eiger server

* new strategy for finding zmq based on cppzmq

.clang-tidy

@@ -18,9 +18,7 @@ Checks:          '*,
                     -google-readability-todo, 
                     -google-readability-braces-around-statements,
                     -modernize-use-trailing-return-type,
-                    -readability-isolate-declaration,
-                    -readability-implicit-bool-conversion,
-                    -llvmlibc-*'
+                    -readability-isolate-declaration'
 
 HeaderFilterRegex: \.h
 AnalyzeTemporaryDtors: false

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "python/pybind11"]
+	path = libs/pybind11
+	url = https://github.com/pybind/pybind11.git

CMakeLists.txt

@@ -1,15 +1,13 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 cmake_minimum_required(VERSION 3.12)
 project(slsDetectorPackage)
-set(PROJECT_VERSION 7.0.1)
-
+set(PROJECT_VERSION 5.1.0)
+include(CheckIPOSupported)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
 
 cmake_policy(SET CMP0074 NEW)
 include(cmake/project_version.cmake)
-include(cmake/SlsAddFlag.cmake)
-include(cmake/SlsFindZeroMQ.cmake)
+
+# Include additional modules that are used unconditionally
 include(GNUInstallDirs)
 
 # If conda build, always set lib dir to 'lib'
@@ -23,7 +21,7 @@ string(TOLOWER "${PROJECT_NAME}" PROJECT_NAME_LOWER)
 
 # Set targets export name (used by slsDetectorPackage and dependencies)
 set(TARGETS_EXPORT_NAME "${PROJECT_NAME_LOWER}-targets")
-set(namespace "sls::")
+#set(namespace "${PROJECT_NAME}::")
 
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 
@@ -34,21 +32,15 @@ if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
     set(SLS_MASTER_PROJECT ON)
 endif()
 
-
-
 option (SLS_USE_HDF5 "HDF5 File format" OFF)
-option(SLS_BUILD_SHARED_LIBRARIES "Build shared libaries" ON)
 option (SLS_USE_TEXTCLIENT "Text Client" ON)
-option(SLS_USE_DETECTOR "Detector libs" ON)
 option (SLS_USE_RECEIVER "Receiver" ON)
-option(SLS_USE_RECEIVER_BINARIES "Receiver binaries" ON)
 option (SLS_USE_GUI "GUI" OFF)
 option (SLS_USE_SIMULATOR "Simulator" OFF)
 option (SLS_USE_TESTS "TESTS" OFF)
 option (SLS_USE_INTEGRATION_TESTS "Integration Tests" OFF)
 option(SLS_USE_SANITIZER "Sanitizers for debugging" OFF)
 option(SLS_USE_PYTHON "Python bindings" OFF)
-option(SLS_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/python/" OFF)
 option(SLS_USE_CTBGUI "ctb GUI" OFF)
 option(SLS_BUILD_DOCS "docs" OFF)
 option(SLS_BUILD_EXAMPLES "examples" OFF)
@@ -56,35 +48,7 @@ option(SLS_TUNE_LOCAL "tune to local machine" OFF)
 option(SLS_DEVEL_HEADERS "install headers for devel" OFF)
 option(SLS_USE_MOENCH "compile zmq and post processing for Moench" OFF)
 
-#Convenience option to switch off defaults when building Moench binaries only
-option(SLS_BUILD_ONLY_MOENCH "compile only Moench" OFF)
-if(SLS_BUILD_ONLY_MOENCH)
-    message(STATUS "Build MOENCH binaries only!")
-    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_DETECTOR OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_RECEIVER OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_MOENCH ON CACHE BOOL "Enable" FORCE)
-endif()
-
-
-option(SLS_EXT_BUILD "external build of part of the project" OFF)
-if(SLS_EXT_BUILD)
-    message(STATUS "External build using already installed libraries")
-    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_DETECTOR OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_RECEIVER OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_MASTER_PROJECT OFF CACHE BOOL "No master proj in case of extbuild" FORCE) 
-endif()
-
-#Maybe have an option guarding this?
-set(SLS_INTERNAL_RAPIDJSON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libs/rapidjson)
-
-set(SLS_INTERNAL_QWT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libs/qwt-6.1.5)
-
+# set(ClangFormat_BIN_NAME clang-format)
 set(ClangFormat_EXCLUDE_PATTERNS    "build/" 
                                     "libs/" 
                                     "slsDetectorCalibration/" 
@@ -95,6 +59,11 @@ set(ClangFormat_EXCLUDE_PATTERNS    "build/"
                                     ${CMAKE_BINARY_DIR})
 find_package(ClangFormat)
 
+#Enable LTO if available
+check_ipo_supported(RESULT SLS_LTO_AVAILABLE)
+message(STATUS "SLS_LTO_AVAILABLE:" ${SLS_LTO_AVAILABLE})
+
+
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
@@ -103,36 +72,14 @@ if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
 endif()
 
 
-#Enable LTO if available
-include(CheckIPOSupported)
-check_ipo_supported(RESULT SLS_LTO_AVAILABLE)
-if((CMAKE_BUILD_TYPE STREQUAL "Release") AND SLS_LTO_AVAILABLE)
-    message(STATUS "Building with link time optimization")
-else()
-    message(STATUS "Building without link time optimization")
-endif()
-
-
-if(SLS_EXT_BUILD)
-    # Find ourself in case of external build
-    find_package(slsDetectorPackage ${PROJECT_VERSION} REQUIRED)
-endif()
-
-
-
-# slsProjectOptions and slsProjectWarnings are used
-# to control options for the libraries
-if(NOT TARGET slsProjectOptions)
+#Add two fake libraries to manage options
 add_library(slsProjectOptions INTERFACE)
-    target_compile_features(slsProjectOptions INTERFACE cxx_std_11)
-endif()
-
-if (NOT TARGET slsProjectWarnings)
 add_library(slsProjectWarnings INTERFACE)
+target_compile_features(slsProjectOptions INTERFACE cxx_std_11)
 target_compile_options(slsProjectWarnings INTERFACE 
                                             -Wall
                                             -Wextra
-        -Wno-unused-parameter
+                                            -Wno-unused-parameter #Needs to be slowly mitigated
                                             # -Wold-style-cast
                                             -Wnon-virtual-dtor
                                             -Woverloaded-virtual
@@ -143,37 +90,38 @@ if (NOT TARGET slsProjectWarnings)
                                             -Wvla
                                             -Wdouble-promotion
                                             -Werror=return-type
-    )
-    # Add or disable warnings depending on if the compiler supports them 
-    # The function checks internally and sets HAS_warning-name
-    sls_enable_cxx_warning("-Wnull-dereference")
-    sls_enable_cxx_warning("-Wduplicated-cond")
-    sls_disable_cxx_warning("-Wclass-memaccess")
 
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5 AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+                                 )
+
+
+#Testing for minimum version for compilers
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.2)
+        message(FATAL_ERROR "Clang version must be at least 3.2!")
+    endif()
+    target_compile_options(slsProjectWarnings INTERFACE -Wshadow) #Clag does not warn on constructor
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8)
+            message(FATAL_ERROR "GCC version must be at least 4.8!")
+    endif()
+
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
             target_compile_options(slsProjectWarnings INTERFACE 
                                              -Wno-missing-field-initializers)
     endif()
     
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+        target_compile_options(slsProjectWarnings INTERFACE 
+                                                -Wno-misleading-indentation # mostly in rapidjson remove using clang format
+                                                -Wduplicated-cond
+                                                -Wnull-dereference )
 
     endif()
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.0)
+        target_compile_options(slsProjectWarnings INTERFACE 
+                                                -Wno-class-memaccess )
 
-
-if (NOT TARGET slsProjectCSettings)
-    #Settings for C code
-    add_library(slsProjectCSettings INTERFACE)
-    target_compile_options(slsProjectCSettings INTERFACE 
-                                                -std=gnu99 #fixed
-                                                -Wall
-                                                -Wextra
-                                                -Wno-unused-parameter
-                                                -Wdouble-promotion
-                                                -Wformat=2
-                                                -Wredundant-decls
-                                                -Wdouble-promotion
-                                                -Werror=return-type
-                                    )
-    sls_disable_c_warning("-Wstringop-truncation")
+    endif()
 endif()
 
 
@@ -189,22 +137,47 @@ if(SLS_TUNE_LOCAL)
 endif()
 
 
-if(SLS_MASTER_PROJECT)
-install(TARGETS slsProjectOptions slsProjectWarnings 
+#rapidjson
+add_library(rapidjson INTERFACE)
+target_include_directories(rapidjson INTERFACE
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/libs/rapidjson>  
+)
+
+# Install fake the libraries
+install(TARGETS slsProjectOptions slsProjectWarnings rapidjson
     EXPORT "${TARGETS_EXPORT_NAME}"
     LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
     ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
     PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
 )
-endif()
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 set(CMAKE_INSTALL_RPATH $ORIGIN)
+# set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 
 
-custom_find_zmq()
 
+#From: https://github.com/zeromq/cppzmq/
+if (NOT TARGET libzmq)
+  find_package(ZeroMQ 4 QUIET)
+
+  # libzmq autotools install: fallback to pkg-config
+  if(NOT ZeroMQ_FOUND)
+    message(STATUS "CMake libzmq package not found, trying again with pkg-config (normal install of zeromq)")
+    list (APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/libzmq-pkg-config)
+    find_package(ZeroMQ 4 REQUIRED)
+  endif()
+
+  # TODO "REQUIRED" above should already cause a fatal failure if not found, but this doesn't seem to work
+  if(NOT ZeroMQ_FOUND)
+    message(FATAL_ERROR "ZeroMQ was not found, neither as a CMake package nor via pkg-config")
+  endif()
+
+  if (ZeroMQ_FOUND AND NOT TARGET libzmq)
+    message(FATAL_ERROR "ZeroMQ version not supported!")
+  endif()
+endif()
 
 if (SLS_USE_TESTS)
     enable_testing()
@@ -212,20 +185,20 @@ if (SLS_USE_TESTS)
 endif(SLS_USE_TESTS)
 
 
-if(NOT SLS_EXT_BUILD)
-    add_subdirectory(slsSupportLib)
-endif()
 
-if (SLS_USE_DETECTOR OR SLS_USE_TEXTCLIENT)
+
+# Common functionallity to detector and receiver
+add_subdirectory(slsSupportLib)
+
+if (SLS_USE_TEXTCLIENT)
     add_subdirectory(slsDetectorSoftware)
-endif ()
+endif (SLS_USE_TEXTCLIENT)
 
 if (SLS_USE_RECEIVER)
     add_subdirectory(slsReceiverSoftware) 
 endif (SLS_USE_RECEIVER)
 
 if (SLS_USE_GUI)   
-    add_subdirectory(libs/qwt)  
     add_subdirectory(slsDetectorGui)
 endif (SLS_USE_GUI)
 
@@ -239,7 +212,7 @@ endif (SLS_USE_INTEGRATION_TESTS)
 
 if (SLS_USE_PYTHON)
     find_package (Python 3.6 COMPONENTS Interpreter Development)
-    add_subdirectory(libs/pybind  ${CMAKE_BINARY_DIR}/bin/)
+    add_subdirectory(libs/pybind11)
     add_subdirectory(python)
 endif(SLS_USE_PYTHON)
 
@@ -259,13 +232,16 @@ if(SLS_BUILD_DOCS)
     add_subdirectory(docs)
 endif(SLS_BUILD_DOCS)
 
+
 if(SLS_USE_MOENCH)
-    add_subdirectory(slsDetectorCalibration/tiffio)
     add_subdirectory(slsDetectorCalibration/moenchExecutables)
 endif(SLS_USE_MOENCH)
 
 if(SLS_MASTER_PROJECT)
+    # Set install dir CMake packages
     set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
+    # Set the list of exported targets
     set(PROJECT_LIBRARIES slsSupportShared slsDetectorShared slsReceiverShared)
+    # Generate and install package config file and version
     include(cmake/package_config.cmake)
 endif()

COPYING

@@ -1,17 +0,0 @@
-The SLS Detector Package is provided under:
-
-	SPDX-License-Identifier: LGPL-3.0-or-later
-
-Being under the terms of the GNU Lesser General Public License version 3 or later, 
-according with:
-
-	LICENSES/LGPL-3.0
-
-Source code under the Apache 2.0 License have the SPDX Identifier and are 
-according with:
-
-	LICENSES/ThirdParty/Apache-2.0
-
-All contributions to the SLS Detector Package are subject to this COPYING file.
-
-

LICENSES/GPL-3.0

@@ -1,688 +0,0 @@
-Valid-License-Identifier: GPL-3.0
-Valid-License-Identifier: GPL-3.0+
-SPDX-URL: https://spdx.org/licenses/GPL-3.0-or-later.html
-Usage-Guide:
-  To use this license in source code, put one of the following SPDX
-  tag/value pairs into a comment according to the placement
-  guidelines in the licensing rules documentation.
-  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
-    SPDX-License-Identifier: GPL-3.0
-  For 'GNU Library General Public License (LGPL) version 3.0 or any later
-  version' use:
-    SPDX-License-Identifier: GPL-3.0-or-later
-License-Text:
-
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
-  The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works.  By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors.  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
-  To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights.  Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received.  You must make sure that they, too, receive
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-know their rights.
-
-  Developers that use the GNU GPL protect your rights with two steps:
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LICENSES/LGPL-3.0

@@ -1,179 +0,0 @@
-Valid-License-Identifier: LGPL-3.0
-Valid-License-Identifier: LGPL-3.0+
-SPDX-URL: https://spdx.org/licenses/LGPL-3.0-or-later.html
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-License-Text:
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-                   GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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LICENSES/Third Party/Apache-2.0

@@ -1,210 +0,0 @@
-Valid-License-Identifier: Apache-2.0
-SPDX-URL: https://spdx.org/licenses/Apache-2.0.html
-Usage-Guide:
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README.md

@@ -1,233 +1,92 @@
-## Dependencies
-Before building from source make sure that you have the [software wiki](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing packages with pip. 
+### Note
 
-## Documentaion
-Detailed documentation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
+Please do not update to any xxxx.xx.xx.dev0 tags. They are not releases, but tags for internal usage.
+Use only releases with tags such as x.x.x or x.x.x-rcx.
 
-## Installation
-
-### 1. Install binaries using conda
-Conda is not only useful to manage python environments but can also
-be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
-are from the developer branch. Please use released tags for stability.
-
-We have three different packages available:
-* **slsdetlib** shared libraries and command line utilities 
-* **slsdetgui** GUI
-* **slsdet** Python bindings
+### Documentation
+Detailed documentation on the latest release of 5.0.0 can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
 
+### Binaries
+Binaries for the slsDetectorPackage are available through conda. 
 ```
-#Add channels for dependencies and our library
+#Add conda channels
 conda config --add channels conda-forge
 conda config --add channels slsdetectorgroup
 conda config --set channel_priority strict
 
-#create and activate an environment with our library
-#replace 6.1.1 with the required tag
-conda create -n myenv slsdetlib=6.1.1
-conda activate myenv
+conda install slsdetlib   #only shared lib and command line
+conda install slsdet      #python bindings (includes slsdetlib)
+conda install slsdetgui   #gui (includes qt4)
 
-#ready to use
-sls_detector_get exptime
-etc ...
-```
+#Install specific version
+conda install slsdet=2020.03.02.dev0 #developer version from 3 March 2020
 
 ```
-# List available versions
-# lib and binaries
-conda search slsdetlib
-# python
-conda search slsdet
-# gui
-conda search slsdetgui
+
+### Source code
+One can also obtain the source code from this repository and compile.
 ```
-
-### 2. Build from source
-
-##### 2.1 Download Source Code from github
-```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.0.0
-```
-
-**Pybind for Python**<br>
-* **v7.0.0+**:
-pybind11 packaged into 'libs/pybind'. No longer a submodule. No need for "recursive" or "submodule update".
- 
-* **Older versions**:
-   pybind11 is a submodule. Must be cloned using "recursive" and updated when switching between versions using the following commands.
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
-# clone using recursive to get pybind11 submodule
-git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
+#### Dependencies 
 
-# update submodule when switching between releases
-cd slsDetectorPackage
-git submodule update --init
-```
-
-##### 2.2 Build from source
+Refer [this page](https://slsdetectorgroup.github.io/devdoc/dependencies.html)  for dependencies.
 
 
-###### Build using CMake
+#### Compilation 
 
-```
-# outside slsDetecorPackage folder
-mkdir build && cd build
+Compiling can be done in two ways. Either with the convenience script
+cmk.sh or directly with cmake for more control.
 
-# configure & generate Makefiles using cmake
-# by listing all your options (alternately use ccmake described below)
-# cmake3 for some systems
-cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-
-# compiled to the build/bin directory
-make -j12 #or whatever number of cores you are using to build
-
-# install headers and libs in /your/install/path directory
-make install
-```
-
-Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.
-
-
-```
-# ccmake3 for some systems
-ccmake ..
- 
-# choose the options
-# first press [c] - configure
-# then press [g] - generate
-```
-
-|Example cmake options|Comment|
-|---|---|
-| -DSLS_USE_PYTHON=ON            | Python                                 |   
-| -DPython_FIND_VIRTUALENV=ONLY  | Python from only the conda environment |
-| -DZeroMQ_HINT=/usr/lib64       | Use system zmq instead                 |    
-| -DSLS_USE_GUI=ON               | GUI                                    |
-
-
-###### Build using in-built cmk.sh script
+**1. Compile using script cmk.sh**<br>
 
+These are mainly aimed at those not familiar with using ccmake and cmake. 
 ```
     The binaries are generated in slsDetectorPackage/build/bin directory.
 
-Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of threads>] 
-[-k <CMake command>] [-l <Install directory>] [m] [n] [-p] [-q <Zmq hint directory>] 
-[r] [s] [t] [u] [z]  
+    Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [n] [-h] [z] [-d <HDF5 directory>] [-l Install directory] [-k <CMake command>] [-j <Number of threads>]
     -[no option]: only make
--b: Builds/Rebuilds CMake files normal mode
     -c: Clean
--d: HDF5 Custom Directory
--e: Debug mode
--g: Build/Rebuilds gui
+    -b: Builds/Rebuilds CMake files normal mode
+    -p: Builds/Rebuilds Python API
     -h: Builds/Rebuilds Cmake files with HDF5 package
--i: Builds tests
--j: Number of threads to compile through
+    -d: HDF5 Custom Directory
     -k: CMake command
     -l: Install directory
+    -t: Build/Rebuilds only text client
+    -r: Build/Rebuilds only receiver
+    -g: Build/Rebuilds only gui
+    -s: Simulator
+    -u: Chip Test Gui
+    -j: Number of threads to compile through
+    -e: Debug mode
+    -i: Builds tests
     -m: Manuals
     -n: Manuals without compiling doxygen (only rst)
--p: Builds/Rebuilds Python API
--q: Zmq hint directory
--r: Build/Rebuilds only receiver
--s: Simulator
--t: Build/Rebuilds only text client
--u: Chip Test Gui
     -z: Moench zmq processor
     
-    
-# display all options
+    # get all options
     ./cmk.sh -?
 
-# new build and compile in parallel (recommended basic option):
-./cmk.sh -cbj5
-
-# new build, python and compile in parallel:
-./cmk.sh -cbpj5
-
-#To use the system zmq (/usr/lib64) instead
-./cmk.sh -cbj5 -q /usr/lib64
+    # new build  and compile in parallel:
+    ./cmk.sh -bj5
 ```
  
-###### Build on old distributions
-
-If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
-it's possible to install a newer gcc using conda and build the slsDetectorPackage
-using this compiler
-
+**2. Compile without script**<br>
+Use cmake to create out-of-source builds, by creating a build folder parallel to source directory. This would create a debug build with address sanitizers.
+```
+    $ mkdir build
+    $ cd build
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON
+    $ make -j12 #or whatever number of threads wanted
 ```
-#Create an environment with the dependencies
-conda create -n myenv gxx_linux-64 cmake zmq
-conda activate myenv
 
