4 @@
-.. _detector udp header config:
+.. _detector udp header:
 
 
 Config file

docs/src/udpheader.rst

@@ -99,7 +99,6 @@ Detector Enum
     MYTHEN3             6
     GOTTHARD2           7    
     ================    ========
-    
     * deprecated since v10.0.0
 
 

docs/src/virtualserver.rst

@@ -1,5 +1,4 @@
 .. _Virtual Detector Servers:
-
 Simulators
 ===========
 

psi-pmodules/DetectorSoftware/slsDetectorPackage/files/variants

@@ -13,5 +13,5 @@ slsDetectorPackage/8.0.2_rh7 stable cmake/3.15.5 Qt/5.12.10
 slsDetectorPackage/8.0.2_rh8 stable cmake/3.15.5 Qt/5.12.10
 slsDetectorPackage/9.0.0_rh8 stable cmake/3.15.5 Qt/5.12.10
 slsDetectorPackage/9.1.0_rh8 stable cmake/3.15.5 Qt/5.12.10
-slsDetectorPackage/9.1.1_rh8 stable cmake/3.15.5 Qt/5.12.10
-slsDetectorPackage/9.2.0_rh8 stable cmake/3.15.5 Qt/5.12.10
+
+

pyproject.toml

@@ -11,13 +11,9 @@ build-backend = "scikit_build_core.build"
 [project]
 name = "slsdet"
 dynamic = ["version"]
-dependencies = [
-    "numpy", 
-]
 
 [tool.cibuildwheel]
 before-all = "uname -a"
-build = "cp{311,312,313}-manylinux_x86_64"
 
 [tool.scikit-build.build]
 verbose = true

python/CMakeLists.txt

@@ -65,9 +65,6 @@ configure_file( scripts/test_virtual.py
     ${CMAKE_BINARY_DIR}/test_virtual.py 
 )
 
-configure_file(scripts/frameSynchronizerPullSocket.py 
-   ${CMAKE_BINARY_DIR}/bin/frameSynchronizerPullSocket.py COPYONLY)
-
 configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/../VERSION  
     ${CMAKE_BINARY_DIR}/bin/slsdet/VERSION
 )

python/scripts/generate_functions.py

@@ -13,17 +13,13 @@ import subprocess
 import argparse
 import sys
 import time
-import ctypes.util, re  # to check libclang version 
 from pathlib import Path
 from parse import system_include_paths, clang_format_version
 
 REDC = "\033[91m"
 GREENC = "\033[92m"
-YELLOWC = "\033[93m"
 ENDC = "\033[0m"
 
-def yellow(msg):
-    return f"{YELLOWC}{msg}{ENDC}"
 
 def red(msg):
     return f"{REDC}{msg}{ENDC}"
@@ -33,25 +29,6 @@ def green(msg):
     return f"{GREENC}{msg}{ENDC}"
 
 
-def check_libclang_version(required="12"):
-    # Use already-loaded libclang, or let cindex resolve it
-    lib = ctypes.CDLL(cindex.Config.library_file or ctypes.util.find_library("clang"))
-
-    # Get version string
-    lib.clang_getClangVersion.restype = ctypes.c_void_p
-    version_ptr = lib.clang_getClangVersion()
-    version_str = ctypes.cast(version_ptr, ctypes.c_char_p).value.decode()
-
-    # Parse and check version
-    match = re.search(r"version\s+(\d+)", version_str)
-    if not match or match.group(1) != required:
-        msg = red(f"libclang version {match.group(1) if match else '?'} found, but version {required} required. Bye!")
-        print(msg)
-        sys.exit(1)
-    msg = green(f"Found libclang version {required}")
-    print(msg)
-
-
 def check_clang_format_version(required_version):
     if (ver := clang_format_version()) != required_version:
         msg = red(
@@ -143,24 +120,6 @@ def time_return_lambda(node, args):
 
 
 def visit(node):
-
-    loc = node.location
-    # skip if ndoe is outside project directory
-    if loc.file and not str(loc.file).startswith(str(cargs.build_path.parent)):
-        return
-    
-    '''
-    # to see which file was causing the error (not in Detector.h, so skipping others in the above code)
-    try:
-        kind = node.kind
-    except ValueError as e:
-        loc = node.location
-        file_name = loc.file.name if loc.file else "<unknown file>"
-        msg = yellow(f"\nWarning: skipping node with unknown CursorKind id {node._kind_id} at {file_name}:{loc.line}:{loc.column}")
-        print(msg)
-        return 
-    '''
-        
     if node.kind == cindex.CursorKind.CLASS_DECL:
         if node.displayname == "Detector":
             for child in node.get_children():
@@ -202,7 +161,6 @@ if __name__ == "__main__":
     )
     cargs = parser.parse_args()
 
-    check_libclang_version("12")
     check_clang_format_version(12)
     check_for_compile_commands_json(cargs.build_path)
 

python/slsdet/__init__.py

@@ -15,8 +15,6 @@ from .gaincaps import Mythen3GainCapsWrapper
 from .PatternGenerator import PatternGenerator
 
 from . import _slsdet
-from ._slsdet import freeSharedMemory, getUserDetails
-
 xy = _slsdet.xy
 defs = _slsdet.slsDetectorDefs
 

python/slsdet/detector.py

@@ -15,7 +15,7 @@ defs = slsDetectorDefs
 
 from .utils import element_if_equal, all_equal, get_set_bits, list_to_bitmask
 from .utils import Geometry, to_geo, element, reduce_time, is_iterable, hostname_list
-from ._slsdet import xy, freeSharedMemory, getUserDetails
+from ._slsdet import xy
 from .gaincaps import Mythen3GainCapsWrapper
 from . import utils as ut
 from .proxy import JsonProxy, SlowAdcProxy, ClkDivProxy, MaxPhaseProxy, ClkFreqProxy, PatLoopProxy, PatNLoopProxy, PatWaitProxy, PatWaitTimeProxy 
@@ -90,7 +90,7 @@ class Detector(CppDetectorApi):
 
     def free(self):
         """Free detector shared memory"""
-        freeSharedMemory(self.getShmId())
+        self.freeSharedMemory()
 
     @property
     def config(self):
@@ -1537,7 +1537,7 @@ class Detector(CppDetectorApi):
         """
         Retrieve user details from shared memory (hostname, type, PID, User, Date)
         """
-        return getUserDetails(self.getShmId())
+        return self.getUserDetails()
 
     @property
     @element
@@ -2184,7 +2184,6 @@ class Detector(CppDetectorApi):
 
         :setter: It loads trim files from settingspath.\n [Mythen3] An energy of -1 will pick up values from detector.
         """
-        
         if self.type == detectorType.MYTHEN3:
             return self.getAllThresholdEnergy()
         return self.getThresholdEnergy()

python/slsdet/utils.py

@@ -281,6 +281,6 @@ def hostname_list(args):
 
 
 def validate_port(value):
-    if value < 1024 or value > 65535:
-        raise ValueError("port must be in range 1024 - 65535")
+    if value <= 0 or value > 65535:
+        raise ValueError("port must be in range 1 - 65535")
 

python/src/detector.cpp

@@ -25,9 +25,6 @@ void init_det(py::module &m) {
           (void (*)(const int, const int)) & sls::freeSharedMemory,
           py::arg() = 0, py::arg() = -1);
 
-    m.def("getUserDetails", (std::string(*)(const int)) & sls::getUserDetails,
-          py::arg() = 0);
-
     py::class_<Detector> CppDetectorApi(m, "CppDetectorApi");
     CppDetectorApi.def(py::init<int>());
 
@@ -112,13 +109,6 @@ void init_det(py::module &m) {
                        (Result<defs::xy>(Detector::*)(sls::Positions) const) &
                            Detector::getModuleSize,
                        py::arg() = Positions{});
-    CppDetectorApi.def("getPortPerModuleGeometry",
-                       (defs::xy(Detector::*)() const) &
-                           Detector::getPortPerModuleGeometry);
-    CppDetectorApi.def("getPortSize",
-                       (Result<defs::xy>(Detector::*)(sls::Positions) const) &
-                           Detector::getPortSize,
-                       py::arg() = Positions{});
     CppDetectorApi.def("getDetectorSize", (defs::xy(Detector::*)() const) &
                                               Detector::getDetectorSize);
     CppDetectorApi.def("setDetectorSize",
@@ -934,14 +924,15 @@ void init_det(py::module &m) {
                        (void (Detector::*)(bool, sls::Positions)) &
                            Detector::setRxArping,
                        py::arg(), py::arg() = Positions{});
-    CppDetectorApi.def("getRxROI",
-                       (std::vector<defs::ROI>(Detector::*)(int) const) &
-                           Detector::getRxROI,
-                       py::arg() = -1);
-    CppDetectorApi.def("setRxROI",
-                       (void (Detector::*)(const std::vector<defs::ROI> &)) &
-                           Detector::setRxROI,
+    CppDetectorApi.def("getIndividualRxROIs",
+                       (Result<defs::ROI>(Detector::*)(sls::Positions) const) &
+                           Detector::getIndividualRxROIs,
                        py::arg());
+    CppDetectorApi.def("getRxROI",
+                       (defs::ROI(Detector::*)() const) & Detector::getRxROI);
+    CppDetectorApi.def(
+        "setRxROI", (void (Detector::*)(const defs::ROI)) & Detector::setRxROI,
+        py::arg());
     CppDetectorApi.def("clearRxROI",
                        (void (Detector::*)()) & Detector::clearRxROI);
     CppDetectorApi.def(
@@ -1352,11 +1343,10 @@ void init_det(py::module &m) {
         (void (Detector::*)(const int, const std::string &, sls::Positions)) &
             Detector::setVetoFile,
         py::arg(), py::arg(), py::arg() = Positions{});
-    CppDetectorApi.def(
-        "getBurstMode",
-        (Result<defs::burstMode>(Detector::*)(sls::Positions) const) &
-            Detector::getBurstMode,
-        py::arg() = Positions{});
+    CppDetectorApi.def("getBurstMode",
+                       (Result<defs::burstMode>(Detector::*)(sls::Positions)) &
+                           Detector::getBurstMode,
+                       py::arg() = Positions{});
     CppDetectorApi.def("setBurstMode",
                        (void (Detector::*)(defs::burstMode, sls::Positions)) &
                            Detector::setBurstMode,
@@ -2066,5 +2056,7 @@ void init_det(py::module &m) {
                        (Result<sls::ns>(Detector::*)(sls::Positions) const) &
                            Detector::getMeasurementTime,
                        py::arg() = Positions{});
+    CppDetectorApi.def("getUserDetails", (std::string(Detector::*)() const) &
+                                             Detector::getUserDetails);
     ;
 }

python/src/detector_in.cpp

@@ -19,8 +19,6 @@ void init_det(py::module &m) {
     using sls::Result;
 
     m.def("freeSharedMemory", (void (*)(const int, const int)) &sls::freeSharedMemory, py::arg() = 0, py::arg() = -1);
-
-    m.def("getUserDetails", (std::string (*)(const int)) &sls::getUserDetails, py::arg() = 0);
     
     py::class_<Detector> CppDetectorApi(m, "CppDetectorApi");
     CppDetectorApi.def(py::init<int>());

serverBin/ctbDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServer_developer

serverBin/eigerDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServer_developer

serverBin/gotthard2DetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServer_developer

serverBin/gotthardDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServer_developer

serverBin/jungfrauDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServer_developer

serverBin/moenchDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServer_developer

serverBin/mythen3DetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServer_developer

serverBin/xilinx_ctbDetectorServer_developer

@@ -0,0 +1 @@
+../slsDetectorServers/xilinx_ctbDetectorServer/bin/xilinx_ctbDetectorServer_developer

slsDetectorCalibration/analogDetector.h

@@ -3,14 +3,14 @@
 #ifndef ANALOGDETECTOR_H
 #define ANALOGDETECTOR_H
 
-//#include <mutex>
+#include <mutex>
 
 #include "commonModeSubtractionNew.h"
 #include "ghostSummation.h"
 #include "pedestalSubtraction.h"
+#include "sls/tiffIO.h"
 #include "slsDetectorData.h"
 #include "slsInterpolation.h"
-#include "sls/tiffIO.h"
 #include <pthread.h>
 
 #ifdef ROOTSPECTRUM
@@ -90,6 +90,8 @@ template <class dataType> class analogDetector {
         ymin = 0;
         ymax = ny;
         fMode = ePedestal;
+        dMode = eInterpolating;
+        // std::cout << "dMode " << dMode << std::endl;
         thr = 0;
         myFile = NULL;
 #ifdef ROOTSPECTRUM
@@ -111,15 +113,20 @@ template <class dataType> class analogDetector {
        destructor. Deletes the pdestalSubtraction array and the image
     */
     virtual ~analogDetector() {
+        // std::cout << "#### Debug: Destructing analogDetector! ####"
+        //           << std::endl;
         for (int i = 0; i < ny; i++) {
-            delete[] stat[i];
+            if (stat[i]) { delete[] stat[i]; stat[i] = nullptr; }
+            // delete[] stat[i];
             /* delete [] pedMean[i];  */
             /* delete [] pedVariance[i]; */
-        };
+        }
         /* delete [] pedMean;  */
         /* delete [] pedVariance; */
-        delete[] stat;
-        delete[] image;
+        // delete[] stat;
+        // delete[] image;
+        if (stat) { delete[] stat; stat = nullptr; }
+        if (image) { delete[] image; image = nullptr; }
 #ifdef ROOTSPECTRUM
         delete hs;
 #ifdef ROOTCLUST
@@ -137,6 +144,8 @@ template <class dataType> class analogDetector {
      */
     analogDetector(analogDetector *orig) {
         /* copy construction from orig*/
+        // std::cout << "#### Debug: Calling analogDetector cloning method! ####"
+        //           << std::endl;
         det = orig->det;
         nx = orig->nx;
         ny = orig->ny;
@@ -152,6 +161,8 @@ template <class dataType> class analogDetector {
         thr = orig->thr;
         // nSigma=orig->nSigma;
         fMode = orig->fMode;
+        dMode = orig->dMode;
+        // std::cout << "dMode " << dMode << std::endl;
         myFile = orig->myFile;
 
         stat = new pedestalSubtraction *[ny];
@@ -216,12 +227,75 @@ template <class dataType> class analogDetector {
             ghSum = NULL;
     }
 
+    /**
+       constructor creating a deep copy of another analog detector
+       \param other analog Detector structure to be copied
+     */
+    analogDetector(const analogDetector &other)
+        : det(other.det), nx(other.nx), ny(other.ny), dataSign(other.dataSign),
+          iframe(other.iframe), gmap(other.gmap), id(other.id),
+          xmin(other.xmin), xmax(other.xmax), ymin(other.ymin),
+          ymax(other.ymax), thr(other.thr), fMode(other.fMode),
+          dMode(other.dMode), myFile(NULL) {
+
+        // std::cout << "#### Debug: Calling analogDetector copy constructor! ####"
+        //           << std::endl;
+
+        // Deep copy the stat array
+        stat = new pedestalSubtraction *[ny];
+        for (int i = 0; i < ny; i++) {
+            stat[i] = new pedestalSubtraction[nx];
+            std::copy(other.stat[i], other.stat[i] + nx, stat[i]);
+        }
+
+        // Deep copy image array
+        image = new int[nx * ny];
+        std::copy(other.image, other.image + (nx * ny), image);
+
+        // Copy common-mode subtraction object (if it exists)
+        if (other.cmSub) {
+            cmSub = other.cmSub->Clone();
+            std::cout << "Copying cmSub" << std::endl;
+        } else {
+            cmSub = nullptr;
+        }
+
+        // Copy ghost summation object (if it exists)
+        if (other.ghSum) {
+            ghSum = other.ghSum->Clone();
+            std::cout << "Copying ghSum" << std::endl;
+        } else {
+            ghSum = nullptr;
+        }
+
+        // Ensure pedestal values are copied properly
+        int nped = other.GetNPedestals(0, 0);
+        for (int iy = 0; iy < ny; ++iy) {
+            for (int ix = 0; ix < nx; ++ix) {
+                stat[iy][ix].SetNPedestals(nped);
+                setPedestal(ix, iy, other.getPedestal(ix, iy),
+                            other.getPedestalRMS(ix, iy),
+                            other.GetNPedestals(ix, iy));
+            }
+        }
+    }
+
     /**
        clone. Must be virtual!
        \returns a clone of the original analog detector
      */
     virtual analogDetector *Clone() = 0;
 
+    /**
+       Deep copy. Must be virtual!
+       This is a new addition because of multithreaded storage cell data (where
+       each sc has its own mutex). If the pure virtual function exists here,
+       EVERY derived class has to overwrite it! That means a Copy() function
+       must also be implemented in any derived class. \returns a deep copy of
+       the original analog detector
+     */
+    virtual analogDetector *Copy() = 0;
+
     /**
        Gives an id to the structure. For debugging purposes in case of
        multithreading. \param i is to be set \returns current id
@@ -548,6 +622,11 @@ template <class dataType> class analogDetector {
         return ped;
     };
 
+    // Const version for use in the copy constructor
+    virtual double getPedestal(int ix, int iy, int cm = 0) const {
+        return stat[iy][ix].getPedestal();
+    };
+
     /**
        gets  pedestal rms (i.e. noise)
        \param ix pixel x coordinate
@@ -566,6 +645,11 @@ template <class dataType> class analogDetector {
         return ped;
     };
 
+    // Const version for use in the copy constructor
+    virtual double getPedestalRMS(int ix, int iy) const {
+        return stat[iy][ix].getPedestalRMS();
+    };
+
     /**
        sets  pedestal
        \param ix pixel x coordinate
@@ -1226,7 +1310,7 @@ template <class dataType> class analogDetector {
     /** gets number of samples for moving average pedestal calculation
            \returns actual number of samples
        */
-    int GetNPedestals(int ix, int iy) {
+    int GetNPedestals(int ix, int iy) const {
         if (ix >= 0 && ix < nx && iy >= 0 && iy < ny)
             return stat[iy][ix].GetNPedestals();
         else

slsDetectorCalibration/circularFifo.h

@@ -50,6 +50,8 @@ template <typename Element> class CircularFifo {
     mutable sem_t data_mutex;
     mutable sem_t free_mutex;
     unsigned int increment(unsigned int idx_) const;
+    int id_;
+    int thread_id_;
 };
 
 template <typename Element> int CircularFifo<Element>::getDataValue() const {
@@ -74,14 +76,18 @@ template <typename Element> int CircularFifo<Element>::getFreeValue() const {
 template <typename Element>
 bool CircularFifo<Element>::push(Element *&item_, bool no_block) {
     // check for fifo full
-    if (no_block && isFull())
-        return false;
+    if (no_block && isFull()) {
+        //std::cout << "Full Fifo at push. Returning." << std::endl;
+        return false; // No space, return immediately
+    }
 
-    sem_wait(&free_mutex);
-    array[tail] = item_;
-    tail = increment(tail);
-    sem_post(&data_mutex);
-    return true;
+    //std::cout << "Thread " << thread_id_ <<" Push Fifo " << id_ << " item " << static_cast<void*>(item_) << std::endl;
+
+    sem_wait(&free_mutex); // Wait for space
+    array[tail] = item_; // Add item to the buffer
+    tail = increment(tail); // Move the tail pointer
+    sem_post(&data_mutex); // Signal that there is new data
+    return true; // Success
 }
 
 /** Consumer only: Removes and returns item from the queue
@@ -94,14 +100,18 @@ bool CircularFifo<Element>::push(Element *&item_, bool no_block) {
 template <typename Element>
 bool CircularFifo<Element>::pop(Element *&item_, bool no_block) {
     // check for fifo empty
-    if (no_block && isEmpty())
-        return false;
+    if (no_block && isEmpty()) {
+        //std::cout << "Empty Fifo at pop. Returning." << std::endl;
+        return false; // No data in fifo, return immediately
+    }
 
-    sem_wait(&data_mutex);
-    item_ = array[head];
-    head = increment(head);
-    sem_post(&free_mutex);
-    return true;
+    //std::cout << "Thread " << thread_id_ << " Pop Fifo " << id_ << " item " << static_cast<void*>(item_) << std::endl;
+
+    sem_wait(&data_mutex); // Wait for data
+    item_ = array[head]; // Retreive item from the current head of the buffer
+    head = increment(head); // Move the head pointer (to point to the next item)
+    sem_post(&free_mutex); // Signal that there is new free space available 
+    return true; //Success
 }
 
