release txt fix

Jfcalib

.clang-tidy

@@ -18,7 +18,8 @@ Checks:          '*,
                     -google-readability-todo, 
                     -google-readability-braces-around-statements,
                     -modernize-use-trailing-return-type,
-                    -readability-isolate-declaration'
+                    -readability-isolate-declaration,
+                    -llvmlibc-*'
 
 HeaderFilterRegex: \.h
 AnalyzeTemporaryDtors: false

CMakeLists.txt

@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.12)
 project(slsDetectorPackage)
-set(PROJECT_VERSION 5.0.0)
+set(PROJECT_VERSION 5.1.0)
 include(CheckIPOSupported)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
 
@@ -32,13 +32,16 @@ if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
     set(SLS_MASTER_PROJECT ON)
 endif()
 
-option (SLS_USE_HDF5 "HDF5 File format" OFF)
-option (SLS_USE_TEXTCLIENT "Text Client" ON)
-option (SLS_USE_RECEIVER "Receiver" ON)
-option (SLS_USE_GUI "GUI" OFF)
-option (SLS_USE_SIMULATOR "Simulator" OFF)
-option (SLS_USE_TESTS "TESTS" OFF)
-option (SLS_USE_INTEGRATION_TESTS "Integration Tests" OFF)
+option(SLS_USE_HDF5 "HDF5 File format" OFF)
+option(SLS_BUILD_SHARED_LIBRARIES "Build shared libaries" ON)
+option(SLS_USE_TEXTCLIENT "Text Client" ON)
+option(SLS_USE_DETECTOR "Detector libs" ON)
+option(SLS_USE_RECEIVER "Receiver" ON)
+option(SLS_USE_RECEIVER_BINARIES "Receiver binaries" ON)
+option(SLS_USE_GUI "GUI" OFF)
+option(SLS_USE_SIMULATOR "Simulator" OFF)
+option(SLS_USE_TESTS "TESTS" OFF)
+option(SLS_USE_INTEGRATION_TESTS "Integration Tests" OFF)
 option(SLS_USE_SANITIZER "Sanitizers for debugging" OFF)
 option(SLS_USE_PYTHON "Python bindings" OFF)
 option(SLS_USE_CTBGUI "ctb GUI" OFF)
@@ -93,6 +96,20 @@ target_compile_options(slsProjectWarnings INTERFACE
 
                                  )
 
+#Settings for C code
+add_library(slsProjectCSettings INTERFACE)
+target_compile_features(slsProjectCSettings INTERFACE c_std_99)
+target_compile_options(slsProjectCSettings INTERFACE 
+                                            -Wall
+                                            -Wextra
+                                            -Wno-unused-parameter
+                                            -Wdouble-promotion
+                                            -Wformat=2
+                                            -Wredundant-decls
+                                            -Wdouble-promotion
+                                            -Werror=return-type
+                                )
+
 
 #Testing for minimum version for compilers
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
@@ -157,8 +174,37 @@ set(CMAKE_INSTALL_RPATH $ORIGIN)
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 
 
+set(ZeroMQ_HINT "" CACHE STRING "Hint where ZeroMQ could be found")
+#Adapted from: https://github.com/zeromq/cppzmq/
+if (NOT TARGET libzmq)
+    if(ZeroMQ_HINT)
+        message(STATUS "Looking for ZeroMQ in: ${ZeroMQ_HINT}")
+        find_package(ZeroMQ 4 
+            NO_DEFAULT_PATH
+            HINTS ${ZeroMQ_DIR}
+        )
+    else()
+        find_package(ZeroMQ 4 QUIET)
+    endif()
+    
 
-find_package(ZeroMQ 4 REQUIRED)
+
+  # libzmq autotools install: fallback to pkg-config
+  if(NOT ZeroMQ_FOUND)
+    message(STATUS "CMake libzmq package not found, trying again with pkg-config (normal install of zeromq)")
+    list (APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/libzmq-pkg-config)
+    find_package(ZeroMQ 4 REQUIRED)
+  endif()
+
+  # TODO "REQUIRED" above should already cause a fatal failure if not found, but this doesn't seem to work
+  if(NOT ZeroMQ_FOUND)
+    message(FATAL_ERROR "ZeroMQ was not found, neither as a CMake package nor via pkg-config")
+  endif()
+
+  if (ZeroMQ_FOUND AND NOT TARGET libzmq)
+    message(FATAL_ERROR "ZeroMQ version not supported!")
+  endif()
+endif()
 
 if (SLS_USE_TESTS)
     enable_testing()
@@ -171,9 +217,9 @@ endif(SLS_USE_TESTS)
 # Common functionallity to detector and receiver
 add_subdirectory(slsSupportLib)
 
-if (SLS_USE_TEXTCLIENT)
+if (SLS_USE_DETECTOR OR SLS_USE_TEXTCLIENT)
     add_subdirectory(slsDetectorSoftware)
-endif (SLS_USE_TEXTCLIENT)
+endif ()
 
 if (SLS_USE_RECEIVER)
     add_subdirectory(slsReceiverSoftware) 

LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+  If the program does terminal interaction, make it output a short
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+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
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+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
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+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

LICENSE.lesser

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
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+
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+
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+
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README.md

@@ -4,7 +4,11 @@ Please do not update to any xxxx.xx.xx.dev0 tags. They are not releases, but tag
 Use only releases with tags such as x.x.x or x.x.x-rcx.
 
 ### Documentation
-Detailed documentation on the latest release of 5.0.0 can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html) and on the [official site](https://www.psi.ch/en/detectors/software).
+##### 5.0.0 - Latest Release
+Detailed documentation on the latest release 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).
+
+##### Older Releases
+Documentation is found in the package.
 
 ### Binaries
 Binaries for the slsDetectorPackage are available through conda. 
@@ -45,7 +49,7 @@ These are mainly aimed at those not familiar with using ccmake and cmake.
 ```
     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>]
+    Usage: ./cmk.sh [-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
@@ -65,6 +69,7 @@ These are mainly aimed at those not familiar with using ccmake and cmake.
     -m: Manuals
     -n: Manuals without compiling doxygen (only rst)
     -z: Moench zmq processor
+
     
     # get all options
     ./cmk.sh -?
@@ -90,3 +95,8 @@ To install binaries using CMake
     make -j12 #or whatever number of cores you are using to build
     make install
 ```
+
+
+### Support
+    dhanya.thattil@psi.ch
+    erik.frojdh@psi.ch

RELEASE.txt

@@ -1,13 +1,13 @@
-SLS Detector Package 5.0.1 released on 25.11.2020 (Bug Fix Release)
-===================================================================
+SLS Detector Package 6.0.0-rc1 released on 08.10.2021 (Release Candidate 1)
+===========================================================================
 
-This document describes the differences between 5.0.1 and 5.0.0 releases.   
+This document describes the differences between v6.0.0-rc1 and v5.1.0.   
 
 
 
     CONTENTS
     --------
-    1.  Topics Concerning
+    1.  New or Changed Features
     2.  Resolved Issues
     3.  Known Issues
     4.  Firmware Requirements
@@ -15,56 +15,313 @@ This document describes the differences between 5.0.1 and 5.0.0 releases.
 
 
 
-1. Topics Concerning
-====================
 
-    - Python bindings
-    - CMake improvements
+1. New or Changed Features
+==========================
 
+    Client 
+    ------
+
+    1.  [Jungfrau] Chip version 
+        Features for chipv1.1 incorporated
+        Command line: chipversion, API: getchipVersion 
+        gets chip version (1.0 or 1.1)
+        chipv1.1 requires config_jungfrau.txt on detector server.
+    
+    2.  [Jungfrau] Chip configuration (only chipv1.1)
+        powering on the chip and changing settings will configure the chip.
+        Hence, required before acquisition.
+
+    3.  [Jungfrau] Settings and Gain mode 
+        Settings can be gain0 and highgain0. Gain mode can be dynamicgain, 
+        forceswitchg1, forceswitchg2, fixg1, fixg2, fixg0. fixg0 must be 
+        used with EXTRA caution as you can damage the detector.
+        Changing settings also changes dac values of 3 dacs () and reconfigures
+        chip (only v1.1)
+
+    4.  [Jungfrau] Storage cells (only chipv1.1)
+        Additional number of storage cells not applicable for chipv1.1.
+        Storage cell start is only allowed from 0 - 3 for chipv1.1 
+        (0 - 15 for chipv1.0).
+    
+    5.  [Gotthard2][Jungfrau] Filter Resistor 
+        Command line: filterresistor, API: getFilterResistor/ setFilterResistor
+        Previous Command: filter, setFilter/ getFilter
+        Set Filter resistor. Increasing values for increasing resistance.
+        [Jungfrau] only for chipv1.1. Options: [0|1]. Default is 1.
+        [Gotthard2] Options: [0|1|2|3]. Default is 0.
+
+    6.  [Jungfrau] Filter cell (only chipv1.1)
+        Command line: filtercell, API: getFilterCell/ setFilterCell
+        Set filter cell. Options: [0-12]. Advanced user command.
+
+    7.  [Jungfrau] Comparator disable time (only chipv1.1)
+        Command line: comp_disable_time, API: getComparatorDisableTime/ 
+        setComparatorDisableTime 
+        One can customize the period to disable comparator.
+
+    8.  [Eiger][Jungfrau] Flip rows
+        Command line: fliprows, API: getFlipRows/ setFlipRows
+        Previous command: flippeddatax, setBottom/ getBottom
+        [Jungfrau] Flips rows in detector only for HW v2.0.
+        slsReceiver and slsDetectorGui will not flip them again.
+        [Eiger] same as before.
+
+    9.  [Eiger][Jungfrau] Read n rows
+        Command line: readnrows, API: getReadNRows/ setReadNRows
+        Previous Command: readnlines, getPartialReadout/ setPartialReadout
+        [Eiger] same as before
+        [Jungfrau] Options: 8 - 512, multiples of 8. Default is 512.
+
+    10. [Gotthard2][Jungfrau] Current source 
+        Command line: currentsource, API: getCurrentSource, setCurrentSource
+        Enable or disable current source. Default is disabled.
+        [Gotthard2] Can only enable or disable.
+        [Jungfrau] Can choose to fix, select source and choose normal or low 
+        current. Normal/ low only for chipv1.1. 
+        Select source is 0-63 for chipv1.0 and a 64 bit mask for chipv1.1. 
+
+    11. Default dac 
+        Command line: defaultdac, API: getDefaultDac/ setDefaultDac
+        change default value of a dac
+        [Jungfrau][Mythen3] Also change default value of dac for particular 
+        setting.
+
+    12. Reset dacs
+        Command line: resetdacs, API: resetToDefaultDacs
+        Previous command: defaultdacs
+        Resets dacs to their default values or hard coded values.
+        
+    13. [Mythen3] Gain Capacitance
+        Command line: gaincaps, API: getGainCaps/ setGainCaps
+        Set various gain capacitances.
+
+    14. [Gotthard2] Veto Streaming from chip
+        Command line: veto, API: getVeto/ setVeto
+        This command used to mean veto streaming from detector. Now, it means
+        veto streaming from chip (New feature). Default is disabled.
+
+    15. [Gotthard2] Veto streaming from detector
+        Command line: vetostream, API: getVetoStream, setVetoStream
+        Options: None, local link interface, 10 10GbE, Both
+        Default: None
+        10GbE (as before) will enable 2 udp interfaces in receiver.
+
+    16. [Gotthard2] Veto algorithm
+        Command line: vetoalg, API: getVetoAlgorithm/ setVetoAlgorithm
+        Set veto algorithm for each interface.
+        Options: hits, raw
+        
+    17. [Eiger][Gotthard2][Mythen3] Module ID
+        Command line: moduleid, API: getModuleId
+        Previous command (Eiger only): serialnumber, getSerialNumber
+        Unique id read from txt file on detector and streamed out in udp header.
+    
+    18. [Gotthard2]
+        Command line: dbitpipeline, API: getDBITPipeline/ setDBITPipeline 
+        Set pipeline to latch digital bits. Options: 0-7
+
+    19. [Eiger][Jungfrau] Round Robin commands
+        Command line, udp_dstlist, API: getDestinationUDPList/ 
+        setDestinationUDPList
+        Round robin commands at the moment does not configure the receiver.
+        Set multiple udp destinations in the detector to stream udp data packets 
+        to. Upto 32 destinations. Refer documentation for details.
+
+        Command line, udp_numdst, API: getNumberofUDPDestinations
+
+        [Jungfrau] Command line, udp_firstdst, API: getFirstUDPDestination/ 
+        setFirstUDPDestination
+    
+    20. Command Line Parsing 
+        Parsing of detector index and module index has been modified to 
+        integrate round robin index.
+        [detector index]-[module index]:[round robin index] [command]
+
+        It is backwards compatible.
+        For ease, one can also execute
+        sls_detector_put [module index] [command]
+
+    21. Clear Udp Destination
+        Command line, udp_cleardst, API: clearUDPDestinations
+        This is useful when changing receivers for a detector or for round robin
+        system.
+
+    22. Shared Memory Naming
+        Shared memory name has been changed to reflect a more appropriate naming 
+        scheme.
+
+    23. [Eiger][Mythen3] Blocking trigger 
+        Command line: blockingtrigger, API: sendSoftwareTrigger
+        Sends software trigger signal to detector and blocks till frames are
+        sent out for that trigger.
+
+    24. [Eiger] Data stream enable for ports
+        Command line: datastream, API: getDataStream/ setDataStream
+        Enable or disable each port. Default: enabled
+
+    25. Changing TCP ports
+        This will only affect shared memory and will not try to change the
+        current tcp port of the control/stop server in detector.
+
+    26. [Eiger][Jungfrau][Gotthard2] Speed 
+        Command line: readoutspeed, readoutspeedlist API: getReadoutSpeed/ setReadoutSpeed /
+        getReadoutSpeedList
+        Previous command: speed, setSpeed/ getSpeed
+        [Eiger][Jungfrau] same as before.
+        [Gotthard2] New command to set readout speed. Options: 108, 144 (in MHz)
+        
+
+    Detector servers
+    ----------------
+
+    1.  [Gotthard2] Bad Channels moved to a new register, default settings 
+        including clock frequency changed
+
+    2.  [Gotthard2] Updated config file in detector server
+    
+
+    Virtual servers
+    ----------------
+
+    1.  Artifical pixel values increasing by every packet, instead of every pixel.
+
+    2.  All possible features updated.
+
+
+    Receiver
+    --------
+
+    1.  Frames caught in metadata
+        Frames caught by the master receiver is added to master file metadata.
+        Hdf5 and Binary version numbers changed to 6.3
+
+    2.  Removed Padding option for Deactivated half modules.
+
+    3.  Changing Receiver TCP ports
+        This will only affect shared memory and will not try to change the
+        current tcp port of the receiver.
+
+    Gui
+    ----
+
+    1. [Mythen3] counters added in settings tab
 
 
 2. Resolved Issues
 ==================
 
-    Python bindings
-    ---------------
+    Detector Servers
+    ----------------
 
-    1.  Fixed function signatures for getRxUDPSocketBufferSize, 
-        setRxUDPSocketBufferSize and getRxRealUDPSocketBufferSize. 
+    1.  [Gotthard2] Tolerance in time parameters. 
+        Eg. 220 ns was being set to 215 ns, instead of 222ns.
 
-    2.  Updated pybind11 to v2.6.1 to remove warnings with Python 3.9 and 
-        better handling of C++ standard. 
+    2.  [Jungfrau] Stopping in trigger mode and then switching to auto timing mode 
+        blocks data streaming from detector. Workaround fix made in 
+        detector server to reset core until next firmware release.
 
-    3.  Added missing properties in Python. 
+    3.  [Jungfrau][CTB][Moench][Gotthard][Gotthard2][Mythen3] Firmware Programming
+        Firmware programming incorporates more validations such as checksum of 
+        program. Always ensure client and server are of same release before 
+        programming firmware.
+
+    4.  [Eiger] Stop sends last frame
+        Stop acquisition will now also send out all complete frames in fifo.
+
+    5.  [Eiger] Bottom not rotated in quad mode. Fixed.
+
+    6.  [Mythen3] counter mask effect on vthreshold
+        Setting counter mask changes vth daac values (ie. disabling sets to 2800),
+        vthreshold only changes for enabled counters, setting vth overwrites
+        dac even if counter disabled and when counters enabled, remembers set 
+        values.
+    
+    7.  [Eiger] fast quad fix for loading trimbits
+    
+    Receiver
+    --------
+
+    1.  Disabled port or deactivated (half) modules will not create files.
 
 
-    CMake improvements
-    ------------------
-
-    1. Explicitly state Python 3.6 or greater.
-
-    2. Finds the Python of the activated environment when using conda 
-       without having to supply additional arguments.  
-
-    3. Removed redundant libraries for linking targets. 
-
+- better control of what is built (PR)?
+- cmake package has hardcoded path to zeromq library
 
 
 3. Firmware Requirements
 ========================
         
-    No updates from 5.0.0
+    Eiger
+    =====  
+    Compatible version : 08.10.2021 (v29)
+    
+    Jungfrau
+    ========       
+    Compatible version : 31.08.2021 (v1.2, PCB v1.0) 
+                       : 08.10.2021 (v2.2, PCB v2.0)
+
+    Gotthard
+    ========   
+    Compatible version : 08.02.2018 (50um and 25um Master)
+                       : 09.02.2018 (25 um Slave) 
+
+    Mythen3
+    =======
+    Compatible version : 10.09.2021 (development)
+
+    Gotthard2
+    =========
+    Compatible version : 27.05.2021 (v1.0)
+
+    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
 
 
 
-4. Known Issues
+
+
+5. Known Issues
 ===============
 
-    No updates from 5.0.0
+    Receiver
+    --------
+    1.  It does not handle readnrows or partial readout. Only the summary
+        is adjusted to print in red. However, it will still write complete
+        images with missing data padded. Roi will be implemented in future
+        that can be complimented with this feature to remove the additional
+        data in files.
+
+    2.  Round robin is not implemented in receiver side, ie. one cannot configure
+        more than 1 receiver at a time. This will/might be done in the future.
 
 
 
-5. Download, Documentation & Support
+6. Download, Documentation & Support
 ====================================
 
     Download

cmake/FindZeroMQ.cmake

@@ -1,112 +0,0 @@
-
-# This file is originally from https://github.com/zeromq/azmq and distributed 
-# under Boost Software Lincese 1.0
-# Boost Software License - Version 1.0 - August 17th, 2003
-
-# Permission is hereby granted, free of charge, to any person or organization
-# obtaining a copy of the software and accompanying documentation covered by
-# this license (the "Software") to use, reproduce, display, distribute,
-# execute, and transmit the Software, and to prepare derivative works of the
-# Software, and to permit third-parties to whom the Software is furnished to
-# do so, all subject to the following:
-
-# The copyright notices in the Software and this entire statement, including
-# the above license grant, this restriction and the following disclaimer,
-# must be included in all copies of the Software, in whole or in part, and
-# all derivative works of the Software, unless such copies or derivative
-# works are solely in the form of machine-executable object code generated by
-# a source language processor.
-
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
-# SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
-# FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
-# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-# DEALINGS IN THE SOFTWARE.
-# --------------------------------------------------------------------------------
-
-# Find ZeroMQ Headers/Libs
-
-# Variables
-# ZMQ_ROOT - set this to a location where ZeroMQ may be found
-#
-# ZeroMQ_FOUND - True of ZeroMQ found
-# ZeroMQ_INCLUDE_DIRS - Location of ZeroMQ includes
-# ZeroMQ_LIBRARIES - ZeroMQ libraries
-
-include(FindPackageHandleStandardArgs)
-
-if (NOT ZMQ_ROOT)
-    set(ZMQ_ROOT "$ENV{ZMQ_ROOT}")
-endif()
-
-if (NOT ZMQ_ROOT)
-    find_path(_ZeroMQ_ROOT NAMES include/zmq.h)
-else()
-    set(_ZeroMQ_ROOT "${ZMQ_ROOT}")
-endif()
-
-find_path(ZeroMQ_INCLUDE_DIRS NAMES zmq.h HINTS ${_ZeroMQ_ROOT}/include)
-
-if (ZeroMQ_INCLUDE_DIRS)
-    set(_ZeroMQ_H ${ZeroMQ_INCLUDE_DIRS}/zmq.h)
-
-    function(_zmqver_EXTRACT _ZeroMQ_VER_COMPONENT _ZeroMQ_VER_OUTPUT)
-        set(CMAKE_MATCH_1 "0")
-        set(_ZeroMQ_expr "^[ \\t]*#define[ \\t]+${_ZeroMQ_VER_COMPONENT}[ \\t]+([0-9]+)$")
-        file(STRINGS "${_ZeroMQ_H}" _ZeroMQ_ver REGEX "${_ZeroMQ_expr}")
-        string(REGEX MATCH "${_ZeroMQ_expr}" ZeroMQ_ver "${_ZeroMQ_ver}")
-        set(${_ZeroMQ_VER_OUTPUT} "${CMAKE_MATCH_1}" PARENT_SCOPE)
-    endfunction()
-
-    _zmqver_EXTRACT("ZMQ_VERSION_MAJOR" ZeroMQ_VERSION_MAJOR)
-    _zmqver_EXTRACT("ZMQ_VERSION_MINOR" ZeroMQ_VERSION_MINOR)
-    _zmqver_EXTRACT("ZMQ_VERSION_PATCH" ZeroMQ_VERSION_PATCH)
-
-    message(STATUS "ZeroMQ version: ${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}.${ZeroMQ_VERSION_PATCH}")
-
-    # We should provide version to find_package_handle_standard_args in the same format as it was requested,
-    # otherwise it can't check whether version matches exactly.
-    if (ZeroMQ_FIND_VERSION_COUNT GREATER 2)
-        set(ZeroMQ_VERSION "${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}.${ZeroMQ_VERSION_PATCH}")
-    else()
-        # User has requested ZeroMQ version without patch part => user is not interested in specific patch =>
-        # any patch should be an exact match.
-        set(ZeroMQ_VERSION "${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}")
-    endif()
-
-    if (NOT ${CMAKE_CXX_PLATFORM_ID} STREQUAL "Windows")
-        find_library(ZeroMQ_LIBRARIES NAMES zmq HINTS ${_ZeroMQ_ROOT}/lib)
-    else()
-        find_library(
-            ZeroMQ_LIBRARY_RELEASE
-            NAMES
-                libzmq
-                "libzmq-${CMAKE_VS_PLATFORM_TOOLSET}-mt-${ZeroMQ_VERSION_MAJOR}_${ZeroMQ_VERSION_MINOR}_${ZeroMQ_VERSION_PATCH}"
-            HINTS
-                ${_ZeroMQ_ROOT}/lib
-            )
-
-        find_library(
-            ZeroMQ_LIBRARY_DEBUG
-            NAMES
-                libzmq_d
-                "libzmq-${CMAKE_VS_PLATFORM_TOOLSET}-mt-gd-${ZeroMQ_VERSION_MAJOR}_${ZeroMQ_VERSION_MINOR}_${ZeroMQ_VERSION_PATCH}"
-            HINTS
-                ${_ZeroMQ_ROOT}/lib)
-
-        # On Windows we have to use corresponding version (i.e. Release or Debug) of ZeroMQ because of `errno` CRT global variable
-        # See more at http://www.drdobbs.com/avoiding-the-visual-c-runtime-library/184416623
-        set(ZeroMQ_LIBRARIES optimized "${ZeroMQ_LIBRARY_RELEASE}" debug "${ZeroMQ_LIBRARY_DEBUG}")
-    endif()
-endif()
-
-find_package_handle_standard_args(ZeroMQ FOUND_VAR ZeroMQ_FOUND
-    REQUIRED_VARS ZeroMQ_INCLUDE_DIRS ZeroMQ_LIBRARIES
-    VERSION_VAR ZeroMQ_VERSION)
-
-if (ZeroMQ_FOUND)
-    mark_as_advanced(ZeroMQ_INCLUDE_DIRS ZeroMQ_LIBRARIES ZeroMQ_VERSION
-        ZeroMQ_VERSION_MAJOR ZeroMQ_VERSION_MINOR ZeroMQ_VERSION_PATCH)
-endif()

cmake/package_config.cmake

@@ -25,6 +25,12 @@ install(FILES
   DESTINATION ${CMAKE_INSTALL_DIR}
 )
 
