Merge branch 'main-rc' into b5.0.0

Callbacksafe

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,42 @@
+---
+name: Bug Report
+about: Create a report to help us improve 
+title: New Bug Report
+labels: action - Bug, priority - Unclassified, status - Pending
+template: bug_report.md
+---
+<!-- Preview changes before submitting -->
+<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
+<!-- This is a comment, the syntax is a bit different from c++ or bash -->
+
+##### *Distribution: 
+<!-- RHEL7, RHEL6, Fedora, etc -->
+
+
+##### *Detector type: 
+<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
+
+##### *Software Package Version: 
+<!-- developer, 4.2.0, 4.1.1, etc -->
+
+##### Priority:
+<!-- Super Low, Low, Medium, High, Super High -->
+
+##### *Describe the bug
+<!--  A clear and concise description of what the bug is -->
+
+##### Expected behavior
+<!--  A clear and concise description of what you expected to happen. -->
+
+##### To Reproduce
+<!--  Steps to reproduce the behavior: -->
+<!--  1. Go to '...' -->
+<!--  2. Click on '....' -->
+<!--  3. Scroll down to '....' -->
+<!--  4. See error -->
+
+##### Screenshots
+<!--  If applicable, add screenshots to help explain your problem. -->
+
+##### Additional context
+<!--  Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/change_request.md

@@ -0,0 +1,28 @@
+---
+name: Change Request
+about: Suggest a change to an existing feature
+title: New Change Request
+labels: action - Change, priority - Unclassified, status - Pending
+template: change_request.md
+---
+<!-- Preview changes before submitting -->
+<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
+<!-- This is a comment, the syntax is a bit different from c++ or bash -->
+
+##### *Detector type: 
+<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
+
+##### *Software Package Version: 
+<!-- developer, 4.2.0, 4.1.1, etc -->
+
+##### Priority:
+<!-- Super Low, Low, Medium, High, Super High -->
+
+##### *State the change request:
+<!--  A clear and concise description of what the change is to an existing feature -->
+
+##### Is your change request related to a problem. Please describe:
+<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
+
+##### Additional context:
+<!--  Add any other context about the feature here -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,34 @@
+---
+name: Feature Request
+about: Suggest a feature, documentation or submit a question
+title: New Feature Request
+labels: action - Enhancement, priority - Unclassified, status - Pending
+template: feature_request.md
+---
+<!-- Preview changes before submitting -->
+<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
+<!-- This is a comment, the syntax is a bit different from c++ or bash -->
+
+##### *Detector type: 
+<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
+
+##### *Software Package Version: 
+<!-- developer, 4.2.0, 4.1.1, etc -->
+
+##### Priority:
+<!-- Super Low, Low, Medium, High, Super High -->
+
+##### *State the feature:
+<!--  A clear and concise description of what the feature is -->
+
+##### Is your feature request related to a problem. Please describe:
+<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
+
+##### Describe the solution you'd like:
+<!-- A clear and concise description of what you want to happen -->
+
+##### Describe alternatives you've considered:
+<!-- A clear and concise description of any alternative solutions or features you've considered -->
+
+##### Additional context:
+<!--  Add any other context about the feature here -->

.travis.yml

@@ -31,7 +31,7 @@ script:
 
 deploy:
   provider: script
-  script: find $HOME/miniconda/envs/testenv/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  script: find $HOME/miniconda/envs/testenv/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -v --show-traceback -t $CONDA_TOKEN upload --force {} \;
   on:
     branch: developer
     tags: true

CMakeLists.txt

@@ -49,7 +49,7 @@ option(SLS_DEVEL_HEADERS "install headers for devel" OFF)
 option(SLS_USE_MOENCH "compile zmq and post processing for Moench" OFF)
 
 # set(ClangFormat_BIN_NAME clang-format)
-set(ClangFormat_EXCLUDE_PATTERNS  "build/" 
+set(ClangFormat_EXCLUDE_PATTERNS    "build/" 
                                     "libs/" 
                                     "slsDetectorCalibration/" 
                                     "ctbGui/" 
@@ -61,19 +61,9 @@ find_package(ClangFormat)
 
 #Enable LTO if available
 check_ipo_supported(RESULT SLS_LTO_AVAILABLE)
+message(STATUS "SLS_LTO_AVAILABLE:" ${SLS_LTO_AVAILABLE})
 
 
-# Use ld.gold if it is available and isn't disabled explicitly
-option(SLS_USE_LD_GOLD "Use GNU gold linker" ON)
-if (SLS_USE_LD_GOLD)
-    execute_process(COMMAND ${CMAKE_C_COMPILER} -fuse-ld=gold -Wl,--version ERROR_QUIET OUTPUT_VARIABLE LD_VERSION)
-    if ("${LD_VERSION}" MATCHES "GNU gold")
-        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fuse-ld=gold")
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fuse-ld=gold")
-    else ()
-        message(WARNING "GNU gold linker isn't available, using the default system linker.")
-    endif ()
-endif ()
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
@@ -97,6 +87,7 @@ target_compile_options(slsProjectWarnings INTERFACE
                                             -Wformat=2
                                             -Wredundant-decls
                                             # -Wconversion
+                                            -Wvla
                                             -Wdouble-promotion
                                             -Werror=return-type
 
@@ -184,20 +175,12 @@ if (SLS_USE_TEXTCLIENT)
     add_subdirectory(slsDetectorSoftware)
 endif (SLS_USE_TEXTCLIENT)
 
-
 if (SLS_USE_RECEIVER)
-    if (SLS_USE_HDF5)
-        find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
-    endif (SLS_USE_HDF5)
     add_subdirectory(slsReceiverSoftware) 
 endif (SLS_USE_RECEIVER)
 
 if (SLS_USE_GUI)   
-    find_package(Qt4 REQUIRED)
-    find_package(Qwt 6.1 REQUIRED)
-    if (QT4_FOUND AND QWT_FOUND)
-        add_subdirectory(slsDetectorGui)
-    endif()
+    add_subdirectory(slsDetectorGui)
 endif (SLS_USE_GUI)
 
 if (SLS_USE_SIMULATOR)
@@ -239,7 +222,7 @@ 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 slsSupportLib slsDetectorShared slsReceiverShared)
+    set(PROJECT_LIBRARIES slsSupportShared slsDetectorShared slsReceiverShared)
     # Generate and install package config file and version
     include(cmake/package_config.cmake)
 endif()

README.md

@@ -1,5 +1,10 @@
+### Note
+
+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.
+
 ### Documentation
-Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
+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. 
@@ -7,6 +12,7 @@ Binaries for the slsDetectorPackage are available through conda.
 #Add conda channels
 conda config --add channels conda-forge
 conda config --add channels slsdetectorgroup
+conda config --set channel_priority strict
 
 conda install slsdetlib   #only shared lib and command line
 conda install slsdet      #python bindings (includes slsdetlib)
@@ -24,10 +30,8 @@ git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Dependencies 
-* Lib: c++11 compiler (gcc=>4.8), ZeroMQ 4
-* Gui: Qt 4.8 and Qwt 6.0
-* Calibration wizards and ctbGUI: ROOT
-* Optional: HDF5
+
+Refer [this page](https://slsdetectorgroup.github.io/devdoc/dependencies.html)  for dependencies.
 
 
 #### Compilation 
@@ -37,27 +41,38 @@ cmk.sh or directly with cmake for more control.
 
 **1. Compile using script cmk.sh**<br>
 
-After compiling, the libraries and executables will be found in `slsDetectorPackage/build/bin` directory<br>
+These are mainly aimed at those not familiar with using ccmake and cmake. 
+```
+    The binaries are generated in slsDetectorPackage/build/bin directory.
 
-Usage: [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [-h] [-d <HDF5 directory>] [-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
- -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
-  
-eg. Rebuild when you switch to a new build and compile in parallel:
-./cmk.sh -bj5
+    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
+```
+ 
 **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.
 ```
@@ -66,3 +81,12 @@ Use cmake to create out-of-source builds, by creating a build folder parallel to
     $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON
     $ make -j12 #or whatever number of threads wanted
 ```
+
+To install binaries using CMake
+```
+    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
+```

RELEASE.txt

@@ -1,2 +1,390 @@
-Draft
-- dr 4, 8, 16 in eiger -> speed 0, 32 stays same (speed 1)
+SLS Detector Package 5.0.0 released on 18.11.2020 (Major Release)
+=================================================================
+
+    CONTENTS
+    --------
+    1.	Topics Concerning
+    2.  New Features
+    3.  Resolved Issues
+    4.  Known Issues
+    5.  Firmware Requirements
+    6.  Download, Documentation & Support
+
+
+
+1. Topics Concerning
+====================
+
+    - Compilation requirements
+    - Manuals
+    - Client API complete change
+    - Exceptions
+    - Scan mode (dacs and trimbit)
+    - Timing commands
+    - Enum list (daclist, dacvalues, settingslist, drlist etc.)
+    - Command line (return code)
+    - Command line (dac)
+    - UDP configuration change
+    - Gappixels
+    - Detector Simulators
+    - (Jungfrau server) settings and default dacs
+    - (Servers) Shared Memory
+    - (Jungfrau) two interfaces
+    - (Eiger, Jungfrau server) starting frame number
+    - (Eiger server) Server Config File
+    - (Eiger server) Partial Readout
+    - (Eiger server) Removed Features
+    - (Eiger server) Deactivation
+    - Zmq interface (ZmqSocket.h)
+    - slsReceiver (Metadata)
+    - slsReceiver (Shared Memory)
+    - slsReceiver (UDP IP)
+    - (Eiger Custom Receiver) Header packet
+    - Gui (zmq high water mark)
+    - (Eiger Server) Blocked server
+    - (Eiger Firmware) Extra 8 byte Packets
+ 
+
+
+2. New Features
+===============
+
+    Client
+    ------
+    1.  Compilation requirements
+        They are very different now and can be accessed at
+            https://slsdetectorgroup.github.io/devdoc/dependencies.html
+        Gui not included in default cmk.sh script. Must be explicitly asked for.
+
+    2.  Manuals 
+        They can be compiled in the package. 
+            https://slsdetectorgroup.github.io/devdoc/installation.html#build-this-documentation
+        Or refer to the documentation provided in 
+            https://slsdetectorgroup.github.io/devdoc/index.html
+
+    3.  API
+        Changed to Detector class. 
+        C++: Detector.h
+            Documentation:
+                https://slsdetectorgroup.github.io/devdoc/detector.html
+            Examples to use the Detector class:
+                https://github.com/slsdetectorgroup/api-examples
+
+        Python API Documentation: 
+            https://slsdetectorgroup.github.io/devdoc/pydetector.html
+
+        Command line:
+            Many commands have become deprecated. They will still execute, 
+            but give a warning.
+            Documentation:
+                https://slsdetectorgroup.github.io/devdoc/commandline.html
+            Help on a command:
+                sls_detector_help [command], or
+                sls_detector_get -h [command]
+    
+    4.  Exceptions
+        They are thrown instead of providing error codes.
+            sls_detector_exceptions.h
+        Make sure you catch all exceptions in custom gui and handle them or 
+        inform the user.
+        Exceptions thrown in callbacks are also handled.
+            - An exception in startAcquisitionCallBack will need to be handled in 
+            startReceiver or acquire()
+            - An exception in acquisitionFinishedCallBack will need to be handled in
+            stopReceiver or acquire()
+            - An exception in rawDataReadyCallBack or rawDataModifyReadyCallBack
+            will only print and skip image to free it in memory. If address is
+            incorrect after callback, expect undefined behavior.
+
+    5.  Scan mode
+        One can do scans for dacs or trimbits. Trimbits are only for Eiger or 
+        Mythen3. Enable scan mode and then acquire using blocking or non blocking
+        method. Command: scan.
+
+    6.  Timing Commands
+        In command line, all timing commands (eg. peiod) can now specify unit. 
+            eg 100ms 10us, 1s, 100ns
+        In C++ API, one must use chrono library.
+            eg. std::chrono::duration<double, std::milli> t1{232.57};
+                det.setExptime(std::chrono::duration_cast<std::chrono::nanoseconds>(t1));
+        In Python API, one must use timedelta library. 
+            eg. d.exptime = dt.timedelta(seconds = 1.2)
+
+    7.  Enum list (daclist)
+        Command line and API now has features to get the list of enums/commands
+        for dacs, settings, dynamic range, timing modes and temperatures for 
+        the detector in shared memory. 
+            eg. daclist, settingslist, drlist, timinglist, templist
+        Command line also has commands to get their values.
+            eg. dacvalues, tempvalues
+        Python has commands to get their values (detector specific class).
+            eg. d.temp, d.dacs
+
+    8.  Command Line (return code)
+        Return code of the client command line applications now return 0 for 
+        success and 1 for failure.
+        
+    9.  Command Line (Dac)
+        All dac commands have been converted to a single "dac" command with 
+        the previous dac commands as arguments.
+            eg. sls_detector_get vcmp_ll
+            is now
+            sls_detector_get dac vcmp_ll
+    
+    10. UDP Configuration
+        Once all the udp details are set in the detector, the detector's
+        destination is then configured automatically. If the detector is not 
+        configured, it will  fail when acquiring. If any of these parameters
+        are also changed, then this is configured again. Hence, configuremac 
+        command has been removed. Instead, there are commands such as
+        udp_validate (to validate if it has been configured) and
+        udp_reconfigure (to reconfigure).
+
+    11. Gap Pixels
+        Gap pixels are now only available in client call back or gui (not in 
+        receiver anymore). It can be enabled for Eiger and Jungfrau and 
+        includes inter chip and inter module gap pixels.
+
+    Detector Servers
+    ----------------
+
+    1.  Detector Simulators 
+        Or virtual detector servers for every detector have been provided. 
+        They are compiled along with the client by enabling its option. 
+        They should also send fake data (increasing pixel/channel value).  
+
+    2.  (Jungfrau) settings
+        Settings command do not implicitly set default dacs from now on.
+        One can use the command 'defaultdacs' to set them explicitly.
+
+    3.  Shared Memory
+        Almost all the detector parameters removed from shared memory.
+        Therefore, they are all fetched directly from detector.
+
+    4.  (Jungfrau) Two 10G data interfaces
+        Only Jungfrau PCBs with version 2.0 can run at full speed using both
+        the 10G UDP interfaces to stream out data. This is available from 
+        the current firmware and software. To enable two interfaces, one has 
+        to enable two interfaces using "numinterfaces" to 2 and set corresponding
+        udp_dstip2, udp_dstport2 etc. One can also decide to select which of 
+        the two interfaces to use, when using only 1 interface.
+
+    5.  (Eiger, Jungfrau) Next Frame number
+        Both now have running frame numbers that is only reset at boot up
+        and increments continuously through acquisitions. One is able to 
+        set the next frame number now. Command: nextframenumber.
+
+    6.  (Eiger) Server Config file (config_eiger.txt)
+        A config file on the detector can take in 2 parameters "master" 
+        and "top" being set to 1 or 0 to enable or disable the same.
+        When server is started without this file, it is set to hardware
+        settings.
+
+    7.  (Eiger) Partial readout
+        It is possible for partial readouts, where you specify the number
+        of pixel rows to read out. Not all values are allowed. The current
+        slsReceiver does not complain about missing packets, but only puts 
+        this partial image into the complete image (padding the rest). One
+        can cut out required subimage using callbacks, but this feature
+        is probably more useful for custom receivers. Command: readnlines.
+
+    8.  (Eiger) Removed Features
+        storeinram, safe speed and ability to set settings via the settings 
+        command has been removed.
+
+    9.  (Eiger) Deactivation
+        The detector is deactivated by default upon boot up and activated only 
+        upon setting hostname in the client. This is to ensure if the 
+        network of a board or a board is broken and one cannot connect
+        to this board, then it is deactivated by default upon reboot. 
+        Therefore, one can use other half modules of the detector.
+
+    Receiver
+    --------
+
+    1.  Zmq
+        The static library and the zmq.h is no longer provided with package.
+        One must install ZeroMQ version 4.
+        ZmqSocket.h API has changed, especially in parsing receiving JSON header.
+        One must pick up needed parameters  from exposed struct zmqHeader in 
+        ZmqSocket.h.
+
+    2.  Metadata
+        Detector dependant metadata has been added to the master files.
+
+    3.  Shared Memory
+        Almost all receiver parameters have been removed from client shared memory.
+        Therefore the receiver process needs to be alive to access any receiver
+        parameter as they are now fetched directly from the receiver.
+
+    4.  UDP IP
+        Since all the parameters are fetched from receiver or detector directly 
+        (not shared memory), the udp desintation ip (previously rx_udpip) is safer 
+        to be specified before setting rx_hostname. Setting it before has the
+        advantage that the detector is updated first before the receiver is
+        requested for the udp mac. This helps when changing pc and the receiver
+        cannot find the udp ip to get the udp mac.
+
+    5.  (Eiger) Header packet
+        The header packets of Eiger are not sent in this firmware version. So, 
+        custom receivers should handle accordingly.
+
+    Gui
+    ---
+    
+    1.  Zmq high water mark
+        When opening the Gui, the zmq send and receiver high water mark is set to 2
+        instead of default (1000 for zmq library version 4). This is to ensure
+        fast and large detectors can still see latest data on the gui at the cost of
+        losing images in between.
+        When using a different processor or client data call back to handle zmq data, 
+        please ensure this is set back to default to get every zmq packet. Setting it to 
+        -1 sets it to library defaults.
+
+    
+    
+
+3. Resolved Issues
+==================
+
+    Detector Server
+    ---------------
+
+    1.  (Eiger) Blocked Server
+        Very rarely, Eiger control or stop server would block and would require a restart
+        of server. This is due to both servers accessing the same link to get to FEB
+        registers. Locking has been implemented in server shared memory to resolve.
+
+
+
+4. Known Issues
+===============
+
+    1.  (Eiger) Extra 8 byte Packets
+        When stopping detector acquisition while acquiring for more than 128 frames,
+        the next acquisition sends out first an 8 byte packet. This is discarded
+        by the slsReceiver/slsMultiReceiver. Please handle this in custom receivers.
+
+
+
+5. Firmware Requirements
+========================
+        
+        Eiger
+        =====  
+        Compatible version : 08.09.2020 (v27)
+        
+        Jungfrau
+        ========       
+        Compatible version : 24.07.2020 (v1.1, PCB v1.0) 
+                           : 21.07.2020 (v2.1, PCB v2.0)
+
+        Gotthard
+        ========   
+        Compatible version : 08.02.2018 (50um and 25um Master)
+                           : 09.02.2018 (25 um Slave) 
+
+        Mythen3
+        =======
+        Compatible version : 25.09.2020 (development)
+
+        Gotthard2
+        =========
+        Compatible version : 25.09.2020 (development)
+
+        Moench
+        ======
+        Compatible version : 05.10.2020 (v1.0)
+
+        Ctb
+        ===
+        Compatible version : 05.10.2020 (v1.0)
+
+        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>
+
+        The following cannot be upgraded remotely:
+        Gotthard   
+
+        Instructions available at
+            https://slsdetectorgroup.github.io/devdoc/firmware.html
+        and
+            https://slsdetectorgroup.github.io/devdoc/serverupgrade.html
+
+    
+6. Download, Documentation & Support
+====================================
+
+    Download
+    --------
+    
+    The Source Code:
+         https://github.com/slsdetectorgroup/slsDetectorPackage
+            
+    Documentation
+    -------------
+    
+    Installation:
+        https://slsdetectorgroup.github.io/devdoc/installation.html#
+        
+    Firmware Upgrade:
+        https://slsdetectorgroup.github.io/devdoc/firmware.html
+
+    Detector Server upgrade:
+        https://slsdetectorgroup.github.io/devdoc/serverupgrade.html
+
+    Detector Simulators:
+        https://slsdetectorgroup.github.io/devdoc/virtualserver.html
+
+    Consuming slsDetectorPackage:
+        https://slsdetectorgroup.github.io/devdoc/consuming.html
+        
+    API Examples:
+        https://github.com/slsdetectorgroup/api-examples
+
+    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
+       
+    C++ API Example:
+        https://slsdetectorgroup.github.io/devdoc/examples.html#
+        
+    Python API Documentation:
+        https://slsdetectorgroup.github.io/devdoc/pygettingstarted.html
+
+    Python API Example:
+        https://slsdetectorgroup.github.io/devdoc/pyexamples.html
+
+    Receivers (including custom receiver):
+        https://slsdetectorgroup.github.io/devdoc/receivers.html
+        https://slsdetectorgroup.github.io/devdoc/slsreceiver.html
+
+    TroubleShooting:
+        https://slsdetectorgroup.github.io/devdoc/troubleshooting.html
+        
+    Further Documentation:
+        https://www.psi.ch/en/detectors/documentation
+        
+    Info on Releases:
+        https://www.psi.ch/en/detectors/software
+
+
+    Support
+    -------
+
+        dhanya.thattil@psi.ch
+        erik.frojdh@psi.ch
+

cmake/FindSphinx.cmake

@@ -1,6 +1,6 @@
 #Look for an executable called sphinx-build
 find_program(SPHINX_EXECUTABLE
-             NAMES sphinx-build
+             NAMES sphinx-build sphinx-build-3.6
              DOC "Path to sphinx-build executable")
  
 include(FindPackageHandleStandardArgs)

cmk.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
+CMAKE="cmake3"
 BUILDDIR="build"
+INSTALLDIR=""
 HDF5DIR="/opt/hdf5v1.10.0"
 HDF5=0
 COMPILERTHREADS=0
@@ -12,6 +14,7 @@ TESTS=0
 SIMULATOR=0
 CTBGUI=0
 MANUALS=0
+MANUALS_ONLY_RST=0
 MOENCHZMQ=0
 
