Merge pull request #1239 from slsdetectorgroup/dev/wheels

added workflow for python wheels

.github/workflows/build_wheel.yml

@@ -0,0 +1,64 @@
+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

@@ -21,6 +21,7 @@ if (${CMAKE_VERSION} VERSION_GREATER "3.24")
 endif()
 include(cmake/project_version.cmake)
 include(cmake/SlsAddFlag.cmake)
+include(cmake/helpers.cmake)
 
 
 
@@ -193,11 +194,9 @@ find_package(ClangFormat)
 
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
-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()
-
+default_build_type("Release")
+set_std_fs_lib()
+message(STATUS "Extra linking to fs lib:${STD_FS_LIB}")
 
 #Enable LTO if available
 include(CheckIPOSupported)

cmake/FindClangFormat.cmake

@@ -25,7 +25,9 @@ mark_as_advanced(
     ClangFormat_BIN)
 
 if(ClangFormat_FOUND)
-    exec_program(${ClangFormat_BIN} ${CMAKE_CURRENT_SOURCE_DIR} ARGS --version OUTPUT_VARIABLE CLANG_VERSION_TEXT)
+    execute_process(COMMAND ${ClangFormat_BIN} --version
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+                 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

@@ -0,0 +1,46 @@
+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

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

docs/CMakeLists.txt

@@ -42,6 +42,7 @@ 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

docs/src/commandline.rst

@@ -6,6 +6,8 @@ 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/index.rst

@@ -28,6 +28,12 @@ Welcome to slsDetectorPackage's documentation!
     receiver_api
     examples
 
+.. toctree::
+    :caption: how to
+    :maxdepth: 2
+
+    multidet
+
 .. toctree::
     :caption: Python API
     :maxdepth: 2
@@ -81,8 +87,9 @@ Welcome to slsDetectorPackage's documentation!
     :caption: Receiver
     :maxdepth: 2
 
-    receivers
     slsreceiver
+    receivers
+    
 
 .. toctree::
     :caption: Receiver Files

docs/src/installation.rst

@@ -6,18 +6,33 @@
 Installation
 ===============
 
-One can either install pre-built binaries using conda or build from source.
+.. 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.
+
+
 
-.. 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:
 
-
-Install binaries using conda
-----------------------------------
+1. Install pre-built binaries using conda (Recommended)
+--------------------------------------------------------
 
 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) 
@@ -63,12 +78,29 @@ 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:
 
-1. Download Source Code from github
+3. Build from source
+-------------------------
+
+3.1. Download Source Code from github
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
@@ -83,12 +115,12 @@ Build from source
 
 
 
-2. Build from Source
+3.2. Build from Source
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 One can either build using cmake or use the in-built cmk.sh script.
 
-Build using CMake
+3.2.1. Build using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
@@ -135,7 +167,7 @@ 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>` 
 
 
-Build using in-built cmk.sh script
+3.2.2. Build using in-built cmk.sh script
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 
@@ -185,8 +217,8 @@ Build using in-built cmk.sh script
     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>` 
 
 
-Build on old distributions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+3.3. Build on old distributions using conda
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 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
@@ -210,7 +242,7 @@ using this compiler
 
 
 
-Build slsDetectorGui (Qt5)
+3.4. Build slsDetectorGui (Qt5)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 1. Using pre-built binary on conda
@@ -271,7 +303,7 @@ Build slsDetectorGui (Qt5)
 
 
 
-Build this documentation
+3.5. Build this documentation
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The documentation for the slsDetectorPackage is build using a combination 
@@ -294,8 +326,8 @@ is to use conda
     make rst # rst only, saves time in case the API did not change
 
 
-Pybind and Zeromq
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+4. Pybind and Zeromq
+-------------------------
 
 .. _pybind for different slsDetectorPackage versions:
 

docs/src/multidet.rst

@@ -0,0 +1,228 @@
+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

@@ -123,6 +123,47 @@ 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/receivers.rst

@@ -1,25 +1,25 @@
-Receivers
+Custom Receiver
 =================
 
-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.
+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>`.
 
 
-To know more about detector receiver configuration, please check out :ref:`detector udp header and udp commands in the config file <detector udp header>`
+| Please note the following when using a custom receiver:
 
-Custom Receiver
-----------------
+* **udp_dstmac** must be configured in the config file. This parameter is not required when using an in-built receiver.
 
-| 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.
+* Cannot use "auto" for **udp_dstip**.
 
-| Cannot use "auto" for **udp_dstip**.
+* No **rx_** commands in the config file. These commands are for configuring the slsReceiver.
 
-| Also ensure that there are no **rx_** commands in the config file. These commands are for configuring the slsReceiver.
+
+
+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.
 
 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/serverupgrade.rst

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

docs/src/slsreceiver.rst

@@ -1,16 +1,55 @@
-slsReceiver/ slsMultiReceiver
+In-built Receiver   
 ================================
 
-| One has to start the slsReceiver before loading config file or using any receiver commands (prefix: **rx_** )
 
+
+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
+-------------------------
 For a Single Module
     .. code-block:: bash  
+        
+        slsReceiver # default port 1954
 
-        # default port 1954
-        slsReceiver
-
-        # custom port 2012
-        slsReceiver -t2012
+        slsReceiver -t2012 # custom port 2012
 
 
 For Multiple Modules
@@ -18,57 +57,66 @@ For Multiple Modules
 
         # each receiver (for each module) requires a unique tcp port (if all on same machine)
 
-        # using slsReceiver in multiple consoles
+        # option 1 (one for each module)
         slsReceiver
         slsReceiver -t1955
 
-        # slsMultiReceiver [starting port] [number of receivers]
+        # option 2
         slsMultiReceiver 2012 2
 
-        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
-        slsMultiReceiver 2012 2 1
+        # option 3
+        slsFrameSynchronizer 2012 2
+
 
 
 Client Commands 
 -----------------
 
-| One can remove **udp_dstmac** from the config file, as the slsReceiver fetches this from the **udp_ip**.
+* Client commands to the receiver begin with **rx_** or **f_** (file commands).
 
-| One can use "auto" for **udp_dstip** if one wants to use default ip of **rx_hostname**.
+* **rx_hostname** has to be the first command to the receiver so the client knows which receiver process to communicate with.
 
-| The first command to the receiver (**rx_** commands) should be **rx_hostname**. The following are the different ways to establish contact.
+* 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.
 
     .. code-block:: bash  
 
-        # default receiver tcp port (1954)
+        # ---single module---
+
+        # default receiver port at 1954
+        rx_hostname xxx
+       
+        # custom receiver port
+        rx_hostname xxx:1957 # option 1
+       
+        rx_tcpport 1957  # option 2
         rx_hostname xxx
 
-        # custom receiver port
-        rx_hostname xxx:1957
 
-        # custom receiver port
-        rx_tcpport 1954
-        rx_hostname xxx
+        # ---multi module---
 
-        # multi modules with custom ports
-        rx_hostname xxx:1955+xxx:1956+
-        
-        
-        # multi modules using increasing tcp ports when using multi detector command
+        # using increasing tcp ports
         rx_tcpport 1955
         rx_hostname xxx
 
-        # or specify multi modules with custom ports on same rxr pc
-        0:rx_tcpport 1954
+        # custom ports
+        rx_hostname xxx:1955+xxx:1958+ # option 1
+
+        0:rx_tcpport 1954 # option 2
         1:rx_tcpport 1955
         2:rx_tcpport 1956
         rx_hostname xxx
 
-        # multi modules with custom ports on different rxr pc
+        # custom ports on different receiver machines
         0:rx_tcpport 1954
         0:rx_hostname xxx
         1:rx_tcpport 1955
-        1:rx_hostname yyy
+        1:rx_hostname yyyrxr
 
 
 | Example commands:
@@ -91,6 +139,32 @@ Client Commands
         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/udpconfig.rst

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

docs/src/virtualserver.rst

@@ -1,4 +1,5 @@
 .. _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

@@ -11,9 +11,13 @@ 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

@@ -65,6 +65,9 @@ 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
 )

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
@@ -90,8 +90,6 @@ 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
@@ -113,20 +111,15 @@ 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++) {
-            if (stat[i]) { delete[] stat[i]; stat[i] = nullptr; }
-            // delete[] stat[i];
+            delete[] stat[i];
             /* delete [] pedMean[i];  */
             /* delete [] pedVariance[i]; */
-        }
+        };
         /* delete [] pedMean;  */
         /* delete [] pedVariance; */
-        // delete[] stat;
-        // delete[] image;
-        if (stat) { delete[] stat; stat = nullptr; }
-        if (image) { delete[] image; image = nullptr; }
+        delete[] stat;
+        delete[] image;
 #ifdef ROOTSPECTRUM
         delete hs;
 #ifdef ROOTCLUST
@@ -144,8 +137,6 @@ 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;
@@ -161,8 +152,6 @@ 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];
@@ -227,75 +216,12 @@ 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
@@ -622,11 +548,6 @@ 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
@@ -645,11 +566,6 @@ 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
@@ -1310,7 +1226,7 @@ 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) const {
+    int GetNPedestals(int ix, int iy) {
         if (ix >= 0 && ix < nx && iy >= 0 && iy < ny)
             return stat[iy][ix].GetNPedestals();
         else

slsDetectorCalibration/circularFifo.h

@@ -50,8 +50,6 @@ 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 {
@@ -76,18 +74,14 @@ 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()) {
-        //std::cout << "Full Fifo at push. Returning." << std::endl;
-        return false; // No space, return immediately
-    }
+    if (no_block && isFull())
+        return false;
 
-    //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
+    sem_wait(&free_mutex);
+    array[tail] = item_;
+    tail = increment(tail);
+    sem_post(&data_mutex);
+    return true;
 }
 
 /** Consumer only: Removes and returns item from the queue
@@ -100,18 +94,14 @@ 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()) {
-        //std::cout << "Empty Fifo at pop. Returning." << std::endl;
-        return false; // No data in fifo, return immediately
-    }
+    if (no_block && isEmpty())
+        return false;
 
-    //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
+    sem_wait(&data_mutex);
+    item_ = array[head];
+    head = increment(head);
+    sem_post(&free_mutex);
+    return true;
 }
 
 /** Useful for testinng and Consumer check of status

slsDetectorCalibration/dataStructures/HDF5File.cpp

@@ -1,482 +0,0 @@
-#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

@@ -1,159 +0,0 @@
-#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

@@ -1,422 +0,0 @@
-// 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

@@ -1,432 +0,0 @@
-// 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

@@ -28,10 +28,6 @@
     @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;
@@ -81,7 +77,7 @@ 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 = 0; // CHANGE IF YOU CHANGE MODULE!
+constexpr int bond_shift_y = 1; // CHANGE IF YOU CHANGE MODULE!
 
 } // namespace strixelSingleChip
 
@@ -101,13 +97,6 @@ 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;
@@ -226,113 +215,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         }
     }
 
-
-    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) {
+    void remapROI(uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax) {
         // determine group and chip selected by ROI
-      int group, xmin, xmax, ymin, ymax;
-      std::tie( mchip, group, xmin, xmax, ymin, ymax ) = roi;
-	/*
+        int group;
         if (ymax <= c1g1_yend + bond_shift_y) {
             group = 1;
             mchip = 1;
@@ -358,17 +243,18 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	  group = -1;
 	  mchip = -1;
 	}
-	*/
-      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;
+        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;
 
         // make sure loop bounds are correct
-	/*
         if (y0 < ymin)
             std::cout << "Error ymin" << std::endl;
         if (y1 > ymax)
@@ -378,27 +264,24 @@ 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;
-	  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;
-	}
-      }
+                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;
+            }
+        }
     }
 
   public:
@@ -424,31 +307,16 @@ 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) {
 
-	  // 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);
+            dataSize =
+                (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
+            std::cout << "datasize " << dataSize << std::endl;
+            remapROI(xmin, xmax, ymin, ymax);
 
         } else {
 

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -3,7 +3,6 @@
 #ifndef JUNGFRAUMODULEDATA_H
 #define JUNGFRAUMODULEDATA_H
 #include <cstdint>
-#include "sls/sls_detector_defs.h"
 #include "slsDetectorData.h"
 
 //#define VERSION_V2
@@ -28,7 +27,7 @@ typedef struct {
     uint64_t bunchNumber; /**< is the frame number */
     uint64_t pre;         /**< something */
 
-} jf_header; //Aldo's header!
+} jf_header;
 
 using namespace std;  
 class jungfrauModuleData : public slsDetectorData<uint16_t> {
@@ -43,56 +42,20 @@ 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(header)
+#define off sizeof(jf_header)
 #endif
 #ifdef ZMQ
 #define off 0
 #endif
 
 
- jungfrauModuleData(uint16_t xmin=0, uint16_t xmax=0,
-		    uint16_t ymin=0, uint16_t ymax=0)
+    jungfrauModuleData()
         : slsDetectorData<uint16_t>(1024, 512,
                                     1024* 512 * 2 + off) {
-
-      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) {
+  
+        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;
@@ -100,7 +63,7 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
             }
         }
 
-      }
+
 
 
         iframe = 0;
@@ -187,7 +150,7 @@ 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

@@ -1,226 +0,0 @@
-// 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

@@ -54,10 +54,6 @@ 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)
@@ -70,28 +66,10 @@ 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

@@ -6,86 +6,18 @@
 
 set(JUNGFRAU_EXECUTABLES)
 
-#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)
-
-
+find_package(fmt REQUIRED)
 
 # 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)
@@ -126,22 +58,6 @@ 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})
@@ -151,16 +67,11 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         ../interpolations
         ../dataStructures 
         ../interpolations/etaVEL
-        ../../slsSupportLib/include/sls/
+        ../../slsSupportLib/include/
         ../../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
@@ -168,7 +79,6 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         pthread 
         tiffio
         fmt::fmt
-	    nlohmann_json::nlohmann_json
           #-L/usr/lib64/
         #-lm  -lstdc++  -lrt
 
@@ -176,11 +86,7 @@ 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
@@ -192,8 +98,4 @@ 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 CHIP
+    !defined JFSTRXCHIP6
 #ifndef MODULE
 #include "jungfrauHighZSingleChipData.h"
 #endif
@@ -20,10 +20,6 @@
 #endif
 #endif
 
-#ifdef CHIP
-#include "jungfrauSingleChipData.h"
-#endif
-
 #ifdef JFSTRX
 #include "jungfrauLGADStrixelsData_new.h"
 #endif
@@ -45,9 +41,6 @@
 #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("/");
@@ -68,24 +61,20 @@ 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) {
-    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 if (fsuffix.length()!=0)
+    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 < 6) {
+    if (argc < 5) {
         std::cout
             << "Usage is " << argv[0]
-            << "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]"
+            << "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
+               "[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
+               "[nframes] [xmin xmax ymin ymax] [gainmap]"
             << std::endl;
         std::cout
             << "threshold <0 means analog; threshold=0 means cluster finder; "
@@ -117,131 +106,94 @@ 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 >= 8) {
-        runmin = atoi(argv[7]);
+    if (argc >= 6) {
+        runmin = atoi(argv[5]);
     }
+
     int runmax = runmin;
-    if (argc >= 9) {
-        runmax = atoi(argv[8]);
+
+    if (argc >= 7) {
+        runmax = atoi(argv[6]);
     }
 
     std::string pedfilename{};
-    if (argc >= 10) {
-        pedfilename = argv[9];
+    if (argc >= 8) {
+        pedfilename = argv[7];
     }
     double thr = 0;
     double thr1 = 1;
 
-    if (argc >= 11) {
-        thr = atof(argv[10]);
+    if (argc >= 9) {
+        thr = atof(argv[8]);
     }
 
     int nframes = 0;
 
-    if (argc >= 12) {
-        nframes = atoi(argv[11]);
+    if (argc >= 10) {
+        nframes = atoi(argv[9]);
     }
-
-    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 CHIP
+    !defined JFSTRXCHIP6
 #ifndef MODULE
     jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
     int nx = 256, ny = 256;
 #endif
 #ifdef MODULE
-    jungfrauModuleData *decoder = new jungfrauModuleData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
+    jungfrauModuleData *decoder = new jungfrauModuleData();
     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
-    std::cout << "Jungfrau strixel full module readout" << std::endl;
+    cout << "Jungfrau strixel full module readout" << endl;
+    // ROI
+    uint16_t xxmin = 0;
+    uint16_t xxmax = 0;
+    uint16_t yymin = 0;
+    uint16_t yymax = 0;
 
 #ifndef ALDO
-    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
+    { //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
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-      new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
+        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
     int nx = 1024 / 3, ny = 512 * 5;
 #endif
 #ifdef JFSTRXCHIP1
@@ -266,20 +218,19 @@ 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;
-    if (argc >= 16) {
-        xmin = atoi(argv[12]);
-        xmax = atoi(argv[13]);
-        ymin = atoi(argv[14]);
-        ymax = atoi(argv[15]);
+    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]);
     }
-    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+    std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
               << std::endl;
 
     char *gainfname = NULL;
-    if (argc > 17) {
-        gainfname = argv[17];
+    if (argc > 14) {
+        gainfname = argv[14];
         std::cout << "Gain map file name is: " << gainfname << std::endl;
     }
 