 /** Useful for testinng and Consumer check of status

slsDetectorCalibration/dataStructures/HDF5File.cpp

@@ -0,0 +1,482 @@
+#include "HDF5File.h"
+
+#include "ansi.h"
+
+#include <algorithm>
+#include <fmt/ranges.h>
+
+/*
+ * No class member helper functions
+ */
+std::string vectorToString(std::vector<hsize_t> const& v) {
+    return fmt::format("({})", fmt::join(v, ", "));
+}
+
+/*
+ * increment frame offset (if s dimension exists, loop through all before incrementing z) 
+ * should also work if file_dims[1] is not s but x (in that case we ignore it)
+ */
+void conditionalIncrement(std::vector<hsize_t>& vec, hsize_t max_value) {
+
+    if (vec.size() < 3) {
+        throw std::invalid_argument("Vector must have at least 3 elements.");
+    }
+
+    // If vector has 4 elements, increment vec[1] first
+    if (vec.size() == 4) {
+        if (++vec[1] >= max_value) { //max_value is never reached!
+            vec[1] = 0;  // Reset and increment vec[0]
+            ++vec[0];
+        }
+    }
+    // If vector has 3 elements, increment vec[0] directly
+    else if (vec.size() == 3) {
+        ++vec[0];
+    }
+}
+
+void printDatatypeSize(hid_t dataset) {
+
+	hid_t datatype = H5Dget_type(dataset);
+	H5T_class_t class_id = H5Tget_class(datatype);
+	size_t type_size = H5Tget_size(datatype);
+
+	H5Tclose(datatype);
+
+	std::cout << " dataset type class: " << class_id 
+          	  << ", size: " << type_size << " bytes\n";
+
+	//Ensure the read datatype matches a system native type correctly
+	//hid_t read_type = (type_size == 8) ? H5T_NATIVE_LLONG : H5T_NATIVE_UINT;
+
+	//return read_type;
+
+}
+
+
+/* **********************
+ * Class member functions
+ * **********************
+ */
+
+// Default constructor
+/*
+HDF5File::HDF5File () {
+  //InitializeParameters(); //old
+}
+*/
+
+/*
+HDF5File::~HDF5File () {
+	
+	if(current_image)
+		delete [] current_image;
+	
+}
+*/
+
+void HDF5File::SetImageDataPath (std::string const& name) { 
+	std::cout << "Image dataset path set to " << name << std::endl;
+	data_datasetname = name; 
+}
+
+void HDF5File::SetFrameIndexPath (std::string const& name) { 
+	std::cout << "Frame index dataset path set to " << name << std::endl;
+	index_datasetname = name; 
+}
+
+void HDF5File::InitializeDimensions () {
+
+	rank = H5Sget_simple_extent_ndims(dataspace);
+    file_dims.resize(rank);
+    H5Sget_simple_extent_dims(dataspace, file_dims.data(), nullptr);
+
+    std::cout << "Dataset dimensions: " << vectorToString(file_dims) << "\n";
+
+}
+
+std::vector<hsize_t> HDF5File::GetDatasetDimensions() {
+	return file_dims;
+}
+
+std::vector<hsize_t> HDF5File::GetChunkDimensions() {
+	return chunk_dims;
+}
+
+hsize_t HDF5File::GetRank() {
+	return rank;
+}
+
+bool HDF5File::ValidateDimensions () {
+
+	// validate rank
+	if(rank != RANK) {
+		cprintf(RED,"rank found %llu. Expected %d\n", rank, RANK);
+		std::cerr << "Error: Rank could not be validated\n";
+		return false;
+	}
+
+	// validate file dimensions of x and y (assuming those are the last two dimensions of the dataset)
+	if ( (file_dims[file_dims.size()-2] != DEFAULT_X_DIMS) || (file_dims[file_dims.size()-1] != DEFAULT_Y_DIMS) ) {
+		cprintf(RED,"file dimensions of x found %llu. Expected %d\n", file_dims[file_dims.size()-2], DEFAULT_X_DIMS);
+		cprintf(RED,"file dimensions of y found %llu. Expected %d\n", file_dims[file_dims.size()-1], DEFAULT_Y_DIMS);
+		std::cerr << "Error: Dataset dimensions could not be validated\n";
+		return false;
+	}
+
+	cprintf(GREEN, "File rank & dimensions validated.");
+	return true;	
+}
+
+bool HDF5File::ReadChunkDimensions () {
+
+	// Get layout
+	hid_t plist_id = H5Dget_create_plist(dataset);
+
+	if (H5Pget_layout (plist_id) != H5D_CHUNKED)  {
+		cprintf(RED,"NOTE: Dataset is not chunked!\n");
+		std::cerr << "Error: Dataset is not chunked\n";
+		return false;
+	}
+
+	// Get Chunk Dimensions
+	int rank_chunk = H5Pget_chunk (plist_id, 0, nullptr);
+	chunk_dims.resize(rank_chunk);
+	H5Pget_chunk (plist_id, rank_chunk, chunk_dims.data());
+
+	std::cout << "Chunk dimensions: " << vectorToString(chunk_dims) << "\n";
+
+	H5Pclose (plist_id);
+
+	return true;
+
+}
+
+bool HDF5File::ValidateChunkDimensions () {
+
+	// validate rank
+	if(chunk_dims.size() != rank) {
+		cprintf(RED,"Chunk rank does not match dataset rank! Found %lu. Expected %llu\n", chunk_dims.size(), rank);
+		std::cerr << "Error: Chunk rank does not match dataset rank\n";
+		return false;
+	}
+
+	// validate chunk dimensions of x and y (assuming those are the last two dimensions of the dataset)
+	if ( (chunk_dims[chunk_dims.size()-2] != DEFAULT_CHUNK_X_DIMS) || (chunk_dims[chunk_dims.size()-1] != DEFAULT_CHUNK_Y_DIMS) ) {
+		cprintf(RED,"file dimensions of x found %llu. Expected %d\n", chunk_dims[chunk_dims.size()-2], DEFAULT_CHUNK_X_DIMS);
+		cprintf(RED,"file dimensions of y found %llu. Expected %d\n", chunk_dims[chunk_dims.size()-1], DEFAULT_CHUNK_Y_DIMS);
+		std::cerr << "Error: Chunk dimensions could not be validated\n";
+		return false;
+	}
+
+	cprintf(GREEN, "Chunk rank & dimensions validated.");
+	return true;
+
+}
+
+bool HDF5File::OpenFrameIndexDataset() {
+
+	// Get all the frame numbers
+	// Open frame index dataset
+	hid_t fi_dataset = H5Dopen2 (file, index_datasetname.c_str(), H5P_DEFAULT);
+	if (fi_dataset < 0){
+		cprintf (RED,"Could not open frame index dataset %s\n", index_datasetname.c_str());
+		std::cerr << "Error: Could not open frame index dataset\n";
+		return false;
+	}
+
+	hid_t fi_dataspace = H5Dget_space (fi_dataset);
+	int fi_rank = H5Sget_simple_extent_ndims(fi_dataspace);
+	std::vector<hsize_t> fi_dims(fi_rank);
+	H5Sget_simple_extent_dims (fi_dataspace, fi_dims.data(), nullptr);
+
+	std::cout << "Frame index dataset dimensions: " << vectorToString(fi_dims) << "\n";
+
+	// validate size
+	if (fi_dims[0] != file_dims[0]) {
+		cprintf (RED,"Frame index dimensions of z found %llu. Expected %llu\n", fi_dims[0], file_dims[0]);
+		std::cerr << "Error: Z dimension of frame index dataset does not align with z dimension of image dataset\n";
+		H5Sclose (fi_dataspace);
+		H5Dclose (fi_dataset);
+		return false;
+	}
+
+	// allocate frame index memory
+	frame_index_list.resize(fi_dims[0]); //file_dims
+
+	// read and print datatype size of dataset
+	std::cout << "Frame index";
+	printDatatypeSize(fi_dataset);
+
+	// make sure we only read the first column of the frame index dataset (not all storage cells)
+	//NOTE: For XFEL datasets, this may mean that some frame numbers are skipped
+	//(because they assign a unique frame number to every storage cell)
+	//Possibly, there is a cleaner fix for this...
+	std::vector<hsize_t> start(fi_rank,0);
+	std::vector<hsize_t> count(fi_rank,1);
+	count[0] = fi_dims[0];
+	hid_t memspace = H5Screate_simple (fi_rank, count.data(), nullptr);
+	if (memspace < 0) {
+    	std::cerr << "Error: Failed to create memory space for HDF5 read operation\n";
+		H5Sclose(memspace);
+		H5Sclose(fi_dataspace);
+		H5Dclose(fi_dataset);
+    	return false;
+	}
+
+	// Create hyperslab selection
+	if (H5Sselect_hyperslab(fi_dataspace, H5S_SELECT_SET, start.data(), nullptr, count.data(), nullptr) < 0 ) {
+		cprintf (RED,"Could not create hyperslab for %s\n", vectorToString(start).c_str());
+		std::cerr << "Error: Hyperslab creation failed for " << vectorToString(start) << "\n";
+		H5Sclose(memspace);
+		H5Sclose (fi_dataspace);
+		H5Dclose(fi_dataset);
+		return false;
+	}
+
+	//read frame index values
+	//Is u32 correct? I would think not. But I get a segmentation fault if I use u64.
+	if (H5Dread (fi_dataset, H5T_STD_U64LE, memspace, fi_dataspace, H5P_DEFAULT, frame_index_list.data()) < 0) {
+		cprintf (RED,"Could not read frame index dataset %s\n", index_datasetname.c_str());
+		std::cerr << "Error: Could not read frame index dataset\n";
+		H5Sclose(memspace);
+		H5Sclose (fi_dataspace);
+		H5Dclose (fi_dataset);
+		return false;
+	}
+
+	H5Sclose(memspace);
+	H5Sclose (fi_dataspace);
+	H5Dclose(fi_dataset);
+	return true;
+}
+
+int HDF5File::OpenResources (char const*const fname, bool validate) {
+
+	std::cout << "Debug HDF5File.cpp: Attempting to open file " << fname << std::endl;
+	// Open File
+	file = H5Fopen (fname, H5F_ACC_RDONLY, H5P_DEFAULT);
+	if (file < 0) {
+	  cprintf(RED,"Could not open hdf5 file\n");
+	  std::cerr << "Error: H5Fopen failed\n";
+	  return 0;
+	}
+	cprintf(BLUE, "Opened File: %s\n", fname);
+
+	// Open Dataset
+	dataset = H5Dopen2 (file, data_datasetname.c_str(), H5P_DEFAULT);
+	if (dataset < 0){
+	  cprintf(RED,"Could not open dataset\n");
+	  std::cerr << "Error: H5Dopen2 failed\n";
+	  CloseResources ();
+	  return 0;
+	}
+	cprintf(BLUE, "Opened Dataset: %s\n", data_datasetname.c_str());
+
+	// print datatype size of dataset
+	std::cout << "Image";
+	printDatatypeSize(dataset);
+
+	// Create Dataspace
+	dataspace = H5Dget_space (dataset);
+	if (dataspace < 0){
+	  cprintf(RED,"Could not open dataspace\n");
+	  std::cerr << "Error: H5Dget_space failed\n";
+	  CloseResources ();
+	  return 0;
+	}
+
+	// Get Dimensions
+	InitializeDimensions();
+	// Get chunk dimensions
+	if (!ReadChunkDimensions()) {
+		CloseResources();
+		return 0;
+	}
+
+	// validate file dimensions
+	if (validate) {
+		if ( !ValidateDimensions() || !ValidateChunkDimensions() ) {
+			CloseResources();
+			return 0;		
+		}
+	}
+
+	//Read frame indices
+	if (!OpenFrameIndexDataset()) {
+		CloseResources();
+		return 0;
+	}
+	
+	return 1;
+}
+
+
+void HDF5File::CloseResources () {
+	if (dataspace >=0 ) 	{
+		H5Sclose(dataspace);
+		dataspace = -1;
+	}
+	if (dataset >=0 ) 	{
+		H5Dclose(dataset);
+		dataset = -1;
+	}
+	if (file >=0 ) 		{
+		H5Fclose(file);
+		file = -1;
+	}
+}
+
+/*
+ * Function takes uint16_t* argument to make explicit that the caller has to handle memory allocation and deallocation.
+ * This is legacy caused by the structure with which the slsDetectorCalibration cluster finder is written.
+ * (Best practice for modern C++ would be using smart pointers.)
+ *
+ * Originially, this function took uint16_t** which may lead to memory management issues since image gets redirected
+ * to point to current_image, which is owned by HDF5File.
+ * (Good practice in classic C-style. HDF5File needs to clean up the resource at destruction.)
+ * 
+ * \param image pointer to uint16_t, buffer which the image is read into. (Memory handled by caller!)
+ * \param offset contains iFrame at [0] and storage cell number at [1],
+ * depending on dimensionality of the dataset, the storage cell number may not be included.
+ * Note that frame number (as read from file) may (likely) differ from frame index (in the dataset)!
+ */
+int HDF5File::ReadImage (uint16_t* image, std::vector<hsize_t>& offset ) {
+
+	// Validate input arguments
+    if (!image) {
+        std::cerr << "Error: image buffer is null.\n";
+        return -99;
+    }
+  	if ( offset.size() != rank-2 ) {
+		cprintf ( RED,"Offset vector must have size %llu. Found %lu\n", rank-2, offset.size() );
+        std::cerr << "Error: Wrong offset vector size\n";
+		CloseResources ();
+        return -99;
+    }
+
+	// Initialize frame_offset
+	if (frame_offset.empty())
+		frame_offset.resize(rank,0);
+
+	// Check if we reached the end of file
+	// Compares that the offsets of frame and storage cell (Z and S) have reached the end of file
+	// Excludes X and Y indices (of the image dataset) from the comparison
+	// As it is now, this never triggers, because frame_offset[1] is never equals file_dims[1]=16
+	/*
+	if( std::equal( frame_offset.cbegin(), frame_offset.cend()-2, file_dims.cbegin() ) ) {
+		printf("End of file reached\n");
+		return -1;
+	}
+	*/
+	if (frame_offset[0] == file_dims[0]) {
+		printf("End of file reached\n");
+		return -1;
+	}
+	/* //old
+	if (frame_offset[0] == file_dims[0]-1) {
+		printf("end of file\n");
+		return -1;
+	}
+	*/
+
+	// Validate frame_offset index
+    if (frame_offset[0] >= frame_index_list.size()) {
+        std::cerr << "Error: frame_offset[0] = " << frame_offset[0] << " of bounds.\n";
+        return -99;
+    }
+
+	// Check if images exist at the current frame offset
+	if (frame_index_list[frame_offset[0]] == 0) {
+		cprintf (RED,"No images at this frame offset %llu\n", frame_offset[0]);
+		std::cerr << "Error: Framenumber 0 at this frame offset\n";
+		CloseResources ();
+		return -99;
+	}
+
+	// Optional: Ensure dataset and dataspace are valid
+    if (dataset < 0) {
+        std::cerr << "Error: Invalid dataset ID.\n";
+        return -99;
+    }
+    if (dataspace < 0) {
+        std::cerr << "Error: Invalid dataspace.\n";
+        return -99;
+    }
+
+	// Define the size of the hyperslab to read
+	std::vector<hsize_t> frame_size(rank, 1);
+	std::copy(file_dims.begin() + rank-2, file_dims.end(), frame_size.begin() + rank-2);
+	/*
+	for ( int d=0; d < rank; ++d ) {
+		if (d < rank-2)
+			frame_size[d] = 1;
+		if ( d >= rank-2 )
+			frame_size[d] = file_dims[d];
+	}
+	*/
+
+	// Define memory space
+	hid_t memspace = H5Screate_simple (rank, frame_size.data(), nullptr);
+	if (memspace < 0) {
+    	std::cerr << "Error: Failed to create memory space for HDF5 read operation\n";
+    	CloseResources();
+    	return -99;
+	}
+
+	// Create hyperslab selection
+	// This aligns dataspace such that we read the correct frame
+	if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, frame_offset.data(), nullptr, frame_size.data(), nullptr) < 0 ) {
+		cprintf (RED,"Could not create hyperslab for frame offset %s\n", vectorToString(frame_offset).c_str());
+		std::cerr << "Error: Hyperslab creation failed for frame offset " << vectorToString(frame_offset) << "\n";
+		CloseResources();
+		H5Sclose(memspace);
+		return -99;
+	}
+
+	// Read dataset into image buffer (previously read to current_image owned by HDF5File)
+	if (H5Dread(dataset, H5T_STD_U16LE, memspace, dataspace, H5P_DEFAULT, image) < 0 ) {
+		cprintf (RED,"Could not read dataset for frame offset %s\n", vectorToString(frame_offset).c_str());
+		std::cerr << "Error: Reading of dataset failed for given start frame offset " << vectorToString(frame_offset) << "\n";
+		CloseResources ();
+		H5Sclose(memspace);
+		return -99;
+	}
+
+	// Clean up memory space
+	H5Sclose(memspace);
+
+	//*image = current_image; //if uint16_t** is passed, HDF5File owns the resource image points to, which is potentially dangerous
+
+	// Return frame number
+	unsigned int retval = frame_index_list[frame_offset[0]];
+	
+	// Pass updated frame offset value(s) via offset parameter vector
+	std::copy_n(frame_offset.begin(), offset.size(), offset.begin());
+	/*
+	std::transform( offset.begin(), offset.end(), offset.begin(), 
+    	[&, i = 0](size_t) mutable { return frame_offset[i++]; } );
+	*/
+
+	// Increment frame offset correctly
+	conditionalIncrement(frame_offset, file_dims[1]);
+	//++frame_offset[0]; //old
+
+	return retval;
+}
+
+void HDF5File::PrintCurrentImage (uint16_t* image) {
+	printf("\n");
+	printf("Frame %llu, Image: %llu\n", frame_offset[0]-1, frame_index_list[frame_offset[0]-1]);
+
+	hsize_t size = file_dims[rank-1] * file_dims[rank-2];
+	for (hsize_t i = 0; i < size; ++i){
+		printf("%u ", image[i]);
+		if (!((i+1) % file_dims[rank-2] ))
+			printf("\n\n");
+	}
+	printf("\n\n\n\n");
+}
+
+
+

slsDetectorCalibration/dataStructures/HDF5File.h

@@ -0,0 +1,159 @@
+#pragma once
+/************************************************
+ * @file HDF5Fle.h
+ * @short functions to open/close/read HDF5 File
+ * Adapted for generalization, accepts rank 3 and 4
+ * Supports control over storage cells
+ ***********************************************/
+/**
+ *@short functions to open/close/read HDF5 File
+ */
+
+
+#include <iostream>
+#include <vector>
+#include <string>
+
+#include "hdf5.h"
+#include "hdf5_hl.h"
+
+
+//#define MAX_STR_LENGTH	1000
+
+#define RANK	4                       // Dimension of the image dataset, only for validation
+#define DEFAULT_Z_DIMS	10000			// only for validation
+#define DEFAULT_Y_DIMS	1024			// only for validation
+#define DEFAULT_X_DIMS	512				// only for validation
+//#define DEFAULT_S_DIMS	1       	// Storage cells
+
+#define DEFAULT_CHUNK_Z_DIMS	1		// only for validation
+#define DEFAULT_CHUNK_Y_DIMS	1024	// only for validation
+#define DEFAULT_CHUNK_X_DIMS	512		// only for validation
+//#define DEFAULT_CHUNK_S_DIMS	1
+
+
+#define DATA_DATASETNAME	"/data/JF18T01V01/data" //Furka JF
+#define INDEX_DATASETNAME	"/data/JF18T01V01/frame_index"
+
+//enum{Z,S,X,Y}; //S is the storage cell //enum is not used
+
+class HDF5File {
+
+public:
+
+	/**
+	 * Constructor
+	 */
+	//HDF5File () = default; //No need to declare if it is default
+
+	/**
+	 * Destructor
+	 */
+	//~HDF5File () = default; //Since the destructor is default (and copy and move are default too)
+
+
+	std::vector<hsize_t> GetDatasetDimensions ();
+
+	std::vector<hsize_t> GetChunkDimensions ();
+
+	hsize_t GetRank ();
+
+	void SetImageDataPath (std::string const& name);
+
+	void SetFrameIndexPath (std::string const& name);
+
+
+
+	/**
+	 * Open HDF5 file and dataset,
+	 * reads frame index dataset to array
+	 * @param fname file name
+	 * @param validate true if one must validate if file is
+	 * chunked with dims [? x 128 x 512] and chunk dims [1 x 128 x 512]
+	 * @returns 1 if successful, else 0 if fail
+	 */
+	int OpenResources (const char* const fname, bool validate); 
+
+	/**
+	 * Close Open resources
+	 */
+	void CloseResources ();
+
+	/**
+	 * Read an image into current_image,
+	 * increment Z-offset (frame) and (if rank==4) storage cell
+	 * @returns frame number read from file,
+	 */
+	int ReadImage (uint16_t* image, std::vector<hsize_t>& offset);
+
+	/**
+	 * Print current image in memory
+	 */
+	void PrintCurrentImage (uint16_t* image);
+
+private:
+
+	/**
+	 * Initialize dimensions of image dataset for each new file
+	 */
+	void InitializeDimensions ();
+
+	bool ReadChunkDimensions ();
+
+	bool ValidateDimensions ();
+
+	bool ValidateChunkDimensions ();
+
+	/**
+	 * Open dataset containing the frame numbers
+	 */
+	bool OpenFrameIndexDataset ();
+
+
+	/** file name */
+	std::string file_name{};
+	/** dataset name for image data */
+	std::string data_datasetname = DATA_DATASETNAME;
+	/** dataset name for frame index data */
+	std::string index_datasetname = INDEX_DATASETNAME;
+
+	/** file handle */
+	hid_t file{};
+	/** dataspace handle */
+	hid_t dataspace{};
+	/** memory space handle */
+	//hid_t memspace; //old
+	/** dataset handle */
+	hid_t dataset{};
+
+	/** file dimensions */
+	std::vector<hsize_t> file_dims{};
+	//hsize_t file_dims[RANK]{}; //static array (dimensions are known)
+
+	/** chunk dimensions 
+	 ** not necessarily required
+	 ** useful for optimization or validation */
+	std::vector<hsize_t> chunk_dims{};
+	//hsize_t chunk_dims[RANK]{};
+
+	/** Rank of the image dataset */
+	hsize_t rank{};
+
+	/** number of frames */
+	unsigned int number_of_frames{};
+
+	/** frame index list */
+	std::vector<hsize_t> frame_index_list{};
+
+	/** Current image
+	 ** dynamic array 
+	 ** uint16_t pointer format is chosen to support use with slsDetectorCalibration cluster finder */
+	//uint16_t* current_image{nullptr};
+	//uint16_t current_chunk[DEFAULT_CHUNK_Z_DIMS][DEFAULT_CHUNK_Y_DIMS][DEFAULT_CHUNK_X_DIMS];
+
+	/** Current frame offset
+	 ** (Z-offset, S-offset, 0, 0) or (Z-offset, 0, 0), increments automatically with ReadImage */
+	std::vector<hsize_t> frame_offset{};
+	//hsize_t frame_offset[RANK]{};
+
+};