 
@@ -21,13 +24,15 @@ CMAKE_PRE=""
 CMAKE_POST=""
 
 usage() { echo -e "
-Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [-h] [z] [-d <HDF5 directory>] [-j] <Number of threads>
+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
@@ -37,6 +42,7 @@ Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [-h] [z] [-d <HDF5 dire
  -e: Debug mode
  -i: Builds tests
  -m: Manuals
+ -n: Manuals without compiling doxygen (only rst)
  -z: Moench zmq processor
 
 Rebuild when you switch to a new build and compile in parallel:
@@ -73,7 +79,7 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bpchd:j:trgeisumz" opt ; do
+while getopts ":bpchd:k:l:j:trgeisumnz" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -97,6 +103,14 @@ while getopts ":bpchd:j:trgeisumz" opt ; do
 		echo "New HDF5 directory: $OPTARG" 
 		HDF5DIR=$OPTARG
 		;;
+	l)
+		echo "CMake install directory: $OPTARG"
+		INSTALLDIR="$OPTARG"
+		;;
+	k)
+		echo "CMake command: $OPTARG"
+		CMAKE="$OPTARG"
+		;;
 	j) 
 		echo "Number of compiler threads: $OPTARG" 
 		COMPILERTHREADS=$OPTARG
@@ -132,6 +146,10 @@ while getopts ":bpchd:j:trgeisumz" opt ; do
 		echo "Compiling Manuals"
 		MANUALS=1
 		;;
+	n)	
+		echo "Compiling Manuals (Only RST)"
+		MANUALS_ONLY_RST=1
+		;;
 	z)	
 		echo "Compiling Moench Zmq Processor"
 		MOENCHZMQ=1
@@ -246,7 +264,15 @@ else
 fi
 
 
+#install
+if [ -n "$INSTALLDIR" ]; then
+	CMAKE_POST+=" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR"
+	CMAKE_POST+=" -DCMAKE_FIND_ROOT_PATH=$INSTALLDIR"
+fi
+
+
 #enter build dir
+#pushd $BUILDDIR;
 cd $BUILDDIR;
 echo "in "$PWD
 
@@ -255,7 +281,7 @@ echo "in "$PWD
 #cmake
 if [ $REBUILD -eq 1 ]; then
 	rm -f CMakeCache.txt
-	BUILDCOMMAND="$CMAKE_PRE cmake3 $CMAKE_POST .."
+	BUILDCOMMAND="$CMAKE_PRE $CMAKE $CMAKE_POST .."
 	echo $BUILDCOMMAND
 	eval $BUILDCOMMAND
 fi
@@ -268,25 +294,45 @@ fi
 
 #make
 if [ $COMPILERTHREADS -gt 0 ]; then
-	BUILDCOMMAND="make -j$COMPILERTHREADS"
-	echo $BUILDCOMMAND
-	eval $BUILDCOMMAND
-	if [ $MANUALS -eq 1 ]; then
-		BUILDCOMMAND="make docs -j$COMPILERTHREADS"
+	if [ $MANUALS -eq 0 ] && [ $MANUALS_ONLY_RST -eq 0 ]; then
+		BUILDCOMMAND="make -j$COMPILERTHREADS"
 		echo $BUILDCOMMAND
 		eval $BUILDCOMMAND
+	else
+		if [ $MANUALS -eq 1 ]; then
+			BUILDCOMMAND="make docs -j$COMPILERTHREADS"
+			echo $BUILDCOMMAND
+			eval $BUILDCOMMAND
+		else
+			BUILDCOMMAND="make rst -j$COMPILERTHREADS"
+			echo $BUILDCOMMAND
+			eval $BUILDCOMMAND		
+		fi
 	fi 
 else
-	echo "make"
-	make
-	if [ $MANUALS -eq 1 ]; then
-		echo "make docs"
-		make docs
+	if [ $MANUALS -eq 0 ] && [ $MANUALS_ONLY_RST -eq 0 ]; then
+		echo "make"
+		make
+	else
+		if [ $MANUALS -eq 1 ]; then
+			echo "make docs"
+			make docs
+		else
+			echo "make rst"
+			make rst
+		fi
 	fi 
 fi
 
 
+#install
+if [ -n "$INSTALLDIR" ]; then
+	make install
+#	popd
+#	$CMAKE --build $BUILDDIR --target install
+fi
+
+
 
 
 
-

conda-recepie/conda_build_config.yaml

@@ -2,6 +2,7 @@ python:
     - 3.6
     - 3.7
     - 3.8
+    - 3.9
     
 numpy: 
     - 1.17

conda-recepie/copy_lib.sh

@@ -1,14 +1,10 @@
 
 mkdir $PREFIX/lib
 mkdir $PREFIX/bin
-mkdir $PREFIX/include
-mkdir $PREFIX/include/slsDetectorPackage
+mkdir -p $PREFIX/include/sls
+# mkdir $PREFIX/include/slsDetectorPackage
 
 #Shared and static libraries
-# cp build/bin/libSlsDetector.so $PREFIX/lib/.
-# cp build/bin/libSlsReceiver.so $PREFIX/lib/.
-# cp build/bin/libSlsSupport.so $PREFIX/lib/.
-
 cp build/install/lib/* $PREFIX/lib/
 
 #Binaries
@@ -20,5 +16,5 @@ cp build/install/bin/slsReceiver $PREFIX/bin/.
 cp build/install/bin/slsMultiReceiver $PREFIX/bin/.
 
 
-cp build/install/include/* $PREFIX/include/
+cp build/install/include/sls/* $PREFIX/include/sls
 cp -r build/install/share/ $PREFIX/share

conda-recepie/meta.yaml

@@ -33,6 +33,7 @@ requirements:
     - {{ cdt('libselinux') }}            # [linux]
     - {{ cdt('libxdamage') }}            # [linux]
     - {{ cdt('libxxf86vm') }}            # [linux]
+    - expat
 
   host:
     - libstdcxx-ng
@@ -45,6 +46,7 @@ requirements:
     - xorg-libxau
     - xorg-libxrender
     - xorg-libxfixes
+    - expat
 
   run:
     - zeromq
@@ -96,3 +98,4 @@ outputs:
         - {{ pin_subpackage('slsdetlib', exact=True) }}
         - qwt 6.*
         - qt 4.8.*
+        - expat

ctbGui/CMakeLists.txt

@@ -59,14 +59,13 @@ set( HEADERS
 #set(ROOT_INCLUDE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
 
 # ROOT dictionary generation 
-include("${ROOT_DIR}/modules/RootNewMacros.cmake")
+include("${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})
 target_link_libraries(ctbRootLib PUBLIC 
     ROOT::Core 
     slsDetectorShared
-    slsSupportLib
     ${ROOT_LIBRARIES} 
     ${ROOT_EXE_LINKER_FLAGS}
 )
@@ -78,7 +77,6 @@ set_target_properties(
 
 target_link_libraries(ctbGui PUBLIC 
     slsDetectorShared
-    slsSupportLib
     ctbRootLib
     ${TIFF_LIBRARIES}
 )

ctbGui/ctbAcquisition.cpp

@@ -16,6 +16,7 @@
 #include <TColor.h>
 #include <TTimer.h>
 #include <TH2F.h>
+#include <TSystem.h>
 
 
 #include <stdio.h>
@@ -25,8 +26,8 @@
 
 #include "ctbAcquisition.h"
 #include "ctbDefs.h"
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 #include "ctbMain.h"
 #include "moench03CtbData.h" 
 //#include "moench03TCtbData.h" 
@@ -43,7 +44,7 @@
 #include "moench04CtbZmqData.h"
 #include "moench04CtbZmq10GbData.h"
 #include "deserializer.h"
-#include "detectorData.h"
+#include "sls/detectorData.h"
 #include "imageZmq16bit.h"
 #include "imageZmq32bit.h"
 

ctbGui/ctbAdcs.cpp

@@ -25,7 +25,7 @@
 
 #include "ctbAdcs.h"
 #include "ctbDefs.h"
-#include "Detector.h"
+#include "sls/Detector.h"
 
 using namespace std;
 

ctbGui/ctbDacs.cpp

@@ -10,8 +10,8 @@
 
 #include "ctbDacs.h"
 #include "ctbDefs.h"
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 
 using namespace std;
 

ctbGui/ctbDefs.h

@@ -4,8 +4,8 @@
 #include <stdexcept>
 #include <chrono>
 
-//#include "sls_detector_exceptions.h"
-//#include "ansi.h"
+//#include "sls/sls_detector_exceptions.h"
+//#include "sls/ansi.h"
 #define RED    	 	"\x1b[31m"
 #define RESET   	"\x1b[0m"
 #define BOLD    	"\x1b[1m"

ctbGui/ctbGui.cpp

@@ -9,8 +9,8 @@
 #include <fstream>
 #include <string>
 
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 //#include "sls_receiver_defs.h"
 #include "ctbMain.h"
 #include "ctbDefs.h"

ctbGui/ctbMain.cpp

@@ -34,7 +34,7 @@
 #include <fstream>
 #include <string>
 
-#include "Detector.h"
+#include "sls/Detector.h"
 #include "ctbDefs.h"
 #include "ctbMain.h"
 #include "ctbDacs.h"

ctbGui/ctbPattern.cpp

@@ -25,7 +25,7 @@
 
 #include "ctbPattern.h"
 #include "ctbDefs.h"
-#include "Detector.h"
+#include "sls/Detector.h"
 #include <chrono>
 using namespace std;
 

ctbGui/ctbPowers.cpp

@@ -13,8 +13,8 @@
 #include "ctbDefs.h"
 #include "ctbDacs.h"
 #include "ctbPowers.h"
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 
 using namespace std;
 

ctbGui/ctbSignals.cpp

@@ -35,7 +35,7 @@
 
 #include "ctbSignals.h"
 #include "ctbDefs.h"
-#include "Detector.h"
+#include "sls/Detector.h"
 
 using namespace std;
 

ctbGui/ctbSlowAdcs.cpp

@@ -10,8 +10,8 @@
 
 #include "ctbSlowAdcs.h"
 #include "ctbDefs.h"
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 
 using namespace std;
 

docs/CMakeLists.txt

@@ -38,12 +38,21 @@ set(SPHINX_SOURCE_FILES
   src/pydetector.rst
   src/pyenums.rst
   src/pyexamples.rst
-  src/receiver.rst
+  src/servers.rst
+  src/receiver_api.rst
   src/result.rst
   src/type_traits.rst
   src/ToString.rst
   src/examples.rst
-  
+  src/pygettingstarted.rst
+  src/firmware.rst
+  src/serverupgrade.rst
+  src/virtualserver.rst
+  src/serverdefaults.rst
+  src/quick_start_guide.rst
+  src/troubleshooting.rst
+  src/receivers.rst
+  src/slsreceiver.rst
 )
 
 foreach(filename ${SPHINX_SOURCE_FILES})
@@ -56,8 +65,21 @@ configure_file(
   "${SPHINX_BUILD}/conf.py"
   @ONLY)
 
+configure_file(
+  "${CMAKE_CURRENT_SOURCE_DIR}/gen_server_doc.py.in"
+  "${SPHINX_BUILD}/gen_server_doc.py"
+  @ONLY)
+
+  configure_file(
+  "${CMAKE_CURRENT_SOURCE_DIR}/static/extra.css"
+  "${SPHINX_BUILD}/static/css/extra.css"
+  @ONLY)
+
+add_custom_target(server_rst python gen_server_doc.py)  
+
 add_custom_target(docs
               gendoc
+              COMMAND python gen_server_doc.py
               COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
               COMMAND ${SPHINX_EXECUTABLE} -a -b html
               -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
@@ -73,3 +95,4 @@ add_custom_target(rst
               ${SPHINX_BUILD}/src 
               ${SPHINX_BUILD}/html
               COMMENT "Generating documentation with Sphinx")
+

docs/conf.py.in

@@ -59,4 +59,8 @@ html_theme = "sphinx_rtd_theme"
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+html_static_path = ['static']
+
+
+def setup(app):
+    app.add_stylesheet('css/extra.css')  # may also be an URL

docs/gen_server_doc.py.in

@@ -0,0 +1,86 @@
+import os 
+import re
+from pathlib import Path
+def remove_comments(text):
+    def replacer(match):
+        s = match.group(0)
+        if s.startswith('/'):
+            return " " # note: a space and not an empty string
+        else:
+            return s
+    pattern = re.compile(
+        r'//.*?$|/\*.*?\*/|\'(?:\\.|[^\\\'])*\'|"(?:\\.|[^\\"])*"',
+        re.DOTALL | re.MULTILINE
+    )
+    return re.sub(pattern, replacer, text)
+
+
+# @CMAKE_CURRENT_BINARY_DIR@
+
+print('\n\n\n\n SERVER CSV')
+
+src = Path('@CMAKE_SOURCE_DIR@')/'slsDetectorServers/'
+detectors = ['Mythen3', 'Gotthard2', 'Eiger', 
+            'Jungfrau', 'Moench', 'Gotthard', 'Ctb']
+
+
+for det in detectors:
+    print(det)
+    in_fname = src/f'{det.lower()}DetectorServer/slsDetectorServer_defs.h'
+    #print(f'Reading: {in_fname}')
+    with open(in_fname) as f:
+        lines = f.read().replace('\\\n', '')
+        lines = lines.splitlines(keepends = True)
+
+    lines = [l.strip('#define').strip(' ') for l in lines if l.startswith('#define')]
+    output = []
+    signals = []
+    fields = ['Name,', 'Value', 'Comment']
+    excluded = ['DAC_NAMES', 'DEFAULT_DAC_VALS', 'CLK_NAMES', 'ONCHIP_DAC_NAMES']
+    header = f'{fields[0]:35}{fields[1]:35}\n'
+    output.append(header)
+    signals.append(header)
+    dac_names = []
+    dac_values = []
+    for line in lines:
+        name, *parts = line.split()
+        arg = ' '.join(parts)
+        value, *comments = arg.split('//') 
+        value = value.strip('() ')
+        # value = value.replace(', ', ' ')
+        value = value.replace('\"', '')
+        if name not in excluded:
+            name += ','
+            if name.startswith('SIGNAL_'):
+                signals.append(f'{name:35}{value}\n')
+            else:
+                output.append(f'{name:35}\"{value}\"\n')
+        elif name == 'DAC_NAMES':
+            dac_names = [v.strip(', ') for v in value.split()]
+            dac_names = [n+',' for n in dac_names]
+        elif name == 'DEFAULT_DAC_VALS':
+            dac_values = remove_comments(value).strip('{}; ')
+            dac_values = dac_values.replace(',', '').split()
+            dac_values = [v.strip('') for v in dac_values]
+
+    print(f"dac_names: {len(dac_names)}, dac_values={len(dac_values)}")
+    if len(dac_values) == 0:
+        dac_values = ['N/A']*len(dac_names)
+
+    
+
+    rstpath = Path('@CMAKE_SOURCE_DIR@')/'docs/src/'
+
+    out_fname = Path.cwd()/f'src/{det.lower()}.csv'
+    out_dac_fname = Path.cwd()/f'src/{det.lower()}-dacs.csv'
+    #print(f'Writing: {out_fname}')
+    with open(out_fname, 'w') as f:
+        f.writelines(output)
+
+    output = [f'{n:35}{v}\n' for n,v in zip(dac_names, dac_values)]
+    output.insert(0, header)
+
+    with open(out_dac_fname, 'w') as f:
+        f.writelines(output)
+
+print('END\n\n\n\n')

docs/src/commandline.rst

@@ -4,13 +4,44 @@ Command line interface
 Usage
 -------------
 
-Commands can be uses either with sls_detector_get or sls_detector_put
+Commands can be used either with sls_detector_get or sls_detector_put
 
 .. code-block::
 
     sls_detector_get vrf
 
+Help
+--------
+
+.. code-block::
+
+    # get list of commands
+    sls_detector_get list
+
+    # search for a particular command using a word
+    sls_detector_get list | grep adc
+
+    # get help for a particular command
+    sls_detector_get -h fpath
+    sls_detector_help fpath
+  
+
 Commands
 -----------
 
 .. include:: ../commands.rst
+
+
+Depreciated commands
+------------------------
+
+.. note ::
+	All the dac commands are preceded with the **dac** command. Use command **daclist** to get correct list of dac command arguments for current detector.
+
+.. csv-table:: Depreciated commands
+   :file: ../depreciated.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+
+

docs/src/consuming.rst

@@ -6,7 +6,7 @@ slsDetectorPackage there are a few different ways to
 consume our package. The recommended way is to use one of the 
 CMake approaches. 
 
-
+One can test with :ref:`detector simulators<Virtual Detector Servers>` before testing the API with a real detector or when a real detector is not at hand.
 
 CMake: slsDetectorPackage as submodule in your project
 ---------------------------------------
@@ -91,7 +91,7 @@ manually when invoking g++. This can sometimes be handy for a quick try.
 
 .. code-block:: cpp
 
-    #include "Detector.h"
+    #include "sls/Detector.h"
     #include <iostream>
     int main(){
 

docs/src/dependencies.rst

@@ -42,7 +42,7 @@ The documentation that you are reading now is built with
 
  * Doxygen (to extract C++ classes etc.)
  * Breathe (Sphinx plugin to handle doxygen xml)
- * Sphinx 
+ * Sphinx with sphinx_rtd_theme 
 
 -----------------------
 Packaged in libs/

docs/src/examples.rst

@@ -36,7 +36,7 @@ Running a config file [e1]
 
 .. code-block:: cpp
 
-    #include "Detector.h"
+    #include "sls/Detector.h"
     ...
     sls::Detector det;
     det.loadConfig("path/to/config/file.config");
@@ -105,7 +105,7 @@ as converting to floating point.
 
 .. code-block:: cpp
 
-    #include "Detector.h"
+    #include "sls/Detector.h"
     #include <chrono>
     ...
     std::chrono::microseconds t0{500};