@@ -288,8 +239,6 @@ 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)
@@ -370,7 +319,7 @@ int main(int argc, char *argv[]) {
 
 	  mt->setFrameMode(ePedestal);
 
-	  std::ifstream pedefile(fname, ios::in | ios::binary);
+	  ifstream pedefile(fname, ios::in | ios::binary);
 	  //      //open file
 	  if (pedefile.is_open()) {
 	    std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
@@ -431,27 +380,26 @@ int main(int argc, char *argv[]) {
     }
 
     ifr = 0;
-    int ioutfile = 0;
+    int ifile = 0;
 
     mt->setFrameMode(eFrame);
 
     FILE *of = NULL;
     
-    for (int irun = runmin; irun <= runmax; ++irun) {
-      for (int ifile = fmin; ifile <= fmax; ++ifile) {
+    for (int irun = runmin; irun <= runmax; irun++) {
         std::cout << "DATA ";
 	std::string fsuffix{};
-	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 );
+	auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
+	auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
+	auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
         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;
-	std::ifstream filebin(fname, ios::in | ios::binary);
+        ifstream filebin(fname, ios::in | ios::binary);
         //      //open file
-        ioutfile = 0;
+        ifile = 0;
         if (filebin.is_open()) {
             if (thr <= 0 && cf != 0) { // cluster finder
                 if (of == NULL) {
@@ -488,10 +436,10 @@ 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, ioutfile );
+		      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
 		      mt->writeImage(imgfname.c_str(), thr1);
                         mt->clearImage();
-                        ioutfile++;
+                        ifile++;
                     }
                 }
                 // } else
@@ -505,7 +453,7 @@ int main(int argc, char *argv[]) {
             }
             if (nframes >= 0) {
                 if (nframes > 0)
-		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
+		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
                 std::cout << "Writing tiff to " << imgfname << " " << thr1
                           << std::endl;
                 mt->writeImage(imgfname.c_str(), thr1);
@@ -521,10 +469,9 @@ 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", runmin, 0, fmin, -1 );
+      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -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 JFSTRXQ && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6 && !defined CHIP
+#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
+    !defined JFSTRXCHIP6
 #ifndef MODULE
 #include "jungfrauHighZSingleChipData.h"
 #endif
@@ -20,16 +20,9 @@
 #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
@@ -48,9 +41,6 @@
 #include <ctime>
 #include <fmt/core.h>
 
-#include <nlohmann/json.hpp>
-using json = nlohmann::json;
-
 
 std::string getRootString( const std::string& filepath ) {
   size_t pos1;
@@ -81,11 +71,11 @@ 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 < 11) {
+    if (argc < 10) {
         std::cout
             << "Usage is " << argv[0]
-            << " filestxt outdir [json master] [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
-               "[threshold] [nframes] [optional: bool read rxroi from data file header]"
+            << " filestxt outdir [pedfile (raw or tiff)] [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
@@ -115,19 +105,19 @@ int main(int argc, char *argv[]) {
 
     const std::string txtfilename(argv[1]);
     const std::string outdir(argv[2]);
-    const std::string jsonmastername(argv[3]);
-    const std::string pedfilename(argv[4]);
+    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]);
 
     double thr = 0;
     double thr1 = 1;
-    thr = atof(argv[9]);
+    thr = atof(argv[8]);
 
     int nframes = 0;
-    nframes = atoi(argv[10]);
-
-    bool readrxroifromdatafile = false;
-    if (argc > 11)
-      readrxroifromdatafile = atoi(argv[11]);
+    nframes = atoi(argv[9]);
 
     //Get vector of filenames from input txt-file
     std::vector<std::string> filenames{};
@@ -156,34 +146,10 @@ 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 JFSTRXQ && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
-    !defined JFSTRXCHIP6 && !defined CHIP
+#if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
+    !defined JFSTRXCHIP6
 #ifndef MODULE
     jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
     int nx = 256, ny = 256;
@@ -194,60 +160,52 @@ 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
-    std::cout << "Jungfrau strixel full module readout" << std::endl;
+    cout << "Jungfrau strixel full module readout" << endl;
+    // ROI
+    uint16_t xxmin = 0;
+    uint16_t xxmax = 0;
+    uint16_t yymin = 0;
+    uint16_t yymax = 0;
 
 #ifndef ALDO
-    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
+    { //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
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-        new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
+        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
     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 =
@@ -270,16 +228,7 @@ 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;
@@ -290,7 +239,6 @@ int main(int argc, char *argv[]) {
     }
     std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
               << std::endl;
-    */
 
     /*
     char *gainfname = NULL;
@@ -462,7 +410,7 @@ int main(int argc, char *argv[]) {
       std::time(&end_time);
       std::cout << std::ctime(&end_time) << std::endl;
 
-      std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      ifstream filebin(filenames[ifile], ios::in | ios::binary);
       //      //open file
       ioutfile = 0;
       if (filebin.is_open()) {

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxtH5.cpp

@@ -1,457 +0,0 @@
-// 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

@@ -1,468 +0,0 @@
-// 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/moenchZmqProcess.cpp

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

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -23,9 +23,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <unistd.h>
-#include <mutex>
-#include <algorithm>
-#include<unordered_map>
+//#include <mutex>
 
 using namespace std;
 
@@ -49,20 +47,12 @@ 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)
-            std::cout << "Could allocate only " << i << " frames";
+            cout << "Could allocate only " << i << " frames";
 
         busy = 0;
         stop = 1;
@@ -112,50 +102,24 @@ class threadedAnalogDetector {
     };
 
     virtual ~threadedAnalogDetector() {
-
-        // std::cout << "#### Debug: Destructing threadedAnalogDetector! ####" << std::endl;
-
         StopThread();
-
-        if (fifoFree) { delete fifoFree; fifoFree = nullptr; }
-        if (fifoData) { delete fifoData; fifoData = nullptr; }
-        if (det) { 
-            delete det; // Call destructor for singlePhotonDetector
-            det = nullptr; 
-        } 
+        delete fifoFree;
+        delete fifoData;
     }
 
     /** Returns true if the thread was successfully started, false if there was
      * an error starting the thread */
     virtual bool StartThread() {
         stop = 0;
-        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;
-
+        cout << "Detector number " << det->getId() << endl;
+        cout << "common mode is " << det->getCommonModeSubtraction() << endl;
+        cout << "ghos summation is " << det->getGhostSummation() << endl;
         return (pthread_create(&_thread, NULL, processData, this) == 0);
     }
 
     virtual void StopThread() {
         stop = 1;
-        //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;
-        }
+        (void)pthread_join(_thread, NULL);
     }
 
     virtual bool pushData(char *&ptr) { return fifoData->push(ptr); }
@@ -302,8 +266,6 @@ 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();
@@ -316,118 +278,55 @@ 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 num_threads,
-                                int fs = 1000, int num_sc = 1)
-        : stop(0), nThreads(num_threads), nSC(num_sc) {
-
-        /*
+    multiThreadedAnalogDetector(analogDetector<uint16_t> *d, int n,
+                                int fs = 1000)
+        : stop(0), nThreads(n), ithread(0) {
         dd[0] = d;
         if (nThreads == 1)
             dd[0]->setId(100);
         else
             dd[0]->setId(0);
-        */
-
-        // 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;
+        for (int i = 1; i < nThreads; i++) {
+            dd[i] = d->Clone();
+            dd[i]->setId(i);
         }
 
-        // 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);
         }
 
-        // Set all thread counters to zero for each storage cell
-        thread_counters_by_sc.resize(nSC,0);
-
-        image = nullptr;
+        image = NULL;
         ff = NULL;
         ped = NULL;
-        //std::cout << "Ithread is " << ithread << std::endl;
+        cout << "Ithread is " << ithread << endl;
     }
 
     virtual ~multiThreadedAnalogDetector() {
-        // 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;
-        }
-        
+        StopThreads();
+        for (int i = 0; i < nThreads; i++)
+            delete dets[i];
+        /* for (int i=1; i<nThreads; i++)  */
+        /*   delete dd[i]; */
+        // delete [] image;
     }
 
     virtual int setFrameMode(int fm) {
@@ -460,52 +359,36 @@ class multiThreadedAnalogDetector {
             dets[i]->newDataSet();
     };
 
-    // Storage cell sensitive
-    virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy, int sc = 0) {
-        //int *img;
+    virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy) {
+        int *img;
         // int nnx, nny, ns;
         // int nnx, nny, ns;
         int nn = dets[0]->getImageSize(nnx, nny, ns, nsy);
-
-        if (sc_images[sc]) {
-            delete[] sc_images[sc];
-            sc_images[sc] = nullptr;
+        if (image) {
+            delete[] image;
+            image = NULL;
         }
-
-        // Allocate memory for image and zero-initialize
-        sc_images[sc] = new int[nn]();
+        image = new int[nn];
         // int nn=dets[0]->getImageSize(nnx, nny, ns);
         // for (i=0; i<nn; i++) image[i]=0;
 
-        // 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 ii = 0; ii < nThreads; ii++) {
+            // cout << ii << " " << nn << " " << nnx << " " << nny << " " << ns
+            // << endl;
+            img = dets[ii]->getImage();
             for (int i = 0; i < nn; i++) {
-
-                /* std::cout << " # pixel " << i
-                          << " # value " << tmp_img[i]
-                          << " ## " << std::endl; */
-
-                
-                sc_images[sc][i] += tmp_img[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];
                 // if (img[i])	  cout << "det " << ii << " pix " << i << " val
                 // " <<  img[i] << " " << image[i] << endl;
             }
         }
-        return sc_images[sc];
+        return image;
     }
 
     virtual void clearImage() {
@@ -515,7 +398,7 @@ class multiThreadedAnalogDetector {
         }
     }
 
-    virtual void *writeImage(char const* base_imgname, double t = 1) {
+    virtual void *writeImage(const char *imgname, double t = 1) {
         /* #ifdef SAVE_ALL   */
         /*      for (int ii=0; ii<nThreads; ii++) { */
         /*        char tit[10000];cout << "m" <<endl; */
@@ -524,30 +407,11 @@ 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);
-
-        // 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
+        float *gm = new float[nn];
+        if (gm) {
             for (int ix = 0; ix < nn; ix++) {
                 if (t) {
                     if (image[ix] < 0)
@@ -560,18 +424,11 @@ class multiThreadedAnalogDetector {
                 // if (image[ix]>0 && ix/nnx<350) cout << ix/nnx << " " <<
                 // ix%nnx << " " << image[ix]<< " " << gm[ix] << 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;
-            }
-            
-        }
-        
+            // cout << "image " << nnx << " " << nny << endl;
+            WriteToTiff(gm, imgname, nnx, nny);
+            delete[] gm;
+        } else
+            cout << "Could not allocate float image " << endl;
         return NULL;
     }
 
@@ -582,7 +439,6 @@ class multiThreadedAnalogDetector {
     }
 
     virtual void StopThreads() {
-        std::cout << "Stopping all threads ..." << std::endl;
         for (int i = 0; i < nThreads; i++)
             dets[i]->StopThread();
     }
@@ -597,133 +453,76 @@ class multiThreadedAnalogDetector {
         return ret;
     }
 
-/*
-    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 pushData(char *&ptr) { return dets[ithread]->pushData(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 bool popFree(char *&ptr) {
+        //  cout << ithread << endl;
+        return dets[ithread]->popFree(ptr);
     }
 
-    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 int nextThread() {
+        ithread++;
+        if (ithread == nThreads)
+            ithread = 0;
+        return ithread;
     }
 
-    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) {
+    virtual double *getPedestal() {
         int nx, ny;
         dets[0]->getDetectorSize(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
+        if (ped)
+            delete[] ped;
+        ped = new double[nx * ny];
         double *p0 = new double[nx * ny];
 
-        // 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 ) {
+        for (int i = 0; i < nThreads; i++) {
             // inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
             //   cout << i << endl;
-            //p0 = dets[thread_id]->getPedestal(p0);
-            dets[thread_id]->getPedestal(p0);
-
-            if (p0) { /*
+            p0 = dets[i]->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 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] << " ";
+                    for (int ib = 0; ib < nx * ny; ib++) {
+                        ped[ib] += p0[ib] / ((double)nThreads);
+                        //  cout << p0[ib] << " ";
+                    }
                 }
-                //}
             }
         }
         delete[] p0;
-        return sc_pedestals[sc];
+        return ped;
     };
 
-    // Storage cell sensitive
-    virtual double *getPedestalRMS(int sc = 0) {
+    virtual double *getPedestalRMS() {
         int nx, ny;
         dets[0]->getDetectorSize(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];
+        // if (ped) delete [] ped;
+        double *rms = new double[nx * ny];
         double *p0 = new double[nx * ny];
 
-        // 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) {
+        for (int i = 0; i < nThreads; i++) {
             // inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
             //   cout << i << endl;
-            //p0 = dets[thread_id]->getPedestalRMS(p0);
-            dets[thread_id]->getPedestalRMS(p0);
-
+            p0 = dets[i]->getPedestalRMS(p0);
             if (p0) {
-                for (int ib = 0; ib < nx * ny; ib++) {
-                    sc_pedestals_rms[sc][ib] += (p0[ib] * p0[ib]) / ((double)num_threads);
+                if (i == 0) {
+
+                    for (int ib = 0; ib < nx * ny; ib++) {
+                        rms[ib] = p0[ib] * p0[ib] / ((double)nThreads);
                         //  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;
 
@@ -734,117 +533,64 @@ class multiThreadedAnalogDetector {
         /* 	rms[ib]=0; */
         /* } */
 
-        return sc_pedestals_rms[sc];
+        return rms;
     };
 
-    /**
-     * Sets pedestal for given storage cell
-     * \param h pedestal
-     * \param sc storage cell
-     * \returns NULL
-     */
-    virtual double *setPedestal(double *h = NULL, int sc = 0) {
+    virtual double *setPedestal(double *h = NULL) {
         // int nb=0;
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
         if (h == NULL)
             h = ped;
-        for (auto i : sc_to_threads[sc]) {
+        for (int i = 0; i < nThreads; i++) {
             dets[i]->setPedestal(h);
         }
 
         return NULL;
     };
 
-    // Storage cell sensitive
-    virtual void *writePedestal(char const* base_imgname) {
+    virtual void *writePedestal(const char *imgname) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
 
-        //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
-            /*
+        getPedestal();
+        float *gm = new float[nx * ny];
+        if (gm) {
             for (int ix = 0; ix < nx * ny; ix++) {
-                gm[ix] = sc_pedestals[sc][ix];
+                gm[ix] = ped[ix];
             }
-            */
-            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;
-            }
-        }
+            WriteToTiff(gm, imgname, nx, ny);
+            delete[] gm;
+        } else
+            cout << "Could not allocate float image " << endl;
 
         return NULL;
     };
 
-    // Storage cell sensitive
-    virtual void *writePedestalRMS(char const* base_imgname) {
+    virtual void *writePedestalRMS(const char *imgname) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
 
-        //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
-            /*
+        double *rms = getPedestalRMS();
+        float *gm = new float[nx * ny];
+        if (gm) {
             for (int ix = 0; ix < nx * ny; ix++) {
-                    gm[ix] = rms[ix];
+                gm[ix] = rms[ix];
             }
-            */
-            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;
-            }  
-        }
+            WriteToTiff(gm, imgname, nx, ny);
+            delete[] gm;
+            delete[] rms;
+        } else
+            cout << "Could not allocate float image " << endl;
 
         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, int sc = 0) {
+                               double emin = 1, double emax = 0) {
 
         int nx, ny;
         dets[0]->getDetectorSize(nx, ny);
@@ -864,68 +610,36 @@ class multiThreadedAnalogDetector {
         }
         delete[] gm;
 
-        return setPedestal(NULL, sc);
+        return setPedestal();
     };
 
-    /** Sets file pointer where to write the clusters to
+    /** sets file pointer where to write the clusters to
         \param f file pointer
-        \param sc storage cell index
-        \returns current file pointer, or nullptr if invalid
+        \returns current file pointer
     */
-    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;
+    virtual FILE *setFilePointer(FILE *f) {
+        for (int i = 0; i < nThreads; i++) {
+            dets[i]->setFilePointer(f);
+            // dets[i]->setMutex(&fmutex);
         }
-
-        // 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;
+        return dets[0]->getFilePointer();
     };
 
-    /** Gets file pointer where to write the clusters to
-        \param sc storage cell index
-        \returns current file pointer, or nullptr if invalid
+    /** gets file pointer where to write the clusters to
+        \returns current file pointer
     */
-    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;
-    };
+    virtual FILE *getFilePointer() { return dets[0]->getFilePointer(); };
 
   protected:
     bool stop;
     const int nThreads;
     threadedAnalogDetector *dets[MAXTHREADS];
     analogDetector<uint16_t> *dd[MAXTHREADS];
-    //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
+    int ithread;
+    int *image;
+    int *ff;
+    double *ped;
+    pthread_mutex_t fmutex;
 };
 