-# outside slsDetecorPackage folder
+To install binaries using CMake
+```
+    git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
     mkdir build && cd build
-cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
-make -j12
+    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
+    make -j12 #or whatever number of cores you are using to build
+    make install
 ```
-
-###### Build slsDetectorGui (Qt5)
-
-1. Using pre-built binary on conda
-```
-conda create -n myenv slsdetgui=7.0.0
-conda activate myenv
-```
-
-2. Using system installation on RHEL7
-```
-yum install qt5-qtbase-devel.x86_64
-yum install qt5-qtsvg-devel.x86_64 
-```
-
-3. Using conda
-```
-#Add channels for dependencies and our library
-conda config --add channels conda-forge
-conda config --add channels slsdetectorgroup
-conda config --set channel_priority strict
-
-# create environment to compile
-# on rhel7
-conda create -n slsgui zeromq gxx_linux-64 gxx_linux-64 mesa-libgl-devel-cos6-x86_64 qt
-# on fedora or newer systems
-conda create -n slsgui zeromq qt
-
-# when using conda compilers, would also need libgl, but no need for it on fedora unless maybe using it with ROOT
-
-# activate environment
-conda activate slsgui
-
-# compile with cmake outside slsDetecorPackage folder
-mkdir build && cd build
-cmake ../slsDetectorPackage -DSLS_USE_GUI=ON
-make -j12
-
-# or compile with cmk.sh
-cd slsDetectorPackage
-./cmk.sh -cbgj9
-```
-
-###### Build documentation from package
-The documentation for the slsDetectorPackage is build using a combination 
-of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
-is to use conda 
-
-```
-conda create -n myenv python sphinx_rtd_theme breathe
-```
-
-```
-# using cmake or ccmake to enable DSLS_BUILD_DOCS
-# outside slsDetecorPackage folder
-mkdir build && cd build
-cmake ../slsDetectorPackage -DSLS_BUILD_DOCS=ON
-
-make docs # generate API docs and build Sphinx RST
-make rst # rst only, saves time in case the API did not change
-```
-
-
-## Support
-    dhanya.thattil@psi.ch
-    erik.frojdh@psi.ch

RELEASE.txt

@@ -1,161 +1,94 @@
-SLS Detector Package Major Release 7.0.1 released on 24.03.2023
-===============================================================
+SLS Detector Package 5.1.0 released on xx.xx.2020 (Minor Release)
+===================================================================
 
-This document describes the differences between v7.0.1 and v7.0.0   
+This document describes the differences between 5.1.0 and 5.x.x releases.   
 
 
 
     CONTENTS
     --------
-    1   Resolved Issues
-    2   On-board Detector Server Compatibility
-    3   Firmware Requirements
-    4   Kernel Requirements
-    5   Download, Documentation & Support
+    1.  Topics Concerning
+    2.  New Features
+    2.  Resolved Issues
+    3.  Known Issues
+    4.  Firmware Requirements
+    5.  Download, Documentation & Support
 
 
 
+1. Topics Concerning
+====================
 
-1 Resolved Issues
-=================
+    - potentital memory leak in receiver
+    - scanParameters in Python
+    - cmk.sh refactored
+    - m3 settings and threshold
+
+
+2. New Features
+===============
+
+    Client
+    ------
+
+    1. Aded settings and threshold features for Mythen3.
+    2. Internal modification of acquire for Mythen3.
+    3. Added getMaster for Mythen3
+    4. Mythen3, API function to set pattern from memory
+
+
+    Mythen3 server
+    -----------------
+
+    1. Setting timing to auto, sets timing to trigger for slaves
+    
+
+3. Resolved Issues
+==================
 
 
     Receiver
     --------
 
-
-    *   HDF5 Compilation
-        Compilation issues from 7.0.0 fixed.
-
-    
-    *   Arping error
-        Cmdline: rx_arping
-        API: setRxArping/ getRxArping
-        Even if arping was successful, it gave an error. Fixed.
-
+    1.  Current code only calls Implementation::setDetectorType from constructor, 
+	    but potential memory leak if called out of constructor context. Fixed.
 
 
     Client
     ------
 
+    1.  Fixed missing scanParameters class in Python 
 
-    *   Detector Server Version from previous Releases
-        Hostname command would hang with 7.0.0 client if the detector server
-        was from a previous release (eg. 6.1.2). In this case, the user cannot
-        get the detector server version.
+    2.  cmk.sh refactored to have better option handling
 
-        Fixed that the hostname command will throw an exception about 
-        incompatible server with its version in the message. Now, the user can 
-        get the version number without having to telnet or ssh to the detector.
-        With this info, one can then update to matching client for that server
-        and start the detector updation process.
+    Server
+    --------
 
-
-2  On-board Detector Server Compatibility
-==========================================
-
-
-    Eiger       7.0.0
-    Jungfrau    7.0.0
-    Mythen3     7.0.0
-    Gotthard2   7.0.0
-    Gotthard    7.0.0
-    Moench      7.0.0
-    Ctb         7.0.0
-    
-
-    On-board Detector Server Upgrade
-    --------------------------------
-
-    From v6.1.0 (without tftp):
-        Using command 'updatedetectorserver'
-    From 5.0.0 (with tftp):
-        Using command 'copydetectorserver'
-
-    Instructions available at
-        https://slsdetectorgroup.github.io/devdoc/serverupgrade.html
+    1.  Bottom port not mirrored correctly for Eiger quad
 
 
 
 
-3 Firmware Requirements
+
+4. Firmware Requirements
 ========================
         
+    Mythen3: 0x210201
+    Jungfrau: 0x210218 (1.0 pcb)
+              0x200721 (2.0 pcb, not changed)
 
-    Eiger       20.02.2023 (v31)
-    
-    Jungfrau    04.11.2022 (v1.4, HW v1.0) 
-                03.11.2022 (v2.4, HW v2.0)
-
-    Mythen3     24.01.2023 (v1.4)
-
-    Gotthard2   23.11.2022 (v0.3)
-
-    Gotthard    08.02.2018 (50um and 25um Master)
-                09.02.2018 (25 um Slave) 
-
-    Moench      05.12.2022 (v0.3)
-
-    Ctb         05.12.2022 (v1.1)
-
-
-    Detector Upgrade
-    ----------------
-
-    The following can be upgraded remotely:
-
-    Eiger      via bit files
-    Jungfrau   via command <.pof>
-    Mythen3    via command <.rbf>
-    Gotthard2  via command <.rbf>
-    Moench     via command <.pof>
-    Ctb        via command <.pof>
-
-    Gotthard cannot be upgraded remotely  
-
-    Except Eiger, 
-        upgrade 
-            Using command 'programfpga' or
-
-        udpate both server and firmware simultaneously
-            Using command 'update'
-
-
-    Instructions available at
-        https://slsdetectorgroup.github.io/devdoc/firmware.html
+    Other detectors no updates from 5.0.0
 
 
 
+5. Known Issues
+===============
 
-4 Kernel Requirements
-======================
-
-    Blackfin 
-    --------
-    Latest version: Fri Oct 29 00:00:00 2021
-    
-    Older ones will work, but might have issues with programming firmware via
-    the package.
-
-    Nios
-    -----
-    Compatible version: Mon May 10 18:00:21 CEST 2021
-
-    Kernel Upgrade
-    ---------------
-    Eiger   via bit files
-    Others  via command
-
-    Commands: udpatekernel, kernelversion
-    Instructions available at
-        https://slsdetectorgroup.github.io/devdoc/commandline.html
-        https://slsdetectorgroup.github.io/devdoc/detector.html
-        https://slsdetectorgroup.github.io/devdoc/pydetector.html
+    No updates from 5.0.0
 
 
 
-
-5 Download, Documentation & Support
+6. Download, Documentation & Support
 ====================================
 
     Download
@@ -168,10 +101,7 @@ This document describes the differences between v7.0.1 and v7.0.0
     -------------
     
     Installation:
-        https://slsdetectorgroup.github.io/devdoc/installation.html
-
-    Quick Start Guide:
-        https://slsdetectorgroup.github.io/devdoc/quick_start_guide.html
+        https://slsdetectorgroup.github.io/devdoc/installation.html#
         
     Firmware Upgrade:
         https://slsdetectorgroup.github.io/devdoc/firmware.html
@@ -191,6 +121,9 @@ This document describes the differences between v7.0.1 and v7.0.0
     Command Line Documentation:
         https://slsdetectorgroup.github.io/devdoc/commandline.html
 
+    Quick Start Guide:
+        https://slsdetectorgroup.github.io/devdoc/quick_start_guide.html
+        
     C++ API Documentation:
         https://slsdetectorgroup.github.io/devdoc/detector.html
        
@@ -207,16 +140,8 @@ This document describes the differences between v7.0.1 and v7.0.0
         https://slsdetectorgroup.github.io/devdoc/receivers.html
         https://slsdetectorgroup.github.io/devdoc/slsreceiver.html
 
-    Detector UDP Header:
-        https://slsdetectorgroup.github.io/devdoc/udpheader.html
-        https://slsdetectorgroup.github.io/devdoc/udpdetspec.html
-
-    slsReceiver Zmq Format:
-        https://slsdetectorgroup.github.io/devdoc/slsreceiver.html#zmq-json-header-format
-
     TroubleShooting:
         https://slsdetectorgroup.github.io/devdoc/troubleshooting.html
-        https://slsdetectorgroup.github.io/devdoc/troubleshooting.html#receiver-pc-tuning-options
         
     Further Documentation:
         https://www.psi.ch/en/detectors/documentation

cmake/FindQwt.cmake

@@ -0,0 +1,118 @@
+# Qt Widgets for Technical Applications
+# available at http://www.http://qwt.sourceforge.net/
+#
+# The module defines the following variables:
+#  QWT_FOUND - the system has Qwt
+#  QWT_INCLUDE_DIR - where to find qwt_plot.h
+#  QWT_INCLUDE_DIRS - qwt includes
+#  QWT_LIBRARY - where to find the Qwt library
+#  QWT_LIBRARIES - aditional libraries
+#  QWT_MAJOR_VERSION - major version
+#  QWT_MINOR_VERSION - minor version
+#  QWT_PATCH_VERSION - patch version
+#  QWT_VERSION_STRING - version (ex. 5.2.1)
+#  QWT_ROOT_DIR - root dir (ex. /usr/local)
+
+#=============================================================================
+# Copyright 2010-2013, Julien Schueller
+# All rights reserved.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met: 
+# 
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer. 
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution. 
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+# The views and conclusions contained in the software and documentation are those
+# of the authors and should not be interpreted as representing official policies, 
+# either expressed or implied, of the FreeBSD Project.
+#=============================================================================
+
+
+find_path ( QWT_INCLUDE_DIR
+  NAMES qwt_plot.h
+  HINTS $ENV{QWTDIR} $ENV{QWTDIR}/src ${QT_INCLUDE_DIR}
+  PATH_SUFFIXES qwt qwt-qt3 qwt-qt4 qwt-qt5
+)
+
+set ( QWT_INCLUDE_DIRS ${QWT_INCLUDE_DIR} )
+
+# version
+set ( _VERSION_FILE ${QWT_INCLUDE_DIR}/qwt_global.h )
+if ( EXISTS ${_VERSION_FILE} )
+  file ( STRINGS ${_VERSION_FILE} _VERSION_LINE REGEX "define[ ]+QWT_VERSION_STR" )
+  if ( _VERSION_LINE )
+    string ( REGEX REPLACE ".*define[ ]+QWT_VERSION_STR[ ]+\"(.*)\".*" "\\1" QWT_VERSION_STRING "${_VERSION_LINE}" )
+    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\1" QWT_MAJOR_VERSION "${QWT_VERSION_STRING}" )
+    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\2" QWT_MINOR_VERSION "${QWT_VERSION_STRING}" )
+    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\3" QWT_PATCH_VERSION "${QWT_VERSION_STRING}" )
+  endif ()
+endif ()
+
+
+# check version
+set ( _QWT_VERSION_MATCH TRUE )
+if ( Qwt_FIND_VERSION AND QWT_VERSION_STRING )
+  if ( Qwt_FIND_VERSION_EXACT )
+    if ( NOT Qwt_FIND_VERSION VERSION_EQUAL QWT_VERSION_STRING )
+      set ( _QWT_VERSION_MATCH FALSE )
+    endif ()
+  else ()
+    if ( QWT_VERSION_STRING VERSION_LESS Qwt_FIND_VERSION )
+      set ( _QWT_VERSION_MATCH FALSE )
+    endif ()
+  endif ()
+endif ()
+
+
+find_library ( QWT_LIBRARY
+  NAMES qwt qwt-qt3 qwt-qt4 qwt-qt5
+  HINTS $ENV{QWTDIR}/lib ${QT_LIBRARY_DIR}
+)
+
+set ( QWT_LIBRARIES ${QWT_LIBRARY} )
+
+
+# try to guess root dir from include dir
+if ( QWT_INCLUDE_DIR )
+  string ( REGEX REPLACE "(.*)/include.*" "\\1" QWT_ROOT_DIR ${QWT_INCLUDE_DIR} )
+# try to guess root dir from library dir
+elseif ( QWT_LIBRARY )
+  string ( REGEX REPLACE "(.*)/lib[/|32|64].*" "\\1" QWT_ROOT_DIR ${QWT_LIBRARY} )
+endif ()
+
+
+# handle the QUIETLY and REQUIRED arguments
+include ( FindPackageHandleStandardArgs )
+if ( CMAKE_VERSION LESS 2.8.3 )
+  find_package_handle_standard_args( Qwt DEFAULT_MSG QWT_LIBRARY QWT_INCLUDE_DIR _QWT_VERSION_MATCH )
+else ()
+  find_package_handle_standard_args( Qwt REQUIRED_VARS QWT_LIBRARY QWT_INCLUDE_DIR _QWT_VERSION_MATCH VERSION_VAR QWT_VERSION_STRING )
+endif ()
+
+
+mark_as_advanced (
+  QWT_LIBRARY 
+  QWT_LIBRARIES
+  QWT_INCLUDE_DIR
+  QWT_INCLUDE_DIRS
+  QWT_MAJOR_VERSION
+  QWT_MINOR_VERSION
+  QWT_PATCH_VERSION
+  QWT_VERSION_STRING
+  QWT_ROOT_DIR
+)

cmake/SlsAddFlag.cmake

@@ -1,64 +0,0 @@
-include(CheckCXXCompilerFlag)
-include(CheckCCompilerFlag)
-
-
-function(enable_cxx_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_cxx_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        target_compile_options(${target} INTERFACE ${flag})
-        message(STATUS "Adding: ${flag} to ${target}")
-    else()
-        message(STATUS "Flag: ${flag} not supported")
-    endif()
-endfunction()
-
-function(enable_c_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_c_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        target_compile_options(${target} INTERFACE ${flag})
-        message(STATUS "Adding: ${flag} to ${target}")
-    else()
-        message(STATUS "Flag: ${flag} not supported")
-    endif()
-endfunction()
-
-
-function(disable_cxx_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_cxx_compiler_flag(${flag} ${flag_name})
-
-    if(${flag_name})
-        string(REPLACE "-W" "-Wno-" neg_flag ${flag})
-        message(STATUS "Adding: ${neg_flag} to ${target}")
-        target_compile_options(${target} INTERFACE ${neg_flag})
-    else()
-        message(STATUS "Warning: ${flag} not supported no need to disable")
-    endif()
-endfunction()
-
-function(disable_c_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_c_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        string(REPLACE "-W" "-Wno-" neg_flag ${flag})
-        message(STATUS "Adding: ${neg_flag} to ${target}")
-        target_compile_options(${target} INTERFACE ${neg_flag})
-    else()
-        message(STATUS "Warning: ${flag} not supported no need to disable")
-    endif()
-endfunction()
-
-
-function(sls_disable_c_warning flag)
-    disable_c_warning(${flag} slsProjectCSettings)
-endfunction()
-
-function(sls_enable_cxx_warning flag)
-    enable_cxx_warning(${flag} slsProjectWarnings)
-endfunction()
-
-function(sls_disable_cxx_warning flag)
-    disable_cxx_warning(${flag} slsProjectWarnings)
-endfunction()

cmake/SlsFindZeroMQ.cmake

@@ -1,38 +0,0 @@
-function(custom_find_zmq)
-    set(ZeroMQ_HINT "" CACHE STRING "Hint where ZeroMQ could be found")
-    #Adapted from: https://github.com/zeromq/cppzmq/
-    if (NOT TARGET libzmq)
-        if(ZeroMQ_HINT)
-            message(STATUS "Looking for ZeroMQ in: ${ZeroMQ_HINT}")
-            find_package(ZeroMQ 4 
-                NO_DEFAULT_PATH
-                HINTS ${ZeroMQ_HINT}
-            )
-        else()
-            find_package(ZeroMQ 4 QUIET)
-        endif()
-        
-    # libzmq autotools install: fallback to pkg-config
-    if(ZeroMQ_FOUND)
-        message(STATUS "Found libzmq using find_package")
-    else()
-        message(STATUS "CMake libzmq package not found, trying again with pkg-config (normal install of zeromq)")
-        list (APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake/libzmq-pkg-config)
-        find_package(ZeroMQ 4 REQUIRED)
-    endif()
-
-    # TODO "REQUIRED" above should already cause a fatal failure if not found, but this doesn't seem to work
-    if(NOT ZeroMQ_FOUND)
-        message(FATAL_ERROR "ZeroMQ was not found, neither as a CMake package nor via pkg-config")
-    endif()
-
-    if (ZeroMQ_FOUND AND NOT TARGET libzmq)
-        message(FATAL_ERROR "ZeroMQ version not supported!")
-    endif()
-    endif()
-
-    get_target_property(VAR libzmq IMPORTED_LOCATION)
-    message(STATUS "Using libzmq: ${VAR}")
-
-
-endfunction()

cmake/libzmq-pkg-config/FindZeroMQ.cmake

@@ -1,36 +0,0 @@
-#From: https://github.com/zeromq/cppzmq/
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH ON)
-find_package(PkgConfig)
-pkg_check_modules(PC_LIBZMQ QUIET libzmq)
-
-set(ZeroMQ_VERSION ${PC_LIBZMQ_VERSION})
-
-find_path(ZeroMQ_INCLUDE_DIR zmq.h
-        PATHS ${ZeroMQ_DIR}/include
-        ${PC_LIBZMQ_INCLUDE_DIRS}
-)
-
-find_library(ZeroMQ_LIBRARY
-        NAMES zmq
-        PATHS ${ZeroMQ_DIR}/lib
-        ${PC_LIBZMQ_LIBDIR}
-        ${PC_LIBZMQ_LIBRARY_DIRS}
-)
-
-if(ZeroMQ_LIBRARY OR ZeroMQ_STATIC_LIBRARY)
-    set(ZeroMQ_FOUND ON)
-    message(STATUS "Found libzmq using PkgConfig")
-endif()
-
-set ( ZeroMQ_LIBRARIES ${ZeroMQ_LIBRARY} )
-set ( ZeroMQ_INCLUDE_DIRS ${ZeroMQ_INCLUDE_DIR} )
-
-if (NOT TARGET libzmq)
-    add_library(libzmq UNKNOWN IMPORTED)
-    set_target_properties(libzmq PROPERTIES
-            IMPORTED_LOCATION ${ZeroMQ_LIBRARIES}
-            INTERFACE_INCLUDE_DIRECTORIES ${ZeroMQ_INCLUDE_DIRS})
-endif()
-
-include ( FindPackageHandleStandardArgs )
-find_package_handle_standard_args ( ZeroMQ DEFAULT_MSG ZeroMQ_LIBRARIES ZeroMQ_INCLUDE_DIRS )

cmake/package_config.cmake

@@ -26,7 +26,7 @@ install(FILES
 )
 
 install(FILES
-  "${CMAKE_SOURCE_DIR}/cmake/libzmq-pkg-config/FindZeroMQ.cmake"
+  "${CMAKE_SOURCE_DIR}/libzmq-pkg-config/FindZeroMQ.cmake"
   COMPONENT devel
   DESTINATION ${CMAKE_INSTALL_DIR}/libzmq-pkg-config
 )

cmk.sh

@@ -1,6 +1,4 @@
 #!/bin/bash
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 CMAKE="cmake3"
 BUILDDIR="build"
 INSTALLDIR=""
@@ -18,7 +16,6 @@ CTBGUI=0
 MANUALS=0
 MANUALS_ONLY_RST=0
 MOENCHZMQ=0
-ZMQ_HINT_DIR=""
 
 
 CLEAN=0
@@ -27,26 +24,25 @@ CMAKE_PRE=""
 CMAKE_POST=""
 
 usage() { echo -e "
-Usage: $0 [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of threads>] [-k <CMake command>] [-l <Install directory>] [m] [n] [-p] [-q <Zmq hint directory>] [r] [s] [t] [u] [z]  
+Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [n] [-h] [z] [-d <HDF5 directory>] [-l Install directory] [-k <CMake command>] [-j <Number of threads>]
  -[no option]: only make
- -b: Builds/Rebuilds CMake files normal mode
  -c: Clean
- -d: HDF5 Custom Directory
- -e: Debug mode
- -g: Build/Rebuilds gui
+ -b: Builds/Rebuilds CMake files normal mode
+ -p: Builds/Rebuilds Python API
  -h: Builds/Rebuilds Cmake files with HDF5 package
- -i: Builds tests
- -j: Number of threads to compile through
+ -d: HDF5 Custom Directory
  -k: CMake command
  -l: Install directory
+ -t: Build/Rebuilds only text client
+ -r: Build/Rebuilds only receiver
+ -g: Build/Rebuilds only gui
+ -s: Simulator
+ -u: Chip Test Gui
+ -j: Number of threads to compile through
+ -e: Debug mode
+ -i: Builds tests
  -m: Manuals
  -n: Manuals without compiling doxygen (only rst)
- -p: Builds/Rebuilds Python API
- -q: Zmq hint directory
- -r: Build/Rebuilds only receiver
- -s: Simulator
- -t: Build/Rebuilds only text client
- -u: Chip Test Gui
  -z: Moench zmq processor
 
 Rebuild when you switch to a new build and compile in parallel:
@@ -83,49 +79,68 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bcd:eghij:k:l:mnpq:rstuz" opt ; do
+while getopts ":bpchd:k:l:j:trgeisumnz" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
 		REBUILD=1
 		;;
+	p)
+    	echo "Compiling Options: Python" 
+		PYTHON=1
+		REBUILD=1
+		;;   
 	c) 
 		echo "Clean Required"
 		CLEAN=1
 		;;
+	h) 
+		echo "Building of CMake files with HDF5 option Required"
+		HDF5=1
+		REBUILD=1
+		;;
 	d) 
 		echo "New HDF5 directory: $OPTARG" 
 		HDF5DIR=$OPTARG
 		;;
-	e)
-		echo "Compiling Options: Debug" 
-		DEBUG=1
+	l)
+		echo "CMake install directory: $OPTARG"
+		INSTALLDIR="$OPTARG"
+		;;
+	k)
+		echo "CMake command: $OPTARG"
+		CMAKE="$OPTARG"
+		;;
+	j) 
+		echo "Number of compiler threads: $OPTARG" 
+		COMPILERTHREADS=$OPTARG
+		;;
+	t) 
+    	echo "Compiling Options: Text Client" 
+		TEXTCLIENT=1
+		REBUILD=1
+		;;      
+	r) 
+		echo "Compiling Options: Receiver" 
+		RECEIVER=1
+		REBUILD=1
 		;;      
 	g) 
 		echo "Compiling Options: GUI" 
 		GUI=1
 		REBUILD=1
 		;;  
-	h) 
-		echo "Building of CMake files with HDF5 option Required"
-		HDF5=1
-		REBUILD=1
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
 		;;   
 	i)
 		echo "Compiling Options: Tests" 
 		TESTS=1
 		;;   
-	j) 
-		echo "Number of compiler threads: $OPTARG" 
-		COMPILERTHREADS=$OPTARG
-		;;
-	k)
-		echo "CMake command: $OPTARG"
-		CMAKE="$OPTARG"
-		;;
-	l)
-		echo "CMake install directory: $OPTARG"
-		INSTALLDIR="$OPTARG"
+	s)
+		echo "Compiling Options: Simulator" 
+		SIMULATOR=1
 		;; 
 	m)	
 		echo "Compiling Manuals"
@@ -135,37 +150,14 @@ while getopts ":bcd:eghij:k:l:mnpq:rstuz" opt ; do
 		echo "Compiling Manuals (Only RST)"
 		MANUALS_ONLY_RST=1
 		;;
-	p)
-    	echo "Compiling Options: Python" 
-		PYTHON=1
-		REBUILD=1
-		;;   
-	q) 
-		echo "Zmq hint directory: $OPTARG" 
-		ZMQ_HINT_DIR=$OPTARG
-		;;
-	r) 
-		echo "Compiling Options: Receiver" 
-		RECEIVER=1
-		REBUILD=1
-		;;      
-	s)
-		echo "Compiling Options: Simulator" 
-		SIMULATOR=1
-		;; 
-	t) 
-    	echo "Compiling Options: Text Client" 
-		TEXTCLIENT=1
-		REBUILD=1
+	z)	
+		echo "Compiling Moench Zmq Processor"
+		MOENCHZMQ=1
 		;;
 	u)
 		echo "Compiling Options: Chip Test Gui"
 		CTBGUI=1
 		;;
-	z)	
-		echo "Compiling Moench Zmq Processor"
-		MOENCHZMQ=1
-		;;
   \?)
     echo "Invalid option: -$OPTARG" 
 		usage
@@ -260,12 +252,6 @@ if [ $TESTS -eq 1 ]; then
 	echo "Tests Option enabled"
 fi 
 
-#zmq hint dir
-if [ -n "$ZMQ_HINT_DIR" ]; then
-	CMAKE_POST+=" -DZeroMQ_HINT="$ZMQ_HINT_DIR
-	CMAKE_POST+=" -DZeroMQ_DIR="
-#	echo "Enabling Zmq Hint Directory: $ZMQ_HINT_DIR"
-fi 
 
 #hdf5 rebuild
 if [ $HDF5 -eq 1 ]; then

conda-recepie/build.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 mkdir build
 mkdir install
@@ -10,7 +8,6 @@ cmake .. \
       -DSLS_USE_TEXTCLIENT=ON \
       -DSLS_USE_RECEIVER=ON \
       -DSLS_USE_GUI=ON \
-      -DSLS_USE_MOENCH=ON\
       -DSLS_USE_TESTS=ON \
       -DSLS_USE_PYTHON=OFF \
       -DCMAKE_BUILD_TYPE=Release \
@@ -21,4 +18,4 @@ echo "Building using: ${NCORES} cores"
 cmake --build . -- -j${NCORES}
 cmake --build . --target install
 
-CTEST_OUTPUT_ON_FAILURE=1 ctest -j 1
+CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2

conda-recepie/build_pylib.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 echo "|<-------- starting python build"
 cd python

conda-recepie/conda_build_config.yaml

@@ -1,8 +1,8 @@
 python:
+    - 3.6
+    - 3.7
     - 3.8
     - 3.9
-    - 3.10
-    - 3.11
     
 numpy: 
     - 1.17

conda-recepie/copy_ctbgui.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 mkdir $PREFIX/lib
 mkdir $PREFIX/bin
 mkdir $PREFIX/include

conda-recepie/copy_gui.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 #Copy the GUI 
 mkdir -p $PREFIX/bin
 cp build/install/bin/slsDetectorGui $PREFIX/bin/.

conda-recepie/copy_lib.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 mkdir -p $PREFIX/lib
 mkdir -p $PREFIX/bin
@@ -19,4 +17,4 @@ cp build/install/bin/slsMultiReceiver $PREFIX/bin/.
 
 
 cp build/install/include/sls/* $PREFIX/include/sls
-cp -rv build/install/share $PREFIX
+cp -r build/install/share/ $PREFIX/share

conda-recepie/copy_moench.sh

@@ -1,6 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-
-#Copy the Moench executables 
-mkdir -p $PREFIX/bin
-cp build/install/bin/moench* $PREFIX/bin/.

conda-recepie/meta.yaml

@@ -17,7 +17,8 @@ requirements:
     - {{ compiler('c') }}
     - {{compiler('cxx')}}
     - cmake
-    - qt 5.*
+    - qwt 6.*
+    - qt 4.8.*
     - zeromq
     - xorg-libx11
     - xorg-libice
@@ -110,22 +111,10 @@ outputs:
         - {{ compiler('c') }}
         - {{compiler('cxx')}}
         - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - qwt 6.*
 
       run:
         - {{ pin_subpackage('slsdetlib', exact=True) }}
-        - qt 5.*
-        - expat
-
-  - name: moenchzmq
-    script: copy_moench.sh
-    requirements:
-
-      build:
-        - {{ compiler('c') }}
-        - {{compiler('cxx')}}
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
-
-
-      run:
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - qwt 6.*
+        - qt 4.8.*
         - expat

conda-recepie/run_test.sh

@@ -1,3 +1 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 ctest -j2

ctbGui/CMakeLists.txt

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 find_package(ROOT CONFIG REQUIRED  COMPONENTS Core Gui)
@@ -34,7 +32,7 @@ add_executable(ctbGui
     ctbAdcs.cpp
     ctbPattern.cpp
     ctbAcquisition.cpp
-    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/tiffio/src/tiffIO.cpp
+    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/tiffIO.cpp
 )
 
 
@@ -43,7 +41,6 @@ target_include_directories(ctbGui PRIVATE
     ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/dataStructures
     ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/interpolations
     ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/
-    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/tiffio/include/
 )
 
 # Headders needed for ROOT dictionary generation
@@ -62,6 +59,7 @@ set( HEADERS
 #set(ROOT_INCLUDE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
 
 # ROOT dictionary generation 
+include("${ROOT_DIR}/RootMacros.cmake")
 root_generate_dictionary(ctbDict ${HEADERS} LINKDEF ctbLinkDef.h)
 add_library(ctbRootLib SHARED ctbDict.cxx)
 target_include_directories(ctbRootLib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
@@ -87,4 +85,3 @@ set_target_properties(ctbGui PROPERTIES
     RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
 
 )
-

ctbGui/Makefile.root5

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 INCS=ctbMain.h ctbDacs.h   ctbPattern.h  ctbSignals.h  ctbAdcs.h ctbAcquisition.h ctbPowers.h   ctbSlowAdcs.h 

ctbGui/Makefile.root6

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 INCS=ctbMain.h ctbDacs.h   ctbPattern.h  ctbSignals.h  ctbAdcs.h ctbAcquisition.h ctbPowers.h   ctbSlowAdcs.h  

ctbGui/ctbAcquisition.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 //#define TESTADC
 
 
@@ -828,14 +826,14 @@ void ctbAcquisition::setCanvas(TCanvas* c) {
   myCanvas->AddExec("dynamic",Form("((ctbAcquisition*)%p)->canvasClicked()",this));
   // myCanvas->AddExec("ex","canvasClicked()");
 }
-void ctbAcquisition::dataCallback(sls::detectorData *data, long unsigned int index, unsigned int dum, void* pArgs) {
+void ctbAcquisition::dataCallback(detectorData *data, long unsigned int index, unsigned int dum, void* pArgs) {
 
   // return 
   ((ctbAcquisition*)pArgs)->plotData(data,index);
 }
 
 
-int ctbAcquisition::plotData(sls::detectorData *data, int index) {
+int ctbAcquisition::plotData(detectorData *data, int index) {
 
   /*
 ******************************************************************
@@ -988,7 +986,7 @@ sample1 (dbit0 + dbit1 +...)if (cmd == "rx_dbitlist") {
 	ped=0;
 	aval=dataStructure->getValue(data->data,x,y);
 	//aval=dataStructure->getChannel(data->data,x,y);
-	// cout << x << " " <<y << " "<< aval << endl;
+	cout << x << " " <<y << " "<< aval << endl;
 	if (cbGetPedestal->IsOn()) {
 	  if (photonFinder) {
 	    photonFinder->addToPedestal(aval,x,y);

ctbGui/ctbAcquisition.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #ifndef CTBACQUISITION_H
 #define CTBACQUISITION_H
 #include  <TGFrame.h>
@@ -28,8 +26,8 @@ class TGTextButton;
 namespace sls
 {
    class Detector;
-   class detectorData;
 };
+class detectorData;
 
 template <class dataType> class slsDetectorData;
 
@@ -201,10 +199,10 @@ class ctbAcquisition : public TGGroupFrame {
    void setBitGraph (int i ,int en, Pixel_t col);
    void startAcquisition();
    static   void progressCallback(double,void*);
-   static void dataCallback(sls::detectorData*, long unsigned int, unsigned int,  void*);
+   static void dataCallback(detectorData*, long unsigned int, unsigned int,  void*);
    int StopFlag;
    
-   int plotData(sls::detectorData*, int);
+   int plotData(detectorData*, int);
 
    void setPatternFile(const char* t);
 

ctbGui/ctbAdcs.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include <TApplication.h>
 #include <TGClient.h>
 #include <TCanvas.h>