docs/src/firmware.rst

@@ -0,0 +1,511 @@
+Firmware Upgrade
+=================
+
+
+
+Eiger
+-------------
+
+Download 
+^^^^^^^^^^^^^
+- `bcp script <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/bcp>`__
+
+- detector server corresponding to package in slsDetectorPackage/serverBin
+
+- bit files
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - 
+         - 08.09.2020
+         - `v27 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v27/>`__
+         - 
+       * - v4.0.0 - v4.2.0
+         - 
+         - 30.07.2019
+         - `v24 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v24/>`__
+         - 
+       * - v3.1.0 - v3.1.5
+         - 
+         - 17.08.2017
+         - `v20 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v20/>`__
+         -
+
+
+Upgrade
+^^^^^^^^
+#. Tftp must be already installed on your pc to use the bcp script.
+
+#. Kill the on-board servers and copy new servers to the board. 
+
+    .. 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.
+    
+    * **Manual:**
+    
+        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
+
+            ssh root@bebxxx
+            cd executables
+            ./boot_recovery
+
+#. Start a terminal for each half module and run the following to see progress.
+
+    .. code-block:: bash
+    
+    	nc -p 3000 -u bebxxx 3000
+        # Press enter twice to see prompt with board name.
+        > bebxxx
+        # After each bcp command, wait for this terminal to print "Success".
+
+
+#. In another terminal, run the following to update firmware. Please update bit files with great caution as it could make your board inaccessible, if done incorrectly.
+
+    .. code-block:: bash
+    
+        #update back end fpga
+        bcp download.bit bebxxx:/fw0
+
+        #update front left fpga
+        bcp download.bit bebxxx:/febl
+
+        #update front right fpga
+        bcp download.bit bebxxx:/febr
+
+        #update kernel (only if required by the SLS Detector Group)
+        bcp download.bit bebxxx:/kernel
+
+#. Reboot the detector.
+
+Jungfrau
+-------------
+
+Download 
+^^^^^^^^^^^^^
+- detector server corresponding to package in slsDetectorPackage/serverBin
+
+- pof files
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - 2.0
+         - 21.07.2020
+         - `v2.1 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v2_1/jungfrau_v2_1.pof>`__
+         - 
+       * - v5.0.0-rcx
+         - 1.0
+         - 24.07.2020
+         - `v1.1 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v1_1/jungfrau_v1_1.pof>`__
+         - 
+       * - v4.0.1 - v4.2.0
+         - 1.0
+         - 06.12.2018
+         - `v0.7 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v0_7/jungfrau_v0_7.pof>`__
+         - 
+       * - v3.1.0 - v3.1.5
+         - 1.0
+         - 13.11.2017
+         - `v0.6 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v0_6/jungfrau_v0_6.pof>`__
+         -
+
+
+
+Upgrade (from v4.x.x)
+^^^^^^^^^^^^^^^^^^^^^^
+
+Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
+
+#. Tftp must be installed on pc.
+
+#. Update client package to the latest (5.0.0-rc1).
+
+#. Disable server respawning or kill old server
+    .. code-block:: bash
+
+        # 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-rcx)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
+
+
+#. Program from console
+    .. code-block:: bash
+
+        # 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
+
+        # Or only program firmware
+        sls_detector_put programfpga xxx.pof
+
+
+
+Gotthard
+---------
+
+Download 
+^^^^^^^^^^^^^
+- detector server corresponding to package in slsDetectorPackage/serverBin
+
+- pof files
+    .. list-table:: 
+       :widths: 15 15 15 15 5
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - All versions
+         - 50um
+         - 08.02.2018
+         - `50um <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/50um/gotthard_I_50um.pof>`__
+         - 
+       * - All versions
+         - 25um (master)
+         - 08.02.2018
+         - `25um (master) <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/25um/master/gotthard_I_25um_master.pof>`__
+         - 
+       * - All versions
+         - 25um (slave)
+         - 09.02.2018
+         - `25um (slave) <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/25um/slave/gotthard_I_25um_slave.pof>`__
+         - 
+
+.. _firmware upgrade using blaster for blackfin:
+
+Upgrade
+^^^^^^^^
+.. warning ::
+    | Gotthard firmware cannot be upgraded remotely and requires the use of USB-Blaster.
+    | 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>`__.
+   
+
+#. Start Quartus programmer, click on Hardware Setup. In the "Currently selected hardware" window, select USB-Blaster.
+
+#. In the Mode combo box, select "Active Serial Programming".
+
+#. 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 the SLS Detector group.
+
+#. Check "Program/Configure" and "Verify". Push the start button. Wait until the programming process is finished.
+
+#. In case of error messages, check the polarity of cable (that pin1 corresponds) and that the correct programming connector is selected.
+
+#. Reboot the detector.
+
+
+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
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - 
+         - 25.09.2020
+         - 
+         - development
+
+
+Upgrade (from v5.0.0-rcx)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+#. Program from console
+    .. code-block:: bash
+
+        # copies server from tftp folder of pc, programs fpga,
+        # and reboots (new server not respawned currently)
+        sls_detector_put update mythen3DetectorServervxxx pcxxx xxx.rbf
+
+        # Or only program firmware
+        sls_detector_put programfpga xxx.rbf
+
+
+
+Gotthard2
+-------------
+
+.. 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
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - 
+         - 25.09.2020
+         - 
+         - development
+
+Upgrade (from v5.0.0-rcx)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+#. Program from console
+    .. code-block:: bash
+
+        # copies server from tftp folder of pc, programs fpga,
+        # and reboots (new server not respawned currently)
+        sls_detector_put update gotthard2DetectorServervxxx pcxxx xxx.rbf
+
+        # Or only program firmware
+        sls_detector_put programfpga xxx.rbf
+
+
+
+Moench
+-------
+
+Download 
+^^^^^^^^^^^^^
+- detector server corresponding to package in slsDetectorPackage/serverBin
+
+- pof files
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - EPCQ128
+         - 05.10.2020
+         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/moench/EPCQ128/v1_0/moench_v1_0_201005.pof>`__
+         - 
+       * - v5.0.0-rcx
+         - EPCS128
+         - 05.10.2020
+         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/moench/EPCS128/v1_0/moench_v1_0_201005.pof>`__
+         - 
+
+Upgrade (from v5.0.0-rcx)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
+
+#. Program from console
+    .. code-block:: bash
+
+        # 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
+
+        # Or only program firmware
+        sls_detector_put programfpga xxx.pof
+
+Ctb
+----
+
+Download 
+^^^^^^^^^^^^^
+- detector server corresponding to package in slsDetectorPackage/serverBin
+
+- pof files
+    .. list-table:: 
+       :widths: 25 10 30 25 10
+       :header-rows: 1
+
+       * - Software
+         - Hardware
+         - Firmware Date
+         - Firmware Link
+         - Comments
+       * - v5.0.0-rcx
+         - EPCQ128
+         - 05.10.2020
+         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/ctb/EPCQ128/v1_0/ctb_v1_0_201005.pof>`__
+         - 
+       * - v5.0.0-rcx
+         - EPCS128
+         - 05.10.2020
+         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/ctb/EPCS128/v1_0/ctb_v1_0_201005.pof>`__
+         - 
+
+Upgrade (from v5.0.0-rcx)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
+
+#. Program from console
+    .. code-block:: bash
+
+        # 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
+
+        # Or only program firmware
+        sls_detector_put programfpga xxx.pof
+
+
+.. _blackfin firmware troubleshooting:
+
+Firmware Troubleshooting with blackfin
+----------------------------------------
+
+#. v4.x.x client after programming will most likely reboot the blackfin processor, regardless of error.
+
+#. v5.x.x-rcx client after programming will not reboot the blackfin processor, if error occurred.
+
+#. If a reboot occured with an incomplete firmware in flash, the blackfin will most likely not find the mtd3 drive. To see if this drive exists:
+  .. code-block:: bash
+    
+    # connect to the board
+    telnet bchipxxx
+
+    # view of mtd3 existing
+    root:/> more /proc/mtd
+    dev:    size   erasesize  name
+    mtd0: 00040000 00020000 "bootloader(nor)"
+    mtd1: 00100000 00020000 "linux kernel(nor)"
+    mtd2: 002c0000 00020000 "file system(nor)"
+    mtd3: 01000000 00010000 "bitfile(spi)"
+
+4. If one can see the mtd3 drive, one can already try to flash again using the **programfpga** command (without rebooting blackfin or detector). 
+
+#. 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
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This might take a few reruns (maybe even 10) until the mtd drive is accessed by the blackfin upon linux startup.
+
+  .. code-block:: bash
+    
+    # step 1: connect to the board
+    telnet bchipxxx
+
+    # step 2: check if mtd3 drive listed
+    more /proc/mtd
+
+    # 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 4: repeat steps 1 - 3 until you see the mtd3 drive
+
+
+Last Resort using USB Blaster
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If none of these steps work, the last resort might be physically upgrading the firmware using a USB blaster, which also requires opening up the detector. Instructions for all the blackfin detectors are the same as the one for :ref:`gotthard firmware upgrade <firmware upgrade using blaster for blackfin>`.

docs/src/gendoc.cpp

@@ -10,8 +10,8 @@
 #include <vector>
 
 #include "CmdProxy.h"
-#include "Detector.h"
-#include "sls_detector_defs.h"
+#include "sls/Detector.h"
+#include "sls/sls_detector_defs.h"
 
 std::string replace_all(const std::string &src, const std::string &from,
                         const std::string &to) {
@@ -48,7 +48,14 @@ int main() {
         auto tmp = os.str().erase(0, cmd.size());
         auto usage = tmp.substr(0, tmp.find_first_of('\n'));
         tmp.erase(0, usage.size());
-        auto help = replace_all(tmp, "\n\t", "\n\t\t");
+        auto help = replace_all(tmp, "\n\t", "\n\t\t| ");
         fs << '\t' << cmd << usage << help << "\n";
     }
-}
+
+    std::ofstream fs2("depreciated.csv");
+    fs2 << "Old, New\n";
+    auto cmds = proxy.GetDepreciatedCommands();
+    for (auto it : cmds) {
+        fs2 << it.first << ", " << it.second << '\n';
+    }
+}

docs/src/index.rst

@@ -25,13 +25,14 @@ Welcome to slsDetectorPackage's documentation!
 
     detector
     result
-    receiver
+    receiver_api
     examples
 
 .. toctree::
     :caption: Python API
     :maxdepth: 2
 
+    pygettingstarted
     pydetector
     pyenums
     pyexamples
@@ -41,6 +42,7 @@ Welcome to slsDetectorPackage's documentation!
     :maxdepth: 2
 
     commandline  
+    quick_start_guide
 
 .. toctree::
     :caption: Developer
@@ -49,6 +51,34 @@ Welcome to slsDetectorPackage's documentation!
     type_traits
     ToString
 
+.. toctree::
+    :caption: Firmware
+    :maxdepth: 2
+
+    firmware 
+
+.. toctree::
+    :caption: Detector Server
+    :maxdepth: 2
+
+    servers
+    serverupgrade
+    virtualserver
+    serverdefaults
+
+.. toctree::
+    :caption: Receiver
+    :maxdepth: 2
+
+    receivers
+    slsreceiver
+
+.. toctree::
+    :caption: Troubleshooting
+
+    troubleshooting
+
+
 .. Indices and tables
 .. ==================
 

docs/src/installation.rst

@@ -1,9 +1,5 @@
 
-Installation
-==============================================
 
-Build from source using CMake
----------------------------------
 
 .. note :: 
 
@@ -13,17 +9,93 @@ Build from source using CMake
     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.
+    
+
+.. _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 https://github.com/slsdetectorgroup/slsDetectorPackage.git
+    git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
     mkdir build && cd build
     cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-    make -j12
+    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. 
+
+We have three different packages available:
+
+ * **slsdetlib**, shared libraries and command line utilities 
+ * **slsdetgui**, GUI
+ * **slsdet**, Python bindings
+
+
 .. code-block:: bash
 
     #Add channels for dependencies and our library
@@ -32,14 +104,20 @@ Install binaries using conda
     conda config --set channel_priority strict
 
     #cerate an environment with our library, then activate
-    conda create -n myenv slsdetlib=2020.03.18.dev2
-    codna activate myenv
+    #replace 2020.07.20.dev0 with the required tag
+    conda create -n myenv slsdetlib=2020.07.23.dev0
+    conda activate myenv
 
     #ready to use
     sls_detector_get exptime
     etc ...
 
 
+.. code-block:: bash
+
+    #List available versions
+    conda search slsdet
+
 
 Build from source on old distributions
 -----------------------------------------
@@ -66,4 +144,11 @@ is to use conda
 
 .. code-block:: bash
 
-    conda create -n myenv python sphinx sphinx_rtd_theme
+    conda create -n myenv python sphinx sphinx_rtd_theme
+
+Then enable the option SLS_BUILD_DOCS to create the targets
+
+.. code-block:: bash
+
+    make docs # generate API docs and build Sphinx RST
+    make rst # rst only, saves time in case the API did not change

docs/src/pydetector.rst

@@ -6,4 +6,5 @@ Detector
 .. autoclass:: Detector
     :members:  
     :undoc-members:
-    :show-inheritance:
+    :show-inheritance:
+    :inherited-members:

docs/src/pyenums.rst

@@ -4,9 +4,74 @@ Enums
 These enums are defined in slsDetectorDefs in the C++ package and 
 exposed to Python through pybind11.
 
+
+::  
+
+    # Most settings are represented as enums that can be 
+    # explicitly imported
+
+    from slsdet import Detector, fileFormat
+    d = Detector()
+    d.fformat = fileFormat.BINARY
+
+    # Altough not recommended for convenience all enums 
+    # and some other things can be impored using *
+
+    from slsdet import *
+    d.speed = speedLevel.FULL_SPEED 
+
+    # To list the available enums, use dir()
+
+    import slsdet.enums
+    for enum in dir(slsdet.enums):
+        # filter out special memebers
+        if not enum.startswith('_'):
+            print(enum)
+
+
 .. py:currentmodule:: slsdet
 
 .. autoclass:: runStatus
-    :members:  
     :undoc-members:
-    :show-inheritance:
+
+.. autoclass:: detectorType
+    :undoc-members:
+
+.. autoclass:: frameDiscardPolicy
+    :undoc-members:
+
+.. autoclass:: fileFormat
+    :undoc-members:
+
+.. autoclass:: dimension
+    :undoc-members:
+
+.. autoclass:: externalSignalFlag
+    :undoc-members:
+
+.. autoclass:: timingMode
+    :undoc-members:
+
+.. autoclass:: dacIndex
+    :undoc-members:
+
+.. autoclass:: detectorSettings
+    :undoc-members:
+
+.. autoclass:: clockIndex
+    :undoc-members:
+
+.. autoclass:: speedLevel
+    :undoc-members:
+
+.. autoclass:: readoutMode
+    :undoc-members:
+
+.. autoclass:: masterFlags
+    :undoc-members:
+
+.. autoclass:: burstMode
+    :undoc-members:
+
+.. autoclass:: timingSourceType
+    :undoc-members:

docs/src/pyexamples.rst

@@ -1,7 +1,73 @@
 Examples
 ================
 
-Some short hints on how to use the detector
+Some short examples on how to use slsdet. If something is missing don't hesitate to
+open an issue in our our  `github repo
+<https://github.com/slsdetectorgroup/slsDetectorPackage>`_. 
+
+
+------------------------------------
+Setting exposure time 
+------------------------------------
+
+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
+
+    # Setting exposure time using timedelta
+    import datetime as dt
+    >>> d.exptime = dt.timedelta(seconds = 1.2)
+
+    # With timedelta any arbitrary combination of units can be used
+    >>> t = dt.timedelta(microseconds = 100, seconds = 5.3, minutes = .3)
+
+    # 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]) 
+
+
+
+------------------------------------
+Converting numbers to hex
+------------------------------------
+
+Python support entering numbers in  format by using the 0x prefix. However, when reading 
+back you will get a normal integer. This can then be converted to a hex string representation
+using the built in hex() function. 
+
+.. code-block :: python
+
+    from slsdet import Detector
+    >>> d = Detector()
+    >>> d.patwait0 = 0xaa
+    >>> d.patwait0
+    170
+
+    # Convert to  string
+    >>> hex(d.patwait0)
+    '0xaa'
+
+For multiple values one can use a list comprehension to loop over the values. 
+
+.. code-block :: python
+
+    >>> values = [1,2,3,4,5]
+    >>> [(v) for v in values]
+    ['0x1', '0x2', '0x3', '0x4', '0x5']
+
+    # or to a single string by passing the list to .join
+    >>> ', '.join([hex(v) for v in values])
+    '0x1, 0x2, 0x3, 0x4, 0x5'
+
+
+
+    
 
 ------------------------
 Simple threshold scan
@@ -74,37 +140,39 @@ But lets start looking at the at the manual way:
 ::
 
     import time
-    from slsdet import Eiger
-    d = Eiger()
+    from slsdet import Detector, runStatus
 
-    n = 10
-    t = 1
 
-    d.exposure_time = t
-    d.n_frames = n
-    d.reset_frames_caught()
+    n_frames = 10
+    t_exp = 1
 
-    #Start the measurement
+    # Set exposure time and number of frames
+    d = Detector()
+    d.exptime = t_exp
+    d.frames = n_frames
+
+    # Start the measurement
     t0 = time.time()
-    d.start_receiver()
-    d.start_detector()
+    d.startDetector()
+    d.startReceiver()
 
-    #Wait for the detector to be ready or do other important stuff
-    time.sleep(t*n)
+    # Wait for the detector to be ready or do other important stuff
+    time.sleep(t_exp * n_frames)
 
-    #check if the detector is ready otherwise wait a bit longer
-    while d.status != 'idle':
+    # check if the detector is ready otherwise wait a bit longer
+    while d.status != runStatus.IDLE:
         time.sleep(0.1)
 
-    #Stop the receiver after we got the frames
-    #Detector is already idle so we don't need to stop it
-    d.stop_receiver()
+    # Stop the receiver after we got the frames
+    # Detector is already idle so we don't need to stop it
+    d.stopReceiver()
+
+    lost = d.rx_framescaught - n_frames
+    print(
+        f"{n_frames} frames of {t_exp}s took {time.time()-t0:{.3}}s with {lost} frames lost "
+    )
 
-    lost = d.frames_caught - n
-    print(f'{n} frames of {t}s took {time.time()-t0:{.3}}s with {lost} frames lost ')
 
-    #Reset to not interfere with a potential next measurement
-    d.reset_frames_caught()
 
 Instead launching d.acq() from a different process is a bit easier since the control of receiver and detector
 is handled in the acq call. However, you need to join the process used otherwise a lot of zombie processes would
@@ -114,30 +182,104 @@ hang around until the main process exits.
 
     import time
     from multiprocessing import Process
-    from slsdet import Eiger
+    from slsdet import Detector, runStatus
 
-    def acquire():
-        """
-        Create a new Eiger object that still referes to the same actual detector
-        and same shared memory. Then launch acq.
-        """
-        detector = Eiger()
-        detector.acq()
 
-    #This is the detector we use throughout the session
-    d = Eiger()
+    d = Detector()
 
-    #Process to run acquire
-    p = Process(target=acquire)
+    #Create a separate process to run acquire in
+    p = Process(target=d.acquire)
 
     #Start the thread and short sleep to allow the acq to start
     p.start()
     time.sleep(0.01)
 
     #Do some other work
-    while d.busy is True:
-        print(d.busy)
+    while d.status != runStatus.IDLE:
+        print("Working")
         time.sleep(0.1)
 
     #Join the process
-    p.join()
+    p.join()
+
+
+------------------------------
+Setting and getting times
+------------------------------
+
+::
+
+    import datetime as dt
+    from slsdet import Detector
+    from slsdet.utils import element_if_equal
+
+    d = Detector()
+
+    # The simplest way is to set the exposure time in 
+    # seconds by using the exptime property
+    # This sets the exposure time for all modules
+    d.exptime = 0.5
+
+    # 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
+
+    # or combination of units
+    t = dt.timedelta(minutes = 3, seconds = 1.23)
+    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 datetime.timedelta
+
+    >>> d.getExptime()
+    [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 
+    # value
+
+    >>> t = d.getExptime()
+    >>> element_if_equal(t)
+    datetime.timedelta(seconds=1)
+
+--------------
+Reading dacs
+--------------
+
+::
+
+    from slsdet import Detector, Eiger, dacIndex
+
+    #using the specialized class
+    e = Eiger()
+    >>> e.dacs
+    ========== DACS =========
+    vsvp      :    0    0
+    vtrim     : 2480 2480
+    vrpreamp  : 3300 3300
+    vrshaper  : 1400 1400
+    vsvn      : 4000 4000
+    vtgstv    : 2556 2556
+    vcmp_ll   : 1000 1000
+    vcmp_lr   : 1000 1000
+    vcal      :    0    0
+    vcmp_rl   : 1000 1000
+    rxb_rb    : 1100 1100
+    rxb_lb    : 1100 1100
+    vcmp_rr   : 1000 1000
+    vcp       : 1000 1000
+    vcn       : 2000 2000
+    vishaper  : 1550 1550
+    iodelay   :  650  650
+
+    # or using the general class and the list
+    d = Detector()
+    for dac in d.daclist:
+        r = d.getDAC(dac, False)
+        print(f'{dac.name:10s} {r}')

docs/src/pygettingstarted.rst

@@ -0,0 +1,228 @@
+Getting Started 
+==================
+
+
+--------------------
+Which Python?  
+--------------------
+
+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. 
+
+Using something like conda also allows you to quickly switch beteen different Python 
+environments. 
+
+.. warning ::
+
+    If you use conda avoid also installing packages with pip. 
+
+---------------------
+PYTHONPATH 
+---------------------
+
+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. 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? 
+--------------------------------------
+
+We provide a generic class called Detector and detector specific 
+versions like, Eiger, Jungfrau etc. The most or all functionality 
+is there in the base class except the convenient access to dacs
+and temperatures. 
+
+:: 
+
+    from slsdet import Detector, Eiger
+
+    d = Detector()
+    e = Eiger()
+
+    # Both classes can be used to control an Eiger detector
+    d.exptime = 0.5
+    e.period = 1
+
+    # But Eiger gives a simpler interface to the dacs
+    >>> e.dacs
+    ========== DACS =========
+    vsvp           :    0
+    vtrim          : 2480
+    vrpreamp       : 3300
+    vrshaper       : 1400
+    vsvn           : 4000
+    vtgstv         : 2556
+    vcmp_ll        : 1000
+    vcmp_lr        : 1000
+    vcal           :    0
+    vcmp_rl        : 1000
+    rxb_rb         : 1100
+    rxb_lb         : 1100
+    vcmp_rr        : 1000
+    vcp            : 1000
+    vcn            : 2000
+    vishaper       : 1550
+    iodelay        :  650
+
+
+.. note ::
+
+    Depending on user feedback we might move some detector specific
+    functionality to the specialized classes.
+
+
+----------------------------------
+Hey, there seems to be two APIs?
+----------------------------------
+
+To make the Python API approachable, both if you come from the command line 
+or are using the C++ API, we provide two interfaces to the detector. 
+One is property based and tries to stay as close to the command line syntax
+as is possible, and the other one directly maps the C++ API found in Detector.h.
+There is also an underlying design reason for the two APIs since we auto 
+generate the bindings to the C++ code using a mix of pybind11 and clang-tools. 
+The property based API covers most of the functionality but in some cases 
+you have to reach for the C++ like interface. 
+
+
+::  
+
+    d = Detector()
+
+    # C++ like API 
+    d.setExptime(0.1)
+
+    # or a bit more pythonic
+    d.exptime = 0.1
+
+The c++ style API offers more control over access to individual modules
+in a large detector.
+
+:: 
+
+    # Set exposure time for module 1, 5 and 7
+    d.setExptime(0.1, [1,5,7])
+
+--------------------
+Finding functions 
+--------------------
+
+To find out which properties and methods that a Python object have you
+can use dir()
+
+::
+
+    >>> from slsdet import Detector
+    >>> d = Detector()
+    >>> dir(d)
+    ['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', 
+    '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', 
+    '__hash__', '__init__', '__init_subclass__', '__le__', '__len__', 
+    '__lt__', '__module__', '__ne__', '__new__', '__reduce__', 
+    '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', 
+    '__str__', '__subclasshook__', '_adc_register', '_frozen', 
+    '_register', 'acquire', 'adcclk', 'adcphase', 'adcpipeline', 
+    'adcreg', 'asamples', 'auto_comp_disable', 'clearAcquiringFlag', 
+    '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. 
+The following example gives you properties and methods containing time in 
+their name.
+
+:: 
+
+    >>> [item for item in dir(d) if 'time' in item]
+    ['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
+while find returns a list of names. 
+
+::
+
+    from slsdet.lookup import view, find
+
+    >>> view('exptime')
+    exptime
+    getExptime
+    getExptimeForAllGates
+    getExptimeLeft
+    getSubExptime
+    setExptime
+    setSubExptime
+    subexptime
+
+    >>> find('exptime')
+    ['exptime', 'getExptime', 'getExptimeForAllGates', 'getExptimeLeft', 
+    'getSubExptime', 'setExptime', 'setSubExptime', 'subexptime']
+
+
+------------------------------------
+Finding out what the function does
+------------------------------------
+
+To access the documentation of a function directly from the Python prompt use help(). 
+
+.. code-block :: python
+
+    >>> help(Detector.period)
+    Help on property:
+
+        Period between frames, accepts either a value in seconds or datetime.timedelta
+
+        Note
+        -----
+        :getter: always returns in seconds. To get in datetime.delta, use getPeriod
+
+        Examples
+        -----------
+        >>> d.period = 1.05
+        >>> d.period = datetime.timedelta(minutes = 3, seconds = 1.23)
+        >>> d.period
+        181.23
+        >>> d.getPeriod()
+        [datetime.timedelta(seconds=181, microseconds=230000)]
+
+
+----------------------
+Where are the ENUMs?
+----------------------
+
+To set some of the detector settings like file format you have
+to pass in an enum. 
+
+:: 
+
+    >>> d.setFileFormat(fileFormat.BINARY)
+    
+The enums can be found in slsdet.enums 
+
+::
+
+    import slsdet
+    >>> [e for e in dir(slsdet.enums) if not e.startswith('_')]
+    ['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: 
+    >>> from slsdet.enums import *