 #endif

slsDetectorCalibration/multiThreadedCountingDetector.h

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

slsDetectorCalibration/multiThreadedInterpolatingDetector.h

@@ -70,6 +70,7 @@ 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);
@@ -78,9 +79,9 @@ class multiThreadedInterpolatingDetector
             image = NULL;
         }
         image = new int[nn];
-        int* tmp_img = dets[0]->getImage();
+        img = dets[0]->getImage();
         for (int i = 0; i < nn; i++) {
-            image[i] = tmp_img[i];
+            image[i] = img[i];
         }
         return image;
     };

slsDetectorCalibration/singlePhotonDetector.h

@@ -51,6 +51,7 @@ 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,
@@ -59,11 +60,10 @@ 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), ownsMutex(true) {    // The original object owns the mutex {
+          quad(UNDEFINED_QUADRANT), tot(0), quadTot(0) {
 
-        //fm = new pthread_mutex_t;
-	    //pthread_mutex_init(fm, NULL);
-        fm = new std::mutex();
+        fm = new pthread_mutex_t;
+	pthread_mutex_init(fm, NULL);
 
         eventMask = new eventType *[ny];
         //  val=new double*[ny];
@@ -86,31 +86,24 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         nphFrame = 0;
     };
     /**
-       Destructor. Deletes the cluster structure, event mask, and destroys the mutex.
+       destructor. Deletes the cluster structure, the pdestalSubtraction and the
+       image array
     */
     virtual ~singlePhotonDetector() {
-        // 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
-            }
-        }
-        
+        delete[] clusters;
+        for (int i = 0; i < ny; i++)
+            delete[] eventMask[i];
+        delete[] eventMask;
     };
 
     /**
-       pointer-based copy constructor (cloner)
+       copy constructor
        \param orig detector to be copied
+
     */
+
     singlePhotonDetector(singlePhotonDetector *orig)
-        : analogDetector<uint16_t>(orig), fm(orig->fm), ownsMutex(false) {
+        : analogDetector<uint16_t>(orig) {
 
         nDark = orig->nDark;
         myFile = orig->myFile;
@@ -133,12 +126,11 @@ 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;
@@ -151,67 +143,13 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     }
 
     /**
-     * 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)
-    */
-    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
+       duplicates the detector structure
        \returns new single photon detector with same parameters
-       that shares the mutex of the original
+
     */
-    virtual singlePhotonDetector* Clone() {
+    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
@@ -443,7 +381,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
 
         // int ir, ic;
         eventType ee;
-        double max = 0, tl = 0, tr = 0, bl = 0, br = 0, v = 0;//, *v;
+        double max = 0, tl = 0, tr = 0, bl = 0, br = 0, *v;
         int cm = 0;
         int good = 1;
         int ir, ic;
@@ -465,8 +403,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
             cm = 1;
         }
 
-        //double *val = new double[ny * nx];
-        std::vector<double> val( ny * nx );
+        double *val = new double[ny * nx];
 
         for (int iy = ymin; iy < ymax; ++iy) {
             for (int ix = xmin; ix < xmax; ++ix) {
@@ -498,34 +435,26 @@ 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]);
-                            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;
-			                //}
+			  }
+			  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;
+			  //}
                         }
                     }
                 }
@@ -595,19 +524,19 @@ 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)
@@ -632,7 +561,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         // cout <<id << " **********************************"<< iframe << " " <<
         // det->getFrameNumber(data) << " " << nphFrame << endl;
         writeClusters(det->getFrameNumber(data));
-        //delete[] val;
+        delete[] val;
         return image;
     };
 
@@ -738,14 +667,13 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     void writeClusters(int fn) {
         if (myFile) {
             // cout << "++" << endl;
-            //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
+            pthread_mutex_lock(fm);
             //   cout <<"**********************************"<< fn << " " <<
             //   nphFrame << endl;
             writeClusters(myFile, clusters, nphFrame, fn);
             // for (int i=0; i<nphFrame; i++)
             //  (clusters+i)->write(myFile);
-            //pthread_mutex_unlock(fm); // unsafe
+            pthread_mutex_unlock(fm);
             // cout << "--" << endl;
         }
     };
@@ -783,14 +711,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
         ema = eMax;
     };
 
-    //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;
-    };
+    void setMutex(pthread_mutex_t *m) { fm = m; };
 
   protected:
     int nDark; /**< number of frames to be used at the beginning of the dataset
@@ -812,9 +733,7 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
     int nphFrame;
 
     //    double **val;
-    //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
+    pthread_mutex_t *fm;
 };
 
 #endif

slsDetectorServers/compileAllServers.sh

@@ -1,16 +1,19 @@
 # SPDX-License-Identifier: LGPL-3.0-or-other
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 
-# empty branch = developer branch in updateAPIVersion.sh
-branch=""
 det_list=("ctbDetectorServer  
 	gotthard2DetectorServer 
 	jungfrauDetectorServer 
 	mythen3DetectorServer 
 	moenchDetectorServer
-	xilinx_ctbDetectorServer" 
+	xilinx_ctbDetectorServer"
 	)
-usage="\nUsage: compileAllServers.sh [server|all(opt)] [branch(opt)]. \n\tNo arguments mean all servers with 'developer' branch. \n\tNo 'branch' input means 'developer branch'"
+usage="\nUsage: compileAllServers.sh [server|all(opt)] [update_api(opt)]. \n\tNo arguments mean all servers with 'developer' branch. \n\tupdate_api if true updates the api to version in VERSION file"
+
+update_api=true
+target=version
+
+
 
 # arguments
 if [ $# -eq 0 ]; then
@@ -34,15 +37,12 @@ elif [ $# -eq 1 ] || [ $# -eq 2 ]; then
 		declare -a det=("${1}")
 		#echo "Compiling only $1"
 	fi
-	# branch
+
 	if [ $# -eq 2 ]; then
-		# arg in list
-		if [[ $det_list == *$2* ]]; then
-			echo -e "Invalid argument 2: $2. $usage"
-			return 1
+		update_api=$2
+		if not $update_api ; then
+			target=clean
 		fi
-		branch+=$2
-		#echo "with branch $branch"
 	fi
 else
 	echo -e "Too many arguments.$usage"
@@ -53,6 +53,9 @@ declare -a deterror=("OK" "OK" "OK" "OK" "OK" "OK")
 
 echo -e "list is ${det[@]}"
 
+if $update_api; then
+	echo "updating api to $(cat ../VERSION)"
+fi
 # compile each server
 idet=0
 for i in ${det[@]}
@@ -62,14 +65,13 @@ do
 	echo -e "Compiling $dir [$file]"
 	cd $dir
 	make clean
-	if make version API_BRANCH=$branch; then
+	if make $target; then
 		deterror[$idet]="OK"
 	else
 		deterror[$idet]="FAIL"
 	fi
 	mv bin/$dir bin/$file
 	git add -f bin/$file
-	cp bin/$file /tftpboot/
 	cd ..
 	echo -e "\n\n"
 	((++idet))

slsDetectorServers/compileAllServers_noAPIUpdate.sh

@@ -1,86 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-
-# empty branch = developer branch in updateAPIVersion.sh
-branch=""
-det_list=("ctbDetectorServer" 
-	"gotthard2DetectorServer"
-	"jungfrauDetectorServer"
-	"mythen3DetectorServer"
-	"moenchDetectorServer"
-	"xilinx_ctbDetectorServer"
-	)
-usage="\nUsage: compileAllServers.sh [server|all(opt)] [branch(opt)]. \n\tNo arguments mean all servers with 'developer' branch. \n\tNo 'branch' input means 'developer branch'"
-
-# arguments
-if [ $# -eq 0 ]; then
-	# no argument, all servers
-	declare -a det=${det_list[@]}
-	echo "Compiling all servers"
-elif [ $# -eq 1 ] || [ $# -eq 2 ]; then
-	# 'all' servers
-	if [[ $1 == "all" ]]; then
-		declare -a det=${det_list[@]}
-		echo "Compiling all servers"
-	else
-		# only one server
-		# arg not in list
-		if [[ $det_list != *$1* ]]; then
-			echo -e "Invalid argument 1: $1. $usage"
-			return -1
-		fi
-		declare -a det=("${1}")
-		#echo "Compiling only $1"
-	fi
-	# branch
-	if [ $# -eq 2 ]; then
-		# arg in list
-		if [[ $det_list == *$2* ]]; then
-			echo -e "Invalid argument 2: $2. $usage"
-			return -1
-		fi
-		branch+=$2
-		#echo "with branch $branch"
-	fi
-else
-	echo -e "Too many arguments.$usage"
-	return -1
-fi
-
-declare -a deterror=("OK" "OK" "OK" "OK" "OK" "OK")
-
-echo -e "list is ${det[@]}"
-
-# compile each server
-idet=0
-for i in ${det[@]}
-do
-	dir=$i
-	file="${i}_developer"
-	echo -e "Compiling $dir [$file]"
-	cd $dir
-	make clean
-	if make API_BRANCH=$branch; then
-		deterror[$idet]="OK"
-	else
-		deterror[$idet]="FAIL"
-	fi
-	mv bin/$dir bin/$file
-	git add -f bin/$file
-	cp bin/$file /tftpboot/
-	cd ..
-	echo -e "\n\n"
-	((++idet))
-done
-
-echo -e "Results:"
-idet=0
-for i in ${det[@]}
-do
-	printf "%s\t\t= %s\n" "$i" "${deterror[$idet]}"
-	((++idet))
-done
-	
-
-
-

slsDetectorServers/compileEigerServer.sh

@@ -3,21 +3,31 @@
 deterror="OK"
 dir="eigerDetectorServer"
 file="${dir}_developer"
-branch=""
+
+usage="\nUsage: compileAllServers.sh [update_api(opt)]. \n\t update_api if true updates the api to version in VERSION file"
+
+update_api=true
+target=version
 
 # arguments
 if [ $# -eq 1 ]; then
-	branch+=$1
-	#echo "with branch $branch"
+	update_api=$1
+	if not $update_api ; then
+		target=clean
+		
+	fi
 elif [ ! $# -eq 0 ]; then
-	echo -e "Only one optional argument allowed for branch."
+	echo -e "Only one optional argument allowed for update_api."
 	return -1
 fi
 
+if $update_api; then
+	echo "updating api to $(cat ../VERSION)"
+fi
+
 echo -e "Compiling $dir [$file]"
 cd $dir
-make clean
-if make version API_BRANCH=$branch; then
+if make $target; then
 	deterror="OK"
 else
 	deterror="FAIL"
@@ -25,7 +35,6 @@ fi
 
 mv bin/$dir bin/$file
 git add -f bin/$file
-cp bin/$file /tftpboot/
 cd ..
 echo -e "\n\n"
 printf "Result:\t\t= %s\n"  "${deterror}"

slsDetectorServers/ctbDetectorServer/Makefile

@@ -25,11 +25,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APICTB
 version_path=slsDetectorServers/ctbDetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/ctbDetectorServer/slsDetectorFunctionList.c

@@ -15,6 +15,7 @@
 #include "loadPattern.h"
 
 #include <netinet/in.h>
+#include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <unistd.h> // usleep
@@ -93,6 +94,10 @@ void basictests() {
     LOG(logINFOBLUE, ("********* Chip Test Board Virtual Server *********\n"));
 #else
     LOG(logINFOBLUE, ("************* Chip Test Board Server *************\n"));
+    initError = enableBlackfinAMCExternalAccessExtension(initErrorMessage);
+    if (initError == FAIL) {
+        return;
+    }
     initError = defineGPIOpins(initErrorMessage);
     if (initError == FAIL) {
         return;
@@ -438,6 +443,32 @@ uint32_t getDetectorIP() {
     return res;
 }
 
+int enableBlackfinAMCExternalAccessExtension(char *mess) {
+    unsigned int value;
+    const char *file_path = BFIN_AMC_ACCESS_EXTENSION_FNAME;
+    FILE *file = fopen(file_path, "r");
+    if (!file) {
+        strcpy(mess, "Failed to enable blackfin AMC access extension. Could "
+                     "not read EBIU_AMBCTL1\n");
+        LOG(logERROR, (mess));
+        return FAIL;
+    }
+    fscanf(file, "%x", &value);
+    fclose(file);
+
+    value |= BFIN_AMC_ACCESS_EXTENSION_ENA_VAL;
+    file = fopen(file_path, "w");
+    if (!file) {
+        strcpy(mess, "Failed to enable blackfin AMC access extension. Could "
+                     "not write EBIU_AMBCTL1\n");
+        LOG(logERROR, (mess));
+        return FAIL;
+    }
+    fprintf(file, "0x%x", value);
+    fclose(file);
+    return OK;
+}
+
 /* initialization */
 
 void initControlServer() {

slsDetectorServers/eigerDetectorServer/Makefile

@@ -25,11 +25,10 @@ version: clean versioning $(PROGS) #hv9m_blackfin_server
 	
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIEIGER
 version_path=slsDetectorServers/eigerDetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS):  $(OBJS)

slsDetectorServers/gotthard2DetectorServer/Makefile

@@ -24,11 +24,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIGOTTHARD2
 version_path=slsDetectorServers/gotthard2DetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/jungfrauDetectorServer/Makefile

@@ -24,11 +24,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIJUNGFRAU
 version_path=slsDetectorServers/jungfrauDetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/moenchDetectorServer/Makefile

@@ -24,11 +24,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIMOENCH
 version_path=slsDetectorServers/moenchDetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/mythen3DetectorServer/Makefile

@@ -25,11 +25,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIMYTHEN3
 version_path=slsDetectorServers/mythen3DetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/slsDetectorServer/include/blackfin.h

@@ -5,6 +5,23 @@
 #include <inttypes.h>
 #include <sys/types.h>
 
+/** enable support for ARDY signal on interface to FPGA
+ * needed to properly translate avalon_mm_waitrequest in the CTB firmware
+ * https://www.analog.com/media/en/dsp-documentation/processor-manuals/bf537_hwr_Rev3.2.pdf
+ * page 274
+ * */
+#define BFIN_EBIU_AMBCTL1_B2_ARDY_ENA_OFST (0)
+#define BFIN_EBIU_AMBCTL1_B2_ARDY_ENA_MSK                                      \
+    (1 << BFIN_EBIU_AMBCTL1_B2_ARDY_ENA_OFST)
+#define BFIN_EBIU_AMBCTL1_B2_ARDY_POL_OFST (1)
+#define BFIN_EBIU_AMBCTL1_B2_ARDY_POL_MSK                                      \
+    (1 << BFIN_EBIU_AMBCTL1_B2_ARDY_POL_OFST)
+
+#define BFIN_AMC_ACCESS_EXTENSION_ENA_VAL                                      \
+    (BFIN_EBIU_AMBCTL1_B2_ARDY_ENA_MSK | BFIN_EBIU_AMBCTL1_B2_ARDY_POL_MSK)
+#define BFIN_AMC_ACCESS_EXTENSION_FNAME                                        \
+    "/sys/kernel/debug/blackfin/ebiu_amc/EBIU_AMBCTL1"
+
 /** I2C defines */
 #define I2C_CLOCK_MHZ (131.25)
 

slsDetectorServers/slsDetectorServer/include/slsDetectorFunctionList.h

@@ -113,6 +113,10 @@ void setModuleId(int modid);
 u_int64_t getDetectorMAC();
 u_int32_t getDetectorIP();
 
+#if defined(CHIPTESTBOARDD)
+int enableBlackfinAMCExternalAccessExtension(char *mess);
+#endif
+
 // initialization
 void initControlServer();
 void initStopServer();

slsDetectorServers/xilinx_ctbDetectorServer/Makefile

@@ -36,11 +36,10 @@ version: clean versioning $(PROGS)
 
 boot: $(OBJS) 
 
-version_branch=$(API_BRANCH)
 version_name=APIXILINXCTB
 version_path=slsDetectorServers/xilinx_ctbDetectorServer
 versioning: 
-	cd ../../ && echo $(PWD) && echo `tput setaf 6; ./updateAPIVersion.sh $(version_name) $(version_path) $(version_branch);  tput sgr0;`
+	cd ../../ && echo $(PWD) && echo `tput setaf 6; python updateAPIVersion.py $(version_name) $(version_path);  tput sgr0;`
 
 
 $(PROGS): $(OBJS)

slsDetectorServers/xilinx_ctbDetectorServer/slsDetectorFunctionList.c

@@ -1537,8 +1537,12 @@ void *start_timer(void *arg) {
                     packetSize, packetsPerFrame));
 
     // Generate Data
-    char imageData[imageSize];
+    char *imageData = (char *)malloc(imageSize);
     memset(imageData, 0, imageSize);
+    if (imageData == NULL) {
+        LOG(logERROR, ("Can not allocate image.\n"));
+        return NULL;
+    }
     for (int i = 0; i < imageSize; i += sizeof(uint16_t)) {
         *((uint16_t *)(imageData + i)) = i;
     }
@@ -1561,6 +1565,7 @@ void *start_timer(void *arg) {
         usleep(expUs);
 
         int srcOffset = 0;
+        int dataSent = 0;
         // loop packet
         for (int i = 0; i != packetsPerFrame; ++i) {
 