+install(FILES
+  "${CMAKE_SOURCE_DIR}/libzmq-pkg-config/FindZeroMQ.cmake"
+  COMPONENT devel
+  DESTINATION ${CMAKE_INSTALL_DIR}/libzmq-pkg-config
+)
+
 if (PROJECT_LIBRARIES OR PROJECT_STATIC_LIBRARIES)
   install(
     EXPORT "${TARGETS_EXPORT_NAME}"

cmake/project-config.cmake.in

@@ -12,8 +12,21 @@ include(CMakeFindDependencyMacro)
 
 set(SLS_USE_HDF5 "@SLS_USE_HDF5@")
 
-# Add optional dependencies here
+
+find_package(ZeroMQ 4 QUIET)
+# libzmq autotools install: fallback to pkg-config
+if(NOT ZeroMQ_FOUND)
+    list (APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/libzmq-pkg-config)
+    find_package(ZeroMQ 4 REQUIRED)
+endif()
+
+if(NOT ZeroMQ_FOUND)
+    message(FATAL_ERROR "ZeroMQ was NOT found!")
+endif()
+
 find_dependency(Threads)
+
+# Add optional dependencies here
 if (SLS_USE_HDF5)
     find_dependency(HDF5)
 endif ()

conda-recepie/build.sh

@@ -8,13 +8,15 @@ cmake .. \
       -DSLS_USE_TEXTCLIENT=ON \
       -DSLS_USE_RECEIVER=ON \
       -DSLS_USE_GUI=ON \
+      -DSLS_USE_MOENCH=ON\
       -DSLS_USE_TESTS=ON \
       -DSLS_USE_PYTHON=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DSLS_USE_HDF5=OFF\
      
-
-cmake --build . -- -j10
+NCORES=$(getconf _NPROCESSORS_ONLN)
+echo "Building using: ${NCORES} cores"
+cmake --build . -- -j${NCORES}
 cmake --build . --target install
 
-CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2
+CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2

conda-recepie/copy_gui.sh

@@ -1,3 +1,3 @@
 #Copy the GUI 
-mkdir $PREFIX/bin
-cp build/bin/slsDetectorGui $PREFIX/bin/.
+mkdir -p $PREFIX/bin
+cp build/install/bin/slsDetectorGui $PREFIX/bin/.

conda-recepie/copy_lib.sh

@@ -1,6 +1,6 @@
 
-mkdir $PREFIX/lib
-mkdir $PREFIX/bin
+mkdir -p $PREFIX/lib
+mkdir -p $PREFIX/bin
 mkdir -p $PREFIX/include/sls
 # mkdir $PREFIX/include/slsDetectorPackage
 

conda-recepie/copy_moench.sh

@@ -0,0 +1,4 @@
+#Copy the Moench executables 
+mkdir -p $PREFIX/bin
+cp build/install/bin/moench04ZmqProcess $PREFIX/bin/.
+cp build/install/bin/moenchZmqProcess $PREFIX/bin/.

conda-recepie/meta.yaml

@@ -59,6 +59,16 @@ outputs:
     script: copy_lib.sh
 
     requirements:
+      build:
+        - {{ compiler('c') }}
+        - {{compiler('cxx')}}
+        - libstdcxx-ng
+        - libgcc-ng
+        - zeromq
+
+      host:
+        - zeromq
+
       run: 
         - libstdcxx-ng
         - libgcc-ng
@@ -78,6 +88,8 @@ outputs:
 
       host:
         - python
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+
 
       run:
         - libstdcxx-ng
@@ -94,8 +106,29 @@ outputs:
   - name: slsdetgui
     script: copy_gui.sh
     requirements:
+
+      build:
+        - {{ compiler('c') }}
+        - {{compiler('cxx')}}
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - qwt 6.*
+
       run:
         - {{ pin_subpackage('slsdetlib', exact=True) }}
         - qwt 6.*
         - qt 4.8.*
         - expat
+
+  - name: moenchzmq
+    script: copy_moench.sh
+    requirements:
+
+      build:
+        - {{ compiler('c') }}
+        - {{compiler('cxx')}}
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+
+
+      run:
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - expat

docs/src/firmware.rst

@@ -154,6 +154,8 @@ Upgrade (from v5.0.0)
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
+Always ensure that the client and server software are of the same release.
+
 
 #. Program from console
     .. code-block:: bash
@@ -222,6 +224,8 @@ Download
 Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Always ensure that the client and server software are of the same release.
+
 #. Program from console
     .. code-block:: bash
 
@@ -251,6 +255,8 @@ Download
 Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Always ensure that the client and server software are of the same release.
+
 #. Program from console
     .. code-block:: bash
 
@@ -278,6 +284,8 @@ Upgrade (from v5.0.0)
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
+Always ensure that the client and server software are of the same release.
+
 #. Program from console
     .. code-block:: bash
 
@@ -304,6 +312,8 @@ Upgrade (from v5.0.0)
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
 
+Always ensure that the client and server software are of the same release.
+
 #. Program from console
     .. code-block:: bash
 
@@ -344,26 +354,43 @@ Firmware Troubleshooting with blackfin
 
 5. If one can't list it, read the next section to try to get the blackfin to list it.
 
-How to get back mtd3 drive remotely
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-This might take a few reruns (maybe even 10) until the mtd drive is accessed by the blackfin upon linux startup.
+How to get back mtd3 drive remotely (copying new kernel)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
   .. code-block:: bash
     
-    # step 1: connect to the board
+    # step 1: get the kernel image (uImage.lzma) from slsdetectorgroup
+    # and copy it to pc's tftp folder
+
+    # step 2: connect to the board
     telnet bchipxxx
 
-    # step 2: check if mtd3 drive listed
-    more /proc/mtd
+    #step 3: go to directory for space
+    cd /var/tmp/
 
-    # 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;
+    # step 3: copy kernel to board
+    tftp pcxxx -r uImage.lzma -g
+
+    # step 4: verify kernel copied properly
+    ls -lrt
+    
+    # step 5: erase flash
+    flash_eraseall /dev/mtd1
+    
+    # step 6: copy new image to kernel drive
+    cat uImage.lzma > /dev/mtd1
+    
+    # step 7:
+    sync
+    
+    # step 8:
     reboot
-
-    # step 4: repeat steps 1 - 3 until you see the mtd3 drive
-
+    
+    # step 9: verification
+    telnet bchipxxx
+    uname -a # verify kernel date
+    more /proc/mtd # verify mtd3 is listed
+    
 
 Last Resort using USB Blaster
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/src/pyenums.rst

@@ -67,9 +67,6 @@ exposed to Python through pybind11.
 .. autoclass:: readoutMode
     :undoc-members:
 
-.. autoclass:: masterFlags
-    :undoc-members:
-
 .. autoclass:: burstMode
     :undoc-members:
 

docs/src/pygettingstarted.rst

@@ -219,7 +219,7 @@ The enums can be found in slsdet.enums
     >>> [e for e in dir(slsdet.enums) if not e.startswith('_')]
     ['burstMode', 'clockIndex', 'dacIndex', 
     'detectorSettings', 'detectorType', 'dimension', 'externalSignalFlag', 
-    'fileFormat', 'frameDiscardPolicy', 'masterFlags', 
+    'fileFormat', 'frameDiscardPolicy', 
     'readoutMode', 'runStatus', 'speedLevel', 'timingMode', 
     'timingSourceType']
 

docs/src/servers.rst

@@ -34,3 +34,62 @@ Detector Servers include:
       *  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.
+
+
+Automatic start 
+------------------
+
+One can start the on-board detector server automatically upon powering on the board.
+
+#. Create a soft link to the binary on board 
+   :
+      .. code-block:: bash
+      
+         ln -sf someDetectorServervx.x.x someDetectorServer
+
+
+
+#. Do the following depending on the detector type :
+
+   Eiger
+      .. code-block:: bash
+         
+         # create script in rc5.d on the board
+         vi /etc/rc5.d/S50board_com.sh
+
+         # enter the following (edit server name)
+         #! /bin/sh
+         /home/root/executables/eigerDetectorServer &> /dev/null &
+         exit 0
+
+   Jungfrau | Moench | CTB | Gotthard I
+      .. code-block:: bash
+
+         # Edit inittab on board
+         vi /etc/inittab
+
+         # enter the following line
+         ttyS0::respawn:/./xxxDetectorServer
+
+
+   Gotthard II | Mythen III
+      .. code-block:: bash
+         
+         # create script in init.d on board
+         vi /etc/init.d/S99detServer.sh
+
+         # enter the following (edit server name)
+         #! /bin/sh
+         cd /root >> /dev/null
+         /root/xxxDetectorServer >> /dev/null &
+
+
+#. Sync, reboot and verify
+   :
+      .. code-block:: bash
+      
+         sync
+         reboot
+
+         # verify
+         ps -ef | grep xxxDetectorServer

examples/moench03_T1.config

@@ -1,7 +1,8 @@
-initialchecks 0
+#initialchecks 0
 #############################################
 ### edit with hostname or IP address of your detector 
 ############################################
+#hostname bchip181+
 hostname bchip181+
 
 #############################################
@@ -27,7 +28,7 @@ rx_zmqport 50003
 #############################################
 ### edit with 1 Gbs IP of PC where you will run the GUI
 ############################################
-zmqip 129.129.202.136
+zmqip 129.129.202.98
 zmqport 50001
 
 
@@ -39,11 +40,12 @@ rx_zmqstream 1
 
 frames 100000
 period 0.0006
+exptime 0.00035
 
 #############################################
 ### edit with directory you want to write to
 ############################################
-fpath /mnt/moench_data/scratch/
+fpath /mnt/moench_data/scratch1/
 
 fwrite 0
 

integrationTests/test-integrationDectector.cpp

@@ -488,7 +488,7 @@ TEST_CASE("Eiger or Jungfrau nextframenumber",
     CHECK(m.getNextFrameNumber() == (val + 1));
 }
 
-TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {
+TEST_CASE("Eiger partialread", "[.eigerintegration][partialread]") {
     SingleDetectorConfig c;
 
     // pick up multi detector from shm id 0
@@ -501,16 +501,16 @@ TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {
 
     m.setDynamicRange(16);
     m.enableTenGigabitEthernet(0);
-    m.setReadNLines(256);
-    CHECK(m.getReadNLines() == 256);
-    m.setReadNLines(1);
-    CHECK(m.getReadNLines() == 1);
+    m.setPartialReadout(256);
+    CHECK(m.getPartialReadout() == 256);
+    m.setPartialReadout(1);
+    CHECK(m.getPartialReadout() == 1);
 
     m.setDynamicRange(8);
-    m.setReadNLines(256);
-    CHECK(m.getReadNLines() == 256);
-    CHECK_THROWS_AS(m.setReadNLines(1), sls::RuntimeError);
-    CHECK(m.getReadNLines() == 256);
-    CHECK_THROWS_AS(m.setReadNLines(0), sls::RuntimeError);
-    m.setReadNLines(256);
+    m.setPartialReadout(256);
+    CHECK(m.getPartialReadout() == 256);
+    CHECK_THROWS_AS(m.setPartialReadout(1), sls::RuntimeError);
+    CHECK(m.getPartialReadout() == 256);
+    CHECK_THROWS_AS(m.setPartialReadout(0), sls::RuntimeError);
+    m.setPartialReadout(256);
 }

libzmq-pkg-config/FindZeroMQ.cmake

@@ -0,0 +1,27 @@
+#From: https://github.com/zeromq/cppzmq/
+set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH ON)
+find_package(PkgConfig)
+pkg_check_modules(PC_LIBZMQ QUIET libzmq)
+
+set(ZeroMQ_VERSION ${PC_LIBZMQ_VERSION})
+find_library(ZeroMQ_LIBRARY NAMES libzmq.so libzmq.dylib libzmq.dll
+             PATHS ${PC_LIBZMQ_LIBDIR} ${PC_LIBZMQ_LIBRARY_DIRS})
+find_library(ZeroMQ_STATIC_LIBRARY NAMES libzmq-static.a libzmq.a libzmq.dll.a
+             PATHS ${PC_LIBZMQ_LIBDIR} ${PC_LIBZMQ_LIBRARY_DIRS})
+
+if(ZeroMQ_LIBRARY OR ZeroMQ_STATIC_LIBRARY)
+    set(ZeroMQ_FOUND ON)
+endif()
+
+if (TARGET libzmq)
+    # avoid errors defining targets twice
+    return()
+endif()
+
+add_library(libzmq SHARED IMPORTED)
+set_property(TARGET libzmq PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PC_LIBZMQ_INCLUDE_DIRS})
+set_property(TARGET libzmq PROPERTY IMPORTED_LOCATION ${ZeroMQ_LIBRARY})
+
+add_library(libzmq-static STATIC IMPORTED ${PC_LIBZMQ_INCLUDE_DIRS})
+set_property(TARGET libzmq-static PROPERTY INTERFACE_INCLUDE_DIRECTORIES ${PC_LIBZMQ_INCLUDE_DIRS})
+set_property(TARGET libzmq-static PROPERTY IMPORTED_LOCATION ${ZeroMQ_STATIC_LIBRARY})

notice_to_add_for_every_file

@@ -0,0 +1,16 @@
+    Copyright (C) 2021 Contributors to the SLS Detector Package
+    
+    This file is part of the SLS Detecotor Package.
+
+    SLS Detecotor Package is free software: you can redistribute it and/or modify
+    it under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    SLS Detecotor Package is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser General Public License
+    along with SLS Detecotor Package.  If not, see <https://www.gnu.org/licenses/>.

python/CMakeLists.txt

@@ -4,6 +4,9 @@ pybind11_add_module(_slsdet
     src/enums.cpp
     src/detector.cpp
     src/network.cpp
+    src/pattern.cpp
+    src/scan.cpp
+    src/current.cpp
 )
 
 target_link_libraries(_slsdet PUBLIC 
@@ -28,6 +31,7 @@ set( PYTHON_FILES
     enums.py
     errors.py
     gotthard.py
+    pattern.py
     gotthard2.py
     moench.py
     proxy.py

python/examples/manipulate_pattern.py

@@ -0,0 +1,14 @@
+
+
+from slsdet import Detector, patternParameters
+
+d = Detector()
+pat = patternParameters()
+
+#Access to members of the structure using numpy arrays
+pat.patlimits = 0x0, 0xa
+
+d.setPattern(pat)
+
+#Load pattern from file
+pat.load("/some/dir/some.pat")

python/examples/use_currentsource.py

@@ -0,0 +1,11 @@
+from slsdet import Detector, currentSrcParameters
+
+s = currentSrcParameters()
+s.enable = 1
+s.fix= 1
+s.normal = 1
+s.select = 10
+
+
+d = Detector()
+d.currentsource = s

python/examples/use_enum.py

@@ -6,7 +6,7 @@ d = Detector()
 d.fformat = fileFormat.BINARY
 
 # Altough not recommended for convenience all enums 
-# and some other things can be impored using *
+# and some other things can be imported using *
 
 from slsdet import *
 d.speed = speedLevel.FULL_SPEED 
@@ -15,6 +15,6 @@ d.speed = speedLevel.FULL_SPEED
 
 import slsdet.enums
 for enum in dir(slsdet.enums):
-    # filter out special memebers
+    # filter out special members
     if not enum.startswith('_'):
         print(enum)

python/examples/using_scan.py

@@ -0,0 +1,21 @@
+
+from slsdet import Mythen3, scanParameters, dacIndex
+
+#Configure scan
+sp = scanParameters()
+sp.enable = 1 
+sp.dacInd = dacIndex.VTH1
+sp.startOffset = 0
+sp.stopOffset = 1000
+sp.stepSize = 100
+sp.dacSettleTime_ns = int(1e9)
+
+
+# Send scan to detector
+d = Mythen3()
+d.setScan(sp)
+
+#or d.scan = sp
+
+
+

python/scripts/basic.py

@@ -10,6 +10,8 @@ from slsdet.lookup import view, find
 import slsdet
 
 
+
+
 d = Detector()
 e = Eiger()
 c = Ctb()

python/scripts/compile_servers.py

@@ -0,0 +1,80 @@
+import subprocess
+import os
+import sys
+from pathlib import Path
+import shutil as sh
+from argparse import ArgumentParser
+
+class color:
+    HEADER = "\033[95m"
+    BLUE = "\033[94m"
+    CYAN = "\033[96m"
+    GREEN = "\033[92m"
+    YELLOW = "\033[93m"
+    RED = "\033[91m"
+    ENDC = "\033[0m"
+    BOLD = "\033[1m"
+    UNDERLINE = "\033[4m"
+    MAGENTA = "\033[35m"
+
+    @staticmethod
+    def red(s):
+        return f"{color.RED}{s}{color.ENDC}"
+
+    @staticmethod
+    def green(s):
+        return f"{color.GREEN}{s}{color.ENDC}"
+
+def add_to_path():
+    paths = [
+        "/opt/uClinux/bfin-uclinux/bin",
+        "/opt/nios2-gcc/bin",
+        "/opt/eldk-5.1/powerpc-4xx-softfloat/sysroots/i686-eldk-linux/usr/bin/ppc405-linux",
+    ]
+    os.environ["PATH"] += os.pathsep + os.pathsep.join(paths)
+
+
+def rc_to_string(rc):
+    if rc == 0:
+        return color.green("OK")
+    else:
+        return color.red("FAIL")
+
+
+
+parser = ArgumentParser()
+parser.add_argument('-t', '--tag', help = 'Tag added to server file name', default='developer')
+parser.add_argument('-g', '--git', help='Add new servers to the git repo', action="store_true")
+args = parser.parse_args()
+
+
+servers = [
+#     "eigerDetectorServer",
+#     "jungfrauDetectorServer",
+      "mythen3DetectorServer",
+#     "gotthard2DetectorServer",
+#     "gotthardDetectorServer",
+#     "ctbDetectorServer",
+#     "moenchDetectorServer",
+]
+
+
+server_root = Path("../../slsDetectorServers/").resolve()
+
+add_to_path()
+for server in servers:
+    bin_name = f"{server}_{args.tag}"
+    path = server_root / server
+    print(f"{bin_name} - ", end="")
+    os.chdir(path)
+    try: 
+        sh.rmtree(path/'bin')
+    except FileNotFoundError:
+        pass
+    p = subprocess.run(["make"], stdout=subprocess.DEVNULL)
+    print(rc_to_string(p.returncode))
+    if p.returncode == 0:
+        sh.move(f"bin/{server}", f"bin/{bin_name}")
+        if args.git:
+            print("Adding to git")
+            subprocess.run(['git', 'add', 'bin', '-f'])

python/scripts/generate_enums.py

@@ -11,14 +11,30 @@ import subprocess
 
 from parse import remove_comments
 
+allow_bitwise_op = ["M3_GainCaps"]
+allow_bitwise_op = ["streamingInterface"]
+
+op_key = {"operator|": "__or__", 
+          "operator&" : "__and__"}
+
 def single_line_enum(line):
     sub = line[line.find('{')+1:line.find('}')]
     return sub.strip().split(',')
 
 def extract_enums(lines):
+
+    # deal with enum class streamingInterface : int32_t
+    # and normal enum burstMode {
+
     line_iter = iter(lines)
     enums = {}
     for line in line_iter:
+        #Hack away class enum defs
+        if "class" in line:
+            line = line.replace("class", "")
+            line = line.replace(line[line.find(':'):line.find('{')], "")
+            line = line.replace("  ", " ")
+
         m = re.search("(?<=enum )\w+(?= {)", line)
         if m:
             enum_name = m.group()
@@ -44,25 +60,80 @@ def extract_enums(lines):
                         pass
             fields = [f.strip() for f in fields]
             enums[enum_name] = fields
+
+
+    #Loop again to find operators
+    for key in enums:
+        for line in lines:
+            if key in line and "operator" in line:
+                pos = line.find("operator")
+                op_type = line[pos:pos+9]
+                enums[key].append(op_type)
     return enums
 
+
 def generate_enum_string(enums):
     data = []
     for key, value in enums.items():
-        data.append(f'py::enum_<slsDetectorDefs::{key}>(Defs, "{key}")\n')
+        if key in allow_bitwise_op:
+            tag=", py::arithmetic()"
+        else:
+            tag=""
+        data.append(f'py::enum_<slsDetectorDefs::{key}>(Defs, "{key}"{tag})\n')
+        operators = []
         for v in value:
-            data.append(f'\t.value("{v}", slsDetectorDefs::{key}::{v})\n')
-        data.append('.export_values();\n\n')
+            if "operator" not in v:
+                data.append(f'\t.value("{v}", slsDetectorDefs::{key}::{v})\n')
+            else:
+                operators.append(v)
+        data.append('\t.export_values()')
+
+        #Here add the operators 
+        for op in operators:
+            data.append(f"\n\t.def(\"{op_key[op]}\", py::overload_cast< const slsDetectorDefs::streamingInterface&,  const slsDetectorDefs::streamingInterface&>(&{op}))")
+
+
+        data.append(';\n\n')
     return ''.join(data)
 
-with open('../../slsSupportLib/include/sls_detector_defs.h') as f:
+
+def remove_ifdefs(lines):
+    """Keeps C++ version of the code"""
+    out = []
+    it = iter(lines)
+    skip = False
+    for line in it:
+        
+        if "#ifdef __cplusplus" in line:
+            line = next(it)
+
+        if "#else" in line:
+            skip = True
+
+        if "#endif" in line:
+            skip = False
+
+        if not skip and "#endif" not in line:    
+            out.append(line)
+    return out
+    
+
+with open('../../slsSupportLib/include/sls/sls_detector_defs.h') as f:
     data = f.read()
 
 data = remove_comments(data)
 data = data.splitlines()
+data = remove_ifdefs(data)
 enums = extract_enums(data)
+
+
 s = generate_enum_string(enums)
 