docs/src/quick_start_guide.rst

@@ -0,0 +1,140 @@
+Quick Start Guide
+=================
+
+Detector
+--------
+Start up detector (with cooling if required). Ensure both control server and stop server is running on-board.
+
+Or use a detector simulator to test. Click :ref:`here<Virtual Detector Servers>` for further instructions.
+
+Receiver
+--------
+
+| One has to start the slsReceiver before loading config file or using any receiver commands (prefix: **rx_** )
+
+For a Single Module
+    .. code-block:: bash  
+
+        # default port 1954
+        slsReceiver
+
+        # custom port 2012
+        slsReceiver -t2012
+
+
+For Multiple Modules
+    .. code-block:: bash  
+
+        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
+        slsMultiReceiver 2012 2 0 
+
+
+Client
+------
+
+Refer :ref:`Sample Config file` to create config file.
+
+.. code-block:: bash  
+
+    # load config file
+    sls_detector_put config /path/sample.config
+
+    # set number of frames
+    sls_detector_put frames 5
+
+    # acquire
+    sls_detector_acquire
+
+
+.. _Sample Config file:
+
+Sample Config file
+^^^^^^^^^^^^^^^^^^
+There are sample config files for each detector in slsDetectorPackage/examples folder.
+
+For a Single Module
+    .. code-block:: bash  
+
+        # connects to module
+        hostname bchipxxx
+
+        # connects to receiver at default port
+        rx_hostname mpc1922
+        # or to connect to specific port
+        # rx_hostname mpc1922:2012
+
+        # sets destination udp ports (not needed, default is 50001)
+        udp_dstport 50012
+
+        # 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
+
+        # set file path
+        fpath /tmp
+
+For a Single Module with custom Receiver (not slsReceiver)
+    .. code-block:: bash  
+
+        # connects to module
+        hostname bchipxxx
+
+        # sets destination udp ports (not needed, default is 50001)
+        udp_dstport 50012
+
+        # source udp ips must be same subnet at destintaion udp ips
+        udp_srcip 192.168.1.112
+
+        # destination udp ip 
+        udp_dstip 192.168.1.100
+
+        # source udp mac 
+        udp_srcmac aa:bb:cc:dd:ee:ff
+        
+        # destination udp mac 
+        udp_dstmac 3c:ab:98:bf:50:60
+
+        # set file path
+        fpath /tmp
+
+For Multiple Modules
+    .. code-block:: bash  
+
+        # connects to mulitple modules
+        hostname bchipxxx+bchipyyy+
+
+        # connects to receivers at ports 2012 and 2014
+        rx_hostname mpc1922:2012+mpc1922:2013+
+
+        # sets differernt destination udp ports
+        0:udp_dstport 50012
+        1:udp_dstport 50014
+
+        # source udp ips must be same subnet at destintaion udp ips
+        0:udp_srcip 192.168.1.112
+        1:udp_srcip 192.168.1.114
+
+        # destination udp ip picked up from rx_hostname (if auto)
+        udp_dstip auto
+
+        # set file path
+        fpath /tmp
+
+Gui
+----
+
+Compile with SLS_USE_GUI=ON in cmake or -g option in cmk.sh script. One can also just use the conda binary. Refer :ref:`installation instructions<Installation>`.
+
+.. code-block:: bash  
+
+    slsDetectorGui
+
+
+.. note ::
+    | The streaming high water mark (commmand: rx_zmqhwm) and the receiving high water mark (command: zmqhwm) is by default the lib zmq's default (currently 1000).
+    | At Gui startup, these values are set to 2. Hence, for very fast detectors, many frames will be dropped to be able to view the latest in the gui.
+    | One can still change this setting in the gui in the Plot tab (ZMQ Streaming), from the command line or API.
+    | Both hwm's can be set to a -1 to use the lib's default.
+    | Since the dummy end of acquisition packet streamed from receiver might also be lost, receiver restreams until gui acknowledges.

docs/src/receiver_api.rst

@@ -1,6 +1,6 @@
 Receiver
 ==============================================
 
-.. doxygenclass:: slsReceiver
+.. doxygenclass:: sls::Receiver
    :members:
 ..    :undoc-members:

docs/src/receivers.rst

@@ -0,0 +1,71 @@
+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.
+ 
+
+Custom Receiver
+----------------
+
+| When using  custom receiver with our package, ensure that **udp_dstmac** is also configured in the config file. This parameter is not required when using slsReceiver.
+
+| Cannot use "auto" for **udp_dstip**.
+
+| Also ensure that there are no **rx_** commands in the config file. These commands are for configuring the slsReceiver.
+
+Example of a custom receiver config file
+
+* The main difference is the lack of **rx_** commands or file commands (eg. fwrite, fpath) and the udp_dstmac is required in config file.
+
+.. code-block:: bash
+
+    # detector hostname
+    hostname bchip052
+
+    # udp destination port (receiver)
+    udp_dstport 50004
+
+    # udp destination ip (receiver)
+    udp_dstip 10.0.1.100
+
+    # udp source ip (same subnet as udp_dstip)
+    udp_srcip 10.0.1.184
+
+    # udp destination mac
+    udp_dstmac 22:47:d5:48:ad:ef

docs/src/serverdefaults.rst

@@ -0,0 +1,106 @@
+Default Values
+==============================================
+
+Mythen3
+-------------
+
+.. csv-table:: Default values
+   :file: mythen3.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Mythen3 DACS
+   :file: mythen3-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Gotthard2
+-------------
+
+.. csv-table:: Default values
+   :file: gotthard2.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Gotthard 2 DACS
+   :file: gotthard2-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Moench
+-------------
+
+.. csv-table:: Default values
+   :file: moench.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Moench DACS
+   :file: moench-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Ctb
+-------------
+
+.. csv-table:: Default values
+   :file: ctb.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Eiger
+-------------
+
+.. csv-table:: Default values
+   :file: eiger.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Eiger DACS
+   :file: eiger-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Jungfrau
+-------------
+
+.. csv-table:: Default values
+   :file: jungfrau.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Jungfrau DACS
+   :file: jungfrau-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+Gotthard
+-------------
+
+.. csv-table:: Default values
+   :file: gotthard.csv
+   :widths: 35, 35
+   :header-rows: 1
+
+DACS
+^^^^^^^^^^^^^
+
+.. csv-table:: Gotthard DACS
+   :file: gotthard-dacs.csv
+   :widths: 35, 35
+   :header-rows: 1

docs/src/servers.rst

@@ -0,0 +1,36 @@
+Detector Servers
+=================
+
+Location
+---------
+   slsDetectorPackage/serverBin/ folder in every release.
+
+
+.. _Detector Server Arguments:
+
+Arguments
+---------
+
+   .. code-block:: bash  
+
+      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.
+      -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. 
+      -s, --stopserver         : Stop server. Do not use as it is created by control server 
+
+
+Basics
+------------
+
+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.

docs/src/serverupgrade.rst

@@ -0,0 +1,114 @@
+Detector Server Upgrade
+=======================
+
+
+
+Eiger
+-------------
+
+
+**Location:** slsDetectorPackage/serverBin/ folder for every release.
+
+
+#. Kill old server and copy new server
+    .. 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
+
+
+#. Reboot the detector.
+
+
+Jungfrau
+-------------
+
+**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 jungfrauDetectorServerxxx pcxxx
+
+
+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
+
+        # copies new server from pc tftp folder, respawns and reboots
+        sls_detector_put copydetectorserver gotthardDetectorServerxxx pcxxx
+
+
+
+Mythen3
+-------
+
+**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
+
+
+Gotthard2
+----------
+
+**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

@@ -0,0 +1,170 @@
+slsReceiver/ slsMultiReceiver
+================================
+
+| One has to start the slsReceiver before loading config file or using any receiver commands (prefix: **rx_** )
+
+For a Single Module
+    .. code-block:: bash  
+
+        # default port 1954
+        slsReceiver
+
+        # custom port 2012
+        slsReceiver -t2012
+
+
+For Multiple Modules
+    .. code-block:: bash  
+
+        # each receiver (for each module) requires a unique tcp port (if all on same machine)
+
+        # using slsReceiver in multiple consoles
+        slsReceiver
+        slsReceiver -t1955
+
+        # slsMultiReceiver [starting port] [number of receivers]
+        slsMultiReceiver 2012 2
+
+        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
+        slsMultiReceiver 2012 2 1
+
+
+Client Commands 
+-----------------
+
+| One can remove **udp_dstmac** from the config file, as the slsReceiver fetches this from the **udp_ip**.
+
+| One can use "auto" for **udp_dstip** if one wants to use default ip of **rx_hostname**.
+
+| The first command to the receiver (**rx_** commands) should be **rx_hostname**. The following are the different ways to establish contact.
+
+    .. code-block:: bash  
+
+        # default receiver tcp port (1954)
+        rx_hostname xxx
+
+        # custom receiver port
+        rx_hostname xxx:1957
+
+        # custom receiver port
+        rx_tcpport 1954
+        rx_hostname xxx
+
+        # multi modules with custom ports
+        rx_hostname xxx:1955+xxx:1956+
+
+        # multi modules with custom ports on same rxr pc
+        0:rx_tcpport 1954
+        1:rx_tcpport 1955
+        2:rx_tcpport 1956
+        rx_hostname xxx
+
+        # multi modules with custom ports on different rxr pc
+        0:rx_tcpport 1954
+        0:rx_hostname xxx
+        1:rx_tcpport 1955
+        1:rx_hostname yyy
+
+
+| Example commands:
+
+    .. code-block:: bash 
+
+        # to get a list of receiver commands (these dont include file commands)
+        sls_detector_get list | grep rx_
+
+        # some file commands are:
+        fwrite
+        foverwrite
+        findex
+        fpath
+        fname
+        fmaster
+        fformat
+
+        # to get help on a single commands
+        sls_detector_get -h rx_framescaught
+
+
+File 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.
+
+* 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:
+
+    .. code-block:: bash
+
+        # first file
+        path-to-file/run_d0_f0_0.raw
+
+        # second file after reaching max frames in first file
+        path-to-file/run_d0_f1_0.raw
+        
+        # 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.
+
+* 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. 
+
+* 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.
+
+
+**HDF5 file formats**
+
+#. Compile the package with HDF5 option enabled
+
+    #. Using cmk script: ./cmk.sh -hj9 -d [path of hdf5 dir]
+
+    #. Enable using cmake **-DCMAKE_INSTALL_PREFIX=/path/to/hdf/installation** and **-DSLS_USE_HDF5=ON**
+
+#. Start Receiver process
+
+#. Load config file
+
+#. Set file format from client or in config file
+    .. code-block:: bash
+
+        sls_detector_put fformat hdf5
+
+
+| For multiple, modules, a virtual file linking all the modules is created. Both the data files and virtual files are linked in the master file.
+
+
+Performance 
+-------------
+
+Please refer to Receiver PC Tuning options and slsReceiver Tuning under `Troubleshooting <https://slsdetectorgroup.github.io/devdoc/troubleshooting.html>`_.
+
+
+Using Callbacks
+----------------
+
+One can get a callback in the receiver for each frame to:
+    * manipulate the data that will be written to file, or
+    * disable file writing in slsReceiver and take care of the data for each call back
+
+When handling callbacks, the control should be returned as soon as possible, to prevent packet loss from fifo being full.
+
+**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 is provided :ref:`here <build from source using cmake>`.
+    * compile the example **e4-rxr** by:
+
+        .. code-block:: bash
+
+            cmake ../path/to/your/source -DCMAKE_PREFIX_PATH=/path/to/sls/install
+            make
+            

docs/src/troubleshooting.rst

@@ -0,0 +1,299 @@
+Troubleshooting
+=================
+
+If something is missing, don't hesitate to
+open an issue at our  `github repo issues
+<https://github.com/slsdetectorgroup/slsDetectorPackage/issues>`_. 
+
+Common
+------
+
+Missing Packets
+^^^^^^^^^^^^^^^
+Possible causes could be the following:
+
+#. 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>`
+
+#. Wiring
+    * Faulty wiring or connecting cable to incorrect interface.
+
+#. Link up and speed
+    * 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
+            # keep executing this command to see if the number of frames left keeps decreasing,
+            # which means the detector is acquiring.
+            sls_detector_get framesl 
+
+    .. note ::
+    
+        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
+
+#. 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.
+
+#. 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.
+
+
+
+.. _Receiver PC Tuning:
+
+Receiver PC Tuning Options
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+#. Increase maximum receive socket buffer size and socket input packet queue. 
+    * Temporarily (until shut down)
+        .. code-block:: bash
+            
+            # check size
+            sysctl -a | grep rmem
+            sysctl -a | grep backlog
+
+            # set max and default (use 1Gb for Jungfrau and 100Mb for others)
+            sysctl net.core.rmem_max=$((100*1024*1024)) 
+            sysctl net.core.rmem_default=$((100*1024*1024))
+            sysctl net.core.netdev_max_backlog=250000
+
+
+    * Permanently
+            .. code-block:: bash
+
+                # edit /etc/sysctl.conf file
+                # set max and default (use 1Gb for Jungfrau and 100Mb for others)
+                net.core.rmem_max = 104857600
+                net.core.rmem_default= 104857600
+                net.core.netdev_max_backlog = 250000
+
+                # save file and run the following
+                sysctl -p
+
+    .. note ::
+        This is the most basic setting, which is sometimes more than enough.
+
+#. For 10Gb,
+    * MTU must be set up to 9000 for jumbo frames on detector, switch and server NIC
+    
+    * Set up static MAC address tables with separated VLANs
+
+#. Write to memory if not a large disk and pc not fast enough.
+    .. code-block:: bash
+
+        mount -t tmpfs none /ramdisk_folder
+        # or
+        mount -t tmpfs none /mnt/ramdisk -o size=10G
+        # check how many GB memory you can allocate, to avoid swapping otherwise    
+
+
+#. Modify ethtool settings. 
+    * rx ring parameters
+        .. code-block:: bash
+
+            # check 
+            ethtool -g xth1
+
+            # set to max value in your pc settings
+            ethtool -G xth1 rx 4096 
+
+    * coalesce settings (might not always work)
+        .. code-block:: bash
+
+            # check 
+            ethtool -c xth1
+
+            # set to max value in your pc settings
+            ethtool -C xth1 rx-usecs 100 
+
+    * pause parameters
+        .. code-block:: bash
+
+            # check 
+            ethtool -a xth1
+
+            # set to max value in your pc settings
+            ethtool -A xth1 rx on
+ 
+    .. note ::
+
+        | xth1 is example interface name. 
+        | These settings are lost at pc reboot.
+
+#. Give user speicific user scheduling privileges.
+    .. code-block:: bash
+
+        # edit /etc/security/limits.conf
+        # add following line or similar depending on your distribution
+        username rtprio 99
+
+    .. note ::
+
+        This is also set if slsReceiver is run as root user.
+        
+        
+#. Disable power saving in CPU frequency 
+    .. code-block:: bash
+
+        # or similar command depending on your distribution
+        cpupower frequency-info
+        cpupower frequency-set -g performance
+
+        # or
+        cpufreq-info
+        for i in ‘seq 0 7‘; do cpufreq-set -c $i -g performance; done
+
+
+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 fifo depth between listening and processing threads.
+    .. code-block:: bash
+
+        sls_detector_get rx_fifodepth
+        # 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
+        sls_detector_put rx_framesperfile 20000
+        # writes all frames into a single file
+        sls_detector_put rx_framesperfile 0
+
+
+Shared memory error
+^^^^^^^^^^^^^^^^^^^
+| 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
+        
+        ll /dev/shm/slsDetectorPackage*
+        -rw-------. 1 l_d l_d  136 Oct  1 11:42 /dev/shm/slsDetectorPackage_multi_0
+        -rw-------. 1 l_d l_d 3476 Oct  1 11:42 /dev/shm/slsDetectorPackage_multi_0_sls_0
+        -rw-------. 1 l_d l_d 3476 Oct  1 11:42 /dev/shm/slsDetectorPackage_multi_0_sls_1
+
+Cannot connect to detector
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Ensure both control and stop servers are running on the detector.
+    .. code-block:: bash
+
+        ps -ef | grep jungfrauDetectorServer*
+
+Cannot connect to receiver
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Start receiver before running a client command that needs to communicate with receiver.
+
+Receiver: cannot bind socket
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+#. slsReceiver or slsMultiReceiver is already open somewhere.
+    * Kill it and restart it.
+
+#. Tcp port is in use by another application.
+    * Start Receiver with a different tcp port and adjust it config file
+        .. code-block:: bash
+
+            # restart receiver with different port
+            slsReceiver -t1980
+
+            # adjust in config file
+            rx_hostname pcxxxx:1980
+
+.. _common troubleshooting multi module data:
+
+Cannot get multi module data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Possible causes could be the following:
+
+#. Network
+    * If you have a direct connection, check to see if the network cables are connected correctly to corresponding interfaces on the PC side. Check also the network configuration and that the detectors and receivers are in the corresponding subnet.
+
+#. Power Supply
+    * Check power supply current limit.
+    * For Jungfrau, refer to :ref:`Jungfrau Power Supply Troubleshooting<Jungfrau Troubleshooting Power Supply>`.
+
+
+
+Gotthard
+----------
+
+
+Missing first frame or next frame after a delay
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Connect the data link from the Module directly to receiver pc or to a private network.
+
+
+Jungfrau
+---------
+
+Temperature event occured
+^^^^^^^^^^^^^^^^^^^^^^^^^
+This will occur only if:
+* temp_threshold (threshold temperature) has been set to a value
+* temp_control (temperature control) set to 1
+* and the temperature overshooted the threshold temperature.
+
+**Consequence**
+* sls_detector_get temp_event will give 1 # temperature event occured
+* the chip will be powered off
+
+**Solution**
+* Even after fixing the cooling, any subsequent powerchip command will fail unless the temperature event has been cleared.
+
+* Clear the temperature event
+    .. code-block:: bash
+        
+        # gives the current chip power status (zero currently as chip powered off)
+        sls_detector_get powerchip 
+
+        # clear temperature event
+        sls_detector_put temp_event 0
+
+        # power on the chip
+        sls_detector_put powerchip 1 
+
+
+.. _Jungfrau Troubleshooting Power Supply:
+
+Cannot get multi module data
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+#. Check :ref:`Common Multi Module Troubleshooting<common troubleshooting multi module data>`
+#. Power Supply
+    * 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/virtualserver.rst