@@ -1577,10 +1582,12 @@ void *start_timer(void *arg) {
             header->column = detPos[X];
 
             // fill data
+            int remaining = imageSize - dataSent;
+            int dataSize = remaining < maxDataSize ? remaining : maxDataSize;
             memcpy(packetData + sizeof(sls_detector_header),
-                   imageData + srcOffset,
-                   (imageSize < maxDataSize ? imageSize : maxDataSize));
-            srcOffset += maxDataSize;
+                   imageData + srcOffset, dataSize);
+            srcOffset += dataSize;
+            dataSent += dataSize;
 
             sendUDPPacket(0, 0, packetData, packetSize);
         }

slsDetectorSoftware/CMakeLists.txt

@@ -100,7 +100,6 @@ if(SLS_USE_TEXTCLIENT)
         target_link_libraries(${val1} 
         slsDetectorStatic
         pthread
-        rt
         )
         SET_SOURCE_FILES_PROPERTIES( src/Caller.cpp PROPERTIES COMPILE_FLAGS "-Wno-unused-variable -Wno-unused-but-set-variable")
 

slsDetectorSoftware/tests/Caller/test-Caller-chiptestboard.cpp

@@ -17,6 +17,119 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("ctb_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::CHIPTESTBOARD ||
+        det_type == defs::XILINX_CHIPTESTBOARD) {
+        int num_frames_to_acquire = 2;
+        // all the test cases
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            test_ctb_config.dbit_offset = 16;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_AND_DIGITAL;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::DIGITAL_AND_TRANSCEIVER;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::DIGITAL_AND_TRANSCEIVER;
+            test_ctb_config.dbit_offset = 16;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::DIGITAL_AND_TRANSCEIVER;
+            test_ctb_config.dbit_list.clear();
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::DIGITAL_AND_TRANSCEIVER;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::DIGITAL_AND_TRANSCEIVER;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::TRANSCEIVER_ONLY;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+        {
+            testCtbAcquireInfo test_ctb_config;
+            test_ctb_config.readout_mode = defs::ANALOG_ONLY;
+            test_ctb_config.dbit_offset = 16;
+            test_ctb_config.dbit_list.clear();
+            test_ctb_config.dbit_reorder = true;
+            REQUIRE_NOTHROW(test_ctb_acquire_with_receiver(
+                test_ctb_config, num_frames_to_acquire, det, caller));
+        }
+    }
+}
+
 /* dacs */
 
 TEST_CASE("dacname", "[.cmdcall]") {

slsDetectorSoftware/tests/Caller/test-Caller-eiger.cpp

@@ -17,6 +17,70 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("eiger_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::EIGER) {
+
+        // save previous state
+        testFileInfo prev_file_info = get_file_state(det);
+        testCommonDetAcquireInfo prev_det_config_info =
+            get_common_acquire_config_state(det);
+
+        // save previous specific det type config
+        auto exptime = det.getExptime().tsquash("inconsistent exptime to test");
+        auto n_rows =
+            det.getReadNRows().tsquash("inconsistent number of rows to test");
+        auto dynamic_range =
+            det.getDynamicRange().tsquash("inconsistent dynamic range to test");
+        REQUIRE(false ==
+                det.getTenGiga().tsquash("inconsistent 10Giga to test"));
+
+        // defaults
+        int num_frames_to_acquire = 2;
+        testFileInfo test_file_info;
+        set_file_state(det, test_file_info);
+        testCommonDetAcquireInfo det_config;
+        det_config.num_frames_to_acquire = num_frames_to_acquire;
+        set_common_acquire_config_state(det, det_config);
+
+        // set default specific det type config
+        det.setExptime(std::chrono::microseconds{200});
+        det.setReadNRows(256);
+        det.setDynamicRange(16);
+
+        // acquire
+        test_acquire_with_receiver(caller, det);
+
+        // check frames caught
+        test_frames_caught(det, num_frames_to_acquire);
+
+        // check file size (assuming local pc)
+        {
+            detParameters par(det_type);
+            // data split into half due to 2 udp interfaces per half module
+            int num_chips = (par.nChipX / 2);
+            int bytes_per_pixel = (dynamic_range / 8);
+            size_t expected_image_size =
+                par.nChanX * par.nChanY * num_chips * bytes_per_pixel;
+            test_acquire_binary_file_size(test_file_info, num_frames_to_acquire,
+                                          expected_image_size);
+        }
+
+        // restore previous state
+        set_file_state(det, prev_file_info);
+        set_common_acquire_config_state(det, prev_det_config_info);
+
+        // restore previous specific det type config
+        det.setExptime(exptime);
+        det.setReadNRows(n_rows);
+        det.setDynamicRange(dynamic_range);
+    }
+}
+
 /** temperature */
 
 TEST_CASE("temp_fpgaext", "[.cmdcall]") {

slsDetectorSoftware/tests/Caller/test-Caller-global.cpp

@@ -4,6 +4,7 @@
 #include "Caller.h"
 #include "catch.hpp"
 #include "sls/Detector.h"
+#include "sls/logger.h"
 #include "tests/globals.h"
 
 namespace sls {
@@ -88,4 +89,227 @@ void test_onchip_dac_caller(defs::dacIndex index, const std::string &dacname,
     }
 }
 
+testFileInfo get_file_state(const Detector &det) {
+    return testFileInfo{
+        det.getFilePath().tsquash("Inconsistent file path"),
+        det.getFileNamePrefix().tsquash("Inconsistent file prefix"),
+        det.getAcquisitionIndex().tsquash(
+            "Inconsistent file acquisition index"),
+        det.getFileWrite().tsquash("Inconsistent file write state"),
+        det.getFileOverWrite().tsquash("Inconsistent file overwrite state"),
+        det.getFileFormat().tsquash("Inconsistent file format")};
+}
+
+void set_file_state(Detector &det, const testFileInfo &file_info) {
+    if (!file_info.file_path.empty())
+        det.setFilePath(file_info.file_path);
+    det.setFileNamePrefix(file_info.file_prefix);
+    det.setAcquisitionIndex(file_info.file_acq_index);
+    det.setFileWrite(file_info.file_write);
+    det.setFileOverWrite(file_info.file_overwrite);
+    det.setFileFormat(file_info.file_format);
+}
+
+void test_acquire_binary_file_size(const testFileInfo &file_info,
+                                   uint64_t num_frames_to_acquire,
+                                   uint64_t expected_image_size) {
+    assert(file_info.file_format == defs::BINARY);
+    std::string fname = file_info.file_path + "/" + file_info.file_prefix +
+                        "_d0_f0_" + std::to_string(file_info.file_acq_index) +
+                        ".raw";
+    uint64_t expected_file_size =
+        num_frames_to_acquire *
+        (expected_image_size + sizeof(defs::sls_receiver_header));
+    auto actual_file_size = std::filesystem::file_size(fname);
+    REQUIRE(actual_file_size == expected_file_size);
+}
+
+void test_frames_caught(const Detector &det, int num_frames_to_acquire) {
+    auto frames_caught = det.getFramesCaught().tsquash(
+        "Inconsistent number of frames caught")[0];
+    REQUIRE(frames_caught == num_frames_to_acquire);
+}
+
+void test_acquire_with_receiver(Caller &caller, const Detector &det) {
+    REQUIRE_NOTHROW(caller.call("rx_start", {}, -1, PUT));
+    REQUIRE_NOTHROW(caller.call("start", {}, -1, PUT));
+    bool idle = false;
+    while (!idle) {
+        std::ostringstream oss;
+        REQUIRE_NOTHROW(caller.call("status", {}, -1, GET));
+        auto statusList = det.getDetectorStatus();
+        if (statusList.any(defs::ERROR)) {
+            throw std::runtime_error("error status while acquiring");
+        }
+        if (statusList.contains_only(defs::IDLE, defs::STOPPED)) {
+            idle = true;
+        }
+    }
+    REQUIRE_NOTHROW(caller.call("rx_stop", {}, -1, PUT));
+}
+
+testCommonDetAcquireInfo get_common_acquire_config_state(const Detector &det) {
+    return testCommonDetAcquireInfo{
+        det.getTimingMode().tsquash("Inconsistent timing mode"),
+        det.getNumberOfFrames().tsquash("Inconsistent number of frames"),
+        det.getNumberOfTriggers().tsquash("Inconsistent number of triggers"),
+        det.getPeriod().tsquash("Inconsistent period")};
+}
+
+void set_common_acquire_config_state(
+    Detector &det, const testCommonDetAcquireInfo &det_config_info) {
+    det.setTimingMode(det_config_info.timing_mode);
+    det.setNumberOfFrames(det_config_info.num_frames_to_acquire);
+    det.setNumberOfTriggers(det_config_info.num_triggers);
+    det.setPeriod(det_config_info.period);
+}
+
+testCtbAcquireInfo get_ctb_config_state(const Detector &det) {
+    testCtbAcquireInfo ctb_config_info{
+        det.getReadoutMode().tsquash("inconsistent readout mode to test"),
+        true,
+        det.getNumberOfAnalogSamples().tsquash(
+            "inconsistent number of analog samples to test"),
+        det.getNumberOfDigitalSamples().tsquash(
+            "inconsistent number of digital samples to test"),
+        det.getNumberOfTransceiverSamples().tsquash(
+            "inconsistent number of transceiver samples to test"),
+        0,
+        det.getTenGigaADCEnableMask().tsquash(
+            "inconsistent ten giga adc enable mask to test"),
+        det.getRxDbitOffset().tsquash("inconsistent rx dbit offset to test"),
+        det.getRxDbitList().tsquash("inconsistent rx dbit list to test"),
+        det.getRxDbitReorder().tsquash("inconsistent rx dbit reorder to test"),
+        det.getTransceiverEnableMask().tsquash(
+            "inconsistent transceiver mask to test")};
+
+    if (det.getDetectorType().tsquash("inconsistent detector type to test") ==
+        slsDetectorDefs::CHIPTESTBOARD) {
+        ctb_config_info.ten_giga =
+            det.getTenGiga().tsquash("inconsistent ten giga enable to test");
+        ctb_config_info.adc_enable_1g = det.getADCEnableMask().tsquash(
+            "inconsistent adc enable mask to test");
+    }
+    return ctb_config_info;
+}
+
+void set_ctb_config_state(Detector &det,
+                          const testCtbAcquireInfo &ctb_config_info) {
+    det.setReadoutMode(ctb_config_info.readout_mode);
+    if (det.getDetectorType().tsquash("inconsistent detector type to test") ==
+        slsDetectorDefs::CHIPTESTBOARD) {
+        det.setTenGiga(ctb_config_info.ten_giga);
+        det.setADCEnableMask(ctb_config_info.adc_enable_1g);
+    }
+    det.setNumberOfAnalogSamples(ctb_config_info.num_adc_samples);
+    det.setNumberOfDigitalSamples(ctb_config_info.num_dbit_samples);
+    det.setNumberOfTransceiverSamples(ctb_config_info.num_trans_samples);
+    det.setTenGigaADCEnableMask(ctb_config_info.adc_enable_10g);
+    det.setRxDbitOffset(ctb_config_info.dbit_offset);
+    det.setRxDbitList(ctb_config_info.dbit_list);
+    det.setRxDbitReorder(ctb_config_info.dbit_reorder);
+    det.setTransceiverEnableMask(ctb_config_info.transceiver_mask);
+}
+
+uint64_t calculate_ctb_image_size(const testCtbAcquireInfo &test_info) {
+    uint64_t num_analog_bytes = 0, num_digital_bytes = 0,
+             num_transceiver_bytes = 0;
+    if (test_info.readout_mode == defs::ANALOG_ONLY ||
+        test_info.readout_mode == defs::ANALOG_AND_DIGITAL) {
+        uint32_t adc_enable_mask =
+            (test_info.ten_giga ? test_info.adc_enable_10g
+                                : test_info.adc_enable_1g);
+        int num_analog_chans = __builtin_popcount(adc_enable_mask);
+        const int num_bytes_per_sample = 2;
+        num_analog_bytes =
+            num_analog_chans * num_bytes_per_sample * test_info.num_adc_samples;
+        LOG(logDEBUG1) << "[Analog Databytes: " << num_analog_bytes << ']';
+    }
+
+    // digital channels
+    if (test_info.readout_mode == defs::DIGITAL_ONLY ||
+        test_info.readout_mode == defs::ANALOG_AND_DIGITAL ||
+        test_info.readout_mode == defs::DIGITAL_AND_TRANSCEIVER) {
+        int num_digital_samples = test_info.num_dbit_samples;
+        if (test_info.dbit_offset > 0) {
+            uint64_t num_digital_bytes_reserved =
+                num_digital_samples * sizeof(uint64_t);
+            num_digital_bytes_reserved -= test_info.dbit_offset;
+            num_digital_samples = num_digital_bytes_reserved / sizeof(uint64_t);
+        }
+        int num_digital_chans = test_info.dbit_list.size();
+        if (num_digital_chans == 0) {
+            num_digital_chans = 64;
+        }
+        if (!test_info.dbit_reorder) {
+            uint32_t num_bits_per_sample = num_digital_chans;
+            if (num_bits_per_sample % 8 != 0) {
+                num_bits_per_sample += (8 - (num_bits_per_sample % 8));
+            }
+            num_digital_bytes = (num_bits_per_sample / 8) * num_digital_samples;
+        } else {
+            uint32_t num_bits_per_bit = num_digital_samples;
+            if (num_bits_per_bit % 8 != 0) {
+                num_bits_per_bit += (8 - (num_bits_per_bit % 8));
+            }
+            num_digital_bytes = num_digital_chans * (num_bits_per_bit / 8);
+        }
+        LOG(logDEBUG1) << "[Digital Databytes: " << num_digital_bytes << ']';
+    }
+    // transceiver channels
+    if (test_info.readout_mode == defs::TRANSCEIVER_ONLY ||
+        test_info.readout_mode == defs::DIGITAL_AND_TRANSCEIVER) {
+        int num_transceiver_chans =
+            __builtin_popcount(test_info.transceiver_mask);
+        const int num_bytes_per_channel = 8;
+        num_transceiver_bytes = num_transceiver_chans * num_bytes_per_channel *
+                                test_info.num_trans_samples;
+        LOG(logDEBUG1) << "[Transceiver Databytes: " << num_transceiver_bytes
+                       << ']';
+    }
+
+    uint64_t image_size =
+        num_analog_bytes + num_digital_bytes + num_transceiver_bytes;
+    LOG(logDEBUG1) << "Expected image size: " << image_size;
+    return image_size;
+}
+
+void test_ctb_acquire_with_receiver(const testCtbAcquireInfo &test_info,
+                                    int64_t num_frames_to_acquire,
+                                    Detector &det, Caller &caller) {
+
+    // save previous state
+    testFileInfo prev_file_info = get_file_state(det);
+    testCommonDetAcquireInfo prev_det_config_info =
+        // overwrite exptime if not using virtual ctb server
+        get_common_acquire_config_state(det);
+    testCtbAcquireInfo prev_ctb_config_info = get_ctb_config_state(det);
+
+    // defaults
+    testFileInfo test_file_info;
+    set_file_state(det, test_file_info);
+    testCommonDetAcquireInfo det_config;
+    det_config.num_frames_to_acquire = num_frames_to_acquire;
+    set_common_acquire_config_state(det, det_config);
+
+    // set ctb config
+    set_ctb_config_state(det, test_info);
+
+    // acquire
+    REQUIRE_NOTHROW(test_acquire_with_receiver(caller, det));
+
+    // check frames caught
+    REQUIRE_NOTHROW(test_frames_caught(det, num_frames_to_acquire));
+
+    // check file size (assuming local pc)
+    uint64_t expected_image_size = calculate_ctb_image_size(test_info);
+    REQUIRE_NOTHROW(test_acquire_binary_file_size(
+        test_file_info, num_frames_to_acquire, expected_image_size));
+
+    // restore previous state
+    set_file_state(det, prev_file_info);
+    set_common_acquire_config_state(det, prev_det_config_info);
+    set_ctb_config_state(det, prev_ctb_config_info);
+}
+
 } // namespace sls

slsDetectorSoftware/tests/Caller/test-Caller-global.h

@@ -1,9 +1,46 @@
 // SPDX-License-Identifier: LGPL-3.0-or-other
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 #pragma once
+
+class Caller;
+#include "sls/Detector.h"
 #include "sls/sls_detector_defs.h"
 