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataQuad.h

@@ -0,0 +1,422 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef JUNGFRAULGADSTRIXELSDATAQUAD_H
+#define JUNGFRAULGADSTRIXELSDATAQUAD_H
+#ifdef CINT
+#include "sls/sls_detector_defs_CINT.h"
+#else
+#include "sls/sls_detector_defs.h"
+#endif
+#include "slsDetectorData.h"
+
+// #define VERSION_V2
+/**
+    @short  structure for a Detector Packet or Image Header
+    @li frameNumber is the frame number
+    @li expLength is the subframe number (32 bit eiger) or real time exposure
+   time in 100ns (others)
+    @li packetNumber is the packet number
+    @li bunchId is the bunch id from beamline
+    @li timestamp is the time stamp with 10 MHz clock
+    @li modId is the unique module id (unique even for left, right, top, bottom)
+    @li xCoord is the x coordinate in the complete detector system
+    @li yCoord is the y coordinate in the complete detector system
+    @li zCoord is the z coordinate in the complete detector system
+    @li debug is for debugging purposes
+    @li roundRNumber is the round robin set number
+    @li detType is the detector type see :: detectorType
+    @li version is the version number of this structure format
+*/
+
+#include <algorithm>
+#include <numeric>
+#include <tuple>
+
+namespace strixelQuad {
+  constexpr int nc_rawimg = 1024; // for full images  //256;
+  constexpr int nc_quad = 512;
+  constexpr int nr_rawimg = 512;
+  constexpr int nr_chip = 256;
+  constexpr int gr = 9;
+
+  //shift due to extra pixels
+  constexpr int shift_x = 2; //left
+  
+  constexpr int nc_strixel = ( nc_quad - shift_x - 2*gr ) / 3; //164
+  constexpr int nr_strixel = ( nr_chip - 1 - gr ) * 3; //one half (-1 because double sided pixel) //738
+  constexpr int nr_center = 12; //double sided pixels to be skipped
+
+  // boundaries in ASIC coordinates (pixels at both bounds are included)
+  constexpr int xstart = 256 + gr;             // 265
+  constexpr int xend = 255 + nc_quad - gr;     // 758
+  constexpr int bottom_ystart = gr;            //   9
+  constexpr int bottom_yend = nr_chip - 2;     // 254
+  constexpr int top_ystart = nr_chip + 1;      // 257
+  constexpr int top_yend = nr_chip*2 - gr - 1; // 502
+
+  // x shift because of 2-pixel strixels on one side
+  constexpr int shift = 2;
+
+} // namespace strixelQuad
+
+//to account for module rotation
+enum rotation {
+  NORMAL = 0,
+  INVERSE = 1
+};
+
+const int rota = NORMAL;
+
+typedef struct {
+    uint64_t bunchNumber; /**< is the frame number */
+    uint64_t pre;         /**< something */
+
+} jf_header; // Aldo's header
+
+using namespace strixelQuad;
+
+class jungfrauLGADStrixelsDataQuad : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+    int x0, y0, x1, y1, shifty;
+    struct {
+      uint16_t xmin;
+      uint16_t xmax;
+      uint16_t ymin;
+      uint16_t ymax;
+      int nc;
+    } globalROI;
+
+    //to account for the inverted routing of the two different quad halfs
+    enum location {
+      BOTTOM = 0,
+      TOP = 1
+    };
+
+    int multiplicator = 3;
+    std::vector<int> mods{ 0, 1, 2 };
+
+    void reverseVector( std::vector<int>& v ) {
+      std::reverse( v.begin(), v.end() );
+      std::cout << "mods reversed ";
+      for ( auto i : v )
+	std::cout << i << " ";
+      std::cout << '\n';
+    }
+
+    void setMappingShifts( const int rot, const int half ) {
+
+      x0 = xstart;
+      x1 = xend;
+
+      if (rot==NORMAL) {
+	x0 += shift;
+      } else {
+	x1-=shift;
+        reverseVector(mods);
+      }
+
+      if (half==BOTTOM) {
+	y0 = bottom_ystart;
+	y1 = bottom_yend;
+	shifty = 0;
+      } else {
+	y0 = top_ystart;
+	y1 = top_yend;
+	reverseVector(mods);
+	shifty = nr_strixel + nr_center; //double-sided pixels in the center have to be jumped
+      }
+
+    }
+
+    void remap( int xmin=0, int xmax=0, int ymin=0, int ymax=0 ) {
+
+      int ix, iy = 0;
+      // remapping loop
+        for (int ipy = y0; ipy <= y1; ipy++) {
+            for (int ipx = x0; ipx <= x1; ipx++) {
+
+                ix = int((ipx - x0) / multiplicator);
+                for (int m = 0; m < multiplicator; ++m) {
+                    if ((ipx - x0) % multiplicator == m)
+                        iy = (ipy - y0) * multiplicator + mods[m] + shifty;
+                }
+
+                //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
+		if (xmin < xmax && ymin < ymax) {
+		  if ( ipx>=xmin && ipx<=xmax && ipy>=ymin && ipy <=ymax )
+		    dataMap[iy][ix] =
+		      sizeof(header) + (globalROI.nc * (ipy - globalROI.ymin) + (ipx - globalROI.xmin)) * 2;
+		} else {
+		  dataMap[iy][ix] = sizeof(header) + (nc_rawimg * ipy + ipx) * 2;
+		}
+            }
+        }
+
+    }
+
+    void remapQuad(const int rot) {
+
+        setMappingShifts( rot, BOTTOM );
+	remap();
+	setMappingShifts( rot, TOP );
+	remap();
+
+    }
+
+
+    std::tuple< uint16_t, uint16_t, uint16_t, uint16_t > adjustROItoLimits(uint16_t xmin,
+									   uint16_t xmax,
+									   uint16_t ymin,
+									   uint16_t ymax,
+									   uint16_t lim_roi_xmin,
+									   uint16_t lim_roi_xmax,
+									   uint16_t lim_roi_ymin,
+									   uint16_t lim_roi_ymax) {
+      uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
+      if ( xmin < lim_roi_xmin)
+        xmin_roi = lim_roi_xmin;
+      else
+        xmin_roi = xmin;
+      if ( xmax > lim_roi_xmax )
+        xmax_roi = lim_roi_xmax;
+      else
+        xmax_roi = xmax;
+      if ( ymin < lim_roi_ymin )
+        ymin_roi = lim_roi_ymin;
+      else
+        ymin_roi = ymin;
+      if ( ymax > lim_roi_ymax )
+        ymax_roi = lim_roi_ymax;
+      else
+        ymax_roi = ymax;
+      return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
+    }
+
+    std::vector < std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > > mapSubROIs(uint16_t xmin,
+											 uint16_t xmax,
+											 uint16_t ymin,
+											 uint16_t ymax) {
+      bool bottom = false;
+      bool top = false;
+
+      for ( int x=xmin; x!=xmax+1; ++x ) {
+	for ( int y=ymin; y!=ymax; ++y ) {
+	  if ( xstart<=x && x<=xend && bottom_ystart<=y && y<=bottom_yend )
+	    bottom = true;
+	  if ( xstart<=x && x<=xend && top_ystart<=y && y<=top_yend )
+	    top = true;
+	}
+      }
+
+      uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
+      std::vector < std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > > rois{};
+
+      if (bottom) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     xstart, xend, bottom_ystart, bottom_yend );
+	rois.push_back( std::make_tuple( BOTTOM, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (top) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     xstart, xend, top_ystart, top_yend );
+	rois.push_back( std::make_tuple( TOP, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+
+      return rois;
+    }
+
+    void remapROI(std::tuple< int, uint16_t, uint16_t, uint16_t, uint16_t > roi, const int rot ) {
+
+      int half, xmin, xmax, ymin, ymax;
+      std::tie( half, xmin, xmax, ymin, ymax ) = roi;
+	
+      setMappingShifts(rot, half);
+
+      std::cout << "remapping roi: "
+		<< ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
+		<< ", y1: " << y1 << std::endl;
+      std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]" << std::endl;
+
+      remap( xmin, xmax, ymin, ymax );
+    }
+
+  public:
+
+    using header = sls::defs::sls_receiver_header;
+
+    jungfrauLGADStrixelsDataQuad(uint16_t xmin = 0, uint16_t xmax = 0,
+				 uint16_t ymin = 0, uint16_t ymax = 0)
+        : slsDetectorData<uint16_t>(
+              nc_strixel,
+              nr_strixel * 2 + nr_center,
+              nc_strixel * ( nr_strixel * 2 + nr_center ) * 2 + sizeof(header)) {
+        std::cout << "Jungfrau strixels quad with full module data "
+                  << std::endl;
+
+        // Fill all strixels with dummy values
+        for (int ix = 0; ix != nc_strixel; ++ix) {
+            for (int iy = 0; iy != nr_strixel * 2 + nr_center; ++iy) {
+                dataMap[iy][ix] = sizeof(header);
+            }
+        }
+
+	globalROI.xmin = xmin;
+	globalROI.xmax = xmax;
+	globalROI.ymin = ymin;
+	globalROI.ymax = ymax;
+
+        std::cout << "sizeofheader = " << sizeof(header) << std::endl;
+        std::cout << "Jungfrau strixels quad with full module data "
+                  << std::endl;
+
+        if (xmin < xmax && ymin < ymax) {
+
+	  // get ROI raw image number of columns
+	  globalROI.nc = xmax - xmin + 1;
+	  std::cout << "nc_roi = " << globalROI.nc << std::endl;
+	  
+	  dataSize =
+	    (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
+	  std::cout << "datasize " << dataSize << std::endl;
+
+	  auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
+	  //function to fill vector of rois from globalROI
+
+	  for ( auto roi : rois )
+	    remapROI(roi, rota);
+
+        } else {
+
+	  remapQuad( rota );
+
+        }
+
+        iframe = 0;
+        std::cout << "data struct created" << std::endl;
+    };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    virtual double getValue(char *data, int ix, int iy = 0) {
+
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+        return val;
+    };
+
+    /**
+
+    Returns the frame number for the given dataset. Purely virtual func.
+    \param buff pointer to the dataset
+    \returns frame number
+
+    */
+
+    int getFrameNumber(char *buff) {
+#ifdef ALDO                                      // VH
+        return ((jf_header *)buff)->bunchNumber; // VH
+#endif                                           // VH
+        return ((header *)buff)->detHeader.frameNumber;
+    };
+
+    /**
+
+       Returns the packet number for the given dataset. purely virtual func
+       \param buff pointer to the dataset
+       \returns packet number number
+
+
+
+    */
+    int getPacketNumber(char *buff) {
+#ifdef ALDO // VH
+        // uint32_t fakePacketNumber = 1000;
+        // return fakePacketNumber; //VH //TODO: Keep in mind in case of bugs!
+        // //This is definitely bad!
+        return 1000;
+#endif // VH
+        return ((header *)buff)->detHeader.packetNumber;
+    };
+
+    char *readNextFrame(std::ifstream &filebin) {
+        int ff = -1, np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(std::ifstream &filebin, int &ff) {
+        int np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(std::ifstream &filebin, int &ff, int &np) {
+        char *data = new char[dataSize];
+        char *d = readNextFrame(filebin, ff, np, data);
+        if (d == NULL) {
+            delete[] data;
+            data = NULL;
+        }
+        return data;
+    };
+
+    char *readNextFrame(std::ifstream &filebin, int &ff, int &np, char *data) {
+      //char *retval = 0;
+      //int nd;
+      //int fnum = -1;
+        np = 0;
+        //int pn;
+
+        //std::cout << dataSize << std::endl;
+        //if (ff >= 0) {
+          //  fnum = ff; }
+
+        if (filebin.is_open()) {
+            if (filebin.read(data, dataSize)) {
+                std::cout << "*";
+                ff = getFrameNumber(data);
+                np = getPacketNumber(data);
+                return data;
+            }
+	    std::cout << "#";
+        } else {
+	  std::cout << "File not open" << std::endl;
+	}
+        return NULL;
+    };
+
+    /*    Loops over a memory slot until a complete frame is found (i.e. all */
+    /*    packets 0 to nPackets, same frame number). purely virtual func \param
+     */
+    /*    data pointer to the memory to be analyzed \param ndata reference to
+     * the */
+    /*    amount of data found for the frame, in case the frame is incomplete at
+     */
+    /*    the end of the memory slot \param dsize size of the memory slot to be
+     */
+    /*    analyzed \returns pointer to the beginning of the last good frame
+     * (might */
+    /*    be incomplete if ndata smaller than dataSize), or NULL if no frame is
+     */
+    /*    found */
+
+    /* *\/ */
+    virtual char *findNextFrame(char *data, int &ndata, int dsize) {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    };
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataQuadH5.h

@@ -0,0 +1,432 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef JUNGFRAULGADSTRIXELSDATAQUADH5_H
+#define JUNGFRAULGADSTRIXELSDATAQUADH5_H
+#ifdef CINT
+#include "sls/sls_detector_defs_CINT.h"
+#else
+#include "sls/sls_detector_defs.h"
+#endif
+#include "slsDetectorData.h"
+
+// This needs to be linked correctly
+#include "HDF5File.cpp"
+#include "HDF5File.h" //this includes hdf5.h and hdf5_hl.h
+
+// #define VERSION_V2
+/**
+    @short  structure for a Detector Packet or Image Header
+    @li frameNumber is the frame number
+    @li expLength is the subframe number (32 bit eiger) or real time exposure
+   time in 100ns (others)
+    @li packetNumber is the packet number
+    @li bunchId is the bunch id from beamline
+    @li timestamp is the time stamp with 10 MHz clock
+    @li modId is the unique module id (unique even for left, right, top, bottom)
+    @li xCoord is the x coordinate in the complete detector system
+    @li yCoord is the y coordinate in the complete detector system
+    @li zCoord is the z coordinate in the complete detector system
+    @li debug is for debugging purposes
+    @li roundRNumber is the round robin set number
+    @li detType is the detector type see :: detectorType
+    @li version is the version number of this structure format
+*/
+
+// #include <algorithm>
+#include <numeric>
+#include <tuple>
+
+namespace strixelQuad {
+constexpr int nc_rawimg = 1024; // for full images  //256;
+constexpr int nc_quad = 512;
+constexpr int nr_rawimg = 512;
+constexpr int nr_chip = 256;
+constexpr int gr = 9;
+
+// shift due to extra pixels
+constexpr int shift_x = 2; // left
+
+constexpr int nc_strixel = (nc_quad - shift_x - 2 * gr) / 3; // 164
+constexpr int nr_strixel =
+    (nr_chip - 1 - gr) * 3;   // one half (-1 because double sided pixel) //738
+constexpr int nr_center = 12; // double sided pixels to be skipped
+
+// boundaries in ASIC coordinates (pixels at both bounds are included)
+constexpr int xstart = 256 + gr;               // 265
+constexpr int xend = 255 + nc_quad - gr;       // 758
+constexpr int bottom_ystart = gr;              //   9
+constexpr int bottom_yend = nr_chip - 2;       // 254
+constexpr int top_ystart = nr_chip + 1;        // 257
+constexpr int top_yend = nr_chip * 2 - gr - 1; // 502
+
+// x shift because of 2-pixel strixels on one side
+constexpr int shift = 2;
+
+} // namespace strixelQuad
+
+// to account for module rotation
+enum rotation { NORMAL = 0, INVERSE = 1 };
+
+const int rota = NORMAL;
+
+typedef struct {
+    uint64_t bunchNumber; /**< is the frame number */
+    uint64_t pre;         /**< something */
+
+} jf_header; // Aldo's header
+
+using namespace strixelQuad;
+
+class jungfrauLGADStrixelsDataQuadH5 : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+    int x0, y0, x1, y1, shifty;
+    struct {
+        uint16_t xmin;
+        uint16_t xmax;
+        uint16_t ymin;
+        uint16_t ymax;
+        int nc;
+    } globalROI;
+
+    // to account for the inverted routing of the two different quad halfs
+    enum location { BOTTOM = 0, TOP = 1 };
+
+    int multiplicator = 3;
+    std::vector<int> mods{0, 1, 2};
+
+    void reverseVector(std::vector<int> &v) {
+        std::reverse(v.begin(), v.end());
+        std::cout << "mods reversed ";
+        for (auto i : v)
+            std::cout << i << " ";
+        std::cout << '\n';
+    }
+
+    void setMappingShifts(const int rot, const int half) {
+
+        x0 = xstart;
+        x1 = xend;
+
+        if (rot == NORMAL) {
+            x0 += shift;
+        } else {
+            x1 -= shift;
+            reverseVector(mods);
+        }
+
+        if (half == BOTTOM) {
+            y0 = bottom_ystart;
+            y1 = bottom_yend;
+            shifty = 0;
+        } else {
+            y0 = top_ystart;
+            y1 = top_yend;
+            reverseVector(mods);
+            shifty = nr_strixel + nr_center; // double-sided pixels in the
+                                             // center have to be jumped
+        }
+    }
+
+    void remap(int xmin = 0, int xmax = 0, int ymin = 0, int ymax = 0) {
+
+        int ix, iy = 0;
+        // remapping loop
+        for (int ipy = y0; ipy <= y1; ++ipy) {
+            for (int ipx = x0; ipx <= x1; ++ipx) {
+
+                ix = int((ipx - x0) / multiplicator);
+                for (int m = 0; m < multiplicator; ++m) {
+                    if ((ipx - x0) % multiplicator == m)
+                        iy = (ipy - y0) * multiplicator + mods[m] + shifty;
+                }
+
+                //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
+                if (xmin < xmax && ymin < ymax) { // if ROI
+                    if (ipx >= xmin && ipx <= xmax && ipy >= ymin &&
+                        ipy <= ymax)
+                        dataMap[iy][ix] =
+                            (globalROI.nc * (ipy - globalROI.ymin) +
+                             (ipx - globalROI.xmin)) *
+                            2;
+                } else { // if full Quad
+                    dataMap[iy][ix] = (nc_rawimg * ipy + ipx) * 2;
+                }
+            }
+        }
+    }
+
+    void remapQuad(const int rot) {
+
+        setMappingShifts(rot, BOTTOM);
+        remap();
+        setMappingShifts(rot, TOP);
+        remap();
+    }
+
+    std::tuple<uint16_t, uint16_t, uint16_t, uint16_t>
+    adjustROItoLimits(uint16_t xmin, uint16_t xmax, uint16_t ymin,
+                      uint16_t ymax, uint16_t lim_roi_xmin,
+                      uint16_t lim_roi_xmax, uint16_t lim_roi_ymin,
+                      uint16_t lim_roi_ymax) {
+        uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
+        if (xmin < lim_roi_xmin)
+            xmin_roi = lim_roi_xmin;
+        else
+            xmin_roi = xmin;
+        if (xmax > lim_roi_xmax)
+            xmax_roi = lim_roi_xmax;
+        else
+            xmax_roi = xmax;
+        if (ymin < lim_roi_ymin)
+            ymin_roi = lim_roi_ymin;
+        else
+            ymin_roi = ymin;
+        if (ymax > lim_roi_ymax)
+            ymax_roi = lim_roi_ymax;
+        else
+            ymax_roi = ymax;
+        return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
+    }
+
+    // The strixel Quad has a mirrored symmetry from the center axis
+    // So we need to distinguish between bottom and top half for remapping
+    std::vector<std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t>>
+    mapSubROIs(uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax) {
+        bool bottom = false;
+        bool top = false;
+
+        for (int x = xmin; x != xmax + 1; ++x) {
+            for (int y = ymin; y != ymax; ++y) {
+                if (xstart <= x && x <= xend && bottom_ystart <= y &&
+                    y <= bottom_yend)
+                    bottom = true;
+                if (xstart <= x && x <= xend && top_ystart <= y &&
+                    y <= top_yend)
+                    top = true;
+            }
+        }
+
+        uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
+        std::vector<std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t>>
+            rois{};
+
+        if (bottom) {
+            std::tie(xmin_roi, xmax_roi, ymin_roi, ymax_roi) =
+                adjustROItoLimits(xmin, xmax, ymin, ymax, xstart, xend,
+                                  bottom_ystart, bottom_yend);
+            rois.push_back(std::make_tuple(BOTTOM, xmin_roi, xmax_roi, ymin_roi,
+                                           ymax_roi));
+        }
+        if (top) {
+            std::tie(xmin_roi, xmax_roi, ymin_roi, ymax_roi) =
+                adjustROItoLimits(xmin, xmax, ymin, ymax, xstart, xend,
+                                  top_ystart, top_yend);
+            rois.push_back(
+                std::make_tuple(TOP, xmin_roi, xmax_roi, ymin_roi, ymax_roi));
+        }
+
+        return rois;
+    }
+
+    void remapROI(std::tuple<int, uint16_t, uint16_t, uint16_t, uint16_t> roi,
+                  const int rot) {
+
+        int half, xmin, xmax, ymin, ymax;
+        std::tie(half, xmin, xmax, ymin, ymax) = roi;
+
+        setMappingShifts(rot, half);
+
+        std::cout << "remapping roi: "
+                  << ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
+                  << ", y1: " << y1 << std::endl;
+        std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin
+                  << ", " << ymax << "]" << std::endl;
+
+        remap(xmin, xmax, ymin, ymax);
+    }
+
+    // The following functions are pure virtual in the base class. But I don't
+    // want them to be accessible here! Implement the functions as private (to
+    // satisfy the linker) int getFrameNumber(char* buff){return 0;} //This is
+    // actually needed because the cluster finder writes the framenumber
+    int getPacketNumber(char *buff) { return 0; } // Not provided
+
+    // Mark overwritten functions as override final
+    char *readNextFrame(std::ifstream &filebin) override final {
+        return nullptr;
+    }
+
+  public:
+    using header = sls::defs::sls_receiver_header;
+
+    jungfrauLGADStrixelsDataQuadH5(uint16_t xmin = 0, uint16_t xmax = 0,
+                                   uint16_t ymin = 0, uint16_t ymax = 0)
+        : slsDetectorData<uint16_t>(
+              // nc_strixel,
+              // nr_strixel * 2 + nr_center,
+              // nc_strixel * ( nr_strixel * 2 + nr_center ) * 2
+              512 / 2, 1024 * 2, 512 * 1024 * 2) {
+        std::cout << "Jungfrau strixels quad with full module data "
+                  << std::endl;
+
+        // Fill all strixels with dummy values
+        // for (int ix = 0; ix != nc_strixel; ++ix) {
+        //    for (int iy = 0; iy != nr_strixel * 2 + nr_center; ++iy) {
+        for (int ix = 0; ix != 512 / 2; ++ix) {
+            for (int iy = 0; iy != 1024 * 2; ++iy) {
+                // Set everything to dummy value
+                dataMap[iy][ix] = sizeof(header);
+            }
+        }
+
+        globalROI.xmin = xmin;
+        globalROI.xmax = xmax;
+        globalROI.ymin = ymin;
+        globalROI.ymax = ymax;
+
+        // std::cout << "sizeofheader = " << sizeof(header) << std::endl;
+        std::cout << "Jungfrau strixels quad with full module data "
+                  << std::endl;
+
+        if (xmin < xmax && ymin < ymax) {
+
+            // get ROI raw image number of columns
+            globalROI.nc = xmax - xmin + 1;
+            std::cout << "nc_roi = " << globalROI.nc << std::endl;
+
+            dataSize = (xmax - xmin + 1) * (ymax - ymin + 1) * 2;
+            std::cout << "datasize " << dataSize << std::endl;
+
+            auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
+            // function to fill vector of rois from globalROI
+
+            for (auto roi : rois)
+                remapROI(roi, rota);
+
+        } else {
+            remapQuad(rota);
+        }
+
+        iframe = 0;
+        std::cout << "data struct created" << std::endl;
+    };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    virtual double getValue(char *data, int ix, int iy = 0) {
+
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+        return val;
+    };
+
+    char *readNextFrame(HDF5File &hfile) {
+        int fn = 0;
+        std::vector<hsize_t> h5offset(1);
+        return readNextFrame(hfile, fn, h5offset);
+    };
+
+    char *readNextFrame(HDF5File &hfile, int &fn) {
+        std::vector<hsize_t> h5offset(1);
+        return readNextFrame(hfile, fn, h5offset);
+    };
+
+    char *readNextFrame(HDF5File &hfile, int &fn,
+                        std::vector<hsize_t> &h5offset) {
+
+        // Ensure dataSize is a valid size for allocation
+        if (dataSize <= 0) {
+            // Handle error case appropriately, e.g., log an error message
+            return nullptr;
+        }
+
+        char *data = new char[dataSize];
+        char *readResult = readNextFrame(hfile, fn, h5offset, data);
+
+        // Check if reading failed
+        if (readResult == nullptr) {
+            delete[] data;  // Free allocated memory
+            data = nullptr; // Set to nullptr to avoid dangling pointer
+        }
+
+        return data; // returning data is equivalent to returning
+                     // reinterpret_cast<char*>(data_ptr) as they both point to
+                     // the same memory
+    };
+
+    /*
+     * This is the most recent function. This is used in the cluster finder!
+     * The overloads are legacy!
+     * Note that caller has to allocate and deallocate memory for data!
+     * \param hfile object of type HDF5File (reader class)
+     * \param framenumber frame number as read from the HDF5 file
+     * \param h5offset vector defining offset parameters for HDF5 hyperslab
+     * selection (dimensions Z and S), incremented automatially
+     * \param data pointer to image buffer (converted to hold uint16_t by
+     * definition of HDF5File)
+     */
+    char *readNextFrame(HDF5File &hfile, int &framenumber,
+                        std::vector<hsize_t> &h5offset, char *data) {
+
+        if (framenumber >= 0) {
+            if (h5offset[0] % 10 == 0)
+                std::cout << "*";
+
+            // Storing the reinterpret_cast in the variable data_ptr ensures
+            // that I can pass it to a function that expects at uint16_t*
+            uint16_t *data_ptr = reinterpret_cast<uint16_t *>(
+                data); // now data_ptr points where data points (thus modifies
+                       // the same memory)
+
+            framenumber = hfile.ReadImage(data_ptr, h5offset);
+            iframe = h5offset[0]; // iframe is a class member!
+            return data; // return reinterpret_cast<char*>(data_ptr); //
+                         // Equivalent
+        }
+
+        std::cout << "#";
+        return nullptr;
+    };
+
+    int getFrameNumber(char *buff) {
+        return iframe;
+    } // Provided via public method readNextFrame
+    // It is debatable if one might not instead want to provide the "real" frame
+    // number as read from the file here For now, this is the frame offset
+    // counter (that always has to start at 0 for each new file)
+
+    /*    Loops over a memory slot until a complete frame is found (i.e. all */
+    /*    packets 0 to nPackets, same frame number). purely virtual func \param
+     */
+    /*    data pointer to the memory to be analyzed \param ndata reference to
+     * the */
+    /*    amount of data found for the frame, in case the frame is incomplete at
+     */
+    /*    the end of the memory slot \param dsize size of the memory slot to be
+     */
+    /*    analyzed \returns pointer to the beginning of the last good frame
+     * (might */
+    /*    be incomplete if ndata smaller than dataSize), or NULL if no frame is
+     */
+    /*    found */
+
+    /* *\/ */
+    virtual char *findNextFrame(char *data, int &ndata, int dsize) {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    };
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h

@@ -28,6 +28,10 @@
     @li version is the version number of this structure format
 */
 
+#include <algorithm>
+#include <numeric>
+#include <tuple>
+
 namespace strixelSingleChip {
 constexpr int nc_rawimg = 1024; // for full images  //256;
 constexpr int nr_rawimg = 512;
@@ -77,7 +81,7 @@ constexpr int c6g1_ystart = c6g2_yend + 1;        // 448
 constexpr int c6g1_yend = c6g2_yend + 64 - gr;    // 502
 
 // y shift due to faulty bonding (relevant for M408)
-constexpr int bond_shift_y = 1; // CHANGE IF YOU CHANGE MODULE!
+constexpr int bond_shift_y = 0; // CHANGE IF YOU CHANGE MODULE!
 