@@ -0,0 +1,149 @@
+.. _Virtual Detector Servers:
+Detector Simulators
+===================
+
+Compilation
+-----------
+
+* Using CMake, turn on the option 
+    .. code-block:: bash  
+        
+        SLS_USE_SIMULATOR=ON
+
+* Using cmk.sh script,
+     .. code-block:: bash  
+        
+        ./cmk.sh -bsj9 #option s is for simulator
+
+
+Binaries
+^^^^^^^^
+    .. code-block:: bash  
+
+        eigerDetectorServerMaster_virtual
+        eigerDetectorServerSlaveTop_virtual
+        eigerDetectorServerSlaveBottom_virtual
+        jungfrauDetectorServer_virtual
+        gotthardDetectorServer_virtual
+        gotthard2DetectorServer_virtual
+        mythen3DetectorServer_virtual
+        moenchDetectorServer_virtual
+        ctbDetectorServer_virtual
+
+
+Arguments
+---------
+
+The arguments are the same as the :ref:`normal server arguments<Detector Server Arguments>`.
+
+When using multiple modules, use different ports for each virtual server.
+    .. code-block:: bash  
+
+        # will start control server at port 1912 and stop server at port 1913
+        jungfrauDetectorServer --port 1912 &
+
+        # will start second control server at port 1914 and stop server at port 1915
+        jungfrauDetectorServer --port 1914 &
+
+
+Client
+------
+
+.. code-block:: bash  
+
+    # hostname should include the port (if not default)
+    sls_detector_put hostname localhost:1912+localhost:1914+
+
+    # or use virtual command, instead of hostname
+    # connects to 2 servers at localhost 
+    # (control servers: 1912, 1914; stop servers: 1913, 1915)
+    sls_detector_put virtual 2 1912 
+
+Use the same in the config file.
+Detector API has a method 'isVirtualDetectorServer' to check if on-board detector server is virtual.
+
+
+Sample Config file
+^^^^^^^^^^^^^^^^^^
+There are sample config files for each detector in slsDetectorPackage/examples folder.
+
+For a Single Module
+    .. code-block:: bash  
+
+        # connects to control port 1912
+        hostname localhost:1912+
+
+        # connects to receiver at ports 2012
+        rx_hostname mpc1922:2012+
+
+        # sets destination udp ports (not needed, default is 50001)
+        udp_dstport 50012
+
+        # 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
+
+        # set file path
+        fpath /tmp
+
+For Multiple Modules
+    .. code-block:: bash  
+
+        # connects to control ports 1912, 1914 and stop ports 1913, 1915
+        virtual 2 1912
+        # or hostname localhost:1912+localhost:1914+
+
+        # connects to receivers at ports 2012 and 2014
+        rx_hostname mpc1922:2012+mpc1922:2013+
+
+        # sets differernt destination udp ports
+        0:udp_dstport 50012
+        1:udp_dstport 50014
+
+        # source udp ips must be same subnet at destintaion udp ips
+        0:udp_srcip 192.168.1.112
+        1:udp_srcip 192.168.1.114
+
+        # destination udp ip picked up from rx_hostname (if auto)
+        udp_dstip auto
+
+        # set file path
+        fpath /tmp
+
+Receivers
+----------
+Same as if you would use an actual detector
+
+For a Single Module
+    .. code-block:: bash  
+
+        slsReceiver -t2012
+
+
+For Multiple Modules
+    .. code-block:: bash  
+
+        # slsMultiReceiver [starting port] [number of receivers] [print each frame header for debugging]
+        slsMultiReceiver 2012 2 0 
+
+Gui
+----
+| Same as if you would use an actual detector.
+| Compile with SLS_USE_GUI=ON in cmake or -g option in cmk.sh script.
+
+.. code-block:: bash  
+
+    slsDetectorGui
+
+Limitations
+-----------
+
+#. 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.
+
+#. Triggers are counted as number of virtual frames. trigger command to send a software trigger (Mythen3 & Eiger) is not implemented in virtual server.
+
+#. firmware version and serial number will give 0.

docs/static/extra.css

@@ -0,0 +1,4 @@
+/* override table no-wrap */
+.wy-table-responsive table td, .wy-table-responsive table th {
+    white-space: normal;
+}

examples/eiger_10Gb.config

@@ -1,33 +1,37 @@
-detsizechan 1024 512 
-#detetctor geometry, long side of the module first
+# detetctor geometry, long side of the module first
+detsize 1024 512 
+
+# detector hostname for controls
 hostname beb059+beb058+ 
-#1Gb detector hostname for controls
 
-0:rx_tcpport 1991 
-#tcpport for the first halfmodule                 
-0:rx_udpport 50011 
-#udp port first quadrant, first halfmodule       
-0:rx_udpport2 50012 
-#udp port second quadrant, first halfmodule       
-0:rx_udpip 10.0.30.210 
-#udp IP of the receiver over 10Gb              
-0:detectorip 10.0.30.100 
-#first half module 10 Gb IP 
+# 1Gb receiver pc hostname with tcp port to configure receiver
+rx_hostname x12sa-vcons:1991+x12sa-vcons:1992
 
-1:rx_tcpport 1992 
-#tcpport for the second halfmodule                  
-1:rx_udpport 50013 
-#udp port first quadrant, second halfmodule     
-1:rx_udpport2 50014 
-#udp port second quadrant, second halfmodule  
-1:rx_udpip 10.0.40.210  
-#udp IP of the receiver over 10Gb, 
-#can be the same or different from 0:rx_udpip                                   
-1:detectorip 10.0.40.101 
-#second half module 10 Gb IP 
+# udp port first quadrant, first halfmodule         
+0:udp_dstport 50011 
 
-rx_hostname x12sa-vcons 
-#1Gb receiver pc hostname
+# udp port second quadrant, first halfmodule       
+0:udp_dstport2 50012 
 
-outdir /sls/X12SA/data/x12saop/Data10/Eiger0.5M
-threaded 1
+# udp IP of the receiver over 10Gb              
+0:udp_dstip 10.0.30.210 
+
+# first half module 10 Gb IP (same subnet as 0:udp_dstip)
+0:udp_srcip 10.0.30.100 
+
+# udp port first quadrant, second halfmodule       
+1:udp_dstport 50013 
+
+# udp port second quadrant, second halfmodule  
+1:udp_dstport2 50014 
+    
+# udp IP of the receiver over 10Gb, 
+1:udp_dstip 10.0.40.210  
+
+# second half module 10 Gb IP 
+# can be the same or different from 0:rx_udpip 
+# butsame subnet as 1:udp_dstip                              
+1:udp_srcip 10.0.40.101 
+
+# output directory
+fpath /sls/X12SA/data/x12saop/Data10/Eiger0.5M

examples/eiger_1Gb.config

@@ -1,24 +1,21 @@
-detsizechan 1024 512 
-#detetctor geometry, long side of the module first
+# detetctor geometry, long side of the module first
+detsize 1024 512 
+
+# detector hostname for controls
 hostname beb059+beb058+ 
-#1Gb detector hostname for controls
 
-0:rx_tcpport 1991 
-#tcpport for the first halfmodule                 
-0:rx_udpport 50011 
-#udp port first quadrant, first halfmodule         
-0:rx_udpport2 50012 
+# 1Gb receiver pc hostname with tcp port to configure receiver
+rx_hostname x12sa-vcons:1991+x12sa-vcons:1992
+
+# udp port first quadrant, first halfmodule         
+0:udp_dstport 50011 
 #udp port second quadrant, first halfmodule       
+0:udp_dstport2 50012 
 
-1:rx_tcpport 1992 
-#tcpport for the second halfmodule               
-1:rx_udpport 50013 
-#udp port first quadrant, second halfmodule       
-1:rx_udpport2 50014 
-#udp port second quadrant, second halfmodule  
+# udp port first quadrant, second halfmodule       
+1:udp_dstport 50013 
+# udp port second quadrant, second halfmodule  
+1:udp_dstport2 50014 
     
-rx_hostname x12sa-vcons 
-#1Gb receiver pc hostname
-
-outdir /sls/X12SA/data/x12saop/Data10/Eiger0.5M
-threaded 1
+# output directory
+fpath /sls/X12SA/data/x12saop/Data10/Eiger0.5M

examples/gotthard.config

@@ -1,27 +1,12 @@
+# detector hostname
 hostname bchip007
 
-#0:port 1952
-#0:stopport 1953
-#0:rx_tcpport 1956 must also have this in receiver config file
-0:angdir 1.000000
-0:moveflag 0.000000
-0:extsig:0 off
-#0:detectorip 129.129.202.9
-0:detectormac 00:aa:bb:cc:dd:ee
-0:rx_udpport 50004
-0:rx_udpip 129.129.202.98
-0:rx_hostname pc6898
-0:outdir /bigRAID/datadir_gotthard/rec_test_data
-0:vhighvoltage 120
-master -1
-sync none
-outdir /bigRAID/datadir_gotthard/rec_test_data
-headerbefore none
-headerafter none
-headerbeforepar none
-headerafterpar none
-badchannels none
-angconv none
-globaloff 0.000000
-binsize 0.001000
+# receiver pc hostname of 1Gb IP of the machine
+rx_hostname my_receiver_hostname
+
+# output directory
+fpath  /bigRAID/datadir_gotthard/rec_test_data
+
+# high voltage
+highvoltage 120
 

examples/gotthard2_veto_file.txt

@@ -0,0 +1,129 @@
+#Gain index    ADU value (12 bit)
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655
+1               3655

examples/gotthard2_veto_photon.txt

@@ -1,132 +1,129 @@
-#G1 Energy #G2 Energy
-300	7000
-
-#G0 pedestal    G1 pedestal    G2 pedestal    G0 gain    G1 gain    G2 gain (for every channel) ADU
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
-100        100        100        10        1        0.1
+#G0 pedestal    G1 pedestal    G2 pedestal    G0 gain    G1 gain    G2 gain     #G1 Energy      #G2 Energy
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000
+100             100             100             10        1             0.1     300	            7000

examples/gotthard_II.config

@@ -1,29 +1,34 @@
+# detector hostname
 hostname strip3
 
+# receiver pc hostname with tcp port
+rx_hostname pc12365:1982
+
+# udp source ip
 udp_srcip 10.1.1.184
+
+# udp destination ip (receiver interface ip)
 udp_dstip 10.1.1.107
 
+# only needed for debugging veto signals
+# udp destination port must be different from udp_dstport (default of 50001)
 udp_dstport2 50084
 udp_srcip2 10.1.1.185
 udp_dstip2 10.1.1.107
 
-rx_hostname pc12365:1954
-#udp_dstmac 3c:fd:fe:d2:a4:25
+# output directory
 fpath  /tmp
-fname run
+
+# disable file writing
 fwrite 0
 
-bursts 10
-frames 2700
-burstperiod 100ms
-
+# to enable 2nd interface for veto debugging
 numinterfaces 2
+
+# enable veto data streaming
 veto 1
 
-#fixing data looks
 # Sampling pipeline 1 clk
 reg 0x120 0x00000010
 clkphase 1 135 deg
 
-
-

examples/gotthard_setup.det

@@ -1,32 +0,0 @@
-fname run
-index 0
-dr 16
-settings veryhighgain
-threshold 0
-exptime 0.000002990
-period 0.000024984
-delay 0.999999968
-gates 1
-frames 300000.000000000
-triggers 1.000000000
-timing auto
-fineoff 0.000000
-startscript none
-startscriptpar none
-stopscript none
-stopscriptpar none
-scriptbefore none
-scriptbeforepar none
-scriptafter none
-scriptafterpar none
-scan0script none
-scan0par none
-scan0prec 0
-scan0steps 0 
-scan1script none
-scan1par none
-scan1prec 0
-scan1steps 0 
-ratecorr 0.000000
-flatfield none
-badchannels none

examples/gotthard_two.config

@@ -1,17 +1,17 @@
-detsizechan 2560 1
-
+# detector hostname
 hostname bchip074+bchip075+
 
+# receiver pc hostname of 1Gb IP of the machine (with tcpport)
+rx_hostname my_receiver_hostname+my_receiver_hostname:1955
 
-0:extsig:0 trigger_in_rising_edge
-0:rx_tcpport 1954
-0:rx_udpport 50001
-0:vhighvoltage 0
+# default udp destination port 50001
+1:udp_dstport 50002
 
-1:extsig:0 trigger_in_rising_edge
-1:rx_tcpport 1955
-1:rx_udpport 50002
-1:vhighvoltage 0
+# output directory
+fpath  /tmp
+
+extsig 0 trigger_in_rising_edge
+highvoltage 0
 
 ##############################################################################
 #########
@@ -19,39 +19,27 @@ hostname bchip074+bchip075+
 #########
 ##############################################################################
 
-# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
-#0:rx_zmqip my_receiver_hostname 
-#0:rx_zmqport 30003
-# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
-#0:zmqip my_client_hostname 
-#0:zmqport  40003
+## receiver pc hostname of 1Gb IP of the machine
+#rx_zmqip my_receiver_hostname 
+## client/gui or softIOc pc hostname
+#zmqip my_client_hostname 
 
-# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
-#1:rx_zmqip my_receiver_hostname 
+## rxr zmq streaming out port
+#0:rx_zmqport 30003
+## client zmq listening port
+#0:zmqport  40003
+## rxr zmq streaming out port
 #1:rx_zmqport 30004
-# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
-#1:zmqip  my_client_hostname 
+## client zmq listening port
 #1:zmqport  40004
 
+## stream out every frame via zmq
+#rx_zmqfreq 1
+## enable zmq streaming
+#rx_zmqstream 1
+
 ##############################################################################
 #########
 ######### until here
 #########
 ##############################################################################
-
-
-r_readfreq 1
-rx_datastream 1
-
-#replace my_receiver_hostname with the hostname of 1Gb IP of the machine where the receiver runs
-rx_hostname my_receiver_hostname
-rx_datastream 1
-outdir /tmp/
-
-
-settings veryhighgain
-exptime 0.000005
-period 0.0001
-
-vhighvoltage 90
-

examples/jctb_moench03_T1.config

@@ -8,8 +8,6 @@ adcclk 20
 dbitclk 40
 
 
-
-
 patword 0000 0000000000000000
 patword 0001 0000000000000000
 patword 0002 0008000900080000
@@ -424,21 +422,24 @@ patwaittime1 0
 patwait2 0400
 patwaittime2 0
 
-
-#0:rx_tcpport 1977
+#############################################
+### edit with hostname or 1Gbs IP address of your server
+############################################
+rx_hostname mpc2011
+#rx_hostname mpc2011:1977
 
 #############################################
 ### edit with 10 Gbs IP of your server
 ############################################
-0:udp_dstip 10.1.1.102
-#0:udp_dstip 129.129.202.136
+udp_dstip 10.1.1.102
+#udp_dstip 129.129.202.136
 #############################################
 ### edit with any number in the subnet of your server (first 3 numbers as above)
 ############################################
-0:udp_srcip 10.1.1.19
-#0:udp_srcip 129.129.202.13
+udp_srcip 10.1.1.19
+#udp_srcip 129.129.202.13
 
-0:udp_dstport 33410
+udp_dstport 33410
 #############################################
 ### edit with 10 Gbs IP of your server
 ############################################
@@ -452,15 +453,9 @@ patwaittime2 0
 #zmqport 50001
 
 
-#############################################
-### edit with hostname or 1Gbs IP address of your server
-############################################
-rx_hostname mpc2011
-
 tengiga 1
-
-rx_datastream 1
-rx_readfreq 1
+rx_zmqstream 1
+rx_zmqfreq 1
 
 
 dac 6 800
@@ -496,6 +491,5 @@ rx_jsonpara detectorMode analog
 #flags newpedestal
 #flags analog
 
-reg 0x5e 0x00010000
-#powerchip 1
-vhighvoltage 90
+powerchip 1
+highvoltage 90

examples/jungfrau.config

@@ -1,16 +1,38 @@
-hostname localhost
+# detector hostname
+hostname bchip052
 
-0:rx_udpport 50004
-0:rx_udpip 172.24.8.84
-0:detectorip 172.24.8.254
-rx_hostname localhost
+# 1Gb receiver pc hostname (default tcpport: 1954)
+rx_hostname pcmoench01
 
-#powerchip 1
-#vhighvoltage 200
+# udp destination port (receiver)
+udp_dstport 50004
 
-#extsig:0 trigger_in_rising_edge
-#timing trigger
+# udp destination ip (receiver)
+udp_dstip 10.0.1.100
 
-outdir /tmp/slsdetector
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 10.0.1.184
 
+# PCBv2.0 (using 2 interfaces, top)
+udp_dstport2 50005
+udp_dstip2 10.0.2.100 
+udp_srcip2 10.0.2.184
+# enable two interfaces
+numinterfaces 2
+# select inner interface(effective only when numinterfaces is 1)
+#selinterface 1
 
+# power on chip
+powerchip 1
+
+# high voltage
+highvoltage 200
+
+# timing to trigger
+timing trigger
+
+# output file directory
+fpath /external_pool/jungfrau_data/softwaretest
+
+# disable file writing
+fwrite 0

examples/jungfrau_custom_receiver.config

@@ -0,0 +1,39 @@
+# detector hostname
+hostname bchip052
+
+# do not use any rx_ or "file" (eg. fwrite, fpath) commands, which go to slsReceiver/slsMultiReceiver
+
+# udp destination port (receiver)
+udp_dstport 50004
+
+# udp destination ip (receiver)
+udp_dstip 10.0.1.100
+
+# udp source ip (same subnet as udp_dstip)
+udp_srcip 10.0.1.184
+
+# udp destination mac
+udp_dstmac 22:47:d5:48:ad:ef
+
+
+# PCBv2.0 (using 2 interfaces, top)
+udp_dstport2 50005
+udp_dstip2 10.0.2.100 
+udp_srcip2 10.0.2.184
+udp_dstmac2 22:47:d5:48:ad:ff
+
+
+# enable two interfaces
+numinterfaces 2
+# select inner interface(effective only when numinterfaces is 1)
+#selinterface 1
+
+# power on chip
+powerchip 1
+
+# high voltage
+highvoltage 200
+
+# timing to trigger
+timing trigger
+

examples/jungfrau_two.config

@@ -1,26 +1,49 @@
-detsizechan 1024 1024
+# detector geometry x, y
+detsize 1024 1024
+
+# detector hostname
 hostname bchip048+bchip052+
 
-0:rx_udpport 50004
-0:rx_udpip 10.1.1.100
-0:rx_udpmac F4:52:14:2F:32:00
-0:detectorip 10.1.1.10
-0:detectormac 00:aa:bb:cc:dd:33
+# 1Gb receiver pc hostname  (default tcpport: 1954)
+rx_hostname pcmoench01+pcmoench01:1955
 
-1:rx_tcpport 1955
-1:rx_udpport 50005
-1:rx_udpip 10.1.1.100
-1:rx_udpmac F4:52:14:2F:32:00
-1:detectorip 10.1.1.11
-1:detectormac 00:aa:bb:cc:dd:33
 
-rx_hostname pcmoench01
 
+# udp configurations for 1st module
+# udp destination port (receiver)
+0:udp_dstport 50004
+
+# udp destination ip (receiver)
+0:udp_dstip 10.1.1.100
+
+# udp source ip (same subnet as 0:udp_dstip)
+0:udp_srcip 10.1.1.10
+
+
+
+# udp configurations for 2nd module
+# udp destination port (receiver)
+1:udp_dstport 50005
+
+# udp destination ip (receiver)
+1:udp_dstip 10.1.1.100
+
+# udp source ip (same subnet as 1:udp_dstip)
+1:udp_srcip 10.1.1.11
+
+
+
+# power on chip
 powerchip 1
-vhighvoltage 200
-#extsig:0 trigger_in_rising_edge
-#timing trigger
 
-outdir /external_pool/jungfrau_data/softwaretest
+# high voltage
+highvoltage 200
 
+# timing to trigger
+timing trigger
 
+# output file directory
+fpath /external_pool/jungfrau_data/softwaretest
+
+# disable file writing
+fwrite 0

examples/measurement_setup.det

@@ -0,0 +1,32 @@
+# file name prefix
+fname measurement1
+
+# file acquisition index
+findex 3000
+
+# dynamic range (only for Mythen3 and Eiger)
+dr 32
+
+# settings 
+settings veryhighgain
+
+# exposure time
+exptime 100us
+
+# period
+period 2ms
+
+# frames per trigger
+frames 30000
+
+# timing mode
+timing trigger
+
+# triggers
+triggers 10
+
+# delay after trigger
+delay 1ms
+
+
+

examples/moench03_T1.config

@@ -9,7 +9,6 @@ hostname bchip181+
 ############################################
 rx_hostname mpc2011
 
-rx_tcpport 1954
 #############################################
 ### edit with 10 Gbs IP of your server
 ############################################
@@ -33,20 +32,20 @@ zmqport 50001
 
 
 