ctbGui/ctbAdcs.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 

ctbGui/ctbDacs.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 #include <stdio.h>
 #include <iostream>

ctbGui/ctbDacs.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 #ifndef CTBDACS_H

ctbGui/ctbDefs.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #pragma once
 
 #include <string>

ctbGui/ctbGui.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include <TApplication.h>
 #include <TColor.h>
 

ctbGui/ctbLinkDef.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #pragma link C++ class ctbMain;
 #pragma link C++ class ctbDacs;
 #pragma link C++ class ctbDac;

ctbGui/ctbMain.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include <TApplication.h>
 #include <TGClient.h>
 #include <TCanvas.h>

ctbGui/ctbMain.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #ifndef CTBMAIN_H
 #define CTBMAIN_H
 #include <TGFrame.h>

ctbGui/ctbPattern.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include <TApplication.h>
 #include <TGClient.h>
 #include <TCanvas.h>

ctbGui/ctbPattern.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #ifndef CTBPATTERN_H
 #define CTBPATTERN_H
 #include  <TGFrame.h>

ctbGui/ctbPowers.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include  <TGFrame.h>
 
 

ctbGui/ctbPowers.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #ifndef CTBPOWERS_H
 #define CTBPOWERS_H
 

ctbGui/ctbSignals.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include <TApplication.h>
 #include <TGClient.h>
 #include <TCanvas.h>

ctbGui/ctbSignals.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #ifndef CTBSIGNALS_H
 #define CTBSIGNALS_H
 #include  <TGFrame.h>

ctbGui/ctbSlowAdcs.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 #include <stdio.h>
 #include <iostream>

ctbGui/ctbSlowAdcs.h

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 
 #ifndef CTBSLOWADCS_H

ctbGui/patternGenerator/deserializer.cpp

@@ -0,0 +1,110 @@
+
+#include <stdlib.h>  
+#include <stdint.h>  
+#include <string.h>  
+#include <sys/utsname.h>   
+#include <sys/types.h>
+#include <unistd.h>  
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <math.h>
+#include <fcntl.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+int main(int argc, char *argv[]) {
+
+  int iarg;
+  char fname[10000];
+  uint64_t word;
+  int val[64];
+  int bit[64];
+  FILE *fdin;
+  
+  int nb=2;
+  int off=0;
+  int ioff=0;
+  int dr=24;
+  int idr=0;
+  int ib=0;
+  int iw=0;
+  bit[0]=19;
+  bit[1]=8;
+  //  for (iarg=0; iarg<argc; iarg++) printf("%d %s\n",iarg, argv[iarg]);
+  
+  if (argc<2) printf("Error: usage is %s fname [dr off  b0 b1 bn]\n");
+  
+  if (argc>2) dr=atoi(argv[2]);
+  if (argc>3) off=atoi(argv[3]);
+  if (argc>4) {
+  for (ib=0; ib<64; ib++) {
+    if (argc>4+ib) {
+      bit[ib]=atoi(argv[4+ib]);
+      nb++;
+    }
+  }
+  
+  }
+  
+  idr=0;
+  for (ib=0; ib<nb; ib++) {
+    val[ib]=0;
+  }
+  
+  
+  fdin=fopen(argv[1],"rb");
+  if (fdin==NULL) {
+    printf("Cannot open input file %s for reading\n",argv[1]);
+    return 200;
+  } 
+  
+  while (fread((void*)&word, 8, 1, fdin)) {
+    //   printf("%llx\n",word);
+    if (ioff<off) ioff++;
+    else {
+      
+      for (ib=0; ib<nb; ib++) {
+	if (word&(1<<bit[ib])) 	  val[ib]|=(1<<idr);
+      }
+      idr++;
+      if (idr==dr) {
+	idr=0;
+	fprintf(stdout,"%d\t",iw++);
+	for (ib=0; ib<nb; ib++) {
+#ifdef HEX
+	  fprintf(stdout,"%08llx\t",val[ib]);
+#else
+	  fprintf(stdout,"%lld\t",val[ib]);
+	  
+#endif
+	  
+	  val[ib]=0;
+	}
+	fprintf(stdout,"\n");
+      }
+      
+    }
+
+  }
+  if (idr!=0) {
+    fprintf(stdout,"%d\t",iw++);
+    for (ib=0; ib<nb; ib++) {
+#ifdef HEX
+	  fprintf(stdout,"%08llx\t",val[ib]);
+#else
+	  fprintf(stdout,"%lld\t",val[ib]);
+	  
+#endif
+	  
+	  val[ib]=0;
+    }
+    fprintf(stdout,"\n");
+  }
+
+  fclose(fdin);
+
+  return 0;
+}

ctbGui/patternGenerator/generate.sh

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 if [ "$#" -eq 0 ]; then
     echo "Wrong number of arguments: usage should be $0 patname"
     exit 1
@@ -21,10 +19,9 @@ fi
 
 if [ -f "$infile" ]
 then
-dir=$(dirname $infile)
-gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c -I$dir; 
+gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c ; 
 echo compiling
-echo gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c  -I$dir; 
+echo gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c ; 
 $exe ; 
 echo cleaning
 rm $exe

ctbGui/patternGenerator/generator.c

@@ -0,0 +1,177 @@
+/****************************************************************************
+usage to generate a patter test.pat from test.p
+
+gcc -DINFILE="\"test.p\"" -DOUTFILE="\"test.pat\"" -o test.exe generator.c ; ./test.exe ; rm test.exe
+
+
+*************************************************************************/
+
+#include <stdlib.h>  
+#include <stdint.h>  
+#include <string.h>  
+#include <sys/utsname.h>   
+#include <sys/types.h>
+#include <unistd.h>  
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <math.h>
+#include <fcntl.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+#define MAXLOOPS 3
+#define MAXTIMERS 3
+#define MAXWORDS 1024
+
+
+
+uint64_t pat=0;
+uint64_t iopat=0;
+uint64_t clkpat=0;
+
+int iaddr=0;
+int waitaddr[3]={MAXWORDS,MAXWORDS,MAXWORDS};
+int startloopaddr[3]={MAXWORDS,MAXWORDS,MAXWORDS}; 
+int stoploopaddr[3]={MAXWORDS,MAXWORDS,MAXWORDS}; 
+int start=0, stop=0;
+uint64_t waittime[3]={0,0,0};
+int nloop[3]={0,0,0};
+
+char infile[10000], outfile[10000];
+
+FILE *fd, *fd1;
+uint64_t PAT[MAXWORDS];
+
+
+int i,ii,iii,j,jj,jjj,pixx,pixy,memx,memy,muxout,memclk,colclk,rowclk,muxclk,memcol,memrow,loopcounter;
+
+void setstart() {
+  start=iaddr;
+}
+
+void setstop() {
+  stop=iaddr;
+}
+
+void setinput(int bit) {
+  uint64_t mask=1;
+  mask=mask<<bit;
+  iopat &= ~mask;
+}
+
+void setoutput(int bit) {
+  uint64_t mask=1;
+  mask=mask<<bit;
+  iopat |= mask;
+}
+
+void setclk(int bit) {
+  uint64_t mask=1;
+  mask=mask<<bit;
+  iopat |= mask;
+  clkpat |= mask;
+}
+
+void clearbit(int bit){
+  uint64_t mask=1;
+  mask=mask<<bit;
+  pat &= ~mask;
+}
+void setbit(int bit){
+  uint64_t mask=1;
+  mask=mask<<bit;
+  pat |= mask;
+}
+
+int checkbit(int bit) {
+  uint64_t mask=1;
+  mask=mask<<bit;
+  return (pat & mask ) >>bit;
+}
+
+void setstartloop(int iloop) {
+  if (iloop>=0 && iloop<MAXLOOPS)
+    startloopaddr[iloop]=iaddr;
+}
+
+
+void setstoploop(int iloop) {
+  if (iloop>=0 && iloop<MAXLOOPS)
+    stoploopaddr[iloop]=iaddr;
+}
+
+
+void setnloop(int iloop, int n) {
+  if (iloop>=0 && iloop<MAXLOOPS)
+    nloop[iloop]=n;
+}
+
+void setwaitpoint(int iloop) {
+  if (iloop>=0 && iloop<MAXTIMERS)
+    waitaddr[iloop]=iaddr;
+}
+
+
+void setwaittime(int iloop, uint64_t t) {
+  if (iloop>=0 && iloop<MAXTIMERS)
+    waittime[iloop]=t;
+}
+
+
+
+
+void pw(){
+  if (iaddr<MAXWORDS)
+    PAT[iaddr]= pat;
+  fprintf(fd,"patword 0x%04x 0x%016llx\n",iaddr, pat);
+  iaddr++;
+  if (iaddr>=MAXWORDS) printf("ERROR: too many word in the pattern (%d instead of %d)!",iaddr, MAXWORDS);
+}
+
+int parseCommand(int clk, int cmdbit, int cmd, int length) {
+  int ibit;
+  clearbit(clk);
+  for (ibit=0; ibit<length; ibit++) {
+    if (cmd&(1>>ibit))
+      setbit(cmdbit);
+    else
+      clearbit(cmdbit);
+    pw();
+    /******/
+    setbit(clk);
+    pw();
+    /******/
+  }
+};
+
+
+
+main(void) {
+  int iloop=0;
+  fd=fopen(OUTFILE,"w");
+#include INFILE
+
+  fprintf(fd,"patioctrl 0x%016llx\n",iopat);
+  fprintf(fd,"patclkctrl 0x%016llx\n",clkpat);
+  fprintf(fd,"patlimits 0x%04x 0x%04x\n",start, stop);
+
+  for (iloop=0; iloop<MAXLOOPS; iloop++) {
+    fprintf(fd,"patloop%d 0x%04x 0x%04x\n",iloop, startloopaddr[iloop], stoploopaddr[iloop]);
+    if ( startloopaddr[iloop]<0 || stoploopaddr[iloop]<= startloopaddr[iloop]) nloop[iloop]=0;
+    fprintf(fd,"patnloop%d %d\n",iloop, nloop[iloop]);
+  }
+
+  for (iloop=0; iloop<MAXTIMERS; iloop++) {
+    fprintf(fd,"patwait%d 0x%04x\n",iloop, waitaddr[iloop]);
+    if (waitaddr[iloop]<0) waittime[iloop]=0;
+    fprintf(fd,"patwaittime%d %lld\n",iloop, waittime[iloop]);
+  }
+  
+  close((int)fd);
+  fd1=fopen(OUTFILEBIN,"w");
+  fwrite(PAT,sizeof(uint64_t),iaddr, fd1);
+  close((int)fd1);
+}

ctbGui/patternGenerator/test.p

@@ -0,0 +1,201 @@
+//define signals and directions (Input, outputs, clocks)
+
+
+#define compTestIN 1
+setoutput(compTestIN);
+
+#define curON 32
+setoutput(curON);
+
+#define side_clk 2
+setclk(side_clk);
+
+#define side_din 3
+setoutput(side_din);
+
+#define clear_shr 4
+setoutput(clear_shr);
+
+#define bottom_din 5
+setoutput(bottom_din);
+
+#define bottom_clk 6
+setclk(bottom_clk);
+
+#define gHG 7
+setoutput(gHG);
+
+#define bypassCDS 31
+setoutput(bypassCDS);
+
+
+#define ENprechPRE 8
+setoutput(ENprechPRE);
+
+
+#define res 9
+setoutput(res);
+
+#define pulseOFF 30
+setoutput(pulseOFF);
+
+#define connCDS 27
+setoutput(connCDS);
+
+#define Dsg_1 24
+setoutput(Dsg_1);
+
+
+#define Dsg_2 25
+setoutput(Dsg_2);
+
+
+#define Dsg_3 23
+setoutput(Dsg_3);
+
+#define sto0 10
+setoutput(sto0);
+
+#define sto1 11
+setoutput(sto1);
+
+#define sto2 12
+setoutput(sto2);
+
+#define resCDS 13
+setoutput(resCDS);
+
+#define prechargeConnect 14
+setoutput(prechargeConnect);
+
+#define pulse 15
+setoutput(pulse);
+
+#define PCT_mode 21
+setoutput(PCT_mode);
+
+#define res_DGS 16
+setoutput(res_DGS);
+
+#define adc_ena 17
+setoutput(adc_ena);
+
+
+#define CLKBIT 18
+setclk(CLKBIT);
+
+
+#define adc_sync 63
+setoutput(adc_sync);
+
+
+
+
+
+	  
+#define PW pw()
+#define SB(x) setbit(x) 
+#define CB(x) clearbit(x)
+#define CLOCK  clearbit(CLKBIT); pw();setbit(CLKBIT);pw()
+#define LCLOCK  clearbit(CLKBIT); pw();setbit(CLKBIT);pw();clearbit(CLKBIT); pw()
+#define CLOCKS(x) for (i=0;i<x;i++) {clearbit(CLKBIT);pw(); setbit(CLKBIT); pw();}
+#define STOP setstop();
+#define START setstart();
+#define REPEAT(x) for (i=0;i<(x);i++) {pw();}
+#define DOFOR(x) for (j=0;j<(x);j++) {
+// }				     
+#define STARTUP1 CB(compTestIN);SB(clear_shr);CB(side_clk);CB(side_din);CB(bottom_din);CB(bottom_clk);
+#define STARTUP2 CB(pulse);SB(PCT_mode);SB(pulseOFF);CB(curON);
+#define STARTUP3 SB(res);SB(gHG);SB(ENprechPRE);
+#define STARTUP4 SB(bypassCDS); CB(connCDS);CB(sto0);SB(sto1);SB(sto2);
+#define STARTUP5 SB(resCDS);CB(Dsg_1);CB(Dsg_2);SB(Dsg_3);CB(prechargeConnect);SB(res_DGS);
+#define STARTUP STARTUP1 STARTUP2 STARTUP3 STARTUP4 STARTUP5 PW;
+
+
+
+
+
+//****NOTES****//
+//FUNCTIONS
+//Declare functions at the beginning 
+void load_pix(int nx, int ny)
+{//SELECT PIXEL 1,1 for readout
+SB(clear_shr);PW;PW;
+CB(clear_shr);PW;PW;PW;PW;
+
+SB(side_din);PW;
+SB(side_clk);PW;
+CB(side_din);
+setstartloop(0); //loop on the rows
+SB(side_clk);PW;
+setstoploop(0);  //finish loop on the rows
+setnloop(0,ny); //set number row selected -can be changed dynamically
+CB(side_clk);PW;
+SB(bottom_din);PW;
+SB(bottom_clk);PW;
+CB(bottom_din);
+setstartloop(1); //loop on the columns
+SB(bottom_clk);PW;
+setstoploop(1); //loop on the columns
+setnloop(1,ny); //set number columns selected -can be changed dynamically
+}
+   
+void load_col(void)
+{//SELECT COLUMN 1 for readout
+SB(clear_shr);PW;PW;
+CB(clear_shr);PW;PW;PW;PW;
+SB(bottom_din);PW;
+SB(bottom_clk);PW;
+CB(bottom_clk);PW;
+CB(bottom_din);PW;
+}
+//END of FUNCTIONS
+////////////////////////////////////////////////////////
+//LET BYPASS PREAMP AND CDS and write on preamp out.//
+//THIS ALLOWS CHECKING SOURCE FOLLOWERS               //
+////////////////////////////////////////////////////////
+
+   
+PW;
+   
+SB(5); PW;
+
+CB(5); PW;
+
+START; //pattern starts from here
+STARTUP;
+setwaitpoint(0); //set wait points
+PW;
+setwaittime(0,20); //wait time - can be changed dynamically
+SB(adc_ena);PW;
+   printf("ADC sync %x %d %llx\n",iaddr,adc_sync, pat);
+SB(adc_sync);PW;
+   printf("ADC sync %x %d  %llx\n",iaddr, adc_sync, pat);
+CB(gHG);
+setwaitpoint(1); //set wait points
+setwaittime(1,16); //wait time - can be changed dynamically
+CB(adc_sync);PW;
+load_pix(10, 20);
+
+CB(res);
+//CB(Dsg_3);PW;
+CB(res_DGS);
+setwaitpoint(2); //set wait points
+setwaittime(2,1000); //wait time - can be changed dynamically
+
+//SB(res_DGS);
+//PW;
+//SB(Dsg_3);
+//
+//CB(connCDS);
+//TEST SIGNALS END
+//
+REPEAT(20)
+
+//****************//
+//*FINAL COMMANDS*//
+//****************//
+CB(adc_ena);PW;
+//STARTUP;
+STOP; PW; //stops here
+//REPEAT(4);

docs/CMakeLists.txt

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 find_package(Doxygen REQUIRED)
 find_package(Sphinx REQUIRED)
 
@@ -55,9 +53,6 @@ set(SPHINX_SOURCE_FILES
   src/troubleshooting.rst
   src/receivers.rst
   src/slsreceiver.rst
-  src/udpheader.rst
-  src/udpconfig.rst
-  src/udpdetspec.rst
 )
 
 foreach(filename ${SPHINX_SOURCE_FILES})

docs/src/dependencies.rst

@@ -21,8 +21,10 @@ the shared libraries these are needed:
 GUI
 -----------------------
 
- * Qt 5.9
- * Qwt 6.1.5 (packaged in libs/)
+The GUI is currently using Qt4 but watch out for an upgrade to 5. 
+
+ * Qt 4.8
+ * Qwt 6.1
 
 -----------------------
 Python bindings
@@ -32,12 +34,6 @@ Python bindings
  * pybind11 (packaged in libs/)
 
 
------------------------
-Moench executables
------------------------
-
- * libtiff
-
 -----------------------
 Documentation
 -----------------------

docs/src/firmware.rst

@@ -1,6 +1,8 @@
 Firmware Upgrade
 =================
 
+
+
 Eiger
 -------------
 
@@ -16,9 +18,30 @@ Upgrade
 ^^^^^^^^
 #. Tftp must be already installed on your pc to use the bcp script.
 
-#. Copy new servers to the board. See :ref:`how to upgrade detector servers<Detector Server Upgrade>` for more detals. A reboot should have started the new linked servers automatically. For Eiger, do not reboot yet as we need to program the firmware via bit files.
+#. Kill the on-board servers and copy new servers to the board. 
 
-    * This step is crucial when registers between firmwares change. Failure to do so will result in linux on boards to crash and boards can't be pinged anymore.
+    .. code-block:: bash
+
+        # Option 1: from detector console
+        # kill old server
+        ssh root@bebxxx
+        killall eigerDetectorServer
+
+        # copy new server
+        cd executables
+        scp user@pc:/path/eigerDetectorServerxxx .
+        chmod 777 eigerDetectorServerxxx
+        ln -sf eigerDetectorServerxxx eigerDetectorServer
+        sync
+
+        # Options 2: from client console for multiple modules
+        for i in bebxxx bebyyy;
+        do ssh root@$i killall eigerDetectorServer;
+        scp eigerDetectorServerxxx root@$i:~/executables/eigerDetectorServer;
+        ssh root@$i sync; done
+
+
+    * This is crucial when registers between firmwares change. Failure to do so will result in linux on boards to crash and boards can't be pinged anymore.
 
 #. Bring the board into programmable mode using either of the 2 ways. Both methods result in only the central LED blinking.
     
@@ -27,13 +50,8 @@ Upgrade
         Do a hard reset for each half module on back panel boards, between the LEDs, closer to each of the 1G ethernet connectors. Push until all LEDs start to blink.
     
     * Software:  
-
         .. code-block:: bash
 
-            # Option 1: if the old server is still running:
-            sls_detector_put execcommand "./boot_recovery"
-
-            # Option 2:
             ssh root@bebxxx
             cd executables
             ./boot_recovery
@@ -61,24 +79,11 @@ Upgrade
         #update front right fpga
         bcp download.bit bebxxx:/febr
 
-        #update kernel (only if required by us)
+        #update kernel (only if required by the SLS Detector Group)
         bcp download.bit bebxxx:/kernel
 
 #. Reboot the detector.
 
-    .. code-block:: bash
-
-        # In the first terminal where we saw "Succeess"
-        # reconfig febX is necessary only if you have flashed a new feb firmware
-        reconfig febl
-        reconfig febr
-        # will reboot controller
-        reconfig fw0
-
-.. note :: 
-
-    If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
-
 Jungfrau
 -------------
 
@@ -89,50 +94,82 @@ Download
 - `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
 
-Upgrade
-^^^^^^^^
+Upgrade (from v4.x.x)
+^^^^^^^^^^^^^^^^^^^^^^
 
-.. warning ::
+Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
-    In case you have had issues in the past with programming via software:
+#. Tftp must be installed on pc.
 
-    * 6.1.2 server has a fix for seamless fpga programming
+#. Update client package to the latest (5.x.x).
 
-    * We recommend first updating the on-board detector server to 6.1.2 (with client 6.1.x) using command 'updatedetectorserver' or 'copydetectorserver'.
+#. Disable server respawning or kill old server
+    .. code-block:: bash
 
-    * Then use command 'programfpga' to only update firmware or use command 'update' to update firmware and server to the latest release.
+        # Option 1: if respawning enabled
+        telnet bchipxxx
+        # edit /etc/inittab
+        # comment out line #ttyS0::respawn:/jungfrauDetectorServervxxx
+        reboot
+        # ensure servers did not start up after reboot
+        telnet bchipxxx
+        ps
+
+        #  Option 2: if respawning already disabled
+        telnet bchipxxx
+        killall jungfrauDetectorServerv*
+
+#. Copy new server and start in update mode
+    .. code-block:: bash
+
+        tftp pcxxx -r jungfrauDetectorServervxxx -g
+        chmod 777 jungfrauDetectorServervxxx
+        ./jungfrauDetectorServervxxx -u
+
+#. Program fpga from the client console
+    .. code-block:: bash
+
+        sls_detector_get free
+        # Crucial that the next command executes without any errors
+        sls_detector_put hostname bchipxxx
+        sls_detector_put programfpga xxx.pof
+
+#. After programming, kill 'update server' using Ctrl + C in server console.
+
+#. Enable server respawning if needed
+    .. code-block:: bash
+
+        telnet bchipxxx
+        # edit /etc/inittab
+        # uncomment out line #ttyS0::respawn:/jungfrauDetectorServervxxx
+        # ensure the line has the new server name
+        reboot
+        # ensure both servers are running using ps
+        jungfrauDetectorServervxxx
+        jungfrauDetectorServervxxx --stop-server 1953
 
 
+Upgrade (from v5.0.0)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
 
-
-
-Program from console
+#. Program from console
     .. code-block:: bash
 
-        # These instructions are for upgrades from v5.0.0. For earlier versions, please contact us.
-
-        # Always ensure that the client and server software are of the same release.
-
-        # copies server, links new server to jungfrauDetectorServer, 
-        # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga, reboots
-
-        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
+        # copies server from tftp folder of pc, programs fpga,
+        # removes old server from respawn, sets up new server to respawn
+        # and reboots
         sls_detector_put update jungfrauDetectorServervxxx pcxxx xx.pof
 
-        # v6.1.1 - present (copies server from the full path provided)
-        sls_detector_put update jungfrauDetectorServervxxx xx.pof
-
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 
 
 
-Gotthard I
------------
+Gotthard
+---------
 
 Download 
 ^^^^^^^^^^^^^
@@ -147,7 +184,7 @@ Upgrade
 ^^^^^^^^
 .. warning ::
     | Gotthard firmware cannot be upgraded remotely and requires the use of USB-Blaster.
-    | It is generally updated by us.
+    | It is generally updated by the SLS Detector group.
 
 #. Download `Altera Quartus software or Quartus programmer <https://fpgasoftware.intel.com/20.1/?edition=standard&platform=linux&product=qprogrammer#tabs-4>`__.
    
@@ -158,7 +195,7 @@ Upgrade
 
 #. Plug the end of your USB-Blaster with the adaptor provided to the connector 'AS config' on the Gotthard board.
 
-#. Click on 'Add file'. Select programming (pof) file provided by us.
+#. Click on 'Add file'. Select programming (pof) file provided by the SLS Detector group.
 
 #. Check "Program/Configure" and "Verify". Push the start button. Wait until the programming process is finished.
 
@@ -167,75 +204,64 @@ Upgrade
 #. Reboot the detector.
 
 
-Mythen III
------------
+Mythen3
+-------
+
+.. note :: 
+
+  As it is still in developement, the rbf files must be picked up from the SLS Detector Group.
 
 Download 
 ^^^^^^^^^^^^^
 
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- `rbf files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
+- rbf files (in developement)
 
 
-Upgrade
-^^^^^^^^
+Upgrade (from v5.0.0)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Program from console
+#. Program from console
     .. code-block:: bash
 
-        # Always ensure that the client and server software are of the same release.
-
-        # copies server, links new server to mythen3DetectorServer, 
-        # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga, reboots
-
-        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
+        # copies server from tftp folder of pc, programs fpga,
+        # and reboots (new server not respawned currently)
         sls_detector_put update mythen3DetectorServervxxx pcxxx xxx.rbf
 
-        # v6.1.1 - present (copies server from the full path provided)
-        sls_detector_put update mythen3DetectorServervxxx xxx.rbf
-
         # Or only program firmware
         sls_detector_put programfpga xxx.rbf
 
+
+
+Gotthard2
+-------------
+
 .. note :: 
 
-    If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
-
-Gotthard II
--------------
+  As it is still in developement, the rbf files must be picked up from the SLS Detector Group.
 
 Download 
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- `rbf files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
+- rbf files (in development)
 
-Upgrade
-^^^^^^^^
 
-Program from console
+Upgrade (from v5.0.0)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+#. Program from console
     .. code-block:: bash
 
-        # Always ensure that the client and server software are of the same release.
-        
-        # copies server, links new server to gotthard2DetectorServer, 
-        # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga, reboots
-
-        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
+        # copies server from tftp folder of pc, programs fpga,
+        # and reboots (new server not respawned currently)
         sls_detector_put update gotthard2DetectorServervxxx pcxxx xxx.rbf
 
-        # v6.1.1 - present (copies server from the full path provided)
-        sls_detector_put update gotthard2DetectorServervxxx xxx.rbf
-
         # Or only program firmware
         sls_detector_put programfpga xxx.rbf
 
-.. note :: 
 
-    If the detector servers did not start up automatically after reboot, you need to add scripts to do that. See :ref:`Automatic start<Automatic start servers>` for more details.
 
 Moench
 -------
@@ -247,40 +273,19 @@ Download
 - `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
 
-
-Upgrade
-^^^^^^^^
-
-.. warning ::
-
-    In case you have had issues in the past with programming via software:
-
-    * 6.1.2 server has a fix for seamless fpga programming
-
-    * We recommend first updating the on-board detector server to 6.1.2 (with client 6.1.x) using command 'updatedetectorserver' or 'copydetectorserver'.
-
-    * Then use command 'programfpga' to only update firmware or use command 'update' to update firmware and server to the latest release.
-
-
+Upgrade (from v5.0.0)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
-
-Program from console
+#. Program from console
     .. code-block:: bash
 
-        # Always ensure that the client and server software are of the same release.
-
-        # copies server, links new server to moenchDetectorServer, 
-        # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga, reboots
-
-        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
+        # copies server from tftp folder of pc, programs fpga,
+        # removes old server from respawn, sets up new server to respawn
+        # and reboots
         sls_detector_put update moenchDetectorServervxxx pcxxx xx.pof
 
-        # v6.1.1 - present (copies server from the full path provided)
-        sls_detector_put update moenchDetectorServervxxx xx.pof
-
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 
@@ -294,28 +299,19 @@ Download
 - `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
 
-
-Upgrade
-^^^^^^^^
+Upgrade (from v5.0.0)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
-
-Program from console
+#. Program from console
     .. code-block:: bash
 
-        # Always ensure that the client and server software are of the same release.
-        
-        # copies server, links new server to ctbDetectorServer, 
-        # removes old server from respawn, sets up new lnked server to respawn
-        # programs fpga, reboots
-
-        # v5.0.0 - 6.0.0 (copies server from tftp folder of the pc)
+        # copies server from tftp folder of pc, programs fpga,
+        # removes old server from respawn, sets up new server to respawn
+        # and reboots
         sls_detector_put update ctbDetectorServervxxx pcxxx xx.pof
 
-        # v6.1.1 - present (copies server from the full path provided)
-        sls_detector_put update ctbDetectorServervxxx xx.pof
-
         # Or only program firmware
         sls_detector_put programfpga xxx.pof
 
@@ -348,52 +344,25 @@ Firmware Troubleshooting with blackfin
 
 5. If one can't list it, read the next section to try to get the blackfin to list it.
 
-How to get back mtd3 drive remotely (udpating kernel)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-    You have 2 alternatives to update the kernel.
-
-    1. Commands via software (>= v6.0.0)
+How to get back mtd3 drive remotely
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This might take a few reruns (maybe even 10) until the mtd drive is accessed by the blackfin upon linux startup.
 
   .. code-block:: bash
     
-            sls_detector_put updatekernel /home/...path-to-kernel-image
-
-
-    2. or command line 
-    
-        .. code-block:: bash
-            
-            # step 1: get the kernel image (uImage.lzma) from slsdetectorgroup
-            # and copy it to pc's tftp folder
-
-            # step 2: connect to the board
+    # step 1: connect to the board
     telnet bchipxxx
 
-            #step 3: go to directory for space
-            cd /var/tmp/
+    # step 2: check if mtd3 drive listed
+    more /proc/mtd
 
-            # step 3: copy kernel to board
-            tftp pcxxx -r uImage.lzma -g
-
-            # step 4: verify kernel copied properly
-            ls -lrt
-            
-            # step 5: erase flash
-            flash_eraseall /dev/mtd1
-            
-            # step 6: copy new image to kernel drive
-            cat uImage.lzma > /dev/mtd1
-            
-            # step 7:
-            sync
-            
-            # step 8:
+    # step 3: tell fpga not to touch flash and reboot
+    echo 9 > /sys/class/gpio/export; 
+    echo out > /sys/class/gpio/gpio9/direction; 
+    echo 0 > /sys/class/gpio/gpio9/value;
     reboot
 
-            # step 9: verification
-            telnet bchipxxx
-            uname -a # verify kernel date
-            more /proc/mtd # verify mtd3 is listed
+    # step 4: repeat steps 1 - 3 until you see the mtd3 drive
 
 
 Last Resort using USB Blaster

docs/src/gendoc.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 /**
  * Utility program to generate input files for the command line
  * documentation. Uses the string returned from sls_detector_help cmd
@@ -45,7 +43,6 @@ int main() {
 
     for (const auto &cmd : commands) {
         std::ostringstream os;
-        std::cout << cmd << '\n';
         proxy.Call(cmd, {}, -1, slsDetectorDefs::HELP_ACTION, os);
 
         auto tmp = os.str().erase(0, cmd.size());

docs/src/index.rst

@@ -66,15 +66,6 @@ Welcome to slsDetectorPackage's documentation!
     virtualserver
     serverdefaults
 
-
-.. toctree::
-    :caption: Detector UDP Header
-    :maxdepth: 2
-
-    udpheader
-    udpconfig
-    udpdetspec
-
 .. toctree::
     :caption: Receiver
     :maxdepth: 2

docs/src/installation.rst

@@ -1,28 +1,100 @@
+
+
+
+.. note :: 
+
+    The default branch of our git repository is developer. It contains the 