+#include <chrono>
+#include <filesystem>
+#include <thread>
+
 namespace sls {
+struct testFileInfo {
+    std::string file_path{"/tmp"};
+    std::string file_prefix{"sls_test"};
+    int64_t file_acq_index{0};
+    bool file_write{true};
+    bool file_overwrite{true};
+    slsDetectorDefs::fileFormat file_format{slsDetectorDefs::BINARY};
+};
+
+struct testCommonDetAcquireInfo {
+    slsDetectorDefs::timingMode timing_mode{slsDetectorDefs::AUTO_TIMING};
+    int64_t num_frames_to_acquire{2};
+    int64_t num_triggers{1};
+    std::chrono::nanoseconds period{std::chrono::milliseconds{2}};
+};
+
+struct testCtbAcquireInfo {
+    defs::readoutMode readout_mode{defs::ANALOG_AND_DIGITAL};
+    bool ten_giga{false};
+    int num_adc_samples{5000};
+    int num_dbit_samples{6000};
+    int num_trans_samples{288};
+    uint32_t adc_enable_1g{0xFFFFFF00};
+    uint32_t adc_enable_10g{0xFF00FFFF};
+    int dbit_offset{0};
+    std::vector<int> dbit_list{0, 12, 2, 43};
+    bool dbit_reorder{false};
+    uint32_t transceiver_mask{0x3};
+};
+
 void test_valid_port_caller(const std::string &command,
                             const std::vector<std::string> &arguments,
                             int detector_id, int action);
@@ -13,4 +50,26 @@ void test_dac_caller(slsDetectorDefs::dacIndex index,
 void test_onchip_dac_caller(slsDetectorDefs::dacIndex index,
                             const std::string &dacname, int dacvalue);
 
+testFileInfo get_file_state(const Detector &det);
+void set_file_state(Detector &det, const testFileInfo &file_info);
+void test_acquire_binary_file_size(const testFileInfo &file_info,
+                                   uint64_t num_frames_to_acquire,
+                                   uint64_t expected_image_size);
+
+void test_frames_caught(const Detector &det, int num_frames_to_acquire);
+
+void test_acquire_with_receiver(Caller &caller, const Detector &det);
+
+testCommonDetAcquireInfo get_common_acquire_config_state(const Detector &det);
+void set_common_acquire_config_state(
+    Detector &det, const testCommonDetAcquireInfo &det_config_info);
+
+testCtbAcquireInfo get_ctb_config_state(const Detector &det);
+void set_ctb_config_state(Detector &det,
+                          const testCtbAcquireInfo &ctb_config_info);
+uint64_t calculate_ctb_image_size(const testCtbAcquireInfo &test_info);
+void test_ctb_acquire_with_receiver(const testCtbAcquireInfo &test_info,
+                                    int64_t num_frames_to_acquire,
+                                    Detector &det, Caller &caller);
+
 } // namespace sls

slsDetectorSoftware/tests/Caller/test-Caller-gotthard2.cpp

@@ -17,6 +17,69 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("gotthard2_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::GOTTHARD2) {
+
+        // save previous state
+        testFileInfo prev_file_info = get_file_state(det);
+        testCommonDetAcquireInfo prev_det_config_info =
+            get_common_acquire_config_state(det);
+
+        // save previous specific det type config
+        auto exptime = det.getExptime().tsquash("inconsistent exptime to test");
+        auto burst_mode =
+            det.getBurstMode().tsquash("inconsistent burst mode to test");
+        auto number_of_bursts = det.getNumberOfBursts().tsquash(
+            "inconsistent number of bursts to test");
+        auto burst_period =
+            det.getBurstPeriod().tsquash("inconsistent burst period to test");
+
+        // defaults
+        int num_frames_to_acquire = 2;
+        testFileInfo test_file_info;
+        set_file_state(det, test_file_info);
+        testCommonDetAcquireInfo det_config;
+        det_config.num_frames_to_acquire = num_frames_to_acquire;
+        set_common_acquire_config_state(det, det_config);
+
+        // set default specific det type config
+        det.setExptime(std::chrono::microseconds{200});
+        det.setBurstMode(defs::CONTINUOUS_EXTERNAL);
+        det.setNumberOfBursts(1);
+        det.setBurstPeriod(std::chrono::milliseconds{0});
+
+        // acquire
+        test_acquire_with_receiver(caller, det);
+
+        // check frames caught
+        test_frames_caught(det, num_frames_to_acquire);
+
+        // check file size (assuming local pc)
+        {
+            detParameters par(det_type);
+            int bytes_per_pixel = det.getDynamicRange().squash() / 8;
+            size_t expected_image_size =
+                par.nChanX * par.nChipX * bytes_per_pixel;
+            test_acquire_binary_file_size(test_file_info, num_frames_to_acquire,
+                                          expected_image_size);
+        }
+        // restore previous state
+        set_file_state(det, prev_file_info);
+        set_common_acquire_config_state(det, prev_det_config_info);
+
+        // restore previous specific det type config
+        det.setExptime(exptime);
+        det.setBurstMode(burst_mode);
+        det.setNumberOfBursts(number_of_bursts);
+        det.setBurstPeriod(burst_period);
+    }
+}
+
 // time specific measurements for gotthard2
 TEST_CASE("timegotthard2", "[.cmdcall]") {
     Detector det;

slsDetectorSoftware/tests/Caller/test-Caller-jungfrau.cpp

@@ -15,6 +15,65 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("jungfrau_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::JUNGFRAU) {
+
+        // save previous state
+        testFileInfo prev_file_info = get_file_state(det);
+        testCommonDetAcquireInfo prev_det_config_info =
+            get_common_acquire_config_state(det);
+
+        // save previous specific det type config
+        auto exptime = det.getExptime().tsquash("inconsistent exptime to test");
+        auto num_udp_interfaces = det.getNumberofUDPInterfaces().tsquash(
+            "inconsistent number of udp interfaces");
+        auto n_rows =
+            det.getReadNRows().tsquash("inconsistent number of rows to test");
+
+        // defaults
+        int num_frames_to_acquire = 2;
+        testFileInfo test_file_info;
+        set_file_state(det, test_file_info);
+        testCommonDetAcquireInfo det_config;
+        det_config.num_frames_to_acquire = num_frames_to_acquire;
+        set_common_acquire_config_state(det, det_config);
+
+        // set default specific det type config
+        det.setExptime(std::chrono::microseconds{200});
+        det.setReadNRows(512);
+
+        // acquire
+        test_acquire_with_receiver(caller, det);
+
+        // check frames caught
+        test_frames_caught(det, num_frames_to_acquire);
+
+        // check file size (assuming local pc)
+        {
+            detParameters par(det_type);
+            int bytes_per_pixel = det.getDynamicRange().squash() / 8;
+            // if 2 udp interfaces, data split into half
+            size_t expected_image_size = (par.nChanX * par.nChanY * par.nChipX *
+                                          par.nChipY * bytes_per_pixel) /
+                                         num_udp_interfaces;
+            test_acquire_binary_file_size(test_file_info, num_frames_to_acquire,
+                                          expected_image_size);
+        }
+        // restore previous state
+        set_file_state(det, prev_file_info);
+        set_common_acquire_config_state(det, prev_det_config_info);
+
+        // restore previous specific det type config
+        det.setExptime(exptime);
+        det.setReadNRows(n_rows);
+    }
+}
+
 /* dacs */
 
 TEST_CASE("Setting and reading back Jungfrau dacs", "[.cmdcall][.dacs]") {

slsDetectorSoftware/tests/Caller/test-Caller-moench.cpp

@@ -15,6 +15,66 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("moench_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::MOENCH) {
+
+        // save previous state
+        testFileInfo prev_file_info = get_file_state(det);
+        testCommonDetAcquireInfo prev_det_config_info =
+            get_common_acquire_config_state(det);
+
+        // save previous specific det type config
+        auto exptime = det.getExptime().tsquash("inconsistent exptime to test");
+        auto num_udp_interfaces = det.getNumberofUDPInterfaces().tsquash(
+            "inconsistent number of udp interfaces");
+        auto n_rows =
+            det.getReadNRows().tsquash("inconsistent number of rows to test");
+
+        // defaults
+        int num_frames_to_acquire = 2;
+        testFileInfo test_file_info;
+        set_file_state(det, test_file_info);
+        testCommonDetAcquireInfo det_config;
+        det_config.num_frames_to_acquire = num_frames_to_acquire;
+        set_common_acquire_config_state(det, det_config);
+
+        // set default specific det type config
+        det.setExptime(std::chrono::microseconds{200});
+        det.setReadNRows(400);
+
+        // acquire
+        test_acquire_with_receiver(caller, det);
+
+        // check frames caught
+        test_frames_caught(det, num_frames_to_acquire);
+
+        // check file size (assuming local pc)
+        {
+            detParameters par(det_type);
+            int bytes_per_pixel = det.getDynamicRange().squash() / 8;
+            // if 2 udp interfaces, data split into half
+            size_t expected_image_size = (par.nChanX * par.nChanY * par.nChipX *
+                                          par.nChipY * bytes_per_pixel) /
+                                         num_udp_interfaces;
+            test_acquire_binary_file_size(test_file_info, num_frames_to_acquire,
+                                          expected_image_size);
+        }
+
+        // restore previous state
+        set_file_state(det, prev_file_info);
+        set_common_acquire_config_state(det, prev_det_config_info);
+
+        // restore previous specific det type config
+        det.setExptime(exptime);
+        det.setReadNRows(n_rows);
+    }
+}
+
 /* dacs */
 
 TEST_CASE("Setting and reading back moench dacs", "[.cmdcall][.dacs]") {

slsDetectorSoftware/tests/Caller/test-Caller-mythen3.cpp

@@ -17,6 +17,74 @@ namespace sls {
 using test::GET;
 using test::PUT;
 
+TEST_CASE("mythen3_acquire_check_file_size", "[.cmdcall]") {
+    Detector det;
+    Caller caller(&det);
+    auto det_type =
+        det.getDetectorType().tsquash("Inconsistent detector types to test");
+
+    if (det_type == defs::MYTHEN3) {
+
+        // save previous state
+        testFileInfo prev_file_info = get_file_state(det);
+        testCommonDetAcquireInfo prev_det_config_info =
+            get_common_acquire_config_state(det);
+
+        // save previous specific det type config
+        auto exptime =
+            det.getExptimeForAllGates().tsquash("inconsistent exptime to test");
+        auto dynamic_range =
+            det.getDynamicRange().tsquash("inconsistent dynamic range to test");
+        uint32_t counter_mask =
+            det.getCounterMask().tsquash("inconsistent counter mask to test");
+
+        // defaults
+        int num_frames_to_acquire = 2;
+        testFileInfo test_file_info;
+        set_file_state(det, test_file_info);
+        testCommonDetAcquireInfo det_config;
+        det_config.num_frames_to_acquire = num_frames_to_acquire;
+        set_common_acquire_config_state(det, det_config);
+
+        // set default specific det type config
+        det.setExptime(-1, std::chrono::microseconds{200});
+        int test_dynamic_range = 16;
+        det.setDynamicRange(test_dynamic_range);
+        int test_counter_mask = 0x3;
+        int num_counters = __builtin_popcount(test_counter_mask);
+        det.setCounterMask(test_counter_mask);
+
+        // acquire
+        test_acquire_with_receiver(caller, det);
+
+        // check frames caught
+        test_frames_caught(det, num_frames_to_acquire);
+
+        // check file size (assuming local pc)
+        {
+            detParameters par(det_type);
+            int bytes_per_pixel = test_dynamic_range / 8;
+            int num_channels_per_counter = par.nChanX / 3;
+            size_t expected_image_size = num_channels_per_counter *
+                                         num_counters * par.nChipX *
+                                         bytes_per_pixel;
+            test_acquire_binary_file_size(test_file_info, num_frames_to_acquire,
+                                          expected_image_size);
+        }
+
+        // restore previous state
+        set_file_state(det, prev_file_info);
+        set_common_acquire_config_state(det, prev_det_config_info);
+
+        // restore previous specific det type config
+        for (int iGate = 0; iGate < 3; ++iGate) {
+            det.setExptime(iGate, exptime[iGate]);
+        }
+        det.setDynamicRange(dynamic_range);
+        det.setCounterMask(counter_mask);
+    }
+}
+
 /* dacs */
 
 TEST_CASE("Setting and reading back MYTHEN3 dacs", "[.cmdcall][.dacs]") {

slsDetectorSoftware/tests/Caller/test-Caller.cpp

@@ -12,6 +12,7 @@
 #include <thread>
 
 #include "tests/globals.h"
+#include <filesystem>
 
 namespace sls {
 

slsReceiverSoftware/src/DataProcessor.cpp

@@ -352,16 +352,20 @@ void DataProcessor::ProcessAnImage(sls_receiver_header &header, size_t &size,
     if (framePadding && nump < generalData->packetsPerFrame)
         PadMissingPackets(header, data);
 
-    // rearrange ctb digital bits
-    if (!generalData->ctbDbitList.empty()) {
-        ArrangeDbitData(size, data);
-    } else if (generalData->ctbDbitReorder) {
-        std::vector<int> ctbDbitList(64);
-        std::iota(ctbDbitList.begin(), ctbDbitList.end(), 0);
-        generalData->SetctbDbitList(ctbDbitList);
-        ArrangeDbitData(size, data);
-    } else if (generalData->ctbDbitOffset > 0) {
-        RemoveTrailingBits(size, data);
+    if (generalData->readoutType == slsDetectorDefs::DIGITAL_ONLY ||
+        generalData->readoutType == slsDetectorDefs::ANALOG_AND_DIGITAL ||
+        generalData->readoutType == slsDetectorDefs::DIGITAL_AND_TRANSCEIVER) {
+        // rearrange ctb digital bits
+        if (!generalData->ctbDbitList.empty()) {
+            ArrangeDbitData(size, data);
+        } else if (generalData->ctbDbitReorder) {
+            std::vector<int> ctbDbitList(64);
+            std::iota(ctbDbitList.begin(), ctbDbitList.end(), 0);
+            generalData->SetctbDbitList(ctbDbitList);
+            ArrangeDbitData(size, data);
+        } else if (generalData->ctbDbitOffset > 0) {
+            RemoveTrailingBits(size, data);
+        }
     }
 
     // 'stream Image' check has to be done here before crop image
@@ -675,11 +679,11 @@ void DataProcessor::ArrangeDbitData(size_t &size, char *data) {
     memcpy(data + nAnalogDataBytes, result.data(),
            totalNumBytes * sizeof(uint8_t));
 
-    LOG(logDEBUG1) << "totalNumBytes: " << totalNumBytes
+    LOG(logDEBUG1) << "nDigitalDataBytes: " << totalNumBytes
                    << " nAnalogDataBytes:" << nAnalogDataBytes
                    << " ctbDbitOffset:" << ctbDbitOffset
                    << " nTransceiverDataBytes:" << nTransceiverDataBytes
-                   << " size:" << size;
+                   << " toal size:" << size;
 }
 
 void DataProcessor::CropImage(size_t &size, char *data) {

slsReceiverSoftware/src/DataProcessor.h

@@ -168,7 +168,7 @@ class DataProcessor : private virtual slsDetectorDefs, public ThreadObject {
     uint32_t streamingTimerInMs;
     uint32_t streamingStartFnum;
     uint32_t currentFreqCount{0};
-    struct timespec timerbegin{};
+    struct timespec timerbegin {};
     bool framePadding;
     std::atomic<bool> startedFlag{false};
     std::atomic<uint64_t> firstIndex{0};

slsReceiverSoftware/src/FrameSynchronizerApp.cpp

@@ -104,11 +104,11 @@ void zmq_free(void *data, void *hint) { delete[] static_cast<char *>(data); }
 void print_frames(const PortFrameMap &frame_port_map) {
     LOG(sls::logDEBUG) << "Printing frames";
     for (const auto &it : frame_port_map) {
-        uint16_t udpPort = it.first;
+        const uint16_t udpPort = it.first;
         const auto &frame_map = it.second;
         LOG(sls::logDEBUG) << "UDP port: " << udpPort;
         for (const auto &frame : frame_map) {
-            uint64_t fnum = frame.first;
+            const uint64_t fnum = frame.first;
             const auto &msg_list = frame.second;
             LOG(sls::logDEBUG)
                 << "  acq index: " << fnum << '[' << msg_list.size() << ']';
@@ -127,30 +127,26 @@ std::set<uint64_t> get_valid_fnums(const PortFrameMap &port_frame_map) {
 
     // collect all unique frame numbers from all ports
     std::set<uint64_t> unique_fnums;
-    for (auto it = port_frame_map.begin(); it != port_frame_map.begin(); ++it) {
-        const FrameMap &frame_map = it->second;
-        for (auto frame = frame_map.begin(); frame != frame_map.end();
-             ++frame) {
-            unique_fnums.insert(frame->first);
+    for (const auto &it : port_frame_map) {
+        const FrameMap &frame_map = it.second;
+        for (const auto &frame : frame_map) {
+            unique_fnums.insert(frame.first);
         }
     }
 