 } // namespace strixelSingleChip
 
@@ -97,6 +101,13 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
     int chip_x0;
     int chip_y0;
     int x0, y0, x1, y1, shifty;
+    struct {
+      uint16_t xmin;
+      uint16_t xmax;
+      uint16_t ymin;
+      uint16_t ymax;
+      int nc;
+    } globalROI;
 
     int getMultiplicator(const int group) {
         int multiplicator;
@@ -215,9 +226,113 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         }
     }
 
-    void remapROI(uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax) {
+
+    std::tuple< uint16_t, uint16_t, uint16_t, uint16_t > adjustROItoLimits(uint16_t xmin,
+									   uint16_t xmax,
+									   uint16_t ymin,
+									   uint16_t ymax,
+									   uint16_t lim_roi_xmin,
+									   uint16_t lim_roi_xmax,
+									   uint16_t lim_roi_ymin,
+									   uint16_t lim_roi_ymax) {
+      uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
+      if ( xmin < lim_roi_xmin)
+        xmin_roi = lim_roi_xmin;
+      else
+        xmin_roi = xmin;
+      if ( xmax > lim_roi_xmax )
+        xmax_roi = lim_roi_xmax;
+      else
+        xmax_roi = xmax;
+      if ( ymin < lim_roi_ymin )
+        ymin_roi = lim_roi_ymin;
+      else
+        ymin_roi = ymin;
+      if ( ymax > lim_roi_ymax )
+        ymax_roi = lim_roi_ymax;
+      else
+        ymax_roi = ymax;
+      return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
+    }
+
+    std::vector < std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > > mapSubROIs(uint16_t xmin,
+											      uint16_t xmax,
+											      uint16_t ymin,
+											      uint16_t ymax) {
+      bool chip_1_1 = false;
+      bool chip_1_2 = false;
+      bool chip_1_3 = false;
+      bool chip_6_1 = false;
+      bool chip_6_2 = false;
+      bool chip_6_3 = false;
+
+      for ( int x=xmin; x!=xmax+1; ++x ) {
+	for ( int y=ymin; y!=ymax; ++y ) {
+	  if ( c1g1_xstart<=x && x<=c1_xend && (c1g1_ystart+bond_shift_y)<=y && y<=(c1g1_yend+bond_shift_y) )
+	    chip_1_1 = true;
+	  if ( c1g2_xstart<=x && x<=c1_xend && (c1g2_ystart+bond_shift_y)<=y && y<=(c1g2_yend+bond_shift_y) )
+	    chip_1_2 = true;
+	  if ( c1g3_xstart<=x && x<=c1_xend && (c1g3_ystart+bond_shift_y)<=y && y<=(c1g3_yend+bond_shift_y) )
+	    chip_1_3 = true;
+	  if ( c6_xstart<=x && x<=c6g1_xend && (c6g1_ystart-bond_shift_y)<=y && y<=(c6g1_yend-bond_shift_y) )
+	    chip_6_1 = true;
+	  if ( c6_xstart<=x && x<=c6g2_xend && (c6g2_ystart-bond_shift_y)<=y && y<=(c6g2_yend-bond_shift_y) )
+	    chip_6_2 = true;
+	  if ( c6_xstart<=x && x<=c6g3_xend && (c6g3_ystart-bond_shift_y)<=y && y<=(c6g3_yend-bond_shift_y) )
+	    chip_6_3 = true;
+	}
+      }
+
+      uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
+       //[ chip, group, xmin, xmax, ymin, ymax ]
+      std::vector < std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > > rois{};
+
+      if (chip_1_1) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g1_xstart, c1_xend, 0, c1g1_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 1, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_1_2) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g2_xstart, c1_xend, c1g2_ystart+bond_shift_y, c1g2_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 2, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_1_3) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g3_xstart, c1_xend, c1g3_ystart+bond_shift_y, c1g3_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 3, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_3) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g3_xend, c6g3_ystart-bond_shift_y, c6g3_yend-bond_shift_y );
+	rois.push_back( std::make_tuple( 6, 3, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_2) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g2_xend, c6g2_ystart-bond_shift_y, c6g2_yend-bond_shift_y );
+	rois.push_back( std::make_tuple( 6, 2, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_1) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g1_xend, c6g1_ystart-bond_shift_y, 511 );
+	rois.push_back( std::make_tuple( 6, 1, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+
+      return rois;
+
+    }
+
+    void remapROI(std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > roi) {
         // determine group and chip selected by ROI
-        int group;
+      int group, xmin, xmax, ymin, ymax;
+      std::tie( mchip, group, xmin, xmax, ymin, ymax ) = roi;
+	/*
         if (ymax <= c1g1_yend + bond_shift_y) {
             group = 1;
             mchip = 1;
@@ -243,18 +358,17 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	  group = -1;
 	  mchip = -1;
 	}
-        int multiplicator = getMultiplicator(group);
-        setMappingShifts(group);
-
-        std::cout << "chip: " << mchip << ", group: " << group << ", m: " << multiplicator
-                  << ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
-                  << ", y1: " << y1 << std::endl;
-
-        // get ROI raw image number of columns
-        int nc_roi = xmax - xmin + 1;
-        std::cout << "nc_roi = " << nc_roi << std::endl;
+	*/
+      int multiplicator = getMultiplicator(group);
+      setMappingShifts(group);
+      
+      std::cout << "remapping chip: " << mchip << ", group: " << group << ", m: " << multiplicator
+		<< ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
+		<< ", y1: " << y1 << std::endl;
+      std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]" << std::endl;
 
         // make sure loop bounds are correct
+	/*
         if (y0 < ymin)
             std::cout << "Error ymin" << std::endl;
         if (y1 > ymax)
@@ -264,24 +378,27 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
             std::cout << "Error xmin" << std::endl;
         if (x1 > xmax)
             std::cout << "Error xmax" << std::endl;
+	*/
 
         // remapping loop
-        int ix, iy = 0;
-        for (int ipy = y0; ipy <= y1; ++ipy) {
-            for (int ipx = x0; ipx <= x1; ++ipx) {
+      int ix, iy = 0;
+      for (int ipy = y0; ipy <= y1; ++ipy) {
+	for (int ipx = x0; ipx <= x1; ++ipx) {
 
-                ix = int((ipx - x0 /*-xmin*/) / multiplicator);
-                for (int m = 0; m < multiplicator; m++) {
-                    if ((ipx - x0 /*-xmin*/) % multiplicator == m)
-                        iy = (ipy - y0 /*-ymin*/) * multiplicator + m + shifty;
-                }
-
-                //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
-                dataMap[iy][ix] =
-                    sizeof(header) + (nc_roi * (ipy - ymin) + (ipx - xmin)) * 2;
-                groupmap[iy][ix] = group - 1;
-            }
-        }
+	  ix = int((ipx - x0 /*-xmin*/) / multiplicator);
+	  for (int m = 0; m < multiplicator; m++) {
+	    if ((ipx - x0 /*-xmin*/) % multiplicator == m)
+	      iy = (ipy - y0 /*-ymin*/) * multiplicator + m + shifty;
+	  }
+	  
+	  //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
+	  if ( ipx>=xmin && ipx<=xmax && ipy>=ymin && ipy <=ymax )
+	    dataMap[iy][ix] =
+	      sizeof(header) + (globalROI.nc * (ipy - globalROI.ymin) + (ipx - globalROI.xmin)) * 2;
+	  else dataMap[iy][ix] = sizeof(header);
+	  groupmap[iy][ix] = group - 1;
+	}
+      }
     }
 
   public:
@@ -307,16 +424,31 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
             }
         }
 
+	globalROI.xmin = xmin;
+	globalROI.xmax = xmax;
+	globalROI.ymin = ymin;
+	globalROI.ymax = ymax;
+
         std::cout << "sizeofheader = " << sizeof(header) << std::endl;
         std::cout << "Jungfrau strixels 2X single chip with full module data "
                   << std::endl;
 
         if (xmin < xmax && ymin < ymax) {
 
-            dataSize =
-                (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
-            std::cout << "datasize " << dataSize << std::endl;
-            remapROI(xmin, xmax, ymin, ymax);
+	  // get ROI raw image number of columns
+	  globalROI.nc = xmax - xmin + 1;
+	  std::cout << "nc_roi = " << globalROI.nc << std::endl;
+	  
+	  dataSize =
+	    (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
+	  std::cout << "datasize " << dataSize << std::endl;
+
+	  //[ chip, group, xmin, xmax, ymin, ymax ]
+	  auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
+	  //function to fill vector of rois from globalROI
+
+	  for ( auto roi : rois )
+	    remapROI(roi);
 
         } else {
 

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -3,6 +3,7 @@
 #ifndef JUNGFRAUMODULEDATA_H
 #define JUNGFRAUMODULEDATA_H
 #include <cstdint>
+#include "sls/sls_detector_defs.h"
 #include "slsDetectorData.h"
 
 //#define VERSION_V2
@@ -27,7 +28,7 @@ typedef struct {
     uint64_t bunchNumber; /**< is the frame number */
     uint64_t pre;         /**< something */
 
-} jf_header;
+} jf_header; //Aldo's header!
 
 using namespace std;  
 class jungfrauModuleData : public slsDetectorData<uint16_t> {
@@ -42,20 +43,56 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
        1286 large etc.) \param c crosstalk parameter for the output buffer
 
    */
+
+#ifdef ALDO
+    using header = jf_header;
+#else
+    using header = sls::defs::sls_receiver_header;
+#endif
+
 #ifndef ZMQ
-#define off sizeof(jf_header)
+#define off sizeof(header)
 #endif
 #ifdef ZMQ
 #define off 0
 #endif
 
 
-    jungfrauModuleData()
+ jungfrauModuleData(uint16_t xmin=0, uint16_t xmax=0,
+		    uint16_t ymin=0, uint16_t ymax=0)
         : slsDetectorData<uint16_t>(1024, 512,
                                     1024* 512 * 2 + off) {
-  
-        for (int ix = 0; ix < 1024; ix++) {
-            for (int iy = 0; iy < 512; iy++) {
+
+      for (int ix = 0; ix != 1024; ++ix) {
+	for (int iy = 0; iy != 512; ++iy) {
+	  dataMap[iy][ix] = off;
+	}
+      }
+
+      if (xmin < xmax && ymin < ymax) {
+
+	int nc_roi = xmax - xmin + 1;
+	int nr_roi = ymax - ymin + 1;
+	std::cout << "nc_roi = " << nc_roi << std::endl;
+	std::cout << "nr_roi = " << nr_roi << std::endl;
+	  
+	dataSize =
+	  (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + off;
+	std::cout << "datasize " << dataSize << std::endl;
+
+	for (int ix = xmin; ix < xmax+1; ++ix) {
+            for (int iy = ymin; iy < ymax+1; ++iy) {
+                dataMap[iy][ix] = off + (nc_roi * iy + ix) * 2;
+#ifdef HIGHZ
+                dataMask[iy][ix] = 0x3fff;
+#endif
+            }
+        }
+
+      } else {
+	  
+        for (int ix = 0; ix < 1024; ++ix) {
+            for (int iy = 0; iy < 512; ++iy) {
                 dataMap[iy][ix] = off + (1024 * iy + ix) * 2;
 #ifdef HIGHZ
                 dataMask[iy][ix] = 0x3fff;
@@ -63,7 +100,7 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
             }
         }
 
-
+      }
 
 
         iframe = 0;
@@ -150,7 +187,7 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
         //int pn;
 
         //  cout << dataSize << endl;
-        if (ff >= 0)
+        //if (ff >= 0)
 	  //fnum = ff;
 
         if (filebin.is_open()) {

slsDetectorCalibration/dataStructures/jungfrauSingleChipData.h

@@ -0,0 +1,226 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef JUNGFRAUSINGLECHIPDATA_H
+#define JUNGFRAUSINGLECHIPDATA_H
+#include <cstdint>
+#include "sls/sls_detector_defs.h"
+#include "slsDetectorData.h"
+
+//#define VERSION_V2
+/**
+    @short  structure for a Detector Packet or Image Header
+    @li frameNumber is the frame number
+    @li expLength is the subframe number (32 bit eiger) or real time exposure
+   time in 100ns (others)
+    @li packetNumber is the packet number
+    @li bunchId is the bunch id from beamline
+    @li timestamp is the time stamp with 10 MHz clock
+    @li modId is the unique module id (unique even for left, right, top, bottom)
+    @li xCoord is the x coordinate in the complete detector system
+    @li yCoord is the y coordinate in the complete detector system
+    @li zCoord is the z coordinate in the complete detector system
+    @li debug is for debugging purposes
+    @li roundRNumber is the round robin set number
+    @li detType is the detector type see :: detectorType
+    @li version is the version number of this structure format
+*/
+typedef struct {
+    uint64_t bunchNumber; /**< is the frame number */
+    uint64_t pre;         /**< something */
+
+} jf_header; //Aldo's header!
+
+using namespace std;  
+class jungfrauSingleChipData : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+
+  public:
+    /**
+       Implements the slsReceiverData structure for the moench02 prototype read
+       out by a module i.e. using the slsReceiver (160x160 pixels, 40 packets
+       1286 large etc.) \param c crosstalk parameter for the output buffer
+
+   */
+
+#ifdef ALDO
+    using header = jf_header;
+#else
+    using header = sls::defs::sls_receiver_header;
+#endif
+
+#ifndef ZMQ
+#define off sizeof(header)
+#endif
+#ifdef ZMQ
+#define off 0
+#endif
+
+
+ jungfrauSingleChipData(uint16_t xmin=0, uint16_t xmax=0,
+		    uint16_t ymin=0, uint16_t ymax=0)
+        : slsDetectorData<uint16_t>(256, 256,
+                                    256* 256 * 2 + off) {
+
+      for (int ix = 0; ix != 256; ++ix) {
+	for (int iy = 0; iy != 256; ++iy) {
+	  dataMap[iy][ix] = off;
+	}
+      }
+
+      if (xmin < xmax && ymin < ymax) {
+
+	int nc_roi = xmax - xmin + 1;
+	int nr_roi = ymax - ymin + 1;
+	std::cout << "nc_roi = " << nc_roi << std::endl;
+	std::cout << "nr_roi = " << nr_roi << std::endl;
+	  
+	dataSize =
+	  (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + off;
+	std::cout << "datasize " << dataSize << std::endl;
+
+	for (int ix = xmin; ix < xmax+1; ++ix) {
+            for (int iy = ymin; iy < ymax+1; ++iy) {
+                dataMap[iy][ix] = off + (nc_roi * iy + ix) * 2;
+#ifdef HIGHZ
+                dataMask[iy][ix] = 0x3fff;
+#endif
+            }
+        }
+
+      } else {
+	  
+        for (int ix = 0; ix < 256; ++ix) {
+            for (int iy = 0; iy < 256; ++iy) {
+                dataMap[iy][ix] = off + (256 * iy + ix) * 2;
+#ifdef HIGHZ
+                dataMask[iy][ix] = 0x3fff;
+#endif
+            }
+        }
+
+      }
+
+
+        iframe = 0;
+        //  cout << "data struct created" << endl;
+    };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    virtual double getValue(char *data, int ix, int iy = 0) {
+
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+	/* if (ix==0 && iy==0) */
+	/*   cout << val << endl; */
+        return val;
+    };
+
+   
+
+    /**
+
+    Returns the frame number for the given dataset. Purely virtual func.
+    \param buff pointer to the dataset
+    \returns frame number
+
+ */
+
+    /* class jfrau_packet_header_t { */
+    /*  public: */
+    /* 	unsigned char reserved[4]; */
+    /* 	unsigned char packetNumber[1]; */
+    /* 	unsigned char frameNumber[3]; */
+    /* 	unsigned char bunchid[8]; */
+    /* }; */
+
+    int getFrameNumber(char *buff) {
+        return ((jf_header *)buff)->bunchNumber;
+    };
+  
+    /**
+
+       Returns the packet number for the given dataset. purely virtual func
+       \param buff pointer to the dataset
+       \returns packet number number
+
+
+
+    */
+    int getPacketNumber(char *buff) {
+        return 0;
+    };
+
+   
+    char *readNextFrame(ifstream &filebin) {
+        int ff = -1, np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(ifstream &filebin, int &ff) {
+        int np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(ifstream &filebin, int &ff, int &np) {
+        char *data = new char[dataSize];
+        char *d = readNextFrame(filebin, ff, np, data);
+        if (d == NULL) {
+            delete[] data;
+            data = NULL;
+        }
+        return data;
+    };
+
+    char *readNextFrame(ifstream &filebin, int &ff, int &np,char *data) {
+      //char *retval = 0;
+      //int nd;
+      //int fnum = -1;
+        np = 0;
+        //int pn;
+
+        //  cout << dataSize << endl;
+        //if (ff >= 0)
+	  //fnum = ff;
+
+        if (filebin.is_open()) {
+            if (filebin.read(data, dataSize)) {
+                ff = getFrameNumber(data);
+                np = getPacketNumber(data);
+                return data;
+            }
+        }
+        return NULL;
+    };
+
+    /**
+
+       Loops over a memory slot until a complete frame is found (i.e. all
+       packets 0 to nPackets, same frame number). purely virtual func \param
+       data pointer to the memory to be analyzed \param ndata reference to the
+       amount of data found for the frame, in case the frame is incomplete at
+       the end of the memory slot \param dsize size of the memory slot to be
+       analyzed \returns pointer to the beginning of the last good frame (might
+       be incomplete if ndata smaller than dataSize), or NULL if no frame is
+       found
+
+    */
+    virtual char *findNextFrame(char *data, int &ndata, int dsize) {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    };
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/interpolatingDetector.h

@@ -54,6 +54,10 @@ class interpolatingDetector : public singlePhotonDetector {
         pthread_mutex_init(fi, NULL);
     };
 
+    /**
+       pointer-based copy constructor (cloner)
+       \param orig detector to be copied
+    */
     interpolatingDetector(interpolatingDetector *orig)
         : singlePhotonDetector(orig) {
         // if (orig->interp)
@@ -66,10 +70,28 @@ class interpolatingDetector : public singlePhotonDetector {
         fi = orig->fi;
     }
 
+    /**
+     * copy constructor (deep copy)
+     * stricly, TODO: Implement Rule of Five!
+     * (copy op=, move ctor, and move op= would need to be defined)
+    */
+    interpolatingDetector(interpolatingDetector const& other)
+        : singlePhotonDetector(other) {
+
+        interp = other.interp;
+
+        id = other.id;
+        fi = other.fi;
+    }
+
     virtual interpolatingDetector *Clone() {
         return new interpolatingDetector(this);
     }
 
+    virtual interpolatingDetector *Copy() {
+        return new interpolatingDetector(*this);
+    }
+
     virtual int setId(int i) {
         id = i;
         //  interp->setId(id);

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -6,18 +6,86 @@
 
 set(JUNGFRAU_EXECUTABLES)
 
-find_package(fmt REQUIRED)
+#find_package(fmt REQUIRED)
+
+#nlohmann_json
+#If the library was INSTALLED (i.e. sudo dnf install nlohmann-json3-dev), do stuff described in the repo under CMake -> External
+#find_package(nlohmann_json 3.2.0 REQUIRED)
+#find_package(nlohmann_json 3.11.2 REQUIRED)
+#find_package(nlohmann_json 3.11.3 REQUIRED)
+#
+#If the library was not installed but just cloned from https://github.com/nlohmann/json.git (possible, because it is a header-only library),
+# do stuff described in the repo under CMake -> Embedded
+#set(JSON_BuildTests OFF CACHE INTERNAL "")
+# If you only include this third party in PRIVATE source files, you do not
+# need to install it when your main project gets installed.
+# set(JSON_Install OFF CACHE INTERNAL "")
+#add_subdirectory(nlohmann_json) #Put the actual path to json
+#
+#Alternative: Fetch and install it from remote
+include(FetchContent)
+FetchContent_Declare(
+  json
+  GIT_REPOSITORY https://github.com/nlohmann/json.git
+  GIT_TAG v3.11.3  # Replace with the version you need
+)
+#FetchContent_Declare(json URL https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz) #Alternative (from the repo documentation)
+FetchContent_MakeAvailable(json)
+
+FetchContent_Declare(
+  fmt
+  GIT_REPOSITORY https://github.com/fmtlib/fmt.git
+  GIT_TAG master
+)
+FetchContent_MakeAvailable(fmt)
+
+# HDF5 file writing 
+if (SLS_USE_HDF5)
+    find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
+	    list (APPEND SOURCES 
+	        HDF5File.cpp 
+	    )
+endif (SLS_USE_HDF5)
+
+
 
 # jungfrauRawDataProcess
 add_executable(jungfrauRawDataProcess jungfrauRawDataProcess.cpp)
 target_compile_definitions(jungfrauRawDataProcess PRIVATE MODULE)
 list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcess)
 
+# jungfrauRawDataProcessChipAldo
+add_executable(jungfrauRawDataProcessChipAldo jungfrauRawDataProcess_filetxt.cpp)
+target_compile_definitions(jungfrauRawDataProcessChipAldo PRIVATE CHIP ALDO)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessChipAldo)
+
 # jungfrauRawDataProcessStrx
 add_executable(jungfrauRawDataProcessStrx jungfrauRawDataProcess_filetxt.cpp)
 target_compile_definitions(jungfrauRawDataProcessStrx PRIVATE JFSTRX)
 list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrx)
 
+# jungfrauRawDataProcessStrxQuad
+add_executable(jungfrauRawDataProcessStrxQuad jungfrauRawDataProcess_filetxt.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxQuad PRIVATE JFSTRXQ)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxQuad)
+
+# jungfrauRawDataProcessStrxQuadH5
+# HDF5
+if (SLS_USE_HDF5)
+    if (HDF5_FOUND)
+       add_executable(jungfrauRawDataProcessStrxQuadH5 jungfrauRawDataProcess_filetxtH5.cpp)
+       #target_compile_definitions(jungfrauRawDataProcessStrxQuadH5 PRIVATE JFSTRXQH5)
+       list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxQuadH5)
+       target_include_directories(jungfrauRawDataProcessStrxQuadH5 PRIVATE ${HDF5_INCLUDE_DIRS}  ${CMAKE_INSTALL_PREFIX}/include)
+       target_link_libraries(jungfrauRawDataProcessStrxQuadH5 PRIVATE ${HDF5_LIBRARIES})
+
+       add_executable(jungfrauRawDataProcessStrxQuadH5SC jungfrauRawDataProcess_filetxtH5_SC.cpp)
+       #target_compile_definitions(jungfrauRawDataProcessStrxQuadH5 PRIVATE JFSTRXQH5)
+       list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxQuadH5SC)
+       target_include_directories(jungfrauRawDataProcessStrxQuadH5SC PRIVATE ${HDF5_INCLUDE_DIRS}  ${CMAKE_INSTALL_PREFIX}/include)
+       target_link_libraries(jungfrauRawDataProcessStrxQuadH5SC PRIVATE ${HDF5_LIBRARIES})
+    endif ()
+endif (SLS_USE_HDF5)
 
 # jungfrauRawDataProcessStrxChip1
 add_executable(jungfrauRawDataProcessStrxChip1 jungfrauRawDataProcess.cpp)
@@ -58,6 +126,22 @@ list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxOldAldo)
 # others to be added if needed (might already be there in Makefile.cluster_finder TO BE CHECKED)
 
 
+if (SLS_USE_HDF5)
+   if (HDF5_FOUND)
+        target_include_directories(jungfrauRawDataProcessStrxQuadH5 PRIVATE 
+								    ${HDF5_INCLUDE_DIRS}
+								    ${CMAKE_INSTALL_PREFIX}/include
+								    )
+	    target_link_libraries(jungfrauRawDataProcessStrxQuadH5 PRIVATE ${HDF5_LIBRARIES})
+
+        target_include_directories(jungfrauRawDataProcessStrxQuadH5SC PRIVATE 
+								    ${HDF5_INCLUDE_DIRS}
+								    ${CMAKE_INSTALL_PREFIX}/include
+								    )
+	    target_link_libraries(jungfrauRawDataProcessStrxQuadH5SC PRIVATE ${HDF5_LIBRARIES})
+
+   endif ()
+endif (SLS_USE_HDF5)
 
 
 foreach(exe ${JUNGFRAU_EXECUTABLES})
@@ -67,11 +151,16 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         ../interpolations
         ../dataStructures 
         ../interpolations/etaVEL
-        ../../slsSupportLib/include/
+        ../../slsSupportLib/include/sls/
         ../../slsReceiverSoftware/include/
         ../tiffio/include
         ${fmt_INCLUDE_DIRS}
     )
+#    if (SLS_USE_HDF5)
+#       if (HDF5_FOUND)
+#       	  target_include_directories(${exe} PRIVATE ${HDF5_INCLUDE_DIRS}  ${CMAKE_INSTALL_PREFIX}/include)
+#       endif ()
+#    endif (SLS_USE_HDF5)
 
     target_link_libraries(${exe} 
         PUBLIC
@@ -79,6 +168,7 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         pthread 
         tiffio
         fmt::fmt
+	    nlohmann_json::nlohmann_json
           #-L/usr/lib64/
         #-lm  -lstdc++  -lrt
 