+    latest development version. It is expected to compile and work but 
+    features might be added or tweaked. In some cases the API might also change
+    without being communicated. If absolute stability of the API is needed please
+    use one of the release versions. 
+
 .. 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. 
+    manage the dependencies.
     
 
 .. _Installation:
 
-
 Installation
-===============
+==============================================
+
+.. _build from source using cmake:
+
+Build from source using CMake
+---------------------------------
+
+Note that on some systems, for example RH7,  cmake v3+ is available under the cmake3 alias.
+It is also required to clone with the option --recursive to get the git submodules used
+in the package. 
+
+
+.. code-block:: bash
+
+    git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
+    mkdir build && cd build
+    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
+    make -j12 #or whatever number of cores you are using to build
+    make install
+
+The easiest way to configure options is to use the ccmake utility. 
+
+.. code-block:: bash
+
+    #from the build directory
+    ccmake .
+
+
+Build using cmk.sh script
+-------------------------
+These are mainly aimed at those not familiar with using ccmake and cmake.
+
+.. code-block:: bash
+
+    The binaries are generated in slsDetectorPackage/build/bin directory.
+
+    Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [n] [-h] [z] [-d <HDF5 directory>] [-l Install directory] [-k <CMake command>] [-j <Number of threads>]
+    -[no option]: only make
+    -c: Clean
+    -b: Builds/Rebuilds CMake files normal mode
+    -p: Builds/Rebuilds Python API
+    -h: Builds/Rebuilds Cmake files with HDF5 package
+    -d: HDF5 Custom Directory
+    -k: CMake command
+    -l: Install directory
+    -t: Build/Rebuilds only text client
+    -r: Build/Rebuilds only receiver
+    -g: Build/Rebuilds only gui
+    -s: Simulator
+    -u: Chip Test Gui
+    -j: Number of threads to compile through
+    -e: Debug mode
+    -i: Builds tests
+    -m: Manuals
+    -n: Manuals without compiling doxygen (only rst)
+    -z: Moench zmq processor
+    
+    # get all options
+    ./cmk.sh -?
+
+    # new build  and compile in parallel:
+    ./cmk.sh -bj5
+
 
 Install binaries using conda
--------------------------------
+--------------------------------
 
 Conda is not only useful to manage python environments but can also
-be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
-are from the developer branch. Please use released tags for stability.
+be used as a user space package manager. 
 
 We have three different packages available:
 
-    * **slsdetlib** shared libraries and command line utilities 
-    * **slsdetgui** GUI
-    * **slsdet** Python bindings
+ * **slsdetlib**, shared libraries and command line utilities 
+ * **slsdetgui**, GUI
+ * **slsdet**, Python bindings
+
 
 .. code-block:: bash
 
@@ -31,9 +103,9 @@ We have three different packages available:
     conda config --add channels slsdetectorgroup
     conda config --set channel_priority strict
 
-    #create and activate an environment with our library
-    #replace 6.1.1 with the required tag
-    conda create -n myenv slsdetlib=6.1.1
+    #cerate an environment with our library, then activate
+    #replace 2020.07.20.dev0 with the required tag
+    conda create -n myenv slsdetlib=2020.07.23.dev0
     conda activate myenv
 
     #ready to use
@@ -44,145 +116,11 @@ We have three different packages available:
 .. code-block:: bash
 
     #List available versions
-    # lib and binaries
-    conda search slsdetlib
-    # python
     conda search slsdet
-    # gui
-    conda search slsdetgui
 
 
-
-
-Build from source
--------------------
-
-
-1. Download Source Code from github
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. code-block:: bash
-
-    git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 6.1.1
-
-
-| **Pybind for Python**
-| v7.0.0+:
-|   pybind11 packaged into 'libs/pybind'. No longer a submodule. No need for "recursive" or "submodule update".
-| 
-| Older versions:
-|   pybind11 is a submodule. Must be cloned using "recursive" and updated when switching between versions using the following commands.
-
-.. code-block:: bash
-    
-    # clone using recursive to get pybind11 submodule
-    git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
-
-    # update submodule when switching between releases
-    cd slsDetectorPackage
-    git submodule update --init
-   
-
-.. _build from source using cmake:
-
-
-
-2. Build from Source
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Build using CMake
-^^^^^^^^^^^^^^^^^^^^^^
-
-.. code-block:: bash
-
-    # outside slsDetecorPackage folder
-    mkdir build && cd build
-
-    # configure & generate Makefiles using cmake
-    # by listing all your options (alternately use ccmake described below)
-    # cmake3 for some systems
-    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-
-    # compiled to the build/bin directory
-    make -j12 #or whatever number of cores you are using to build
-
-    # install headers and libs in /your/install/path directory
-    make install
-
-
-Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.
-
-.. code-block:: bash
-
-    # ccmake3 for some systems
-    ccmake ..
- 
-    # choose the options
-    # first press [c] - configure
-    # then press [g] - generate
-
-
-
-===============================     ===========================================
-Example cmake options               Comment
-===============================     ===========================================
--DSLS_USE_PYTHON=ON                 Python
--DPython_FIND_VIRTUALENV=ONLY       Python from only the conda environment 
--DZeroMQ_HINT=/usr/lib64            Use system zmq instead
--DSLS_USE_GUI=ON                    GUI
-===============================     ===========================================
-
-
-
-Build using in-built cmk.sh script
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-.. code-block:: bash
-
-    The binaries are generated in slsDetectorPackage/build/bin directory.
-
-    Usage: ./cmk.sh [-b] [-c] [-d <HDF5 directory>] [e] [g] [-h] [i] [-j <Number of threads>] 
-    [-k <CMake command>] [-l <Install directory>] [m] [n] [-p] [-q <Zmq hint directory>] 
-    [r] [s] [t] [u] [z]  
-    -[no option]: only make
-    -b: Builds/Rebuilds CMake files normal mode
-    -c: Clean
-    -d: HDF5 Custom Directory
-    -e: Debug mode
-    -g: Build/Rebuilds gui
-    -h: Builds/Rebuilds Cmake files with HDF5 package
-    -i: Builds tests
-    -j: Number of threads to compile through
-    -k: CMake command
-    -l: Install directory
-    -m: Manuals
-    -n: Manuals without compiling doxygen (only rst)
-    -p: Builds/Rebuilds Python API
-    -q: Zmq hint directory
-    -r: Build/Rebuilds only receiver
-    -s: Simulator
-    -t: Build/Rebuilds only text client
-    -u: Chip Test Gui
-    -z: Moench zmq processor
-
-    
-    # display all options
-    ./cmk.sh -?
-
-    # new build and compile in parallel (recommended basic option):
-    ./cmk.sh -cbj5
-
-    # new build, python and compile in parallel:
-    ./cmk.sh -cbpj5
-
-    #To use the system zmq (/usr/lib64) instead
-    ./cmk.sh -cbj5 -q /usr/lib64
-
-
-
-Build on old distributions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Build from source on old distributions
+-----------------------------------------
 
 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
@@ -193,64 +131,12 @@ using this compiler
     #Create an environment with the dependencies
     conda create -n myenv gxx_linux-64 cmake zmq
     conda activate myenv
-
-    # outside slsDetecorPackage folder
-    mkdir build && cd build
     cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
     make -j12
 
 
-
-Build slsDetectorGui (Qt5)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-1. Using pre-built binary on conda
-    .. code-block:: bash
-
-        conda create -n myenv slsdetgui=7.0.0
-        conda activate myenv
-
-
-2. Using system installation on RHEL7
-    .. code-block:: bash
-
-        yum install qt5-qtbase-devel.x86_64
-        yum install qt5-qtsvg-devel.x86_64 
-
-
-3. Using conda
-    .. code-block:: bash
-
-        #Add channels for dependencies and our library
-        conda config --add channels conda-forge
-        conda config --add channels slsdetectorgroup
-        conda config --set channel_priority strict
-
-        # create environment to compile
-        # on rhel7
-        conda create -n slsgui zeromq gxx_linux-64 gxx_linux-64 mesa-libgl-devel-cos6-x86_64 qt
-        # on fedora or newer systems
-        conda create -n slsgui zeromq qt
-
-        # when using conda compilers, would also need libgl, but no need for it on fedora unless maybe using it with ROOT
-
-        # activate environment
-        conda activate slsgui
-
-        # compile with cmake outside slsDetecorPackage folder
-        mkdir build && cd build
-        cmake ../slsDetectorPackage -DSLS_USE_GUI=ON
-        make -j12
-
-        # or compile with cmk.sh
-        cd slsDetectorPackage
-        ./cmk.sh -cbgj9
-
-
-
-
 Build this documentation
-^^^^^^^^^^^^^^^^^^^^^^^^
+-------------------------------
 
 The documentation for the slsDetectorPackage is build using a combination 
 of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
@@ -258,15 +144,11 @@ is to use conda
 
 .. code-block:: bash
 
-    conda create -n myenv python sphinx_rtd_theme breathe
+    conda create -n myenv python sphinx sphinx_rtd_theme
 
+Then enable the option SLS_BUILD_DOCS to create the targets
 
 .. code-block:: bash
 
-    # using cmake or ccmake to enable DSLS_BUILD_DOCS
-    # outside slsDetecorPackage folder
-    mkdir build && cd build
-    cmake ../slsDetectorPackage -DSLS_BUILD_DOCS=ON
-
     make docs # generate API docs and build Sphinx RST
     make rst # rst only, saves time in case the API did not change

docs/src/pyenums.rst

@@ -67,23 +67,11 @@ exposed to Python through pybind11.
 .. autoclass:: readoutMode
     :undoc-members:
 
+.. autoclass:: masterFlags
+    :undoc-members:
+
 .. autoclass:: burstMode
     :undoc-members:
 
 .. autoclass:: timingSourceType
     :undoc-members:
-
-.. autoclass:: M3_GainCaps
-    :undoc-members:    
-
-.. autoclass:: portPosition
-    :undoc-members:
-
-.. autoclass:: streamingInterface
-    :undoc-members:
-
-.. autoclass:: vetoAlgorithm
-    :undoc-members:
-
-.. autoclass:: gainMode
-    :undoc-members:

docs/src/pyexamples.rst

@@ -10,46 +10,27 @@ open an issue in our our  `github repo
 Setting exposure time 
 ------------------------------------
 
-Setting and reading back exposure time can be done either using a Python 
-datetime.timedelta, DurationWrapper or by setting the time in seconds. 
+Setting and reading back exposure time can be done either using a Python datetime.timedelta
+or by setting the time in seconds. 
 
 ::
 
     # Set exposure time to 1.2 seconds
     >>> d.exptime = 1.2
-    >>> d.exptime = 5e-07
 
-    # Setting exposure time using timedelta (upto microseconds precision)
+    # Setting exposure time using timedelta
     import datetime as dt
     >>> d.exptime = dt.timedelta(seconds = 1.2)
-    >>> d.exptime = dt.timedelta(seconds = 1, microseconds = 3)
 
     # With timedelta any arbitrary combination of units can be used
     >>> t = dt.timedelta(microseconds = 100, seconds = 5.3, minutes = .3)
 
-    # using DurationWrapper to set in seconds
-    >>> from slsdet import DurationWrapper
-    >>> d.exptime = DurationWrapper(1.2)
-    
-    # using DurationWrapper to set in ns
-    >>> t = DurationWrapper()
-    >>> t.set_count(500)
-    >>> d.exptime = t
-
     # To set exposure time for individual detector one have to resort
     # to the C++ style API.
     # Sets exposure time to 1.2 seconds for module 0, 6 and 12
     >>> d.setExptime(1.2, [0, 6, 12]) 
     >>> d.setExptime(dt.timedelta(seconds = 1.2), [0, 6, 12]) 
 
-    # to get in seconds
-    >>> d.period
-    181.23
-
-    # to get in DurationWrapper
-    >>> d.getExptime()
-    [sls::DurationWrapper(total_seconds: 181.23 count: 181230000000)]
-
 
 
 ------------------------------------
@@ -239,7 +220,8 @@ Setting and getting times
     # This sets the exposure time for all modules
     d.exptime = 0.5
 
-    # exptime also accepts a python datetime.timedelta (upto microseconds resolution)
+    # exptime also accepts a python datetime.timedelta
+    # which can be used to set the time in almost any unit
     t = dt.timedelta(milliseconds = 2.3)
     d.exptime = t
 
@@ -247,25 +229,16 @@ Setting and getting times
     t = dt.timedelta(minutes = 3, seconds = 1.23)
     d.exptime = t
 
-    # using DurationWrapper to set in seconds
-    >>> from slsdet import DurationWrapper
-    >>> d.exptime = DurationWrapper(1.2)
-    
-    # using DurationWrapper to set in ns
-    >>> t = DurationWrapper()
-    >>> t.set_count(500)
-    >>> d.exptime = t
-
     # exptime however always returns the time in seconds
     >>> d.exptime
     181.23 
 
     # To get back the exposure time for each module 
     # it's possible to use getExptime, this also returns
-    # the values as  DurationWrapper
+    # the values as datetime.timedelta
 
     >>> d.getExptime()
-    [sls::DurationWrapper(total_seconds: 181.23 count: 181230000000)]
+    [datetime.timedelta(seconds=181, microseconds=230000), datetime.timedelta(seconds=181, microseconds=230000)]
 
     # In case the values are the same it's possible to use the
     # element_if_equal function to reduce the values to a single 
@@ -273,8 +246,7 @@ Setting and getting times
 
     >>> t = d.getExptime()
     >>> element_if_equal(t)
-    sls::DurationWrapper(total_seconds: 1.2 count: 1200000000)
-
+    datetime.timedelta(seconds=1)
 
 --------------
 Reading dacs

docs/src/pygettingstarted.rst

@@ -6,7 +6,7 @@ Getting Started
 Which Python?  
 --------------------
 
-We require at least Python 3.6 and strongly recommended that you don't use the system
+We require at lest Python 3.6 and strongly recommended that you don't use the system
 Python installation. The examples in this documentation uses `conda
 <https://docs.conda.io/en/latest/miniconda.html>`_ since it provides good support
 also for non Python packages but there are also other alternatives like, pyenv. 
@@ -14,35 +14,28 @@ also for non Python packages but there are also other alternatives like, pyenv.
 Using something like conda also allows you to quickly switch beteen different Python 
 environments. 
 
----------------------
-Building from Source 
----------------------
-
-If you are not installing slsdet binaries from conda, but instead building from 
-source, please refer to  :ref:`the installation section<Installation>` for details.
-
-Don't forget to compile with the option SLS_USE_PYTHON=ON to enable the Python 
-bindings or if you use the cmk.sh script -p.
-
-.. note ::
-
-    Ensure that the sls det python lib compiled is for the expected python version.
-    For example, build/bin/_slsdet.cpython-39-x86_64-linux-gnu.so for Python v3.9.x
+.. warning ::
 
+    If you use conda avoid also installing packages with pip. 
 
 ---------------------
 PYTHONPATH 
 ---------------------
 
-If you install slsdet binaries using conda everything is set up and you can
+If you install slsdet using conda everything is set up and you can
 directly start using the Python bindings. However, if you build 
-from source you need to tell Python where to find slsdet to use it. This
-can be done by adding your build/bin directory to PYTHONPATH. 
+from source you need to tell Python where to find slsdet. This
+is be done by adding your build/bin directory to PYTHONPATH. 
 
 .. code-block:: bash
 
     export PYTHONPATH = /path/to/your/build/bin:$PYTHONPATH
 
+.. note ::
+
+    Don't forget to compile with the option SLS_USE_PYTHON=ON to enable
+    the Python bindings or if you use the cmk.sh script -p.
+
 --------------------------------------
 Which detector class should I use? 
 --------------------------------------
@@ -143,7 +136,7 @@ can use dir()
     '__str__', '__subclasshook__', '_adc_register', '_frozen', 
     '_register', 'acquire', 'adcclk', 'adcphase', 'adcpipeline', 
     'adcreg', 'asamples', 'auto_comp_disable', 'clearAcquiringFlag', 
-    'clearBit', 'clearROI', 'client_version', 'config',  
+    'clearBit', 'clearROI', 'client_version', 'config', 'copyDetectorServer', 
     'counters', 'daclist', 'dacvalues', 'dbitclk', 'dbitphase' ...
 
 Since the list for Detector is rather long it's an good idea to filter it. 
@@ -153,11 +146,9 @@ their name.
 :: 
 
     >>> [item for item in dir(d) if 'time' in item]
-    ['compdisabletime', 'exptime', 'exptimel', 'frametime', 'getExptime', 
-    'getExptimeForAllGates', 'getExptimeLeft', 'getSubExptime', 'patwaittime', 
-    'patwaittime0', 'patwaittime1', 'patwaittime2', 'runtime', 'setExptime', 
-    'setSubExptime', 'subdeadtime', 'subexptime']
-
+    ['exptime', 'getExptime', 'getExptimeForAllGates', 'getExptimeLeft', 
+    'getSubExptime', 'patwaittime0', 'patwaittime1', 'patwaittime2', 
+    'setExptime', 'setSubExptime', 'subdeadtime', 'subexptime']
 
 The above method works on any Python object but for convenience we also 
 included two functions to find names. View prints the names one per line
@@ -169,7 +160,6 @@ while find returns a list of names.
 
     >>> view('exptime')
     exptime
-    exptimel
     getExptime
     getExptimeForAllGates
     getExptimeLeft
@@ -178,7 +168,6 @@ while find returns a list of names.
     setSubExptime
     subexptime
 
-
     >>> find('exptime')
     ['exptime', 'getExptime', 'getExptimeForAllGates', 'getExptimeLeft', 
     'getSubExptime', 'setExptime', 'setSubExptime', 'subexptime']
@@ -199,36 +188,16 @@ To access the documentation of a function directly from the Python prompt use he
 
         Note
         -----
-        :getter: always returns in seconds. To get in DurationWrapper, use getPeriod
+        :getter: always returns in seconds. To get in datetime.delta, use getPeriod
 
-        Example
+        Examples
         -----------
-        >>> # setting directly in seconds
         >>> d.period = 1.05
-        >>>
-        >>> # setting directly in seconds
-        >>> d.period = 5e-07
-        >>> 
-        >>> # using timedelta (up to microseconds precision)
-        >>> from datatime import timedelta
-        >>> d.period = timedelta(seconds = 1, microseconds = 3)
-        >>> 
-        >>> # using DurationWrapper to set in seconds
-        >>> from slsdet import DurationWrapper
-        >>> d.period = DurationWrapper(1.2)
-        >>> 
-        >>> # using DurationWrapper to set in ns
-        >>> t = DurationWrapper()
-        >>> t.set_count(500)
-        >>> d.period = t
-        >>>
-        >>> # to get in seconds
+        >>> d.period = datetime.timedelta(minutes = 3, seconds = 1.23)
         >>> d.period
         181.23
-        >>> 
-        >>> d.getExptime()
-        [sls::DurationWrapper(total_seconds: 181.23 count: 181230000000)]
-
+        >>> d.getPeriod()
+        [datetime.timedelta(seconds=181, microseconds=230000)]
 
 
 ----------------------
@@ -248,12 +217,11 @@ The enums can be found in slsdet.enums
 
     import slsdet
     >>> [e for e in dir(slsdet.enums) if not e.startswith('_')]
-    ['M3_GainCaps', 'burstMode', 'clockIndex', 'cls', 'dacIndex', 'detectorSettings', 
-    'detectorType', 'dimension', 'externalSignalFlag', 'fileFormat', 
-    'frameDiscardPolicy', 'gainMode', 'name', 'polarity', 'portPosition', 
-    'readoutMode', 'runStatus', 'speedLevel', 'streamingInterface', 'timingMode', 
-    'timingSourceType', 'vetoAlgorithm']
-
+    ['burstMode', 'clockIndex', 'dacIndex', 
+    'detectorSettings', 'detectorType', 'dimension', 'externalSignalFlag', 
+    'fileFormat', 'frameDiscardPolicy', 'masterFlags', 
+    'readoutMode', 'runStatus', 'speedLevel', 'timingMode', 
+    'timingSourceType']
 
     # Even though importing using * is not recommended one could
     # get all the enums like this: 

docs/src/quick_start_guide.rst

@@ -66,15 +66,11 @@ For a Single Module
         # sets destination udp ports (not needed, default is 50001)
         udp_dstport 50012
 
-        # 1g data out
         # source udp ips must be same subnet at destintaion udp ips
-        # udp_srcip 192.168.1.112
-        # destination udp ip picked up from rx_hostname (if auto)
-        # udp_dstip auto
+        udp_srcip 192.168.1.112
 
-        # 10g data out
-        udp_srcip 10.30.20.200
-        udp_dstip 10.30.20.6
+        # destination udp ip picked up from rx_hostname (if auto)
+        udp_dstip auto
 
         # set file path
         fpath /tmp

docs/src/receivers.rst

@@ -4,8 +4,41 @@ Receivers
 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.
 
+Detector UDP Header
+---------------------
+
+| The UDP data format for the packets consist of a common header for all detectors, followed by the data for that one packet.
+
+**The SLS Detector Header**
+
+.. table:: <-------------------------------- 8 bytes -------------------------------->
+    :align: center
+    :widths: 30,30,30,30
+
+    +--------------------------------------------------------------------+
+    |frameNumber                                                         |
+    +---------------------------------+----------------------------------+
+    |expLength                        |packetNumber                      |
+    +---------------------------------+----------------------------------+
+    |bunchId                                                             |
+    +--------------------------------------------------------------------+
+    |timestamp                                                           |
+    +----------------+----------------+----------------+-----------------+
+    |modId           |row             |column          |reserved         |
+    +----------------+----------------+----------------+--------+--------+
+    |debug                            |roundRNumber    |detType |version |
+    +---------------------------------+----------------+--------+--------+
+
+UDP configuration in Config file
+----------------------------------
+
+#. UDP source port is hardcoded in detector server, starting at 32410.
+#. **udp_dstport** : UDP destination port number. Port in receiver pc to listen to packets from the detector.
+#. **udp_dstip** : IP address of UDP destination interface. IP address of interface in receiver pc to listen to packets from detector. If **auto** is used (only when using slsReceiver/ slsMultiReceiver), the IP of **rx_hostname** is picked up.
+#. **udp_dstmac** : Mac address of UDP destination interface. MAC address of interface in receiver pc to list to packets from detector. Only required when using custom receiver, else slsReceiver/slsMultiReceiver picks it up from **udp_dstip**.
+#. **udp_srcip** : IP address of UDP source interface. IP address of detector UDP interface to send packets from. Do not use for Eiger 1Gb interface (uses its hardware IP). For others, must be in the same subnet as **udp_dstip**.
+#. **udp_srcmac** : MAC address of UDP source interface. MAC address of detector UDP interface to send packets from. Do not use for Eiger (uses hardware mac). For others, it is not necessary, but can help for switch and debugging to put unique values for each module.
  
-To know more about detector receiver configuration, please check out :ref:`detector udp header and udp commands in the config file <detector udp header>`
 
 Custom Receiver
 ----------------

docs/src/servers.rst

@@ -1,14 +1,5 @@
-Getting Started
-===============
-
-Detector Servers include:
-   * Control server [default port: 1952]
-      * Almost all client communication.
-   * Stop server [default port: 1953]
-      *  Client requests for detector status, stop acquisition, temperature, advanced read/write registers.
-
-When using a blocking acquire command (sls_detector_acquire or Detector::acquire), the control server is blocked until end of acquisition. However, stop server commands could be used in parallel.
-
+Detector Servers
+=================
 
 Location
 ---------
@@ -25,76 +16,21 @@ Arguments
       Possible arguments are:
       -v, --version            : Software version
       -p, --port <port>        : TCP communication port with client. 
-         -g, --nomodule           : [Mythen3][Gotthard2] 
-                                    Generic or No Module mode. Skips detector type checks. 
+      -g, --nomodule           : [Mythen3][Gotthard2] Generic or No Module mode. 
+                                 Skips detector type checks.
       -f, --phaseshift <value> : [Gotthard] only. Sets phase shift. 
       -d, --devel              : Developer mode. Skips firmware checks. 
       -u, --update             : Update mode. Skips firmware checks and initial detector setup. 
-         -i, --ignore-config      : [Eiger][Jungfrau][Gotthard][Gotthard2][Moench] 
-                                    Ignore config file. 
-         -m, --master <master>    : [Eiger][Mythen3][Gotthard][Gotthard2] 
-                                    Set Master to 0 or 1. Precedence over config file. Only for virtual servers except Eiger. 
-         -t, --top <top>          : [Eiger] Set Top to 0 or 1. Precedence over config file. 
       -s, --stopserver         : Stop server. Do not use as it is created by control server 
 
 
-.. _Automatic start servers:
-Automatic start 
-------------------
+Basics
+------------
 
-One can start the on-board detector server automatically upon powering on the board.
+Detector Servers include:
+   * Control server [default port: 1952]
+      * Almost all client communication.
+   * Stop server [default port: 1953]
+      *  Client requests for detector status, stop acquisition, temperature, advanced read/write registers.
 
-#. Create a soft link to the binary on board 
-   :
-      .. code-block:: bash
-      
-         ln -sf someDetectorServervx.x.x someDetectorServer
-
-
-
-#. Do the following depending on the detector type :
-
-   Eiger
-      .. code-block:: bash
-         
-         # create script in rc5.d on the board
-         vi /etc/rc5.d/S50board_com.sh
-
-         # enter the following (edit server name)
-         #! /bin/sh
-         /home/root/executables/eigerDetectorServer &> /dev/null &
-         exit 0
-
-   Jungfrau | Moench | CTB | Gotthard I
-      .. code-block:: bash
-
-         # Edit inittab on board
-         vi /etc/inittab
-
-         # enter the following line
-         ttyS0::respawn:/./xxxDetectorServer
-
-
-   Gotthard II | Mythen III
-      .. code-block:: bash
-         
-         # create script in init.d on board
-         vi /etc/init.d/S99detServer.sh
-
-         # enter the following (edit server name)
-         #! /bin/sh
-         cd /root >> /dev/null
-         /root/xxxDetectorServer >> /dev/null &
-
-
-#. Sync, reboot and verify
-   :
-      .. code-block:: bash
-      
-         sync
-
-         # physically reboot for Gotthard II or Mythen III
-         reboot
-
-         # verify
-         ps -ef | grep xxxDetectorServer
+When using a blocking acquire command (sls_detector_acquire or Detector::acquire), the control server is blocked until end of acquisition. However, stop server commands could be used in parallel.

docs/src/serverupgrade.rst

@@ -1,66 +1,114 @@
-.. _Detector Server Upgrade:
-Upgrade
-========
+Detector Server Upgrade
+=======================
+
+
+
+Eiger
+-------------
 
 
 **Location:** slsDetectorPackage/serverBin/ folder for every release.
 
-.. note :: 
-
-    For Mythen3, Gotthard2 and Eiger, you need to add scripts to automatically start detector server upon power on. See :ref:`Automatic start<Automatic start servers>` for more details.
-
- .. note :: 
-
-    Eiger requires a manual reboot. Or killall the servers and restart the new linked one. If you are in the process of updating firmware, then don't reboot yet.
-
-
-6.1.1+ (no tftp required)
----------------------------------------
-
-#. Program from console
 
+#. Kill old server and copy new server
     .. code-block:: bash
 
-        # the following command copies new server, creates a soft link to xxxDetectorServerxxx
-        # [Jungfrau][CTB][Moench] also deletes the old server binary and edits initttab to respawn server on reboot