+# print(s)
+# for i, line in enumerate(data):
+#     print(i, line)
+
+
 with open('../src/enums_in.cpp') as f:
     data = f.read()
 

python/scripts/test_virtual.py

@@ -101,15 +101,11 @@ def test_module_size(virtual_jf_detectors):
 
 def test_settings(virtual_jf_detectors):
     d = ExperimentalDetector()
-    assert d.settings == detectorSettings.DYNAMICGAIN
+    assert d.settings == detectorSettings.GAIN0
 
     gain_list = [
-        detectorSettings.FIXGAIN1,
-        detectorSettings.FIXGAIN2,
-        detectorSettings.FORCESWITCHG1,
-        detectorSettings.FORCESWITCHG2,
-        detectorSettings.DYNAMICHG0,
-        detectorSettings.DYNAMICGAIN,
+        detectorSettings.GAIN0,
+        detectorSettings.HIGHGAIN0,
     ]
 
     # Set all viable gain for Jungfrau to make sure nothing is crashing
@@ -117,15 +113,14 @@ def test_settings(virtual_jf_detectors):
         d.settings = gain
         assert d.settings == gain
 
-    d.setSettings(detectorSettings.FORCESWITCHG1, [1])
+    d.setSettings(detectorSettings.GAIN0, [1])
     assert d.settings == [
-        detectorSettings.DYNAMICGAIN,
-        detectorSettings.FORCESWITCHG1,
-        detectorSettings.DYNAMICGAIN,
+        detectorSettings.GAIN0,
+        detectorSettings.HIGHGAIN0,
     ]
 
-    d.settings = detectorSettings.DYNAMICGAIN
-    assert d.settings == detectorSettings.DYNAMICGAIN
+    d.settings = detectorSettings.GAIN0
+    assert d.settings == detectorSettings.GAIN0
 
 def test_frames(virtual_jf_detectors):
     d = ExperimentalDetector()
@@ -161,4 +156,34 @@ def test_period(virtual_jf_detectors):
     d.period  = t
     assert d.period == 10e-6
 
-    
+def test_gainmode(virtual_jf_detectors):
+    d = ExperimentalDetector()
+    assert d.gainMode == gainMode.NORMAL_GAIN_MODE
+
+    gain_list = [
+        gainMode.DYNAMIC,
+        gainMode.FORCE_SWITCH_G1,
+        gainMode.FORCE_SWITCH_G2,
+        gainMode.FIX_G1,
+        gainMode.FIX_G2,
+        gainMode.FIX_G0
+    ]
+
+    # Set all viable gain for Jungfrau to make sure nothing is crashing
+    for gain in gain_list:
+        d.gainMode = gain
+        assert d.gainMode == gain
+
+    d.setGainMode(gainMode.FORCE_SWITCH_G1, [1])
+    assert d.gainMode == [
+        gainMode.DYNAMIC,
+        gainMode.FORCE_SWITCH_G1,
+        gainMode.FORCE_SWITCH_G2,
+        gainMode.FIX_G1,
+        gainMode.FIX_G2,
+        gainMode.FIX_G0
+    ]
+
+    d.gainMode = gainMode.FORCE_SWITCH_G1
+    assert d.gainMode == gainMode.FORCE_SWITCH_G1
+    

python/setup.py

@@ -2,11 +2,12 @@
 Setup file for slsdet
 Build upon the pybind11 example found here: https://github.com/pybind/python_example
 """
-from setuptools import setup, Extension, find_packages
-from setuptools.command.build_ext import build_ext
-import sys
-import setuptools
+
 import os
+import sys
+sys.path.append('../libs/pybind11')
+from setuptools import setup, find_packages
+from pybind11.setup_helpers import Pybind11Extension, build_ext
 
 __version__ = os.environ.get('GIT_DESCRIBE_TAG', 'developer')
 
@@ -19,109 +20,29 @@ def get_conda_path():
     return os.environ['CONDA_PREFIX']
 
 
-# class get_pybind_include(object):
-#     """Helper class to determine the pybind11 include path
-#     The purpose of this class is to postpone importing pybind11
-#     until it is actually installed, so that the ``get_include()``
-#     method can be invoked. """
-
-#     def __init__(self, user=False):
-#         self.user = user
-
-#     def __str__(self):
-#         import pybind11
-#         return pybind11.get_include(self.user)
-
-
+#TODO migrate to CMake build? 
 ext_modules = [
-    Extension(
+    Pybind11Extension(
         '_slsdet',
         ['src/main.cpp',
         'src/enums.cpp',
         'src/detector.cpp',
-        'src/network.cpp'],
+        'src/network.cpp',
+        'src/pattern.cpp',
+        'src/scan.cpp',],
         include_dirs=[
-            # Path to pybind11 headers
-            # get_pybind_include(),
-            # get_pybind_include(user=True),
             os.path.join('../libs/pybind11/include'),
             os.path.join(get_conda_path(), 'include'),
 
         ],
-        libraries=['SlsDetector', 'SlsReceiver', 'zmq'],
+        libraries=['SlsDetector', 'SlsSupport', 'SlsReceiver', 'zmq'],
         library_dirs=[
             os.path.join(get_conda_path(), 'lib'),
-            os.path.join(get_conda_path(), 'bin'),
         ],
-
         language='c++'
     ),
 ]
 
-
-# As of Python 3.6, CCompiler has a `has_flag` method.
-# cf http://bugs.python.org/issue26689
-def has_flag(compiler, flagname):
-    """Return a boolean indicating whether a flag name is supported on
-    the specified compiler.
-    """
-    import tempfile
-    with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
-        f.write('int main (int argc, char **argv) { return 0; }')
-        try:
-            compiler.compile([f.name], extra_postargs=[flagname])
-        except setuptools.distutils.errors.CompileError:
-            return False
-    return True
-
-
-def cpp_flag(compiler):
-    """Return the -std=c++[11/14] compiler flag.
-    The c++14 is prefered over c++11 (when it is available).
-    """
-    if has_flag(compiler, '-std=c++14'):
-        return '-std=c++14'
-    elif has_flag(compiler, '-std=c++11'):
-        return '-std=c++11'
-    else:
-        raise RuntimeError('Unsupported compiler -- at least C++11 support '
-                           'is needed!')
-
-
-class BuildExt(build_ext):
-    """A custom build extension for adding compiler-specific options."""
-    c_opts = {
-        'msvc': ['/EHsc'],
-        'unix': [],
-    }
-
-    if sys.platform == 'darwin':
-        c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.7']
-
-    def build_extensions(self):
-        ct = self.compiler.compiler_type
-        opts = self.c_opts.get(ct, [])
-        if ct == 'unix':
-            opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
-            opts.append(cpp_flag(self.compiler))
-            if has_flag(self.compiler, '-fvisibility=hidden'):
-                opts.append('-fvisibility=hidden')
-        elif ct == 'msvc':
-            opts.append('/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version())
-        for ext in self.extensions:
-            ext.extra_compile_args = opts
-
-        print('**************************************************')
-        print(ct)
-        print(opts)
-        print('**************************************************')
-        build_ext.build_extensions(self)
-        
-
-
-def get_shared_lib():
-    return [f for f in os.listdir('.') if '_slsdet' in f]
-
 setup(
     name='slsdet',
     version=__version__,
@@ -132,6 +53,6 @@ setup(
     long_description='',
     packages=find_packages(exclude=['contrib', 'docs', 'tests']),
     ext_modules=ext_modules,
-    cmdclass={'build_ext': BuildExt},
+    cmdclass={"build_ext": build_ext},
     zip_safe=False,
 )

python/slsdet/__init__.py

@@ -8,6 +8,8 @@ from .mythen3 import Mythen3
 from .gotthard2 import Gotthard2
 from .gotthard import Gotthard
 from .moench import Moench
+from .pattern import Pattern, patternParameters
+
 
 import _slsdet
 xy = _slsdet.xy
@@ -18,3 +20,5 @@ from .enums import *
 
 IpAddr = _slsdet.IpAddr
 MacAddr = _slsdet.MacAddr
+scanParameters = _slsdet.scanParameters
+currentSrcParameters = _slsdet.currentSrcParameters

python/slsdet/detector.py

@@ -7,6 +7,9 @@ timingMode = slsDetectorDefs.timingMode
 speedLevel = slsDetectorDefs.speedLevel
 dacIndex = slsDetectorDefs.dacIndex
 detectorType = slsDetectorDefs.detectorType
+streamingInterface = slsDetectorDefs.streamingInterface
+
+defs = slsDetectorDefs
 
 from .utils import element_if_equal, all_equal, get_set_bits, list_to_bitmask
 from .utils import Geometry, to_geo, element, reduce_time, is_iterable
@@ -308,7 +311,7 @@ class Detector(CppDetectorApi):
         -----
         
         [Eiger] Use threshold command to load settings
-        [Jungfrau] DYNAMICGAIN, DYNAMICHG0, FIXGAIN1, FIXGAIN2, FORCESWITCHG1, FORCESWITCHG2 \n
+        [Jungfrau] GAIN0, HIGHGAIN0 \n
         [Gotthard] DYNAMICGAIN, HIGHGAIN, LOWGAIN, MEDIUMGAIN, VERYHIGHGAIN \n
         [Gotthard2] DYNAMICGAIN, FIXGAIN1, FIXGAIN2 \n
         [Moench] G1_HIGHGAIN, G1_LOWGAIN, G2_HIGHCAP_HIGHGAIN, G2_HIGHCAP_LOWGAIN, G2_LOWCAP_HIGHGAIN, G2_LOWCAP_LOWGAIN, G4_HIGHGAIN, G4_LOWGAIN \n
@@ -359,6 +362,21 @@ class Detector(CppDetectorApi):
         """
         return self.getNumberOfFramesFromStart()
 
+
+    @property
+    @element
+    def scan(self):
+        """
+        Pass in a scanParameters object 
+        see python/examples/use_scan.py
+
+        """
+        return self.getScan()
+
+    @scan.setter
+    def scan(self, s):
+        ut.set_using_dict(self.setScan, s)
+
     @property
     @element
     def powerchip(self):
@@ -367,7 +385,7 @@ class Detector(CppDetectorApi):
         Note
         ----
         [Moench] Default is disabled. \n
-        [Jungfrau] Default is disabled. Get will return power status. Can be off if temperature event occured (temperature over temp_threshold with temp_control enabled. \n
+        [Jungfrau] Default is disabled. Get will return power status. Can be off if temperature event occured (temperature over temp_threshold with temp_control enabled. Will configure chip (only chip v1.1).\n
         [Mythen3][Gotthard2] Default is 1. If module not connected or wrong module, powerchip will fail.
         """
         return self.getPowerChip()
@@ -1627,20 +1645,22 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def speed(self):
+    def readoutspeed(self):
         """
-        [Eiger][Jungfrau] Readout speed of chip. Enum: speedLevel
+        [Eiger][Jungfrau|Gotthard2] Readout speed of chip. Enum: speedLevel
         Note
         -----
-        Options: FULL_SPEED, HALF_SPEED, QUARTER_SPEED \n
-        [Jungfrau] FULL_SPEED option only available from v2.0 boards and with setting number of interfaces to 2.  \n
+        [Jungfrau] FULL_SPEED, HALF_SPEED (Default), QUARTER_SPEED
+        [Eiger] FULL_SPEED (Default), HALF_SPEED, QUARTER_SPEED
+        [Gottthard2] G2_108MHZ (Default), G2_144MHZ
+        [Jungfrau] FULL_SPEED option only available from v2.0 boards and is recommended to set number of interfaces to 2.  \n
         Also overwrites adcphase to recommended default.
         """
-        return element_if_equal(self.getSpeed())
+        return element_if_equal(self.getReadoutSpeed())
 
-    @speed.setter
-    def speed(self, value):
-        ut.set_using_dict(self.setSpeed, value)
+    @readoutspeed.setter
+    def readoutspeed(self, value):
+        ut.set_using_dict(self.setReadoutSpeed, value)
 
     @property
     def rx_jsonpara(self):
@@ -1696,6 +1716,8 @@ class Detector(CppDetectorApi):
         To change settings as well or set threshold without trimbits, use setThresholdEnergy.
         :setter: It loads trim files from settingspath.
         """
+        if self.type == detectorType.MYTHEN3:
+            return self.getAllThresholdEnergy()
         return self.getThresholdEnergy()
 
     @threshold.setter
@@ -1747,7 +1769,7 @@ class Detector(CppDetectorApi):
         Note
         ----
         [Eiger] Sets vcmp_ll, vcmp_lr, vcmp_rl, vcmp_rr and vcp to the same value. \n
-        [Mythen3] Sets vth1, vth2 and vth3 to the same value.
+        [Mythen3] Sets vth1, vth2 and vth3 to the same value for enabled counters.
         """
         return self.getDAC(dacIndex.VTHRESHOLD)
 
@@ -1785,10 +1807,25 @@ class Detector(CppDetectorApi):
 
     """
 
-    <<<-----------------------Eiger specific----------------------->>>
+    <<<Eiger>>>
 
     """
 
+    @property
+    def datastream(self):
+        """
+        datastream [left|right] [0, 1]
+	    [Eiger] Enables or disables data streaming from left or/and right side of detector. 1 (enabled) by default.
+        """
+        result = {}
+        for port in [defs.LEFT, defs.RIGHT]:
+            result[port] = element_if_equal(self.getDataStream(port))
+        return result
+
+    @datastream.setter
+    def datastream(self, value):
+        ut.set_using_dict(self.setDataStream, *value)
+
     @property
     @element
     def quad(self):
@@ -1826,19 +1863,21 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def readnlines(self):
+    def readnrows(self):
         """
-        [Eiger] Number of lines to read out per half module 
+        [Eiger] Number of rows to read out per half module starting from the centre.
+        [Jungfrau] Number of rows to read per module starting from the centre.
         Note
         ----
-        Options: 0 - 256. 256 is default. \n
-        The permissible values depend on dynamic range and 10Gbe enabled.
+        [Eiger] Options: 1 - 256. 256 is default. \n
+        [Eiger]The permissible values depend on dynamic range and 10Gbe enabled.\n\n
+        [Jungfrau] Options: 8 - 512 (multiples of 8)
         """
-        return self.getPartialReadout()
+        return self.getReadNRows()
 
-    @readnlines.setter
-    def readnlines(self, value):
-        ut.set_using_dict(self.setPartialReadout, value)
+    @readnrows.setter
+    def readnrows(self, value):
+        ut.set_using_dict(self.setReadNRows, value)
 
 
     @property
@@ -1969,9 +2008,23 @@ class Detector(CppDetectorApi):
         return ut.reduce_time(self.getMeasuredSubFramePeriod())
 
     """
-    Jungfrau specific
+    ------------------<<<Jungfrau specific>>>-------------------------
     """
 
+    @property
+    @element
+    def chipversion(self):
+        """
+        [Jungfrau] Chip version of module. Can be 1.0 or 1.1.
+
+        Example
+        -------
+        >>> d.chipversion
+        '1.0'
+        """
+        return self.getChipVersion()
+
+
     @property
     @element
     def auto_comp_disable(self):
@@ -1979,14 +2032,39 @@ class Detector(CppDetectorApi):
 
         Note
         -----
-        By default, the on-chip gain switching is active during the entire exposure. This mode disables the on-chip gain switching comparator automatically after 93.75% of exposure time (only for longer than 100us).\n
+        By default, the on-chip gain switching is active during the entire exposure. This mode disables the on-chip gain switching comparator automatically after 93.75% of exposure time (only for longer than 100us). The % is only for chipv1.0, the duration can be set for chipv1.1.\n
         Default is 0 or this mode disabled (comparator enabled throughout). 1 enables mode. 0 disables mode. 
         """
-        return self.getAutoCompDisable()
+        return self.getAutoComparatorDisable()
 
     @auto_comp_disable.setter
     def auto_comp_disable(self, value):
-        ut.set_using_dict(self.setAutoCompDisable, value)
+        ut.set_using_dict(self.setAutoComparatorDisable, value)
+
+    @property
+    @element
+    def comp_disable_time(self):
+        """[Jungfrau] Time before end of exposure when comparator is disabled. 
+
+        Note
+        -----
+        It is only possible for chipv1.1.
+        :getter: always returns in seconds. To get in datetime.delta, use getComparatorDisableTime
+
+        Example
+        -----------
+        >>> d.comp_disable_time = 1.05
+        >>> d.comp_disable_time = datetime.timedelta(minutes = 3, seconds = 1.23)
+        >>> d.comp_disable_time
+        181.23
+        >>> d.getComparatorDisableTime()
+        [datetime.timedelta(seconds=181, microseconds=230000)]
+        """
+        return ut.reduce_time(self.getComparatorDisableTime())
+
+    @comp_disable_time.setter
+    def comp_disable_time(self, value):
+       ut.set_time_using_dict(self.setComparatorDisableTime, value)
 
 
     @property
@@ -2006,7 +2084,7 @@ class Detector(CppDetectorApi):
         [Jungfrau] Number of additional storage cells. 
         Note
         ----
-        For advanced users only. \n
+        Only for chip v1.0. For advanced users only. \n
         Options: 0 - 15. Default is 0.
         The #images = #frames x #triggers x (#storagecells + 1)
         """
@@ -2025,7 +2103,7 @@ class Detector(CppDetectorApi):
         Note
         ----
         For advanced users only.
-        Options 0-15. Default is 15. \n
+        Options 0-max. max is 15 (default) for chipv1.0 and 3 (default) for chipv1.1. \n
         """
         return self.getStorageCellStart()
 
@@ -2039,7 +2117,7 @@ class Detector(CppDetectorApi):
         [Jungfrau] Additional time delay between 2 consecutive exposures in burst mode, accepts either a value in seconds or datetime.timedelta
         Note
         -----
-        For advanced users only \n
+        Only applicable for chipv1.0. For advanced users only \n
         Value: 0-1638375 ns (resolution of 25ns) \n
         :getter: always returns in seconds. To get in datetime.delta, use getStorageCellDelay
 
@@ -2131,6 +2209,40 @@ class Detector(CppDetectorApi):
     def selinterface(self, i):
         ut.set_using_dict(self.selectUDPInterface, i)
 
+    @property
+    def gainmodelist(self):
+        """List of gainmode implemented for this detector."""
+        return self.getGainModeList()
+
+    @property
+    def gainmode(self):
+        """
+        [Jungfrau] Detector gain mode. Enum: gainMode
+        Note
+        -----
+        [Jungfrau] DYNAMIC, FORCE_SWITCH_G1, FORCE_SWITCH_G2, FIX_G1, FIX_G2, FIX_G0 \n
+        CAUTION: Do not use FIX_G0 without caution, you can damage the detector!!!
+        """
+        return element_if_equal(self.getGainMode())
+
+    @gainmode.setter
+    def gainmode(self, value):
+        self.setGainMode(value)
+
+    @property
+    @element
+    def currentsource(self):
+        """
+        Pass in a currentSrcParameters object
+        see python/examples/use_currentsource.py
+
+        """
+        return self.getCurrentSource()
+
+    @currentsource.setter
+    def currentsource(self, cs):
+        ut.set_using_dict(self.setCurrentSource, cs)
+
     """
     ---------------------------<<<Gotthard2 specific>>>---------------------------
     """
@@ -2159,18 +2271,37 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def filter(self):
-        """[Gotthard2] Set filter resistor. 
+    def filterresistor(self):
+        """
+        [Gotthard2][Jungfrau] Set filter resistor. Increasing values for increasing "
+        "resistance.
         Note
         ----
-        Default is 0. Options: 0-3.
+        Advanced user command.
+        [Gotthard2] Default is 0. Options: 0-3.
+        [Jungfrau] Default is 1. Options: 0-1.
         """
-        return self.getFilter()
+        return self.getFilterResistor()
 
-    @filter.setter
-    def filter(self, value):
-        ut.set_using_dict(self.setFilter, value)
+    @filterresistor.setter
+    def filterresistor(self, value):
+        ut.set_using_dict(self.setFilterResistor, value)
 
+    @property
+    @element
+    def filtercell(self):
+        """
+        [Jungfrau] Set filter capacitor. 
+        Note
+        ----
+        [Jungfrau] Options: 0-12. Default: 0. Advanced user command. Only for chipv1.1.
+        """
+        return self.getFilterCell()
+
+    @filtercell.setter
+    def filtercell(self, value):
+        ut.set_using_dict(self.setFilterCell, value)
+        
     @property
     def maxclkphaseshift(self):
         """
@@ -2210,7 +2341,7 @@ class Detector(CppDetectorApi):
     @element
     def veto(self):
         """
-        [Gotthard2] Enable or disable veto data streaming from detector. 
+        [Gotthard2] Enable or disable veto data from chip. 
         Note
         ----
         Default is 0.
@@ -2330,6 +2461,49 @@ class Detector(CppDetectorApi):
         ut.set_using_dict(self.setVetoReference, *args)
 
 
+    @property
+    @element
+    def vetostream(self):
+        """[Gotthard2] Enabling/ disabling veto interface
+        Note
+        ----
+        Default: both off
+        Options: NONE, LOW_LATENCY_LINK, 10GBE (debugging)
+        Debugging interface also enables second interface in receiver (separate file), which also restarts zmq streaming if enabled.
+        """
+        return self.getVetoStream()
+
+    @vetostream.setter
+    def vetostream(self, args):
+        if not isinstance(args, tuple):
+            args = (args,)
+        ut.set_using_dict(self.setVetoStream, *args)
+
+    @property
+    def vetoalg(self):
+        """[Gotthard2] Algorithm used for veto. Enum: vetoAlgorithm, streamingInterface
+        Note
+        ----
+        Options:
+        (vetoAlgorithm): ALG_HITS (default), ALG_RAW
+        (streamingInterface): ETHERNET_10GB, LOW_LATENCY_LINK
+        Example
+        ----------
+        >>> d.vetoalg = defs.ALG_HITS, defs.ETHERNET_10GB
+        """
+        result = {}
+        interface = [streamingInterface.LOW_LATENCY_LINK, streamingInterface.ETHERNET_10GB]
+        for eth in interface:
+            result[eth] = element_if_equal(self.getVetoAlgorithm(eth))
+        return result
+
+
+    @vetoalg.setter
+    def vetoalg(self, args):
+        if not isinstance(args, tuple):
+            args = (args,)
+        ut.set_using_dict(self.setVetoAlgorithm, *args)
+
     """
     Mythen3 specific
     """
@@ -2379,6 +2553,7 @@ class Detector(CppDetectorApi):
         Note
         -----
         Each element in list can be 0 - 2 and must be non repetitive.
+        Enabling counters sets vth dacs to remembered values and disabling sets them to disabled values.
 