-
 tengiga 1
-rx_datastream 1
+rx_zmqstream 1
 
 
 
 frames 100000
 period 0.0006
+
 #############################################
 ### edit with directory you want to write to
 ############################################
 fpath /mnt/moench_data/scratch/
+
 fwrite 0
-rx_datastream 1
 
 rx_jsonpara frameMode frame
 rx_jsonpara detectorMode counting
@@ -56,7 +55,7 @@ rx_discardpolicy discardpartial
 adcpipeline 15
 
 powerchip 1
-vhighvoltage 90
+highvoltage 90
 
 #adcreg 0x14 0x40
 

examples/two_gotthard.config

@@ -1,55 +0,0 @@
-#####Any line with a # is not read######
-
-detsizechan 2560 1
-
-hostname bchip007+bchip009+
-
-#0:hostname bchip007
-#0:port 1952
-#0:stopport 1953
-#0:rx_tcpport 1956 
-0:angdir 1.000000
-0:moveflag 0.000000
-0:ffdir /home/l_msdetect
-0:extsig:0 off
-
-0:detectorip 10.1.1.2
-#0:detectormac 00:aa:bb:cc:dd:ee
-#0:rx_udpport 50001
-0:rx_udpip 10.1.1.1
-0:rx_hostname 129.129.202.134 
-0:outdir /data/speedt
-0:vhighvoltage 120
-
-
-#1:hostname bchip009
-#1:port 1952
-#1:stopport 1953
-1:rx_tcpport 1957
-1:angdir 1.000000
-1:moveflag 0.000000
-1:ffdir /home/l_msdetect
-1:extsig:0 off
-
-1:detectorip 10.1.2.2
-#1:detectormac 00:aa:bb:cc:dd:ee
-1:rx_udpport 50004
-1:rx_udpip 10.1.2.1
-1:rx_hostname 129.129.202.134 
-1:outdir /data/speedt
-1:vhighvoltage 120
-
-
-master -1
-sync none
-outdir /data/speedt
-ffdir /home/l_msdetect
-headerbefore none
-headerafter none
-headerbeforepar none
-headerafterpar none
-badchannels none
-angconv none
-globaloff 0.000000
-binsize 0.001000
-

examples/virtual_ctb_moench.config

@@ -0,0 +1,477 @@
+# detector hostname
+hostname localhost:1910
+
+# 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
+
+# disable file writing
+fwrite 0
+
+
+# default clocks
+runclk 40
+adcclk 20
+dbitclk 40
+
+
+# patterns
+patword 0x0000 0x0000000000000000
+patword 0x0001 0x0000000000000000
+patword 0x0002 0x0008000900080000
+patword 0x0003 0x0008000900080000
+patword 0x0004 0x0008000900080000
+patword 0x0005 0x0008000900080000
+patword 0x0006 0x0008000900080000
+patword 0x0007 0x0008000900080000
+patword 0x0008 0x0008000900080000
+patword 0x0009 0x0008000900080000
+patword 0x000a 0x0008000900080000
+patword 0x000b 0x0008000900080000
+patword 0x000c 0x0008000900080000
+patword 0x000d 0x0008000900080000
+patword 0x000e 0x0008000900080000
+patword 0x000f 0x0008000900080000
+patword 0x0010 0x0008000900080000
+patword 0x0011 0x0008000900080000
+patword 0x0012 0x0008000900080000
+patword 0x0013 0x0008000900080000
+patword 0x0014 0x0008000900080000
+patword 0x0015 0x0008000900080000
+patword 0x0016 0x0008400900080020
+patword 0x0017 0x0008400900080020
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+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
+dac 0 1300
+dac 4 1428
+dac 1 1000
+dac 7 900
+dac 3 680
+dac 2 1400
+dac 5 1200
+
+
+adcinvert 4a342593
+
+# analog samples
+asamples 5000
+
+# digital samples
+dsamples 0
+
+# adc phase
+adcphase 30 deg
+
+# adc pipeline
+adcpipeline 14
+
+# analog readout
+romode analog
+
+# frames
+frames 1
+
+# period
+period 1ms
+
+

examples/virtual_eiger_1_half_module.config

@@ -0,0 +1,22 @@
+# detector hostname
+hostname localhost:1900
+
+# receiver hostname
+rx_hostname mpc1922:2000
+
+# udp destination ports
+udp_dstport 50000
+udp_dstport2 50001
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
+# output file directory
+fpath /tmp
+
+# disable file writing
+fwrite 0
+
+#imagetest 1
+
+

examples/virtual_eiger_2_half_modules.config

@@ -0,0 +1,23 @@
+# 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
+
+# udp destination ip from rx_hostname
+udp_dstip auto
+
+# output file directory
+fpath /tmp
+
+# disable file writing
+fwrite 0
+
+#imagetest 1
+

examples/virtual_gotthard.config

@@ -0,0 +1,23 @@
+# detector hostname
+hostname localhost:1904
+
+# 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
+
+# disable file writing
+fwrite 0
+
+
+

examples/virtual_gotthard2.config

@@ -0,0 +1,37 @@
+# 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
+# udp destination ip (from rx_hostname)
+udp_dstip2 auto
+# udp source ip (same subnet as udp_dstip)
+udp_srcip2 192.168.1.100
+
+# to enable 2nd interface for veto debugging
+numinterfaces 2
+
+# enable veto data streaming
+veto 1
+
+
+

examples/virtual_jungfrau.config

@@ -0,0 +1,32 @@
+# detector hostname
+hostname localhost:1906
+
+# receiver hostname
+rx_hostname mpc1922:2006
+
+# udp destination ports
+udp_dstport 50006
+udp_dstport2 50007
+
+# 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
+
+# disable file writing
+fwrite 0
+
+#imagetest 1
+#frames 1
+
+# enable two interfaces
+numinterfaces 2
+
+# select inner interface(effective only when numinterfaces is 1)
+#selinterface 1

examples/virtual_jungfrau_4.config

@@ -0,0 +1,47 @@
+# detector geometry
+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
+1:udp_dstport 50003
+1:udp_dstport2 50004
+2:udp_dstport 50005
+2:udp_dstport2 50006
+3:udp_dstport 50007
+3:udp_dstport2 50008
+
+# 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
+2:txndelay_frame 2
+3:txndelay_frame 3
+
+# output file directory
+fpath /tmp
+
+# disable file writing
+fwrite 0
+
+#imagetest 1
+#frames 1
+
+

examples/virtual_moench.config

@@ -0,0 +1,21 @@
+# detector hostname
+hostname localhost:1908
+
+# 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
+
+# disable file writing
+fwrite 0
+

examples/virtual_mythen3.config

@@ -0,0 +1,24 @@
+# detector hostname
+hostname localhost:1912
+
+# 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
+
+# disable file writing
+fwrite 0
+
+# load ascii pattern file
+#pattern ../pat.txt
+

integrationTests/test-eigerIntegration.cpp

@@ -1,6 +1,6 @@
 #include "DetectorImpl.h"
 #include "catch.hpp"
-#include "string_utils.h"
+#include "sls/string_utils.h"
 #include "tests/globals.h"
 #include <iostream>
 

integrationTests/test-integrationDectector.cpp

@@ -1,14 +1,14 @@
 
 #include "catch.hpp"
 
-#include "ClientSocket.h"
 #include "DetectorImpl.h"
 #include "Module.h"
-#include "logger.h"
-#include "sls_detector_defs.h"
+#include "sls/ClientSocket.h"
+#include "sls/logger.h"
+#include "sls/sls_detector_defs.h"
 
-#include "Timer.h"
-#include "sls_detector_funcs.h"
+#include "sls/Timer.h"
+#include "sls/sls_detector_funcs.h"
 #include <iostream>
 #include <vector>
 #define VERBOSE
@@ -446,8 +446,8 @@ TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert",
     CHECK(m.readRegister(0x7b) == 0x1003E);
 }
 
-TEST_CASE("Eiger or Jungfrau startingfnum",
-          "[.eigerintegration][.jungfrauintegration][startingfnum]") {
+TEST_CASE("Eiger or Jungfrau nextframenumber",
+          "[.eigerintegration][.jungfrauintegration][nextframenumber]") {
     SingleDetectorConfig c;
 
     // pick up multi detector from shm id 0
@@ -465,8 +465,8 @@ TEST_CASE("Eiger or Jungfrau startingfnum",
     // starting fnum
     uint64_t val = 8;
 
-    m.setStartingFrameNumber(val);
-    CHECK(m.getStartingFrameNumber() == val);
+    m.setNextFrameNumber(val);
+    CHECK(m.getNextFrameNumber() == val);
     CHECK(m.acquire() == slsDetectorDefs::OK);
     CHECK(m.getReceiverCurrentFrameIndex() == val);
 
@@ -474,18 +474,18 @@ TEST_CASE("Eiger or Jungfrau startingfnum",
     CHECK(m.acquire() == slsDetectorDefs::OK);
     CHECK(m.getReceiverCurrentFrameIndex() == val);
 
-    CHECK_THROWS_AS(m.setStartingFrameNumber(0), sls::RuntimeError);
+    CHECK_THROWS_AS(m.setNextFrameNumber(0), sls::RuntimeError);
 
     if (m.getDetectorTypeAsString() == "Eiger") {
         val = 281474976710655;
     } else if (m.getDetectorTypeAsString() == "Jungfrau") {
         val = 18446744073709551615;
     }
-    m.setStartingFrameNumber(val);
-    CHECK(m.getStartingFrameNumber() == val);
+    m.setNextFrameNumber(val);
+    CHECK(m.getNextFrameNumber() == val);
     CHECK(m.acquire() == slsDetectorDefs::OK);
     CHECK(m.getReceiverCurrentFrameIndex() == val);
-    CHECK(m.getStartingFrameNumber() == (val + 1));
+    CHECK(m.getNextFrameNumber() == (val + 1));
 }
 
 TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {

integrationTests/test-integrationMulti.cpp

@@ -1,6 +1,6 @@
 #include "DetectorImpl.h"
 #include "catch.hpp"
-#include "string_utils.h"
+#include "sls/string_utils.h"
 #include "tests/globals.h"
 #include <iostream>
 

manual/Makefile

@@ -1,51 +0,0 @@
-DESTDIR?=docs
-
-
-#manual-api manual-calwiz manual-client manual-gui manual-main
-
-
-
-MAINDIRS= manual-main manual-api  manual-calwiz manual-client manual-gui
-#manual-calwiz manual-calwiz manual-gui manual-client manual-api
-CLEANDIRS=$(MAINDIRS:manual-%=clean-%)
-PDFDIRS=$(MAINDIRS:manual-%=pdf-%)
-HTMLDIRS=$(MAINDIRS:manual-%=html-%)
-ALLDIRS=$(MAINDIRS:manual-%=all-%)
-
-
-all: $(ALLDIRS)
-#	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
-#	mv pdf $(DESTDIR)
-#	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
-#	mv html $(DESTDIR)
-	
-pdf: $(PDFDIRS)
-#	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
-#	mv pdf $(DESTDIR)
-
-html: $(HTMLDIRS)
-#	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
-#	mv html $(DESTDIR)
-
-clean: $(CLEANDIRS)
-	rm -fr $(DESTDIR)/pdf
-	rm -fr $(DESTDIR)/html	
-
-all-%:
-	echo 
-	cd  $(@:all-%=manual-%) && make all
-
-pdf-%:
-	cd  $(@:pdf-%=manual-%) && make pdf
-
-html-%:
-	cd  $(@:html-%=manual-%) && make html
-
-clean-%: 
-	cd  $(@:clean-%=manual-%) && make clean	
-
-
-#<23><>$(@D)<29><>    The directory part of the file name of the target, with the trailing slash removed. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@D)<29><> is dir. This value is . if <20><>$@<40><> does not contain a slash.
-#<23><>$(@F)<29><>    The file-within-directory part of the file name of the target. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@F)<29><> is foo.o. <20><>$(@F)<29><> is equivalent to <20><>$(notdir $@)<29><>.
-
-

manual/index.html

@@ -1,65 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-
-<!--Converted with LaTeX2HTML 2002-2-1 (1.71)
-original version by:  Nikos Drakos, CBLU, University of Leeds
-* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
-  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>SLS Detector Software Documentation</TITLE>
-<META NAME="description" CONTENT="SLS Detector Software Documentation">
-<META NAME="keywords" CONTENT="SLS Detectors">
-<META NAME="resource-type" CONTENT="document">
-<META NAME="distribution" CONTENT="global">
-
-<LINK REL="next" HREF="node1.html">
-</HEAD>
-
-<BODY >
-<P>
-
-<H1 ALIGN="CENTER">SLS Detector Software Documentation</H1>
-<DIV>
-</DIV>
-<BR><HR>
-<!--Table of Child-Links-->
-<A NAME="CHILD_LINKS"></A>
-
-<UL> 
-
-<LI><A HREF="slsDetectors-FAQ/index.html">SLS Detectors Frequently Asked Questions</A>  <BR>
-Documents with general remarks about the detectors and the software that all users should read.
-<A HREF="../pdf/slsDetectors-FAQ.pdf">*pdf*</A>    <BR>
- <BR>
-<LI><A HREF="slsDetectorInstall/index.html">Installation</A> <BR>
-Documentation for the installation of the SLS Detectors software library
-<A HREF="../pdf/slsDetectorInstall.pdf">*pdf*</A> <BR>
- <BR>
-<LI><A HREF="slsDetectorClientHowTo/index.html">Command Line Interface</A>  <BR>
-Reference documentation for the command line interface sls_detector_put, sls_detector_get, sls_detector_acquire, sls_detector_help 
-<A HREF="../pdf/slsDetectorClientHowTo.pdf">*pdf*</A>  <BR>
- <BR>
-<LI><A HREF="slsDetectorGuiHowTo/index.html">Graphical Users Interface</A>  <BR>
-Reference documentation for the GUI
-<A HREF="../pdf/slsDetectorGuiHowTo.pdf">*pdf*</A>  <BR>
- <BR>
-<LI><A HREF="calibrationWizardsHowTo/index.html">Calibration Wizards</A> 
-<UL> 
-<LI> Energy calibration <A HREF="../pdf/energyCalibrationHowTo.pdf">*pdf*</A> 
-<LI> Angular calibration <A HREF="../pdf/angularCalibrationHowTo.pdf">*pdf*</A>     
-</UL>
- <BR>
-
-<LI><A HREF="slsDetectorUsersDocs/index.html">Application Program Interface</A>  <BR>
-Doxygen documentation for using the slsDetectorUsers class
-<A HREF="../pdf/slsDetectorUsersDocs.pdf">*pdf*</A>  <BR>
-   <BR>        
-</UL>
-
-<BR><HR>
-<ADDRESS>
-Anna Bergamaschi
-</ADDRESS>
-</BODY>
-</HTML>

manual/manual-api/CMakeLists.txt

@@ -1,32 +0,0 @@
-set(SOURCES
-    mainReceiver.cpp
-)
-
-include_directories(
-    ../../slsSupportLib/include
-    ../../slsReceiverSoftware/include
-    ../../build/bin 
-    ../../slsdetectorSoftware/slsDetector 
-)
-
-add_executable(slsMultiReceiver
-    ${SOURCES}
-)
-
-target_link_libraries(slsMultiReceiver
-    slsReceiverShared
-    pthread
-    ${ZeroMQ_LIBRARIES}
-    rt
-)
-
-if (HDF5_FOUND)
-    target_link_libraries(slsMultiReceiver ${HDF5_LIBRARIES})
-endif ()
-
-
-set_target_properties(slsMultiReceiver PROPERTIES
-    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
-)
-
-install(TARGETS slsMultiReceiver DESTINATION bin)

manual/manual-api/Makefile

@@ -1,62 +0,0 @@
-PKGDIR		=	../..
-LIBDIR		=   $(PKGDIR)/bin
-INCLUDES	=   -I . -I$(PKGDIR)/slsSupportLib/include -I$(LIBDIR) -I$(PKGDIR)/slsDetectorSoftware/slsDetector  -I$(PKGDIR)/slsReceiversoftware/include
-SRC_DET		= 	mainClient.cpp 	
-SRC_REC		=   mainReceiver.cpp
-ZMQLIBDIR	= 	$(PKGDIR)/slsSupportLib/include
-LDFLAG_DET 	=	-I. -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread -lrt -L$(ZMQLIBDIR) -Wl,-rpath=$(ZMQLIBDIR) -lzmq
-LDFLAG_REC 	=	-I. -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread -lrt -L$(ZMQLIBDIR) -Wl,-rpath=$(ZMQLIBDIR) -lzmq
-DESTDIR		?=	../docs
-
-HDF5 		?=	no
-HDF5_DIR 	?=	/opt/hdf5v1.10.0
-
-ifeq ($(HDF5),yes)
-	LDFLAG_REC += -L$(HDF5_DIR)/lib  -Wl,-rpath=$(HDF5_DIR)/lib -lhdf5 -lhdf5_cpp -lsz -lz -DHDF5C 
-endif
-
-all: docs detUser slsMultiReceiver 
-#all: docs
-
-docs: createdocs docspdf docshtml removedocs
-
-createdocs: slsDetectorUsers.doxy mainClient.cpp mainReceiver.cpp
-	doxygen slsDetectorUsers.doxy	
-
-docspdf: 
-	cd slsDetectorUsersDocs/latex && make 
-	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
-	$(shell test -d $(DESTDIR)/pdf || mkdir -p $(DESTDIR)/pdf)
-	mv slsDetectorUsersDocs/latex/refman.pdf $(DESTDIR)/pdf/slsDetectorUsersDocs.pdf
-
-docshtml: 
-	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
-	$(shell test -d $(DESTDIR)/html || mkdir -p $(DESTDIR)/html)
-	$(shell test -d $(DESTDIR)/html/slsDetectorUsersDocs && rm -r $(DESTDIR)/html/slsDetectorUsersDocs)
-	mv slsDetectorUsersDocs/html $(DESTDIR)/html/slsDetectorUsersDocs
-	
-removedocs:
-	rm -rf 	slsDetectorUsersDocs;
-	
-detUser:$(SRC_DET)
-	echo "creating client"
-	mkdir -p bin
-	g++ -o bin/detUser $(SRC_DET) $(INCLUDES) $(LDFLAG_DET) -lm -lstdc++
-
-slsMultiReceiver:$(SRC_REC)
-	echo "creating receiver"
-	echo $LDFLAG_REC
-	mkdir -p bin
-	g++ -o bin/slsMultiReceiver $(SRC_REC) $(INCLUDES) $(LDFLAG_REC) -lm -lstdc++
-	cp bin/slsMultiReceiver $(LIBDIR)
-	
-clean:
-	echo "cleaning for manual-api"
-	rm -rf bin/detUser bin/slsMultiReceiver bin/detReceiver slsDetectorUsersDocs
-	rm -rf slsDetectorUsersDocs
-	rm -rf $(DESTDIR)/html/slsDetectorUsersDocs
-	rm -rf $(DESTDIR)/pdf/slsDetectorUsersDocs.pdf
-	rm -rf $(LIBDIR)/slsMultiReceiver
-	
-
-

manual/manual-api/mainClient.cpp

@@ -1,106 +0,0 @@
-/**
-\file mainClient.cpp
-
-This file is an example of how to implement the slsDetectorUsers class 
-You can compile it linking it to the slsDetector library
-
-g++ mainClient.cpp -L lib -lSlsDetector -L/usr/lib64/ -L lib2 -lzmq  -pthread -lrt -lm -lstdc++
-
-where,
-
-lib is the location of libSlsDetector.so
-
-lib2 is the location of the libzmq.a.
-[ libzmq.a is required only when using data call backs and enabling data streaming from receiver to client.
-It is linked in manual/manual-api from slsReceiverSoftware/include ]
-
- */
-
-#include "slsDetectorUsers.h"
-#include "detectorData.h"
-#include <iostream>
-#include <cstdlib>
-
-/**
- * Data Call back function defined
- * @param pData pointer to data structure received from the call back
- * @param iframe frame number of data passed
- * @param isubframe sub frame number of data passed ( only valid for EIGER in 32 bit mode)
- * @param pArg pointer to object
- * \returns integer that is currently ignored
- */
-int dataCallback(detectorData *pData, int iframe, int isubframe, void *pArg)
-{
-	std::cout  	<< " DataCallback:"
-				<< "\n nx           : " << pData->npoints
-				<< "\n ny           : " << pData->npy
-				<< "\n Frame number : " << iframe << std::endl;
-}
-
-
-/**
- * Example of a main program using the slsDetectorUsers class
- *
- * - Arguments are optional
- * 		- argv[1] : Configuration File
- * 		- argv[2] : Measurement Setup File
- * 		- argv[3] : Detector Id (default is zero)
- */
-int main(int argc,  char **argv) {
-	/** - if specified, set ID from argv[3] */
-	int id=0;
-	if (argc>=4)
-		id=atoi(argv[3]);
-
-
-	/** - slsDetectorUsers Object is instantiated with appropriate ID */
-	int ret = 1;
-	slsDetectorUsers *pDetector = new slsDetectorUsers (ret, id);
-	if (ret == 1) {
-		std::cout << "Error: Could not instantiate slsDetectorUsers" << std::endl;
-		return EXIT_FAILURE;
-	}
-
-
-	/** - if specified, load configuration file (necessary at least the first time it is called to properly configure advanced settings in the shared memory) */
-	if (argc>=2){
-		pDetector->readConfigurationFile(argv[1]);
-		std::cout << "Detector configured" << std::endl;
-	}
-
-	/** - set detector in shared memory online (in case no config file was used) */
-	pDetector->setOnline(1);
-
-	/** - set receiver in shared memory online (in case no config file was used) */
-	pDetector->setReceiverOnline(1);
-
-	/** - registering data callback */
-	pDetector->registerDataCallback(&dataCallback, NULL);
-
-
-	/** - ensuring detector status is idle before starting acquisition. exiting if not idle */
-	int status = pDetector->getDetectorStatus();
-	if (status  !=  0){
-		std::cout << "Detector not ready: " << slsDetectorUsers::runStatusType(status) << std::endl;
-		return 1;
-	}
-
-	/** - if provided, load detector settings */
-	if (argc>=3){
-		pDetector->retrieveDetectorSetup(argv[2]);
-		std::cout << "Detector measurement set-up done" << std::endl;
-	}
-
-
-	/** - start measurement */
-	pDetector->startMeasurement();
-	std::cout << "measurement finished" << std::endl;
-
-	/** - returning when acquisition is finished or data are avilable */
-
-	/** - delete slsDetectorUsers object */
-	delete pDetector;
-
-	return 0;
-}
-