-        # Then, the detector controller will reboot (except Eiger)
-        sls_detector_put updatedetectorserver /complete-path-to-binary/xxxDetectorServerxxx
+        # Option 1: from detector console
+        # kill old server
+        ssh root@bebxxx
+        killall eigerDetectorServer
 
-#. Copy the detector server specific config files or any others required to the detector:
+        # copy new server
+        cd executables
+        scp user@pc:/path/eigerDetectorServerxxx .
+        chmod 777 eigerDetectorServerxxx
+        ln -sf eigerDetectorServerxxx eigerDetectorServer
+        sync
 
-   .. code-block:: bash
+        # Options 2: from client console for multiple modules
+        for i in bebxxx bebyyy;
+        do ssh root@$i killall eigerDetectorServer;
+        scp eigerDetectorServerxxx root@$i:~/executables/eigerDetectorServer;
+        ssh root@$i sync; done
 
-        sls_detector_put execcommand "tftp pcxxx -r configxxx -g"
 
-5.0.0 - 6.1.1
---------------
+#. Reboot the detector.
+
+
+Jungfrau
+-------------
+
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
 
 #. Install tftp and copy detector server binary to tftp folder
-#. Program from console
-
+#. Program from console (only from 5.0.0-rcx)
     .. code-block:: bash
 
-        # the following command copies new server from pc tftp folder, creates a soft link to xxxDetectorServerxxx
-        # [Jungfrau][CTB][Moench] also edits initttab to respawn server on reboot
-        # Then, the detector controller will reboot (except Eiger)
-        sls_detector_put copydetectorserver xxxDetectorServerxxx pcxxx
+        # copies new server from pc tftp folder, respawns and reboots
+        sls_detector_put copydetectorserver jungfrauDetectorServerxxx pcxxx
 
-#. Copy the detector server specific config files or any others required to the detector:
 
+Gotthard
+---------
+
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+#. Install tftp and copy detector server binary to tftp folder
+#. Program from console (only from 5.0.0-rcx)
     .. code-block:: bash
 
-        sls_detector_put execcommand "tftp pcxxx -r configxxx -g"
+        # copies new server from pc tftp folder, respawns and reboots
+        sls_detector_put copydetectorserver gotthardDetectorServerxxx pcxxx
 
 
-Troubleshooting with tftp
-^^^^^^^^^^^^^^^^^^^^^^^^^
 
-#. tftp write error: There is no space left. Please delete some old binaries and try again.
+Mythen3
+-------
 
-#. text file busy: You are trying to copy the same server.
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+#. Install tftp and copy detector server binary to tftp folder
+#. Program from console (only from 5.0.0-rcx)
+    .. code-block:: bash
+
+        # copies new server from pc tftp folder and reboots (does not respawn)
+        sls_detector_put copydetectorserver mythen3DetectorServerxxx pcxxx
 
 
-< 5.0.0
---------
+Gotthard2
+----------
 
-Please contact us.
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+#. Install tftp and copy detector server binary to tftp folder
+#. Program from console (only from 5.0.0-rcx)
+    .. code-block:: bash
+
+        # copies new server from pc tftp folder and reboots (does not respawn)
+        sls_detector_put copydetectorserver gotthard2DetectorServerxxx pcxxx
+
+
+Moench
+------
+
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+#. Install tftp and copy detector server binary to tftp folder
+#. Program from console (only from 5.0.0-rcx)
+    .. code-block:: bash
+
+        # copies new server from pc tftp folder, respawns and reboots
+        sls_detector_put copydetectorserver moenchDetectorServerxxx pcxxx
+
+
+Ctb
+---
+
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+#. Install tftp and copy detector server binary to tftp folder
+#. Program from console (only from 5.0.0-rcx)
+    .. code-block:: bash
+
+        # copies new server from pc tftp folder, respawns and reboots
+        sls_detector_put copydetectorserver ctbDetectorServerxxx pcxxx

docs/src/slsreceiver.rst

@@ -86,199 +86,16 @@ Client Commands
         sls_detector_get -h rx_framescaught
 
 
-ZMQ: Json Header Format
-------------------------
-
-
-**Change in field names from slsDetectorPackage v6.x.x to v7.0.0**
-
-* detSpec1 <- bunchId
-* detSpec2 <- reserved
-* detSpec3 <- debug
-* detSpec4 <- roundRNumber
-
-
-**Format**
-
-    .. code-block:: bash 
-
-        {
-            "jsonversion": unsigned int,
-            "bitmode": unsigned int,
-            "fileIndex": unsigned long int,
-            "detshape": [
-                unsigned int,
-                unsigned int
-            ],
-            "shape": [
-                unsigned int,
-                unsigned int
-            ],
-            "size": unsigned int,
-            "acqIndex": unsigned long int,
-            "frameIndex": unsigned long int,
-            "progress": double,
-            "fname": string,
-            "data": unsigned int,
-            "completeImage": unsigned int,
-
-            "frameNumber": unsigned long long int,
-            "expLength": unsigned int,
-            "packetNumber": unsigned int,
-            "detSpec1": unsigned long int,
-            "timestamp": unsigned long int,
-            "modId": unsigned int,
-            "row": unsigned int,
-            "column": unsigned int,
-            "detSpec2": unsigned int,
-            "detSpec3": unsigned int,
-            "detSpec4": unsigned int,
-            "detType": unsigned int,
-            "version": unsigned int,
-            
-            "flipRows": unsigned int,
-            "quad": unsigned int,
-            "addJsonHeader": {
-                string : string
-            }
-        }
-
-   +--------------+----------------------------------------------+
-   |   Field      |       Description                            |
-   +--------------+----------------------------------------------+
-   | jsonversion  | Version of the json header.                  |
-   |              | Value at 4 for v6.x.x and v7.x.x             |
-   +--------------+----------------------------------------------+
-   | bitmode      | Bits per pixel [4|8|16|32]                   |
-   +--------------+----------------------------------------------+
-   | fileIndex    | Current file acquisition index               |
-   +--------------+----------------------------------------------+
-   | detshape     | Geometry of the entire detector              |
-   +--------------+----------------------------------------------+
-   | shape        | Geometry of the current port streamed out    |
-   +--------------+----------------------------------------------+
-   | size         | Size of image of current port in bytesout    |
-   +--------------+----------------------------------------------+
-   | acqIndex     | Frame number from the detector (redundant)   |
-   +--------------+----------------------------------------------+
-   | frameIndex   | Frame number of current acquisition          |
-   |              | (Starting at 0)                              |
-   +--------------+----------------------------------------------+
-   | progress     | Progress of current acquisition in %         |
-   +--------------+----------------------------------------------+
-   | fname        | Current file name                            |
-   +--------------+----------------------------------------------+
-   | data         | 1 if there is data following                 |
-   |              | 0 if dummy header                            |
-   +--------------+----------------------------------------------+
-   | completeImage| 1 if no missing packets for this frame       |
-   |              | in this port, else 0                         |
-   +--------------+----------------------------------------------+
-   | frameNumber  | Frame number                                 |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | expLength    | subframe number (32 bit eiger)               |
-   |              | or real time exposure time in 100ns (others) |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | packetNumber | Number of packets caught for that frame      |
-   +--------------+----------------------------------------------+
-   | detSpec1     | See :ref:`here<Detector Specific Fields>`    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | timestamp    | Timestamp with 10 MHz clock                  |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | modId        | Module Id                                    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | row          | Row number in detector                       |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | column       | Column number in detector                    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | detSpec2     | See :ref:`here<Detector Specific Fields>`    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | detSpec3     | See :ref:`here<Detector Specific Fields>`    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | detSpec4     | See :ref:`here<Detector Specific Fields>`    |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | detType      | Detector type enum                           |
-   | detSpec3     | See :ref:`Detector enum<Detector Enum>`      |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | version      | Detector header version. At 2                |
-   |              | [From detector udp header]                   |
-   +--------------+----------------------------------------------+
-   | flipRows     | 1 if rows should be flipped.                 |
-   |              | Usually for Eiger bottom.                    |
-   +--------------+----------------------------------------------+
-   | quad         | 1 if its an Eiger quad.                      |
-   +--------------+----------------------------------------------+
-   | addJsonHeader| Optional custom parameters that is required  |
-   |              | for processing code.                         |
-   +--------------+----------------------------------------------+
-
-
-SLS Receiver Header Format
---------------------------
-
-It is 112 bytes and consists of:
-    * 48 bytes of the SLS Detector Header (described in :ref:`the current detector header <detector udp header>`)
-    * 64 bytes of packet mask
-
-.. code-block:: cpp 
-    
-    typedef struct {
-        uint64_t frameNumber;
-        uint32_t expLength;
-        uint32_t packetNumber;
-        uint64_t detSpec1;
-        uint64_t timestamp;
-        uint16_t modId;
-        uint16_t row;
-        uint16_t column;
-        uint16_t detSpec2;
-        uint32_t detSpec3;
-        uint16_t detSpec4;
-        uint8_t detType;
-        uint8_t version;
-    } sls_detector_header;
-
-    struct sls_receiver_header {
-        sls_detector_header detHeader; /**< is the detector header */
-        sls_bitset packetsMask;        /**< is the packets caught bit mask */
-    };
-
-
-.. note :: 
-
-    | The packetNumber in the SLS Receiver Header will be modified to number of packets caught by receiver for that frame. For eg. Jungfrau will have 128 packets per frame. If it is less, then this is a partial frame due to missing packets.
-    
-    | Furthermore, the bit mask will specify which packets have been received.
-
-
-
-
 File format
 --------------
 
-Master file is in json format.
+* The file name format is [fpath]/[fname]_dx_fy_[findex].raw, where x is module index and y is file index. **fname** is file name prefix and by default "run". **fpath** is '/' by default.
 
-The file name format is [fpath]/[fname]_dx_fy_[findex].raw, where x is module index and y is file index. **fname** is file name prefix and by default "run". **fpath** is '/' by default.
+* Each acquisition will have an increasing acquisition index or findex (if file write enabled). This can be retrieved by using **findex** command. 
 
+* Each acquisition can have multiple files (the file index number **y**), with **rx_framesperfile** being the maximum number of frames per file. The default varies for each detector type.
 
-Each acquisition will have an increasing acquisition index or findex (if file write enabled). This can be retrieved by using **findex** command. 
-
-
-Each acquisition can have multiple files (the file index number **y**), with **rx_framesperfile** being the maximum number of frames per file. The default varies for each detector type.
-
-
-Some file name examples:
+* Some file name examples:
 
     .. code-block:: bash
 
@@ -291,19 +108,17 @@ Some file name examples:
         # second acquisition, first file
         path-to-file/run_d0_f0_1.raw
 
+* Each acquisition will create a master file that can be enabled/disabled using **fmaster**. This should have parameters relevant to the acquisition.
 
-Each acquisition will create a master file that can be enabled/disabled using **fmaster**. This should have parameters relevant to the acquisition.
-
+* SLS Receiver Header consist of SLS Detector Header + 64 bytes of bitmask, altogether 112 bytes. The packetNumber in the sls detector header part, will be updated to number of packets caught by receiver for that frame. Furthermore, the bit mask will specify which packets have been received.
 
 **Binary file format**
 
-This is the default file format. 
+* This is the default file format. 
 
+* Each data file will consist of frames, each consisting of slsReceiver Header followed by data for 1 frame.
 
-Each data file will consist of frames, each consisting of slsReceiver Header followed by data for 1 frame.
-
-
-Master file is of ASCII format and will also include the format of the slsReceiver Header.
+* Master file is of ASCII format and will also include the format of the slsReceiver Header.
 
 
 **HDF5 file formats**
@@ -345,7 +160,7 @@ When handling callbacks, the control should be returned as soon as possible, to
 **Example**
     * `main cpp file <https://github.com/slsdetectorgroup/api-examples/blob/master/e4-receiver_callbacks.cpp>`_ 
     * `cmake file <https://github.com/slsdetectorgroup/api-examples/blob/master/CMakeLists.txt>`_. 
-    * how to install the slsDetectorPackage with cmake is provided :ref:`here <build from source using cmake>`.
+    * how to install the slsDetectorPackage is provided :ref:`here <build from source using cmake>`.
     * compile the example **e4-rxr** by:
 
         .. code-block:: bash

docs/src/troubleshooting.rst

@@ -8,24 +8,21 @@ open an issue at our  `github repo issues
 Common
 ------
 
+Missing Packets
+^^^^^^^^^^^^^^^
+Possible causes could be the following:
 
-1. Total Failure of Packet Delivery
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#. Receiver PC is not tuned for socket buffer size and input packet queue.
+    * Refer to :ref:`Increase rmem_default, rmem_max and max_backlog<Receiver PC Tuning>`
 
-#. Data cable plugged into the wrong interface on board (Jungfrau)
-    * Please ensure that the data cable is plugged into the rightmost interface (default for single interface). The inner one is disabled for PCB v1.0 and must be selected via command for PCB v2.0.
+#. Wiring
+    * Faulty wiring or connecting cable to incorrect interface.
 
 #. Link up and speed
-    * Check ethtool and find if Link Deteced:Yes and Speed is acceptable (>10k).
-    * Check to see if the 10G link is up (blue or red LED on board, close to SFP+). If not:
-
-       * Check transeiver and fibers are compatible (all MMF 850nm or all SMF 1030nm)
-       * Check fiber
-       * Check fiber polarity (if short range, unplug the link anywhere, and look at the light/dark pattern: dark has to mate with light)
+    * Check to see if there is a blue LED on board to signal that the link is up. Check ethtool and find if Link Deteced:Yes and Speed is acceptable (>10k).
 
 #. Detector is not acquiring (Not Eiger)
     * Take an acquisition with many images and using the following steps instead of acquire:
-
         .. code-block:: bash
 
             sls_detector_put status start
@@ -33,63 +30,37 @@ Common
             # which means the detector is acquiring.
             sls_detector_get framesl 
 
-            # If you are using multiple modules, the previous command can return -1 because each module will return different values. Then, check for a single module instead: sls_detector_get 0:framesl
-
-
-#. Detector is not sending data (Except Eiger)
-    * Check the board to see if the green LED close to SFP is blinking (detector is sending data). If not, detector is not operated properly (period too short/long, no trigger in trigger mode) or misconfigured and needs reboot.
-
-#. Power supply
-    * Check if power supply has enough current. 
-    * For Jungfrau, refer to :ref:`Jungfrau Power Supply Troubleshooting<Jungfrau Troubleshooting Power Supply>`.
-
-#. Ethernet interface not configured for Jumbo frames (10Gb)
-    * Ensure that the interfaces (on NIC and the switch) used in receiver pc have MTU 9000 (jumbo frames) enabled.
-
-
-#. Check if 'rx_frames' counter in 'ifconfig' do not increment for interface.
-    * If no, check switch configuration if present. Port counters of switch can also help to identify problem.
-    * If yes, but receiver software does not see it:
-
-        * Check no firewall (eg. firewalld) is present or add rules
-        * Check that selinux is disabled ( or add rules)
-        
-#. Source UDP IP in config file (Not Eiger)
-    * Ensure it is valid and does not end if 0 or 255. Also ensure that the source ip 'udp_srcip' is in the same subnet as destination ip 'udp_dstip' and the masking in the interface configuration ensures this rule.
-    * Eg. If interface IP is 102.10.10.110 and mask is 255.255.255.0, udp_srcip has to be 102.10.10.xxx (same subnet)
-    * Use ifconfig and route commands to verify etheret interface configuration
-
-
-#. Netstat and netcat
-    * Try with netstat to see if its really listening to the right interface. Or netcat to see if you get packets.
-
-#. Wireshark or Tcpdump
-    * Use one of these to confirm that you receive packets (with the right filtering ie. source and destination ports, ip).
-
-
-
-2. Partial or Random Packet Loss (Performance)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
     .. note ::
     
-    The following suggestions are for convenience. Please do not follow blindly, research each parameter and adapt it to your system.
+        If you are using multiple modules, the previous command can return -1 because each module will return different values. Then, check for a single module instead: sls_detector_get 0:framesl
 
-#. Receiver PC is not tuned for socket buffer size and input packet queue or other parameters.
-    * Refer to :ref:`Receiver PC Tuning<Receiver PC Tuning>`
+#. Data cable plugged into the wrong interface on board (Jungfrau)
+    * Please ensure that the data cable is plugged into the rightmost interface. The middle one is disabled for PCB v1.0 and must be selected via command for PCB v2.0.
 
-#. Wiring
-    * Faulty wiring or connecting cable to incorrect interface.
+#. Detector is not sending data
+    * Check the board to see if the green LED is blinking next to the data cable, which means that the detector is sending data.
 
+#. Firewall or security feature
+    * A firewall or some security feature could be blocking the reception of data.
+
+#. Ethernet interface not configured properly
+    * Ensure that the interfaces used are configured properly with the right mask and ip. Eg. use ifconfig and route commands to verify.
+
+#. Ethernet interface not configured for Jumbo frames (10Gb)
+    * Ensure that the interfaces used in receiver pc have MTU 9000 (jumbo frames) enabled.
+
+#. Detector IP (Not Eiger)
+    * Ensure it is valid and does not end if 0 or 255. Also ensure that the detector ip is in the same subnet as rx_udpip and the masking in the interface configuration ensures this rule.
+
+#. Tcpdump or wireshark
+    * Use one of these to confirm that you receive packets (with the right filtering ie. source and destination ports, ip).
+
+#. Check SFP modules
+    * Check if the SFP modules on both sides of the fiber are of same type.
 
 #. Pinging the subnet (receiving only a few number of packets each time)
     * If a switch is used between a receiver pc and detector instead of plugging the cables directly, one might have to ping any ip in the subnet of the Ethernet interface constantly so that it does not forget the ip during operation.
     * Eg. if rx_udpip is 10.2.3.100, then ping constantly 10.2.3.xxx, where xxx is any ip other than 100.
-    * Using slsReceiver, you can use a command that does this for you:
-        .. code-block:: bash
-        
-            # arping the interface in a separate thread every minute
-            sls_detector_put rx_arping 1
 
 
 
@@ -97,12 +68,6 @@ Common
 
 Receiver PC Tuning Options
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. note ::
-
-    | xth1 is example interface name in the following examples. 
-    | These settings are lost at pc reboot.
-
 #. Increase maximum receive socket buffer size and socket input packet queue. 
     * Temporarily (until shut down)
         .. code-block:: bash
@@ -146,7 +111,6 @@ Receiver PC Tuning Options
         # check how many GB memory you can allocate, to avoid swapping otherwise    
 
 
-
 #. Modify ethtool settings. 
     * rx ring parameters
         .. code-block:: bash
@@ -163,9 +127,6 @@ Receiver PC Tuning Options
             # check 
             ethtool -c xth1
 
-            # enable adaptive xoalescence parameters
-            ethtool -C xth1 adaptive-rx on
-
             # set to max value in your pc settings
             ethtool -C xth1 rx-usecs 100 
 
@@ -178,42 +139,10 @@ Receiver PC Tuning Options
             # set to max value in your pc settings
             ethtool -A xth1 rx on
  
-    * generic receiver offload (might not always work)
-        .. code-block:: bash
+    .. note ::
 
-            # check
-            ethtool -k xth1
-
-            # enable generic receiver offload
-            ethtool -K xth1 gro
-        
-
-#. Disable power saving in CPU frequency scaling and set system to performance 
-    * Check current policy (default might be powersave or schedutil)
-        .. code-block:: bash
-            
-            # check current active governor and range of cpu freq policy
-            cpupower frequency-info --policy
-            # list all available governors for this kernel
-            cpupower frequency-info --governors  
-
-    * Temporarily (until shut down)
-        .. code-block:: bash
-            
-            # set to performance
-            sudo cpupower frequency-set -g performance
-
-            # or
-            cpufreq-info
-            for i in ‘seq 0 7‘; do cpufreq-set -c $i -g performance; done
-            
-    * Permanently
-        .. code-block:: bash
-            
-            # edit /etc/sysconfig/cpupower to preference
-
-            # enable or disable permanently
-            sudo systemctl enable cpupower
+        | xth1 is example interface name. 
+        | These settings are lost at pc reboot.
 
 #. Give user speicific user scheduling privileges.
     .. code-block:: bash
@@ -226,29 +155,18 @@ Receiver PC Tuning Options
 
         This is also set if slsReceiver is run as root user.
         
-#. Some more advanced options: 
-    .. warning ::
-        
-        Please do not try if you do not understand
-
-    #. reduce the number of queue per NIC to the number of expected streams: ethtool -L xth0 combined 2 
-    #. assign each queue to its stream:  ethtool -U xth0 flow-type tcp4 dst-port 50004 action 1
-    #. assign to each queue (IRQ) one CPU on the right socket:  echo "3"> /proc/irq/47/smp_affinity_list    #change the numbers looking at /proc/interrupts
-    #. disable irqbalance service 
-    #. Be sure that the switch knows the receiver mac address. Most switches reset the mac lists every few minutes, and since the receiver only receives, there is not a periodic refresh of the mac list. In this case, one can set a fixed mac list in the switch, or setup some kind of script arping or pinging out from that interface (will be available in 7.0.0). 
-    #. assign the receiver numa node (also with -m) to the socket where the NIC is attached. To know it, cat /sys/class/net/ethxxx/device/numa_node
-    #. ensure file system performance can handle sustained high data rate:
-        
-        * One can use dd: 
         
+#. Disable power saving in CPU frequency 
     .. code-block:: bash
 
-                dd if=/dev/zero of=/testpath/testfile bs=1M count=100000
-        * Or better fio (which needs to be installed) 
+        # or similar command depending on your distribution
+        cpupower frequency-info
+        cpupower frequency-set -g performance
 
-            .. code-block:: bash
+        # or
+        cpufreq-info
+        for i in ‘seq 0 7‘; do cpufreq-set -c $i -g performance; done
 
-                fio --name=global –directory=/testpath/ --rw=write --ioengine=libaio --direct=0 --size=200G -- 	numjobs=2 --iodepth=1 --bs=1M –name=job
 
 slsReceiver Tuning
 ^^^^^^^^^^^^^^^^^^
@@ -256,25 +174,18 @@ slsReceiver Tuning
 #. Starting receiver as root to have scheduling privileges.
 
 #. For 10g, enable flow control
-
     .. code-block:: bash
 
         sls_detector_put flowcontrol10g 1
 
-#. Increase slsReceiver ring buffer depth 
-    This can be tuned depending on the number of receivers (modules) and memory available.
-
+#. Increase slsReceiver fifo depth between listening and processing threads.
     .. code-block:: bash
 
-        # sugggested not to use more than half memory of CPU socket in case of NUMA systems) for this
-
         sls_detector_get rx_fifodepth
-        # sets number of frames in fifo to 1024 ~1GB per receiver. Default is 2500
-        sls_detector_put rx_fifodepth 1024
-
-#. Increase number of frames per file 
-    This can reduce time taken to open and close files.
+        # sets number of frames in fifo to 5000
+        sls_detector_put rx_fifodepth 5000
 
+#. Increase number of frames per file to reduce time taken to open and close files.
     .. code-block:: bash
 
         sls_detector_get rx_framesperfile
@@ -282,31 +193,10 @@ slsReceiver Tuning
         # writes all frames into a single file
         sls_detector_put rx_framesperfile 0
 
-#. Disable file write
-    This can ensure it is not the file system performance hampering high date rate.
-
-    .. code-block:: bash
-
-        sls_detector_put fwrite 0
-
 
 Shared memory error
 ^^^^^^^^^^^^^^^^^^^
-For errors due to access or size, use any of the following suggestions.
-    #. Delete shared memory files and try again
-    #. Use environment variable to use a different shared memory ending in jfxx
-        
-        .. code-block:: bash
-
-            # shared memory ending in jfxx
-            export SLSDETNAME=jfxx
-
-    #. USe a different multi shared memory ID
-        .. code-block:: bash
-    
-            sls_detector_put 2-config xxxx.config
-            # or
-            sls_detector_put 2-hostname bchipxxx
+| For errors due to access or size, delete shared memory files nd try again.
 
 To list all shared memory files of sls detector package.
     .. code-block:: bash
@@ -357,19 +247,6 @@ Possible causes could be the following:
     * For Jungfrau, refer to :ref:`Jungfrau Power Supply Troubleshooting<Jungfrau Troubleshooting Power Supply>`.
 
 
-Cannot ping module (Nios)
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If you executed "reboot" command on the board, you cannot ping it anymore unless you power cycle. To reboot the controller, please use the software command ("rebootcontroller"), which talks to the microcontroller.
-
-Gotthard2
----------
-
-Cannot get data without a module attached
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-You cannot get data without a module attached as a specific pin is floating. Attach module to get data.
-
 
 Gotthard
 ----------
@@ -417,7 +294,6 @@ Cannot get multi module data
 
 #. Check :ref:`Common Multi Module Troubleshooting<common troubleshooting multi module data>`
 #. Power Supply
-    * Jungfrau needs a ~4A per module for a short time at startup. If not, it reboots misconfigured.
     * Comment out this line in the config file: powerchip 1