         Example
         -----------
@@ -2519,7 +2694,12 @@ class Detector(CppDetectorApi):
     @property
     @element
     def dbitpipeline(self):
-        """[Ctb] Pipeline of the clock for latching digital bits. """
+        """[Ctb][Gotthard2] Pipeline of the clock for latching digital bits. 
+        Note
+        ----
+        [CTB] Options: 0 - 255
+        [Gotthard2] Options: 0 - 7
+        """
         return self.getDBITPipeline()
 
     @dbitpipeline.setter

python/slsdet/enums.py

@@ -1,17 +1,20 @@
+"""
+Automatically improt all enums from slsDetectorDefs and give an
+alias with their name in the enum module. All names from the enum
+module is later imported into slsdet
+
+Example: detectorType = _slsdet.slsDetectorDefs.detectorType
+Usage can later be:
+
+from slsdet import detectorType
+if dt === detectorType.EIGER:
+    #do something
+
+"""
+
 
 import _slsdet
-runStatus = _slsdet.slsDetectorDefs.runStatus
-speedLevel = _slsdet.slsDetectorDefs.speedLevel
-detectorType = _slsdet.slsDetectorDefs.detectorType
-frameDiscardPolicy = _slsdet.slsDetectorDefs.frameDiscardPolicy
-fileFormat = _slsdet.slsDetectorDefs.fileFormat
-dimension = _slsdet.slsDetectorDefs.dimension
-externalSignalFlag = _slsdet.slsDetectorDefs.externalSignalFlag
-timingMode = _slsdet.slsDetectorDefs.timingMode
-dacIndex = _slsdet.slsDetectorDefs.dacIndex
-detectorSettings = _slsdet.slsDetectorDefs.detectorSettings
-clockIndex = _slsdet.slsDetectorDefs.clockIndex
-readoutMode = _slsdet.slsDetectorDefs.readoutMode
-masterFlags = _slsdet.slsDetectorDefs.masterFlags
-burstMode = _slsdet.slsDetectorDefs.burstMode
-timingSourceType = _slsdet.slsDetectorDefs.timingSourceType
+for name, cls in _slsdet.slsDetectorDefs.__dict__.items():
+    if isinstance(cls, type):
+        exec(f'{name} = {cls.__module__}.{cls.__qualname__}')
+

python/slsdet/pattern.py

@@ -0,0 +1,53 @@
+import _slsdet
+
+from _slsdet import Pattern
+
+
+class patternParameters(_slsdet.patternParameters):
+    def __init__(self):
+        super().__init__()
+        self.view = self.numpy_view()
+        self.names = self.view.dtype.names
+
+    def __getattr__(self, name):
+        if name in self.names:
+            return self.view[name][0]
+        else:
+            raise KeyError(f"Key: {name} not found")
+
+    def __setattr__(self, name, value):
+        if name in ["view", "names"]:
+            self.__dict__[name] = value
+        elif name in self.names:
+            self.view[name] = value
+        else:
+            raise KeyError(f"Key: {name} not found")
+
+    # Provide custom dir for tab completion
+    def __dir__(self):
+        return self.names
+
+
+class Pattern(_slsdet.Pattern):
+    def __init__(self):
+        super().__init__()
+        self.view = self.data().numpy_view()
+        self.names = self.view.dtype.names
+
+    def __getattr__(self, name):
+        if name in self.names:
+            return self.view[name][0]
+        else:
+            raise KeyError(f"Key: {name} not found")
+
+    def __setattr__(self, name, value):
+        if name in ["view", "names"]:
+            self.__dict__[name] = value
+        elif name in self.names:
+            self.view[name] = value
+        else:
+            raise KeyError(f"Key: {name} not found")
+
+    # Provide custom dir for tab completion
+    def __dir__(self):
+        return self.names

python/slsdet/utils.py

@@ -41,7 +41,7 @@ def list_to_bitmask(values):
     return mask
 
 def make_bitmask(args):
-    if isinstance(args, list):
+    if isinstance(args, (list,tuple)):
         return list_to_bitmask(args)
     elif isinstance(args, dict):
         return {key: list_to_bitmask(value) for key, value in args.items()}

python/src/current.cpp

@@ -0,0 +1,26 @@
+#include <pybind11/chrono.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+// #include "sls/Pattern.h"
+#include "sls/ToString.h"
+#include "sls/sls_detector_defs.h"
+
+namespace py = pybind11;
+void init_source(py::module &m) {
+
+    using src = slsDetectorDefs::currentSrcParameters;
+    py::class_<src> currentSrcParameters(m, "currentSrcParameters");
+
+    currentSrcParameters.def(py::init());
+    currentSrcParameters.def_readwrite("enable", &src::enable);
+    currentSrcParameters.def_readwrite("fix", &src::fix);
+    currentSrcParameters.def_readwrite("normal", &src::normal);
+    currentSrcParameters.def_readwrite("select", &src::select);
+    currentSrcParameters.def(pybind11::self == pybind11::self);
+
+    currentSrcParameters.def("__repr__",
+                             [](const src &a) { return sls::ToString(a); });
+}

python/src/detector.cpp

@@ -69,6 +69,10 @@ void init_det(py::module &m) {
              (Result<int64_t>(Detector::*)(sls::Positions) const) &
                  Detector::getSerialNumber,
              py::arg() = Positions{})
+        .def("getModuleId",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getModuleId,
+             py::arg() = Positions{})
         .def("getReceiverVersion",
              (Result<int64_t>(Detector::*)(sls::Positions) const) &
                  Detector::getReceiverVersion,
@@ -102,6 +106,34 @@ void init_det(py::module &m) {
              (void (Detector::*)(defs::detectorSettings, sls::Positions)) &
                  Detector::setSettings,
              py::arg(), py::arg() = Positions{})
+        .def("getThresholdEnergy",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getThresholdEnergy,
+             py::arg() = Positions{})
+        .def("getAllThresholdEnergy",
+             (Result<std::array<int, 3>>(Detector::*)(sls::Positions) const) &
+                 Detector::getAllThresholdEnergy,
+             py::arg() = Positions{})
+        .def("setThresholdEnergy",
+             (void (Detector::*)(int, defs::detectorSettings, bool,
+                                 sls::Positions)) &
+                 Detector::setThresholdEnergy,
+             py::arg(), py::arg() = defs::STANDARD, py::arg() = true,
+             py::arg() = Positions{})
+        .def("setThresholdEnergy",
+             (void (Detector::*)(std::array<int, 3>, defs::detectorSettings,
+                                 bool, sls::Positions)) &
+                 Detector::setThresholdEnergy,
+             py::arg(), py::arg() = defs::STANDARD, py::arg() = true,
+             py::arg() = Positions{})
+        .def("getSettingsPath",
+             (Result<std::string>(Detector::*)(sls::Positions) const) &
+                 Detector::getSettingsPath,
+             py::arg() = Positions{})
+        .def("setSettingsPath",
+             (void (Detector::*)(const std::string &, sls::Positions)) &
+                 Detector::setSettingsPath,
+             py::arg(), py::arg() = Positions{})
         .def("loadTrimbits",
              (void (Detector::*)(const std::string &, sls::Positions)) &
                  Detector::loadTrimbits,
@@ -114,12 +146,27 @@ void init_det(py::module &m) {
              (void (Detector::*)(int, sls::Positions)) &
                  Detector::setAllTrimbits,
              py::arg(), py::arg() = Positions{})
+        .def("getTrimEnergies",
+             (Result<std::vector<int>>(Detector::*)(sls::Positions) const) &
+                 Detector::getTrimEnergies,
+             py::arg() = Positions{})
+        .def("setTrimEnergies",
+             (void (Detector::*)(std::vector<int>, sls::Positions)) &
+                 Detector::setTrimEnergies,
+             py::arg(), py::arg() = Positions{})
         .def("getGapPixelsinCallback",
              (bool (Detector::*)() const) & Detector::getGapPixelsinCallback)
         .def("setGapPixelsinCallback",
              (void (Detector::*)(const bool)) &
                  Detector::setGapPixelsinCallback,
              py::arg())
+        .def("getFlipRows",
+             (Result<bool>(Detector::*)(sls::Positions) const) &
+                 Detector::getFlipRows,
+             py::arg() = Positions{})
+        .def("setFlipRows",
+             (void (Detector::*)(bool, sls::Positions)) & Detector::setFlipRows,
+             py::arg(), py::arg() = Positions{})
         .def("isVirtualDetectorServer",
              (Result<bool>(Detector::*)(sls::Positions) const) &
                  Detector::isVirtualDetectorServer,
@@ -207,14 +254,17 @@ void init_det(py::module &m) {
         .def("getTimingModeList",
              (std::vector<defs::timingMode>(Detector::*)() const) &
                  Detector::getTimingModeList)
-        .def("getSpeed",
+        .def("getReadoutSpeed",
              (Result<defs::speedLevel>(Detector::*)(sls::Positions) const) &
-                 Detector::getSpeed,
+                 Detector::getReadoutSpeed,
              py::arg() = Positions{})
-        .def("setSpeed",
+        .def("setReadoutSpeed",
              (void (Detector::*)(defs::speedLevel, sls::Positions)) &
-                 Detector::setSpeed,
+                 Detector::setReadoutSpeed,
              py::arg(), py::arg() = Positions{})
+        .def("getReadoutSpeedList",
+             (std::vector<defs::speedLevel>(Detector::*)() const) &
+                 Detector::getReadoutSpeedList)
         .def("getADCPhase",
              (Result<int>(Detector::*)(sls::Positions) const) &
                  Detector::getADCPhase,
@@ -318,9 +368,28 @@ void init_det(py::module &m) {
              py::arg(), py::arg() = Positions{})
         .def("getDacList", (std::vector<defs::dacIndex>(Detector::*)() const) &
                                Detector::getDacList)
-        .def("setDefaultDacs",
-             (void (Detector::*)(sls::Positions)) & Detector::setDefaultDacs,
-             py::arg() = Positions{})
+        .def("getDefaultDac",
+             (Result<int>(Detector::*)(defs::dacIndex, sls::Positions)) &
+                 Detector::getDefaultDac,
+             py::arg(), py::arg() = Positions{})
+        .def("setDefaultDac",
+             (void (Detector::*)(defs::dacIndex, int, sls::Positions)) &
+                 Detector::setDefaultDac,
+             py::arg(), py::arg(), py::arg() = Positions{})
+        .def("getDefaultDac",
+             (Result<int>(Detector::*)(defs::dacIndex, defs::detectorSettings,
+                                       sls::Positions)) &
+                 Detector::getDefaultDac,
+             py::arg(), py::arg(), py::arg() = Positions{})
+        .def("setDefaultDac",
+             (void (Detector::*)(defs::dacIndex, int, defs::detectorSettings,
+                                 sls::Positions)) &
+                 Detector::setDefaultDac,
+             py::arg(), py::arg(), py::arg(), py::arg() = Positions{})
+        .def("resetToDefaultDacs",
+             (void (Detector::*)(const bool, sls::Positions)) &
+                 Detector::resetToDefaultDacs,
+             py::arg(), py::arg() = Positions{})
         .def("getDAC",
              (Result<int>(Detector::*)(defs::dacIndex, bool, sls::Positions)
                   const) &
@@ -357,6 +426,39 @@ void init_det(py::module &m) {
              (void (Detector::*)(bool, sls::Positions)) &
                  Detector::setParallelMode,
              py::arg(), py::arg() = Positions{})
+        .def("getFilterResistor",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getFilterResistor,
+             py::arg() = Positions{})
+        .def("setFilterResistor",
+             (void (Detector::*)(int, sls::Positions)) &
+                 Detector::setFilterResistor,
+             py::arg(), py::arg() = Positions{})
+        .def("getCurrentSource",
+             (Result<defs::currentSrcParameters>(Detector::*)(sls::Positions)
+                  const) &
+                 Detector::getCurrentSource,
+             py::arg() = Positions{})
+        .def("setCurrentSource",
+             (void (Detector::*)(defs::currentSrcParameters, sls::Positions)) &
+                 Detector::setCurrentSource,
+             py::arg(), py::arg() = Positions{})
+        .def("getDBITPipeline",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getDBITPipeline,
+             py::arg() = Positions{})
+        .def("setDBITPipeline",
+             (void (Detector::*)(int, sls::Positions)) &
+                 Detector::setDBITPipeline,
+             py::arg(), py::arg() = Positions{})
+        .def("getReadNRows",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getReadNRows,
+             py::arg() = Positions{})
+        .def("setReadNRows",
+             (void (Detector::*)(const int, sls::Positions)) &
+                 Detector::setReadNRows,
+             py::arg(), py::arg() = Positions{})
         .def("acquire", (void (Detector::*)()) & Detector::acquire)
         .def("clearAcquiringFlag",
              (void (Detector::*)()) & Detector::clearAcquiringFlag)
@@ -365,7 +467,9 @@ void init_det(py::module &m) {
         .def("startDetector", (void (Detector::*)()) & Detector::startDetector)
         .def("startDetectorReadout",
              (void (Detector::*)()) & Detector::startDetectorReadout)
-        .def("stopDetector", (void (Detector::*)()) & Detector::stopDetector)
+        .def("stopDetector",
+             (void (Detector::*)(sls::Positions)) & Detector::stopDetector,
+             py::arg() = Positions{})
         .def("getDetectorStatus",
              (Result<defs::runStatus>(Detector::*)(sls::Positions) const) &
                  Detector::getDetectorStatus,
@@ -392,9 +496,9 @@ void init_det(py::module &m) {
                  Detector::setNextFrameNumber,
              py::arg(), py::arg() = Positions{})
         .def("sendSoftwareTrigger",
-             (void (Detector::*)(sls::Positions)) &
+             (void (Detector::*)(const bool, sls::Positions)) &
                  Detector::sendSoftwareTrigger,
-             py::arg() = Positions{})
+             py::arg() = false, py::arg() = Positions{})
         .def("getScan",
              (Result<defs::scanParameters>(Detector::*)(sls::Positions) const) &
                  Detector::getScan,
@@ -455,6 +559,31 @@ void init_det(py::module &m) {
              (void (Detector::*)(const sls::MacAddr, sls::Positions)) &
                  Detector::setSourceUDPMAC2,
              py::arg(), py::arg() = Positions{})
+        .def("getDestinationUDPList",
+             (Result<sls::UdpDestination>(Detector::*)(const uint32_t,
+                                                       sls::Positions) const) &
+                 Detector::getDestinationUDPList,
+             py::arg(), py::arg() = Positions{})
+        .def("setDestinationUDPList",
+             (void (Detector::*)(const sls::UdpDestination, const int)) &
+                 Detector::setDestinationUDPList,
+             py::arg(), py::arg())
+        .def("getNumberofUDPDestinations",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getNumberofUDPDestinations,
+             py::arg() = Positions{})
+        .def("clearUDPDestinations",
+             (void (Detector::*)(sls::Positions)) &
+                 Detector::clearUDPDestinations,
+             py::arg() = Positions{})
+        .def("getFirstUDPDestination",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getFirstUDPDestination,
+             py::arg() = Positions{})
+        .def("setFirstUDPDestination",
+             (void (Detector::*)(const int, sls::Positions)) &
+                 Detector::setFirstUDPDestination,
+             py::arg(), py::arg() = Positions{})
         .def("getDestinationUDPIP",
              (Result<sls::IpAddr>(Detector::*)(sls::Positions) const) &
                  Detector::getDestinationUDPIP,
@@ -783,24 +912,6 @@ void init_det(py::module &m) {
              (void (Detector::*)(sls::ns, sls::Positions)) &
                  Detector::setSubDeadTime,
              py::arg(), py::arg() = Positions{})
-        .def("getThresholdEnergy",
-             (Result<int>(Detector::*)(sls::Positions) const) &
-                 Detector::getThresholdEnergy,
-             py::arg() = Positions{})
-        .def("setThresholdEnergy",
-             (void (Detector::*)(int, defs::detectorSettings, bool,
-                                 sls::Positions)) &
-                 Detector::setThresholdEnergy,
-             py::arg(), py::arg() = defs::STANDARD, py::arg() = true,
-             py::arg() = Positions{})
-        .def("getSettingsPath",
-             (Result<std::string>(Detector::*)(sls::Positions) const) &
-                 Detector::getSettingsPath,
-             py::arg() = Positions{})
-        .def("setSettingsPath",
-             (void (Detector::*)(const std::string &, sls::Positions)) &
-                 Detector::setSettingsPath,
-             py::arg(), py::arg() = Positions{})
         .def("getOverFlowMode",
              (Result<bool>(Detector::*)(sls::Positions) const) &
                  Detector::getOverFlowMode,
@@ -809,21 +920,6 @@ void init_det(py::module &m) {
              (void (Detector::*)(bool, sls::Positions)) &
                  Detector::setOverFlowMode,
              py::arg(), py::arg() = Positions{})
-        .def("getBottom",
-             (Result<bool>(Detector::*)(sls::Positions) const) &
-                 Detector::getBottom,
-             py::arg() = Positions{})
-        .def("setBottom",
-             (void (Detector::*)(bool, sls::Positions)) & Detector::setBottom,
-             py::arg(), py::arg() = Positions{})
-        .def("getTrimEnergies",
-             (Result<std::vector<int>>(Detector::*)(sls::Positions) const) &
-                 Detector::getTrimEnergies,
-             py::arg() = Positions{})
-        .def("setTrimEnergies",
-             (void (Detector::*)(std::vector<int>, sls::Positions)) &
-                 Detector::setTrimEnergies,
-             py::arg(), py::arg() = Positions{})
         .def("getRateCorrection",
              (Result<sls::ns>(Detector::*)(sls::Positions) const) &
                  Detector::getRateCorrection,
@@ -836,14 +932,6 @@ void init_det(py::module &m) {
              (void (Detector::*)(sls::ns, sls::Positions)) &
                  Detector::setRateCorrection,
              py::arg(), py::arg() = Positions{})
-        .def("getPartialReadout",
-             (Result<int>(Detector::*)(sls::Positions) const) &
-                 Detector::getPartialReadout,
-             py::arg() = Positions{})
-        .def("setPartialReadout",
-             (void (Detector::*)(const int, sls::Positions)) &
-                 Detector::setPartialReadout,
-             py::arg(), py::arg() = Positions{})
         .def("getInterruptSubframe",
              (Result<bool>(Detector::*)(sls::Positions) const) &
                  Detector::getInterruptSubframe,
@@ -868,14 +956,6 @@ void init_det(py::module &m) {
              (void (Detector::*)(const bool, sls::Positions)) &
                  Detector::setActive,
              py::arg(), py::arg() = Positions{})
-        .def("getRxPadDeactivatedMode",
-             (Result<bool>(Detector::*)(sls::Positions) const) &
-                 Detector::getRxPadDeactivatedMode,
-             py::arg() = Positions{})
-        .def("setRxPadDeactivatedMode",
-             (void (Detector::*)(bool, sls::Positions)) &
-                 Detector::setRxPadDeactivatedMode,
-             py::arg(), py::arg() = Positions{})
         .def("getPartialReset",
              (Result<bool>(Detector::*)(sls::Positions) const) &
                  Detector::getPartialReset,
@@ -901,6 +981,20 @@ void init_det(py::module &m) {
              py::arg() = Positions{})
         .def("setQuad", (void (Detector::*)(const bool)) & Detector::setQuad,
              py::arg())
+        .def("getDataStream",
+             (Result<bool>(Detector::*)(const defs::portPosition,
+                                        sls::Positions) const) &
+                 Detector::getDataStream,
+             py::arg(), py::arg() = Positions{})
+        .def("setDataStream",
+             (void (Detector::*)(const defs::portPosition, const bool,
+                                 sls::Positions)) &
+                 Detector::setDataStream,
+             py::arg(), py::arg(), py::arg() = Positions{})
+        .def("getChipVersion",
+             (Result<double>(Detector::*)(sls::Positions) const) &
+                 Detector::getChipVersion,
+             py::arg() = Positions{})
         .def("getThresholdTemperature",
              (Result<int>(Detector::*)(sls::Positions) const) &
                  Detector::getThresholdTemperature,
@@ -925,13 +1019,21 @@ void init_det(py::module &m) {
              (void (Detector::*)(sls::Positions)) &
                  Detector::resetTemperatureEvent,
              py::arg() = Positions{})
-        .def("getAutoCompDisable",
+        .def("getAutoComparatorDisable",
              (Result<bool>(Detector::*)(sls::Positions) const) &
-                 Detector::getAutoCompDisable,
+                 Detector::getAutoComparatorDisable,
              py::arg() = Positions{})
-        .def("setAutoCompDisable",
+        .def("setAutoComparatorDisable",
              (void (Detector::*)(bool, sls::Positions)) &
-                 Detector::setAutoCompDisable,
+                 Detector::setAutoComparatorDisable,
+             py::arg(), py::arg() = Positions{})
+        .def("getComparatorDisableTime",
+             (Result<sls::ns>(Detector::*)(sls::Positions) const) &
+                 Detector::getComparatorDisableTime,
+             py::arg() = Positions{})
+        .def("setComparatorDisableTime",
+             (void (Detector::*)(sls::ns, sls::Positions)) &
+                 Detector::setComparatorDisableTime,
              py::arg(), py::arg() = Positions{})
         .def("getNumberOfAdditionalStorageCells",
              (Result<int>(Detector::*)(sls::Positions) const) &
@@ -957,6 +1059,25 @@ void init_det(py::module &m) {
              (void (Detector::*)(sls::ns, sls::Positions)) &
                  Detector::setStorageCellDelay,
              py::arg(), py::arg() = Positions{})
+        .def("getGainModeList",
+             (std::vector<defs::gainMode>(Detector::*)() const) &
+                 Detector::getGainModeList)
+        .def("getGainMode",
+             (Result<defs::gainMode>(Detector::*)(sls::Positions) const) &
+                 Detector::getGainMode,
+             py::arg() = Positions{})
+        .def("setGainMode",
+             (void (Detector::*)(const defs::gainMode, sls::Positions)) &
+                 Detector::setGainMode,
+             py::arg(), py::arg() = Positions{})
+        .def("getFilterCell",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getFilterCell,
+             py::arg() = Positions{})
+        .def("setFilterCell",
+             (void (Detector::*)(int, sls::Positions)) &
+                 Detector::setFilterCell,
+             py::arg(), py::arg() = Positions{})
         .def("getROI",
              (Result<defs::ROI>(Detector::*)(sls::Positions) const) &
                  Detector::getROI,
@@ -1032,21 +1153,6 @@ void init_det(py::module &m) {
         .def("setCDSGain",
              (void (Detector::*)(bool, sls::Positions)) & Detector::setCDSGain,
              py::arg(), py::arg() = Positions{})
-        .def("getFilter",
-             (Result<int>(Detector::*)(sls::Positions) const) &
-                 Detector::getFilter,
-             py::arg() = Positions{})
-        .def("setFilter",
-             (void (Detector::*)(int, sls::Positions)) & Detector::setFilter,
-             py::arg(), py::arg() = Positions{})
-        .def("getCurrentSource",
-             (Result<bool>(Detector::*)(sls::Positions) const) &
-                 Detector::getCurrentSource,
-             py::arg() = Positions{})
-        .def("setCurrentSource",
-             (void (Detector::*)(bool, sls::Positions)) &
-                 Detector::setCurrentSource,
-             py::arg(), py::arg() = Positions{})
         .def("getTimingSource",
              (Result<defs::timingSourceType>(Detector::*)(sls::Positions)
                   const) &
@@ -1064,6 +1170,27 @@ void init_det(py::module &m) {
              (void (Detector::*)(const bool, sls::Positions)) &
                  Detector::setVeto,
              py::arg(), py::arg() = Positions{})
+        .def("getVetoStream",
+             (Result<defs::streamingInterface>(Detector::*)(sls::Positions)
+                  const) &
+                 Detector::getVetoStream,
+             py::arg() = Positions{})
+        .def("setVetoStream",
+             (void (Detector::*)(const defs::streamingInterface,
+                                 sls::Positions)) &
+                 Detector::setVetoStream,
+             py::arg(), py::arg() = Positions{})
+        .def("getVetoAlgorithm",
+             (Result<defs::vetoAlgorithm>(Detector::*)(
+                 const defs::streamingInterface, sls::Positions) const) &
+                 Detector::getVetoAlgorithm,
+             py::arg(), py::arg() = Positions{})
+        .def("setVetoAlgorithm",
+             (void (Detector::*)(const defs::vetoAlgorithm,
+                                 const defs::streamingInterface,
+                                 sls::Positions)) &
+                 Detector::setVetoAlgorithm,
+             py::arg(), py::arg(), py::arg() = Positions{})
         .def("getADCConfiguration",
              (Result<int>(Detector::*)(const int, const int, sls::Positions)
                   const) &
@@ -1122,6 +1249,20 @@ void init_det(py::module &m) {
              (Result<std::array<ns, 3>>(Detector::*)(sls::Positions) const) &
                  Detector::getGateDelayForAllGates,
              py::arg() = Positions{})
+        .def("getMaster",
+             (Result<bool>(Detector::*)(sls::Positions) const) &
+                 Detector::getMaster,
+             py::arg() = Positions{})
+        .def("getChipStatusRegister",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getChipStatusRegister,
+             py::arg() = Positions{})
+        .def("setGainCaps",
+             (void (Detector::*)(int, sls::Positions)) & Detector::setGainCaps,
+             py::arg(), py::arg() = Positions{})
+        .def("getGainCaps",
+             (Result<int>(Detector::*)(sls::Positions)) & Detector::getGainCaps,
+             py::arg() = Positions{})
         .def("getNumberOfAnalogSamples",
              (Result<int>(Detector::*)(sls::Positions) const) &
                  Detector::getNumberOfAnalogSamples,
@@ -1203,14 +1344,6 @@ void init_det(py::module &m) {
         .def("setDBITClock",
              (void (Detector::*)(int, sls::Positions)) & Detector::setDBITClock,
              py::arg(), py::arg() = Positions{})
-        .def("getDBITPipeline",
-             (Result<int>(Detector::*)(sls::Positions) const) &
-                 Detector::getDBITPipeline,
-             py::arg() = Positions{})
-        .def("setDBITPipeline",
-             (void (Detector::*)(int, sls::Positions)) &
-                 Detector::setDBITPipeline,
-             py::arg(), py::arg() = Positions{})
         .def("getMeasuredVoltage",
              (Result<int>(Detector::*)(defs::dacIndex, sls::Positions) const) &
                  Detector::getMeasuredVoltage,
@@ -1271,9 +1404,17 @@ void init_det(py::module &m) {
              (void (Detector::*)(const std::string &, sls::Positions)) &
                  Detector::setPattern,
              py::arg(), py::arg() = Positions{})
+        .def("setPattern",
+             (void (Detector::*)(const sls::Pattern &, sls::Positions)) &
+                 Detector::setPattern,
+             py::arg(), py::arg() = Positions{})
         .def("savePattern",
              (void (Detector::*)(const std::string &)) & Detector::savePattern,
              py::arg())
+        .def("loadDefaultPattern",
+             (void (Detector::*)(sls::Positions)) &
+                 Detector::loadDefaultPattern,
+             py::arg() = Positions{})
         .def("getPatternIOControl",
              (Result<uint64_t>(Detector::*)(sls::Positions) const) &
                  Detector::getPatternIOControl,