     // collect valid frame numbers
     for (auto &fnum : unique_fnums) {
         bool is_valid = true;
-        for (auto it = port_frame_map.begin(); it != port_frame_map.end();
-             ++it) {
-            uint16_t port = it->first;
-            const FrameMap &frame_map = it->second;
+        for (const auto &it : port_frame_map) {
+            const uint16_t port = it.first;
+            const FrameMap &frame_map = it.second;
             auto frame = frame_map.find(fnum);
             // invalid: fnum missing in one port
             if (frame == frame_map.end()) {
                 LOG(sls::logDEBUG)
                     << "Fnum " << fnum << " is missing in port " << port;
-                // invalid: fnum greater than all in that port
-                auto last_frame = std::prev(frame_map.end());
-                auto last_fnum = last_frame->first;
-                if (fnum > last_fnum) {
+                auto upper_frame = frame_map.upper_bound(fnum);
+                if (upper_frame == frame_map.end()) {
                     LOG(sls::logDEBUG) << "And no larger fnum found. Fnum "
                                        << fnum << " is invalid.\n";
                     is_valid = false;
@@ -220,18 +216,26 @@ void Correlate(FrameStatus *stat) {
                 // sending all valid fnum data packets
                 for (const auto &fnum : valid_fnums) {
                     ZmqMsgList msg_list;
-                    PortFrameMap &port_frame_map = stat->frames;
-                    for (auto it = port_frame_map.begin();
-                         it != port_frame_map.end(); ++it) {
-                        uint16_t port = it->first;
-                        const FrameMap &frame_map = it->second;
+                    for (const auto &it : stat->frames) {
+                        const uint16_t port = it.first;
+                        const FrameMap &frame_map = it.second;
                         auto frame = frame_map.find(fnum);
                         if (frame != frame_map.end()) {
                             msg_list.insert(msg_list.end(),
                                             stat->frames[port][fnum].begin(),
                                             stat->frames[port][fnum].end());
-                            // clean up
-                            for (zmq_msg_t *msg : stat->frames[port][fnum]) {
+                        }
+                    }
+                    LOG(printHeadersLevel)
+                        << "Sending data packets for fnum " << fnum;
+                    zmq_send_multipart(socket, msg_list);
+                    // clean up
+                    for (const auto &it : stat->frames) {
+                        const uint16_t port = it.first;
+                        const FrameMap &frame_map = it.second;
+                        auto frame = frame_map.find(fnum);
+                        if (frame != frame_map.end()) {
+                            for (zmq_msg_t *msg : frame->second) {
                                 if (msg) {
                                     zmq_msg_close(msg);
                                     delete msg;
@@ -240,9 +244,6 @@ void Correlate(FrameStatus *stat) {
                             stat->frames[port].erase(fnum);
                         }
                     }
-                    LOG(printHeadersLevel)
-                        << "Sending data packets for fnum " << fnum;
-                    zmq_send_multipart(socket, msg_list);
                 }
             }
             // sending all end packets
@@ -256,6 +257,21 @@ void Correlate(FrameStatus *stat) {
                     }
                 }
                 stat->ends.clear();
+                // clean up old frames
+                for (auto &it : stat->frames) {
+                    FrameMap &frame_map = it.second;
+                    for (auto &frame : frame_map) {
+                        for (zmq_msg_t *msg : frame.second) {
+                            if (msg) {
+                                zmq_msg_close(msg);
+                                delete msg;
+                            }
+                        }
+                        frame.second.clear();
+                    }
+                    frame_map.clear();
+                }
+                stat->frames.clear();
             }
         }
     }

slsReceiverSoftware/src/GeneralData.h

@@ -63,8 +63,8 @@ class GeneralData {
     slsDetectorDefs::frameDiscardPolicy frameDiscardMode{
         slsDetectorDefs::NO_DISCARD};
 
-    GeneralData() {};
-    virtual ~GeneralData() {};
+    GeneralData(){};
+    virtual ~GeneralData(){};
 
     // Returns the pixel depth in byte, 4 bits being 0.5 byte
     float GetPixelDepth() { return float(dynamicRange) / 8; }

slsReceiverSoftware/tests/test-ArrangeDataBasedOnBitList.cpp

@@ -47,8 +47,8 @@ class GeneralDataTest : public GeneralData {
 // dummy DataProcessor class for testing
 class DataProcessorTest : public DataProcessor {
   public:
-    DataProcessorTest() : DataProcessor(0) {};
-    ~DataProcessorTest() {};
+    DataProcessorTest() : DataProcessor(0){};
+    ~DataProcessorTest(){};
     void ArrangeDbitData(size_t &size, char *data) {
         DataProcessor::ArrangeDbitData(size, data);
     }

slsSupportLib/CMakeLists.txt

@@ -88,6 +88,7 @@ message(STATUS "RAPID: ${SLS_INTERNAL_RAPIDJSON_DIR}")
 target_link_libraries(slsSupportObject 
   PUBLIC
     slsProjectOptions 
+    ${STD_FS_LIB} # from helpers.cmake
     
   PRIVATE
     slsProjectWarnings

slsSupportLib/include/sls/StaticVector.h

@@ -113,10 +113,10 @@ template <typename T, size_t Capacity> class StaticVector {
     // auto begin() noexcept -> decltype(data_.begin()) { return data_.begin();
     // }
     const_iterator begin() const noexcept { return data_.begin(); }
-    iterator end() noexcept { return &data_[current_size]; }
-    const_iterator end() const noexcept { return &data_[current_size]; }
+    iterator end() noexcept { return data_.begin()+current_size; }
+    const_iterator end() const noexcept { return data_.begin()+current_size; }
     const_iterator cbegin() const noexcept { return data_.cbegin(); }
-    const_iterator cend() const noexcept { return &data_[current_size]; }
+    const_iterator cend() const noexcept { return  data_.cbegin()+current_size; }
 
     void size_check(size_type s) const {
         if (s > Capacity) {

slsSupportLib/include/sls/ToString.h

@@ -47,6 +47,8 @@ std::string ToString(const defs::polarity s);
 std::string ToString(const defs::timingInfoDecoder s);
 std::string ToString(const defs::collectionMode s);
 
+std::string ToString(bool value);
+
 std::string ToString(const slsDetectorDefs::xy &coord);
 std::ostream &operator<<(std::ostream &os, const slsDetectorDefs::xy &coord);
 std::string ToString(const slsDetectorDefs::ROI &roi);

slsSupportLib/include/sls/Version.h

@@ -11,7 +11,7 @@ class Version {
   private:
     std::string version_;
     std::string date_;
-    const std::string defaultBranch_ = "developer";
+    inline static const std::string defaultVersion_[] = {"developer", "0.0.0"};
 
   public:
     explicit Version(const std::string &s);

slsSupportLib/include/sls/versionAPI.h

@@ -1,12 +1,13 @@
 // SPDX-License-Identifier: LGPL-3.0-or-other
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 /** API versions */
-#define APILIB       "developer 0x241122"
-#define APIRECEIVER  "developer 0x241122"
-#define APICTB       "developer 0x250310"
-#define APIGOTTHARD2 "developer 0x250310"
-#define APIMOENCH    "developer 0x250310"
-#define APIEIGER     "developer 0x250310"
-#define APIXILINXCTB "developer 0x250311"
-#define APIJUNGFRAU  "developer 0x250318"
-#define APIMYTHEN3   "developer 0x250409"
+#define APILIB       "0.0.0 0x250523"
+#define APIRECEIVER  "0.0.0 0x250523"
+#define APICTB       "0.0.0 0x250523"
+#define APIGOTTHARD2 "0.0.0 0x250523"
+#define APIMOENCH    "0.0.0 0x250523"
+#define APIEIGER     "0.0.0 0x250523"
+#define APIXILINXCTB "0.0.0 0x250523"
+#define APIJUNGFRAU  "0.0.0 0x250523"
+#define APIMYTHEN3   "0.0.0 0x250523"
+

slsSupportLib/src/ToString.cpp

@@ -5,6 +5,13 @@
 
 namespace sls {
 
+
+std::string ToString(bool value) {
+    return value ? "1" : "0";
+}
+
+
+
 std::string ToString(const slsDetectorDefs::xy &coord) {
     std::ostringstream oss;
     oss << '[' << coord.x << ", " << coord.y << ']';

slsSupportLib/src/Version.cpp

@@ -21,7 +21,8 @@ Version::Version(const std::string &s) {
 }
 
 bool Version::hasSemanticVersioning() const {
-    return version_ != defaultBranch_;
+
+    return (version_ != defaultVersion_[0]) && (version_ != defaultVersion_[1]);
 }
 
 std::string Version::getVersion() const { return version_; }

slsSupportLib/tests/CMakeLists.txt

@@ -14,6 +14,7 @@ target_sources(tests PRIVATE
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-TypeTraits.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-UdpRxSocket.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-logger.cpp
+                ${CMAKE_CURRENT_SOURCE_DIR}/test-Version.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-ZmqSocket.cpp
                 )
 

slsSupportLib/tests/test-StaticVector.cpp

@@ -8,12 +8,15 @@
 #include <sstream>
 #include <vector>
 
-namespace sls {
+
+using sls::StaticVector;
 
 TEST_CASE("StaticVector is a container") {
-    REQUIRE(is_container<StaticVector<int, 7>>::value == true);
+    REQUIRE(sls::is_container<StaticVector<int, 7>>::value == true);
 }
 
+
+
 TEST_CASE("Comparing StaticVector containers") {
     StaticVector<int, 5> a{0, 1, 2};
     StaticVector<int, 5> b{0, 1, 2};
@@ -90,10 +93,17 @@ TEST_CASE("Copy construct from array") {
     REQUIRE(fcc == arr);
 }
 
+TEST_CASE("Construct from a smaller StaticVector") {
+    StaticVector<int, 3> sv{1, 2, 3};
+    StaticVector<int, 5> sv2{sv};
+    REQUIRE(sv == sv2);
+}
+
 TEST_CASE("Free function and method gives the same iterators") {
     StaticVector<int, 3> fcc{1, 2, 3};
     REQUIRE(std::begin(fcc) == fcc.begin());
 }
+
 SCENARIO("StaticVectors can be sized and resized", "[support]") {
 
     GIVEN("A default constructed container") {
@@ -246,23 +256,23 @@ SCENARIO("Sorting, removing and other manipulation of a container",
                 REQUIRE(a[3] == 90);
             }
         }
-        // WHEN("Sorting is done using free function for begin and end") {
-        //     std::sort(begin(a), end(a));
-        //     THEN("it also works") {
-        //         REQUIRE(a[0] == 12);
-        //         REQUIRE(a[1] == 12);
-        //         REQUIRE(a[2] == 14);
-        //         REQUIRE(a[3] == 90);
-        //     }
-        // }
-        // WHEN("Erasing elements of a certain value") {
-        //     a.erase(std::remove(begin(a), end(a), 12));
-        //     THEN("all elements of that value are removed") {
-        //         REQUIRE(a.size() == 2);
-        //         REQUIRE(a[0] == 14);
-        //         REQUIRE(a[1] == 90);
-        //     }
-        // }
+        WHEN("Sorting is done using free function for begin and end") {
+            std::sort(std::begin(a), std::end(a));
+            THEN("it also works") {
+                REQUIRE(a[0] == 12);
+                REQUIRE(a[1] == 12);
+                REQUIRE(a[2] == 14);
+                REQUIRE(a[3] == 90);
+            }
+        }
+        WHEN("Erasing elements of a certain value") {
+            a.erase(std::remove(std::begin(a), std::end(a), 12));
+            THEN("all elements of that value are removed") {
+                REQUIRE(a.size() == 2);
+                REQUIRE(a[0] == 14);
+                REQUIRE(a[1] == 90);
+            }
+        }
     }
 }
 
@@ -335,4 +345,3 @@ TEST_CASE("StaticVector stream") {
     REQUIRE(oss.str() == "[33, 85667, 2]");
 }
 
-} // namespace sls

slsSupportLib/tests/test-ToString.cpp

@@ -16,6 +16,17 @@ namespace sls {
 
 using namespace sls::time;
 
+TEST_CASE("Convert bool to string", "[support]") {
+    REQUIRE(ToString(true) == "1");
+    REQUIRE(ToString(false) == "0");
+}
+
+TEST_CASE("Convert string to bool", "[support]") {
+    REQUIRE(StringTo<bool>("1") == true);
+    REQUIRE(StringTo<bool>("0") == false);
+}
+
+
 TEST_CASE("Integer conversions", "[support]") {
     REQUIRE(ToString(0) == "0");
     REQUIRE(ToString(1) == "1");

slsSupportLib/tests/test-Version.cpp

@@ -0,0 +1,19 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#include "catch.hpp"
+#include "sls/Version.h"
+
+namespace sls {
+
+TEST_CASE("check if version is semantic", "[.version]") {
+
+    auto [version_string, has_semantic_version] =
+        GENERATE(std::make_tuple("developer 0x250512", false),
+                 std::make_tuple("0.0.0 0x250512", false));
+
+    Version version(version_string);
+
+    CHECK(version.hasSemanticVersioning() == has_semantic_version);
+}
+
+} // namespace sls

tests/CMakeLists.txt

@@ -60,3 +60,5 @@ include(Catch)
 catch_discover_tests(tests)
 
 configure_file(scripts/test_simulators.py ${CMAKE_BINARY_DIR}/bin/test_simulators.py COPYONLY)
+configure_file(scripts/test_frame_synchronizer.py ${CMAKE_BINARY_DIR}/bin/test_frame_synchronizer.py COPYONLY)
+configure_file(scripts/utils_for_test.py ${CMAKE_BINARY_DIR}/bin/utils_for_test.py COPYONLY)

tests/scripts/test_frame_synchronizer.py

@@ -0,0 +1,141 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2021 Contributors to the SLS Detector Package
+'''
+This file is used to start up simulators, frame synchronizer, pull sockets, acquire, test and kill them finally.
+'''
+
+import sys, time
+import traceback, json
+
+from slsdet import Detector
+from slsdet.defines import DEFAULT_TCP_RX_PORTNO
+
+from utils_for_test import (
+    Log,
+    LogLevel,
+    RuntimeException,
+    checkIfProcessRunning,
+    killProcess,
+    cleanup,
+    cleanSharedmemory,
+    startProcessInBackground,
+    startProcessInBackgroundWithLogFile,
+    checkLogForErrors,
+    startDetectorVirtualServer,
+    loadConfig,
+    ParseArguments
+)
+
+LOG_PREFIX_FNAME = '/tmp/slsFrameSynchronizer_test'
+MAIN_LOG_FNAME = LOG_PREFIX_FNAME + '_log.txt'
+PULL_SOCKET_PREFIX_FNAME = LOG_PREFIX_FNAME + '_pull_socket_'
+
+
+def startFrameSynchronizerPullSocket(name, fp):
+    fname = PULL_SOCKET_PREFIX_FNAME + name + '.txt'
+    cmd = ['python', '-u', 'frameSynchronizerPullSocket.py']  
+    startProcessInBackgroundWithLogFile(cmd, fp, fname)
+    time.sleep(1)
+    checkLogForErrors(fp, fname)
+    
+
+
+def startFrameSynchronizer(num_mods, fp):
+    cmd = ['slsFrameSynchronizer', str(DEFAULT_TCP_RX_PORTNO), str(num_mods)]
+    # in 10.0.0
+    #cmd = ['slsFrameSynchronizer', '-p', str(DEFAULT_TCP_RX_PORTNO), '-n', str(num_mods)]
+    startProcessInBackground(cmd, fp)
+    time.sleep(1)
+
+
+def acquire(fp, det):
+    Log(LogLevel.INFO, 'Acquiring')
+    Log(LogLevel.INFO, 'Acquiring', fp)
+    det.acquire()
+
+
+def testFramesCaught(name, det, num_frames):
+    fnum = det.rx_framescaught[0]
+    if fnum != num_frames:
+        raise RuntimeException(f"{name} caught only {fnum}. Expected {num_frames}") 
+    
+    Log(LogLevel.INFOGREEN, f'Frames caught test passed for {name}')
+    Log(LogLevel.INFOGREEN, f'Frames caught test passed for {name}', fp)
+
+
+def testZmqHeadetTypeCount(name, det, num_mods, num_frames, fp):
+
+    Log(LogLevel.INFO, f"Testing Zmq Header type count for {name}")
+    Log(LogLevel.INFO, f"Testing Zmq Header type count for {name}", fp)
+    htype_counts = {
+        "header": 0,
+        "series_end": 0,
+        "module": 0
+    }
+
+    try:
+        # get a count of each htype from file
+        pull_socket_fname = PULL_SOCKET_PREFIX_FNAME + name + '.txt'
+        with open(pull_socket_fname, 'r') as log_fp:
+            for line in log_fp:
+                line = line.strip()
+                if not line or not line.startswith('{'):
+                    continue
+                try:
+                    data = json.loads(line)
+                    htype = data.get("htype")
+                    if htype in htype_counts:
+                        htype_counts[htype] += 1
+                except json.JSONDecodeError:
+                    continue
+
+        # test if file contents matches expected counts
+        num_ports_per_module = 1 if name == "gotthard2" else det.numinterfaces
+        total_num_frame_parts = num_ports_per_module * num_mods * num_frames
+        for htype, expected_count in [("header", num_mods), ("series_end", num_mods), ("module", total_num_frame_parts)]:
+            if htype_counts[htype] != expected_count:
+                msg = f"Expected {expected_count} '{htype}' entries, found {htype_counts[htype]}"
+                raise RuntimeException(msg)
+    except Exception as e:
+        raise RuntimeException(f'Failed to get zmq header count type. Error:{str(e)}') from e
+        
+    Log(LogLevel.INFOGREEN, f"Zmq Header type count test passed for {name}")
+    Log(LogLevel.INFOGREEN, f"Zmq Header type count test passed for {name}", fp)
+
+
+def startTestsForAll(args, fp):
+    for server in args.servers:
+        try:
+            Log(LogLevel.INFOBLUE, f'Synchronizer Tests for {server}')
+            Log(LogLevel.INFOBLUE, f'Synchronizer Tests for {server}', fp)
+            cleanup(fp)
+            startDetectorVirtualServer(server, args.num_mods, fp)
+            startFrameSynchronizerPullSocket(server, fp)
+            startFrameSynchronizer(args.num_mods, fp)
+            d = loadConfig(name=server, rx_hostname=args.rx_hostname, settingsdir=args.settingspath, fp=fp, num_mods=args.num_mods, num_frames=args.num_frames)
+            acquire(fp, d)
+            testFramesCaught(server, d, args.num_frames)
+            testZmqHeadetTypeCount(server, d, args.num_mods, args.num_frames, fp)
+            Log(LogLevel.INFO, '\n')
+        except Exception as e:
+            raise RuntimeException(f'Synchronizer Tests failed') from e
+
+    Log(LogLevel.INFOGREEN, 'Passed all synchronizer tests for all detectors \n' + str(args.servers))
+  
+
+if __name__ == '__main__':
+    args = ParseArguments(description='Automated tests to test frame synchronizer', default_num_mods=2)
+
+    Log(LogLevel.INFOBLUE, '\nLog File: ' + MAIN_LOG_FNAME + '\n') 
+
+    with open(MAIN_LOG_FNAME, 'w') as fp:
+        try:
+            startTestsForAll(args, fp)
+            cleanup(fp)
+        except Exception as e:
+            with open(MAIN_LOG_FNAME, 'a') as fp_error:
+                traceback.print_exc(file=fp_error)
+            cleanup(fp)
+            Log(LogLevel.ERROR, f'Tests Failed.')
+
+