     * Powering on the chip increases the power consumption by a considerable amount. If commenting out this line aids in getting data (strange data due to powered off chip), then it could be the power supply current limit. Fix it (possibly to 8A current limit) and uncomment the powerchip line back in config file.
 

docs/src/udpconfig.rst

@@ -1,37 +0,0 @@
-.. _detector udp header:
-
-
-Config file
-============
-
-Commands to configure the UDP in the config file:
-
-.. note :: 
-
-    These command are recommended to be placed before "rx_hostname" if it is used.
-
-Source Port
------------
-    Hardcoded in detector server, starting at 32410.
-
-udp_srcip - Source IP
----------------------
-    IP address of detector UDP interface to send packets from. Do not use for Eiger 1Gb interface (uses its hardware IP). For others, must be in the same subnet as **udp_dstip**.
-
-udp_srcmac - Source MAC
------------------------
-    MAC address of detector UDP interface to send packets from. Do not use for Eiger (uses hardware mac). For others, it is not necessary, but can help for switch and debugging to put unique values for each module.
- 
-
-udp_dstport - Desintation Port
--------------------------------
-    Port in receiver pc to listen to packets from the detector.
-
-udp_dstip - Destination IP
---------------------------
-    IP address of interface in receiver pc to listen to packets from detector. If **auto** is used (only when using slsReceiver/ slsMultiReceiver), the IP of **rx_hostname** is picked up.
-
-udp_dstmac - Destination MAC
-----------------------------
-    MAC address of interface in receiver pc to list to packets from detector. Only required when using custom receiver, else slsReceiver/slsMultiReceiver picks it up from **udp_dstip**.
-

docs/src/udpdetspec.rst

@@ -1,152 +0,0 @@
-.. _detector specific fields:
-
-Detector Specific Fields
-========================
-
-Please check out :ref:`the current detector header <detector udp header>` to see 
-where the detector specific fields are placed.
-
-
-
-Eiger
-------
-
-.. table:: Detector Specific Field
-   
-   +----------+------------------------------+
-   | expLength| Sub Frame Number             |
-   +----------+------------------------------+
-   | detSpec1 | 0x0                          |
-   +----------+------------------------------+
-   | detSpec2 | 0x0                          |
-   +----------+------------------------------+
-   | detSpec3 | e14a                         |
-   +----------+------------------------------+
-   | detSpec4 | Round Robin Interface Number |
-   +----------+------------------------------+
-
-
-Jungfrau
----------
-
-.. table:: Detector Specific Field
-
-   +----------+------------------------------+
-   | detSpec1 | Bunch Id [#]_                |
-   +----------+------------------------------+
-   | detSpec2 | 0                            |
-   +----------+------------------------------+
-   | detSpec3 | DAQ info                     |
-   +----------+------------------------------+
-   | detSpec4 | 0                            |
-   +----------+------------------------------+
-
-
-.. table:: DAQ Info Field
-
-   +----------+--------------------+----------------------------------------------+
-   |   Bits   |       Name         |   Description                                |
-   +----------+--------------------+-----+----------------------------------------+
-   | 0        | High gain          |  1  | High Gain enabled                      |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | High Gain disabled                     |
-   +----------+--------------------+-----+----------------------------------------+
-   | 1        | Fix gain stage 1   |  1  | Gain stage 1 fixed. The switch that    |
-   |          |                    |     | selects the gains stage 1 is active all|
-   |          |                    |     | the time.                              |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | Gain stage 1 unset. The switch that    |
-   |          |                    |     | selects the gains stage 1 is inactive  |
-   |          |                    |     | all the time.                          |
-   +----------+--------------------+-----+----------------------------------------+
-   | 2        | Fix gain stage 2   |  1  | Gain stage 2 fixed. The switch that    |
-   |          |                    |     | selects the gains stage 2 is active all|
-   |          |                    |     | the time.                              |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | Gain stage 2 unset. The switch that    |
-   |          |                    |     | selects the gains stage 2 is inactive  |
-   |          |                    |     | all the time.                          |
-   +----------+--------------------+-----+----------------------------------------+
-   | 4        | Comparator reset   |  1  | On-chip comparator in reset state.     | 
-   |          |                    |     | Dynamic-gain switching is therefore    |
-   |          |                    |     | disabled.                              |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | On-chip comparator active.             |
-   +----------+--------------------+-----+-----+-----+----------------------------+
-   | 7-5      | Jungfrau chip      |Bit 7|Bit 6|Bit 5| Description                |
-   |          | version            +-----+-----+-----+----------------------------+
-   |          |                    | 0   |   0 |  0  | v1.0                       |
-   |          |                    +-----+-----+-----+----------------------------+
-   |          |                    | 0   |   0 |  1  | v1.1                       |
-   |          |                    +-----+-----+-----+----------------------------+
-   |          |                    | 0   |   1 |  X  | Reserved                   |
-   |          |                    +-----+-----+-----+----------------------------+
-   |          |                    | 1   |   X |  X  | Reserved                   |
-   +----------+--------------------+-----+-----+-----+----------------------------+
-   | 11-8     | Storage cell select|Storage cell used for this exposure. This     |
-   |          |                    |field defines the storage cell that was used  |
-   |          |                    |to acquire the data of this frame             |
-   +----------+--------------------+-----+----------------------------------------+
-   | 12       | Force switching    |  1  | Forced switching to gain stage 1 at the|
-   |          | to gain stage 1    |     | start of the exposure period.          |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | Disabled forced gain switching to gain |
-   |          |                    |     | stage 1. Dynamic gain switching        |
-   |          |                    |     | conditions apply.                      |
-   +----------+--------------------+-----+----------------------------------------+
-   | 13       | Force switching    |  1  | Forced switching to gain stage 2 at the|
-   |          | to gain stage 2    |     | start of the exposure period.          |
-   |          |                    +-----+----------------------------------------+
-   |          |                    | 0   | Disabled forced gain switching to gain |
-   |          |                    |     | stage 2. Dynamic gain switching        |
-   |          |                    |     | conditions apply.                      |
-   +----------+--------------------+-----+-----+-----+----------------------------+
-   | 23-16    |  10-Gigabit event  |The 8-bit event code contains value of the    |
-   |          |  code              |event received over the 10 GbE interface by   |
-   |          |                    |JUNGFRAU detector at the moment of the frame  |
-   |          |                    |acquisition.                                  |
-   +----------+--------------------+-----+----------------------------------------+
-   | 31       | External input flag|  1  | External input flag detected in the    |
-   |          |                    |     | last exposure.                         |
-   |          |                    +-----+----------------------------------------+
-   |          |                    |  0  | External input flag not detected in the|
-   |          |                    |     | last exposure.                         |
-   +----------+--------------------+-----+----------------------------------------+
-
-
-
-Gotthard2
-----------
-
-.. table:: Detector Specific Field
-
-   +----------+------------------------------+
-   | detSpec1 | Train Id [#]_                |
-   +----------+------------------------------+
-   | detSpec2 | Bunch Id [#]_                |
-   +----------+------------------------------+
-   | detSpec3 | 0                            |
-   +----------+------------------------------+
-   | detSpec4 | 0                            |
-   +----------+------------------------------+
-
-
-Mythen3
-----------
-
-.. table:: Detector Specific Field
-
-   +----------+------------------------------+
-   | detSpec1 | 0                            |
-   +----------+------------------------------+
-   | detSpec2 | 0                            |
-   +----------+------------------------------+
-   | detSpec3 | 0                            |
-   +----------+------------------------------+
-   | detSpec4 | 0                            |
-   +----------+------------------------------+
-
-
-.. [#] **Bunch Id**: bunch identification number received by the detector at the moment of frame acquisition.
-.. [#] **Train Id**: train identification number received by the detector at the moment of frame acquisition.
-.. [#] **Bunch Id**: bunch identification number to identify every single exposure during a burst acquisition.

docs/src/udpheader.rst

@@ -1,125 +0,0 @@
-.. _detector udp header:
-
-Format
-=======
-
-The UDP data format for the packets consist of a common header for all detectors, followed by the data for that one packet.
-
-
-Current Version
----------------------------
-
-**v2.0 (slsDetectorPackage v7.0.0+)**
-
-.. table:: <---------------------------------------------------- 8 bytes per row --------------------------------------------->
-    :align: center
-    :widths: 30,30,30,15,15
-
-    +---------------------------------------------------------------+
-    |                          frameNumber                          |
-    +-------------------------------+-------------------------------+
-    |            expLength          |         packetNumber          |
-    +-------------------------------+-------------------------------+
-    |                         **detSpec1**                          |
-    +---------------------------------------------------------------+
-    |                           timestamp                           |
-    +---------------+---------------+---------------+---------------+
-    |     modId     |      row      |     column    |  **detSpec2** |
-    +---------------+---------------+---------------+-------+-------+
-    |          **detSpec3**         |  **detSpec4** |detType|version|
-    +-------------------------------+---------------+-------+-------+
-
-
-.. note :: 
-
-    Since there is no difference in the format of the UDP header from the detector
-    from the previous version (v2.0), the version number stays the same.
-    
-    Only the struture member names have changed in sls_detector_defs.h
-
-
-
-Description
-------------
-
-* **Detector specific field** descriptions are found :ref:`here<detector specific fields>`.
-
-* **frameNumber**: framenumber to which the current packet belongs to.
-
-* **expLength**: measured exposure time of the frame in tenths of microsecond. It is instead the sub frame number for Eiger.
-
-* **packetNumber**: packet number of the frame to which the current data belongs to.
-
-* **timestamp**: time measured at the start of frame exposure since the start of the current measurement. It is expressed in tenths of microsecond.
-
-* **modId**: module ID picked up from det_id_[detector type].txt on the detector cpu.
-
-* **row**: row position of the module in the detector system. It is calculated by the order of the module in hostname command, as well as the detsize command.
-
-* **column**: column position of the module in the detector system.  It is calculated by the order of the module in hostname command, as well as the detsize command.
-
-* **detType**: detector type from enum of detectorType in the package.
-
-* **version**: current version of the detector header (0x2).
-
-
-Detector Enum
---------------
-
-    ================    ========
-    Detector Type        Value
-    ================    ========
-    GENERIC             0
-    EIGER               1
-    GOTTHARD            2    
-    JUNGFRAU            3    
-    CHIPTESTBOARD       4        
-    MOENCH              5
-    MYTHEN3             6
-    GOTTHARD2           7    
-    ================    ========
-
-
-
-Previous Versions
------------------
-**v2.0 (Package v4.0.0 -  6.x.x)**
-
-.. table:: <---------------------------------------------------- 8 bytes ---------------------------------------------------->
-    :align: center
-    :widths: 30,30,30,15,15
-
-    +---------------------------------------------------------------+
-    |                          frameNumber                          |
-    +-------------------------------+-------------------------------+
-    |            expLength          |         packetNumber          |
-    +-------------------------------+-------------------------------+
-    |                            bunchid                            |
-    +---------------------------------------------------------------+
-    |                           timestamp                           |
-    +---------------+---------------+---------------+---------------+
-    |     modId     |    **row**    |   **column**  |  **reserved** |
-    +---------------+---------------+---------------+-------+-------+
-    |             debug             |  roundRNumber |detType|version|
-    +-------------------------------+---------------+-------+-------+
-
-**v1.0 (Package v3.0.0 -  3.1.5)**
-
-.. table:: <---------------------------------------------------- 8 bytes ---------------------------------------------------->
-    :align: center
-    :widths: 30,30,30,15,15
-
-    +---------------------------------------------------------------+
-    |                          frameNumber                          |
-    +-------------------------------+-------------------------------+
-    |            expLength          |         packetNumber          |
-    +-------------------------------+-------------------------------+
-    |                            bunchid                            |
-    +---------------------------------------------------------------+
-    |                           timestamp                           |
-    +---------------+---------------+---------------+---------------+
-    |     modId     |    xCoord     |     yCoord    |    zCoord     |
-    +---------------+---------------+---------------+-------+-------+
-    |             debug             |  roundRNumber |detType|version|
-    +-------------------------------+---------------+-------+-------+
-

docs/src/virtualserver.rst

@@ -1,6 +1,6 @@
 .. _Virtual Detector Servers:
-Simulators
-===========
+Detector Simulators
+===================
 
 Compilation
 -----------
@@ -13,14 +13,16 @@ Compilation
 * Using cmk.sh script,
      .. code-block:: bash  
         
-        ./cmk.sh -bsj9 # option -s is for simulator
+        ./cmk.sh -bsj9 #option s is for simulator
 
 
 Binaries
 ^^^^^^^^
     .. code-block:: bash  
 
-        eigerDetectorServer_virtual
+        eigerDetectorServerMaster_virtual
+        eigerDetectorServerSlaveTop_virtual
+        eigerDetectorServerSlaveBottom_virtual
         jungfrauDetectorServer_virtual
         gotthardDetectorServer_virtual
         gotthard2DetectorServer_virtual
@@ -65,15 +67,7 @@ Sample Config file
 ^^^^^^^^^^^^^^^^^^
 There are sample config files for each detector in slsDetectorPackage/examples folder.
 
-For a Single Module (Basic)
-    .. code-block:: bash  
-
-        hostname localhost
-        rx_hostname localhost
-        udp_dstip auto
-
-
-For a Single Module (With Options)
+For a Single Module
     .. code-block:: bash  
 
         # connects to control port 1912
@@ -146,7 +140,7 @@ Gui
 Limitations
 -----------
 
-#. Data coming out of virtual server is fake. 
+#. Data coming out of virtual server is fake. Value at each pixel/ channel is incremented by 1.
 
 #. A stop will stop the virtual acquisition only at the start of every new frame.
 

evalVersionVariables.sh

@@ -0,0 +1,22 @@
+GITREPO1='git remote -v'
+GITREPO2=" | grep \"fetch\" | cut -d' ' -f1"
+BRANCH1='git branch -v'
+BRANCH2=" | grep '*' | cut -d' ' -f2"
+REPUID1='git log --pretty=format:"%H" -1'
+AUTH1_1='git log --pretty=format:"%cn" -1'
+AUTH1_2=" | cut -d' ' -f1"
+AUTH2_1='git log --pretty=format:"%cn" -1'
+AUTH2_2=" | cut -d' ' -f2"
+FOLDERREV1='git log --oneline . '   #used for all the individual server folders
+FOLDERREV2=" | wc -l"  #used for all the individual server folders
+REV1='git log --oneline  '
+REV2=" | wc -l"
+
+GITREPO=`eval $GITREPO1  $GITREPO2`
+BRANCH=`eval $BRANCH1  $BRANCH2`
+REPUID=`eval $REPUID1`
+AUTH1=`eval $AUTH1_1  $AUTH1_2`
+AUTH2=`eval $AUTH2_1  $AUTH2_2`
+REV=`eval $REV1  $REV2`
+FOLDERREV=`eval $FOLDERREV1  $FOLDERREV2`
+

examples/badchannel.txt

@@ -1,6 +0,0 @@
-0
-10, 30
-40:45 50:52
-1279
-# all bad channels are applied for all counters in deector
-

examples/jungfrau_two.config

@@ -5,7 +5,7 @@ detsize 1024 1024
 hostname bchip048+bchip052+
 
 # 1Gb receiver pc hostname  (default tcpport: 1954)
-rx_hostname pcmoench01:1954+pcmoench01:1955+
+rx_hostname pcmoench01+pcmoench01:1955
 
 
 

examples/moench03_T1.config

@@ -1,9 +1,8 @@
-#initialchecks 0
+initialchecks 0
 #############################################
 ### edit with hostname or IP address of your detector 
 ############################################
-#hostname bchip181+
-hostname bchip135 
+hostname bchip181+
 
 #############################################
 ### edit with hostname or 1Gbs IP address of your server
@@ -28,7 +27,7 @@ rx_zmqport 50003
 #############################################
 ### edit with 1 Gbs IP of PC where you will run the GUI
 ############################################
-zmqip 129.129.202.57
+zmqip 129.129.202.136
 zmqport 50001
 
 
@@ -40,12 +39,11 @@ rx_zmqstream 1
 
 frames 100000
 period 0.0006
-exptime 0.00035
 
 #############################################
 ### edit with directory you want to write to
 ############################################
-fpath /mnt/moench_data/scratch1/
+fpath /mnt/moench_data/scratch/
 
 fwrite 0
 

examples/virtual_ctb_moench.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1910
 
-# udp destination ports
-udp_dstport 50010
-
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-
 # receiver hostname
 rx_hostname mpc1922:2010
 
+# udp destination ports
+udp_dstport 50010
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+
 # output file directory
 fpath /tmp
 
@@ -27,7 +27,418 @@ dbitclk 40
 
 
 # patterns
-pattern /tmp/pattern.pat
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+patword 0x00ea 0x030c799f010858ba
+patword 0x00eb 0x030c799f010858ba
+patword 0x00ec 0x030c599f000850ba
+patword 0x00ed 0x030c599f000850ba
+patword 0x00ee 0x030c599f000850ba
+patword 0x00ef 0x030c599f000850ba
+patword 0x00f0 0x030c599f000850ba
+patword 0x00f1 0x030c599f000850ba
+patword 0x00f2 0x030c599f000850ba
+patword 0x00f3 0x030c599f000850ba
+patword 0x00f4 0x030c599f000850ba
+patword 0x00f5 0x030c599f000850ba
+patword 0x00f6 0x030c599f000850ba
+patword 0x00f7 0x030c599f000850ba
+patword 0x00f8 0x030c599f000850ba
+patword 0x00f9 0x030c599f000850ba
+patword 0x00fa 0x030c599f000850ba
+patword 0x00fb 0x030c599f000850ba
+patword 0x00fc 0x030c599f000850ba
+patword 0x00fd 0x030c599f000850ba
+patword 0x00fe 0x030c599f000850ba
+patword 0x00ff 0x030c599f000850ba
+patword 0x0100 0x030c599f000850ba
+patword 0x0101 0x030c599f000850ba
+patword 0x0102 0x030c599f400850ba
+patword 0x0103 0x030c599f400850ba
+patword 0x0104 0x030c599f600850ba
+patword 0x0105 0x030c599f400850ba
+patword 0x0106 0x030c599f400850ba
+patword 0x0107 0x030c599f400850ba
+patword 0x0108 0x870c599f682e50ba
+patword 0x0109 0x870c599f482850ba
+patword 0x010a 0x870c599f000e50ba
+patword 0x010b 0x870c599f000850ba
+patword 0x010c 0x870c599f000e50ba
+patword 0x010d 0x870c599f000850ba
+patword 0x010e 0x870c599f000e50ba
+patword 0x010f 0x870c599f000850ba
+patword 0x0110 0x870c599f000e50ba
+patword 0x0111 0x870c599f000850ba
+patword 0x0112 0x870c599f000e50ba
+patword 0x0113 0x870c599f000850ba
+patword 0x0114 0x870c599f000e50ba
+patword 0x0115 0x870c599f000850ba
+patword 0x0116 0x870c599f000e50ba
+patword 0x0117 0x870c599f000850ba
+patword 0x0118 0x870c599f000e50ba
+patword 0x0119 0x870c599f000850ba
+patword 0x011a 0x870c599f000e50ba
+patword 0x011b 0x870c599f000850ba
+patword 0x011c 0x870c599f000e50ba
+patword 0x011d 0x870c599f000850ba
+patword 0x011e 0x870c599f000e50ba
+patword 0x011f 0x870c599f000850ba
+patword 0x0120 0x870c599f000e50ba
+patword 0x0121 0x870c599f000850ba
+patword 0x0122 0x870c599f200e50ba
+patword 0x0123 0x870c599f000850ba
+patword 0x0124 0x870c599f000e50ba
+patword 0x0125 0x870c599f000850ba
+patword 0x0126 0x870c599f000e50ba
+patword 0x0127 0x870c599f000850ba
+patword 0x0128 0x870c599f000e50ba
+patword 0x0129 0x870c599f000850ba
+patword 0x012a 0x870c599f000e50ba
+patword 0x012b 0x870c599f000850ba
+patword 0x012c 0x870c599f000e50ba
+patword 0x012d 0x870c599f000850ba
+patword 0x012e 0x870c599f000e50ba
+patword 0x012f 0x870c599f000850ba
+patword 0x0130 0x870c599f000e50ba
+patword 0x0131 0x870c599f000850ba
+patword 0x0132 0x870c599f000e50ba
+patword 0x0133 0x870c599f000850ba
+patword 0x0134 0x870c599f000e50ba
+patword 0x0135 0x870c599f000850ba
+patword 0x0136 0x870c599f000e50ba
+patword 0x0137 0x870c599f000850ba
+patword 0x0138 0x870c599f000e50ba
+patword 0x0139 0x870c599f000850ba
+patword 0x013a 0x870c599f282e50ba
+patword 0x013b 0x870c599f082850ba
+patword 0x013c 0x870c599f000e50ba
+patword 0x013d 0x870c599f000850ba
+patword 0x013e 0x870c599f000e50ba
+patword 0x013f 0x870c599f000850ba
+patword 0x0140 0x870c599f000e50ba
+patword 0x0141 0x870c599f000850ba
+patword 0x0142 0x870c599f000e50ba
+patword 0x0143 0x870c599f000850ba
+patword 0x0144 0x870c599f000e50ba
+patword 0x0145 0x870c599f000850ba
+patword 0x0146 0x870c599f000e50ba
+patword 0x0147 0x870c599f000850ba
+patword 0x0148 0x870c599f000e50ba
+patword 0x0149 0x870c599f000850ba
+patword 0x014a 0x870c599f000e50ba
+patword 0x014b 0x870c599f000850ba
+patword 0x014c 0x870c599f000e50ba
+patword 0x014d 0x870c599f000850ba
+patword 0x014e 0x870c599f000e50ba
+patword 0x014f 0x870c599f000850ba
+patword 0x0150 0x870c599f000e50ba
+patword 0x0151 0x870c599f000850ba
+patword 0x0152 0x870c599f000e50ba
+patword 0x0153 0x870c599f000850ba
+patword 0x0154 0x870c599f200e50ba
+patword 0x0155 0x870c599f000850ba
+patword 0x0156 0x870c599f000e50ba
+patword 0x0157 0x870c599f000850ba
+patword 0x0158 0x870c599f000e50ba
+patword 0x0159 0x870c599f000850ba
+patword 0x015a 0x870c599f000e50ba
+patword 0x015b 0x870c599f000850ba
+patword 0x015c 0x870c599f000e50ba
+patword 0x015d 0x870c599f000850ba
+patword 0x015e 0x870c599f000e50ba
+patword 0x015f 0x870c599f000850ba
+patword 0x0160 0x870c599f000e50ba
+patword 0x0161 0x870c599f000850ba
+patword 0x0162 0x870c599f000e50ba
+patword 0x0163 0x870c599f000850ba
+patword 0x0164 0x870c599f000e50ba
+patword 0x0165 0x870c599f000850ba
+patword 0x0166 0x870c599f000e50ba
+patword 0x0167 0x870c599f000850ba
+patword 0x0168 0x870c599f000e50ba
+patword 0x0169 0x870c599f000850ba
+patword 0x016a 0x870c599f000e50ba
+patword 0x016b 0x870c599f000850ba
+patword 0x016c 0x070c599f000850ba
+patword 0x016d 0x070c599f000850ba
+patword 0x016e 0x000c599f000850ba
+patword 0x016f 0x000c599f000850ba
+patword 0x0170 0x0008599f200e503a
+patword 0x0171 0x0008599f0008503a
+patword 0x0172 0x0008599f200e503a
+patword 0x0173 0x0008599f0008503a
+patword 0x0174 0x0008599f0008503a
+patword 0x0175 0x0008599f0008503a
+patword 0x0176 0x0008599f0008503a
+patword 0x0177 0x0008599f0008503a
+patword 0x0178 0x0008599f0008503a
+patword 0x0179 0x0008599f0008503a
+patword 0x017a 0x0008599f0008503a
+patword 0x017b 0x0008599f0008503a
+patword 0x017c 0x0008599f0008503a
+patword 0x017d 0x0008599f0008503a
+patword 0x017e 0x0008599f0008503a
+patword 0x017f 0x0008599f0008503a
+patword 0x0180 0x0008599f0008503a
+patword 0x0181 0x0008599f0008503a
+patword 0x0182 0x0008599f0008503a
+patword 0x0183 0x0008599f0008503a
+patword 0x0184 0x0008599f0008503a
+patword 0x0185 0x0008599f0008503a
+patword 0x0186 0x0008599f0008503a
+patword 0x0187 0x0008599f0008503a
+patword 0x0188 0x0008599f0008503a
+patword 0x0189 0x0008599f0008503a
+patword 0x018a 0x0008599f0008503a
+patword 0x018b 0x0008599f0008503a
+patword 0x018c 0x0008599f0008503a
+patword 0x018d 0x0008599f0008503a
+patioctrl 0x8f0effff6dbffdbf
+patlimits 0x0000 0x018c
+patloop0 0x013a 0x016b
+patnloop0 0x199
+patloop1 0x0400 0x0400
+patnloop1 0
+patloop2 0x0400 0x0400
+patnloop2 0
+patwait0 0x00aa
+patwaittime0 10000
+patwait1 0x0400
+patwaittime1 0
+patwait2 0x0400
+patwaittime2 0
 
 # dacs
 dac 6 800

examples/virtual_eiger_1_half_module.config

@@ -1,13 +1,13 @@
 # detector hostname
 hostname localhost:1900
 
+# receiver hostname
+rx_hostname mpc1922:2000
+
 # udp destination ports
 udp_dstport 50000
 udp_dstport2 50001
 
-# receiver hostname
-rx_hostname mpc1922:2000
-
 # udp destination ip from rx_hostname
 udp_dstip auto
 

examples/virtual_eiger_2_half_modules.config

@@ -1,15 +1,15 @@
 # detector hostname
 hostname localhost:1900+localhost:1902+
 
+# receiver hostname
+rx_hostname mpc1922:2000+mpc1922:2001+
+
 # udp destination ports
 0:udp_dstport 50000
 0:udp_dstport2 50001
 1:udp_dstport 50002
 1:udp_dstport2 50003
 
-# receiver hostname
-rx_hostname mpc1922:2000+mpc1922:2001+
-
 # udp destination ip from rx_hostname
 udp_dstip auto
 

examples/virtual_gotthard.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1904
 
-# udp destination ports
-udp_dstport 50004
-
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-
 # receiver hostname
 rx_hostname mpc1922:2004
 
+# udp destination ports
+udp_dstport 50004
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+
 # output file directory
 fpath /tmp
 

examples/virtual_gotthard2.config

@@ -1,12 +1,24 @@
 # detector hostname
 hostname localhost:1914
 
+# receiver hostname
+rx_hostname mpc1922:2014
+
 # udp destination ports
 udp_dstport 50014
 
+# udp destination ip from rx_hostname
+udp_dstip auto
+
 # udp source ip (same subnet as udp_dstip)
 udp_srcip 192.168.1.100
 
+# output file directory
+fpath /tmp
+
+# disable file writing
+fwrite 0
+
 # enable 2nd interface for veto debugging
 # udp destination port for veto
 udp_dstport2 50015
@@ -15,18 +27,6 @@ udp_dstip2 auto
 # udp source ip (same subnet as udp_dstip)
 udp_srcip2 192.168.1.100
 
-# receiver hostname
-rx_hostname mpc1922:2014
-
-# udp destination ip from rx_hostname
-udp_dstip auto
-
-# output file directory
-fpath /tmp
-
-# disable file writing
-fwrite 0
-
 # to enable 2nd interface for veto debugging
 numinterfaces 2
 

examples/virtual_jungfrau.config

@@ -1,21 +1,21 @@
 # detector hostname
 hostname localhost:1906
 
+# receiver hostname
+rx_hostname mpc1922:2006
+
 # udp destination ports
 udp_dstport 50006
 udp_dstport2 50007
 
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-udp_srcip2 192.168.1.100
-
-# receiver hostname
-rx_hostname mpc1922:2006
-
 # udp destination ip from rx_hostname
 udp_dstip auto
 udp_dstip2 auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+udp_srcip2 192.168.1.100
+
 # output file directory
 fpath /tmp
 

examples/virtual_jungfrau_4.config

@@ -4,6 +4,13 @@ detsize 2048 1024
 # detector hostname
 virtual 4 1952
 
+# receiver hostname and tcpports
+0:rx_tcpport 1970
+1:rx_tcpport 1971
+2:rx_tcpport 1972
+3:rx_tcpport 1973
+rx_hostname mpc1922
+
 # udp destination ports
 0:udp_dstport2 50001
 0:udp_dstport2 50002
@@ -14,21 +21,14 @@ virtual 4 1952
 3:udp_dstport 50007
 3:udp_dstport2 50008
 
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-udp_srcip2 192.168.1.100