python/src/enums.cpp

@@ -2,10 +2,12 @@
  * warning */
 
 #include <pybind11/chrono.h>
+#include <pybind11/numpy.h>
 #include <pybind11/operators.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
+#include "sls/Pattern.h"
 #include "sls/sls_detector_defs.h"
 namespace py = pybind11;
 void init_enums(py::module &m) {
@@ -208,13 +210,9 @@ void init_enums(py::module &m) {
         .value("LOWGAIN", slsDetectorDefs::detectorSettings::LOWGAIN)
         .value("MEDIUMGAIN", slsDetectorDefs::detectorSettings::MEDIUMGAIN)
         .value("VERYHIGHGAIN", slsDetectorDefs::detectorSettings::VERYHIGHGAIN)
-        .value("DYNAMICHG0", slsDetectorDefs::detectorSettings::DYNAMICHG0)
+        .value("HIGHGAIN0", slsDetectorDefs::detectorSettings::HIGHGAIN0)
         .value("FIXGAIN1", slsDetectorDefs::detectorSettings::FIXGAIN1)
         .value("FIXGAIN2", slsDetectorDefs::detectorSettings::FIXGAIN2)
-        .value("FORCESWITCHG1",
-               slsDetectorDefs::detectorSettings::FORCESWITCHG1)
-        .value("FORCESWITCHG2",
-               slsDetectorDefs::detectorSettings::FORCESWITCHG2)
         .value("VERYLOWGAIN", slsDetectorDefs::detectorSettings::VERYLOWGAIN)
         .value("G1_HIGHGAIN", slsDetectorDefs::detectorSettings::G1_HIGHGAIN)
         .value("G1_LOWGAIN", slsDetectorDefs::detectorSettings::G1_LOWGAIN)
@@ -228,6 +226,7 @@ void init_enums(py::module &m) {
                slsDetectorDefs::detectorSettings::G2_LOWCAP_LOWGAIN)
         .value("G4_HIGHGAIN", slsDetectorDefs::detectorSettings::G4_HIGHGAIN)
         .value("G4_LOWGAIN", slsDetectorDefs::detectorSettings::G4_LOWGAIN)
+        .value("GAIN0", slsDetectorDefs::detectorSettings::GAIN0)
         .value("UNDEFINED", slsDetectorDefs::detectorSettings::UNDEFINED)
         .value("UNINITIALIZED",
                slsDetectorDefs::detectorSettings::UNINITIALIZED)
@@ -251,12 +250,8 @@ void init_enums(py::module &m) {
         .value("FULL_SPEED", slsDetectorDefs::speedLevel::FULL_SPEED)
         .value("HALF_SPEED", slsDetectorDefs::speedLevel::HALF_SPEED)
         .value("QUARTER_SPEED", slsDetectorDefs::speedLevel::QUARTER_SPEED)
-        .export_values();
-
-    py::enum_<slsDetectorDefs::masterFlags>(Defs, "masterFlags")
-        .value("NO_MASTER", slsDetectorDefs::masterFlags::NO_MASTER)
-        .value("IS_MASTER", slsDetectorDefs::masterFlags::IS_MASTER)
-        .value("IS_SLAVE", slsDetectorDefs::masterFlags::IS_SLAVE)
+        .value("G2_108MHZ", slsDetectorDefs::speedLevel::G2_108MHZ)
+        .value("G2_144MHZ", slsDetectorDefs::speedLevel::G2_144MHZ)
         .export_values();
 
     py::enum_<slsDetectorDefs::burstMode>(Defs, "burstMode")
@@ -275,4 +270,52 @@ void init_enums(py::module &m) {
         .value("TIMING_EXTERNAL",
                slsDetectorDefs::timingSourceType::TIMING_EXTERNAL)
         .export_values();
+
+    py::enum_<slsDetectorDefs::M3_GainCaps>(Defs, "M3_GainCaps")
+        .value("M3_C10pre", slsDetectorDefs::M3_GainCaps::M3_C10pre)
+        .value("M3_C15sh", slsDetectorDefs::M3_GainCaps::M3_C15sh)
+        .value("M3_C30sh", slsDetectorDefs::M3_GainCaps::M3_C30sh)
+        .value("M3_C50sh", slsDetectorDefs::M3_GainCaps::M3_C50sh)
+        .value("M3_C225ACsh", slsDetectorDefs::M3_GainCaps::M3_C225ACsh)
+        .value("M3_C15pre", slsDetectorDefs::M3_GainCaps::M3_C15pre)
+        .export_values();
+
+    py::enum_<slsDetectorDefs::portPosition>(Defs, "portPosition")
+        .value("LEFT", slsDetectorDefs::portPosition::LEFT)
+        .value("RIGHT", slsDetectorDefs::portPosition::RIGHT)
+        .value("TOP", slsDetectorDefs::portPosition::TOP)
+        .value("BOTTOM", slsDetectorDefs::portPosition::BOTTOM)
+        .export_values();
+
+    py::enum_<slsDetectorDefs::streamingInterface>(Defs, "streamingInterface",
+                                                   py::arithmetic())
+        .value("NONE", slsDetectorDefs::streamingInterface::NONE)
+        .value("LOW_LATENCY_LINK",
+               slsDetectorDefs::streamingInterface::LOW_LATENCY_LINK)
+        .value("ETHERNET_10GB",
+               slsDetectorDefs::streamingInterface::ETHERNET_10GB)
+        .value("ALL", slsDetectorDefs::streamingInterface::ALL)
+        .export_values()
+        .def("__or__",
+             py::overload_cast<const slsDetectorDefs::streamingInterface &,
+                               const slsDetectorDefs::streamingInterface &>(
+                 &operator|))
+        .def("__and__",
+             py::overload_cast<const slsDetectorDefs::streamingInterface &,
+                               const slsDetectorDefs::streamingInterface &>(
+                 &operator&));
+
+    py::enum_<slsDetectorDefs::vetoAlgorithm>(Defs, "vetoAlgorithm")
+        .value("ALG_HITS", slsDetectorDefs::vetoAlgorithm::ALG_HITS)
+        .value("ALG_RAW", slsDetectorDefs::vetoAlgorithm::ALG_RAW)
+        .export_values();
+
+    py::enum_<slsDetectorDefs::gainMode>(Defs, "gainMode")
+        .value("DYNAMIC", slsDetectorDefs::gainMode::DYNAMIC)
+        .value("FORCE_SWITCH_G1", slsDetectorDefs::gainMode::FORCE_SWITCH_G1)
+        .value("FORCE_SWITCH_G2", slsDetectorDefs::gainMode::FORCE_SWITCH_G2)
+        .value("FIX_G1", slsDetectorDefs::gainMode::FIX_G1)
+        .value("FIX_G2", slsDetectorDefs::gainMode::FIX_G2)
+        .value("FIX_G0", slsDetectorDefs::gainMode::FIX_G0)
+        .export_values();
 }

python/src/enums_in.cpp

@@ -1,18 +1,19 @@
 #include <pybind11/chrono.h>
+#include <pybind11/numpy.h>
 #include <pybind11/operators.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 
 #include "sls/sls_detector_defs.h"
+#include "sls/Pattern.h"
 namespace py = pybind11;
 void init_enums(py::module &m) {
     py::class_<slsDetectorDefs> Defs(m, "slsDetectorDefs");
     py::class_<slsDetectorDefs::xy> xy(m, "xy");
     xy.def(py::init());
-	xy.def(py::init<int,int>());
+    xy.def(py::init<int, int>());
     xy.def_readwrite("x", &slsDetectorDefs::xy::x);
     xy.def_readwrite("y", &slsDetectorDefs::xy::y);
 
-[[ENUMS]]
-
+    [[ENUMS]]
 }

python/src/main.cpp

@@ -19,6 +19,9 @@ void init_enums(py::module &);
 void init_experimental(py::module &);
 void init_det(py::module &);
 void init_network(py::module &);
+void init_pattern(py::module &);
+void init_scan(py::module &);
+void init_source(py::module &);
 PYBIND11_MODULE(_slsdet, m) {
     m.doc() = R"pbdoc(
         C/C++ API
@@ -33,6 +36,9 @@ PYBIND11_MODULE(_slsdet, m) {
      init_enums(m);
      init_det(m);
      init_network(m);
+     init_pattern(m);
+     init_scan(m);
+     init_source(m);
     //  init_experimental(m);
     
 

python/src/pattern.cpp

@@ -0,0 +1,29 @@
+#include <pybind11/chrono.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "sls/Pattern.h"
+#include "sls/sls_detector_defs.h"
+namespace py = pybind11;
+void init_pattern(py::module &m) {
+
+    using pat = sls::patternParameters;
+    py::class_<pat> patternParameters(m, "patternParameters");
+
+    PYBIND11_NUMPY_DTYPE(pat, word, ioctrl, limits, loop, nloop, wait,
+                         waittime);
+
+    patternParameters.def(py::init());
+    patternParameters.def("numpy_view", [](py::object &obj) {
+        pat &o = obj.cast<pat &>();
+        return py::array_t<pat>(1, &o, obj);
+    });
+
+    py::class_<sls::Pattern> Pattern(m, "Pattern");
+    Pattern.def(py::init());
+    Pattern.def("load", &sls::Pattern::load);
+    Pattern.def("data", (pat * (sls::Pattern::*)()) & sls::Pattern::data,
+                py::return_value_policy::reference);
+}

python/src/scan.cpp

@@ -0,0 +1,39 @@
+#include <pybind11/chrono.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+#include <sstream>
+#include "sls/sls_detector_defs.h"
+namespace py = pybind11;
+void init_scan(py::module &m) {
+
+    using sp = slsDetectorDefs::scanParameters;
+    py::class_<sp> scanParameters(m, "scanParameters");
+
+    scanParameters.def(py::init());
+
+    scanParameters.def(py::init<slsDetectorDefs::dacIndex, int, int, int>());
+    scanParameters.def(py::init<slsDetectorDefs::dacIndex, int, int, int, std::chrono::nanoseconds>());
+    scanParameters.def_readwrite("enable", &sp::enable);
+    scanParameters.def_readwrite("dacInd", &sp::dacInd);
+    scanParameters.def_readwrite("startOffset", &sp::startOffset);
+    scanParameters.def_readwrite("stopOffset", &sp::stopOffset);
+    scanParameters.def_readwrite("stepSize", &sp::stepSize);
+    scanParameters.def_readwrite("dacSettleTime_ns", &sp::dacSettleTime_ns);
+    scanParameters.def("__repr__", [](const sp &a){
+        std::ostringstream oss;
+        auto indent = "  ";
+        oss << "<scanParameters>\n";
+        oss << indent << "enable: " <<  a.enable << '\n';
+        oss << indent << "dacInd: " <<  a.dacInd << '\n';
+        oss << indent << "startOffset: " <<  a.startOffset << '\n';
+        oss << indent << "stopOffset: " <<  a.stopOffset << '\n';
+        oss << indent << "stepSize: " <<  a.stepSize << '\n';
+        oss << indent << "dacSettleTime_ns: " <<  a.dacSettleTime_ns;
+        return oss.str();
+    });
+
+
+
+}

serverBin/ctbDetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServerv5.0.0

serverBin/ctbDetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/ctbDetectorServer/bin/ctbDetectorServerv6.0.0-rc1

serverBin/eigerDetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServerv5.0.0

serverBin/eigerDetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/eigerDetectorServer/bin/eigerDetectorServerv6.0.0-rc1

serverBin/gotthard2DetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServerv5.0.0

serverBin/gotthard2DetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/gotthard2DetectorServer/bin/gotthard2DetectorServerv6.0.0-rc1

serverBin/gotthardDetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServerv5.0.0

serverBin/gotthardDetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/gotthardDetectorServer/bin/gotthardDetectorServerv6.0.0-rc1

serverBin/jungfrauDetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServerv5.0.0

serverBin/jungfrauDetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/jungfrauDetectorServer/bin/jungfrauDetectorServerv6.0.0-rc1

serverBin/moenchDetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv5.0.0

serverBin/moenchDetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/moenchDetectorServer/bin/moenchDetectorServerv6.0.0-rc1

serverBin/mythen3DetectorServerv5.0.0

@@ -1 +0,0 @@
-../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv5.0.0

serverBin/mythen3DetectorServerv6.0.0-rc1

@@ -0,0 +1 @@
+../slsDetectorServers/mythen3DetectorServer/bin/mythen3DetectorServerv6.0.0-rc1

settingsdir/mythen/fast/calibration.snxxx

@@ -1 +0,0 @@
-800 10

settingsdir/mythen/fast/fast.cal

@@ -1 +0,0 @@
-829 9.3

settingsdir/mythen/highgain/calibration.snxxx

@@ -1 +0,0 @@
-800 10

settingsdir/mythen/highgain/highgain.cal

@@ -1 +0,0 @@
-804 15.0

settingsdir/mythen/standard/calibration.snxxx

@@ -1 +0,0 @@
-800 10

settingsdir/mythen/standard/standard.cal

@@ -1 +0,0 @@
-817 11.6

slsDetectorCalibration/circularFifo.h

@@ -0,0 +1,156 @@
+#pragma once
+/* CircularFifo.h 
+* Code & platform dependent issues with it was originally
+* published at http://www.kjellkod.cc/threadsafecircularqueue
+* 2009-11-02
+* @author Kjell Hedstr<74>m, hedstrom@kjellkod.cc
+* modified by the sls detetor group
+* */
+
+//#include "sls_receiver_defs.h"
+#include <semaphore.h>
+#include <vector>
+#include <iostream>
+
+typedef  double double32_t;
+typedef  float float32_t;
+typedef  int int32_t;
+
+
+
+/** Circular Fifo (a.k.a. Circular Buffer)
+* Thread safe for one reader, and one writer */
+template<typename Element>
+class CircularFifo {
+public:
+
+   CircularFifo(unsigned int Size) : tail(0), head(0){
+	   Capacity = Size + 1;
+	   array.resize(Capacity);
+	   sem_init(&data_mutex,0,0);
+	   sem_init(&free_mutex,0,Size);
+   }
+   virtual ~CircularFifo() {
+       sem_destroy(&data_mutex);
+	   sem_destroy(&free_mutex);
+   }
+
+   bool push(Element*& item_, bool no_block=false);
+   bool pop(Element*& item_, bool no_block=false);
+
+   bool isEmpty() const;
+   bool isFull() const;
+
+   int getDataValue() const;
+   int getFreeValue() const;
+
+private:
+   std::vector <Element*> array;
+   unsigned int tail; // input index
+   unsigned int head; // output index
+   unsigned int Capacity;
+   mutable sem_t data_mutex;
+   mutable sem_t free_mutex;
+   unsigned int increment(unsigned int idx_) const;
+};
+
+template<typename Element>
+int CircularFifo<Element>::getDataValue() const
+{
+   int value;
+   sem_getvalue(&data_mutex, &value);
+   return value;
+}
+
+template<typename Element>
+int CircularFifo<Element>::getFreeValue() const
+{
+    int value;
+    sem_getvalue(&free_mutex, &value);
+    return value;
+}
+
+
+/** Producer only: Adds item to the circular queue.
+* If queue is full at 'push' operation no update/overwrite
+* will happen, it is up to the caller to handle this case
+*
+* \param item_ copy by reference the input item
+* \param no_block if true, return immediately if fifo is full
+* \return whether operation was successful or not */
+template<typename Element>
+bool CircularFifo<Element>::push(Element*& item_, bool no_block)
+{
+    // check for fifo full
+    if (no_block && isFull())
+        return false;
+
+    sem_wait(&free_mutex);
+    array[tail] = item_;
+    tail = increment(tail);
+    sem_post(&data_mutex);
+    return true;
+}
+
+/** Consumer only: Removes and returns item from the queue
+* If queue is empty at 'pop' operation no retrieve will happen
+* It is up to the caller to handle this case
+*
+* \param item_ return by reference the wanted item
+* \param no_block if true, return immediately if fifo is full
+* \return whether operation was successful or not */
+template<typename Element>
+bool CircularFifo<Element>::pop(Element*& item_, bool no_block)
+{
+    // check for fifo empty
+    if (no_block && isEmpty())
+        return false;
+
+   sem_wait(&data_mutex);
+   item_ = array[head];
+   head = increment(head);
+   sem_post(&free_mutex);
+   return true;
+}
+
+/** Useful for testinng and Consumer check of status
+  * Remember that the 'empty' status can change quickly
+  * as the Procuder adds more items.
+  *
+  * \return true if circular buffer is empty */
+template<typename Element>
+bool CircularFifo<Element>::isEmpty() const
+{
+    return (getDataValue() == 0);
+}
+
+/** Useful for testing and Producer check of status
+  * Remember that the 'full' status can change quickly
+  * as the Consumer catches up.
+  *
+  * \return true if circular buffer is full.  */
+template<typename Element>
+bool CircularFifo<Element>::isFull() const
+{
+    return (getFreeValue() == 0);
+}
+
+/** Increment helper function for index of the circular queue
+* index is inremented or wrapped
+*
+*  \param idx_ the index to the incremented/wrapped
+*  \return new value for the index */
+template<typename Element>
+unsigned int CircularFifo<Element>::increment(unsigned int idx_) const
+{
+   // increment or wrap
+   // =================
+   //    index++;
+   //    if(index == array.lenght) -> index = 0;
+   //
+   //or as written below:
+   //    index = (index+1) % array.length
+   idx_ = (idx_+1) % Capacity;
+   return idx_;
+}
+

slsDetectorCalibration/dataStructures/jungfrauHighZSingleChipData.h

@@ -0,0 +1,238 @@
+#ifndef JUNGFRAUHIGHZSINGLECHIPDATA_H
+#define  JUNGFRAUHIGHZSINGLECHIPDATA_H
+#include "slsDetectorData.h"
+
+//#define VERSION_V2
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t bunchNumber;    /**< is the frame number */
+        uint64_t pre;    /**< something */
+
+    } jf_header;
+
+
+
+
+class jungfrauHighZSingleChipData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+ public:
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+ jungfrauHighZSingleChipData(): slsDetectorData<uint16_t>(256, 256, 256*256*2+sizeof(jf_header)) {
+
+
+     for (int ix=0; ix<256; ix++) {
+       for (int iy=0; iy<256; iy++) {
+	 dataMap[iy][ix]=sizeof(jf_header)+(256*iy+ix)*2;
+#ifdef HIGHZ
+	 dataMask[iy][ix]=0x3fff;
+#endif
+	 }
+     }
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+ 
+  /**
+     Returns the value of the selected channel for the given dataset as double.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \returns data for the selected channel, with inversion if required as double
+
+  */
+  virtual double getValue(char *data, int ix, int iy=0) {
+   
+    uint16_t val=getChannel(data, ix, iy)&0x3fff;
+    return val;
+  };
+
+   
+
+  /* virtual void calcGhost(char *data, int ix, int iy) { */
+  /*   double val=0; */
+  /*   ghost[iy][ix]=0; */
+    
+  /* } */
+
+
+
+  /* virtual void calcGhost(char *data) { */
+  /*   for (int ix=0; ix<25; ix++){ */
+  /*     for (int iy=0; iy<200; iy++) { */
+  /* 	calcGhost(data, ix,iy); */
+  /*     }  */
+  /*   } */
+  /*   // cout << "*" << endl; */
+  /* } */
+
+
+  /* double getGhost(int ix, int iy) { */
+  /*   return 0; */
+  /* }; */
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((jf_header*)buff)->bunchNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+   int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	  return NULL;
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h

@@ -14,6 +14,8 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
   const int nSamples;
   const int offset;
 
+
+
   double ghost[200][25];
   double xtalk;
 