manual/manual-api/mainReceiver.cpp

@@ -1,306 +0,0 @@
-/**
- \file mainReceiver.cpp
-
-This file is an example of how to implement the slsReceiverUsers class
-You can compile it linking it to the slsReceiver library
-
-g++ mainReceiver.cpp -L lib -lSlsReceiver -L/usr/lib64/ -L lib2 -lzmq  -pthread -lrt -lm -lstdc++
-
-where,
-
-lib is the location of lSlsReceiver.so
-
-lib2 is the location of the libzmq.a.
-[ libzmq.a is required only when using data call backs and enabling data streaming from receiver to client.
-It is linked in manual/manual-api from slsReceiverSoftware/include ]
-
- */
-
-#include "sls_detector_defs.h"
-#include "slsReceiverUsers.h"
-
-#include <csignal>	//SIGINT
-#include <cstdlib>		//system
-#include <cstring>
-#include <iostream>
-//#include "utilities.h"
-//#include "logger.h"
-#include <cerrno>
-#include <string>
-#include <sys/types.h>	//wait
-#include <sys/wait.h>	//wait
-#include <syscall.h>	//tid
-#include <unistd.h> 	//usleep
-using namespace std;
-
-
-/** Define Colors to print data call back in different colors for different recievers */
-#define PRINT_IN_COLOR(c,f, ...) 	printf ("\033[%dm" f RESET, 30 + c+1, ##__VA_ARGS__)
-
-
-/** Variable is true to continue running, set to false upon interrupt */
-bool keeprunning;
-
-/**
- * Control+C Interrupt Handler
- * Sets the variable keeprunning to false, to let all the processes know to exit properly
- */
-void sigInterruptHandler(int p){
-	keeprunning = false;
-}
-
-/**
- * prints usage of this example program
- */
-void printHelp() {
-	cprintf(RESET, "Usage:\n"
-			"./slsMultiReceiver(detReceiver) [start_tcp_port] [num_receivers] [1 for call back, 0 for none]\n\n");
-	exit(EXIT_FAILURE);
-}
-
-/**
- * Start Acquisition Call back
- * slsReceiver writes data if file write enabled.
- * Users get data to write using call back if registerCallBackRawDataReady is registered.
- * @param filepath file path
- * @param filename file name
- * @param fileindex file index
- * @param datasize data size in bytes
- * @param p pointer to object
- * \returns ignored
- */
-int StartAcq(char* filepath, char* filename, uint64_t fileindex, uint32_t datasize, void*p){
-	cprintf(BLUE, "#### StartAcq:  filepath:%s  filename:%s fileindex:%llu  datasize:%u ####\n",
-			filepath, filename, (long long unsigned int)fileindex, datasize);
-
-	cprintf(BLUE, "--StartAcq: returning 0\n");
-	return 0;
-}
-
-/**
- * Acquisition Finished Call back
- * @param frames Number of frames caught
- * @param p pointer to object
- */
-void AcquisitionFinished(uint64_t frames, void*p){
-	cprintf(BLUE, "#### AcquisitionFinished: frames:%llu ####\n",(long long unsigned int)frames);
-}
-
-
-/**
- * Get Receiver Data Call back
- * Prints in different colors(for each receiver process) the different headers for each image call back.
- * @param metadata sls_receiver_header metadata
- * @param datapointer pointer to data
- * @param datasize data size in bytes.
- * @param p pointer to object
- */
-void GetData(char* metadata, char* datapointer, uint32_t datasize, void* p){
-	slsDetectorDefs::sls_receiver_header* header = (slsDetectorDefs::sls_receiver_header*)metadata;
-	slsDetectorDefs::sls_detector_header detectorHeader = header->detHeader;
-
-	PRINT_IN_COLOR (detectorHeader.modId?detectorHeader.modId:detectorHeader.row,
-			"#### %d GetData: ####\n"
-			"frameNumber: %lu\t\texpLength: %u\t\tpacketNumber: %u\t\tbunchId: %lu"
-			"\t\ttimestamp: %lu\t\tmodId: %u\t\t"
-			"row: %u\t\tcolumn: %u\t\treserved: %u\t\tdebug: %u"
-			"\t\troundRNumber: %u\t\tdetType: %u\t\tversion: %u"
-			//"\t\tpacketsMask:%s"
-			"\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
-			detectorHeader.row, (long unsigned int)detectorHeader.frameNumber,
-			detectorHeader.expLength, detectorHeader.packetNumber, (long unsigned int)detectorHeader.bunchId,
-			(long unsigned int)detectorHeader.timestamp, detectorHeader.modId,
-			detectorHeader.row, detectorHeader.column, detectorHeader.reserved,
-			detectorHeader.debug, detectorHeader.roundRNumber,
-			detectorHeader.detType, detectorHeader.version,
-			//header->packetsMask.to_string().c_str(),
-            ((uint8_t)(*((uint8_t*)(datapointer)))), datasize);
-}
-
-
-
-/**
- * Get Receiver Data Call back (modified)
- * Prints in different colors(for each receiver process) the different headers for each image call back.
- * @param metadata sls_receiver_header metadata
- * @param datapointer pointer to data
- * @param datasize data size in bytes.
- * @param revDatasize new data size in bytes after the callback.
- * This will be the size written/streamed. (only smaller value is allowed).
- * @param p pointer to object
- */
-void GetData(char* metadata, char* datapointer, uint32_t &revDatasize, void* p){
-	slsDetectorDefs::sls_receiver_header* header = (slsDetectorDefs::sls_receiver_header*)metadata;
-	slsDetectorDefs::sls_detector_header detectorHeader = header->detHeader;
-
-	PRINT_IN_COLOR (detectorHeader.modId?detectorHeader.modId:detectorHeader.row,
-			"#### %d GetData: ####\n"
-			"frameNumber: %llu\t\texpLength: %u\t\tpacketNumber: %u\t\tbunchId: %llu"
-			"\t\ttimestamp: %llu\t\tmodId: %u\t\t"
-			"row: %u\t\tcolumn: %u\t\treserved: %u\t\tdebug: %u"
-			"\t\troundRNumber: %u\t\tdetType: %u\t\tversion: %u"
-			//"\t\tpacketsMask:%s"
-			"\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
-			detectorHeader.row, (long long unsigned int)detectorHeader.frameNumber,
-			detectorHeader.expLength, detectorHeader.packetNumber, (long long unsigned int)detectorHeader.bunchId,
-			(long long unsigned int)detectorHeader.timestamp, detectorHeader.modId,
-			detectorHeader.row, detectorHeader.column, detectorHeader.reserved,
-			detectorHeader.debug, detectorHeader.roundRNumber,
-			detectorHeader.detType, detectorHeader.version,
-			//header->packetsMask.to_string().c_str(),
-			((uint8_t)(*((uint8_t*)(datapointer)))), revDatasize);
-
-	// if data is modified, eg ROI and size is reduced
-	revDatasize = 26000;
-}
-
-
-
-
-/**
- * Example of main program using the slsReceiverUsers class
- *
- * - Defines in file for:
- *  	- Default Number of receivers is 1
- *  	- Default Start TCP port is 1954
- */
-int main(int argc, char *argv[]) {
-
-	/**	- set default values */
-	int numReceivers = 1;
-	int startTCPPort = 1954;
-	int withCallback = 0;
-	keeprunning = true;
-
-	/**	- get number of receivers and start tcp port from command line arguments */
-	if ( (argc != 4) || (!sscanf(argv[1],"%d", &startTCPPort)) || (!sscanf(argv[2],"%d", &numReceivers)) || (!sscanf(argv[3],"%d", &withCallback)) )
-		printHelp();
-	cprintf(BLUE,"Parent Process Created [ Tid: %ld ]\n", (long)syscall(SYS_gettid));
-	cprintf(RESET, "Number of Receivers: %d\n", numReceivers);
-	cprintf(RESET, "Start TCP Port: %d\n", startTCPPort);
-	cprintf(RESET, "Callback Enable: %d\n", withCallback);
-
-
-
-	/** - Catch signal SIGINT to close files and call destructors properly */
-	struct sigaction sa;
-	sa.sa_flags=0;							// no flags
-	sa.sa_handler=sigInterruptHandler;		// handler function
-	sigemptyset(&sa.sa_mask);				// dont block additional signals during invocation of handler
-	if (sigaction(SIGINT, &sa, nullptr) == -1) {
-		cprintf(RED, "Could not set handler function for SIGINT\n");
-	}
-
-	/** - Ignore SIG_PIPE, prevents global signal handler, handle locally,
-	   instead of a server crashing due to client crash when writing, it just gives error */
-	struct sigaction asa;
-	asa.sa_flags=0;							// no flags
-	asa.sa_handler=SIG_IGN;					// handler function
-	sigemptyset(&asa.sa_mask);				// dont block additional signals during invocation of handler
-	if (sigaction(SIGPIPE, &asa, nullptr) == -1) {
-		cprintf(RED, "Could not set handler function for SIGPIPE\n");
-	}
-
-
-	/** - loop over number of receivers */
-	for (int i = 0; i < numReceivers; ++i) {
-
-		/**	- fork process to create child process */
-		pid_t pid = fork();
-
-		/**	- if fork failed, raise SIGINT and properly destroy all child processes */
-		if (pid < 0) {
-			cprintf(RED,"fork() failed. Killing all the receiver objects\n");
-			raise(SIGINT);
-		}
-
-			/**	- if child process */
-		else if (pid == 0) {
-			cprintf(BLUE,"Child process %d [ Tid: %ld ]\n", i, (long)syscall(SYS_gettid));
-
-			char temp[10];
-			sprintf(temp,"%d",startTCPPort + i);
-			char* args[] = {(char*)"ignored", (char*)"--rx_tcpport", temp};
-			int ret = slsDetectorDefs::OK;
-			/**	-  create slsReceiverUsers object with appropriate arguments */
-			slsReceiverUsers *receiver = new slsReceiverUsers(3, args, ret);
-			if(ret==slsDetectorDefs::FAIL){
-				delete receiver;
-				exit(EXIT_FAILURE);
-			}
-
-
-			/**	- register callbacks. remember to set file write enable to 0 (using the client)
-		  if we should not write files and you will write data using the callbacks */
-			if (withCallback) {
-
-				/** - Call back for start acquisition */
-				cprintf(BLUE, "Registering 	StartAcq()\n");
-				receiver->registerCallBackStartAcquisition(StartAcq, nullptr);
-
-				/** - Call back for acquisition finished */
-				cprintf(BLUE, "Registering 	AcquisitionFinished()\n");
-				receiver->registerCallBackAcquisitionFinished(AcquisitionFinished, nullptr);
-
-				/* 	- Call back for raw data */
-				cprintf(BLUE, "Registering     GetData() \n");
-				if (withCallback == 1) receiver->registerCallBackRawDataReady(GetData,nullptr);
-				else if (withCallback == 2) receiver->registerCallBackRawDataModifyReady(GetData,nullptr);
-			}
-
-
-
-			/**	- start tcp server thread */
-			if (receiver->start() == slsDetectorDefs::FAIL){
-				delete receiver;
-				cprintf(BLUE,"Exiting Child Process [ Tid: %ld ]\n", (long)syscall(SYS_gettid));
-				exit(EXIT_FAILURE);
-			}
-
-			/**	- as long as keeprunning is true (changes with Ctrl+C) */
-			while(keeprunning)
-				pause();
-			/**	- interrupt caught, delete slsReceiverUsers object and exit */
-			delete receiver;
-			cprintf(BLUE,"Exiting Child Process [ Tid: %ld ]\n", (long)syscall(SYS_gettid));
-			exit(EXIT_SUCCESS);
-			break;
-		}
-	}
-
-	/** - Parent process ignores SIGINT (exits only when all child process exits) */
-	sa.sa_flags=0;							// no flags
-	sa.sa_handler=SIG_IGN;					// handler function
-	sigemptyset(&sa.sa_mask);				// dont block additional signals during invocation of handler
-	if (sigaction(SIGINT, &sa, nullptr) == -1) {
-		cprintf(RED, "Could not set handler function for SIGINT\n");
-	}
-
-
-	/** - Print Ready and Instructions how to exit */
-	cout << "Ready ... " << endl;
-	cprintf(RESET, "\n[ Press \'Ctrl+c\' to exit ]\n");
-
-	/** - Parent process waits for all child processes to exit */
-	for(;;) {
-		pid_t childPid = waitpid (-1, nullptr, 0);
-
-		// no child closed
-		if (childPid == -1) {
-			if (errno == ECHILD) {
-				cprintf(GREEN,"All Child Processes have been closed\n");
-				break;
-			} else {
-				cprintf(RED, "Unexpected error from waitpid(): (%s)\n",strerror(errno));
-				break;
-			}
-		}
-
-		//child closed
-		cprintf(BLUE,"Exiting Child Process [ Tid: %ld ]\n", (long int) childPid);
-	}
-
-	cout << "Goodbye!" << endl;
-	return 0;
-}
-

manual/manual-api/slsDetectorUsers.doxy

@@ -1,91 +0,0 @@
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
-# documentation are documented, even if no documentation was available. 
-# Private class members and static file members will be hidden unless 
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL            = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
-
-EXTRACT_STATIC         = YES
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS  = YES
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespace are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-INTERNAL_DOCS = NO
-
-SHOW_INCLUDE_FILES = YES
-
-SHOW_FILES = YES
-
-SHOW_NAMESPACES = NO
-
-COMPACT_LATEX = YES
-
-PAPER_TYPE = a4
-
-PDF_HYPERLINKS = YES
-
-USE_PDFLATEX = YES
-
-LATEX_HIDE_INDICES = YES
-
-SOURCE_BROWSER	= YES
-
-PREDEFINED           = __cplusplus
- 
-INPUT            = 		../../slsDetectorSoftware/slsDetector/slsDetectorUsers.h		\
-					 	../../slDetectorSoftware/slsDetectorAnalysis/detectorData.h 	\
-					 	../../slsReceiverSoftware/include/slsReceiverUsers.h 			\
-					 	mainClient.cpp 													\
-					 	mainReceiver.cpp
-
-OUTPUT_DIRECTORY = slsDetectorUsersDocs

manual/manual-calwiz/Makefile

@@ -1,56 +0,0 @@
-DESTDIR?=../docs
-
-
-#manual-api manual-calwiz manual-client manual-gui manual-main
-
-TEX=latex
-
-MAINTEXS= angularCalibrationHowTo.tex energyCalibrationHowTo.tex 
-
-TEXS=ancCal.tex enCal.tex installation.tex 
-
-DVIS = $(MAINTEXS:.tex=.dvi)
-PSS = $(MAINTEXS:.tex=.ps)
-PDFS = $(MAINTEXS:.tex=.pdf)
-HTMLS = $(MAINTEXS:%.tex=%)
-
-
-all: pdf html
-	echo $(PWD)
-	echo $(PDFS)
-	echo $(HTMLS)
-
-
-pdf: $(PDFS)
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-	mv $(PDFS) $(DESTDIR)/pdf	
-
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-$(HTMLS): $(TEXS) $(MAINTEXS)
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-	$(shell test -d $(DESTDIR)/html/$@ && rm -r $(DESTDIR)/html/$@)
-	latex $@.tex
-	latex2html -split 4 $@.tex
-	mv $@ $(DESTDIR)/html
-
-%.dvi : %.tex $(TEXS)
-	latex $<
-	latex $<
-
-%.ps : %.dvi
-	dvips -o $@  $< 
-
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-	ps2pdf  $<  $@
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-	rm -rf *.aux *.log *.toc *.out $(DVIS) $(PSS) $(PDFS) $(HTMLS)
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manual/manual-calwiz/ancCal.tex

@@ -1,171 +0,0 @@
-
-In order to convert from strip number to 2$\theta$-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). \\
-
-For this purpose, a series of patterns of a powder standard with symmetric peaks (e.g. silicon) must acquired while shifting the detector by an angular step of the order of about 2\% of the module size. During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position.\\
-
-In a first step, the   peak is fitted with a Gaussian in order to determine its position $C_{peak}$ in channel number for each of the acquired patterns.\\
-In a second step, for each module $i$, the encoder position  $\Theta_e$  is fitted as a function of the peak position  $C_{peak}$  according to:
-\begin{equation}\label{eq:angcal}
-\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
-\end{equation} 
-where the parameters $\Theta_o^i$ is the angular offset with respect to the diffractometer zero position, $C_{center}^{i}$ is the central channel  and $R^i$ is the distance of the module $i$ from the diffractometer center while $p=50~\mu m$ is the strip pitch of the detector. \\
-Finally, the global offset of the detector system is precisely determined by refining a silicon pattern at a well-defined energy (i.e., knowing the position of the peak).
-
-The same function of equation~\ref{eq:angcal}, with the parameters obtained from the calibration, is used in order to convert from channel number to 2$\theta$-angle.
-
-The parallax at the borders of the modules due to the thickness of the silicon sensor is a function of the X-ray energy (higher energy X-rays are absorbed deeper inside the sensor) and is of the order of 0.2~mdeg at 12~keV and 0.5~mdeg at 30~keV. \\
-The differences in pixel size due to the different portion of solid angle covered by the strips on the border of the modules and  the higher efficiency due to the longer path of the X-rays in the sensor are removed by the flat field correction. This also normalizes additional differences in pixel size between channels which are also present because of mismatches in the strip sensor fabrication and in fluctuations of the channels threshold level.
- 
-Patterns acquired at different detector positions are generally merged together  in order to fill the gaps between the modules and correct possibly bad functioning channels. In this procedure the data from different positions which are closer than 4~mdeg (the average pixel size) are averaged and the new position is set to the mean of the positions of the original points.
-
-
-The position and width of the peaks results from a fit over several detector channels. Geometrical distortions might disturb this determination mainly because of errors in the angular calibration, fluctuations in the encoder position, variations between channels and parallax effects.\\
-The resolution in locating the peak center and determining its width and integrated intensity has been estimated by acquiring several patterns of a LaB$_6$ sample in a 300~$\mu$m capillary with the detector shifted in 5~mdeg steps between 30.4 and 36.5 degrees. The 16~peaks acquired have been fitted with a Gaussian function plus background and the fluctuations on the fitted parameters have been calculated. The resulting average resolutions are  0.63$\pm$0.06~mdeg for the peak center and 0.22$\pm$0.05~mdeg for the peak Full-Width at Half-Maximum (FWHM) for an average peak FWHM of 27.0$\pm$2.5~mdeg. \\
-These results show that  the angular calibration allows a resolution in determining the peaks position and width which is appropriate for structural determination.
-
-\section{Data acquisition}
-
-The angular calibration consists in acquiring a set of diffraction patterns of a well known powder standard (e.g. Silicon) at different encoder positions.  In order to facilitate the procedure, the sample should not emit fluorescent light and should present relatively symmetric peaks. \\
-During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position. In general the highest peak will be used for the calibration, but this is not necessary in case there would be e.g. geometrical limitations for shifting the detector. \\ \textbf{Do not forget to properly position the beam stopper if the detector is scanned in front of the direct beam.}\\
-The detector should be shifted of an angular step of the order of about 2\% of the module size, such that about 50 patterns can contribute to the fitting of the 3 parameters necessary for the angular calibration.\\
- 
-All the angular calibration procedure should be acquired using a trimmed detector with the threshold set at half of the X-ray energy (Assuming no fluorescent element in the standard). A flat field should also be acquired in order to precisely correct the data, while the X-ray intensity should be kept lower than about 100~kHz per strip in order to avoid the need for rate corrections.
-
-A rough angular conversion file starting from a previous calibration or from the geometric characteristics of the mechanics is an advantage. The angular conversion file should contain a line for each module of the detector with its module number $i$, center  $C_{center}^{i}$ and error, conversion radius $p/R^i$ and error, offset $\Theta_o^i$ and error:
-\begin{verbatim}
-module 0 center 639.5 +- 0 conversion 6.56E-05 +- 0 offset 0 +- 0
-\end{verbatim}
-Also the \textit{global offset} value of the beamline should be approximately known i.e. the angular position of channel 0 of module 0 when the motor is set at 0. \\
-All the documentation assumes that the detector is oriented in the same direction as the encoder position i.e. large channel number at higher angles (both per module and absolute). If this is not the case, the \textit{angular direction} should be set to -1. 
-
-\subsection{Software}
-
-For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.\\
-
-Please make sure that you have edited the \\
-\textit{slsDetectorSoftware/usersFunctions/angleFunction.h} \\
-in order to match the angular conversion for your geometry and \\
-\textit{slsDetectorSoftware/usersFunctions/usersFunctions.cpp} \\
-in order to be able to move the detector and read out its position by using the slsDetector software.
-
-In the following the command to acquire a dataset for the angular calibration with an exposure time of 1~s, and position shift 
-\begin{verbatim}
-#setup angular calibration log mode
-> sls_detector_put angcallog 1 
-#set exposure time to 1s
-> sls_detector_put exptime 1. 
-#setup threshold scan
-> sls_detector_put scan0script position 
-#setup the precision for the scan variable in the file name
-> sls_detector_put scan0prec 2 
-#set scan range between 20deg and -60deg, step of -0.1deg
-# (at 12.4 keV the Si(111) peak is at approx 19deg
-> sls_detector_put scan0range 20 -60 -0.1 
-#acquire the data
-> sls_detector_acquire
-#unset angular calibration log mode
-> sls_detector_put angcallog 0
-\end{verbatim}
-
-With the GUI you can obtain the same results by clicking on the \textit{Angular calibration} log button in the advanced tab (see figure~\ref{fig:guiangcallog}) and setting up the motor position scan in the Actions tab (see figure~\ref{fig:guiposscan}). The exposure time should also be set in the measurement tab.
-
-
-
-Additional to the data files, the acquisition will produce a .angcal file containing an header and, for each step of the acquisition, the exect value of the motor position and the file name. \\
-In case you forgot to enable the angcallog flag in the software, you can produce the file with the syntax as follows, assuming that you know the exact values of your encoder for each frame:
-\begin{verbatim}
-type Mythen
-maxmod 32
-nmod 32
-angconv /scratch/angcal20120422/ang.off
-globaloff 5.088
-fineoff 0.0
-angdir 1
-ffdir /scratch/angcal20120422/
-flatfield flatfield_E12keV_T6keV_0.raw
-badchannels /scratch/cal/bad.chans
-19.99998 angcal_S20.00_0
-19.90001 angcal_S19.90_0
-19.79999 angcal_S19.80_0
-19.70002 angcal_S19.70_0
-......
-\end{verbatim}
-
-
-
-\begin{figure}
-\caption{Acquisition GUI window to enable the angular calibration log.} \label{fig:guiangcallog}
-\includegraphics[width=\textwidth]{enable_angcal.eps}
-\end{figure} 
-
-\begin{figure}
-\caption{Acquisition GUI window to setup the motor position scan.} \label{fig:guiposscan}
-\includegraphics[width=\textwidth]{position_scan.eps}
-\end{figure} 
-\newpage
-
-\section{Data analysis}
-
-The data analysis consists in fitting with a gaussian the selected peak of the powder pattern for each position in order to determine its position is channel number as a function of the encoder position. \\
-In a second step, for each module, the channel vs. encoder curve is fitted in order to extrapolate the three parameters necessary for the angular conversion and the result is written to file
-
-\subsection{Software}
-
-The software used for the angular calibration data analysis is based on root (see http://root.cern.ch).\\
-This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
-
-To start the data analysis simply launch:
-\begin{verbatim}
-> ./angularCalibrationWizard 
-\end{verbatim}
-
-\begin{figure}
-\caption{Overview of the nagular calibration dataset.} \label{fig:setangcal}
-\includegraphics[width=\textwidth]{setupAngcal.eps}
-\end{figure} 
-
-To setup the angular calibration dataset, the .angcal file should be selected (or digited) and the load button should be pressed to confirm. The parameters of the angular calibration are then read to the file and the data loaded for a quick overview (see figure~\ref{fig:setangcal}).\\
-The software assumes that the data files (.raw) and the .encal file are in the same directory.\\
-A 2D color plot will show a rebinned overview of the dataset. The peak to be fitted should be visible as a high intensity diagonal line passing through all the channels.
-
-
-\begin{figure}
-\caption{Preview of the fitting of the Si(111) peak for one of the detector positions.} \label{fig:peakfit}
-\includegraphics[width=\textwidth]{peakFit.eps}
-\end{figure} 
-
-For a more detailed view of the data, one can select an angular calibration step from the combo box, select the plot mode (raw data or processed data as a function of channel number, processed angular converted data, flat field data, or again an overview of the whole dataset). \\
-By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.\\
-
-If the bad channel list, angular conversion file or flat field file are changed compared to the acquisition, they can be reloaded by editing the correspondent text entries and pressing enter.
-
-In particular, the angular converted data should be checked in order to view the position of the selected peak. In this case, the plot will be zoomed to the angular region slected in the minimum and maximum angle entries. By pressing fit, the fit of the peak in the selected angular range will be shown (see figure~\ref{fig:peakfit}).  It is useful to check that it works properly in several positions such that then the sequential fitting on all steps can give good results.
-
-To automatically fit all positions simply press \textit{Proceed to Modules Calibration} and wait until all steps are fitted. This can take sometime, depending on the number of steps.
-
-
-\begin{figure}
-\caption{Window for fitting the angular calibration parameters of a module.} \label{fig:anglefit}
-\includegraphics[width=\textwidth]{angleFit.eps}
-\end{figure} 
-
-
-
-
-
-In the module calibration window (see figure~\ref{fig:anglefit}), you will be able to fit the channel number to encoder position curve to estimate the three angular calibration parameters for each module.\\
-The entries show the angular calibration parameters used for approximate angular conversion in the previous step of the calibration. These can be edited and will be used as start parameters for the fit.
-By clicking on the check box next to the parameters, the selected parameter will be set and fixed during the fit. Often the center is used as a fix parameter.\\
-It is possible to navigate between modules by using the Previous and Next module buttons. To refit the current module (e.g. after changing one of the parameters) simply re-click on the module number.
-
-After fitting all modules you can click on the \textit{Write Angular Calibration} button, select the file name to write to and save the calibration angulat calibration data. Please note that the offset of module 0 will always be 0 and the other values will be rescaled to its value. Therefore the global offset of the steup will always need to be specified for a proper angular conversion unless the home of the encoder will not be redifined.
-
-\section{Setup calibration files}
-
-To use the generated angular calibration files, using the text client:
-\begin{verbatim}
-sls_detector_put angconv /scratch/ang_new.off 
-\end{verbatim}
-while for the GUI the file name should be specified in the configuration file (works also for the text client).
-\end{document}
-