-
-# receiver hostname and tcpports
-0:rx_tcpport 1970
-1:rx_tcpport 1971
-2:rx_tcpport 1972
-3:rx_tcpport 1973
-rx_hostname mpc1922
-
 # udp destination ip from rx_hostname
 udp_dstip auto
 udp_dstip2 auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+udp_srcip2 192.168.1.100
+
 # transmission delay frame
 0:txndelay_frame 0
 1:txndelay_frame 1

examples/virtual_moench.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1908
 
-# udp destination ports
-udp_dstport 50008
-
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-
 # receiver hostname
 rx_hostname mpc1922:2008
 
+# udp destination ports
+udp_dstport 50008
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+
 # output file directory
 fpath /tmp
 

examples/virtual_mythen3.config

@@ -1,18 +1,18 @@
 # detector hostname
 hostname localhost:1912
 
-# udp destination ports
-udp_dstport 50012
-
-# udp source ip (same subnet as udp_dstip)
-udp_srcip 192.168.1.100
-
 # receiver hostname
 rx_hostname mpc1922:2012
 
+# udp destination ports
+udp_dstport 50012
+
 # udp destination ip from rx_hostname
 udp_dstip auto
 
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 192.168.1.100
+
 # output file directory
 fpath /tmp
 

genVersionHeader.sh

@@ -0,0 +1,25 @@
+#####! /bin/awk -f
+
+
+if [ $# -lt 3 ] 
+then
+    echo "wrong usage"
+    exit -1
+fi
+
+
+fin=$1
+ftmp=$2
+fout=$3
+
+
+#dat=echo "date '+%Y%m%d'"
+
+echo "Updating $fout"
+#echo "in: $fin tmp: $ftmp out: $fout"
+
+#awk 'NR==FNR {if ($3=="Date:") {l[FNR]=$4; gsub("-","",l[FNR]);} else { if (match($0,"Rev")) {l[FNR]=$(NF);} else {l[FNR]="\""$(NF)"\"";};};next} {$0=$1" "$2" "l[FNR]}1' $fin $ftmp > $fout
+
+awk 'BEGIN {l[0]=0; "date +%Y%m%d" | getline l[1]; l[2]="\"/\""; l[3]="\"nobody\""; l[3]="\"nobody\""; l[4]="\"0000-0000-0000\"";} \
+NR==FNR {if (match($0,"Rev")) {l[0]="0x"$(NF);} else if (match($0,"Date")) {l[1]="0x"$4; gsub("-","",l[1]);} else if (match($0,"URL")) {l[2]="\""$(NF)"\"";} else if (match($0,"Author")) {l[3]="\""$(NF)"\"";} else if (match($0,"UUID")) {l[4]="\""$(NF)"\"";} else if (match($0,"Branch")) {l[5]="\""$(NF)"\"";};next;} 
+{if (match($2,"REV")) {$0=$1" "$2" "l[0];} else if (match($2,"DATE")) {$0=$1" "$2" "l[1];} else if (match($2,"URL")) {$0=$1" "$2" "l[2];} else if (match($2,"AUTH")) {$0=$1" "$2" "l[3];} else if (match($2,"UUID")) {$0=$1" "$2" "l[4];} else if (match($2,"BRANCH")) {$0=$1" "$2" "l[5];}}1' $fin $ftmp > $fout

integrationTests/CMakeLists.txt

@@ -1,5 +1,3 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
 # MESSAGE( STATUS "CMAKE_CURRENT_SOURCE_DIR: " ${CMAKE_CURRENT_SOURCE_DIR} )
 # MESSAGE( STATUS "PROJECT_SOURCE_DIR: " ${PROJECT_SOURCE_DIR} )
 

integrationTests/test-eigerIntegration.cpp

@@ -1,13 +1,9 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include "DetectorImpl.h"
 #include "catch.hpp"
 #include "sls/string_utils.h"
 #include "tests/globals.h"
 #include <iostream>
 
-namespace sls {
-
 class MultiDetectorFixture {
   protected:
     DetectorImpl d;
@@ -138,7 +134,7 @@ TEST_CASE_METHOD(MultiDetectorFixture, "Get ID", "[.eigerintegration][cli]") {
     std::string hn = test::hostname;
     hn.erase(std::remove(begin(hn), end(hn), 'b'), end(hn));
     hn.erase(std::remove(begin(hn), end(hn), 'e'), end(hn));
-    auto hostnames = split(hn, '+');
+    auto hostnames = sls::split(hn, '+');
     CHECK(hostnames.size() == d.getNumberOfDetectors());
     for (int i = 0; i != d.getNumberOfDetectors(); ++i) {
         CHECK(d.getId(defs::DETECTOR_SERIAL_NUMBER, 0) ==
@@ -200,5 +196,3 @@ TEST_CASE_METHOD(MultiDetectorFixture, "rate correction",
     d.setRateCorrection(200);
     CHECK(d.getRateCorrection() == 200);
 }
-
-} // namespace sls

integrationTests/test-integrationDectector.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 
 #include "catch.hpp"
 
@@ -24,8 +22,6 @@
 // extern std::string detector_type;
 // extern dt type;
 
-namespace sls {
-
 TEST_CASE("Single detector no receiver", "[.integration][.single]") {
     auto t = Module::getTypeFromDetector(test::hostname);
     CHECK(t == test::type);
@@ -50,8 +46,8 @@ TEST_CASE("Set control port then create a new object with this control port",
     Is this the best way to initialize the detectors
     Using braces to make the object go out of scope
     */
-    int old_cport = DEFAULT_TCP_CNTRL_PORTNO;
-    int old_sport = DEFAULT_TCP_STOP_PORTNO;
+    int old_cport = DEFAULT_PORTNO;
+    int old_sport = DEFAULT_PORTNO + 1;
     int new_cport = 1993;
     int new_sport = 2000;
     {
@@ -79,7 +75,7 @@ TEST_CASE("Set control port then create a new object with this control port",
 
     Module d(test::type);
     d.setHostname(test::hostname);
-    CHECK(d.getStopPort() == DEFAULT_TCP_STOP_PORTNO);
+    CHECK(d.getStopPort() == DEFAULT_PORTNO + 1);
     d.freeSharedMemory();
 }
 
@@ -285,14 +281,14 @@ TEST_CASE(
     CHECK(m.getRateCorrection() == ratecorr);
 
     // ratecorr fail with dr 4 or 8
-    CHECK_THROWS_AS(m.setDynamicRange(8), RuntimeError);
+    CHECK_THROWS_AS(m.setDynamicRange(8), sls::RuntimeError);
     CHECK(m.getRateCorrection() == 0);
     m.setDynamicRange(16);
     m.setDynamicRange(16);
     m.setRateCorrection(ratecorr);
     m.setDynamicRange(16);
     m.setRateCorrection(ratecorr);
-    CHECK_THROWS_AS(m.setDynamicRange(4), RuntimeError);
+    CHECK_THROWS_AS(m.setDynamicRange(4), sls::RuntimeError);
     CHECK(m.getRateCorrection() == 0);
 }
 
@@ -331,11 +327,11 @@ TEST_CASE("Chiptestboard Loading Patterns", "[.ctbintegration]") {
     m.setPatternWord(addr, word);
     CHECK(m.setPatternWord(addr, -1) == word);
     addr = MAX_ADDR;
-    CHECK_THROWS_AS(m.setPatternWord(addr, word), RuntimeError);
+    CHECK_THROWS_AS(m.setPatternWord(addr, word), sls::RuntimeError);
     CHECK_THROWS_WITH(m.setPatternWord(addr, word),
                       Catch::Matchers::Contains("be between 0 and"));
     addr = -1;
-    CHECK_THROWS_AS(m.setPatternWord(addr, word), RuntimeError);
+    CHECK_THROWS_AS(m.setPatternWord(addr, word), sls::RuntimeError);
     CHECK_THROWS_WITH(m.setPatternWord(addr, word),
                       Catch::Matchers::Contains("be between 0 and"));
 
@@ -410,7 +406,7 @@ TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert",
     CHECK(m.getReceiverDbitList().size() == 10);
 
     list.push_back(64);
-    CHECK_THROWS_AS(m.setReceiverDbitList(list), RuntimeError);
+    CHECK_THROWS_AS(m.setReceiverDbitList(list), sls::RuntimeError);
     CHECK_THROWS_WITH(m.setReceiverDbitList(list),
                       Catch::Matchers::Contains("be between 0 and 63"));
 
@@ -478,7 +474,7 @@ TEST_CASE("Eiger or Jungfrau nextframenumber",
     CHECK(m.acquire() == slsDetectorDefs::OK);
     CHECK(m.getReceiverCurrentFrameIndex() == val);
 
-    CHECK_THROWS_AS(m.setNextFrameNumber(0), RuntimeError);
+    CHECK_THROWS_AS(m.setNextFrameNumber(0), sls::RuntimeError);
 
     if (m.getDetectorTypeAsString() == "Eiger") {
         val = 281474976710655;
@@ -492,7 +488,7 @@ TEST_CASE("Eiger or Jungfrau nextframenumber",
     CHECK(m.getNextFrameNumber() == (val + 1));
 }
 
-TEST_CASE("Eiger partialread", "[.eigerintegration][partialread]") {
+TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {
     SingleDetectorConfig c;
 
     // pick up multi detector from shm id 0
@@ -505,18 +501,16 @@ TEST_CASE("Eiger partialread", "[.eigerintegration][partialread]") {
 
     m.setDynamicRange(16);
     m.enableTenGigabitEthernet(0);
-    m.setPartialReadout(256);
-    CHECK(m.getPartialReadout() == 256);
-    m.setPartialReadout(1);
-    CHECK(m.getPartialReadout() == 1);
+    m.setReadNLines(256);
+    CHECK(m.getReadNLines() == 256);
+    m.setReadNLines(1);
+    CHECK(m.getReadNLines() == 1);
 
     m.setDynamicRange(8);
-    m.setPartialReadout(256);
-    CHECK(m.getPartialReadout() == 256);
-    CHECK_THROWS_AS(m.setPartialReadout(1), RuntimeError);
-    CHECK(m.getPartialReadout() == 256);
-    CHECK_THROWS_AS(m.setPartialReadout(0), RuntimeError);
-    m.setPartialReadout(256);
+    m.setReadNLines(256);
+    CHECK(m.getReadNLines() == 256);
+    CHECK_THROWS_AS(m.setReadNLines(1), sls::RuntimeError);
+    CHECK(m.getReadNLines() == 256);
+    CHECK_THROWS_AS(m.setReadNLines(0), sls::RuntimeError);
+    m.setReadNLines(256);
 }
-
-} // namespace sls

integrationTests/test-integrationMulti.cpp

@@ -1,17 +1,13 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 #include "DetectorImpl.h"
 #include "catch.hpp"
 #include "sls/string_utils.h"
 #include "tests/globals.h"
 #include <iostream>
 
-namespace sls {
-
 using namespace Catch::literals;
 
 TEST_CASE("Initialize a multi detector", "[.integration][.multi]") {
-    auto hostnames = split(test::hostname, '+');
+    auto hostnames = sls::split(test::hostname, '+');
 
     DetectorImpl d(0, true, true);
     d.setHostname(test::hostname.c_str());
@@ -104,5 +100,3 @@ TEST_CASE("Set and read timers", "[.integration][.multi]") {
 
     d.freeSharedMemory();
 }
-
-} // namespace sls

integrationTests/test.cpp

@@ -1,5 +1,3 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
 // tests-main.cpp
 #define CATCH_CONFIG_MAIN
 #include "catch.hpp"

libs/pybind/CMakeLists.txt

@@ -1,299 +0,0 @@
-# CMakeLists.txt -- Build system for the pybind11 modules
-#
-# Copyright (c) 2015 Wenzel Jakob <wenzel@inf.ethz.ch>
-#
-# All rights reserved. Use of this source code is governed by a
-# BSD-style license that can be found in the LICENSE file.
-
-cmake_minimum_required(VERSION 3.4)
-
-# The `cmake_minimum_required(VERSION 3.4...3.22)` syntax does not work with
-# some versions of VS that have a patched CMake 3.11. This forces us to emulate
-# the behavior using the following workaround:
-if(${CMAKE_VERSION} VERSION_LESS 3.22)
-  cmake_policy(VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION})
-else()
-  cmake_policy(VERSION 3.22)
-endif()
-
-# Avoid infinite recursion if tests include this as a subdirectory
-if(DEFINED PYBIND11_MASTER_PROJECT)
-  return()
-endif()
-
-# Extract project version from source
-file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/include/pybind11/detail/common.h"
-     pybind11_version_defines REGEX "#define PYBIND11_VERSION_(MAJOR|MINOR|PATCH) ")
-
-foreach(ver ${pybind11_version_defines})
-  if(ver MATCHES [[#define PYBIND11_VERSION_(MAJOR|MINOR|PATCH) +([^ ]+)$]])
-    set(PYBIND11_VERSION_${CMAKE_MATCH_1} "${CMAKE_MATCH_2}")
-  endif()
-endforeach()
-
-if(PYBIND11_VERSION_PATCH MATCHES [[\.([a-zA-Z0-9]+)$]])
-  set(pybind11_VERSION_TYPE "${CMAKE_MATCH_1}")
-endif()
-string(REGEX MATCH "^[0-9]+" PYBIND11_VERSION_PATCH "${PYBIND11_VERSION_PATCH}")
-
-project(
-  pybind11
-  LANGUAGES CXX
-  VERSION "${PYBIND11_VERSION_MAJOR}.${PYBIND11_VERSION_MINOR}.${PYBIND11_VERSION_PATCH}")
-
-# Standard includes
-include(GNUInstallDirs)
-include(CMakePackageConfigHelpers)
-include(CMakeDependentOption)
-
-if(NOT pybind11_FIND_QUIETLY)
-  message(STATUS "pybind11 v${pybind11_VERSION} ${pybind11_VERSION_TYPE}")
-endif()
-
-# Check if pybind11 is being used directly or via add_subdirectory
-if(CMAKE_SOURCE_DIR STREQUAL PROJECT_SOURCE_DIR)
-  ### Warn if not an out-of-source builds
-  if(CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
-    set(lines
-        "You are building in-place. If that is not what you intended to "
-        "do, you can clean the source directory with:\n"
-        "rm -r CMakeCache.txt CMakeFiles/ cmake_uninstall.cmake pybind11Config.cmake "
-        "pybind11ConfigVersion.cmake tests/CMakeFiles/\n")
-    message(AUTHOR_WARNING ${lines})
-  endif()
-
-  set(PYBIND11_MASTER_PROJECT ON)
-
-  if(OSX AND CMAKE_VERSION VERSION_LESS 3.7)
-    # Bug in macOS CMake < 3.7 is unable to download catch
-    message(WARNING "CMAKE 3.7+ needed on macOS to download catch, and newer HIGHLY recommended")
-  elseif(WINDOWS AND CMAKE_VERSION VERSION_LESS 3.8)
-    # Only tested with 3.8+ in CI.
-    message(WARNING "CMAKE 3.8+ tested on Windows, previous versions untested")
-  endif()
-
-  message(STATUS "CMake ${CMAKE_VERSION}")
-
-  if(CMAKE_CXX_STANDARD)
-    set(CMAKE_CXX_EXTENSIONS OFF)
-    set(CMAKE_CXX_STANDARD_REQUIRED ON)
-  endif()
-
-  set(pybind11_system "")
-
-  set_property(GLOBAL PROPERTY USE_FOLDERS ON)
-else()
-  set(PYBIND11_MASTER_PROJECT OFF)
-  set(pybind11_system SYSTEM)
-endif()
-
-# Options
-option(PYBIND11_INSTALL "Install pybind11 header files?" ${PYBIND11_MASTER_PROJECT})
-option(PYBIND11_TEST "Build pybind11 test suite?" ${PYBIND11_MASTER_PROJECT})
-option(PYBIND11_NOPYTHON "Disable search for Python" OFF)
-set(PYBIND11_INTERNALS_VERSION
-    ""
-    CACHE STRING "Override the ABI version, may be used to enable the unstable ABI.")
-
-cmake_dependent_option(
-  USE_PYTHON_INCLUDE_DIR
-  "Install pybind11 headers in Python include directory instead of default installation prefix"
-  OFF "PYBIND11_INSTALL" OFF)
-
-cmake_dependent_option(PYBIND11_FINDPYTHON "Force new FindPython" OFF
-                       "NOT CMAKE_VERSION VERSION_LESS 3.12" OFF)
-
-# NB: when adding a header don't forget to also add it to setup.py
-set(PYBIND11_HEADERS
-    include/pybind11/detail/class.h
-    include/pybind11/detail/common.h
-    include/pybind11/detail/descr.h
-    include/pybind11/detail/init.h
-    include/pybind11/detail/internals.h
-    include/pybind11/detail/type_caster_base.h
-    include/pybind11/detail/typeid.h
-    include/pybind11/attr.h
-    include/pybind11/buffer_info.h
-    include/pybind11/cast.h
-    include/pybind11/chrono.h
-    include/pybind11/common.h
-    include/pybind11/complex.h
-    include/pybind11/options.h
-    include/pybind11/eigen.h
-    include/pybind11/embed.h
-    include/pybind11/eval.h
-    include/pybind11/gil.h
-    include/pybind11/iostream.h
-    include/pybind11/functional.h
-    include/pybind11/numpy.h
-    include/pybind11/operators.h
-    include/pybind11/pybind11.h
-    include/pybind11/pytypes.h
-    include/pybind11/stl.h
-    include/pybind11/stl_bind.h
-    include/pybind11/stl/filesystem.h)
-
-# Compare with grep and warn if mismatched
-if(PYBIND11_MASTER_PROJECT AND NOT CMAKE_VERSION VERSION_LESS 3.12)
-  file(
-    GLOB_RECURSE _pybind11_header_check
-    LIST_DIRECTORIES false
-    RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}"
-    CONFIGURE_DEPENDS "include/pybind11/*.h")
-  set(_pybind11_here_only ${PYBIND11_HEADERS})
-  set(_pybind11_disk_only ${_pybind11_header_check})
-  list(REMOVE_ITEM _pybind11_here_only ${_pybind11_header_check})
-  list(REMOVE_ITEM _pybind11_disk_only ${PYBIND11_HEADERS})
-  if(_pybind11_here_only)
-    message(AUTHOR_WARNING "PYBIND11_HEADERS has extra files:" ${_pybind11_here_only})
-  endif()
-  if(_pybind11_disk_only)
-    message(AUTHOR_WARNING "PYBIND11_HEADERS is missing files:" ${_pybind11_disk_only})
-  endif()
-endif()
-
-# CMake 3.12 added list(TRANSFORM <list> PREPEND
-# But we can't use it yet
-string(REPLACE "include/" "${CMAKE_CURRENT_SOURCE_DIR}/include/" PYBIND11_HEADERS
-               "${PYBIND11_HEADERS}")
-
-# Cache variable so this can be used in parent projects
-set(pybind11_INCLUDE_DIR
-    "${CMAKE_CURRENT_LIST_DIR}/include"
-    CACHE INTERNAL "Directory where pybind11 headers are located")
-
-# Backward compatible variable for add_subdirectory mode
-if(NOT PYBIND11_MASTER_PROJECT)
-  set(PYBIND11_INCLUDE_DIR
-      "${pybind11_INCLUDE_DIR}"
-      CACHE INTERNAL "")
-endif()
-
-# Note: when creating targets, you cannot use if statements at configure time -
-# you need generator expressions, because those will be placed in the target file.
-# You can also place ifs *in* the Config.in, but not here.
-
-# This section builds targets, but does *not* touch Python
-# Non-IMPORT targets cannot be defined twice
-if(NOT TARGET pybind11_headers)
-  # Build the headers-only target (no Python included):
-  # (long name used here to keep this from clashing in subdirectory mode)
-  add_library(pybind11_headers INTERFACE)
-  add_library(pybind11::pybind11_headers ALIAS pybind11_headers) # to match exported target
-  add_library(pybind11::headers ALIAS pybind11_headers) # easier to use/remember
-
-  target_include_directories(
-    pybind11_headers ${pybind11_system} INTERFACE $<BUILD_INTERFACE:${pybind11_INCLUDE_DIR}>
-                                                  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
-
-  target_compile_features(pybind11_headers INTERFACE cxx_inheriting_constructors cxx_user_literals
-                                                     cxx_right_angle_brackets)
-  if(NOT "${PYBIND11_INTERNALS_VERSION}" STREQUAL "")
-    target_compile_definitions(
-      pybind11_headers INTERFACE "PYBIND11_INTERNALS_VERSION=${PYBIND11_INTERNALS_VERSION}")
-  endif()
-else()
-  # It is invalid to install a target twice, too.
-  set(PYBIND11_INSTALL OFF)
-endif()
-
-include("${CMAKE_CURRENT_SOURCE_DIR}/tools/pybind11Common.cmake")
-
-# Relative directory setting
-if(USE_PYTHON_INCLUDE_DIR AND DEFINED Python_INCLUDE_DIRS)
-  file(RELATIVE_PATH CMAKE_INSTALL_INCLUDEDIR ${CMAKE_INSTALL_PREFIX} ${Python_INCLUDE_DIRS})
-elseif(USE_PYTHON_INCLUDE_DIR AND DEFINED PYTHON_INCLUDE_DIR)
-  file(RELATIVE_PATH CMAKE_INSTALL_INCLUDEDIR ${CMAKE_INSTALL_PREFIX} ${PYTHON_INCLUDE_DIRS})
-endif()
-
-if(PYBIND11_INSTALL)
-  install(DIRECTORY ${pybind11_INCLUDE_DIR}/pybind11 DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
-  set(PYBIND11_CMAKECONFIG_INSTALL_DIR
-      "${CMAKE_INSTALL_DATAROOTDIR}/cmake/${PROJECT_NAME}"
-      CACHE STRING "install path for pybind11Config.cmake")
-
-  if(IS_ABSOLUTE "${CMAKE_INSTALL_INCLUDEDIR}")
-    set(pybind11_INCLUDEDIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}")
-  else()
-    set(pybind11_INCLUDEDIR "\$\{PACKAGE_PREFIX_DIR\}/${CMAKE_INSTALL_INCLUDEDIR}")
-  endif()
-
-  configure_package_config_file(
-    tools/${PROJECT_NAME}Config.cmake.in "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
-    INSTALL_DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
-
-  if(CMAKE_VERSION VERSION_LESS 3.14)
-    # Remove CMAKE_SIZEOF_VOID_P from ConfigVersion.cmake since the library does
-    # not depend on architecture specific settings or libraries.
-    set(_PYBIND11_CMAKE_SIZEOF_VOID_P ${CMAKE_SIZEOF_VOID_P})
-    unset(CMAKE_SIZEOF_VOID_P)
-
-    write_basic_package_version_file(
-      ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
-      VERSION ${PROJECT_VERSION}
-      COMPATIBILITY AnyNewerVersion)
-
-    set(CMAKE_SIZEOF_VOID_P ${_PYBIND11_CMAKE_SIZEOF_VOID_P})
-  else()
-    # CMake 3.14+ natively supports header-only libraries
-    write_basic_package_version_file(
-      ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
-      VERSION ${PROJECT_VERSION}
-      COMPATIBILITY AnyNewerVersion ARCH_INDEPENDENT)
-  endif()
-
-  install(
-    FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
-          ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
-          tools/FindPythonLibsNew.cmake
-          tools/pybind11Common.cmake
-          tools/pybind11Tools.cmake
-          tools/pybind11NewTools.cmake
-    DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
-
-  if(NOT PYBIND11_EXPORT_NAME)
-    set(PYBIND11_EXPORT_NAME "${PROJECT_NAME}Targets")
-  endif()
-
-  install(TARGETS pybind11_headers EXPORT "${PYBIND11_EXPORT_NAME}")
-
-  install(
-    EXPORT "${PYBIND11_EXPORT_NAME}"
-    NAMESPACE "pybind11::"
-    DESTINATION ${PYBIND11_CMAKECONFIG_INSTALL_DIR})
-
-  # Uninstall target
-  if(PYBIND11_MASTER_PROJECT)
-    configure_file("${CMAKE_CURRENT_SOURCE_DIR}/tools/cmake_uninstall.cmake.in"
-                   "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake" IMMEDIATE @ONLY)
-
-    add_custom_target(uninstall COMMAND ${CMAKE_COMMAND} -P
-                                        ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
-  endif()
-endif()
-
-# BUILD_TESTING takes priority, but only if this is the master project
-if(PYBIND11_MASTER_PROJECT AND DEFINED BUILD_TESTING)
-  if(BUILD_TESTING)
-    if(_pybind11_nopython)
-      message(FATAL_ERROR "Cannot activate tests in NOPYTHON mode")
-    else()
-      add_subdirectory(tests)
-    endif()
-  endif()
-else()
-  if(PYBIND11_TEST)
-    if(_pybind11_nopython)
-      message(FATAL_ERROR "Cannot activate tests in NOPYTHON mode")
-    else()
-      add_subdirectory(tests)
-    endif()
-  endif()
-endif()
-
-# Better symmetry with find_package(pybind11 CONFIG) mode.
-if(NOT PYBIND11_MASTER_PROJECT)
-  set(pybind11_FOUND
-      TRUE
-      CACHE INTERNAL "True if pybind11 and all required components found on the system")
-endif()

libs/pybind/LICENSE

@@ -1,29 +0,0 @@
-Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>, All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its contributors
-   may be used to endorse or promote products derived from this software
-   without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Please also refer to the file .github/CONTRIBUTING.md, which clarifies licensing of
-external contributions to this project including patches, pull requests, etc.

libs/pybind/MANIFEST.in

@@ -1,5 +0,0 @@
-recursive-include pybind11/include/pybind11 *.h
-recursive-include pybind11 *.py
-recursive-include pybind11 py.typed
-include pybind11/share/cmake/pybind11/*.cmake
-include LICENSE README.rst pyproject.toml setup.py setup.cfg

libs/pybind/README.rst

@@ -1,180 +0,0 @@
-.. figure:: https://github.com/pybind/pybind11/raw/master/docs/pybind11-logo.png
-   :alt: pybind11 logo
-
-**pybind11 — Seamless operability between C++11 and Python**
-
-|Latest Documentation Status| |Stable Documentation Status| |Gitter chat| |GitHub Discussions| |CI| |Build status|
-
-|Repology| |PyPI package| |Conda-forge| |Python Versions|
-
-`Setuptools example <https://github.com/pybind/python_example>`_
-• `Scikit-build example <https://github.com/pybind/scikit_build_example>`_
-• `CMake example <https://github.com/pybind/cmake_example>`_
-
-.. start
-
-
-**pybind11** is a lightweight header-only library that exposes C++ types
-in Python and vice versa, mainly to create Python bindings of existing
-C++ code. Its goals and syntax are similar to the excellent
-`Boost.Python <http://www.boost.org/doc/libs/1_58_0/libs/python/doc/>`_
-library by David Abrahams: to minimize boilerplate code in traditional
-extension modules by inferring type information using compile-time
-introspection.
-
-The main issue with Boost.Python—and the reason for creating such a
-similar project—is Boost. Boost is an enormously large and complex suite
-of utility libraries that works with almost every C++ compiler in
-existence. This compatibility has its cost: arcane template tricks and
-workarounds are necessary to support the oldest and buggiest of compiler
-specimens. Now that C++11-compatible compilers are widely available,
-this heavy machinery has become an excessively large and unnecessary
-dependency.
-
-Think of this library as a tiny self-contained version of Boost.Python
-with everything stripped away that isn't relevant for binding
-generation. Without comments, the core header files only require ~4K
-lines of code and depend on Python (3.6+, or PyPy) and the C++
-standard library. This compact implementation was possible thanks to
-some of the new C++11 language features (specifically: tuples, lambda
-functions and variadic templates). Since its creation, this library has
-grown beyond Boost.Python in many ways, leading to dramatically simpler
-binding code in many common situations.
-
-Tutorial and reference documentation is provided at
-`pybind11.readthedocs.io <https://pybind11.readthedocs.io/en/latest>`_.
-A PDF version of the manual is available
-`here <https://pybind11.readthedocs.io/_/downloads/en/latest/pdf/>`_.
-And the source code is always available at
-`github.com/pybind/pybind11 <https://github.com/pybind/pybind11>`_.
-
-
-Core features
--------------
-
-
-pybind11 can map the following core C++ features to Python:
-
-- Functions accepting and returning custom data structures per value,
-  reference, or pointer
-- Instance methods and static methods
-- Overloaded functions
-- Instance attributes and static attributes
-- Arbitrary exception types
-- Enumerations
-- Callbacks
-- Iterators and ranges
-- Custom operators
-- Single and multiple inheritance
-- STL data structures
-- Smart pointers with reference counting like ``std::shared_ptr``
-- Internal references with correct reference counting
-- C++ classes with virtual (and pure virtual) methods can be extended
-  in Python
-
-Goodies
--------
-
-In addition to the core functionality, pybind11 provides some extra
-goodies:
-
-- Python 3.6+, and PyPy3 7.3 are supported with an implementation-agnostic
-  interface (pybind11 2.9 was the last version to support Python 2 and 3.5).
-
-- It is possible to bind C++11 lambda functions with captured
-  variables. The lambda capture data is stored inside the resulting
-  Python function object.
-
-- pybind11 uses C++11 move constructors and move assignment operators
-  whenever possible to efficiently transfer custom data types.
-
-- It's easy to expose the internal storage of custom data types through
-  Pythons' buffer protocols. This is handy e.g. for fast conversion
-  between C++ matrix classes like Eigen and NumPy without expensive
-  copy operations.
-
-- pybind11 can automatically vectorize functions so that they are
-  transparently applied to all entries of one or more NumPy array
-  arguments.
-
-- Python's slice-based access and assignment operations can be
-  supported with just a few lines of code.
-
-- Everything is contained in just a few header files; there is no need
-  to link against any additional libraries.
-
-- Binaries are generally smaller by a factor of at least 2 compared to
-  equivalent bindings generated by Boost.Python. A recent pybind11
-  conversion of PyRosetta, an enormous Boost.Python binding project,
-  `reported <https://graylab.jhu.edu/Sergey/2016.RosettaCon/PyRosetta-4.pdf>`_
-  a binary size reduction of **5.4x** and compile time reduction by
-  **5.8x**.
-
-- Function signatures are precomputed at compile time (using
-  ``constexpr``), leading to smaller binaries.
-
-- With little extra effort, C++ types can be pickled and unpickled
-  similar to regular Python objects.
-
-Supported compilers
--------------------
-
-1. Clang/LLVM 3.3 or newer (for Apple Xcode's clang, this is 5.0.0 or
-   newer)
-2. GCC 4.8 or newer
-3. Microsoft Visual Studio 2017 or newer
-4. Intel classic C++ compiler 18 or newer (ICC 20.2 tested in CI)
-5. Cygwin/GCC (previously tested on 2.5.1)
-6. NVCC (CUDA 11.0 tested in CI)
-7. NVIDIA PGI (20.9 tested in CI)
-
-About
------
-
-This project was created by `Wenzel
-Jakob <http://rgl.epfl.ch/people/wjakob>`_. Significant features and/or
-improvements to the code were contributed by Jonas Adler, Lori A. Burns,
-Sylvain Corlay, Eric Cousineau, Aaron Gokaslan, Ralf Grosse-Kunstleve, Trent Houliston, Axel
-Huebl, @hulucc, Yannick Jadoul, Sergey Lyskov Johan Mabille, Tomasz Miąsko,
-Dean Moldovan, Ben Pritchard, Jason Rhinelander, Boris Schäling, Pim
-Schellart, Henry Schreiner, Ivan Smirnov, Boris Staletic, and Patrick Stewart.
-
-We thank Google for a generous financial contribution to the continuous
-integration infrastructure used by this project.
-
-
-Contributing
-~~~~~~~~~~~~
-
-See the `contributing
-guide <https://github.com/pybind/pybind11/blob/master/.github/CONTRIBUTING.md>`_
-for information on building and contributing to pybind11.
-
-License
-~~~~~~~
-
-pybind11 is provided under a BSD-style license that can be found in the
-`LICENSE <https://github.com/pybind/pybind11/blob/master/LICENSE>`_
-file. By using, distributing, or contributing to this project, you agree
-to the terms and conditions of this license.
-
-.. |Latest Documentation Status| image:: https://readthedocs.org/projects/pybind11/badge?version=latest
-   :target: http://pybind11.readthedocs.org/en/latest
-.. |Stable Documentation Status| image:: https://img.shields.io/badge/docs-stable-blue.svg
-   :target: http://pybind11.readthedocs.org/en/stable
-.. |Gitter chat| image:: https://img.shields.io/gitter/room/gitterHQ/gitter.svg
-   :target: https://gitter.im/pybind/Lobby
-.. |CI| image:: https://github.com/pybind/pybind11/workflows/CI/badge.svg
-   :target: https://github.com/pybind/pybind11/actions
-.. |Build status| image:: https://ci.appveyor.com/api/projects/status/riaj54pn4h08xy40?svg=true