@@ -29,17 +31,22 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
   */
   // moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)), xtalk(0.00021) {
- moench03T1ZmqDataNew(int ns=5000, int oo=0): slsDetectorData<uint16_t>(400, 400, ns*32*2+oo), nSamples(ns), offset(oo), xtalk(0.00021) {
-
+ moench03T1ZmqDataNew(int ns=5000, int oo=2*2): slsDetectorData<uint16_t>(400, 400, ns*32*2+oo), nSamples(ns), offset(oo), xtalk(0.00021) {
+    cout << "M0.3" << endl;
     int nadc=32;
     int sc_width=25;
     int sc_height=200;
-
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    
+     int adc_nr[32]={300,325,350,375,300,325,350,375,	\
     		    200,225,250,275,200,225,250,275,\
     		    100,125,150,175,100,125,150,175,\
     		    0,25,50,75,0,25,50,75};
-
+   
+     /*   int adc_nr[32]={350,375,150,175,350,375,150,175,	\
+    		    300,325,100,125,300,325,100,125,\
+    		    250,275,50,75,250,275,50,75,\
+    		    200,225,0,25,200,225,0,25};
+     */
     int row, col;
     
     int isample;
@@ -50,11 +57,11 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
     int i;
     int adc4(0);
   
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
+    //for (int ip=0; ip<npackets; ip++) {
+    // for (int is=0; is<128; is++) {
+    for (i=0; i<nSamples; i++) {
 	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
+	  //i=128*ip+is;
 	  adc4=(int)iadc/4;
 	  if (i<sc_width*sc_height) {
 	    //  for (int i=0; i<sc_width*sc_height; i++) {
@@ -70,7 +77,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	  }
 	}
       }
-    }
+  // }
 
     
     int ii=0;

slsDetectorCalibration/energyCalibration.cpp

@@ -0,0 +1,798 @@
+#include "energyCalibration.h"
+
+#ifdef __CINT
+#define MYROOT
+#endif
+
+
+#ifdef MYROOT
+#include <TMath.h>
+#include <TH1F.h>
+#include <TH2F.h>
+#include <TGraphErrors.h>
+#endif
+
+#include <iostream>
+
+#define max(a,b) ((a) > (b) ? (a) : (b))
+#define min(a,b) ((a) < (b) ? (a) : (b))
+#define ELEM_SWAP(a,b) { register int t=(a);(a)=(b);(b)=t; }
+
+
+using namespace std;
+
+#ifdef MYROOT
+
+Double_t energyCalibrationFunctions::pedestal(Double_t *x, Double_t *par) { 
+    return par[0]-par[1]*sign*x[0];                                      
+}
+
+
+Double_t energyCalibrationFunctions::gaussChargeSharing(Double_t *x, Double_t *par) { 
+  Double_t f, arg=0;
+  // Gaussian exponent
+  if (par[3]!=0) {
+    arg=sign*(x[0]-par[2])/par[3];
+  }
+  // the Gaussian
+  f=TMath::Exp(-1*arg*arg/2.); 
+  // Gaussian + error function
+  f=f+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); 
+  // Gaussian + error function + pedestal
+  return par[4]*f+pedestal(x,par);                                       
+}
+
+Double_t energyCalibrationFunctions::gaussChargeSharingKb(Double_t *x, Double_t *par) { 
+  Double_t f, arg=0,argb=0;
+  // Gaussian exponent
+  if (par[3]!=0) {
+    arg=sign*(x[0]-par[2])/par[3];
+    argb=sign*(x[0]-(par[6]*par[2]))/par[3]; // using absolute kb mean might seem better but like this the ratio can be fixed
+  }
+  // the Gaussian
+  f=TMath::Exp(-1*arg*arg/2.); 
+  f=f+par[7]*(TMath::Exp(-1*argb*argb/2.));
+  // Gaussian + error function
+  f=f+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); 
+  f=f+par[7]*par[5]/2.*(TMath::Erfc(argb/(TMath::Sqrt(2.)))); 
+  // Gaussian + error function + pedestal
+  return par[4]*f+pedestal(x,par);                                       
+}
+
+Double_t energyCalibrationFunctions::gaussChargeSharingKaDoublet(Double_t *x, Double_t *par) { 
+  Double_t f, f2, arg=0, arg2=0;
+  // Gaussian exponent
+  if (par[3]!=0) {
+    arg=sign*(x[0]-par[2])/par[3];
+    arg2=sign*(x[0]-par[6])/par[3];
+  }
+  // the Gaussian
+  f=TMath::Exp(-1*arg*arg/2.); 
+  f2=TMath::Exp(-1*arg2*arg2/2.); 
+  // Gaussian + error function
+  f=f+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); 
+  f2=f2+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); // shouldn't this be arg2?
+  // Gaussian + error function + pedestal
+  return par[4]*f+par[7]*f2+pedestal(x,par);                                       
+}
+
+Double_t energyCalibrationFunctions::gaussChargeSharingPixel(Double_t *x, Double_t *par) { 
+  Double_t f;
+  if (par[3]<=0 || par[2]*(*x)<=0 || par[5]<0 || par[4]<=0) return 0;
+
+  Double_t pp[3];
+
+  pp[0]=0;
+  pp[1]=par[2];
+  pp[2]=par[3];
+  
+
+  f=(par[5]-par[6]*(TMath::Log(*x/par[2])))*erfBox(x,pp);
+  f+=par[4]*TMath::Gaus(*x, par[2], par[3], kTRUE);
+  return f+pedestal(x,par);                                       
+}
+
+Double_t energyCalibrationFunctions::erfBox(Double_t *z, Double_t *par) {
+
+  
+  
+  Double_t m=par[0];
+  Double_t M=par[1];
+  
+  if (par[0]>par[1]) {
+    m=par[1];
+    M=par[0];
+  }
+  
+  if (m==M)
+    return 0;
+
+
+  if (par[2]<=0) {
+    if (*z>=m && *z<=M)
+      return 1./(M-m);
+    else
+      return 0;
+
+  }
+
+  return (TMath::Erfc((z[0]-M)/par[2])-TMath::Erfc((z[0]-m)/par[2]))*0.5/(M-m);
+
+}
+
+
+// basic erf function
+Double_t energyCalibrationFunctions::erfFunction(Double_t *x, Double_t *par) {	
+  double arg=0;
+  if (par[1]!=0) arg=(par[0]-x[0])/par[1];
+  return ((par[2]/2.*(1+TMath::Erf(sign*arg/(TMath::Sqrt(2))))));  
+};
+  
+
+Double_t energyCalibrationFunctions::erfFunctionChargeSharing(Double_t *x, Double_t *par) {	       
+  Double_t f;		
+  
+  f=erfFunction(x, par+2)*(1+par[5]*(par[2]-x[0]))+par[0]-par[1]*x[0]*sign;		
+  return f;								
+};
+  
+  
+Double_t energyCalibrationFunctions::erfFuncFluo(Double_t *x, Double_t *par) {
+  Double_t f;							       
+  f=erfFunctionChargeSharing(x, par)+erfFunction(x, par+6)*(1+par[9]*(par[6]-x[0])); 
+  return f;							
+};
+#endif
+
+double energyCalibrationFunctions::median(double *x, int n){
+  // sorts x into xmed array and returns median 
+  // n is number of values already in the xmed array
+  double xmed[n];
+  int k,i,j;
+
+  for (i=0; i<n; i++) {
+    k=0;
+    for (j=0; j<n; j++) {
+      if(*(x+i)>*(x+j))
+	k++;
+      if (*(x+i)==*(x+j)) {
+	if (i>j) 
+	  k++;
+      }
+    }
+    xmed[k]=*(x+i);
+  }
+  k=n/2;
+  return xmed[k];
+}
+
+
+int energyCalibrationFunctions::quick_select(int arr[], int n){
+    int low, high ;
+    int median;
+    int middle, ll, hh;
+
+    low = 0 ; high = n-1 ; median = (low + high) / 2;
+    for (;;) {
+        if (high <= low) /* One element only */
+            return arr[median] ;
+
+        if (high == low + 1) {  /* Two elements only */
+            if (arr[low] > arr[high])
+                ELEM_SWAP(arr[low], arr[high]) ;
+            return arr[median] ;
+        }
+
+    /* Find median of low, middle and high items; swap into position low */
+    middle = (low + high) / 2;
+    if (arr[middle] > arr[high])    ELEM_SWAP(arr[middle], arr[high]) ;
+    if (arr[low] > arr[high])       ELEM_SWAP(arr[low], arr[high]) ;
+    if (arr[middle] > arr[low])     ELEM_SWAP(arr[middle], arr[low]) ;
+
+    /* Swap low item (now in position middle) into position (low+1) */
+    ELEM_SWAP(arr[middle], arr[low+1]) ;
+
+    /* Nibble from each end towards middle, swapping items when stuck */
+    ll = low + 1;
+    hh = high;
+    for (;;) {
+        do ll++; while (arr[low] > arr[ll]) ;
+        do hh--; while (arr[hh]  > arr[low]) ;
+
+        if (hh < ll)
+        break;
+
+        ELEM_SWAP(arr[ll], arr[hh]) ;
+    }
+
+    /* Swap middle item (in position low) back into correct position */
+    ELEM_SWAP(arr[low], arr[hh]) ;
+
+    /* Re-set active partition */
+    if (hh <= median)
+        low = ll;
+        if (hh >= median)
+        high = hh - 1;
+    }
+}
+
+int energyCalibrationFunctions::kth_smallest(int *a, int n, int k){
+    register int i,j,l,m ;
+    register double x ;
+
+    l=0 ; m=n-1 ;
+    while (l<m) {
+        x=a[k] ;
+        i=l ;
+        j=m ;
+        do {
+            while (a[i]<x) i++ ;
+            while (x<a[j]) j-- ;
+            if (i<=j) {
+                ELEM_SWAP(a[i],a[j]) ;
+                i++ ; j-- ;
+            }
+        } while (i<=j) ;
+        if (j<k) l=i ;
+        if (k<i) m=j ;
+    }
+    return a[k] ;
+}
+
+
+
+#ifdef MYROOT
+Double_t energyCalibrationFunctions::spectrum(Double_t *x, Double_t *par) {
+  return gaussChargeSharing(x,par);	
+}
+
+Double_t energyCalibrationFunctions::spectrumkb(Double_t *x, Double_t *par) {
+  return gaussChargeSharingKb(x,par);	
+}
+
+Double_t energyCalibrationFunctions::spectrumkadoublet(Double_t *x, Double_t *par) {
+  return gaussChargeSharingKaDoublet(x,par);	
+}
+
+Double_t energyCalibrationFunctions::spectrumPixel(Double_t *x, Double_t *par) {
+  return gaussChargeSharingPixel(x,par);	
+}
+
+
+Double_t energyCalibrationFunctions::scurve(Double_t *x, Double_t *par) {
+  return erfFunctionChargeSharing(x,par);
+}
+
+
+Double_t energyCalibrationFunctions::scurveFluo(Double_t *x, Double_t *par) {
+  return erfFuncFluo(x,par);						
+}
+#endif
+
+energyCalibration::energyCalibration() : 
+#ifdef MYROOT	
+					 fit_min(-1),	
+					 fit_max(-1),	
+					 bg_offset(-1),	
+					 bg_slope(-1),	
+					 flex(-1),
+					 noise(-1),
+					 ampl(-1),
+					 cs_slope(-1),
+					 kb_mean(-1),
+					 kb_frac(-1),
+					 mean2(-1),
+					 ampl2(-1),
+					 fscurve(NULL),
+					 fspectrum(NULL),
+					 fspectrumkb(NULL),
+					 fspectrumkadoublet(NULL),
+#endif
+					 funcs(NULL),
+					 plot_flag(1), // fit parameters output to screen
+					 cs_flag(1)
+{
+
+#ifdef MYROOT	
+  funcs=new energyCalibrationFunctions();
+  
+  fscurve=new TF1("fscurve",funcs,&energyCalibrationFunctions::scurve,0,1000,6,"energyCalibrationFunctions","scurve");	
+  fscurve->SetParNames("Background Offset","Background Slope","Inflection Point","Noise RMS", "Number of Photons","Charge Sharing Slope");
+
+  fspectrum=new TF1("fspectrum",funcs,&energyCalibrationFunctions::spectrum,0,1000,6,"energyCalibrationFunctions","spectrum");	
+  fspectrum->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal");
+  fspectrumkb=new TF1("fspectrumkb",funcs,&energyCalibrationFunctions::spectrumkb,0,1000,8,"energyCalibrationFunctions","spectrumkb");	
+  fspectrumkb->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal","kb mean","kb frac");
+
+  fspectrumkadoublet=new TF1("fspectrumkadoublet",funcs,&energyCalibrationFunctions::spectrumkadoublet,0,1000,8,"energyCalibrationFunctions","spectrumkadoublet");	
+  fspectrumkadoublet->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal","ka2 mean","n2");
+
+  fspixel=new TF1("fspixel",funcs,&energyCalibrationFunctions::spectrumPixel,0,1000,7,"energyCalibrationFunctions","spectrumPixel");	
+  fspixel->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal","Corner");
+
+#endif
+
+
+}
+
+
+
+void energyCalibration::fixParameter(int ip, Double_t val){
+  
+  fscurve->FixParameter(ip, val);
+  fspectrum->FixParameter(ip, val);
+  fspectrumkb->FixParameter(ip, val);
+  fspectrumkadoublet->FixParameter(ip, val);
+}
+
+
+void energyCalibration::releaseParameter(int ip){
+
+  fscurve->ReleaseParameter(ip);
+  fspectrum->ReleaseParameter(ip);
+  fspectrumkb->ReleaseParameter(ip);
+  fspectrumkadoublet->ReleaseParameter(ip);
+}
+
+
+
+
+
+
+
+energyCalibration::~energyCalibration(){ 
+#ifdef MYROOT
+  delete fscurve;
+  delete fspectrum;
+  delete fspectrumkb;
+  delete fspectrumkadoublet;
+#endif
+  
+}
+
+#ifdef MYROOT
+
+
+
+
+
+TH1F* energyCalibration::createMedianHistogram(TH2F* h2, int ch0, int nch, int direction) {
+
+  if (h2==NULL || nch==0)
+    return NULL;
+
+  double *x=new double[nch];
+  TH1F *h1=NULL;
+  
+  double val=-1;
+
+  if (direction==0) {
+    h1=new TH1F("median","Median",h2->GetYaxis()->GetNbins(),h2->GetYaxis()->GetXmin(),h2->GetYaxis()->GetXmax());
+    for (int ib=0; ib<h1->GetXaxis()->GetNbins(); ib++) {
+      for (int ich=0; ich<nch; ich++) {
+	x[ich]=h2->GetBinContent(ch0+ich+1,ib+1);
+      }
+      val=energyCalibrationFunctions::median(x, nch);
+      h1->SetBinContent(ib+1,val);
+    }
+  } else if (direction==1) {   
+    h1=new TH1F("median","Median",h2->GetXaxis()->GetNbins(),h2->GetXaxis()->GetXmin(),h2->GetXaxis()->GetXmax());
+    for (int ib=0; ib<h1->GetYaxis()->GetNbins(); ib++) {
+      for (int ich=0; ich<nch; ich++) {
+	x[ich]=h2->GetBinContent(ib+1,ch0+ich+1);
+      }
+      val=energyCalibrationFunctions::median(x, nch);
+      h1->SetBinContent(ib+1,val);
+    }
+  }
+  delete [] x;
+
+  return h1;
+
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+void energyCalibration::setStartParameters(Double_t *par){	
+  bg_offset=par[0];						
+  bg_slope=par[1];						
+  flex=par[2];							
+  noise=par[3];							
+  ampl=par[4];							
+  cs_slope=par[5];						
+}
+
+void energyCalibration::setStartParametersKb(Double_t *par){	
+  bg_offset=par[0];						
+  bg_slope=par[1];						
+  flex=par[2];							
+  noise=par[3];							
+  ampl=par[4];							
+  cs_slope=par[5];						
+  kb_mean=par[6];
+  kb_frac=par[7];
+  //fit_min = 400; // used for soleil flat field
+  //fit_max = 800;
+}
+
+void energyCalibration::setStartParametersKaDoublet(Double_t *par){	
+  bg_offset=par[0];						
+  bg_slope=par[1];						
+  flex=par[2];							
+  noise=par[3];							
+  ampl=par[4];							
+  cs_slope=par[5];						
+  mean2=par[6];
+  ampl2=par[7];
+  //fit_min = 400; // used for soleil flat field
+  //fit_max = 800;
+}
+
+
+void energyCalibration::getStartParameters(Double_t *par){	
+  par[0]=bg_offset;
+  par[1]=bg_slope;
+  par[2]=flex;
+  par[3]=noise;
+  par[4]=ampl;				
+  par[5]=cs_slope;				
+}
+
+#endif
+int energyCalibration::setChargeSharing(int p) {
+  if (p>=0) {
+    cs_flag=p; 
+#ifdef MYROOT  
+    if (p) {
+      fscurve->ReleaseParameter(5);
+      fspectrum->ReleaseParameter(1);
+      fspectrumkb->ReleaseParameter(1);
+      fspectrumkadoublet->ReleaseParameter(1);
+    } else {
+      fscurve->FixParameter(5,0);
+      fspectrum->FixParameter(1,0);
+      fspectrumkb->FixParameter(1,0);
+      fspectrumkadoublet->FixParameter(1,0);
+    }
+#endif
+  } 
+  
+  return cs_flag;
+}
+
+ 
+#ifdef MYROOT  
+void energyCalibration::initFitFunction(TF1 *fun, TH1 *h1) {
+
+ Double_t min=fit_min, max=fit_max; 
+
+ Double_t mypar[6];
+  
+ if (max==-1) 
+    max=h1->GetXaxis()->GetXmax();
+ 
+  if (min==-1) 
+    min=h1->GetXaxis()->GetXmin();
+
+  
+  if (bg_offset==-1)
+    mypar[0]=0;
+  else
+    mypar[0]=bg_offset;
+
+
+  if (bg_slope==-1)
+    mypar[1]=0;
+  else
+    mypar[1]=bg_slope;
+
+
+  if (flex==-1)
+    mypar[2]=(min+max)/2.;
+  else
+    mypar[2]=flex;
+
+
+  if (noise==-1)
+    mypar[3]=0.1;
+  else
+    mypar[3]=noise;
+
+  if (ampl==-1)
+    mypar[4]=h1->GetBinContent(h1->GetXaxis()->FindBin(0.5*(max+min)));
+  else
+    mypar[4]=ampl;
+
+  if (cs_slope==-1)
+    mypar[5]=0;
+  else
+    mypar[5]=cs_slope;
+ 
+  fun->SetParameters(mypar);
+
+  fun->SetRange(min,max);
+
+}
+
+void energyCalibration::initFitFunctionKb(TF1 *fun, TH1 *h1) {
+
+ Double_t min=fit_min, max=fit_max; 
+
+ Double_t mypar[8];
+  
+ if (max==-1) 
+    max=h1->GetXaxis()->GetXmax();
+ 
+  if (min==-1) 
+    min=h1->GetXaxis()->GetXmin();
+
+  
+  if (bg_offset==-1)
+    mypar[0]=0;
+  else
+    mypar[0]=bg_offset;
+
+
+  if (bg_slope==-1)
+    mypar[1]=0;
+  else
+    mypar[1]=bg_slope;
+
+
+  if (flex==-1)
+    mypar[2]=(min+max)/2.;
+  else
+    mypar[2]=flex;
+
+
+  if (noise==-1)
+    mypar[3]=0.1;
+  else
+    mypar[3]=noise;
+
+  if (ampl==-1)
+    mypar[4]=h1->GetBinContent(h1->GetXaxis()->FindBin(0.5*(max+min)));
+  else
+    mypar[4]=ampl;
+
+  if (cs_slope==-1)
+    mypar[5]=0;
+  else
+    mypar[5]=cs_slope;
+
+  if (kb_mean==-1)
+    mypar[6]=0;
+  else
+    mypar[6]=kb_mean;
+
+  if (kb_frac==-1)
+    mypar[7]=0;
+  else
+    mypar[7]=kb_frac;
+ 
+  fun->SetParameters(mypar);
+
+  fun->SetRange(min,max);
+
+}
+
+void energyCalibration::initFitFunctionKaDoublet(TF1 *fun, TH1 *h1) {
+
+ Double_t min=fit_min, max=fit_max; 
+
+ Double_t mypar[8];
+  
+ if (max==-1) 
+    max=h1->GetXaxis()->GetXmax();
+ 
+  if (min==-1) 
+    min=h1->GetXaxis()->GetXmin();
+
+  
+  if (bg_offset==-1)
+    mypar[0]=0;
+  else
+    mypar[0]=bg_offset;
+
+
+  if (bg_slope==-1)
+    mypar[1]=0;
+  else
+    mypar[1]=bg_slope;
+
+
+  if (flex==-1)
+    mypar[2]=(min+max)/2.;
+  else
+    mypar[2]=flex;
+
+
+  if (noise==-1)
+    mypar[3]=0.1;
+  else
+    mypar[3]=noise;
+
+  if (ampl==-1)
+    mypar[4]=h1->GetBinContent(h1->GetXaxis()->FindBin(0.5*(max+min)));
+  else
+    mypar[4]=ampl;
+
+  if (cs_slope==-1)
+    mypar[5]=0;
+  else
+    mypar[5]=cs_slope;
+
+  if (mean2==-1)
+    mypar[6]=0;
+  else
+    mypar[6]=mean2;
+
+  if (ampl2==-1)
+    mypar[7]=0;
+  else
+    mypar[7]=ampl2;
+ 
+  fun->SetParameters(mypar);
+
+  fun->SetRange(min,max);
+
+}
+
+TF1* energyCalibration::fitFunction(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar) {
+
+
+  TF1* fitfun;
+
+  char fname[100];
+
+  strcpy(fname, fun->GetName());
+
+  if (plot_flag) {
+    h1->Fit(fname,"R0Q");
+  } else
+    h1->Fit(fname,"R0Q");
+
+  fitfun= h1->GetFunction(fname);
+  fitfun->GetParameters(mypar);
+  for (int ip=0; ip<6; ip++) {
+    emypar[ip]=fitfun->GetParError(ip);
+  }
+  return fitfun;
+}
+
+TF1* energyCalibration::fitFunctionKb(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar) {
+
+
+  TF1* fitfun;
+
+  char fname[100];
+
+  strcpy(fname, fun->GetName());
+
+  if (plot_flag) {
+    h1->Fit(fname,"R0Q");
+  } else
+    h1->Fit(fname,"R0Q");
+
+  fitfun= h1->GetFunction(fname);
+  fitfun->GetParameters(mypar);
+  for (int ip=0; ip<8; ip++) {
+    emypar[ip]=fitfun->GetParError(ip);
+  }
+  return fitfun;
+}
+
+TF1* energyCalibration::fitFunctionKaDoublet(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar) {
+
+
+  TF1* fitfun;
+
+  char fname[100];
+
+  strcpy(fname, fun->GetName());
+
+  if (plot_flag) {
+    h1->Fit(fname,"R0Q");
+  } else
+    h1->Fit(fname,"R0Q");
+
+
+  fitfun= h1->GetFunction(fname);
+  fitfun->GetParameters(mypar);
+  for (int ip=0; ip<8; ip++) {
+    emypar[ip]=fitfun->GetParError(ip);
+  }
+  return fitfun;
+}
+
+TF1* energyCalibration::fitSCurve(TH1 *h1, Double_t *mypar, Double_t *emypar) {
+  initFitFunction(fscurve,h1);
+  return fitFunction(fscurve, h1, mypar, emypar);
+}
+
+
+
+
+
+TF1* energyCalibration::fitSpectrum(TH1 *h1, Double_t *mypar, Double_t *emypar) {
+  initFitFunction(fspectrum,h1);
+  return fitFunction(fspectrum, h1, mypar, emypar);
+}
+
+TF1* energyCalibration::fitSpectrumKb(TH1 *h1, Double_t *mypar, Double_t *emypar) {
+  initFitFunctionKb(fspectrumkb,h1);
+  return fitFunctionKb(fspectrumkb, h1, mypar, emypar);
+}
+
+TF1* energyCalibration::fitSpectrumKaDoublet(TH1 *h1, Double_t *mypar, Double_t *emypar) {
+  initFitFunctionKaDoublet(fspectrumkadoublet,h1);
+  return fitFunctionKaDoublet(fspectrumkadoublet, h1, mypar, emypar);
+}
+
+
+TGraphErrors* energyCalibration::linearCalibration(int nscan, Double_t *en, Double_t *een, Double_t *fl, Double_t *efl, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff) { 
+ 
+  TGraphErrors *gr;
+ 
+  Double_t  mypar[2];
+ 
+  gr = new TGraphErrors(nscan,en,fl,een,efl);
+
+  if (plot_flag) {
+    gr->Fit("pol1");
+    gr->SetMarkerStyle(20);
+  } else
+    gr->Fit("pol1","0Q");
+        
+  TF1 *fitfun= gr->GetFunction("pol1"); 
+  fitfun->GetParameters(mypar);
+
+  egain=fitfun->GetParError(1);
+  eoff=fitfun->GetParError(0);
+
+  gain=funcs->setScanSign()*mypar[1];
+  
+  off=mypar[0]; 
+  
+  return gr;
+}
+
+
+TGraphErrors* energyCalibration::calibrate(int nscan, Double_t *en, Double_t *een, TH1F **h1, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff, int integral) {
+
+  TH1F *h;
+
+  Double_t mypar[6], emypar[6];
+  Double_t fl[nscan], efl[nscan];
+  
+
+  for (int ien=0; ien<nscan; ien++) {
+    h=h1[ien];
+    if (integral)
+      fitSCurve(h,mypar,emypar);
+    else
+      fitSpectrum(h,mypar,emypar);
+
+    fl[ien]=mypar[2];
+    efl[ien]=emypar[2];
+  }
+  return linearCalibration(nscan,en,een,fl,efl,gain,off, egain, eoff);
+
+}
+
+#endif
+
+
+
+

