dont add detector id for .trim

* Setting pattern from memory (#218)

* ToString accepts c-style arrays

* fixed patwait time bug in validation

* Introduced pattern class

* compile for servers too

* Python binding for Pattern

* added scanParameters in Python

* slsReceiver: avoid potential memory leak around Implementation::generalData

* additional constructors for scanPrameters in python

* bugfix: avoid potentital memory leak in receiver if called outside constructor context

* added scanParameters in Python

* additional constructors for scanPrameters in python

* M3defaultpattern (#227)

* default pattern for m3 and moench including Python bindings

* M3settings (#228)

* some changes to compile on RH7 and in the server to load the default chip status register at startup

* Updated mythen3DeectorServer_developer executable with correct initialization at startup

Co-authored-by: Erik Frojdh <erik.frojdh@gmail.com>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>

* Pattern.h as a public header files (#229)

* fixed buffer overflow but caused by using global instead of local enum

* replacing out of range trimbits with edge values

* replacing dac values that are out of range after interpolation

* updated pybind11 to 2.6.2

* Mythen3 improved synchronization (#231)

Disabling scans for multi module Mythen3, since there is no feedback of the detectors being ready
startDetector first starts the slaves then the master
acquire firs calls startDetector for the slaves then acquire on the master
getMaster to read back from hardware which one is master

* New server for JF to go with the new FW (#232)

* Modified Jungfrau speed settings for HW1.0 - FW fix version 1.1.1, compilation date 210218

* Corrected bug. DBIT clk phase is implemented in both HW version 1.0 and 2.0. Previous version did not update the DBIT phase shift on the configuration of a speed.

* fix for m3 scan with single module

* m3 fw version

* m3 server

* bugfix for bottom when setting quad

* new strategy for finding zmq based on cppzmq



Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>
Co-authored-by: Dhanya Thattil <33750417+thattil@users.noreply.github.com>
Co-authored-by: Alejandro Homs Puron <ahoms@esrf.fr>
Co-authored-by: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Co-authored-by: Xiaoqiang Wang <xiaoqiangwang@gmail.com>
Co-authored-by: lopez_c <carlos.lopez-cuenca@psi.ch>

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")
 
@@ -157,8 +157,37 @@ 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()
@@ -192,7 +221,7 @@ if (SLS_USE_INTEGRATION_TESTS)
 endif (SLS_USE_INTEGRATION_TESTS)
 
 if (SLS_USE_PYTHON)
-    set(PYBIND11_CPP_STANDARD -std=c++11)
+    find_package (Python 3.6 COMPONENTS Interpreter Development)
     add_subdirectory(libs/pybind11)
     add_subdirectory(python)
 endif(SLS_USE_PYTHON)

RELEASE.txt

@@ -1,325 +1,38 @@
-SLS Detector Package 5.0.0 released on 18.11.2020 (Major Release)
-=================================================================
+SLS Detector Package 5.X.X released on XX.XX.2021 (Minor Release)
+===================================================================
+
+This document describes the differences between X and Y releases.   
+
+
 
     CONTENTS
     --------
-    1.	Topics Concerning
-    2.  New Features
-    3.  Resolved Issues
-    4.  Known Issues
-    5.  Firmware Requirements
-    6.  Download, Documentation & Support
+    1.  New Features
+    2.  Resolved Issues
+    3.  Known Issues
+    4.  Firmware Requirements
+    5.  Download, Documentation & Support
 
 
 
-1. Topics Concerning
-====================
 
-    - Compilation requirements
-    - Manuals
-    - Client API complete change
-    - Exceptions
-    - Scan mode (dacs and trimbit)
-    - Timing commands
-    - Enum list (daclist, dacvalues, settingslist, drlist etc.)
-    - Command line (return code)
-    - Command line (dac)
-    - UDP configuration change
-    - Gappixels
-    - Detector Simulators
-    - (Jungfrau server) settings and default dacs
-    - (Servers) Shared Memory
-    - (Jungfrau) two interfaces
-    - (Eiger, Jungfrau server) starting frame number
-    - (Eiger server) Server Config File
-    - (Eiger server) Partial Readout
-    - (Eiger server) Removed Features
-    - (Eiger server) Deactivation
-    - Zmq interface (ZmqSocket.h)
-    - slsReceiver (Metadata)
-    - slsReceiver (Shared Memory)
-    - slsReceiver (UDP IP)
-    - (Eiger Custom Receiver) Header packet
-    - Gui (zmq high water mark)
-    - (Eiger Server) Blocked server
-    - (Eiger Firmware) Extra 8 byte Packets
- 
-
-
-2. New Features
+1. New Features
 ===============
 
-    Client
-    ------
-    1.  Compilation requirements
-        They are very different now and can be accessed at
-            https://slsdetectorgroup.github.io/devdoc/dependencies.html
-        Gui not included in default cmk.sh script. Must be explicitly asked for.
+    Setting Mythen3 gain from command line
 