-   :target: https://ci.appveyor.com/project/wjakob/pybind11
-.. |PyPI package| image:: https://img.shields.io/pypi/v/pybind11.svg
-   :target: https://pypi.org/project/pybind11/
-.. |Conda-forge| image:: https://img.shields.io/conda/vn/conda-forge/pybind11.svg
-   :target: https://github.com/conda-forge/pybind11-feedstock
-.. |Repology| image:: https://repology.org/badge/latest-versions/python:pybind11.svg
-   :target: https://repology.org/project/python:pybind11/versions
-.. |Python Versions| image:: https://img.shields.io/pypi/pyversions/pybind11.svg
-   :target: https://pypi.org/project/pybind11/
-.. |GitHub Discussions| image:: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github
-   :target: https://github.com/pybind/pybind11/discussions

libs/pybind/docs/Doxyfile

@@ -1,21 +0,0 @@
-PROJECT_NAME           = pybind11
-INPUT                  = ../include/pybind11/
-RECURSIVE              = YES
-
-GENERATE_HTML          = NO
-GENERATE_LATEX         = NO
-GENERATE_XML           = YES
-XML_OUTPUT             = .build/doxygenxml
-XML_PROGRAMLISTING     = YES
-
-MACRO_EXPANSION        = YES
-EXPAND_ONLY_PREDEF     = YES
-EXPAND_AS_DEFINED      = PYBIND11_RUNTIME_EXCEPTION
-
-ALIASES                = "rst=\verbatim embed:rst"
-ALIASES               += "endrst=\endverbatim"
-
-QUIET                  = YES
-WARNINGS               = YES
-WARN_IF_UNDOCUMENTED   = NO
-PREDEFINED             = PYBIND11_NOINLINE

libs/pybind/docs/Makefile

@@ -1,192 +0,0 @@
-# Makefile for Sphinx documentation
-#
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-
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-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
-
-# Internal variables.
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-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
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-
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-	      "or in $(BUILDDIR)/linkcheck/output.txt."
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libs/pybind/docs/_static/css/custom.css

@@ -1,3 +0,0 @@
-.highlight .go {
-  color: #707070;
-}

libs/pybind/docs/advanced/cast/chrono.rst

@@ -1,81 +0,0 @@
-Chrono
-======
-
-When including the additional header file :file:`pybind11/chrono.h` conversions
-from C++11 chrono datatypes to python datetime objects are automatically enabled.
-This header also enables conversions of python floats (often from sources such
-as ``time.monotonic()``, ``time.perf_counter()`` and ``time.process_time()``)
-into durations.
-
-An overview of clocks in C++11
-------------------------------
-
-A point of confusion when using these conversions is the differences between
-clocks provided in C++11. There are three clock types defined by the C++11
-standard and users can define their own if needed. Each of these clocks have
-different properties and when converting to and from python will give different
-results.
-
-The first clock defined by the standard is ``std::chrono::system_clock``. This
-clock measures the current date and time. However, this clock changes with to
-updates to the operating system time. For example, if your time is synchronised
-with a time server this clock will change. This makes this clock a poor choice
-for timing purposes but good for measuring the wall time.
-
-The second clock defined in the standard is ``std::chrono::steady_clock``.
-This clock ticks at a steady rate and is never adjusted. This makes it excellent
-for timing purposes, however the value in this clock does not correspond to the
-current date and time. Often this clock will be the amount of time your system
-has been on, although it does not have to be. This clock will never be the same
-clock as the system clock as the system clock can change but steady clocks
-cannot.
-
-The third clock defined in the standard is ``std::chrono::high_resolution_clock``.
-This clock is the clock that has the highest resolution out of the clocks in the
-system. It is normally a typedef to either the system clock or the steady clock
-but can be its own independent clock. This is important as when using these
-conversions as the types you get in python for this clock might be different
-depending on the system.
-If it is a typedef of the system clock, python will get datetime objects, but if
-it is a different clock they will be timedelta objects.
-
-Provided conversions
---------------------
-
-.. rubric:: C++ to Python
-
-- ``std::chrono::system_clock::time_point`` → ``datetime.datetime``
-    System clock times are converted to python datetime instances. They are
-    in the local timezone, but do not have any timezone information attached
-    to them (they are naive datetime objects).
-
-- ``std::chrono::duration`` → ``datetime.timedelta``
-    Durations are converted to timedeltas, any precision in the duration
-    greater than microseconds is lost by rounding towards zero.
-
-- ``std::chrono::[other_clocks]::time_point`` → ``datetime.timedelta``
-    Any clock time that is not the system clock is converted to a time delta.
-    This timedelta measures the time from the clocks epoch to now.
-
-.. rubric:: Python to C++
-
-- ``datetime.datetime`` or ``datetime.date`` or ``datetime.time`` → ``std::chrono::system_clock::time_point``
-    Date/time objects are converted into system clock timepoints. Any
-    timezone information is ignored and the type is treated as a naive
-    object.
-
-- ``datetime.timedelta`` → ``std::chrono::duration``
-    Time delta are converted into durations with microsecond precision.
-
-- ``datetime.timedelta`` → ``std::chrono::[other_clocks]::time_point``
-    Time deltas that are converted into clock timepoints are treated as
-    the amount of time from the start of the clocks epoch.
-
-- ``float`` → ``std::chrono::duration``
-    Floats that are passed to C++ as durations be interpreted as a number of
-    seconds. These will be converted to the duration using ``duration_cast``
-    from the float.
-
-- ``float`` → ``std::chrono::[other_clocks]::time_point``
-    Floats that are passed to C++ as time points will be interpreted as the
-    number of seconds from the start of the clocks epoch.

libs/pybind/docs/advanced/cast/custom.rst

@@ -1,93 +0,0 @@
-Custom type casters
-===================
-
-In very rare cases, applications may require custom type casters that cannot be
-expressed using the abstractions provided by pybind11, thus requiring raw
-Python C API calls. This is fairly advanced usage and should only be pursued by
-experts who are familiar with the intricacies of Python reference counting.
-
-The following snippets demonstrate how this works for a very simple ``inty``
-type that that should be convertible from Python types that provide a
-``__int__(self)`` method.
-
-.. code-block:: cpp
-
-    struct inty { long long_value; };
-
-    void print(inty s) {
-        std::cout << s.long_value << std::endl;
-    }
-
-The following Python snippet demonstrates the intended usage from the Python side:
-
-.. code-block:: python
-
-    class A:
-        def __int__(self):
-            return 123
-
-
-    from example import print
-
-    print(A())
-
-To register the necessary conversion routines, it is necessary to add an
-instantiation of the ``pybind11::detail::type_caster<T>`` template.
-Although this is an implementation detail, adding an instantiation of this
-type is explicitly allowed.
-
-.. code-block:: cpp
-
-    namespace pybind11 { namespace detail {
-        template <> struct type_caster<inty> {
-        public:
-            /**
-             * This macro establishes the name 'inty' in
-             * function signatures and declares a local variable
-             * 'value' of type inty
-             */
-            PYBIND11_TYPE_CASTER(inty, const_name("inty"));
-
-            /**
-             * Conversion part 1 (Python->C++): convert a PyObject into a inty
-             * instance or return false upon failure. The second argument
-             * indicates whether implicit conversions should be applied.
-             */
-            bool load(handle src, bool) {
-                /* Extract PyObject from handle */
-                PyObject *source = src.ptr();
-                /* Try converting into a Python integer value */
-                PyObject *tmp = PyNumber_Long(source);
-                if (!tmp)
-                    return false;
-                /* Now try to convert into a C++ int */
-                value.long_value = PyLong_AsLong(tmp);
-                Py_DECREF(tmp);
-                /* Ensure return code was OK (to avoid out-of-range errors etc) */
-                return !(value.long_value == -1 && !PyErr_Occurred());
-            }
-
-            /**
-             * Conversion part 2 (C++ -> Python): convert an inty instance into
-             * a Python object. The second and third arguments are used to
-             * indicate the return value policy and parent object (for
-             * ``return_value_policy::reference_internal``) and are generally
-             * ignored by implicit casters.
-             */
-            static handle cast(inty src, return_value_policy /* policy */, handle /* parent */) {
-                return PyLong_FromLong(src.long_value);
-            }
-        };
-    }} // namespace pybind11::detail
-
-.. note::
-
-    A ``type_caster<T>`` defined with ``PYBIND11_TYPE_CASTER(T, ...)`` requires
-    that ``T`` is default-constructible (``value`` is first default constructed
-    and then ``load()`` assigns to it).
-
-.. warning::
-
-    When using custom type casters, it's important to declare them consistently
-    in every compilation unit of the Python extension module. Otherwise,
-    undefined behavior can ensue.

libs/pybind/docs/advanced/cast/eigen.rst

@@ -1,310 +0,0 @@
-Eigen
-#####
-
-`Eigen <http://eigen.tuxfamily.org>`_ is C++ header-based library for dense and
-sparse linear algebra. Due to its popularity and widespread adoption, pybind11
-provides transparent conversion and limited mapping support between Eigen and
-Scientific Python linear algebra data types.
-
-To enable the built-in Eigen support you must include the optional header file
-:file:`pybind11/eigen.h`.
-
-Pass-by-value
-=============
-
-When binding a function with ordinary Eigen dense object arguments (for
-example, ``Eigen::MatrixXd``), pybind11 will accept any input value that is
-already (or convertible to) a ``numpy.ndarray`` with dimensions compatible with
-the Eigen type, copy its values into a temporary Eigen variable of the
-appropriate type, then call the function with this temporary variable.
-
-Sparse matrices are similarly copied to or from
-``scipy.sparse.csr_matrix``/``scipy.sparse.csc_matrix`` objects.
-
-Pass-by-reference
-=================
-
-One major limitation of the above is that every data conversion implicitly
-involves a copy, which can be both expensive (for large matrices) and disallows
-binding functions that change their (Matrix) arguments.  Pybind11 allows you to
-work around this by using Eigen's ``Eigen::Ref<MatrixType>`` class much as you
-would when writing a function taking a generic type in Eigen itself (subject to
-some limitations discussed below).
-
-When calling a bound function accepting a ``Eigen::Ref<const MatrixType>``
-type, pybind11 will attempt to avoid copying by using an ``Eigen::Map`` object
-that maps into the source ``numpy.ndarray`` data: this requires both that the
-data types are the same (e.g. ``dtype='float64'`` and ``MatrixType::Scalar`` is
-``double``); and that the storage is layout compatible.  The latter limitation
-is discussed in detail in the section below, and requires careful
-consideration: by default, numpy matrices and Eigen matrices are *not* storage
-compatible.
-
-If the numpy matrix cannot be used as is (either because its types differ, e.g.
-passing an array of integers to an Eigen parameter requiring doubles, or
-because the storage is incompatible), pybind11 makes a temporary copy and
-passes the copy instead.
-
-When a bound function parameter is instead ``Eigen::Ref<MatrixType>`` (note the
-lack of ``const``), pybind11 will only allow the function to be called if it
-can be mapped *and* if the numpy array is writeable (that is
-``a.flags.writeable`` is true).  Any access (including modification) made to
-the passed variable will be transparently carried out directly on the
-``numpy.ndarray``.
-
-This means you can write code such as the following and have it work as
-expected:
-
-.. code-block:: cpp
-
-    void scale_by_2(Eigen::Ref<Eigen::VectorXd> v) {
-        v *= 2;
-    }
-
-Note, however, that you will likely run into limitations due to numpy and
-Eigen's difference default storage order for data; see the below section on
-:ref:`storage_orders` for details on how to bind code that won't run into such
-limitations.
-
-.. note::
-
-    Passing by reference is not supported for sparse types.
-
-Returning values to Python
-==========================
-
-When returning an ordinary dense Eigen matrix type to numpy (e.g.
-``Eigen::MatrixXd`` or ``Eigen::RowVectorXf``) pybind11 keeps the matrix and
-returns a numpy array that directly references the Eigen matrix: no copy of the
-data is performed.  The numpy array will have ``array.flags.owndata`` set to
-``False`` to indicate that it does not own the data, and the lifetime of the
-stored Eigen matrix will be tied to the returned ``array``.
-
-If you bind a function with a non-reference, ``const`` return type (e.g.
-``const Eigen::MatrixXd``), the same thing happens except that pybind11 also
-sets the numpy array's ``writeable`` flag to false.
-
-If you return an lvalue reference or pointer, the usual pybind11 rules apply,
-as dictated by the binding function's return value policy (see the
-documentation on :ref:`return_value_policies` for full details).  That means,
-without an explicit return value policy, lvalue references will be copied and
-pointers will be managed by pybind11.  In order to avoid copying, you should
-explicitly specify an appropriate return value policy, as in the following
-example:
-
-.. code-block:: cpp
-
-    class MyClass {
-        Eigen::MatrixXd big_mat = Eigen::MatrixXd::Zero(10000, 10000);
-    public:
-        Eigen::MatrixXd &getMatrix() { return big_mat; }
-        const Eigen::MatrixXd &viewMatrix() { return big_mat; }
-    };
-
-    // Later, in binding code:
-    py::class_<MyClass>(m, "MyClass")
-        .def(py::init<>())
-        .def("copy_matrix", &MyClass::getMatrix) // Makes a copy!
-        .def("get_matrix", &MyClass::getMatrix, py::return_value_policy::reference_internal)
-        .def("view_matrix", &MyClass::viewMatrix, py::return_value_policy::reference_internal)
-        ;
-
-.. code-block:: python
-
-    a = MyClass()
-    m = a.get_matrix()  # flags.writeable = True,  flags.owndata = False
-    v = a.view_matrix()  # flags.writeable = False, flags.owndata = False
-    c = a.copy_matrix()  # flags.writeable = True,  flags.owndata = True
-    # m[5,6] and v[5,6] refer to the same element, c[5,6] does not.
-
-Note in this example that ``py::return_value_policy::reference_internal`` is
-used to tie the life of the MyClass object to the life of the returned arrays.
-
-You may also return an ``Eigen::Ref``, ``Eigen::Map`` or other map-like Eigen
-object (for example, the return value of ``matrix.block()`` and related
-methods) that map into a dense Eigen type.  When doing so, the default
-behaviour of pybind11 is to simply reference the returned data: you must take
-care to ensure that this data remains valid!  You may ask pybind11 to
-explicitly *copy* such a return value by using the
-``py::return_value_policy::copy`` policy when binding the function.  You may
-also use ``py::return_value_policy::reference_internal`` or a
-``py::keep_alive`` to ensure the data stays valid as long as the returned numpy
-array does.
-
-When returning such a reference of map, pybind11 additionally respects the
-readonly-status of the returned value, marking the numpy array as non-writeable
-if the reference or map was itself read-only.
-
-.. note::
-
-    Sparse types are always copied when returned.
-
-.. _storage_orders:
-
-Storage orders
-==============
-
-Passing arguments via ``Eigen::Ref`` has some limitations that you must be
-aware of in order to effectively pass matrices by reference.  First and
-foremost is that the default ``Eigen::Ref<MatrixType>`` class requires
-contiguous storage along columns (for column-major types, the default in Eigen)
-or rows if ``MatrixType`` is specifically an ``Eigen::RowMajor`` storage type.
-The former, Eigen's default, is incompatible with ``numpy``'s default row-major
-storage, and so you will not be able to pass numpy arrays to Eigen by reference
-without making one of two changes.
-
-(Note that this does not apply to vectors (or column or row matrices): for such
-types the "row-major" and "column-major" distinction is meaningless).
-
-The first approach is to change the use of ``Eigen::Ref<MatrixType>`` to the
-more general ``Eigen::Ref<MatrixType, 0, Eigen::Stride<Eigen::Dynamic,
-Eigen::Dynamic>>`` (or similar type with a fully dynamic stride type in the
-third template argument).  Since this is a rather cumbersome type, pybind11
-provides a ``py::EigenDRef<MatrixType>`` type alias for your convenience (along
-with EigenDMap for the equivalent Map, and EigenDStride for just the stride
-type).
-
-This type allows Eigen to map into any arbitrary storage order.  This is not
-the default in Eigen for performance reasons: contiguous storage allows
-vectorization that cannot be done when storage is not known to be contiguous at
-compile time.  The default ``Eigen::Ref`` stride type allows non-contiguous
-storage along the outer dimension (that is, the rows of a column-major matrix
-or columns of a row-major matrix), but not along the inner dimension.
-
-This type, however, has the added benefit of also being able to map numpy array
-slices.  For example, the following (contrived) example uses Eigen with a numpy
-slice to multiply by 2 all coefficients that are both on even rows (0, 2, 4,
-...) and in columns 2, 5, or 8:
-
-.. code-block:: cpp
-
-    m.def("scale", [](py::EigenDRef<Eigen::MatrixXd> m, double c) { m *= c; });
-
-.. code-block:: python
-
-    # a = np.array(...)
-    scale_by_2(myarray[0::2, 2:9:3])
-
-The second approach to avoid copying is more intrusive: rearranging the
-underlying data types to not run into the non-contiguous storage problem in the
-first place.  In particular, that means using matrices with ``Eigen::RowMajor``
-storage, where appropriate, such as:
-
-.. code-block:: cpp
-
-    using RowMatrixXd = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
-    // Use RowMatrixXd instead of MatrixXd
-
-Now bound functions accepting ``Eigen::Ref<RowMatrixXd>`` arguments will be
-callable with numpy's (default) arrays without involving a copying.
-
-You can, alternatively, change the storage order that numpy arrays use by
-adding the ``order='F'`` option when creating an array:
-
-.. code-block:: python
-
-    myarray = np.array(source, order="F")
-
-Such an object will be passable to a bound function accepting an
-``Eigen::Ref<MatrixXd>`` (or similar column-major Eigen type).
-
-One major caveat with this approach, however, is that it is not entirely as
-easy as simply flipping all Eigen or numpy usage from one to the other: some
-operations may alter the storage order of a numpy array.  For example, ``a2 =
-array.transpose()`` results in ``a2`` being a view of ``array`` that references
-the same data, but in the opposite storage order!
-
-While this approach allows fully optimized vectorized calculations in Eigen, it
-cannot be used with array slices, unlike the first approach.
-
-When *returning* a matrix to Python (either a regular matrix, a reference via
-``Eigen::Ref<>``, or a map/block into a matrix), no special storage
-consideration is required: the created numpy array will have the required
-stride that allows numpy to properly interpret the array, whatever its storage
-order.
-
-Failing rather than copying
-===========================
-
-The default behaviour when binding ``Eigen::Ref<const MatrixType>`` Eigen
-references is to copy matrix values when passed a numpy array that does not
-conform to the element type of ``MatrixType`` or does not have a compatible
-stride layout.  If you want to explicitly avoid copying in such a case, you
-should bind arguments using the ``py::arg().noconvert()`` annotation (as
-described in the :ref:`nonconverting_arguments` documentation).
-
-The following example shows an example of arguments that don't allow data
-copying to take place:
-
-.. code-block:: cpp
-
-    // The method and function to be bound:
-    class MyClass {
-        // ...
-        double some_method(const Eigen::Ref<const MatrixXd> &matrix) { /* ... */ }
-    };
-    float some_function(const Eigen::Ref<const MatrixXf> &big,
-                        const Eigen::Ref<const MatrixXf> &small) {
-        // ...
-    }
-
-    // The associated binding code:
-    using namespace pybind11::literals; // for "arg"_a
-    py::class_<MyClass>(m, "MyClass")
-        // ... other class definitions
-        .def("some_method", &MyClass::some_method, py::arg().noconvert());
-
-    m.def("some_function", &some_function,
-        "big"_a.noconvert(), // <- Don't allow copying for this arg
-        "small"_a            // <- This one can be copied if needed
-    );
-
-With the above binding code, attempting to call the the ``some_method(m)``
-method on a ``MyClass`` object, or attempting to call ``some_function(m, m2)``
-will raise a ``RuntimeError`` rather than making a temporary copy of the array.
-It will, however, allow the ``m2`` argument to be copied into a temporary if
-necessary.
-
-Note that explicitly specifying ``.noconvert()`` is not required for *mutable*
-Eigen references (e.g. ``Eigen::Ref<MatrixXd>`` without ``const`` on the
-``MatrixXd``): mutable references will never be called with a temporary copy.
-
-Vectors versus column/row matrices
-==================================
-
-Eigen and numpy have fundamentally different notions of a vector.  In Eigen, a
-vector is simply a matrix with the number of columns or rows set to 1 at
-compile time (for a column vector or row vector, respectively).  NumPy, in
-contrast, has comparable 2-dimensional 1xN and Nx1 arrays, but *also* has
-1-dimensional arrays of size N.
-
-When passing a 2-dimensional 1xN or Nx1 array to Eigen, the Eigen type must
-have matching dimensions: That is, you cannot pass a 2-dimensional Nx1 numpy
-array to an Eigen value expecting a row vector, or a 1xN numpy array as a
-column vector argument.
-
-On the other hand, pybind11 allows you to pass 1-dimensional arrays of length N
-as Eigen parameters.  If the Eigen type can hold a column vector of length N it
-will be passed as such a column vector.  If not, but the Eigen type constraints
-will accept a row vector, it will be passed as a row vector.  (The column
-vector takes precedence when both are supported, for example, when passing a
-1D numpy array to a MatrixXd argument).  Note that the type need not be
-explicitly a vector: it is permitted to pass a 1D numpy array of size 5 to an
-Eigen ``Matrix<double, Dynamic, 5>``: you would end up with a 1x5 Eigen matrix.
-Passing the same to an ``Eigen::MatrixXd`` would result in a 5x1 Eigen matrix.
-
-When returning an Eigen vector to numpy, the conversion is ambiguous: a row
-vector of length 4 could be returned as either a 1D array of length 4, or as a
-2D array of size 1x4.  When encountering such a situation, pybind11 compromises
-by considering the returned Eigen type: if it is a compile-time vector--that
-is, the type has either the number of rows or columns set to 1 at compile
-time--pybind11 converts to a 1D numpy array when returning the value.  For
-instances that are a vector only at run-time (e.g. ``MatrixXd``,
-``Matrix<float, Dynamic, 4>``), pybind11 returns the vector as a 2D array to
-numpy.  If this isn't want you want, you can use ``array.reshape(...)`` to get
-a view of the same data in the desired dimensions.
-
-.. seealso::
-
-    The file :file:`tests/test_eigen.cpp` contains a complete example that
-    shows how to pass Eigen sparse and dense data types in more detail.

libs/pybind/docs/advanced/cast/functional.rst

@@ -1,109 +0,0 @@
-Functional
-##########
-
-The following features must be enabled by including :file:`pybind11/functional.h`.
-
-
-Callbacks and passing anonymous functions
-=========================================
-
-The C++11 standard brought lambda functions and the generic polymorphic
-function wrapper ``std::function<>`` to the C++ programming language, which
-enable powerful new ways of working with functions. Lambda functions come in
-two flavors: stateless lambda function resemble classic function pointers that
-link to an anonymous piece of code, while stateful lambda functions
-additionally depend on captured variables that are stored in an anonymous
-*lambda closure object*.
-
-Here is a simple example of a C++ function that takes an arbitrary function
-(stateful or stateless) with signature ``int -> int`` as an argument and runs
-it with the value 10.
-
-.. code-block:: cpp
-
-    int func_arg(const std::function<int(int)> &f) {
-        return f(10);
-    }
-
-The example below is more involved: it takes a function of signature ``int -> int``
-and returns another function of the same kind. The return value is a stateful
-lambda function, which stores the value ``f`` in the capture object and adds 1 to
-its return value upon execution.
-
-.. code-block:: cpp
-
-    std::function<int(int)> func_ret(const std::function<int(int)> &f) {
-        return [f](int i) {
-            return f(i) + 1;
-        };
-    }
-
-This example demonstrates using python named parameters in C++ callbacks which
-requires using ``py::cpp_function`` as a wrapper. Usage is similar to defining
-methods of classes:
-
-.. code-block:: cpp
-
-    py::cpp_function func_cpp() {
-        return py::cpp_function([](int i) { return i+1; },
-           py::arg("number"));
-    }
-
-After including the extra header file :file:`pybind11/functional.h`, it is almost
-trivial to generate binding code for all of these functions.
-
-.. code-block:: cpp
-
-    #include <pybind11/functional.h>
-
-    PYBIND11_MODULE(example, m) {
-        m.def("func_arg", &func_arg);
-        m.def("func_ret", &func_ret);
-        m.def("func_cpp", &func_cpp);
-    }
-
-The following interactive session shows how to call them from Python.
-
-.. code-block:: pycon
-
-    $ python
-    >>> import example
-    >>> def square(i):
-    ...     return i * i
-    ...
-    >>> example.func_arg(square)
-    100L
-    >>> square_plus_1 = example.func_ret(square)
-    >>> square_plus_1(4)
-    17L
-    >>> plus_1 = func_cpp()
-    >>> plus_1(number=43)
-    44L
-
-.. warning::
-
-    Keep in mind that passing a function from C++ to Python (or vice versa)
-    will instantiate a piece of wrapper code that translates function
-    invocations between the two languages. Naturally, this translation
-    increases the computational cost of each function call somewhat. A
-    problematic situation can arise when a function is copied back and forth
-    between Python and C++ many times in a row, in which case the underlying
-    wrappers will accumulate correspondingly. The resulting long sequence of
-    C++ -> Python -> C++ -> ... roundtrips can significantly decrease
-    performance.
-
-    There is one exception: pybind11 detects case where a stateless function
-    (i.e. a function pointer or a lambda function without captured variables)
-    is passed as an argument to another C++ function exposed in Python. In this
-    case, there is no overhead. Pybind11 will extract the underlying C++
-    function pointer from the wrapped function to sidestep a potential C++ ->
-    Python -> C++ roundtrip. This is demonstrated in :file:`tests/test_callbacks.cpp`.
-
-.. note::
-
-    This functionality is very useful when generating bindings for callbacks in
-    C++ libraries (e.g. GUI libraries, asynchronous networking libraries, etc.).
-
-    The file :file:`tests/test_callbacks.cpp` contains a complete example
-    that demonstrates how to work with callbacks and anonymous functions in
-    more detail.