@@ -86,7 +176,11 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         slsProjectWarnings
         slsProjectOptions
     )
-
+#    if (SLS_USE_HDF5)
+#       if (HDF5_FOUND)
+#	target_link_libraries(${exe} PRIVATE ${HDF5_LIBRARIES})
+#       endif ()
+#    endif (SLS_USE_HDF5)
 
     set_target_properties(${exe}  PROPERTIES 
         RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
@@ -98,4 +192,8 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
     
 endforeach(exe ${JUNGFRAU_EXECUTABLES})
 
-install(TARGETS ${JUNGFRAU_EXECUTABLES} DESTINATION bin)
+
+
+
+
+install(TARGETS ${JUNGFRAU_EXECUTABLES} DESTINATION bin)

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -11,7 +11,7 @@
 #define RAWDATA
 
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6
+    !defined JFSTRXCHIP6 && !defined CHIP
 #ifndef MODULE
 #include "jungfrauHighZSingleChipData.h"
 #endif
@@ -20,6 +20,10 @@
 #endif
 #endif
 
+#ifdef CHIP
+#include "jungfrauSingleChipData.h"
+#endif
+
 #ifdef JFSTRX
 #include "jungfrauLGADStrixelsData_new.h"
 #endif
@@ -41,6 +45,9 @@
 #include <ctime>
 #include <fmt/core.h>
 
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
 
 std::string getRootString( const std::string& filepath ) {
   size_t pos1 = filepath.find_last_of("/");
@@ -61,20 +68,24 @@ std::string getRootString( const std::string& filepath ) {
 std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int aindex=0, int mindex=0, int findex=0, int outfilecounter=-1 ) {
   if (outfilecounter >= 0)
     return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
-  else if (fsuffix.length()!=0)
-    return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+  else if (fsuffix.length()!=0) {
+    if (fsuffix == "master")
+      return fmt::format("{:s}/{:s}_master_{:d}.{:s}", dir, fprefix, aindex, fext);
+    else
+      return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+  }
   else
     return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
 }
 
 int main(int argc, char *argv[]) {
 
-    if (argc < 5) {
+    if (argc < 6) {
         std::cout
             << "Usage is " << argv[0]
-            << "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
-               "[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
-               "[nframes] [xmin xmax ymin ymax] [gainmap]"
+            << "indir outdir [fprefix(excluding slsDetector standard suffixes and extension)] [fextension] "
+	       "[fmin] [fmax] [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
+               "[nframes] [xmin xmax ymin ymax] [optional: bool read rxroi from data file header] [gainmap]"
             << std::endl;
         std::cout
             << "threshold <0 means analog; threshold=0 means cluster finder; "
@@ -106,94 +117,131 @@ int main(int argc, char *argv[]) {
     std::string outdir(argv[2]);
     std::string fprefix(argv[3]);
     std::string fext(argv[4]);
+
+    int fmin = 0;
+    if (argc >= 6)
+        fmin = atoi(argv[5]);
+    int fmax = fmin;
+    if (argc >= 7)
+        fmax = atoi(argv[6]);
+
     int runmin = 0;
-
     // cout << "argc is " << argc << endl;
-    if (argc >= 6) {
-        runmin = atoi(argv[5]);
+    if (argc >= 8) {
+        runmin = atoi(argv[7]);
     }
-
     int runmax = runmin;
-
-    if (argc >= 7) {
-        runmax = atoi(argv[6]);
+    if (argc >= 9) {
+        runmax = atoi(argv[8]);
     }
 
     std::string pedfilename{};
-    if (argc >= 8) {
-        pedfilename = argv[7];
+    if (argc >= 10) {
+        pedfilename = argv[9];
     }
     double thr = 0;
     double thr1 = 1;
 
-    if (argc >= 9) {
-        thr = atof(argv[8]);
+    if (argc >= 11) {
+        thr = atof(argv[10]);
     }
 
     int nframes = 0;
 
-    if (argc >= 10) {
-        nframes = atoi(argv[9]);
+    if (argc >= 12) {
+        nframes = atoi(argv[11]);
     }
+
+    bool readrxroifromdatafile = false;
+    if (argc >= 17)
+      readrxroifromdatafile = atoi(argv[16]);
     
+    // Receiver ROI
+    uint16_t rxroi_xmin = 0;
+    uint16_t rxroi_xmax = 0;
+    uint16_t rxroi_ymin = 0;
+    uint16_t rxroi_ymax = 0;
+
+    { //protective scope so ifstream gets destroyed properly
+
+      auto jsonmastername = createFileName( indir, fprefix, "master", "json", runmin );
+      std::cout << "json master file " << jsonmastername << std::endl;
+      std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
+      if (masterfile.is_open()) {
+	json j;
+	masterfile >> j;
+	rxroi_xmin = j["Receiver Roi"]["xmin"];
+	rxroi_xmax = j["Receiver Roi"]["xmax"];
+	rxroi_ymin = j["Receiver Roi"]["ymin"];
+	rxroi_ymax = j["Receiver Roi"]["ymax"];
+	masterfile.close();
+	std::cout << "Read Receiver ROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
+		  << rxroi_ymin << ", " << rxroi_ymax << "] from json master file" << std::endl;
+      } else 
+	std::cout << "Could not open master file " << jsonmastername << std::endl;
+    
+    }
+
     // Define decoders...
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6
+    !defined JFSTRXCHIP6 && !defined CHIP
 #ifndef MODULE
     jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
     int nx = 256, ny = 256;
 #endif
 #ifdef MODULE
-    jungfrauModuleData *decoder = new jungfrauModuleData();
+    jungfrauModuleData *decoder = new jungfrauModuleData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024, ny = 512;
 #endif
 #endif
 
+#ifdef CHIP
+    std::cout << "Jungfrau pixel module single chip readout" << std::endl;
+    jungfrauSingleChipData *decoder = new jungfrauSingleChipData();
+    int nx = 256, ny = 256;
+#endif
+
 #ifdef JFSTRX
-    cout << "Jungfrau strixel full module readout" << endl;
-    // ROI
-    uint16_t xxmin = 0;
-    uint16_t xxmax = 0;
-    uint16_t yymin = 0;
-    uint16_t yymax = 0;
+    std::cout << "Jungfrau strixel full module readout" << std::endl;
 
 #ifndef ALDO
-    { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
-      using header = sls::defs::sls_receiver_header;
-      // check if there is a roi in the header
-      typedef struct {
-        uint16_t xmin;
-        uint16_t xmax;
-        uint16_t ymin;
-        uint16_t ymax;
-      } receiverRoi_compact;
-      receiverRoi_compact croi;
-      std::string fsuffix{};
-      auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
-      std::cout << "Reading header of file " << filename << " to check for ROI "
-		<< std::endl;
-      ifstream firstfile(filename, ios::in | ios::binary);
-      if (firstfile.is_open()) {
-        header hbuffer;
-        std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
-        if (firstfile.read((char *)&hbuffer, sizeof(header))) {
-	  memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
-	  std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
-		    << croi.ymin << ", " << croi.ymax << "]" << std::endl;
-	  xxmin = croi.xmin;
-	  xxmax = croi.xmax;
-	  yymin = croi.ymin;
-	  yymax = croi.ymax;
-        } else
-	  std::cout << "reading error" << std::endl;
-        firstfile.close();
-      } else
-        std::cout << "Could not open " << filename << " for reading " << std::endl;
-    } //end of protective scope
+    if (readrxroifromdatafile)
+      { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
+	using header = sls::defs::sls_receiver_header;
+	// check if there is a roi in the header
+	typedef struct {
+	  uint16_t xmin;
+	  uint16_t xmax;
+	  uint16_t ymin;
+	  uint16_t ymax;
+	} receiverRoi_compact;
+	receiverRoi_compact croi;
+	std::string fsuffix{};
+	auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
+	std::cout << "Reading header of file " << filename << " to check for ROI "
+		  << std::endl;
+	ifstream firstfile(filename, ios::in | ios::binary);
+	if (firstfile.is_open()) {
+	  header hbuffer;
+	  std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
+	  if (firstfile.read((char *)&hbuffer, sizeof(header))) {
+	    memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
+	    std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
+		      << croi.ymin << ", " << croi.ymax << "]" << std::endl;
+	    rxroi_xmin = croi.xmin;
+	    rxroi_xmax = croi.xmax;
+	    rxroi_ymin = croi.ymin;
+	    rxroi_ymax = croi.ymax;
+	  } else
+	    std::cout << "reading error" << std::endl;
+	  firstfile.close();
+	} else
+	  std::cout << "Could not open " << filename << " for reading " << std::endl;
+      } //end of protective scope
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
+      new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024 / 3, ny = 512 * 5;
 #endif
 #ifdef JFSTRXCHIP1
@@ -218,19 +266,20 @@ int main(int argc, char *argv[]) {
     decoder->getDetectorSize(nx, ny);
     std::cout << "Detector size is " << nx << " " << ny << std::endl;
 
-    int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
-    if (argc >= 14) {
-        xmin = atoi(argv[10]);
-        xmax = atoi(argv[11]);
-        ymin = atoi(argv[12]);
-        ymax = atoi(argv[13]);
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    if (argc >= 16) {
+        xmin = atoi(argv[12]);
+        xmax = atoi(argv[13]);
+        ymin = atoi(argv[14]);
+        ymax = atoi(argv[15]);
     }
-    std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
               << std::endl;
 
     char *gainfname = NULL;
-    if (argc > 14) {
-        gainfname = argv[14];
+    if (argc > 17) {
+        gainfname = argv[17];
         std::cout << "Gain map file name is: " << gainfname << std::endl;
     }
 
@@ -239,6 +288,8 @@ int main(int argc, char *argv[]) {
     std::cout << "input directory is " << indir << std::endl;
     std::cout << "output directory is " << outdir << std::endl;
     std::cout << "input file prefix is " << fprefix << std::endl;
+    std::cout << "fmin is " << fmin << std::endl;
+    std::cout << "fmax is " << fmax << std::endl;
     std::cout << "runmin is " << runmin << std::endl;
     std::cout << "runmax is " << runmax << std::endl;
     if (pedfilename.length()!=0)
@@ -319,7 +370,7 @@ int main(int argc, char *argv[]) {
 
 	  mt->setFrameMode(ePedestal);
 
-	  ifstream pedefile(fname, ios::in | ios::binary);
+	  std::ifstream pedefile(fname, ios::in | ios::binary);
 	  //      //open file
 	  if (pedefile.is_open()) {
 	    std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
@@ -380,26 +431,27 @@ int main(int argc, char *argv[]) {
     }
 
     ifr = 0;
-    int ifile = 0;
+    int ioutfile = 0;
 
     mt->setFrameMode(eFrame);
 
     FILE *of = NULL;
     
-    for (int irun = runmin; irun <= runmax; irun++) {
+    for (int irun = runmin; irun <= runmax; ++irun) {
+      for (int ifile = fmin; ifile <= fmax; ++ifile) {
         std::cout << "DATA ";
 	std::string fsuffix{};
-	auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
-	auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
-	auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
+	auto fname = createFileName( indir, fprefix, fsuffix, fext, irun, 0, ifile );
+	auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, ifile );
+	auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun, 0, ifile );
         std::cout << fname << " ";
         std::cout << imgfname << std::endl;
         std::time(&end_time);
         std::cout << std::ctime(&end_time) << std::endl;
         //  std::cout <<  fname << " " << outfname << " " << imgfname <<  std::endl;
-        ifstream filebin(fname, ios::in | ios::binary);
+	std::ifstream filebin(fname, ios::in | ios::binary);
         //      //open file
-        ifile = 0;
+        ioutfile = 0;
         if (filebin.is_open()) {
             if (thr <= 0 && cf != 0) { // cluster finder
                 if (of == NULL) {
@@ -436,10 +488,10 @@ int main(int argc, char *argv[]) {
                     std::cout << " " << ifr << " " << ff << std::endl;
                 if (nframes > 0) {
                     if (ifr % nframes == 0) {
-		      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
+		      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
 		      mt->writeImage(imgfname.c_str(), thr1);
                         mt->clearImage();
-                        ifile++;
+                        ioutfile++;
                     }
                 }
                 // } else
@@ -453,7 +505,7 @@ int main(int argc, char *argv[]) {
             }
             if (nframes >= 0) {
                 if (nframes > 0)
-		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
+		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
                 std::cout << "Writing tiff to " << imgfname << " " << thr1
                           << std::endl;
                 mt->writeImage(imgfname.c_str(), thr1);
@@ -469,9 +521,10 @@ int main(int argc, char *argv[]) {
         } else
             std::cout << "Could not open " << fname << " for reading "
                       << std::endl;
+      }
     }
     if (nframes < 0) {
-      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -1 );
+      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", runmin, 0, fmin, -1 );
         std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
         mt->writeImage(imgfname.c_str(), thr1);
     }

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp

@@ -10,8 +10,8 @@
 
 #define RAWDATA
 
-#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6
+#if !defined JFSTRX && !defined JFSTRXQ && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
+    !defined JFSTRXCHIP6 && !defined CHIP
 #ifndef MODULE
 #include "jungfrauHighZSingleChipData.h"
 #endif
@@ -20,9 +20,16 @@
 #endif
 #endif
 
+#ifdef CHIP
+#include "jungfrauSingleChipData.h"
+#endif
+
 #ifdef JFSTRX
 #include "jungfrauLGADStrixelsData_new.h"
 #endif
+#ifdef JFSTRXQ
+#include "jungfrauLGADStrixelsDataQuad.h"
+#endif
 #if defined JFSTRXCHIP1 || defined JFSTRXCHIP6
 #include "jungfrauLGADStrixelsDataSingleChip.h"
 #endif
@@ -41,6 +48,9 @@
 #include <ctime>
 #include <fmt/core.h>
 
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
 
 std::string getRootString( const std::string& filepath ) {
   size_t pos1;
@@ -71,11 +81,11 @@ std::string createFileName( const std::string& dir, const std::string& fprefix="
 //NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
 int main(int argc, char *argv[]) {
 
-    if (argc < 10) {
+    if (argc < 11) {
         std::cout
             << "Usage is " << argv[0]
-            << " filestxt outdir [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
-               "[threshold] [nframes] "
+            << " filestxt outdir [json master] [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
+               "[threshold] [nframes] [optional: bool read rxroi from data file header]"
 	       "NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
             << std::endl;
         std::cout
@@ -105,19 +115,19 @@ int main(int argc, char *argv[]) {
 
     const std::string txtfilename(argv[1]);
     const std::string outdir(argv[2]);
-    const std::string pedfilename(argv[3]);
-
-    int xmin = atoi(argv[4]);
-    int xmax = atoi(argv[5]);
-    int ymin = atoi(argv[6]);
-    int ymax = atoi(argv[7]);
+    const std::string jsonmastername(argv[3]);
+    const std::string pedfilename(argv[4]);
 
     double thr = 0;
     double thr1 = 1;
-    thr = atof(argv[8]);
+    thr = atof(argv[9]);
 
     int nframes = 0;
-    nframes = atoi(argv[9]);
+    nframes = atoi(argv[10]);
+
+    bool readrxroifromdatafile = false;
+    if (argc > 11)
+      readrxroifromdatafile = atoi(argv[11]);
 
     //Get vector of filenames from input txt-file
     std::vector<std::string> filenames{};
@@ -146,10 +156,34 @@ int main(int argc, char *argv[]) {
     }
 
     std::cout << "###############" << std::endl;
-    
+
+    // Receiver ROI
+    uint16_t rxroi_xmin = 0;
+    uint16_t rxroi_xmax = 0;
+    uint16_t rxroi_ymin = 0;
+    uint16_t rxroi_ymax = 0;
+
+    { //protective scope so ifstream gets destroyed properly
+
+      std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
+      if (masterfile.is_open()) {
+	json j;
+	masterfile >> j;
+	rxroi_xmin = j["Receiver Roi"]["xmin"];
+	rxroi_xmax = j["Receiver Roi"]["xmax"];
+	rxroi_ymin = j["Receiver Roi"]["ymin"];
+	rxroi_ymax = j["Receiver Roi"]["ymax"];
+	masterfile.close();
+	std::cout << "Read rxROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
+		      << rxroi_ymin << ", " << rxroi_ymax << "]" << std::endl;
+      } else 
+	std::cout << "Could not open master file " << jsonmastername << std::endl;
+      
+    }
+
     // Define decoders...
-#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6
+#if !defined JFSTRX && !defined JFSTRXQ && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
+    !defined JFSTRXCHIP6 && !defined CHIP
 #ifndef MODULE
     jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
     int nx = 256, ny = 256;
@@ -160,52 +194,60 @@ int main(int argc, char *argv[]) {
 #endif
 #endif
 
+#ifdef CHIP
+    std::cout << "Jungfrau pixel module single chip readout" << std::endl;
+    jungfrauSingleChipData *decoder = new jungfrauSingleChipData();
+    int nx = 256, ny = 256;
+#endif
+
 #ifdef JFSTRX
-    cout << "Jungfrau strixel full module readout" << endl;
-    // ROI
-    uint16_t xxmin = 0;
-    uint16_t xxmax = 0;
-    uint16_t yymin = 0;
-    uint16_t yymax = 0;
+    std::cout << "Jungfrau strixel full module readout" << std::endl;
 
 #ifndef ALDO
-    { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
-      using header = sls::defs::sls_receiver_header;
-      // check if there is a roi in the header
-      typedef struct {
-        uint16_t xmin;
-        uint16_t xmax;
-        uint16_t ymin;
-        uint16_t ymax;
-      } receiverRoi_compact;
-      receiverRoi_compact croi;
-      //std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
-      std::cout << "Reading header of file " << filenames[0] << " to check for ROI "
-		<< std::endl;
-      ifstream firstfile(filenames[0], ios::in | ios::binary);
-      if (firstfile.is_open()) {
-        header hbuffer;
-        std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
-        if (firstfile.read((char *)&hbuffer, sizeof(header))) {
-	  memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
-	  std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
-		    << croi.ymin << ", " << croi.ymax << "]" << std::endl;
-	  xxmin = croi.xmin;
-	  xxmax = croi.xmax;
-	  yymin = croi.ymin;
-	  yymax = croi.ymax;
-        } else
-	  std::cout << "reading error" << std::endl;
-        firstfile.close();
-      } else
-        std::cout << "Could not open " << filenames[0] << " for reading " << std::endl;
-    } //end of protective scope
+    if (readrxroifromdatafile)
+      { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
+	using header = sls::defs::sls_receiver_header;
+	// check if there is a roi in the header
+	typedef struct {
+	  uint16_t xmin;
+	  uint16_t xmax;
+	  uint16_t ymin;
+	  uint16_t ymax;
+	} receiverRoi_compact;
+	receiverRoi_compact croi;
+	//std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
+	std::cout << "Reading header of file " << filenames[0] << " to check for ROI "
+		  << std::endl;
+	std::ifstream firstfile( filenames[0], ios::in | ios::binary);
+	if (firstfile.is_open()) {
+	  header hbuffer;
+	  std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
+	  if (firstfile.read((char *)&hbuffer, sizeof(header))) {
+	    memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
+	    std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
+		      << croi.ymin << ", " << croi.ymax << "]" << std::endl;
+	    rxroi_xmin = croi.xmin;
+	    rxroi_xmax = croi.xmax;
+	    rxroi_ymin = croi.ymin;
+	    rxroi_ymax = croi.ymax;
+	  } else
+	    std::cout << "reading error" << std::endl;
+	  firstfile.close();
+	} else
+	  std::cout << "Could not open " << filenames[0] << " for reading " << std::endl;
+      } //end of protective scope
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
+        new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024 / 3, ny = 512 * 5;
 #endif
+#ifdef JFSTRXQ
+    std::cout << "Jungfrau strixel quad" << std::endl;
+    jungfrauLGADStrixelsDataQuad *decoder =
+        new jungfrauLGADStrixelsDataQuad(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
+    int nx = 1024 / 3, ny = 512 * 3;
+#endif
 #ifdef JFSTRXCHIP1
     std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
     jungfrauLGADStrixelsDataSingleChip *decoder =
@@ -228,7 +270,16 @@ int main(int argc, char *argv[]) {
     decoder->getDetectorSize(nx, ny);
     std::cout << "Detector size is " << nx << " " << ny << std::endl;
 
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    xmin = atoi(argv[5]);
+    xmax = atoi(argv[6]);
+    ymin = atoi(argv[7]);
+    ymax = atoi(argv[8]);
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+              << std::endl;
 
+    /* old
     if ( xmin == xmax ) {
       xmin = 0;
       xmax = nx;
@@ -239,6 +290,7 @@ int main(int argc, char *argv[]) {
     }
     std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
               << std::endl;
+    */
 
     /*
     char *gainfname = NULL;
@@ -410,7 +462,7 @@ int main(int argc, char *argv[]) {
       std::time(&end_time);
       std::cout << std::ctime(&end_time) << std::endl;
 
-      ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
       //      //open file
       ioutfile = 0;
       if (filebin.is_open()) {