tests/scripts/test_simulators.py

@@ -4,251 +4,86 @@
 This file is used to start up simulators, receivers and run all the tests on them and finally kill the simulators and receivers.
 '''
 import argparse
-import os, sys, subprocess, time, colorama
+import sys, subprocess, time, traceback
 
-from colorama import Fore
-from slsdet import Detector, detectorType, detectorSettings
-from slsdet.defines import DEFAULT_TCP_CNTRL_PORTNO, DEFAULT_TCP_RX_PORTNO, DEFAULT_UDP_DST_PORTNO
-HALFMOD2_TCP_CNTRL_PORTNO=1955
-HALFMOD2_TCP_RX_PORTNO=1957
+from slsdet import Detector
+from slsdet.defines import DEFAULT_TCP_RX_PORTNO
 
-colorama.init(autoreset=True)
-
-class RuntimeException (Exception):
-    def __init__ (self, message):
-        super().__init__(Fore.RED + message)
-    
-def Log(color, message):
-    print('\n' + color + message, flush=True)
+from utils_for_test import (
+    Log,
+    LogLevel,
+    RuntimeException,
+    checkIfProcessRunning,
+    killProcess,
+    cleanup,
+    cleanSharedmemory,
+    startProcessInBackground,
+    runProcessWithLogFile,
+    startDetectorVirtualServer,
+    loadConfig,
+    ParseArguments
+)
 
 
-def checkIfProcessRunning(processName):
-    cmd = f"pgrep -f {processName}"
-    res = subprocess.getoutput(cmd)
-    return bool(res.strip())
+LOG_PREFIX_FNAME = '/tmp/slsDetectorPackage_virtual_test'
+MAIN_LOG_FNAME = LOG_PREFIX_FNAME + '_log.txt'
+GENERAL_TESTS_LOG_FNAME = LOG_PREFIX_FNAME + '_results_general.txt'
+CMD_TEST_LOG_PREFIX_FNAME = LOG_PREFIX_FNAME + '_results_cmd_'
 
 
-def killProcess(name):
-    if checkIfProcessRunning(name):
-        Log(Fore.GREEN, 'killing ' + name)
-        p = subprocess.run(['killall', name])
-        if p.returncode != 0:
-            raise RuntimeException('killall failed for ' + name)
+def startReceiver(num_mods, fp):
+    if num_mods == 1:
+        cmd = ['slsReceiver']
     else:
-        print('process not running : ' + name)
+        cmd = ['slsMultiReceiver', str(DEFAULT_TCP_RX_PORTNO), str(num_mods)]
+        # in 10.0.0
+        #cmd = ['slsMultiReceiver', '-p', str(DEFAULT_TCP_RX_PORTNO), '-n', str(num_mods)]
+    startProcessInBackground(cmd, fp)
+    time.sleep(1)
 
-
-def killAllStaleProcesses(fp):
-    killProcess('eigerDetectorServer_virtual')
-    killProcess('jungfrauDetectorServer_virtual')
-    killProcess('mythen3DetectorServer_virtual')
-    killProcess('gotthard2DetectorServer_virtual')
-    killProcess('ctbDetectorServer_virtual')
-    killProcess('moenchDetectorServer_virtual')
-    killProcess('xilinx_ctbDetectorServer_virtual')
-    killProcess('slsReceiver')
-    killProcess('slsMultiReceiver')
-    cleanSharedmemory(fp)
-
-def cleanup(name, fp):
-    '''
-    kill both servers, receivers and clean shared memory
-    '''
-    Log(Fore.GREEN, 'Cleaning up...')
-    killProcess(name + 'DetectorServer_virtual')
-    killProcess('slsReceiver')
-    killProcess('slsMultiReceiver')
-    cleanSharedmemory(fp)
-
-def cleanSharedmemory(fp):
-    Log(Fore.GREEN, 'Cleaning up shared memory...')
+def startGeneralTests(fp):
+    fname = GENERAL_TESTS_LOG_FNAME
+    cmd = ['tests', '--abort', '-s']
     try:
-        p = subprocess.run(['sls_detector_get', 'free'], stdout=fp, stderr=fp)
-    except:
-        Log(Fore.RED, 'Could not free shared memory')
-        raise
-
-def startProcessInBackground(name):
-    try:
-        # in background and dont print output
-        p = subprocess.Popen(name.split(), stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, restore_signals=False) 
-        Log(Fore.GREEN, 'Starting up ' + name + ' ...')
+        cleanup(fp)
+        runProcessWithLogFile('General Tests', cmd, fp, fname)
     except Exception as e:
-        Log(Fore.RED, f'Could not start {name}:{e}')
-        raise
-
-def startServer(name):
-    
-    startProcessInBackground(name + 'DetectorServer_virtual')
-    # second half
-    if name == 'eiger':
-        startProcessInBackground(name + 'DetectorServer_virtual -p' + str(HALFMOD2_TCP_CNTRL_PORTNO))
-    tStartup = 6
-    Log(Fore.WHITE, 'Takes ' + str(tStartup) + ' seconds... Please be patient')
-    time.sleep(tStartup)
-
-def startReceiver(name):
-    startProcessInBackground('slsReceiver')
-    # second half
-    if name == 'eiger':
-        startProcessInBackground('slsReceiver -t' + str(HALFMOD2_TCP_RX_PORTNO))
-    time.sleep(2)
-
-def loadConfig(name, rx_hostname, settingsdir):
-    Log(Fore.GREEN, 'Loading config')
-    try:
-        d = Detector()
-        if name == 'eiger':
-            d.hostname = 'localhost:' + str(DEFAULT_TCP_CNTRL_PORTNO) + '+localhost:' + str(HALFMOD2_TCP_CNTRL_PORTNO)
-            #d.udp_dstport = {2: 50003} 
-            # will set up for every module
-            d.udp_dstport = DEFAULT_UDP_DST_PORTNO
-            d.udp_dstport2 = DEFAULT_UDP_DST_PORTNO + 1
-            d.rx_hostname = rx_hostname + ':' + str(DEFAULT_TCP_RX_PORTNO) + '+' + rx_hostname + ':' + str(HALFMOD2_TCP_RX_PORTNO)
-            d.udp_dstip = 'auto'
-            d.trimen = [4500, 5400, 6400]
-            d.settingspath = settingsdir + '/eiger/'
-            d.setThresholdEnergy(4500, detectorSettings.STANDARD)
-        else:
-            d.hostname = 'localhost'
-            d.rx_hostname = rx_hostname
-            d.udp_dstip = 'auto'
-            d.udp_srcip = 'auto'
-        if d.type == detectorType.JUNGFRAU or d.type == detectorType.MOENCH or d.type == detectorType.XILINX_CHIPTESTBOARD:
-            d.powerchip = 1
-        if d.type == detectorType.XILINX_CHIPTESTBOARD:
-            d.configureTransceiver()
-    except:
-        Log(Fore.RED, 'Could not load config for ' + name)
-        raise
-
-def startCmdTests(name, fp, fname):
-    Log(Fore.GREEN, 'Cmd Tests for ' + name)
-    cmd = 'tests --abort [.cmdcall] -s -o ' + fname
-    try:
-        subprocess.run(cmd.split(), stdout=fp, stderr=fp, check=True, text=True)
-    except subprocess.CalledProcessError as e:
-        pass
-
-    with open (fname, 'r') as f:
-        for line in f:
-            if "FAILED" in line:
-                msg = 'Cmd tests failed for ' + name + '!!!'
-                sys.stdout = original_stdout
-                Log(Fore.RED, msg)
-                Log(Fore.RED, line)
-                sys.stdout = fp
-                raise Exception(msg)
-
-    Log(Fore.GREEN, 'Cmd Tests successful for ' + name)
-
-def startGeneralTests(fp, fname):
-    Log(Fore.GREEN, 'General Tests')
-    cmd = 'tests --abort -s -o ' + fname
-    try:
-        subprocess.run(cmd.split(), stdout=fp, stderr=fp, check=True, text=True)
-    except subprocess.CalledProcessError as e:
-        pass
-
-    with open (fname, 'r') as f:
-        for line in f:
-            if "FAILED" in line:
-                msg = 'General tests failed !!!'
-                sys.stdout = original_stdout
-                Log(Fore.RED, msg + '\n' + line)
-                sys.stdout = fp
-                raise Exception(msg)
-
-    Log(Fore.GREEN, 'General Tests successful')
+        raise RuntimeException(f'General tests failed.') from e
 
 
+def startCmdTestsForAll(args, fp):
+    for server in args.servers:
+        try:
+            num_mods = 2 if server == 'eiger' else 1
+            fname = CMD_TEST_LOG_PREFIX_FNAME + server + '.txt'
+            cmd = ['tests', '--abort', '[.cmdcall]', '-s']
 
-# parse cmd line for rx_hostname and settingspath using the argparse library
-parser = argparse.ArgumentParser(description = 'automated tests with the virtual detector servers')
-parser.add_argument('rx_hostname', nargs='?', default='localhost', help = 'hostname/ip of the current machine')
-parser.add_argument('settingspath', nargs='?', default='../../settingsdir', help = 'Relative or absolut path to the settingspath')
-parser.add_argument('-s', '--servers', help='Detector servers to run', nargs='*')
-args = parser.parse_args()
+            Log(LogLevel.INFOBLUE, f'Starting Cmd Tests for {server}')
+            cleanup(fp)
+            startDetectorVirtualServer(name=server, num_mods=num_mods, fp=fp)
+            startReceiver(num_mods, fp)
+            loadConfig(name=server, rx_hostname=args.rx_hostname, settingsdir=args.settingspath, fp=fp, num_mods=num_mods)
+            runProcessWithLogFile('Cmd Tests for ' + server, cmd, fp, fname)
+        except Exception as e:
+            raise RuntimeException(f'Cmd Tests failed for {server}.') from e
 
-if args.servers is None:
-    servers = [
-        'eiger',
-        'jungfrau',
-        'mythen3',
-        'gotthard2',
-        'ctb',
-        'moench',
-        'xilinx_ctb'
-    ]
-else:
-    servers = args.servers
+    Log(LogLevel.INFOGREEN, 'Passed all tests for all detectors \n' + str(args.servers))
 
 
-Log(Fore.WHITE, 'Arguments:\nrx_hostname: ' + args.rx_hostname + '\nsettingspath: \'' + args.settingspath + '\'') 
+if __name__ == '__main__':
+    args = ParseArguments('Automated tests with the virtual detector servers')
+    if args.num_mods > 1:
+        raise RuntimeException(f'Cannot support multiple modules at the moment (except Eiger).')
 
+    Log(LogLevel.INFOBLUE, '\nLog File: ' + MAIN_LOG_FNAME + '\n') 
 
-# redirect to file
-prefix_fname = '/tmp/slsDetectorPackage_virtual_test'
-original_stdout = sys.stdout
-original_stderr = sys.stderr
-fname = prefix_fname + '_log.txt'
-Log(Fore.BLUE, '\nLog File: ' + fname) 
-
-with open(fname, 'w') as fp:
-
-
-
-    # general tests
-    file_results = prefix_fname + '_results_general.txt'
-    Log(Fore.BLUE, 'General tests (results: ' + file_results + ')')
-    sys.stdout = fp
-    sys.stderr = fp
-    Log(Fore.BLUE, 'General tests (results: ' + file_results + ')')
-
-    try:
-        startGeneralTests(fp, file_results)
-        killAllStaleProcesses(fp)
-
-        testError = False
-        for server in servers:
-            try:
-                # print to terminal for progress
-                sys.stdout = original_stdout
-                sys.stderr = original_stderr
-                file_results = prefix_fname + '_results_cmd_' + server + '.txt'
-                Log(Fore.BLUE, 'Cmd tests for ' + server + ' (results: ' + file_results + ')')
-                sys.stdout = fp
-                sys.stderr = fp
-                Log(Fore.BLUE, 'Cmd tests for ' + server + ' (results: ' + file_results + ')')
-                
-                # cmd tests for det
-                cleanup(server, fp)
-                startServer(server)
-                startReceiver(server)
-                loadConfig(server, args.rx_hostname, args.settingspath)
-                startCmdTests(server, fp, file_results)
-                cleanup(server, fp)
-                
-            except Exception as e:
-                # redirect to terminal
-                sys.stdout = original_stdout
-                sys.stderr = original_stderr
-                Log(Fore.RED, f'Exception caught while testing {server}. Cleaning up...')
-                testError = True
-                break
-
-        # redirect to terminal
-        sys.stdout = original_stdout
-        sys.stderr = original_stderr
-        if not testError:
-            Log(Fore.GREEN, 'Passed all tests for virtual detectors \n' + str(servers))
-
-
-    except Exception as e:
-        # redirect to terminal
-        sys.stdout = original_stdout
-        sys.stderr = original_stderr
-        Log(Fore.RED, f'Exception caught with general testing. Cleaning up...')
-        cleanSharedmemory(sys.stdout)
-        
-
+    with open(MAIN_LOG_FNAME, 'w') as fp:  
+        try:
+            startGeneralTests(fp)
+            startCmdTestsForAll(args, fp)
+            cleanup(fp)
+        except Exception as e:
+            with open(MAIN_LOG_FNAME, 'a') as fp_error:
+                traceback.print_exc(file=fp_error)
+            cleanup(fp)
+            Log(LogLevel.ERROR, f'Tests Failed.')