slsDetectorCalibration/energyCalibration.h

@@ -98,6 +98,8 @@ class energyCalibrationFunctions {
       par[5] is the fractional height of the charge sharing pedestal (scales with par[3])
   */
   Double_t gaussChargeSharing(Double_t *x, Double_t *par);
+  Double_t gaussChargeSharingKb(Double_t *x, Double_t *par);
+  Double_t gaussChargeSharingKaDoublet(Double_t *x, Double_t *par);
   /** 
       Gaussian Function with charge sharing pedestal
       par[0] is the absolute height of the background pedestal
@@ -153,6 +155,8 @@ Double_t erfFuncFluo(Double_t *x, Double_t *par);
       par[5] is the fractional height of the charge sharing pedestal (scales with par[4]
   */
   Double_t spectrum(Double_t *x, Double_t *par);
+  Double_t spectrumkb(Double_t *x, Double_t *par);
+  Double_t spectrumkadoublet(Double_t *x, Double_t *par);
 
   /** 
       static function Gaussian with charge sharing pedestal with the correct scan sign
@@ -285,7 +289,9 @@ class energyCalibration  {
       par[5] is the angual coefficient of the charge sharing slope (scales with par[3]) -- always positive
   */
   void setStartParameters(Double_t *par);
-  
+  void setStartParametersKb(Double_t *par);
+  void setStartParametersKaDoublet(Double_t *par);
+
 /** get start parameters for the s-curve function
     \param par parameters, -1 means auto-calculated
       par[0] is the  pedestal 
@@ -315,16 +321,8 @@ class energyCalibration  {
      \returns the fitted function - can be used e.g. to get the Chi2 or similar
   */
   TF1 *fitSpectrum(TH1 *h1, Double_t *mypar, Double_t *emypar);
-
-
-  /**
-     fits histogram with the spectrum
-     \param h1 1d-histogram to be fitted
-     \param mypar pointer to fit parameters array 
-     \param emypar pointer to fit parameter errors
-     \returns the fitted function - can be used e.g. to get the Chi2 or similar
-  */
-  TF1 *fitSpectrumPixel(TH1 *h1, Double_t *mypar, Double_t *emypar);
+  TF1 *fitSpectrumKb(TH1 *h1, Double_t *mypar, Double_t *emypar);
+  TF1 *fitSpectrumKaDoublet(TH1 *h1, Double_t *mypar, Double_t *emypar);
 
 
   /**
@@ -399,6 +397,8 @@ class energyCalibration  {
 */
   
   void initFitFunction(TF1 *fun, TH1 *h1);
+  void initFitFunctionKb(TF1 *fun, TH1 *h1);
+  void initFitFunctionKaDoublet(TF1 *fun, TH1 *h1);
 
 
   /**
@@ -410,6 +410,8 @@ class energyCalibration  {
      \returns the fitted function - can be used e.g. to get the Chi2 or similar
   */
   TF1 *fitFunction(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar);  
+  TF1 *fitFunctionKb(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar);  
+  TF1 *fitFunctionKaDoublet(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar);  
 
 #endif
 
@@ -423,11 +425,16 @@ class energyCalibration  {
   Double_t noise; /**< start value for the noise */
   Double_t ampl; /**< start value for the number of photons */
   Double_t cs_slope; /**< start value for the charge sharing slope */
-
+  Double_t kb_mean;
+  Double_t kb_frac;
+  Double_t mean2;
+  Double_t ampl2;
 
   TF1 *fscurve; /**< function with which the s-curve will be fitted */
 
   TF1 *fspectrum; /**< function with which the spectrum will be fitted */
+  TF1 *fspectrumkb; /**< function with which the spectrum will be fitted */
+  TF1 *fspectrumkadoublet; /**< function with which the spectrum will be fitted */
 
   TF1 *fspixel; /**< function with which the spectrum will be fitted */
 

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -447,19 +447,6 @@ class slsInterpolation
       etax=(-l+r)/sum;
       etay=(-b+t)/sum;
     }
-    /* if (etax<-1 || etax>1 || etay<-1 || etay>1) { */
-    /*   cout << "**********" << etax << " " << etay << endl; */
-    /*    for (int ix=0; ix<3; ix++) { */
-    /*   for (int iy=0; iy<3; iy++) { */
-    /* 	cout << cl[iy+3*ix] << "\t" ; */
-
-    /*   } */
-    /*   cout << endl; */
-    /* } */
-    /*    cout << sum << " " << l << " " << r << " " << t << " " << b << endl; */
-
-    /* } */
-
 
     if (etax>=0 && etay>=0)
       return TOP_RIGHT;
@@ -479,6 +466,29 @@ class slsInterpolation
   }
 
 
+
+  static int calcEta3X(double *cl, double &etax, double &etay, double &sum) {
+    double l,r,t,b;
+    sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8];
+    if (sum>0) {
+      l=cl[3];
+      r=cl[5];
+      b=cl[1];
+      t=cl[7];
+      etax=(-l+r)/sum;
+      etay=(-b+t)/sum;
+    }
+    return -1;
+  }
+
+  static int calcEta3X(int *cl, double &etax, double &etay, double &sum) {
+    double cli[9];
+    for (int ix=0; ix<9; ix++) cli[ix]=cl[ix];
+    
+    return calcEta3X(cli, etax, etay, sum);
+  }
+
+
   /* static int calcMyEta(double totquad, int quad, double *cl, double &etax, double &etay) { */
   /*   double l,r,t,b, sum; */
   /*   int yoff; */
@@ -537,21 +547,6 @@ class slsInterpolation
 
 
 
-  /* static int calcEta3X(double *cl, double &etax, double &etay, double &sum) { */
-  /*   double l,r,t,b; */
-  /*   sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8]; */
-  /*   if (sum>0) { */
-  /*     l=cl[3]; */
-  /*     r=cl[5]; */
-  /*     b=cl[1]; */
-  /*     t=cl[7]; */
-  /*     etax=(-l+r)/sum; */
-  /*     etay=(-b+t)/sum; */
-  /*   } */
-  /*   return -1; */
-  /* } */
-
-
   /* static int calcEta3X(int *cl, double &etax, double &etay, double &sum) { */
   /*   double l,r,t,b; */
   /*   sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8]; */

slsDetectorCalibration/jungfrauExecutables/Makefile.cluster_finder

@@ -0,0 +1,47 @@
+#module add CBFlib/0.9.5
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ 
+
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
+
+MAIN=jungfrauClusterFinder.cpp
+
+
+all: jungfrauClusterFinder jungfrauMakeEta jungfrauInterpolation jungfrauNoInterpolation jungfrauPhotonCounter jungfrauAnalog
+
+
+
+jungfrauClusterFinder:  jungfrauClusterFinder.cpp  $(INCS) clean
+			 g++ -o jungfrauClusterFinder  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  
+
+
+jungfrauClusterFinderHighZ:  jungfrauClusterFinder.cpp  $(INCS) clean
+			 g++ -o jungfrauClusterFinderHighZ  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DHIGHZ 
+
+
+
+
+jungfrauMakeEta:  jungfrauInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauMakeEta jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
+
+jungfrauInterpolation:  jungfrauInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauInterpolation jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
+
+jungfrauNoInterpolation:  jungfrauNoInterpolation.cpp  $(INCS) clean
+			 g++ -o jungfrauNoInterpolation jungfrauNoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
+
+jungfrauPhotonCounter: jungfrauPhotonCounter.cpp   $(INCS) clean
+			 g++ -o jungfrauPhotonCounter  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
+
+jungfrauAnalog: jungfrauPhotonCounter.cpp  $(INCS) clean
+			 g++ -o jungfrauAnalog  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+
+jungfrauPhotonCounterHighZ: jungfrauPhotonCounter.cpp   $(INCS) clean
+			 g++ -o jungfrauPhotonCounterHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+
+jungfrauAnalogHighZ: jungfrauPhotonCounter.cpp  $(INCS) clean
+			 g++ -o jungfrauAnalogHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
+
+clean: 	
+	rm -f  jungfrauClusterFinder jungfrauMakeEta jungfrauInterpolation jungfrauNoInterpolation jungfrauPhotonCounter jungfrauAnalog
+
+

slsDetectorCalibration/jungfrauExecutables/Makefile.cluster_finder~

@@ -0,0 +1,47 @@
+#module add CBFlib/0.9.5
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/
+
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
+
+MAIN=moench03ClusterFinder.cpp
+
+
+all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
+
+
+
+moenchClusterFinder:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinder  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER 
+
+
+moenchClusterFinderHighZ:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinderHighZ  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER -DHIGHZ 
+
+
+
+
+moenchMakeEta:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEta moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
+
+moenchInterpolation:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolation moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
+
+moenchNoInterpolation:  moench03NoInterpolation.cpp  $(INCS) clean
+			 g++ -o moenchNoInterpolation moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
+
+moenchPhotonCounter: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounter  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
+
+moenchAnalog: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalog  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+
+moenchPhotonCounterHighZ: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+
+moenchAnalogHighZ: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalogHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
+
+clean: 	
+	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
+
+

slsDetectorCalibration/jungfrauExecutables/Makefile.zmq

@@ -0,0 +1,23 @@
+
+INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3  -std=c++11 -Wall -L../../build/bin/ -lSlsSupport
+#-L../../bin -lhdf5  -L.
+
+#DESTDIR?=../bin
+
+all:  moenchZmqProcess moenchZmq04Process
+ #moenchZmqProcessCtbGui
+
+moenchZmqProcess:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP 
+
+moenchZmq04Process:  moenchZmqProcess.cpp   clean
+		      g++ -o moench04ZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DMOENCH04 
+
+#moenchZmqProcessCtbGui:  moenchZmqProcess.cpp   clean
+#		      g++ -o moenchZmqProcessCtbGui  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DCTBGUI
+
+clean: 	
+	rm -f  moenchZmqProcess  
+
+

slsDetectorCalibration/jungfrauExecutables/jungfrauClusterFinder.cpp

@@ -0,0 +1,161 @@
+//#include "sls/ansi.h"
+#include <iostream>
+
+
+//#include "moench03T1ZmqData.h"
+#include "jungfrauHighZSingleChipData.h"
+
+
+#include "multiThreadedAnalogDetector.h"
+#include "singlePhotonDetector.h"
+
+#include <stdio.h>
+#include <map>
+#include <fstream>
+#include <sys/stat.h>
+
+#include <ctime>
+using namespace std;
+
+
+int main(int argc, char *argv[]) {
+
+
+  if (argc<6) {
+    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
+    return 1;
+  }
+  int p=10000;
+  int fifosize=1000;
+  int nthreads=1;
+  int nsubpix=25;
+  int etabins=nsubpix*10;
+  double etamin=-1, etamax=2;
+  int csize=3;
+  int nx=400, ny=400;
+  int save=1;
+  int nsigma=5;
+  int nped=1000;
+  int ndark=100;
+  int ok;
+  int iprog=0;
+
+
+
+
+  jungfrauHighZSingleChipData *decoder=new  jungfrauHighZSingleChipData();
+
+  decoder->getDetectorSize(nx,ny);
+  cout << "nx " << nx << " ny " << ny << endl;
+
+  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
+  //  char tit[10000];
+  cout << "filter " << endl;
+
+
+
+
+  int* image;
+  filter->newDataSet();
+
+
+  int ff, np;
+  int dsize=decoder->getDataSize();
+  cout << " data size is " << dsize;
+  
+
+  char data[dsize];
+
+  ifstream filebin;
+  char *indir=argv[1];
+  char *outdir=argv[2];
+  char *fformat=argv[3];
+  int runmin=atoi(argv[4]);
+  int runmax=atoi(argv[5]);
+  
+  char fname[10000];
+  char outfname[10000];
+  char imgfname[10000];
+  char pedfname[10000];
+  char fn[10000];
+  
+  std::time_t end_time;
+
+  FILE *of=NULL;
+  cout << "input directory is " << indir << endl;
+  cout << "output directory is " << outdir << endl;
+  cout << "fileformat is " << fformat << endl;
+  
+
+  std::time(&end_time);
+  cout << std::ctime(&end_time) <<   endl;
+
+  char* buff;
+  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+
+ 
+  mt->setDetectorMode(ePhotonCounting);
+  mt->setFrameMode(eFrame);
+  mt->StartThreads();
+  mt->popFree(buff);
+
+
+  cout << "mt " << endl;
+
+  int ifr=0;
+ 
+
+  for (int irun=runmin; irun<runmax; irun++) {
+    sprintf(fn,fformat,irun);
+    sprintf(fname,"%s/%s.raw",indir,fn);
+    sprintf(outfname,"%s/%s.clust",outdir,fn);
+    sprintf(imgfname,"%s/%s.tiff",outdir,fn);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<    endl;
+    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+    filebin.open((const char *)(fname), ios::in | ios::binary);
+    //      //open file
+    if (filebin.is_open()){
+      of=fopen(outfname,"w");
+      if (of) {
+  	mt->setFilePointer(of);
+	//	cout << "file pointer set " << endl;
+      } else {
+  	cout << "Could not open "<< outfname << " for writing " << endl;
+  	mt->setFilePointer(NULL);
+  	return 1;
+      }
+      //     //while read frame 
+      ff=-1;
+      while (decoder->readNextFrame(filebin, ff, np,buff)) {
+
+  	mt->pushData(buff);
+  	mt->nextThread();
+  	mt->popFree(buff);
+	ifr++;
+	if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	ff=-1;
+      }
+        cout << "--" << endl;
+      filebin.close();	 
+      while (mt->isBusy()) {;}//wait until all data are processed from the queues
+      if (of)
+  	fclose(of);
+      
+      mt->writeImage(imgfname);
+      mt->clearImage();
+   
+      std::time(&end_time);
+      cout << std::ctime(&end_time) <<   endl;
+
+    } else 
+     cout << "Could not open "<< fname << " for reading " << endl;
+      
+    
+  }
+    
+
+  return 0;
+}
+

slsDetectorCalibration/jungfrauExecutables/jungfrauClusterFinder.cpp~

@@ -0,0 +1,237 @@
+//#include "sls/ansi.h"
+#include <iostream>
+
+
+//#include "moench03T1ZmqData.h"
+#ifdef NEWRECEIVER
+#ifndef RECT
+#include "moench03T1ReceiverDataNew.h"
+#endif
+
+#ifdef RECT
+#include "moench03T1ReceiverDataNewRect.h"
+#endif
+
+#endif
+
+
+#ifdef CSAXS_FP
+#include "moench03T1ReceiverData.h"
+#endif 
+#ifdef OLDDATA
+#include "moench03Ctb10GbT1Data.h"
+#endif 
+
+#ifdef REORDERED
+#include "moench03T1ReorderedData.h"
+#endif
+
+// #include "interpolatingDetector.h"
+//#include "etaInterpolationPosXY.h"
+// #include "linearInterpolation.h"
+// #include "noInterpolation.h"
+#include "multiThreadedAnalogDetector.h"
+#include "singlePhotonDetector.h"
+//#include "interpolatingDetector.h"
+
+#include <stdio.h>
+#include <map>
+#include <fstream>
+#include <sys/stat.h>
+
+#include <ctime>
+using namespace std;
+
+
+int main(int argc, char *argv[]) {
+
+
+  if (argc<6) {
+    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
+    return 1;
+  }
+  int p=10000;
+  int fifosize=1000;
+  int nthreads=1;
+  int nsubpix=25;
+  int etabins=nsubpix*10;
+  double etamin=-1, etamax=2;
+  int csize=3;
+  int nx=400, ny=400;
+  int save=1;
+  int nsigma=5;
+  int nped=1000;
+  int ndark=100;
+  int ok;
+  int iprog=0;
+
+
+
+
+
+#ifdef NEWRECEIVER
+#ifdef RECT
+  cout << "Should be rectangular!" <<endl;
+#endif
+  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
+  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
+#endif
+
+#ifdef CSAXS_FP
+  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
+  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
+#endif
+
+#ifdef OLDDATA
+  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
+  cout << "OLD RECEIVER DATA!"<<endl;
+#endif
+
+#ifdef REORDERED
+  moench03T1ReorderedData *decoder=new  moench03T1ReorderedData();
+  cout << "REORDERED DATA!"<<endl;
+#endif
+
+
+  decoder->getDetectorSize(nx,ny);
+  cout << "nx " << nx << " ny " << ny << endl;
+
+  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
+  //  char tit[10000];
+  cout << "filter " << endl;
+
+
+
+  // filter->readPedestals("/scratch/ped_100.tiff");
+  // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
+  // cout << "filter "<< endl;
+  
+
+  int size = 327680;////atoi(argv[3]);
+  
+  int* image;
+	//int* image =new int[327680/sizeof(int)];
+  filter->newDataSet();
+
+
+  int ff, np;
+  int dsize=decoder->getDataSize();
+  cout << " data size is " << dsize;
+  
+
+  char data[dsize];
+
+  ifstream filebin;
+  char *indir=argv[1];
+  char *outdir=argv[2];
+  char *fformat=argv[3];
+  int runmin=atoi(argv[4]);
+  int runmax=atoi(argv[5]);
+  
+  char fname[10000];
+  char outfname[10000];
+  char imgfname[10000];
+  char pedfname[10000];
+  //  strcpy(pedfname,argv[6]);
+  char fn[10000];
+  
+  std::time_t end_time;
+
+  FILE *of=NULL;
+  cout << "input directory is " << indir << endl;
+  cout << "output directory is " << outdir << endl;
+  cout << "fileformat is " << fformat << endl;
+  
+
+  std::time(&end_time);
+  cout << std::ctime(&end_time) <<   endl;
+ 
+
+
+
+
+
+
+
+  char* buff;
+  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+
+ 
+  mt->setDetectorMode(ePhotonCounting);
+  mt->setFrameMode(eFrame);
+  mt->StartThreads();
+  mt->popFree(buff);
+
+
+  cout << "mt " << endl;
+
+  int ifr=0;
+ 
+
+  for (int irun=runmin; irun<runmax; irun++) {
+    sprintf(fn,fformat,irun);
+    sprintf(fname,"%s/%s.raw",indir,fn);
+    sprintf(outfname,"%s/%s.clust",outdir,fn);
+    sprintf(imgfname,"%s/%s.tiff",outdir,fn);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<    endl;
+    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+    filebin.open((const char *)(fname), ios::in | ios::binary);
+    //      //open file
+    if (filebin.is_open()){
+      of=fopen(outfname,"w");
+      if (of) {
+  	mt->setFilePointer(of);
+	//	cout << "file pointer set " << endl;
+      } else {
+  	cout << "Could not open "<< outfname << " for writing " << endl;
+  	mt->setFilePointer(NULL);
+  	return 1;
+      }
+      //     //while read frame 
+      ff=-1;
+      while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
+	//	cout << ff << " " << np << endl;
+  	//         //push
+	// for (int ix=0; ix<400; ix++)
+	//   for (int iy=0; iy<400; iy++) {
+	//     if (decoder->getChannel(buff, ix, iy)<3000 || decoder->getChannel(buff, ix, iy)>8000) {
+	//       cout <<  ifr << " " << ff << " " << ix << " " << iy << " " << decoder->getChannel(buff, ix, iy) << endl ;
+	//     }
+	//   }
+
+  	mt->pushData(buff);
+  // 	//         //pop
+  	mt->nextThread();
+  // // 		//	cout << " " << (void*)buff;
+  	mt->popFree(buff);
+	ifr++;
+	if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	ff=-1;
+      }
+        cout << "--" << endl;
+      filebin.close();	 
+      //      //close file 
+      //     //join threads
+      while (mt->isBusy()) {;}//wait until all data are processed from the queues
+      if (of)
+  	fclose(of);
+      
+      mt->writeImage(imgfname);
+      mt->clearImage();
+   
+      std::time(&end_time);
+      cout << std::ctime(&end_time) <<   endl;
+
+    } else 
+     cout << "Could not open "<< fname << " for reading " << endl;
+      
+    
+  }
+    
+
+  return 0;
+}
+