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp

@@ -0,0 +1,457 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+// #include "sls/ansi.h"
+//#include <iostream>
+#undef CORR
+
+#define C_GHOST 0.0004
+
+#define CM_ROWS 50
+
+#define RAWDATA
+
+
+#include "jungfrauLGADStrixelsDataQuadH5.h"
+
+#include "multiThreadedCountingDetector.h"
+#include "singlePhotonDetector.h"
+
+#include <fstream>
+#include <map>
+#include <memory>
+#include <stdio.h>
+#include <sys/stat.h>
+
+#include <ctime>
+#include <fmt/core.h>
+
+/*
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+*/
+
+/*Dataset paths according to different beamlines*/
+std::string const data_datasetname_furka("/data/JF18T01V01/data");
+std::string const index_datasetname_furka("/data/JF18T01V01/frame_index");
+std::string const data_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/adc");
+std::string const index_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/frameNumber");
+
+std::string getRootString( std::string const& filepath ) {
+  size_t pos1;
+  if (filepath.find("/") == std::string::npos )
+    pos1 = 0;
+  else
+    pos1 = filepath.find_last_of("/")+1;
+  size_t pos2 = filepath.find_last_of(".");
+  //std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
+  return filepath.substr( pos1, pos2-pos1 );
+}
+
+//Create file name string
+//   dir:     directory
+//   fprefix:   fileprefix (without extension)
+//   fsuffix:   filesuffix (for output files, e.g. "ped")
+//   fext:    file extension (e.g. "raw")
+std::string createFileName( std::string const& dir, std::string const& fprefix="run",
+			    std::string const& fsuffix="", std::string const& fext="raw", int const outfilecounter=-1 ) {
+  std::string return_string;
+  if (outfilecounter >= 0)
+    return_string = fmt::format("{:s}/{:s}_{:s}_f{:05d}", dir, fprefix, fsuffix, outfilecounter);
+  else if (fsuffix.length()!=0)
+    return_string = fmt::format("{:s}/{:s}_{:s}", dir, fprefix, fsuffix);
+  else
+    return_string = fmt::format("{:s}/{:s}", dir, fprefix);
+
+  if (fext.length()!=0)
+    return_string += "." + fext;
+
+  return return_string;
+}
+
+
+//NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
+int main(int argc, char *argv[]) {
+
+    if (argc < 4) {
+        std::cout
+            << "Usage is " << argv[0]
+            << " filestxt outdir [pedfile (h5)] "
+               " optional: [int dataset path; 0 means Furka, 1 means XFEL; overwrites default given in HDF5File.h] "
+               " [bool validate h5 rank] "
+               " [xmin xmax ymin ymax] [threshold] [nframes] "
+	             " NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
+            << std::endl;
+        std::cout
+            << "threshold <0 means analog; threshold=0 means cluster finder; "
+               "threshold>0 means photon counting"
+            << std::endl;
+        std::cout
+            << "nframes <0 means sum everything; nframes=0 means one file per "
+               "run; nframes>0 means one file every nframes"
+            << std::endl;
+        return 1;
+    }
+
+    int const fifosize = 100; //1000;
+    int const nthreads = 10;
+    int const csize = 3; // 3
+    int const nsigma = 5;
+    int const nped = 10000;
+
+    int cf = 0;
+
+    std::string const txtfilename(argv[1]);
+    std::string const outdir(argv[2]);
+    std::string const pedfilename(argv[3]);
+
+    std::string datasetpath{};
+    std::string frameindexpath{};
+    if (argc > 4) {
+      switch (atoi(argv[4])) {
+      case 0:
+        datasetpath = data_datasetname_furka;
+        frameindexpath = index_datasetname_furka;
+        break;
+      case 1:
+        datasetpath = data_datasetname_xfelSCS;
+        frameindexpath = index_datasetname_xfelSCS;
+        break;
+      default:
+        break;
+      }
+    }
+
+    bool validate_rank=true;
+    if (argc > 5)
+      validate_rank = atoi(argv[5]);
+
+    double thr = 0;
+    double thr1 = 1;
+    if (argc > 9)
+      thr = atof(argv[9]);
+
+    int nframes = 0;
+    if (argc > 10)
+      nframes = atoi(argv[10]);
+
+    //Get vector of filenames from input txt-file
+    std::vector<std::string> filenames{};
+    //filenames.reserve(512);
+    { //Safety scope for ifstream
+      ifstream inputs( txtfilename, std::ios::in );
+      if (inputs.is_open()) {
+	    std::cout << "Reading imput filenames from txt-file ..." << std::endl;
+	    std::string line{};
+	    while (!inputs.eof()) {
+	      std::getline(inputs, line);
+        if(line.find(".h5") != std::string::npos) {
+	        filenames.emplace_back(line);
+	        std::cout << line << std::endl; //" line.max_size() " << line.max_size() << " filenames.capacity() " << filenames.capacity() << '\n';
+        }
+	    }
+	    inputs.close();
+	    std::cout << "---- Reached end of txt-file. ----" << std::endl;
+      } else
+	      std::cout << "Could not open " << txtfilename << std::endl;
+      if (filenames.size()>0) {
+	      std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
+	      std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
+      } else {
+	      std::cout << "No files found in txt-file!" << std::endl;
+	      return 1;
+      }
+    }
+
+    std::cout << "###############" << std::endl;
+
+    // Define decoder
+    std::cout << "Jungfrau strixel quad h5" << std::endl;
+    jungfrauLGADStrixelsDataQuadH5* decoder = new jungfrauLGADStrixelsDataQuadH5();
+    //auto decoder = std::make_unique<jungfrauLGADStrixelsDataQuadH5>();
+    int nx = 1024 / 3, ny = 512 * 3;
+
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    if (argc > 9) {
+      xmin = atoi(argv[6]);
+      xmax = atoi(argv[7]);
+      ymin = atoi(argv[8]);
+      ymax = atoi(argv[9]);
+    }
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+              << std::endl;
+
+    decoder->getDetectorSize(nx, ny);
+    std::cout << "Detector size is " << nx << " " << ny << std::endl;
+
+    std::time_t end_time;
+
+    std::cout << "output directory is " << outdir << std::endl;
+    if (pedfilename.length()!=0)
+        std::cout << "pedestal file is " << pedfilename << std::endl;
+    if (thr > 0)
+        std::cout << "threshold is " << thr << std::endl;
+    std::cout << "Nframes is " << nframes << std::endl;
+
+    uint32_t nnx, nny;
+
+    singlePhotonDetector* filter =
+      new singlePhotonDetector(decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, NULL, NULL);
+    //auto filter = std::make_unique<singlePhotonDetector>(decoder.get(), 3, nsigma, 1, nullptr, nped, 200, -1, -1, nullptr, nullptr);
+
+    thr = 0.15 * thr;
+    //filter->newDataSet(); //This only initializes the dataset for the first thread (the other threads are created via cloning)
+    // int dsize = decoder->getDataSize();
+
+    if (thr > 0) {
+        std::cout << "threshold is " << thr << std::endl;
+        filter->setThreshold(thr);
+        cf = 0;
+
+    } else
+        cf = 1;
+
+    filter->setROI(xmin, xmax, ymin, ymax);
+    std::time(&end_time);
+    std::cout << std::ctime(&end_time) << std::endl;
+
+    char* buff;
+
+    multiThreadedCountingDetector* mt =
+        new multiThreadedCountingDetector(filter, nthreads, fifosize);
+    //auto mt = std::make_unique<multiThreadedCountingDetector>(filter.get(), nthreads, fifosize);
+    mt->setClusterSize(csize, csize);
+    mt->newDataSet(); //Initialize new dataset for each thread
+
+#ifndef ANALOG
+    mt->setDetectorMode(ePhotonCounting);
+    std::cout << "Counting!" << std::endl;
+    if (thr > 0) {
+        cf = 0;
+    }
+#endif
+//{
+#ifdef ANALOG
+    mt->setDetectorMode(eAnalog);
+    std::cout << "Analog!" << std::endl;
+    cf = 0;
+    // thr1=thr;
+#endif
+    //  }
+
+    mt->StartThreads();
+    mt->popFree(buff);
+
+    int ifr = 0; //frame counter of while loop
+    int framenumber = 0; //framenumber as read from file (detector)
+    std::vector<hsize_t> h5offset(1,0); //frame counter internal to HDF5File::ReadImage (provided for sanity check/debugging)
+
+    if (pedfilename.length()>1) {
+
+      std::cout << "PEDESTAL " << std::endl;
+
+      if (pedfilename.find(".tif") == std::string::npos) { //not a tiff file
+	      std::string const fname(pedfilename);
+	      std::cout << fname << std::endl;
+	      std::time(&end_time);
+	      std::cout << "aaa " << std::ctime(&end_time) << std::endl;
+
+	      mt->setFrameMode(ePedestal);
+
+	      //HDF5File pedefile;
+	      auto pedefile = std::make_unique<HDF5File>();
+        pedefile->SetFrameIndexPath(frameindexpath);
+        pedefile->SetImageDataPath(datasetpath);
+	      //      //open file
+	      if ( pedefile->OpenResources(fname.c_str(),validate_rank) ) {
+	        std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
+	    
+	        framenumber = 0;
+
+	        while ( decoder->readNextFrame(*pedefile, framenumber, h5offset, buff) ) {
+
+	          if ((ifr + 1) % 100 == 0) {
+	            std::cout
+		            << " ****"
+		            << decoder->getValue(buff, 20, 20); // << std::endl;
+	          }
+	          mt->pushData(buff);
+	          mt->nextThread();
+	          mt->popFree(buff);
+	          ++ifr;
+	          if (ifr % 100 == 0) {
+	            std::cout << " ****" << ifr << " " << framenumber << " " << h5offset[0]
+			                  << std::endl;
+	          } // else
+	      
+	          if (ifr >= 1000)
+	            break;
+	          //framenumber = 0;
+	        }
+	    
+	        pedefile->CloseResources();
+	        while (mt->isBusy()) {
+	          ;
+	        }
+
+	        std::cout << "Writing pedestal to " << getRootString(pedfilename) << "_ped.tiff" << std::endl;
+	        auto imgfname = createFileName( outdir, getRootString(pedfilename), "ped", "");
+	        mt->writePedestal(imgfname.c_str());
+          std::cout << "Writing pedestal rms to " << getRootString(pedfilename) << "_rms.tiff" << std::endl;
+	        imgfname = createFileName( outdir, getRootString(pedfilename), "rms", "");
+	        mt->writePedestalRMS(imgfname.c_str());
+
+	      } else
+	        std::cout << "Could not open pedestal file " << fname
+		                << " for reading " << std::endl;
+
+      } else { //is a tiff file
+
+	      std::vector<double> ped(nx * ny);
+	      float* pp = ReadFromTiff(pedfilename.c_str(), nny, nnx);
+	      if (pp && (int)nnx == nx && (int)nny == ny) {
+	        for (int i = 0; i < nx * ny; i++) {
+	          ped[i] = pp[i];
+	        }
+	        delete[] pp;
+	        mt->setPedestal(ped.data());
+	        std::cout << "Pedestal set from tiff file " << pedfilename
+		                << std::endl;
+	      } else {
+	        std::cout << "Could not open pedestal tiff file " << pedfilename
+		                << " for reading " << std::endl;
+	      }
+      }
+      std::time(&end_time);
+      std::cout << std::ctime(&end_time) << std::endl;
+    }
+    
+    ifr = 0;
+    int ioutfile = 0;
+
+    mt->setFrameMode(eFrame);
+
+    FILE* of = nullptr;
+    
+    //NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
+    for (unsigned int ifile = 0; ifile != filenames.size(); ++ifile) {
+      std::cout << "DATA " << filenames[ifile] << " " << std::endl;
+      auto imgfname( createFileName( outdir, getRootString(filenames[ifile]), "", "" ) );
+      std::string const cfname( createFileName( outdir, getRootString(filenames[ifile]), "", "clust" ) );
+      
+      std::time(&end_time);
+      std::cout << std::ctime(&end_time) << std::endl;
+
+      //HDF5File fileh5;
+      auto fileh5 = std::make_unique<HDF5File>();
+      fileh5->SetFrameIndexPath(frameindexpath);
+      fileh5->SetImageDataPath(datasetpath);
+      //      //open file
+      ioutfile = 0;
+      if ( fileh5->OpenResources(filenames[ifile].c_str(), validate_rank) ) {
+	      if (thr <= 0 && cf != 0) { // cluster finder
+	        if (of == nullptr) {
+	          of = fopen(cfname.c_str(), "w");
+	          if (of) {
+	            if (mt) {
+		            mt->setFilePointer(of);
+		            std::cout << "file pointer set " << std::endl;
+	            } else {
+		            std::cerr << "Error: mt is null." << std::endl;
+		            return 1;
+	            }
+	            //mt->setFilePointer(of);
+	            //std::cout << "file pointer set " << std::endl;
+	            //std::cout << "Here! " << framenumber << " ";
+	          } else {
+	            std::cout << "Could not open " << cfname
+			                  << " for writing " << std::endl;
+	            mt->setFilePointer(nullptr);
+	            return 1;
+	          }
+	        }
+	      }
+	
+	//     //while read frame
+	      framenumber = 0;
+	      h5offset[0] = 0;
+	      ifr = 0;
+	      //std::cout << "Here! " << framenumber << " ";
+	      while ( decoder->readNextFrame(*fileh5, framenumber, h5offset, buff) ) {
+	        //std::cout << "Here! " << framenumber << " ";
+	        //         //push
+	        if ((ifr + 1) % 1000 == 0) {
+	          std::cout << " ****"
+		                  << decoder->getValue(buff, 20, 20); // << std::endl;
+	        }
+	        mt->pushData(buff);
+
+	        // 	//         //pop
+	        mt->nextThread();
+	        mt->popFree(buff); /* In the last execution of the loop,
+                              * this leaves buff outside of the Fifo!
+                              * Free explicitely at the end! */
+	  
+	        ++ifr;
+	        if (ifr % 1000 == 0)
+	          std::cout << " " << ifr << " " << framenumber << " " << h5offset[0]
+                      << std::endl;
+	        if (nframes > 0) {
+	          if (ifr % nframes == 0) {
+	            imgfname = createFileName( outdir, getRootString(filenames[ifile]), "", "", ioutfile );
+	            mt->writeImage(imgfname.c_str(), thr1);
+	            mt->clearImage();
+	            ++ioutfile;
+	          }
+	        }
+
+	        //framenumber = 0;
+	      }
+
+	      //std::cout << "aa --" << std::endl;
+	      fileh5->CloseResources();
+
+	      //std::cout << "bb --" << std::endl;
+	      while (mt->isBusy()) {
+	        ;
+	      }
+
+	      //std::cout << "cc --" << std::endl;
+	      if (nframes >= 0) {
+	        if (nframes > 0)
+	          imgfname = createFileName( outdir, getRootString(filenames[ifile]), "", "", ioutfile );
+	        std::cout << "Writing tiff to " << imgfname << " " << thr1 << ".tiff"
+		                << std::endl;
+	        mt->writeImage(imgfname.c_str(), thr1);
+	        mt->clearImage();
+	        if (of) {
+	          fclose(of);
+	          of = nullptr;
+	          mt->setFilePointer(nullptr);
+	        }
+	      }
+	      std::time(&end_time);
+	      std::cout << std::ctime(&end_time) << std::endl;
+      } else
+	      std::cout << "Could not open " << filenames[ifile] << " for reading "
+		              << std::endl;
+    }
+    if (nframes < 0) {     
+      //std::string fprefix( getRootString(filenames[0]) ); //Possibly, non-ideal name choice for file
+      auto imgfname( createFileName( outdir, getRootString(filenames[0]), "sum", "" ) );
+      std::cout << "Writing tiff to " << imgfname << " " << thr1 << ".tiff" << std::endl;
+      mt->writeImage(imgfname.c_str(), thr1);
+    }
+
+
+    //std::cout << "Calling delete..." << std::endl;
+    /* Info: Previously, 'delete mt' caused crash
+     (double calls of StopThread() in both destructors of
+     multiThreadedAnalogDetector and threadedAnalogDetector)
+     Now fixed! */
+    delete mt; // triggers cleanup of all threads and singlePhotonDetector instances (delete filter is obsolete)
+    delete decoder;
+    free(buff); // Free explicitly as it gets popped out of the Fifo at termination of while(readNextFrame)
+
+    return 0;
+}

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5_SC.cpp

@@ -0,0 +1,468 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+// #include "sls/ansi.h"
+//#include <iostream>
+#undef CORR
+
+#define RAWDATA
+
+
+#include "jungfrauLGADStrixelsDataQuadH5.h"
+
+#include "multiThreadedCountingDetector.h"
+#include "singlePhotonDetector.h"
+
+#include <fstream>
+#include <csignal>
+#include <map>
+#include <memory>
+#include <stdio.h>
+#include <sys/stat.h>
+
+#include <ctime>
+#include <fmt/core.h>
+
+
+/*Dataset paths according to different beamlines*/
+std::string const data_datasetname_furka("/data/JF18T01V01/data");
+std::string const index_datasetname_furka("/data/JF18T01V01/frame_index");
+std::string const data_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/adc");
+std::string const index_datasetname_xfelSCS("/INSTRUMENT/SCS_HRIXS_JUNGF/DET/JNGFR01:daqOutput/data/frameNumber");
+
+std::string getRootString( std::string const& filepath ) {
+  size_t pos1;
+  if (filepath.find("/") == std::string::npos )
+    pos1 = 0;
+  else
+    pos1 = filepath.find_last_of("/")+1;
+  size_t pos2 = filepath.find_last_of(".");
+  //std::cout << "pos1 " << pos1 << " pos2 " << pos2 << " size " << filepath.length() << std::endl;
+  return filepath.substr( pos1, pos2-pos1 );
+}
+
+/* Create file name string
+ * \param dir directory
+ * \param fprefix fileprefix (without extension)
+ * \param fsuffix filesuffix (for output files, e.g. "ped")
+ * \param fext    file extension (e.g. "raw")
+ */
+std::string createFileName( std::string const& dir, std::string const& fprefix="run",
+			                std::string const& fsuffix="", std::string const& fext="raw", int const outfilecounter=-1 ) {
+    std::string return_string;
+    if (outfilecounter >= 0)
+        return_string = fmt::format("{:s}/{:s}_{:s}_f{:05d}", dir, fprefix, fsuffix, outfilecounter);
+    else if (fsuffix.length()!=0)
+        return_string = fmt::format("{:s}/{:s}_{:s}", dir, fprefix, fsuffix);
+    else
+        return_string = fmt::format("{:s}/{:s}", dir, fprefix);
+
+    if (fext.length()!=0)
+        return_string += "." + fext;
+
+    return return_string;
+}
+
+/* Adjusts number of threads to be a multiple of number of storage cells
+ * \param requestedThreads number of threads requested by the user
+ * \param nSC number of storage cells
+ */
+int adjustThreads(int requestedThreads, int nSC) {
+    if (nSC <= 0) {
+        std::cerr << "Error: Number of S values must be greater than zero!" << std::endl;
+        return requestedThreads; // Return the original value as a fallback
+    }
+
+    // Calculate the remainder
+    int remainder = requestedThreads % nSC;
+
+    // If remainder is non-zero, round up by adding the difference
+    int adjustedThreads = (remainder == 0) ? requestedThreads : requestedThreads + (nSC - remainder);
+
+    // Ensure at least `nSC` threads are used
+    if (adjustedThreads < nSC) {
+        adjustedThreads = nSC;
+    }
+
+    std::cout << "Adjusted thread count (rounded up): " << adjustedThreads << " (nearest multiple of " 
+              << nSC << ")" << std::endl;
+
+    return adjustedThreads;
+}
+
+// Signal handler for segmentation faults
+void signal_handler(int signum) {
+    std::cerr << "Caught signal " << signum << ": Segmentation fault (core dump)" << std::endl;
+    // Handle the error (e.g., clean up, abort, etc.)
+    exit(signum);  // Exit program with the signal code
+}
+
+
+int main(int argc, char *argv[]) {
+
+    if (argc < 4) {
+        std::cout
+            << "Usage is " << argv[0]
+            << " filestxt outdir [pedfile (h5)] "
+               " optional: [int dataset path; 0 means Furka, 1 means XFEL; overwrites default given in HDF5File.h] "
+               " [bool validate h5 rank] "
+               " [xmin xmax ymin ymax] [nframes] "
+	             " NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
+            << std::endl;
+        return 1;
+    }
+
+    // Set up the signal handler for segmentation faults
+    signal(SIGSEGV, signal_handler);
+
+    int const fifosize = 100; //1000;
+    int const nthreads = 10;
+    int const csize = 3; // 3
+    int const nsigma = 5;
+    int const nped = 10000;
+
+    //int cf = 0;
+
+    std::string const txtfilename(argv[1]);
+    std::string const outdir(argv[2]);
+    std::string const pedfilename(argv[3]);
+
+    std::string datasetpath{};
+    std::string frameindexpath{};
+    if (argc > 4) {
+      switch (atoi(argv[4])) {
+      case 0:
+        datasetpath = data_datasetname_furka;
+        frameindexpath = index_datasetname_furka;
+        break;
+      case 1:
+        datasetpath = data_datasetname_xfelSCS;
+        frameindexpath = index_datasetname_xfelSCS;
+        break;
+      default:
+        break;
+      }
+    }
+
+    bool validate_rank=true;
+    if (argc > 5)
+      validate_rank = atoi(argv[5]);
+
+    //Get vector of filenames from input txt-file
+    std::vector<std::string> filenames{};
+
+    { //Safety scope for ifstream
+      ifstream inputs( txtfilename, std::ios::in );
+      if (inputs.is_open()) {
+	    std::cout << "Reading imput filenames from txt-file ..." << std::endl;
+	    std::string line{};
+	    while (!inputs.eof()) {
+	      std::getline(inputs, line);
+            if(line.find(".h5") != std::string::npos) {
+	            filenames.emplace_back(line);
+	            std::cout << line << std::endl;
+            }
+	    }
+	    inputs.close();
+	    std::cout << "---- Reached end of txt-file. ----" << std::endl;
+      } else
+	      std::cout << "Could not open " << txtfilename << std::endl;
+      if (filenames.size()>0) {
+	      std::cout << filenames.size() << " filenames found in " << txtfilename << std::endl;
+	      std::cout << "The files will be processed in the same order as found in the txt-file." << std::endl;
+      } else {
+	      std::cout << "No files found in txt-file!" << std::endl;
+	      return 1;
+      }
+    }
+
+    std::cout << "###############" << std::endl;
+
+    // Define decoder
+    std::cout << "Jungfrau strixel quad h5" << std::endl;
+    jungfrauLGADStrixelsDataQuadH5* decoder = new jungfrauLGADStrixelsDataQuadH5();
+    //auto decoder = std::make_unique<jungfrauLGADStrixelsDataQuadH5>();
+    int nx = 1024 / 3, ny = 512 * 3;
+
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    if (argc > 9) {
+      xmin = atoi(argv[6]);
+      xmax = atoi(argv[7]);
+      ymin = atoi(argv[8]);
+      ymax = atoi(argv[9]);
+    }
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+              << std::endl;
+
+    decoder->getDetectorSize(nx, ny);
+    std::cout << "Detector size is " << nx << " " << ny << std::endl;
+
+    std::time_t end_time;
+
+    std::cout << "Output directory is " << outdir << std::endl;
+    if (pedfilename.length()!=0)
+        std::cout << "Pedestal file is " << pedfilename << std::endl;
+
+    //uint32_t nnx, nny;
+
+    singlePhotonDetector* filter =
+      new singlePhotonDetector(decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, NULL, NULL);
+    //auto filter = std::make_unique<singlePhotonDetector>(decoder.get(), 3, nsigma, 1, nullptr, nped, 200, -1, -1, nullptr, nullptr);
+
+    filter->setROI(xmin, xmax, ymin, ymax);
+
+    std::time(&end_time);
+    std::cout << std::ctime(&end_time) << std::endl;
+
+    // Validate number of threads for number of storage cells (if applicable)
+    int nThreads = nthreads;
+    int nSC = 1;
+    // Determine the dimensions of the dataset from the first datafile
+    auto firstfileh5 = std::make_unique<HDF5File>();
+    firstfileh5->SetFrameIndexPath(frameindexpath);
+    firstfileh5->SetImageDataPath(datasetpath);
+    //std::cout << "Debug: Attempting to open file " << filenames[0].c_str() << std::endl;
+    if ( firstfileh5->OpenResources(filenames[0].c_str(), validate_rank) ) {
+
+        // Validate number of threads
+        if( firstfileh5->GetRank() == 4 ) {
+            auto h5dims = firstfileh5->GetDatasetDimensions();
+            nSC = h5dims[1];
+            nThreads = adjustThreads(nthreads,nSC);
+        }
+
+        firstfileh5->CloseResources();
+    } else {
+        std::cerr << "Error: Could not open data file " << filenames[0]
+		          << " for validating rank " << std::endl;
+    }
+
+    multiThreadedCountingDetector* mt =
+        new multiThreadedCountingDetector(filter, nThreads, fifosize, nSC);
+    //auto mt = std::make_unique<multiThreadedCountingDetector>(filter.get(), nthreads, fifosize);
+    mt->setClusterSize(csize, csize);
+    mt->newDataSet(); //Initialize new dataset for each thread
+    mt->setDetectorMode(ePhotonCounting);
+
+    char* buff;
+
+    mt->StartThreads();
+    mt->popFree(buff); // Get the first pointer to write image to
+
+    size_t ifr = 0; //frame counter of while loop
+    int framenumber = 0; //framenumber as read from file (detector)
+    std::vector<hsize_t> h5offset; //hyperslab offset internal to HDF5File::ReadImage
+    hsize_t h5rank;
+
+    if (pedfilename.length()>1) {
+
+        std::string froot = getRootString(pedfilename);
+
+        std::cout << "PEDESTAL " << pedfilename << std::endl;
+	    std::time(&end_time);
+	    std::cout << "aaa " << std::ctime(&end_time) << std::endl;
+
+	    mt->setFrameMode(ePedestal);
+
+	    //HDF5File pedefile;
+	    auto pedefile = std::make_unique<HDF5File>();
+        pedefile->SetFrameIndexPath(frameindexpath);
+        pedefile->SetImageDataPath(datasetpath);
+	    //      //open file
+	    if ( pedefile->OpenResources(pedfilename.c_str(),validate_rank) ) {
+
+            // Initialize offset vector to 0
+            h5rank = pedefile->GetRank();
+	        h5offset.resize(h5rank-2, 0);
+	        framenumber = 0;
+
+	        while ( decoder->readNextFrame(*pedefile, framenumber, h5offset, buff) ) {
+
+	            if ((ifr + 1) % 100 == 0) {
+	                std::cout
+		                << " ****"
+		                << decoder->getValue(buff, 20, 20); // << std::endl;
+	            }
+
+                int storageCell = 0;
+                hsize_t n_storageCells = 1;
+                if (h5rank == 4) {
+                    storageCell = h5offset[1];
+                    n_storageCells = pedefile->GetDatasetDimensions()[1];
+                }
+
+                // push buff into fifoData for a thread corresponding to the active storage cell
+	            mt->pushData(buff, storageCell);
+                // increment (round-robin) the internal thread counter for that storage cell
+	            mt->nextThread(storageCell);
+                // get a free memory address from fifoFree of the active storage cell for the next read operation
+	            mt->popFree(buff, storageCell);
+                /* NOTE: the buff that was popped free from the current thread, will be (likely) pushed into
+                 * the fifoData of a different thread in the next iteration of the loop! */
+
+	            ++ifr;
+	            if (ifr % 100 == 0) {
+	                std::cout << " ****" << ifr << " " << framenumber << " " << h5offset[0];
+                    if (n_storageCells>1)
+			            std::cout << " sc " << storageCell;
+                    std::cout << "\n";
+	            } // else
+	      
+	            if (ifr >= 1000*n_storageCells)
+	                break;
+	          //framenumber = 0;
+	        }
+	    
+	        pedefile->CloseResources();
+	        while (mt->isBusy()) {
+	          ;
+	        }
+
+	        std::cout << "Writing pedestal to " << getRootString(pedfilename) << "_ped_SCxx.tiff" << std::endl;
+	        auto imgfname = createFileName( outdir, getRootString(pedfilename), "ped", "" );
+	        mt->writePedestal(imgfname.c_str());
+            std::cout << "Writing pedestal rms to " << getRootString(pedfilename) << "_rms_SCxx.tiff" << std::endl;
+	        imgfname = createFileName( outdir, getRootString(pedfilename), "rms", "");
+	        mt->writePedestalRMS(imgfname.c_str());
+
+	      } else {
+	        std::cerr << "Error: Could not open pedestal file " << pedfilename
+		                << " for reading " << std::endl;
+          }
+
+      std::time(&end_time);
+      std::cout << std::ctime(&end_time) << std::endl;
+    }
+    
+    ifr = 0;
+    //int ioutfile = 0;
+
+    mt->setFrameMode(eFrame);
+
+    std::vector<FILE*> of(nSC, nullptr);
+    
+    for (unsigned int ifile = 0; ifile != filenames.size(); ++ifile) {
+        std::cout << "DATA " << filenames[ifile] << " " << std::endl;
+        std::time(&end_time);
+        std::cout << std::ctime(&end_time) << std::endl;
+
+        //HDF5File fileh5;
+        auto fileh5 = std::make_unique<HDF5File>();
+        fileh5->SetFrameIndexPath(frameindexpath);
+        fileh5->SetImageDataPath(datasetpath);
+
+        // Open HDF5 file
+        if ( fileh5->OpenResources(filenames[ifile].c_str(), validate_rank) ) {
+
+            std::vector<std::string> cfnames(nSC);
+            for ( int s = 0; s < nSC; ++s ) {
+                std::string fsuffix = "SC" + std::to_string(s);
+                cfnames[s] = createFileName( outdir, getRootString(filenames[ifile]), fsuffix, "clust" );
+            }
+	      
+            //Open output files and set file pointers according to storage cells
+            for ( size_t f = 0; f < of.size(); ++f ) {
+                if (!of[f]) {
+                    of[f] = fopen(cfnames[f].c_str(), "w");
+                    if (of[f])
+                    {
+                        if (mt) {
+		                    mt->setFilePointer(of[f],f); // assumes f == sc
+		                    std::cout << "File pointer set for storage cell " << f << std::endl;
+	                    } else {
+		                    std::cerr << "Error: mt is null." << std::endl;
+		                    return 1;
+	                    }
+                    } else {
+	                    std::cerr << "Error: could not open " << cfnames[f]
+			                      << " for writing " << std::endl;
+	                    mt->setFilePointer(nullptr,f);
+	                    return 1;
+                
+                    }
+                }
+            }
+	      
+	
+	        // Read frames
+	        framenumber = 0;
+	        std::fill(h5offset.begin(), h5offset.end(), 0);
+	        ifr = 0;
+	        
+	        while ( decoder->readNextFrame(*fileh5, framenumber, h5offset, buff) ) {
+	        
+	            if ((ifr + 1) % 1000 == 0) {
+	                std::cout << " ****"
+		                      << decoder->getValue(buff, 20, 20); // << std::endl;
+	            }
+
+                int storageCell = 0;
+                hsize_t n_storageCells = 1;
+                if (h5rank == 4) {
+                    storageCell = h5offset[1];
+                    n_storageCells = fileh5->GetDatasetDimensions()[1];
+                }
+
+	            // push buff into fifoData for a thread corresponding to the active storage cell
+	            mt->pushData(buff, storageCell);
+                // increment (round-robin) the internal thread counter for that storage cell
+	            mt->nextThread(storageCell);
+                // get a free memory address from fifoFree of the active storage cell for the next read operation
+	            mt->popFree(buff, storageCell); /* In the last execution of the loop,
+                                                * this leaves buff outside of the Fifo!
+                                                * Free explicitely at the end! */
+	  
+	            ++ifr;
+	            if (ifr % 1000 == 0) {
+	                std::cout << " " << ifr << " " << framenumber << " " << h5offset[0];
+                    if (n_storageCells>1) std::cout << " sc " << storageCell;
+                    std::cout << "\n";
+                }
+
+	            //framenumber = 0;
+	        }
+
+	        //std::cout << "aa --" << std::endl;
+	        fileh5->CloseResources();
+
+	        //std::cout << "bb --" << std::endl;
+	        while (mt->isBusy()) {
+	            ;
+	        }
+
+	        //std::cout << "cc --" << std::endl;
+	      
+	        auto imgfname = createFileName( outdir, getRootString(filenames[ifile]), "", "" );
+	        std::cout << "Writing tiff to " << imgfname << "_SCxx.tiff" << std::endl;
+	        mt->writeImage(imgfname.c_str());
+	        mt->clearImage();
+
+            // Close output files
+            for ( size_t f = 0; f < of.size(); ++f ) {
+	            if (of[f]) {
+	                fclose(of[f]);
+	                mt->setFilePointer(nullptr,f);
+                    of[f] = nullptr;
+	            }
+            }
+	      
+	        std::time(&end_time);
+	        std::cout << std::ctime(&end_time) << std::endl;
+        } else {
+	        std::cerr << "Error: Could not open " << filenames[ifile] << " for reading "
+		              << std::endl;
+        }
+    }
+    
+
+    //std::cout << "Calling delete..." << std::endl;
+    /* Info: Previously, 'delete mt' caused crash
+     (double calls of StopThread() in both destructors of
+     multiThreadedAnalogDetector and threadedAnalogDetector)
+     Now fixed! */
+    delete mt; // triggers cleanup of all threads and singlePhotonDetector instances (delete filter is obsolete)
+    delete decoder;
+    free(buff); // Free explicitly as it gets popped out of the Fifo at termination of while(readNextFrame)
+
+    return 0;
+}