manual/manual-calwiz/angularCalibrationHowTo.tex

@@ -1,17 +0,0 @@
-\documentclass{article}
-\usepackage{amssymb}
-\usepackage[dvips]{graphicx}
-\usepackage{verbatim}
-\begin{document}
-
-\title{Angular calibration wizard manual}
-\author{Anna Bergamaschi}
-\date{\today}
-\maketitle
-
-
-\section{Introduction}
-\input{ancCal.tex}
-
-\end{document}
-

manual/manual-calwiz/calibrationWizardsHowTo.tex

@@ -1,24 +0,0 @@
-\documentclass{report}
-\usepackage{amssymb}
-\usepackage[dvips]{graphicx}
-\usepackage{verbatim}
-\begin{document}
-
-\title{Calibration wizards manual}
-\author{Anna Bergamaschi}
-\date{\today}
-\maketitle
-\chapter{Installation}
-\input{installation.tex}
-
-\chapter{Energy calibration}
-%\section{Introduction}
-\input{enCal.tex}
-
-
-\chapter{Angular calibration}
-%\section{Introduction}
-\input{ancCal.tex}
-
-\end{document}
-

manual/manual-calwiz/enCal.tex

@@ -1,214 +0,0 @@
-
-The choice of the level of the comparator threshold plays a very important role in counting systems since it influences the efficiency of the detector as well as its spatial resolution (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668).
-
-
-Single-photon-counting detectors are sensitive to single photons and the only limitation on the fluctuations of the number of counts is given by the Poisson-like statistics of the X-ray quanta. 
-The digitized signal does not carry any information concerning the energy of the X-rays and all photons with an energy larger than the threshold are counted as one bit. This means that the choice of the correct comparator threshold level is critical in order to obtain good-quality data.\\
- Figure~\ref{fig:thrscanexpl} shows the expected number of counts as a function of the threshold energy for $N_0$ monochromatic X-rays of energy $E_0$. This is often denominated  S-curve and can be interpreted as the integral of the signal spectrum between the threshold level and infinity.
-The dashed curve represents the behavior of an ideal counting system: nothing is counted for thresholds larger than the photon energy and all the $N_0$ X-rays are counted for thresholds lower than $E_0$.
-The thick solid line represents the physical curve which also takes into account the electronic noise and the charge sharing between channels.
-
-The intrinsic noise on the electronic signal  is defined by the Equivalent Noise Charge ($ENC$). The $ENC$ describes noise in terms of the charge at the detector input needed to create the same output at the end of the analog chain and is normally expressed in electrons. For silicon sensors, it can be converted into energy units by considering 1~$e^-$=3.6~eV.
-The value of the $ENC$ normally depends on the shaping settings of the analog chain and increases with shorter shaping times. 
-The resulting electronic signal spectrum is then  given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation $ENC$.  
-The S-curve for a monochromatic radiation beam is well described by a Gaussian cumulative distribution $D$ with an additional increase at low threshold due to the baseline noise, as shown by the solid thin line. 
-
-Moreover, when a photon is absorbed in the region between two strips of the sensor, the generated charge is partially collected by the two nearest electronic channels. For this reason the physical S-curve is not flat but can be modeled by a decreasing straight line. The number of shared photons  $N_S$ is given by the difference between the number of counts and the number of X-rays whose charge is completely collected by the strip (shown by the dotted line).
-
-The number of counts in the physical case is equal to that in the ideal case for a threshold set at half the photon energy. This defines the optimal threshold level $E_t=E_0/2$.\\
-The detector response $N$ as a function of the threshold energy $E_t$ is given by the sum of the noise counts  $N_n$ and the counts originating from photons $N_\gamma$:
-\begin{equation}
-N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big), \label{eq:thrscan}
-\end{equation}
-where $C_s$ is the fraction of photons which produce a charge cloud which is shared between neighboring strips ($N_s=C_s N_0$).\\
-By assuming a noise of Gaussian type, and considering its bandwidth limited by the shaping time  $\tau_s$, the number of noise counts in the acquisition time $T$ can be approximated as:
-\begin{equation}
-N_n(E_t) \sim \frac{T}{\tau_s}  D \Big(\frac{-E_t}{ENC} \Big). \label{eq:noisescan}
-\end{equation} 
-
-The choice of the comparator threshold level $E_t$ influences not only the counting efficiency and noise performances, but also the spatial resolution and the counting statistics of the detector. 
-If the threshold is set at values higher than the ideal value $E_t=E_0/2$, a fraction of the photons absorbed in the sensor in the region between two strips is not counted thus reducing the detector efficiency but improving its spatial resolution (narrower strip size). On the other hand, if the threshold is set at values lower than $E_t$, part of the X-rays absorbed in the region between two strips are counted by both of them, resulting in a deterioration of the spatial resolution of the detector and of the fluctuations on the number of photons because of the increased multiplicity. 
-
-
-Furthermore, the threshold uniformity is particularly critical with regards to fluorescent radiation emitted by the sample under investigation. Since the emission of fluorescent light is isotropic, the data quality will be improved by setting the threshold high enough in order to discard the fluorescence background (see figure~\ref{fig:thrscanfluo}). \\
-Moreover, setting the threshold too close to the energy of the fluorescent light gives rise to large fluctuations between channels in the number of counts since the threshold sits on the steepest part of the threshold scan curve for the fluorescent background. These differences cannot be corrected by using a flat-field normalization  since the fluorescent component is not present in the reference image. For this reason, it is extremely important that the threshold uniformity over the whole detector is optimized. The threshold level must be set at least $\Sigma>3\,ENC$ away from both the fluorescent energy level and the X-ray energy in order to remove the fluorescence background while efficiently count the diffracted photons. 
-
-The comparator threshold is given by a global level which can be set on a module basis and adds to a component which is individually adjustable for each channel. In order to optimize the uniformity of the detector response it is important to properly adjust the threshold for all channels. \\
-Since both the signal amplification stages and the comparator  are linear, it is necessary to calibrate the detector offset $O$ and gain $G$ in order to correctly set its comparator threshold $V_t$ at the desired energy $E_t$:
-\begin{equation}
-V_{t}=O+G \cdot E_t.\label{eq:encal}
-\end{equation}
-This is initially performed by acquiring measurements while scanning the global threshold using different X-ray energies and calculating the median of the counts at each threshold value for each module $i$. The curves obtained for one of the detector modules at three energies are shown in figure~\ref{fig:modulecalibration}. The experimental data are then fitted according to equation~\ref{eq:thrscan} and for each module a linear relation is found between the X-ray energy and the estimated inflection point, as shown in the inset of figure~\ref{fig:modulecalibration}. The resulting offset  $O_i$ and  gain $G_i$ are used as a conversion factor between the threshold level and the energy. 
-
-
-\begin{figure}
-\caption{Expected counts as a function of a threshold energy for a monochromatic beam of energy $E_0$=12~keV. $N_0$=10000 is the number of photons absorbed by the detector during the acquisition time. The dashed line represents the curve in an ideal case without electronic noise and charge sharing, the solid thin line with noise  $ENC$=1~keV but without charge sharing and the solid thick line is the physical case with noise and $CS=$22~\% charge sharing. $N_S$ is the number of photons whose charge is shared between neighbouring strips ($CS=\frac{N_S}{N_0}$). The dotted line represents the number of photons whose charge is completely collected by a single strip.}\label{fig:thrscanexpl}
-\includegraphics[width=\textwidth]{fig4.eps}
-\end{figure} 
-
-
-
-\begin{figure}
-\caption{Measured threshold scan at 12.5~keV with the three different settings. In the inset the fit of the experimental data with the expected curve as in function~\ref{eq:thrscan} is shown in the region of the inflection point.} \label{fig:expthrscan}
-\includegraphics[width=\textwidth]{fig5.eps}
-\end{figure} 
-
-\begin{figure}
-\caption{Number of counts as a function of the threshold measured from a sample containing iron ($E_f$=5.9~keV) when using X-rays of energy $E_0$=12~keV. In this case, setting the threshold at $E_0/2$, which is very close to $E_f$, would give $\Delta \sim$10\% counts from the fluorescense background. Therefore the threshold should be set at an intermediate level $E_t$ between the two energy components with a distance of at least $\Sigma>3ENC$  from both $E_f$ and $E_0$.}\label{fig:thrscanfluo}
-\includegraphics[width=\textwidth]{fig7.eps}
-\end{figure}
-Differences in gain and offset are present also between individual channels within a module and therefore the use of threshold equalization techniques (trimming) using the internal 6-bit DAC is needed in order to reduce the threshold dispersion.
-Since both gain and offset have variations between channels, the optimal trimming should be performed as a function of the threshold energy.
-Please not that trimming of the channels of the detector should be performed in advanced and is extremely important for a succeful energy calibration of the detector.
-
-All energy calibration procedures should be applied to a trimmed detector and only an improvement of the existing trimbits can be performed afterwards, since it does not significatively affect the energy calibration.
-
-
-\begin{figure}
-\caption{Median of the number of counts as a function of the threshold for X-rays of 12.5, 17.5 and 25~keV for one of the detector modules using \textit{standard} settings. The solid line represents the fit of the experimental points with equation~\ref{eq:thrscan}. In the inset the linear fit between the X-ray energy and the position of the inflection point of the curves is shown.}\label{fig:modulecalibration}
-\includegraphics[width=\textwidth]{fig8.eps}
-\end{figure}
-\newpage
-
-\section{Data acquisition}
-
-The energy calibration consists in acquiring threshold scans using the detector at at least 2 (better 3) energies. A monochromatic beam is ideal in this procedure, but beam obtained from some fluorescent sample is also good.\\
-Please note that the statistic is important to succesfully analyze the data. Normally the exposure time for each step should be chosen in order to achieve at least 1000 counts per step.
-If this is not possible it is better to reduce the scan range or enlarge the scan step rather than acquiring data with a too low statics.
-
-With a quick acquisition or threshold scan it is useful to define the range of the scan and the exposure time. It is important to start from a threshold high enough that (almost) all channels of the detector have a negligible number of counts and that the plateau of the S-curve is long enough to correctly estimate the number of photons.
-
-\subsection{Software}
-
-For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.\\
-
-In the following the command to acquire a dataset for the energy calibration with an exposure time of 1~s, and threshold scan range between 200 and 850 with a setp of 1 DAC unit.
-\begin{verbatim}
-> sls_detector_put encallog 1 #setup energy calibration
-> sls_detector_put exptime 1. #set exposure time to 1s
-> sls_detector_put scan0script threshold #setup threshold scan
-> sls_detector_put scan0range 200 850 1 #set scan range between 200 and 850, step of 1
-> sls_detector_acquire #acquire the data
-> sls_detector_put encallog 0 #unset energy calibration
-\end{verbatim}
-
-With the GUI you can obtain the same results by clicking on the \textit{Energy Calibration} log button in the advanced tab (see figure~\ref{fig:guiencallog}) and setting up the threshold scan in the Actions tab (see figure~\ref{fig:guithrscan}). the exposure time should also be set in the measurement tab.
-
-
-This procedure should be executed at at least 2 (better 3) energies.
-
-Additional to the data files, the acquisition will produce a .encal file containing an header and, for each step of the acquisition, the threshold value and the file name. \\
-In case you forgot to enable the encallog flag in the software, you can produce the file with the syntax as follows:
-\begin{verbatim}
-settings standard
-type Mythen+
-nmod 12
-modulenumber:0 000
-modulenumber:1 111
-modulenumber:2 222
-modulenumber:3 333
-modulenumber:4 444
-modulenumber:5 555
-modulenumber:6 666
-modulenumber:7 777
-modulenumber:8 888
-modulenumber:9 999
-modulenumber:10 aaa
-modulenumber:11 bbb
-450 standard_12_4keV_S450_0
-460 standard_12_4keV_S460_0
-470 standard_12_4keV_S470_0
-480 standard_12_4keV_S480_0
-490 standard_12_4keV_S490_0
-500 standard_12_4keV_S500_0
-510 standard_12_4keV_S510_0
-520 standard_12_4keV_S520_0
-...
-...
-\end{verbatim}
-
-
-
-
-\begin{figure}
-\caption{Acquisition GUI window to enable the energy calibration log.} \label{fig:guiencallog}
-\includegraphics[width=\textwidth]{GUI_Advanced.eps}
-\end{figure} 
-
-\begin{figure}
-\caption{Acquisition GUI window to setup the threshold scan.} \label{fig:guithrscan}
-\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}
-\end{figure} 
-\newpage
-
-\section{Data analysis}
-
-The data analysis consists in fitting the S-curves obtained from the datasets acquired as above and then performing a linear fit between the energy values and the inflection points.
-
-\subsection{Software}
-
-The software used for the energy calibration data analysis is based on root (see http://root.cern.ch).\\
-This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
-
-To start the data analysis simply launch:
-\begin{verbatim}
-> ./energyCalibrationWizard 
-\end{verbatim}
-
-To add anew energy write the energy value and select (or digit) the name of the .encal file corresponding to that energy (see figure~\ref{fig:addenergy}).\\
-The software assumes that the data files (.raw) and the .encal file are in the same directory.
-Press  \textit{Preview} and a 2D color plot will be displayed, showing the channel numbers on the X-axis, the threshold on the Y-axis, and the number of counts as a color scale.
-By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.\\
-If the plot corresponds to your expectations press \textit{Add to list}. The energy value will be shown in the combo box on top and labels will display the settings of the detector, the number of modules, the number of channels per module and the modules serial numbers.
-
-Add then all the other energies to the calibration always by editing the energy value and .encal file name, pressing \textit{preview} and \textit{add to list}.\\
-If the settings, number of modules or serial numbers do not match, you will not be llowed to add the energy.\\
-By using the \textit{selected energy actions} you can navigate in the combo box with list of energies, view the plots and eventually remove the ones you don't want to use in your calibration.\\
-Once you have uploaded at least 2 energies, you will be allowed to  \textit{proceed to module calibration}.
-
-
-
-\begin{figure}
-\caption{Window to add energies to the calibration.} \label{fig:addenergy}
-\includegraphics[width=\textwidth]{addEnergy.eps}
-\end{figure} 
-
-In the module calibration window (see figure~\ref{fig:calibratemodule}), you are still able to look at the calibration summary, and eventually return to the previous windown by pressing \textit{Back to energy setup}.\\
-The canvas will show the plot of the S-curves relative to the median of the selected module, fitted with equation~\ref{eq:thrscan} and the linear fit between the energy values and the fitted inflection points.
-Normally the points lie on a straight line (although often not perfect), therefore it should be simple to spot if there are problems in the fitting of some of the data.\\
-If \textit{Manual save} is unclicked, the calibration files will be saved locally, with the extension automatically generated by using the modules serial numbers, every time a linear fit is performed (i.e. if you mess up wiht the linear fit you overwrite a previous good file!). If you click the checkbox, you need to save the calibration by pressing \textit{Write to file} for each module once you are happy with the fit.
-
-To change the Y scale of the plot, edit the \textit{Counts} entry. After clicking of the energy button (eventually twice) the maximum of the histogram will be set to three times the value.
-
-To re-fit one energy with modified range or start parameters, you should press the central button with the energy value once the energy is selected. The text color tells you which curve you are referring to.\\
-
-You should set the range of the fit. In particular the maximum should be limited in order to avoid to enter the noise range (and can be pretty different for the various modules).\\
-Normally the data are acquired by collecting holes from the detector and therefore the \textit{Invert axis} check button should be ckecked. Uncheck it in case your detector collects electrons (e.g. CdTe, Si n in p)
-
-You can change the start values of the parameters of the fits by editing the number eneries. The label nearby will show you the actual value of the fitted parameters.\\
-By checking the checkboxes you can fix the values to the ones you specify.\\
-Normally it can be useful to fix the pedestal and pedestal slope to 0, unless you have a lot of 3rd armnonics contribution, primary beam background or similar.\\
-Changing the starting value of the inflection point or of the number of counts can often help the fit to converge.\\
-Normally it is not very useful to change the starting value for the noise or charge sharing slope.
-
-The button \textit{Finished} will be enebled only once the calibration files have been generated for all modules.
-
-
-\begin{figure}
-\caption{Window to calibrate the modules.} \label{fig:calibratemodule}
-\includegraphics[width=\textwidth]{calibrateModule.eps}
-\end{figure} 
-\newpage
-
-
-\section{Setup calibration files}
-
-To use the genrated calibration files as default ones, copy them into your default \textit{caldir/settings} renaming them calibration.snxxx, where snxxx is the extension that the genrated files already have, which corresponds to the module serial number.\\
-Fot this scope, a script as following can be used:
-\begin{verbatim}
-for i in $(ls newcal_standard.sn* | awk -F "." '{print $2}'); do \
-mv newcal_standard.$i caldir/standard/calibration.$i; \
-done
-\end{verbatim}
-
-By reloading the default detector settings, the calibration coefficients will be automatically loaded.