slsDetectorCalibration/jungfrauExecutables/jungfrauInterpolation.cpp

@@ -0,0 +1,250 @@
+
+#include "sls/ansi.h"
+#include <iostream>
+
+//#include "moench03T1ZmqData.h"
+//#define DOUBLE_SPH
+//#define MANYFILES
+
+#ifdef DOUBLE_SPH
+#include "single_photon_hit_double.h"
+#endif
+
+#ifndef DOUBLE_SPH
+#include "single_photon_hit.h"
+#endif
+
+//#include "etaInterpolationPosXY.h"
+#include "noInterpolation.h"
+#include "etaInterpolationPosXY.h"
+//#include "etaInterpolationCleverAdaptiveBins.h"
+//#include "etaInterpolationRandomBins.h"
+using namespace std;
+#define NC 400
+#define NR 400
+#define MAX_ITERATIONS (nSubPixels*100)
+
+#define XTALK
+
+int main(int argc, char *argv[]) {
+
+#ifndef FF
+  if (argc<9) {
+    cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile outfile runmin runmax ns cmin cmax" << endl;
+    return 1;
+  }
+#endif
+  
+#ifdef FF
+  if (argc<7) {
+    cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile runmin runmax cmin cmax" << endl;
+    return 1;
+  }
+#endif
+  int iarg=4;
+  char infname[10000];
+  char fname[10000];
+  char outfname[10000];
+#ifndef FF
+  iarg=4;
+#endif
+
+#ifdef FF
+  iarg=3;
+#endif
+  int runmin=atoi(argv[iarg++]);
+  int runmax=atoi(argv[iarg++]); 
+  cout << "Run min: " << runmin << endl;
+  cout << "Run max: " << runmax << endl;
+  
+  int nsubpix=4;
+#ifndef FF
+  nsubpix=atoi(argv[iarg++]);
+  cout << "Subpix: " << nsubpix << endl;
+#endif
+  float cmin=atof(argv[iarg++]);
+  float cmax=atof(argv[iarg++]);
+  cout << "Energy min: " << cmin << endl;
+  cout << "Energy max: " << cmax << endl;
+  //int etabins=500;
+  int etabins=1000;//nsubpix*2*100;
+  double etamin=-1, etamax=2;
+  //double etamin=-0.1, etamax=1.1;
+  double eta3min=-2, eta3max=2;
+  int quad;
+  double sum, totquad;
+  double sDum[2][2];
+  double etax, etay, int_x, int_y;
+  double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
+  int ok;
+  int f0=-1;
+  int ix, iy, isx, isy;
+  int nframes=0, lastframe=-1;
+  double d_x, d_y, res=5, xx, yy;
+  int nph=0, badph=0, totph=0;
+    FILE *f=NULL;
+
+#ifdef DOUBLE_SPH
+    single_photon_hit_double cl(3,3);
+#endif
+
+#ifndef DOUBLE_SPH
+    single_photon_hit cl(3,3);
+#endif
+
+    int nSubPixels=nsubpix;
+#ifndef NOINTERPOLATION
+   eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(NC, NR, nsubpix, etabins, etamin, etamax);
+   //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
+#endif
+#ifdef NOINTERPOLATION
+    noInterpolation *interp=new noInterpolation(NC, NR, nsubpix);  
+#endif
+
+
+ 
+#ifndef FF
+#ifndef NOINTERPOLATION
+    cout << "read ff " << argv[2] << endl;
+    sprintf(fname,"%s",argv[2]);
+    interp->readFlatField(fname);
+    interp->prepareInterpolation(ok);//, MAX_ITERATIONS);
+#endif
+    // return 0;
+#endif
+#ifdef FF
+    cout << "Will write eta file " << argv[2] << endl;
+#endif
+
+    int *img;
+    float *totimg=new float[NC*NR*nsubpix*nsubpix];
+    for (ix=0; ix<NC; ix++) {
+      for (iy=0; iy<NR; iy++) {
+	for (isx=0; isx<nsubpix; isx++) {
+	  for (isy=0; isy<nsubpix; isy++) {
+	    totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]=0;
+	      }
+	}
+      }
+    }
+
+#ifdef FF
+      sprintf(outfname,argv[2]);
+#endif     
+
+    int irun;
+    for (irun=runmin; irun<runmax; irun++) {
+      sprintf(infname,argv[1],irun);
+#ifndef FF
+      sprintf(outfname,argv[3],irun);
+#endif
+ 
+      f=fopen(infname,"r");
+      if (f) {
+	cout << infname << endl;
+	nframes=0;
+	f0=-1;
+
+	while (cl.read(f)) {
+	  totph++;
+	  if (lastframe!=cl.iframe) {
+	    lastframe=cl.iframe;
+	    // cout << cl.iframe << endl;
+	    // f0=cl.iframe;
+	    if (nframes==0) f0=lastframe;
+	    nframes++;
+	  }
+	  //quad=interp->calcQuad(cl.get_cluster(), sum, totquad, sDum);
+	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+	    if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
+	    nph++;
+	    //  if (sum>200 && sum<580) {
+	    //  interp->getInterpolatedPosition(cl.x,cl.y, totquad,quad,cl.get_cluster(),int_x, int_y);
+// #ifdef SOLEIL
+// 	    if (cl.x>210 && cl.x<240 && cl.y>210 && cl.y<240) {
+// #endif
+#ifndef FF
+	    // interp->getInterpolatedPosition(cl.x,cl.y, cl.get_cluster(),int_x, int_y);  
+	    interp->getInterpolatedPosition(cl.x,cl.y, etax, etay, quad,int_x, int_y);
+	      // cout <<"**************"<< endl;
+	      // cout << cl.x << " " << cl.y << " " << sum << endl;
+	      // cl.print();
+	      // cout << int_x << " " << int_y << endl;
+	      // cout <<"**************"<< endl;
+	    //  if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
+	    interp->addToImage(int_x, int_y);
+	    if (int_x<0 || int_y<0 || int_x>400 || int_y>400) {
+	      cout <<"**************"<< endl;
+	      cout << cl.x << " " << cl.y << " " << sum << endl;
+	      cl.print();
+	      cout << int_x << " " << int_y << endl;
+	      cout <<"**************"<< endl;
+	    }
+#endif
+#ifdef FF
+	    //	interp->addToFlatField(cl.get_cluster(), etax, etay);
+// #ifdef UCL
+// 	    if (cl.x>50)
+// #endif
+// 	    if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
+	      interp->addToFlatField(etax, etay);
+	    //  if (etax==0 || etay==0) cout << cl.x << " " << cl.y << endl;
+	     
+#endif
+// #ifdef SOLEIL
+// 	    }
+// #endif
+	    
+	    if (nph%1000000==0) cout << nph << endl;
+	    if (nph%10000000==0) { 
+#ifndef FF
+		interp->writeInterpolatedImage(outfname);
+#endif
+#ifdef FF 
+		interp->writeFlatField(outfname);
+#endif
+		
+		}
+	  }
+	    
+	} 
+	  
+	  
+	fclose(f);
+#ifdef FF
+	interp->writeFlatField(outfname);
+#endif
+	
+#ifndef FF
+	interp->writeInterpolatedImage(outfname); 
+
+	img=interp->getInterpolatedImage();
+	for (ix=0; ix<NC; ix++) {
+	  for (iy=0; iy<NR; iy++) {
+	    for (isx=0; isx<nsubpix; isx++) {
+	      for (isy=0; isy<nsubpix; isy++) {
+		totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]+=img[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)];
+		}
+	    }
+	  }
+	}
+	cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ") nph="<< nph <<endl;
+	interp->clearInterpolatedImage();
+#endif
+	
+      } else
+	cout << "could not open file " << infname << endl;
+    }
+#ifndef FF
+    sprintf(outfname,argv[3],11111);
+    WriteToTiff(totimg, outfname,NC*nsubpix,NR*nsubpix);
+#endif 
+    
+#ifdef FF
+	interp->writeFlatField(outfname);
+#endif
+
+    cout << "Filled " << nph << " (/"<< totph <<") " << endl; 
+    return 0;
+}
+

slsDetectorCalibration/jungfrauExecutables/jungfrauPhotonCounter.cpp

@@ -0,0 +1,453 @@
+//#include "sls/ansi.h"
+#include <iostream>
+#define CORR
+
+#define C_GHOST 0.0004
+
+#define CM_ROWS 50
+
+//#define VERSION_V1
+
+//#include "moench03T1ZmqData.h"
+#ifdef NEWRECEIVER
+#ifndef RECT
+#include "moench03T1ReceiverDataNew.h"
+#endif
+
+#ifdef RECT
+#include "moench03T1ReceiverDataNewRect.h"
+#endif
+
+#endif
+
+
+#ifdef CSAXS_FP
+#include "moench03T1ReceiverData.h"
+#endif 
+#ifdef OLDDATA
+#include "moench03Ctb10GbT1Data.h"
+#endif 
+
+// #include "interpolatingDetector.h"
+//#include "etaInterpolationPosXY.h"
+// #include "linearInterpolation.h"
+// #include "noInterpolation.h"
+#include "multiThreadedCountingDetector.h"
+//#include "multiThreadedAnalogDetector.h"
+#include "singlePhotonDetector.h"
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
+//#include "interpolatingDetector.h"
+
+#include <stdio.h>
+#include <map>
+#include <fstream>
+#include <sys/stat.h>
+
+#include <ctime>
+using namespace std;
+
+
+int main(int argc, char *argv[]) {
+
+
+  if (argc<4) {
+    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
+    cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
+    cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
+    return 1;
+  }
+
+  int p=10000;
+  int fifosize=1000;
+  int nthreads=10;
+  int nsubpix=25;
+  int etabins=nsubpix*10;
+  double etamin=-1, etamax=2;
+  int csize=3;
+  int save=1;
+  int nsigma=5;
+  int nped=10000;
+  int ndark=100;
+  int ok;
+  int iprog=0;
+
+  int cf=0;
+
+#ifdef NEWRECEIVER
+#ifdef RECT
+  cout << "Should be rectangular!" <<endl;
+#endif
+  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
+  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
+#endif
+
+#ifdef CSAXS_FP
+  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
+  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
+#endif
+
+#ifdef OLDDATA
+  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
+  cout << "OLD RECEIVER DATA!"<<endl;
+#endif
+
+  int nx=400, ny=400;
+
+  decoder->getDetectorSize(nx,ny);
+
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs;
+  double *gainmap=NULL;
+  float *gm;
+
+
+
+  int size = 327680;////atoi(argv[3]);
+  
+  int* image;
+	//int* image =new int[327680/sizeof(int)];
+
+  int ff, np;
+  //cout << " data size is " << dsize;
+  
+
+
+  ifstream filebin;
+  char *indir=argv[1];
+  char *outdir=argv[2];
+  char *fformat=argv[3];
+  int runmin=0;
+  
+  // cout << "argc is " << argc << endl;
+ if (argc>=5) {
+   runmin=atoi(argv[4]);
+  }
+
+ int runmax=runmin;
+
+ if (argc>=6) {
+   runmax=atoi(argv[5]);
+  }
+
+  char *pedfile=NULL;
+  if (argc>=7) {
+    pedfile=argv[6];
+  }
+  double thr=0;
+  double thr1=1;
+
+  if (argc>=8) {
+    thr=atof(argv[7]);
+  }
+  
+
+  int nframes=0;
+  
+  if (argc>=9) {
+    nframes=atoi(argv[8]);
+  }
+
+  int xmin=0, xmax=nx, ymin=0, ymax=ny;
+  if (argc>=13) {
+    xmin=atoi(argv[9]);
+    xmax=atoi(argv[10]);
+    ymin=atoi(argv[11]);
+    ymax=atoi(argv[12]);
+  }
+
+  
+  char *gainfname=NULL;
+  if (argc>13) {
+    gainfname=argv[13];
+    cout << "Gain map file name is: " << gainfname << endl;
+  }
+
+  
+
+
+  char ffname[10000];
+  char fname[10000];
+  char imgfname[10000];
+  char cfname[10000];
+  char fn[10000];
+  
+  std::time_t end_time;
+
+  FILE *of=NULL;
+  cout << "input directory is " << indir << endl;
+  cout << "output directory is " << outdir << endl;
+  cout << "input file is " << fformat << endl;
+  cout << "runmin is " << runmin << endl;
+  cout << "runmax is " << runmax << endl;
+  if (pedfile)
+    cout << "pedestal file is " << pedfile << endl;
+ if (thr>0) 
+    cout << "threshold is " << thr << endl;
+ cout << "Nframes is " << nframes << endl;
+ 
+ uint32 nnx, nny;
+ double *gmap;
+
+  // if (gainfname) {
+  //   gm=ReadFromTiff(gainfname, nny, nnx);
+  //   if (gm && nnx==nx && nny==ny) {
+  //     gmap=new double[nx*ny];
+  //     for (int i=0; i<nx*ny; i++) {
+  // 	gmap[i]=gm[i];
+  //     }
+  //     delete gm;
+  //   } else
+  //     cout << "Could not open gain map " << gainfname << endl;
+  // }
+
+#ifdef CORR
+ cout << "Applying common mode  " << ncol_cm << endl;
+  cm=new moench03CommonMode(ncol_cm);
+  
+
+  cout << "Applying ghost corrections " << xt_ghost << endl;
+  gs=new moench03GhostSummation(decoder, xt_ghost);
+#endif
+
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
+
+  if (gainfname) {
+
+    if (filter->readGainMap(gainfname))
+      cout << "using gain map " << gainfname << endl;
+    else
+      cout << "Could not open gain map " << gainfname << endl;
+  } else
+    thr=0.15*thr;
+  filter->newDataSet();
+  int dsize=decoder->getDataSize();
+
+
+  char data[dsize];
+
+
+
+
+
+  //#ifndef ANALOG
+  if (thr>0) {
+    cout << "threshold is " << thr << endl;
+    //#ifndef ANALOG
+    filter->setThreshold(thr);
+    //#endif
+      cf=0;
+
+  } else
+    cf=1;
+  //#endif
+
+
+  filter->setROI(xmin,xmax,ymin,ymax);
+  std::time(&end_time);
+  cout << std::ctime(&end_time) <<   endl;
+
+  char* buff;
+
+  // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+ multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
+#ifndef ANALOG
+    mt->setDetectorMode(ePhotonCounting);
+    cout << "Counting!" << endl;
+  if (thr>0) {
+    cf=0;
+  } 
+#endif
+//{
+#ifdef ANALOG
+      mt->setDetectorMode(eAnalog);
+      cout << "Analog!" << endl;
+      cf=0;
+      //thr1=thr;
+#endif  
+      //  }
+  
+  mt->StartThreads();
+  mt->popFree(buff);
+
+
+  //  cout << "mt " << endl;
+
+  int ifr=0;
+
+  double ped[nx*ny], *ped1;
+
+
+  if (pedfile) {
+
+    cout << "PEDESTAL " << endl;
+    sprintf(imgfname,"%s/pedestals.tiff",outdir);
+
+    if (string(pedfile).find(".tif")==std::string::npos){
+      sprintf(fname,"%s.raw",pedfile);
+      cout << fname << endl ;
+      std::time(&end_time);
+      cout << "aaa" << std::ctime(&end_time) <<   endl;
+      
+      
+      mt->setFrameMode(ePedestal);
+      // sprintf(fn,fformat,irun);
+      filebin.open((const char *)(fname), ios::in | ios::binary);
+      //      //open file
+      if (filebin.is_open()){
+	ff=-1;
+	while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	  if (np==40) {
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    ifr++;
+	    if (ifr%100==0) 
+	      cout << ifr << " " << ff << " " << np << endl;
+	  } else
+	    cout << ifr << " " << ff << " " << np << endl;
+	  ff=-1;
+	}
+	filebin.close();	 
+	while (mt->isBusy()) {;}
+	
+      } else 
+	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
+    } else {
+      float *pp=ReadFromTiff(pedfile, nny, nnx);
+      if (pp && nnx==nx && nny==ny) {
+	for (int i=0; i<nx*ny; i++) {
+	  ped[i]=pp[i];
+	}
+	delete [] pp;
+	mt->setPedestal(ped);
+	// ped1=mt->getPedestal();
+	
+	// for (int i=0; i<nx*ny; i++) {
+
+	//   cout << ped[i]<<"/"<<ped1[i] << " " ;
+	// }
+	cout << "Pedestal set from tiff file " << pedfile << endl;
+      } else {
+	cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
+      }
+    }
+    mt->writePedestal(imgfname);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
+  }
+  
+
+
+  ifr=0;
+  int ifile=0;
+  
+  mt->setFrameMode(eFrame);
+
+  for (int irun=runmin; irun<=runmax; irun++) {
+    cout << "DATA " ;
+    // sprintf(fn,fformat,irun);
+    sprintf(ffname,"%s/%s.raw",indir,fformat);
+    sprintf(fname,ffname,irun);
+    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+    sprintf(imgfname,ffname,irun);
+    sprintf(ffname,"%s/%s.clust",outdir,fformat);
+    sprintf(cfname,ffname,irun);
+    cout << fname << " " ;
+    cout << imgfname << endl;
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<    endl;
+    //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+    filebin.open((const char *)(fname), ios::in | ios::binary);
+    //      //open file
+    ifile=0;
+    if (filebin.is_open()){
+      if (thr<=0 && cf!=0) { //cluster finder
+	  if (of==NULL) {
+	    of=fopen(cfname,"w");
+	    if (of) {
+	    mt->setFilePointer(of);
+	    cout << "file pointer set " << endl;
+	    } else {
+	      cout << "Could not open "<< cfname << " for writing " << endl;
+	      mt->setFilePointer(NULL);
+	      return 1;
+	    }
+	  }
+      }
+      //     //while read frame 
+      ff=-1;
+      ifr=0;
+      while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	if (np==40) {
+	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
+	//	cout << ff << " " << np << endl;
+  	//         //push
+	  mt->pushData(buff);
+	  // 	//         //pop
+	  mt->nextThread();
+	  // // 		//	cout << " " << (void*)buff;
+	  mt->popFree(buff);
+
+
+
+
+	  ifr++;
+	  if (ifr%100==0) cout << ifr << " " << ff << endl;
+	  if (nframes>0) {
+	    if (ifr%nframes==0) {
+	      //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
+	      
+	      sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+	      sprintf(imgfname,ffname,irun);
+	      //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+	      mt->writeImage(imgfname, thr1);
+	      mt->clearImage();
+	      ifile++;
+	    }
+	  }
+	} else
+	  cout << ifr << " " << ff << " " << np << endl;
+	ff=-1;
+      }
+      cout << "--" << endl;
+      filebin.close();	 
+      //      //close file 
+      //     //join threads
+      while (mt->isBusy()) {;}
+      if (nframes>=0) {
+	if (nframes>0) {
+	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+	    sprintf(imgfname,ffname,irun);
+	} else {
+	  sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+	  sprintf(imgfname,ffname,irun);
+	}
+	cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
+	mt->writeImage(imgfname, thr1);
+	mt->clearImage();
+	if (of) {
+	  fclose(of);
+	  of=NULL;
+	  mt->setFilePointer(NULL);
+	}
+      }	
+      std::time(&end_time);
+      cout << std::ctime(&end_time) <<   endl;
+    } else 
+      cout << "Could not open "<< fname << " for reading " << endl;
+  }
+  if (nframes<0){
+    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+    strcpy(imgfname,ffname);
+    cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
+    mt->writeImage(imgfname, thr1);
+  }
+    
+
+
+  return 0;
+}
+

slsDetectorCalibration/moenchExecutables/CMakeLists.txt

@@ -3,11 +3,11 @@ find_package(TIFF REQUIRED)
 
 #Moench ZMQ
 add_executable(moenchZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
-add_compile_definitions(moenchZmqProcess NEWZMQ INTERP)
+target_compile_definitions(moenchZmqProcess PRIVATE NEWZMQ INTERP)
 
 #Moench04 ZMQ
 add_executable(moench04ZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
-add_compile_definitions(moenchZmqProcess NEWZMQ INTERP MOENCH04)
+target_compile_definitions(moench04ZmqProcess PRIVATE NEWZMQ INTERP MOENCH04)
 
 
 #Both executables should have the same includes and output dirs
@@ -41,5 +41,9 @@ foreach(exe ${MOENCH_EXECUTABLES})
         set_property(TARGET ${exe} PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
     endif()
 
+    
+
 
 endforeach(exe ${MOENCH_EXECUTABLES})
+
+install(TARGETS ${MOENCH_EXECUTABLES} DESTINATION bin)

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -1,6 +1,8 @@
 //#define WRITE_QUAD
 #define DEVELOPER
 #undef CORR
+#undef MOENCH04
+
 #define C_GHOST 0.0004
 
 #define CM_ROWS 20
@@ -28,6 +30,7 @@
 #include <fstream> 
 #include "tiffIO.h"
 
+
 #include <rapidjson/document.h> //json header in zmq stream
 
 #include<iostream>
@@ -135,9 +138,11 @@ int main(int argc, char *argv[]) {
 
   //slsDetectorData *det=new moench03T1ZmqDataNew(); 
 #ifndef MOENCH04
+  cout << "This is a Moench03" << endl;
   moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
 #endif
 #ifdef MOENCH04
+  cout << "This is a Moench04" << endl;
   moench04CtbZmq10GbData *det=new moench04CtbZmq10GbData(); 
 #endif
   cout << endl << " det" <<endl;
@@ -614,61 +619,8 @@ int main(int argc, char *argv[]) {
 	      version=zHeader.version;//doc["version"].GetUint();
 	      /*document["bitmode"].GetUint(); zHeader.dynamicRange
 
-document["fileIndex"].GetUint64(); zHeader.fileIndex
 
-document["detshape"][0].GetUint();
-zHeader.ndetx
-
-document["detshape"][1].GetUint();
-zHeader.ndety
-
-document["shape"][0].GetUint();
-zHeader.npixelsx
-
-document["shape"][1].GetUint();
-zHeader.npixelsy
-
-document["size"].GetUint(); zHeader.imageSize
-
-document["acqIndex"].GetUint64(); zHeader.acqIndex
-
-document["frameIndex"].GetUint64(); zHeader.frameIndex
-
-document["fname"].GetString(); zHeader.fname
-
-document["frameNumber"].GetUint64(); zHeader.frameNumber
-
-document["expLength"].GetUint(); zHeader.expLength
-
-document["packetNumber"].GetUint(); zHeader.packetNumber
-
-document["bunchId"].GetUint64(); zHeader.bunchId
-
-document["timestamp"].GetUint64(); zHeader.timestamp
-
-document["modId"].GetUint(); zHeader.modId
-
-document["row"].GetUint(); zHeader.row
-
-document["column"].GetUint(); zHeader.column
-
-document["reserved"].GetUint(); zHeader.reserved
-
-document["debug"].GetUint(); zHeader.debug
-
-document["roundRNumber"].GetUint(); zHeader.roundRNumber
-
-document["detType"].GetUint(); zHeader.detType
-
-document["version"].GetUint(); zHeader.version
-
-document["flippedDataX"].GetUint(); zHeader.flippedDataX
-
-document["quad"].GetUint(); zHeader.quad
-
-document["completeImage"].GetUint(); zHeader.completeImage
 	      */
-	      //dataSize=size;
 
 	      //strcpy(fname,filename.c_str());
 	      fname=filename;