tests/scripts/utils_for_test.py

@@ -0,0 +1,259 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2021 Contributors to the SLS Detector Package
+'''
+This file is used for common utils used for integration tests between simulators and receivers.
+'''
+
+import sys, subprocess, time, argparse
+from enum import Enum
+from colorama import Fore, Style, init
+
+from slsdet import Detector, detectorSettings
+from slsdet.defines import DEFAULT_TCP_RX_PORTNO, DEFAULT_UDP_DST_PORTNO
+SERVER_START_PORTNO=1900
+
+init(autoreset=True)
+
+
+class LogLevel(Enum):
+    INFO = 0
+    INFORED = 1
+    INFOGREEN = 2
+    INFOBLUE = 3
+    WARNING = 4
+    ERROR = 5
+    DEBUG = 6
+
+
+LOG_LABELS = {
+    LogLevel.WARNING: "WARNING: ",
+    LogLevel.ERROR: "ERROR: ",
+    LogLevel.DEBUG: "DEBUG: "
+}
+
+
+LOG_COLORS = {
+    LogLevel.INFO: Fore.WHITE,
+    LogLevel.INFORED: Fore.RED,
+    LogLevel.INFOGREEN: Fore.GREEN,
+    LogLevel.INFOBLUE: Fore.BLUE,
+    LogLevel.WARNING: Fore.YELLOW,
+    LogLevel.ERROR: Fore.RED,
+    LogLevel.DEBUG: Fore.CYAN
+}
+
+
+def Log(level: LogLevel, message: str, stream=sys.stdout):
+    color = LOG_COLORS.get(level, Fore.WHITE)
+    label = LOG_LABELS.get(level, "")
+    print(f"{color}{label}{message}{Style.RESET_ALL}", file=stream, flush=True)
+
+
+class RuntimeException (Exception):
+    def __init__ (self, message):
+        Log(LogLevel.ERROR, message)
+        super().__init__(message)
+
+
+def checkIfProcessRunning(processName):
+    cmd = f"pgrep -f {processName}"
+    res = subprocess.getoutput(cmd)
+    return res.strip().splitlines()
+
+
+def killProcess(name, fp):
+    pids = checkIfProcessRunning(name)
+    if pids:
+        Log(LogLevel.INFO, f"Killing '{name}' processes with PIDs: {', '.join(pids)}", fp)
+        for pid in pids:
+            try:
+                p = subprocess.run(['kill', pid])
+                if p.returncode != 0 and bool(checkIfProcessRunning(name)):
+                    raise RuntimeException(f"Could not kill {name} with pid {pid}")
+            except Exception as e:
+                raise RuntimeException(f"Failed to kill process {name} pid:{pid}. Error: {str(e)}") from e
+    #else:
+    #    Log(LogLevel.INFO, 'process not running : ' + name)
+
+
+def cleanSharedmemory(fp):
+    Log(LogLevel.INFO, 'Cleaning up shared memory', fp)
+    try:
+        p = subprocess.run(['sls_detector_get', 'free'], stdout=fp, stderr=fp)
+    except:
+        raise RuntimeException('Could not free shared memory')
+
+
+def cleanup(fp):
+    Log(LogLevel.INFO, 'Cleaning up')
+    Log(LogLevel.INFO, 'Cleaning up', fp)
+    killProcess('DetectorServer_virtual', fp)
+    killProcess('slsReceiver', fp)
+    killProcess('slsMultiReceiver', fp)
+    killProcess('slsFrameSynchronizer', fp)
+    killProcess('frameSynchronizerPullSocket', fp)
+    cleanSharedmemory(fp)
+
+
+def startProcessInBackground(cmd, fp):
+    Log(LogLevel.INFO, 'Starting up ' + ' '.join(cmd))
+    Log(LogLevel.INFO, 'Starting up ' + ' '.join(cmd), fp)
+    try:
+        p = subprocess.Popen(cmd, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, restore_signals=False) 
+    except Exception as e:
+        raise RuntimeException(f'Failed to start {cmd}:{str(e)}') from e
+
+
+def startProcessInBackgroundWithLogFile(cmd, fp, log_file_name: str):
+    Log(LogLevel.INFOBLUE, 'Starting up ' +  ' '.join(cmd) + '. Log: ' +  log_file_name)
+    Log(LogLevel.INFOBLUE, 'Starting up ' +  ' '.join(cmd) + '. Log: ' +  log_file_name, fp)
+    try:
+        with open(log_file_name, 'w') as log_fp:
+            subprocess.Popen(cmd, stdout=log_fp, stderr=log_fp, text=True)
+    except Exception as e:
+        raise RuntimeException(f'Failed to start {cmd}:{str(e)}') from e
+
+
+def checkLogForErrors(fp, log_file_path: str):
+    try:
+        with open(log_file_path, 'r') as log_file:
+            for line in log_file:
+                if 'Error' in line:
+                    Log(LogLevel.ERROR, f"Error found in log: {line.strip()}")
+                    Log(LogLevel.ERROR, f"Error found in log: {line.strip()}", fp)
+                    raise RuntimeException("Error found in log file")
+    except FileNotFoundError:
+        print(f"Log file not found: {log_file_path}")
+        raise
+    except Exception as e:
+        print(f"Exception while reading log: {e}")
+        raise
+
+
+def runProcessWithLogFile(name, cmd, fp, log_file_name):
+    Log(LogLevel.INFOBLUE, 'Running ' +  name + '. Log: ' +  log_file_name)
+    Log(LogLevel.INFOBLUE, 'Running ' +  name + '. Log: ' +  log_file_name, fp)
+    Log(LogLevel.INFOBLUE, 'Cmd: ' + ' '.join(cmd), fp)
+    try:
+        with open(log_file_name, 'w') as log_fp:
+            subprocess.run(cmd, stdout=log_fp, stderr=log_fp, check=True, text=True)
+    except subprocess.CalledProcessError as e:
+        pass    
+    except Exception as e:
+        Log(LogLevel.ERROR, f'Failed to run {name}:{str(e)}', fp)
+        raise RuntimeException(f'Failed to run {name}:{str(e)}')
+    
+    with open (log_file_name, 'r') as f:
+        for line in f:
+            if "FAILED" in line:
+                raise RuntimeException(f'{line}')
+
+    Log(LogLevel.INFOGREEN, name + ' successful!\n')
+    Log(LogLevel.INFOGREEN, name + ' successful!\n', fp)
+
+
+def startDetectorVirtualServer(name :str, num_mods, fp):
+    for i in range(num_mods):
+        port_no = SERVER_START_PORTNO + (i * 2)
+        cmd = [name + 'DetectorServer_virtual', '-p', str(port_no)]
+        startProcessInBackgroundWithLogFile(cmd, fp, "/tmp/virtual_det_" + name + str(i) + ".txt")
+        match name:
+            case 'jungfrau':
+                time.sleep(7)
+            case 'gotthard2':
+                time.sleep(5)
+            case _:
+                time.sleep(3)
+
+
+def connectToVirtualServers(name, num_mods):
+    try:
+        d = Detector()
+    except Exception as e:
+        raise RuntimeException(f'Could not create Detector object for {name}. Error: {str(e)}') from e
+
+    counts_sec = 5
+    while (counts_sec != 0):
+        try:
+            d.virtual = [num_mods, SERVER_START_PORTNO]
+            break
+        except Exception as e:
+            # stop server still not up, wait a bit longer
+            if "Cannot connect to" in str(e):
+                Log(LogLevel.WARNING, f'Still waiting for {name} virtual server to be up...{counts_sec}s left')
+                time.sleep(1)
+                counts_sec -= 1
+            else:
+                raise
+
+    return d
+
+
+def loadConfig(name, rx_hostname, settingsdir, fp, num_mods = 1, num_frames = 1):
+    Log(LogLevel.INFO, 'Loading config')
+    Log(LogLevel.INFO, 'Loading config', fp)
+    try:
+        d = connectToVirtualServers(name, num_mods)
+        d.udp_dstport = DEFAULT_UDP_DST_PORTNO
+        if name == 'eiger':
+            d.udp_dstport2 = DEFAULT_UDP_DST_PORTNO + 1
+
+        d.rx_hostname = rx_hostname
+        d.udp_dstip = 'auto'
+        if name != "eiger":
+            d.udp_srcip = 'auto'
+
+        if name == "jungfrau" or name == "moench" or name == "xilinx_ctb":
+            d.powerchip = 1
+
+        if name == "xilinx_ctb":
+            d.configureTransceiver()
+
+        if name == "eiger":
+            d.trimen = [4500, 5400, 6400]
+            d.settingspath = settingsdir + '/eiger/'
+            d.setThresholdEnergy(4500, detectorSettings.STANDARD)
+
+        d.frames = num_frames
+    except Exception as e:
+        raise RuntimeException(f'Could not load config for {name}. Error: {str(e)}') from e
+    
+    return d
+
+
+def ParseArguments(description, default_num_mods=1):
+    parser = argparse.ArgumentParser(description)
+
+    parser.add_argument('rx_hostname', nargs='?', default='localhost',
+                        help='Hostname/IP of the current machine')
+    parser.add_argument('settingspath', nargs='?', default='../../settingsdir',
+                        help='Relative or absolute path to the settings directory')
+    parser.add_argument('-n', '--num-mods', nargs='?', default=default_num_mods, type=int,
+                        help='Number of modules to test with')
+    parser.add_argument('-f', '--num-frames', nargs='?', default=1, type=int,
+                        help='Number of frames to test with')
+    parser.add_argument('-s', '--servers', nargs='*',
+                        help='Detector servers to run')
+
+    args = parser.parse_args()
+
+    # Set default server list if not provided
+    if args.servers is None:
+        args.servers = [
+            'eiger',
+            'jungfrau',
+            'mythen3',
+            'gotthard2',
+            'ctb',
+            'moench',
+            'xilinx_ctb'
+        ]
+
+    Log(LogLevel.INFO, 'Arguments:\n' + 
+        'rx_hostname: ' + args.rx_hostname + 
+        '\nsettingspath: \'' + args.settingspath + 
+        '\nservers: \'' + ' '.join(args.servers) + 
+        '\nnum_mods: \'' + str(args.num_mods) + 
+        '\nnum_frames: \'' + str(args.num_frames) + '\'') 
+
+    return args   

updateAPIVersion.py

@@ -0,0 +1,81 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2025 Contributors to the SLS Detector Package
+"""
+Script to update API VERSION file based on the version in VERSION file.
+"""
+
+import argparse
+import sys
+import os
+import re
+import time
+from datetime import datetime
+
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+API_FILE = SCRIPT_DIR + "/slsSupportLib/include/sls/versionAPI.h"
+
+VERSION_FILE = SCRIPT_DIR + "/VERSION"
+
+parser = argparse.ArgumentParser(description = 'updates API version')
+parser.add_argument('api_module_name', choices=["APILIB", "APIRECEIVER", "APICTB", "APIGOTTHARD2", "APIMOENCH", "APIEIGER", "APIXILINXCTB", "APIJUNGFRAU", "APIMYTHEN3"], help = 'module name to change api version options are: ["APILIB", "APIRECEIVER", "APICTB", "APIGOTTHARD2", "APIMOENCH", "APIEIGER", "APIXILINXCTB", "APIJUNGFRAU", "APIMYTHEN3"]')
+parser.add_argument('api_dir', help = 'Relative or absolute path to the module code')
+
+def update_api_file(new_api : str, api_module_name : str, api_file_name : str): 
+
+    regex_pattern = re.compile(rf'#define\s+{api_module_name}\s+')
+    with open(api_file_name, "r") as api_file:
+        lines = api_file.readlines()
+
+    with open(api_file_name, "w") as api_file:
+        for line in lines:
+            if regex_pattern.match(line):
+                api_file.write(f'#define {api_module_name} "{new_api}"\n')
+            else:
+                api_file.write(line)
+
+def get_latest_modification_date(directory : str):
+    latest_time = 0
+    latest_date = None
+
+    for root, dirs, files in os.walk(directory):
+        for file in files:
+            if file.endswith(".o"):
+                continue
+            full_path = os.path.join(root, file)
+            try:
+                mtime = os.path.getmtime(full_path)
+                if mtime > latest_time:
+                    latest_time = mtime
+            except FileNotFoundError:
+                continue
+    
+    latest_date = datetime.fromtimestamp(latest_time).strftime("%y%m%d")            
+
+    return latest_date
+
+
+def update_api_version(api_module_name : str, api_dir : str):
+    api_date = get_latest_modification_date(api_dir)
+    api_date = "0x"+str(api_date)
+
+    with open(VERSION_FILE, "r") as version_file: 
+        api_version = version_file.read().strip()
+
+    api_version = api_version + " " + api_date #not sure if we should give an argument option version_branch 
+
+    update_api_file(api_version, api_module_name, API_FILE)
+
+    print(f"updated {api_module_name} api version to: {api_version}")
+
+if __name__ == "__main__":
+
+    args = parser.parse_args() 
+
+    api_dir = SCRIPT_DIR + "/" + args.api_dir
+    
+
+    update_api_version(args.api_module_name, api_dir)
+
+

updateAPIVersion.sh

@@ -1,65 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-usage="\nUsage: updateAPIVersion.sh [API_NAME] [API_DIR] [API_BRANCH(opt)]."
-
-if [ $# -lt 2 ]; then
-    echo -e "Requires atleast 2 arguments. $usage"
-    return [-1]
-fi
-
-API_NAME=$1
-PACKAGE_DIR=$PWD
-API_DIR=$PACKAGE_DIR/$2
-API_FILE=$PACKAGE_DIR/slsSupportLib/include/sls/versionAPI.h
-CURR_DIR=$PWD
-
-if [ ! -d "$API_DIR" ]; then
-    echo "[API_DIR] does not exist. $usage"
-    return [-1]
-fi
-
-#go to directory
-cd $API_DIR
-
-#deleting line from file
-NUM=$(sed -n '/'$API_NAME' /=' $API_FILE)
-#echo $NUM
-
-
-if [ "$NUM" -gt 0 ]; then
-    sed -i ${NUM}d $API_FILE
-fi
-
-#find new API date
-API_DATE="find .  -printf \"%T@ %CY-%Cm-%Cd\n\"| sort -nr | cut -d' ' -f2- | egrep -v '(\.)o' | head -n 1"
-
-API_DATE=`eval $API_DATE`
-
-API_DATE=$(sed "s/-//g" <<< $API_DATE | awk '{print $1;}' ) 
-
-#extracting only date
-API_DATE=${API_DATE:2:6}
-
-#prefix of 0x
-API_DATE=${API_DATE/#/0x}
-echo "date="$API_DATE
-
-
-# API_VAL concatenates branch and date
-API_VAL=""
-# API branch is defined (3rd argument)
-if [ $# -eq 3 ]; then
-    API_BRANCH=$3
-    echo "branch="$API_BRANCH
-    API_VAL+="\"$API_BRANCH $API_DATE\""
-else
-    # API branch not defined (default is developer)
-    echo "branch=developer"
-    API_VAL+="\"developer $API_DATE\""
-fi
-
-#copy it to versionAPI.h
-echo "#define "$API_NAME $API_VAL >> $API_FILE
-
-#go back to original directory
-cd $CURR_DIR

updateClientAPIVersion.py

@@ -0,0 +1,34 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2025 Contributors to the SLS Detector Package
+"""
+Script to update API VERSION for slsReceiverSoftware or slsDetectorSoftware 
+""" 
+
+import argparse
+import os
+
+from updateAPIVersion import update_api_version
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+parser = argparse.ArgumentParser(description = 'updates API version')
+parser.add_argument('module_name', nargs="?", choices=["slsDetectorSoftware", "slsReceiverSoftware", "all"], default="all", help = 'module name to change api version options are: ["slsDetectorSoftware", "slsReceiverSoftware, "all"]')
+
+if __name__ == "__main__": 
+    args = parser.parse_args()
+
+    if args.module_name == "all": 
+        client_names = ["APILIB", "APIRECEIVER"]
+        client_directories = [SCRIPT_DIR+"/slsDetectorSoftware", SCRIPT_DIR+"/slsReceiverSoftware"]
+    elif args.module_name == "slsDetectorSoftware": 
+        client_names = ["APILIB"]
+        client_directories = [SCRIPT_DIR+"/slsDetectorSoftware"]
+    else: 
+        client_names = ["APIRECEIVER"]
+        client_directories = [SCRIPT_DIR+"/slsReceiverSoftware"]
+	
+    for client_name, client_directory in zip(client_names, client_directories): 
+        update_api_version(client_name, client_directory)
+		
+
+	

updateClientAPIVersion.sh

@@ -1,59 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-branch=""
-client_list=("slsDetectorSoftware" "slsReceiverSoftware")
-usage="\nUsage: updateClientAPI.sh [all|slsDetectorSoftware|slsReceiverSoftware] [branch]. \n\tNo arguments means all with 'developer' branch. \n\tNo 'branch' input means 'developer branch'"
-
-# arguments
-if [ $# -eq 0 ]; then
-	declare -a client=${client_list[@]}
-	echo "API Versioning all"
-elif [ $# -eq 1 ] || [ $# -eq 2 ]; then
-	# 'all' client
-	if [[ $1 == "all" ]]; then
-		declare -a client=${client_list[@]}
-		echo "API Versioning all"
-	else
-		# only one server
-		if [[ $client_list != *$1* ]]; then
-			echo -e "Invalid argument 1: $1. $usage"
-			return -1
-		fi
-		declare -a client=("${1}")
-		#echo "Versioning only $1"
-	fi
-	if [ $# -eq 2 ]; then
-		if [[ $client_list == *$2* ]]; then
-			echo -e "Invalid argument 2: $2. $usage"
-			return -1
-		fi
-		branch+=$2
-		#echo "with branch $branch"
-	fi
-else
-	echo -e "Too many arguments.$usage"
-	return -1
-fi
-
-#echo "list is: ${client[@]}"
-
-# versioning each client
-for i in ${client[@]}
-do
-	dir=$i
-	case $dir in
-		slsDetectorSoftware)
-			declare -a name=APILIB
-			;;
-		slsReceiverSoftware)
-			declare -a name=APIRECEIVER
-			;;
-		*)
-			echo -n "unknown client argument $i"
-			return -1
-			;;
-	esac
-	echo -e "Versioning $dir [$name]"
-	./updateAPIVersion.sh $name $dir $branch
-done
-