slsDetectorCalibration/moenchExecutables/CMakeLists.txt

@@ -48,9 +48,8 @@ add_executable(moench03Interpolation moench03Interpolation.cpp)
 #no compile defs
 list(APPEND MOENCH_EXECUTABLES moench03Interpolation)
 
-add_executable(moench03NoInterpolation moench03Interpolation.cpp)
+add_executable(moench03NoInterpolation moench03NoInterpolation.cpp)
 #no compile defs
-target_compile_definitions(moench03NoInterpolation PRIVATE  NOINTERPOLATION)
 list(APPEND MOENCH_EXECUTABLES moench03NoInterpolation)
 
 
@@ -88,4 +87,4 @@ foreach(exe ${MOENCH_EXECUTABLES})
     
 endforeach(exe ${MOENCH_EXECUTABLES})
 
-install(TARGETS ${MOENCH_EXECUTABLES} DESTINATION bin)
+install(TARGETS ${MOENCH_EXECUTABLES} DESTINATION bin)

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -126,11 +126,11 @@ int main(int argc, char *argv[]) {
 
     int quad; 
 #ifndef FF
-    double int_x, int_y;
-    int *img;
 #ifndef NOINTERPOLATION
     char fname[10000];
     int ok;
+    double int_x, int_y;
+    int *img;
     cout << "read ff " << argv[2] << endl;
     sprintf(fname, "%s", argv[2]);
     interp->readFlatField(fname);

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -336,7 +336,7 @@ int main(int argc, char *argv[]) {
 
     string fname;
     //	int length;
-    int *detimage = NULL;
+    int *detimage = nullptr;
     int nnx, nny, nnsx, nnsy;
     // uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0,
     // uint32_t  dynamicRange = 0;

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -23,7 +23,9 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <unistd.h>
-//#include <mutex>
+#include <mutex>
+#include <algorithm>
+#include<unordered_map>
 
 using namespace std;
 
@@ -47,12 +49,20 @@ class threadedAnalogDetector {
 
             if (mm) {
                 // memset(mm,0, det->getDataSize());
+                /*
+                if (i == 0) { // debug
+                    first_mm = mm;
+                }
+                */
+                
                 fifoFree->push(mm);
+                //std::cout << "Allocated memory at: " << static_cast<void*>(mm) << " (fifoslot " << i << ")" << std::endl;
             } else
                 break;
         }
+
         if (i < fs)
-            cout << "Could allocate only " << i << " frames";
+            std::cout << "Could allocate only " << i << " frames";
 
         busy = 0;
         stop = 1;
@@ -102,24 +112,50 @@ class threadedAnalogDetector {
     };
 
     virtual ~threadedAnalogDetector() {
+
+        // std::cout << "#### Debug: Destructing threadedAnalogDetector! ####" << std::endl;
+
         StopThread();
-        delete fifoFree;
-        delete fifoData;
+
+        if (fifoFree) { delete fifoFree; fifoFree = nullptr; }
+        if (fifoData) { delete fifoData; fifoData = nullptr; }
+        if (det) { 
+            delete det; // Call destructor for singlePhotonDetector
+            det = nullptr; 
+        } 
     }
 
     /** Returns true if the thread was successfully started, false if there was
      * an error starting the thread */
     virtual bool StartThread() {
         stop = 0;
-        cout << "Detector number " << det->getId() << endl;
-        cout << "common mode is " << det->getCommonModeSubtraction() << endl;
-        cout << "ghos summation is " << det->getGhostSummation() << endl;
+        std::cout << "Detector number " << det->getId() << std::endl;
+        std::cout << "common mode is " << det->getCommonModeSubtraction() << std::endl;
+        std::cout << "ghos summation is " << det->getGhostSummation() << std::endl;
+
         return (pthread_create(&_thread, NULL, processData, this) == 0);
     }
 
     virtual void StopThread() {
         stop = 1;
-        (void)pthread_join(_thread, NULL);
+        //std::cout << "Attempting to stop thread..." << std::endl;
+
+        // Free all remaining allocated memory in fifoFree
+        char *mm = nullptr;
+        while (fifoFree->pop(mm, true)) {  // Use no_block to avoid waiting
+            //std::cout << "fifo Free: Freeing memory at: " << static_cast<void*>(mm) << std::endl;
+            free(mm);  // Free the allocated memory
+        }
+
+        if (_thread) {
+            //(void)pthread_join(_thread, NULL);
+            //std::cout << "Calling pthread_join for thread: " << det->getId() << std::endl;
+            pthread_join(_thread, NULL);
+            _thread = 0;
+            std::cout << "Thread " << det->getId() << " stopped and joined." << std::endl;
+        } else {
+            std::cout << "No thread to join." << std::endl;
+        }
     }
 
     virtual bool pushData(char *&ptr) { return fifoData->push(ptr); }
@@ -266,6 +302,8 @@ class threadedAnalogDetector {
     char *data;
     int *ff;
 
+    //char* first_mm = nullptr; // For debug; to track first allocated block
+
     static void *processData(void *ptr) {
         threadedAnalogDetector *This = ((threadedAnalogDetector *)ptr);
         return This->processData();
@@ -278,55 +316,118 @@ class threadedAnalogDetector {
                 usleep(100);
                 if (fifoData->isEmpty()) {
                     busy = 0;
-                } else
+                } else {
                     busy = 1;
-            } else
+                }
+            } else {
                 busy = 1;
+            }
 
             if (busy == 1) {
+                // Check stop flag before making a blocking call
+                //if (stop) {
+                //    break;
+                //}
+
+                // Blocking call
                 fifoData->pop(data); // blocking!
+
+                // Process data if not stopping
+                //if (!stop) {
                 det->processData(data);
                 fifoFree->push(data);
+                    
+                //}
                 // busy=0;
             }
         }
+
         return NULL;
     }
 };
 
 class multiThreadedAnalogDetector {
   public:
-    multiThreadedAnalogDetector(analogDetector<uint16_t> *d, int n,
-                                int fs = 1000)
-        : stop(0), nThreads(n), ithread(0) {
+    multiThreadedAnalogDetector(analogDetector<uint16_t> *d, int num_threads,
+                                int fs = 1000, int num_sc = 1)
+        : stop(0), nThreads(num_threads), nSC(num_sc) {
+
+        /*
         dd[0] = d;
         if (nThreads == 1)
             dd[0]->setId(100);
         else
             dd[0]->setId(0);
-        for (int i = 1; i < nThreads; i++) {
-            dd[i] = d->Clone();
-            dd[i]->setId(i);
+        */
+
+        // Create separate detectorObjects for each SC (each owns its mutex)
+        std::vector< analogDetector<uint16_t>* > sc_detectors(nSC, nullptr);
+        sc_detectors[0] = d; // First storage cell uses the given detector
+        // std::cout << "#### Debug: Copied analogDetector object for storage cell 0! ####" << std::endl;
+
+        for (int sc = 1; sc < nSC; ++sc) {
+            sc_detectors[sc] = d->Copy(); // Ensure unique mutex for each SC
+            // std::cout << "#### Debug: Copied analogDetector object for storage cell " << sc << "! ####" << std::endl;
         }
 
+        // Distribute threads among storage cells
+        int threads_per_sc = nThreads / nSC;
+        int remaining_threads = nThreads % nSC; // additional safety measure if nThreads is not divisible by nSC
+
+        sc_to_threads.clear();
+        for (int s = 0, thread_idx = 0; s < nSC; ++s) {
+            // Remaining threads (if any) are assigned to the first storage cells
+            int current_sc_threads = threads_per_sc + (s < remaining_threads ? 1 : 0);
+
+            for (int t = 0; t < current_sc_threads; ++t, ++thread_idx) {
+
+                if (t == 0) {
+                    dd[thread_idx] = sc_detectors[s]; // First thread gets main SC detector
+                } else {
+                    dd[thread_idx] = sc_detectors[s]->Clone(); // Other threads get clones
+                }
+
+                std::cout << "Assigned thread " << thread_idx << " to storage cell " << s << std::endl;
+
+                dd[thread_idx]->setId(thread_idx);
+                
+                // Store which threads belong to which SC
+                sc_to_threads[s].push_back(thread_idx);
+            }
+        }
+
+        if (nSC == 1 && nThreads == 1) {
+            dd[0]->setId(100);
+        }
+
+        // Initialize threadedAnalogDetector objects
         for (int i = 0; i < nThreads; i++) {
             cout << "**" << i << endl;
             dets[i] = new threadedAnalogDetector(dd[i], fs);
         }
 
-        image = NULL;
+        // Set all thread counters to zero for each storage cell
+        thread_counters_by_sc.resize(nSC,0);
+
+        image = nullptr;
         ff = NULL;
         ped = NULL;
-        cout << "Ithread is " << ithread << endl;
+        //std::cout << "Ithread is " << ithread << std::endl;
     }
 
     virtual ~multiThreadedAnalogDetector() {
-        StopThreads();
-        for (int i = 0; i < nThreads; i++)
-            delete dets[i];
-        /* for (int i=1; i<nThreads; i++)  */
-        /*   delete dd[i]; */
-        // delete [] image;
+        // std::cout << "#### Debug: Destructing multiThreadedAnalogDetector! ####" << std::endl;
+        //StopThreads(); // Superfluous, leads to double delete
+        
+        /* Reverse loop for destruction.
+         * Deletes clones first, then root object, which owns the mutex
+         * (ensure shared mutex is deleted last).
+         * Optional solution: reference counting (safer but more complex) */
+        for (int i = nThreads - 1; i >= 0; --i) {
+            delete dets[i]; //StopThread() called by each ~threadedAnalogDetector()
+            dets[i] = nullptr;
+        }
+        
     }
 
     virtual int setFrameMode(int fm) {
@@ -359,36 +460,52 @@ class multiThreadedAnalogDetector {
             dets[i]->newDataSet();
     };
 
-    virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy) {
-        int *img;
+    // Storage cell sensitive
+    virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy, int sc = 0) {
+        //int *img;
         // int nnx, nny, ns;
         // int nnx, nny, ns;
         int nn = dets[0]->getImageSize(nnx, nny, ns, nsy);
-        if (image) {
-            delete[] image;
-            image = NULL;
+
+        if (sc_images[sc]) {
+            delete[] sc_images[sc];
+            sc_images[sc] = nullptr;
         }
-        image = new int[nn];
+
+        // Allocate memory for image and zero-initialize
+        sc_images[sc] = new int[nn]();
         // int nn=dets[0]->getImageSize(nnx, nny, ns);
         // for (i=0; i<nn; i++) image[i]=0;
 
-        for (int ii = 0; ii < nThreads; ii++) {
-            // cout << ii << " " << nn << " " << nnx << " " << nny << " " << ns
-            // << endl;
-            img = dets[ii]->getImage();
+        // Get the threads assigned to this storage cell
+        auto const& assigned_threads = sc_to_threads[sc];
+
+        // Only iterate over threads assigned to this storage cell
+        for (int thread_id : assigned_threads) {
+            
+            int* tmp_img = dets[thread_id]->getImage();
+            if (!tmp_img) continue; // Skip if null
+
+            /* std::cout << "## Thread " << ii
+                      << " # image size " << nn
+                      << " # nnx " << nnx
+                      << " # nny " << nny
+                      << " # ns " << ns; */
+
+            // Sum images across threads
             for (int i = 0; i < nn; i++) {
-                if (ii == 0)
-                    //	  if (img[i]>0)
-                    image[i] = img[i];
-                // else
-                //  image[i]=0;
-                else // if (img[i]>0)
-                    image[i] += img[i];
+
+                /* std::cout << " # pixel " << i
+                          << " # value " << tmp_img[i]
+                          << " ## " << std::endl; */
+
+                
+                sc_images[sc][i] += tmp_img[i];
                 // if (img[i])	  cout << "det " << ii << " pix " << i << " val
                 // " <<  img[i] << " " << image[i] << endl;
             }
         }
-        return image;
+        return sc_images[sc];
     }
 
     virtual void clearImage() {
@@ -398,7 +515,7 @@ class multiThreadedAnalogDetector {
         }
     }
 
-    virtual void *writeImage(const char *imgname, double t = 1) {
+    virtual void *writeImage(char const* base_imgname, double t = 1) {
         /* #ifdef SAVE_ALL   */
         /*      for (int ii=0; ii<nThreads; ii++) { */
         /*        char tit[10000];cout << "m" <<endl; */
@@ -407,11 +524,30 @@ class multiThreadedAnalogDetector {
         /*      } */
         /* #endif */
         int nnx, nny, ns, nsy;
-        getImage(nnx, nny, ns, nsy);
-        // int nnx, nny, ns;
         int nn = dets[0]->getImageSize(nnx, nny, ns, nsy);
-        float *gm = new float[nn];
-        if (gm) {
+
+        // Allocate teporary float buffer and zero-initialize
+        std::vector<float> gm(nn);
+
+        // Lambda for pixel conversion
+        auto convert_pixel = [t](int pixel) -> float {
+            return (t > 0) ? static_cast<float>(std::max(0, pixel)) / static_cast<float>(t) : pixel;
+        }; // t ... threshold
+
+        // Loop over each storage cell
+        for (auto const& [sc, _] : sc_to_threads) { // structured bindings [sc, _] only available with -std=c++17
+            std::string imgname(base_imgname);
+            if (nSC > 1) imgname += "_SC" + std::to_string(sc);
+            imgname += ".tiff";
+
+            //Retrieve the image for this storage cell
+            int *image = getImage(nnx, nny, ns, nsy, sc);
+            if (!image) continue; // Skip if null
+
+            // Convert image data to float
+            std::transform(image, image + nn, gm.begin(), convert_pixel);
+
+            /* old loop implementing same logic as convert_pixel
             for (int ix = 0; ix < nn; ix++) {
                 if (t) {
                     if (image[ix] < 0)
@@ -424,11 +560,18 @@ class multiThreadedAnalogDetector {
                 // if (image[ix]>0 && ix/nnx<350) cout << ix/nnx << " " <<
                 // ix%nnx << " " << image[ix]<< " " << gm[ix] << endl;
             }
-            // cout << "image " << nnx << " " << nny << endl;
-            WriteToTiff(gm, imgname, nnx, nny);
-            delete[] gm;
-        } else
-            cout << "Could not allocate float image " << endl;
+            */
+
+            WriteToTiff(gm.data(), imgname.c_str(), nnx, nny);
+
+            // Clean up memory for this storage cell
+            if (sc_images[sc]) {
+                delete[] sc_images[sc];
+                sc_images[sc] = nullptr;
+            }
+            
+        }
+        
         return NULL;
     }
 
@@ -439,6 +582,7 @@ class multiThreadedAnalogDetector {
     }
 
     virtual void StopThreads() {
+        std::cout << "Stopping all threads ..." << std::endl;
         for (int i = 0; i < nThreads; i++)
             dets[i]->StopThread();
     }
@@ -453,76 +597,133 @@ class multiThreadedAnalogDetector {
         return ret;
     }
 
-    virtual bool pushData(char *&ptr) { return dets[ithread]->pushData(ptr); }
+/*
+    virtual std::vector<int> getThreadsForSc(int sc) {
+        return sc_to_threads[sc];
+    }
+*/
+    virtual bool pushData(char *&ptr, int sc=0) {
+        //Additional logic implemented to accommodate storage cells
 
-    virtual bool popFree(char *&ptr) {
-        //  cout << ithread << endl;
-        return dets[ithread]->popFree(ptr);
+        std::unique_lock<std::mutex> lock(map_mutex);
+
+        // Get assigned threads for this storage cell
+        auto& assigned_threads = sc_to_threads[sc];
+        auto& counter = thread_counters_by_sc[sc];
+        
+        // Distribute workload among threads using round-robin
+        int selected_thread = assigned_threads[counter % assigned_threads.size()];
+
+        return dets[selected_thread]->pushData(ptr); 
     }
 
-    virtual int nextThread() {
-        ithread++;
-        if (ithread == nThreads)
-            ithread = 0;
-        return ithread;
+    virtual bool popFree(char *&ptr, int sc=0) {
+        //Additional logic implemented to accommodate storage cells
+
+        std::unique_lock<std::mutex> lock(map_mutex);
+
+        // Get assigned threads for this storage cell
+        auto& assigned_threads = sc_to_threads[sc];
+        auto& counter = thread_counters_by_sc[sc];
+        
+        // Distribute workload among threads using round-robin
+        int selected_thread = assigned_threads[counter % assigned_threads.size()];
+
+        return dets[selected_thread]->popFree(ptr);
     }
 
-    virtual double *getPedestal() {
+    virtual int nextThread(int sc=0) {
+        //Additional logic implemented to accommodate storage cells
+
+        auto& counter = thread_counters_by_sc[sc];
+        //counter++;
+        if (++counter == nThreads/nSC)
+            counter = 0;
+        return counter;
+    }
+
+    // Storage cell sensitive
+    virtual double *getPedestal(int sc = 0) {
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
-        if (ped)
-            delete[] ped;
-        ped = new double[nx * ny];
+
+        if (sc_pedestals.count(sc) && sc_pedestals[sc]) {
+            delete[] sc_pedestals[sc];
+            sc_pedestals[sc] = nullptr;
+        }
+
+        // allocate memory and initialize all values to zero
+        sc_pedestals[sc] = new double[nx * ny](); // parentheses initialize elements to zero
+        //std::fill(sc_pedestals[sc], sc_pedestals[sc] + (nx * ny), 0.0); // explicit zero initialization
         double *p0 = new double[nx * ny];
 
-        for (int i = 0; i < nThreads; i++) {
+        // Get the threads assigned to this storage cell
+        auto const& assigned_threads = sc_to_threads[sc];
+        int num_threads = assigned_threads.size();
+
+        // Only iterate over threads assigned to this storage cell
+        for ( int thread_id : assigned_threads ) {
             // inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
             //   cout << i << endl;
-            p0 = dets[i]->getPedestal(p0);
-            if (p0) {
-                if (i == 0) {
+            //p0 = dets[thread_id]->getPedestal(p0);
+            dets[thread_id]->getPedestal(p0);
 
+            if (p0) { /*
+                if (i == 0) {
+                    // If first thread, initialize ped with first thread's values
                     for (int ib = 0; ib < nx * ny; ib++) {
                         ped[ib] = p0[ib] / ((double)nThreads);
                         //  cout << p0[ib] << " ";
                     }
                 } else {
-                    for (int ib = 0; ib < nx * ny; ib++) {
-                        ped[ib] += p0[ib] / ((double)nThreads);
-                        //  cout << p0[ib] << " ";
-                    }
+                */
+                    // For subsequent threads, accumulate pedestal values
+                // if ( i == 0 ) becomes superfluous if we zero-initialize earlier
+                for (int ib = 0; ib < nx * ny; ib++) {
+                    sc_pedestals[sc][ib] += p0[ib] / ((double)num_threads);
+                    //  cout << p0[ib] << " ";
                 }
+                //}
             }
         }
         delete[] p0;
-        return ped;
+        return sc_pedestals[sc];
     };
 
-    virtual double *getPedestalRMS() {
+    // Storage cell sensitive
+    virtual double *getPedestalRMS(int sc = 0) {
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
-        // if (ped) delete [] ped;
-        double *rms = new double[nx * ny];
+        
+        if (sc_pedestals_rms.count(sc) && sc_pedestals_rms[sc]) {
+            delete[] sc_pedestals_rms[sc];
+            sc_pedestals_rms[sc] = nullptr;
+        }
+
+        // allocate memory and initialize all values to zero
+        sc_pedestals_rms[sc] = new double[nx * ny](); // Zero-initialize
+        //std::fill(sc_pedestals_rms[sc], sc_pedestals_rms[sc] + (nx * ny), 0.0); // explicit zero initialization
+        //double *rms = sc_pedestals_rms[sc];
         double *p0 = new double[nx * ny];
 
-        for (int i = 0; i < nThreads; i++) {
+        // Get the threads assigned to this storage cell
+        auto const& assigned_threads = sc_to_threads[sc];
+        int num_threads = assigned_threads.size();
+
+        // Only iterate over threads assigned to this storage cell
+        for (int thread_id : assigned_threads) {
             // inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
             //   cout << i << endl;
-            p0 = dets[i]->getPedestalRMS(p0);
-            if (p0) {
-                if (i == 0) {
+            //p0 = dets[thread_id]->getPedestalRMS(p0);
+            dets[thread_id]->getPedestalRMS(p0);
 
-                    for (int ib = 0; ib < nx * ny; ib++) {
-                        rms[ib] = p0[ib] * p0[ib] / ((double)nThreads);
+            if (p0) {
+                for (int ib = 0; ib < nx * ny; ib++) {
+                    sc_pedestals_rms[sc][ib] += (p0[ib] * p0[ib]) / ((double)num_threads);
                         //  cout << p0[ib] << " ";
-                    }
-                } else {
-                    for (int ib = 0; ib < nx * ny; ib++) {
-                        rms[ib] += p0[ib] * p0[ib] / ((double)nThreads);
-                        //  cout << p0[ib] << " ";
-                    }
                 }
             }
+            
         }
         delete[] p0;
 
@@ -533,64 +734,117 @@ class multiThreadedAnalogDetector {
         /* 	rms[ib]=0; */
         /* } */
 
-        return rms;
+        return sc_pedestals_rms[sc];
     };
 
-    virtual double *setPedestal(double *h = NULL) {
+    /**
+     * Sets pedestal for given storage cell
+     * \param h pedestal
+     * \param sc storage cell
+     * \returns NULL
+     */
+    virtual double *setPedestal(double *h = NULL, int sc = 0) {
         // int nb=0;
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
         if (h == NULL)
             h = ped;
-        for (int i = 0; i < nThreads; i++) {
+        for (auto i : sc_to_threads[sc]) {
             dets[i]->setPedestal(h);
         }
 
         return NULL;
     };
 
-    virtual void *writePedestal(const char *imgname) {
+    // Storage cell sensitive
+    virtual void *writePedestal(char const* base_imgname) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
 
-        getPedestal();
-        float *gm = new float[nx * ny];
-        if (gm) {
+        //float *gm = new float[nx * ny];
+
+        // Loop over each storage cell
+        for ( auto const& entry : sc_to_threads ) {
+            int sc = entry.first;
+            std::string imgname = std::string(base_imgname);
+            if (nSC>1)
+                imgname += "_SC" + std::to_string(sc);
+            imgname += ".tiff";
+
+            getPedestal(sc); // Compute pedestal for this storage cell
+            std::vector<float> gm(nx * ny);
+
+            // Copy pedestal data into the float array
+            /*
             for (int ix = 0; ix < nx * ny; ix++) {
-                gm[ix] = ped[ix];
+                gm[ix] = sc_pedestals[sc][ix];
             }
-            WriteToTiff(gm, imgname, nx, ny);
-            delete[] gm;
-        } else
-            cout << "Could not allocate float image " << endl;
+            */
+            std::copy(sc_pedestals[sc], sc_pedestals[sc] + (nx * ny), gm.data());
+            WriteToTiff(gm.data(), imgname.c_str(), nx, ny);
+            
+            // Clean up memory
+            if(sc_pedestals[sc]) {
+                delete[] sc_pedestals[sc];
+                sc_pedestals[sc] = nullptr;
+            }
+        }
 
         return NULL;
     };
 
-    virtual void *writePedestalRMS(const char *imgname) {
+    // Storage cell sensitive
+    virtual void *writePedestalRMS(char const* base_imgname) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
 
-        double *rms = getPedestalRMS();
-        float *gm = new float[nx * ny];
-        if (gm) {
+        //float *gm = new float[nx * ny];
+
+        // Loop over each stoarge cell
+        for ( auto const& entry : sc_to_threads ) {
+            int sc = entry.first;
+            std::string imgname = std::string(base_imgname);
+            if (nSC>1)
+                imgname += "_SC" + std::to_string(sc);
+            imgname += ".tiff";
+
+            double *rms = getPedestalRMS(sc); // Compute pedestal RMS for this storage cell
+            std::vector<float> gm(nx * ny);
+
+            // Copy rms data into the float array
+            /*
             for (int ix = 0; ix < nx * ny; ix++) {
-                gm[ix] = rms[ix];
+                    gm[ix] = rms[ix];
             }
-            WriteToTiff(gm, imgname, nx, ny);
-            delete[] gm;
-            delete[] rms;
-        } else
-            cout << "Could not allocate float image " << endl;
+            */
+            std::copy(rms, rms + (nx * ny), gm.data());
+            WriteToTiff(gm.data(), imgname.c_str(), nx, ny);
+
+            // Clean up memory
+            //delete[] rms; //This would cause double-free since the pointer is already handled by sc_pedestals_rms[sc]
+            if(sc_pedestals_rms[sc]) {
+                delete[] sc_pedestals_rms[sc]; 
+                sc_pedestals_rms[sc] = nullptr;
+            }  
+        }
 
         return NULL;
     };
 
+    /** 
+     * Reads pedestal and sets it for given storage cell
+     * \param imgname name of pedestal file
+     * \param nb obsolete
+     * \param emin obsolete
+     * \param emax obsolete
+     * \param sc storage cell
+     * \returns setPedestal(NULL, sc)
+     * */
     virtual void *readPedestal(const char *imgname, int nb = -1,
-                               double emin = 1, double emax = 0) {
+                               double emin = 1, double emax = 0, int sc = 0) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
@@ -610,36 +864,68 @@ class multiThreadedAnalogDetector {
         }
         delete[] gm;
 
-        return setPedestal();
+        return setPedestal(NULL, sc);
     };
 
-    /** sets file pointer where to write the clusters to
+    /** Sets file pointer where to write the clusters to
         \param f file pointer
-        \returns current file pointer
+        \param sc storage cell index
+        \returns current file pointer, or nullptr if invalid
     */
-    virtual FILE *setFilePointer(FILE *f) {
-        for (int i = 0; i < nThreads; i++) {
-            dets[i]->setFilePointer(f);
-            // dets[i]->setMutex(&fmutex);
+    virtual FILE *setFilePointer(FILE *f, int sc = 0) {
+        // Check if the storage cell exists
+        if (sc_to_threads.find(sc) == sc_to_threads.end() || sc_to_threads[sc].empty()) {
+            std::cerr << "Error: Invalid storage cell index " << sc << std::endl;
+            return nullptr;
         }
-        return dets[0]->getFilePointer();
+
+        // Assign file pointer to all threads belonging to this storage cell
+        for (auto i : sc_to_threads[sc]) {
+            if(dets[i]) {
+                dets[i]->setFilePointer(f);
+                // dets[i]->setMutex(&fmutex);
+            } else {
+                std::cerr << "Warning: dets[" << i << "] is null, skipping file pointer set." << std::endl;
+            }
+        }
+        // Return file pointer of the first thread in this storage cell
+        return dets[sc_to_threads[sc][0]] ? dets[sc_to_threads[sc][0]]->getFilePointer() : nullptr;
     };
 
-    /** gets file pointer where to write the clusters to
-        \returns current file pointer
+    /** Gets file pointer where to write the clusters to
+        \param sc storage cell index
+        \returns current file pointer, or nullptr if invalid
     */
-    virtual FILE *getFilePointer() { return dets[0]->getFilePointer(); };
+    virtual FILE *getFilePointer(int sc = 0) {
+        // Ensure storage cell index is valid
+        if (sc_to_threads.find(sc) == sc_to_threads.end() || sc_to_threads[sc].empty()) {
+            std::cerr << "Error: Invalid storage cell index " << sc << std::endl;
+            return nullptr;
+        }
+
+        // Return file pointer of the first thread in this storage cell
+        return dets[sc_to_threads[sc][0]] ? dets[sc_to_threads[sc][0]]->getFilePointer() : nullptr;
+    };
 
   protected:
     bool stop;
     const int nThreads;
     threadedAnalogDetector *dets[MAXTHREADS];
     analogDetector<uint16_t> *dd[MAXTHREADS];
-    int ithread;
-    int *image;
-    int *ff;
-    double *ped;
-    pthread_mutex_t fmutex;
+    //int ithread{0}; // Thread index
+    std::vector<int> thread_counters_by_sc{}; // Counters for threads for each storage cell 
+    int* image;
+    int* ff;
+    double* ped;
+    //pthread_mutex_t fmutex; //unused
+    std::unordered_map<int,std::vector<int>> sc_to_threads; // Maps storage cell -> vector of assigned thread ids
+    std::mutex map_mutex; // Ensure thread-safe access to the map
+    int nSC{1}; // Number of storage cells
+    
+    std::unordered_map<int,int*> sc_images; // Store images per storage cell
+    std::unordered_map<int,double*> sc_pedestals; // Store pedestal arrays per storage cell
+    std::unordered_map<int,double*> sc_pedestals_rms; // Store pedestal RMS arrays per storage cell
+    // at the moment, these maps could be avoided, but this implementation is more robust in allowing future changes
 };
 
 #endif

slsDetectorCalibration/multiThreadedCountingDetector.h

@@ -19,8 +19,8 @@ using namespace std;
 
 class multiThreadedCountingDetector : public multiThreadedAnalogDetector {
   public:
- multiThreadedCountingDetector(singlePhotonDetector *d, int n, int fs = 1000)
-        : multiThreadedAnalogDetector(d, n, fs){};
+ multiThreadedCountingDetector(singlePhotonDetector *d, int num_threads, int fs = 1000, int num_sc = 1)
+        : multiThreadedAnalogDetector(d, num_threads, fs, num_sc){};
     // virtual
     // ~multiThreadedCountingDetector{multiThreadedAnalogDetector::~multiThreadedAnalogDetector();};
     virtual double setNSigma(double n) {

slsDetectorCalibration/multiThreadedInterpolatingDetector.h

@@ -70,7 +70,6 @@ class multiThreadedInterpolatingDetector
         if (getInterpolation() == NULL)
             return multiThreadedAnalogDetector::getImage(nnx, nny, nsx, nsy);
         // if one interpolates, the whole image is stored in detector 0;
-        int *img;
         // int nnx, nny, ns;
         // int nnx, nny, ns;
         int nn = dets[0]->getImageSize(nnx, nny, nsx, nsy);
@@ -79,9 +78,9 @@ class multiThreadedInterpolatingDetector
             image = NULL;
         }
         image = new int[nn];
-        img = dets[0]->getImage();
+        int* tmp_img = dets[0]->getImage();
         for (int i = 0; i < nn; i++) {
-            image[i] = img[i];
+            image[i] = tmp_img[i];
         }
         return image;
     };

slsDetectorCalibration/singlePhotonDetector.h

@@ -51,7 +51,6 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
 
 
     */
-
     singlePhotonDetector(slsDetectorData<uint16_t> *d, int csize = 3,
                          double nsigma = 5, int sign = 1,
                          commonModeSubtraction *cm = NULL, int nped = 1000,
@@ -60,10 +59,11 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm, gs),
           nDark(nd), eventMask(NULL), nSigma(nsigma), eMin(-1), eMax(-1),
           clusterSize(csize), clusterSizeY(csize), c2(1), c3(1), clusters(NULL),
-          quad(UNDEFINED_QUADRANT), tot(0), quadTot(0) {
+          quad(UNDEFINED_QUADRANT), tot(0), quadTot(0), ownsMutex(true) {    // The original object owns the mutex {
 
-        fm = new pthread_mutex_t;
-	pthread_mutex_init(fm, NULL);
+        //fm = new pthread_mutex_t;
+	    //pthread_mutex_init(fm, NULL);
+        fm = new std::mutex();
 
         eventMask = new eventType *[ny];
         //  val=new double*[ny];
@@ -86,24 +86,31 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         nphFrame = 0;
     };
     /**
-       destructor. Deletes the cluster structure, the pdestalSubtraction and the
-       image array
+       Destructor. Deletes the cluster structure, event mask, and destroys the mutex.
     */
     virtual ~singlePhotonDetector() {
-        delete[] clusters;
-        for (int i = 0; i < ny; i++)
-            delete[] eventMask[i];
-        delete[] eventMask;
+        // std::cout << "#### Debug: Destructing singlePhotonDetector! ####" << std::endl;
+        if (clusters) { delete[] clusters; clusters = nullptr; }
+        for (int i = 0; i < ny; i++) {
+            if (eventMask[i]) { delete[] eventMask[i]; eventMask[i] = nullptr; }
+        }
+        if (eventMask) { delete[] eventMask; eventMask = nullptr; }
+        if (ownsMutex) {
+            if (fm) {
+                //pthread_mutex_destroy(fm); // Destroy the mutex (not necessary with std::mutex)
+                delete fm; // Free the memory allocated for the mutex
+                fm = nullptr;  // Set the pointer to nullptr to avoid dangling pointer
+            }
+        }
+        
     };
 
     /**
-       copy constructor
+       pointer-based copy constructor (cloner)
        \param orig detector to be copied
-
     */
-
     singlePhotonDetector(singlePhotonDetector *orig)
-        : analogDetector<uint16_t>(orig) {
+        : analogDetector<uint16_t>(orig), fm(orig->fm), ownsMutex(false) {
 
         nDark = orig->nDark;
         myFile = orig->myFile;
@@ -126,11 +133,12 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         c3 = sqrt(clusterSizeY * clusterSize);
 
         clusters = new single_photon_hit[nx * ny];
+        //std::copy(orig->clusters, orig->clusters + (nx * ny), clusters); //possibly superfluous
 
         // cluster=clusters;
 
         setClusterSize(clusterSize);
-        fm = orig->fm;
+        //fm = orig->fm;
 
         quad = UNDEFINED_QUADRANT;
         tot = 0;
@@ -143,13 +151,67 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     }
 
     /**
-       duplicates the detector structure
-       \returns new single photon detector with same parameters
-
+     * copy constructor (deep copy), creates a new mutex
+     * stricly, TODO: Implement Rule of Five!
+     * (copy op=, move ctor, and move op= would need to be defined)
     */
-    virtual singlePhotonDetector *Clone() {
+    singlePhotonDetector(singlePhotonDetector const& other)
+        : analogDetector<uint16_t>(other), ownsMutex(true) {
+
+        //fm = new pthread_mutex_t; // create a new mutex
+	    //pthread_mutex_init(fm, NULL);
+        fm = new std::mutex();  // New unique mutex per copy
+
+        nDark = other.nDark;
+        myFile = other.myFile;
+
+        eventMask = new eventType *[ny];
+        for (int i = 0; i < ny; i++) {
+            eventMask[i] = new eventType[nx];
+            //std::copy(other.eventMask[i], other.eventMask[i] + nx, eventMask[i]);
+        }
+
+        eMin = other.eMin;
+        eMax = other.eMax;
+
+        nSigma = other.nSigma;
+        clusterSize = other.clusterSize;
+        clusterSizeY = other.clusterSizeY;
+
+        c2 = sqrt((clusterSizeY + 1) / 2 * (clusterSize + 1) / 2);
+        c3 = sqrt(clusterSizeY * clusterSize);
+
+        clusters = new single_photon_hit[nx * ny];
+        //std::copy(other.clusters, other.clusters + (nx * ny), clusters);
+
+        setClusterSize(clusterSize);
+
+        quad = other.quad;
+        tot = other.tot;
+        quadTot = other.quadTot;
+        gmap = other.gmap;
+        nphTot = other.nphTot;
+        nphFrame = other.nphFrame;
+   }
+
+    /**
+       Clones the detector structure
+       \returns new single photon detector with same parameters
+       that shares the mutex of the original
+    */
+    virtual singlePhotonDetector* Clone() {
         return new singlePhotonDetector(this);
     }
+    /**
+       Copies the detector structure
+       \returns new single photon detector with same parameters
+       that owns a new mutex
+    */
+    virtual singlePhotonDetector* Copy() {
+        return new singlePhotonDetector(*this);  // Calls the copy constructor
+    }
+    
+
     /** sets/gets number of rms threshold to detect photons
         \param n number of sigma to be set (0 or negative gets)
         \returns actual number of sigma parameter
@@ -381,7 +443,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
 
         // int ir, ic;
         eventType ee;
-        double max = 0, tl = 0, tr = 0, bl = 0, br = 0, *v;
+        double max = 0, tl = 0, tr = 0, bl = 0, br = 0, v = 0;//, *v;
         int cm = 0;
         int good = 1;
         int ir, ic;
@@ -403,7 +465,8 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
             cm = 1;
         }
 
-        double *val = new double[ny * nx];
+        //double *val = new double[ny * nx];
+        std::vector<double> val( ny * nx );
 
         for (int iy = ymin; iy < ymax; ++iy) {
             for (int ix = xmin; ix < xmax; ++ix) {
@@ -435,26 +498,34 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
                             (ix + ic) >= 0 && (ix + ic) < nx) {
 
 
-			  if ((iy + ir) > iy && (ix + ic) > ix ) {
+			                if ((iy + ir) > iy && (ix + ic) > ix ) {
                             
-			    val[(iy + ir) * nx + ix + ic] =
-			      subtractPedestal(data, ix + ic, iy + ir, cm);
+			                    val[(iy + ir) * nx + ix + ic] =
+			                        subtractPedestal(data, ix + ic, iy + ir, cm);
 			    
 			    
-			  }
-			  v = &(val[(iy + ir) * nx + ix + ic]);
-			  tot += *v;
-			  if (ir <= 0 && ic <= 0)
-			    bl += *v;
-			  if (ir <= 0 && ic >= 0)
-			    br += *v;
-			  if (ir >= 0 && ic <= 0)
-			    tl += *v;
-			  if (ir >= 0 && ic >= 0)
-			  tr += *v;
-			  if (*v > max) //{
-			    max = *v;
-			  //}
+			                }
+			                //v = &(val[(iy + ir) * nx + ix + ic]);
+                            v = val[(iy + ir) * nx + ix + ic];
+			                //tot += *v;
+                            tot += v;
+			                if (ir <= 0 && ic <= 0)
+			                    bl += v;
+                                //bl += *v;
+			                if (ir <= 0 && ic >= 0)
+			                    br += v;
+                                //br += *v;
+			                if (ir >= 0 && ic <= 0)
+			                    tl += v;
+                                //tl += *v;
+			                if (ir >= 0 && ic >= 0)
+			                    tr += v;
+                                //tr += *v;
+			                //if (*v > max) //{
+                                //max = *v;
+                            if (v > max)
+			                    max = v;
+			                //}
                         }
                     }
                 }
@@ -524,19 +595,19 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
                              ic < (clusterSize / 2) + 1; ic++) {
                             if ((iy + ir) >= 0 && (iy + ir) < ny &&
                                 (ix + ic) >= 0 && (ix + ic) < nx) {
-			      (clusters + nph)
+			                    (clusters + nph)
                                     ->set_data(val[(iy + ir) * nx + ix + ic],
                                                ic, ir);
-			      if (val[(iy + ir) * nx + ix + ic]>max) 
-				good=0;
-			    }
+			                    if (val[(iy + ir) * nx + ix + ic]>max) 
+				                    good=0;
+			                }
                         }
                     }
-		    if (good==0) {
-		      (clusters + nph)->print();
-		      cout << max << " " <<  val[iy * nx + ix] << endl;
-		    }
-		    //else (clusters + nph)->print();
+		            if (good==0) {
+		                (clusters + nph)->print();
+		                cout << max << " " <<  val[iy * nx + ix] << endl;
+		            }
+		            //else (clusters + nph)->print();
                     if (eMin > 0 && tot < eMin)
                         good = 0;
                     if (eMax > 0 && tot > eMax)
@@ -561,7 +632,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         // cout <<id << " **********************************"<< iframe << " " <<
         // det->getFrameNumber(data) << " " << nphFrame << endl;
         writeClusters(det->getFrameNumber(data));
-        delete[] val;
+        //delete[] val;
         return image;
     };
 
@@ -667,13 +738,14 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     void writeClusters(int fn) {
         if (myFile) {
             // cout << "++" << endl;
-            pthread_mutex_lock(fm);
+            //pthread_mutex_lock(fm); // This is dangerous! What if writeClusters() throws? Then the mutex is never unlocked!
+            std::lock_guard<std::mutex> lock(*fm); // safer, RAII-based locking
             //   cout <<"**********************************"<< fn << " " <<
             //   nphFrame << endl;
             writeClusters(myFile, clusters, nphFrame, fn);
             // for (int i=0; i<nphFrame; i++)
             //  (clusters+i)->write(myFile);
-            pthread_mutex_unlock(fm);
+            //pthread_mutex_unlock(fm); // unsafe
             // cout << "--" << endl;
         }
     };
@@ -711,7 +783,14 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         ema = eMax;
     };
 
-    void setMutex(pthread_mutex_t *m) { fm = m; };
+    //void setMutex(pthread_mutex_t *m) { fm = m; };
+    void setMutex(std::mutex* m) { 
+        if (ownsMutex && fm) {
+            delete fm;  // Cleanup old mutex
+        }
+        fm = m;
+        ownsMutex = false;
+    };
 
   protected:
     int nDark; /**< number of frames to be used at the beginning of the dataset
@@ -733,7 +812,9 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     int nphFrame;
 
     //    double **val;
-    pthread_mutex_t *fm;
+    //pthread_mutex_t* fm;      // Pointer to the shared mutex
+    std::mutex* fm;           // Pointer to the shared (or unique) mutex (safer version)
+    bool ownsMutex;           // Flag to indicate ownership
 };
 
 #endif