-    2.  Manuals 
-        They can be compiled in the package. 
-            https://slsdetectorgroup.github.io/devdoc/installation.html#build-this-documentation
-        Or refer to the documentation provided in 
-            https://slsdetectorgroup.github.io/devdoc/index.html
-
-    3.  API
-        Changed to Detector class. 
-        C++: Detector.h
-            Documentation:
-                https://slsdetectorgroup.github.io/devdoc/detector.html
-            Examples to use the Detector class:
-                https://github.com/slsdetectorgroup/api-examples
-
-        Python API Documentation: 
-            https://slsdetectorgroup.github.io/devdoc/pydetector.html
-
-        Command line:
-            Many commands have become deprecated. They will still execute, 
-            but give a warning.
-            Documentation:
-                https://slsdetectorgroup.github.io/devdoc/commandline.html
-            Help on a command:
-                sls_detector_help [command], or
-                sls_detector_get -h [command]
-    
-    4.  Exceptions
-        They are thrown instead of providing error codes.
-            sls_detector_exceptions.h
-        Make sure you catch all exceptions in custom gui and handle them or 
-        inform the user.
-        Exceptions thrown in callbacks are also handled.
-            - An exception in startAcquisitionCallBack will need to be handled in 
-            startReceiver or acquire()
-            - An exception in acquisitionFinishedCallBack will need to be handled in
-            stopReceiver or acquire()
-            - An exception in rawDataReadyCallBack or rawDataModifyReadyCallBack
-            will only print and skip image to free it in memory. If address is
-            incorrect after callback, expect undefined behavior.
-
-    5.  Scan mode
-        One can do scans for dacs or trimbits. Trimbits are only for Eiger or 
-        Mythen3. Enable scan mode and then acquire using blocking or non blocking
-        method. Command: scan.
-
-    6.  Timing Commands
-        In command line, all timing commands (eg. peiod) can now specify unit. 
-            eg 100ms 10us, 1s, 100ns
-        In C++ API, one must use chrono library.
-            eg. std::chrono::duration<double, std::milli> t1{232.57};
-                det.setExptime(std::chrono::duration_cast<std::chrono::nanoseconds>(t1));
-        In Python API, one must use timedelta library. 
-            eg. d.exptime = dt.timedelta(seconds = 1.2)
-
-    7.  Enum list (daclist)
-        Command line and API now has features to get the list of enums/commands
-        for dacs, settings, dynamic range, timing modes and temperatures for 
-        the detector in shared memory. 
-            eg. daclist, settingslist, drlist, timinglist, templist
-        Command line also has commands to get their values.
-            eg. dacvalues, tempvalues
-        Python has commands to get their values (detector specific class).
-            eg. d.temp, d.dacs
-
-    8.  Command Line (return code)
-        Return code of the client command line applications now return 0 for 
-        success and 1 for failure.
-        
-    9.  Command Line (Dac)
-        All dac commands have been converted to a single "dac" command with 
-        the previous dac commands as arguments.
-            eg. sls_detector_get vcmp_ll
-            is now
-            sls_detector_get dac vcmp_ll
-    
-    10. UDP Configuration
-        Once all the udp details are set in the detector, the detector's
-        destination is then configured automatically. If the detector is not 
-        configured, it will  fail when acquiring. If any of these parameters
-        are also changed, then this is configured again. Hence, configuremac 
-        command has been removed. Instead, there are commands such as
-        udp_validate (to validate if it has been configured) and
-        udp_reconfigure (to reconfigure).
-
-    11. Gap Pixels
-        Gap pixels are now only available in client call back or gui (not in 
-        receiver anymore). It can be enabled for Eiger and Jungfrau and 
-        includes inter chip and inter module gap pixels.
-
-    Detector Servers
-    ----------------
-
-    1.  Detector Simulators 
-        Or virtual detector servers for every detector have been provided. 
-        They are compiled along with the client by enabling its option. 
-        They should also send fake data (increasing pixel/channel value).  
-
-    2.  (Jungfrau) settings
-        Settings command do not implicitly set default dacs from now on.
-        One can use the command 'defaultdacs' to set them explicitly.
-
-    3.  Shared Memory
-        Almost all the detector parameters removed from shared memory.
-        Therefore, they are all fetched directly from detector.
-
-    4.  (Jungfrau) Two 10G data interfaces
-        Only Jungfrau PCBs with version 2.0 can run at full speed using both
-        the 10G UDP interfaces to stream out data. This is available from 
-        the current firmware and software. To enable two interfaces, one has 
-        to enable two interfaces using "numinterfaces" to 2 and set corresponding
-        udp_dstip2, udp_dstport2 etc. One can also decide to select which of 
-        the two interfaces to use, when using only 1 interface.
-
-    5.  (Eiger, Jungfrau) Next Frame number
-        Both now have running frame numbers that is only reset at boot up
-        and increments continuously through acquisitions. One is able to 
-        set the next frame number now. Command: nextframenumber.
-
-    6.  (Eiger) Server Config file (config_eiger.txt)
-        A config file on the detector can take in 2 parameters "master" 
-        and "top" being set to 1 or 0 to enable or disable the same.
-        When server is started without this file, it is set to hardware
-        settings.
-
-    7.  (Eiger) Partial readout
-        It is possible for partial readouts, where you specify the number
-        of pixel rows to read out. Not all values are allowed. The current
-        slsReceiver does not complain about missing packets, but only puts 
-        this partial image into the complete image (padding the rest). One
-        can cut out required subimage using callbacks, but this feature
-        is probably more useful for custom receivers. Command: readnlines.
-
-    8.  (Eiger) Removed Features
-        storeinram, safe speed and ability to set settings via the settings 
-        command has been removed.
-
-    9.  (Eiger) Deactivation
-        The detector is deactivated by default upon boot up and activated only 
-        upon setting hostname in the client. This is to ensure if the 
-        network of a board or a board is broken and one cannot connect
-        to this board, then it is deactivated by default upon reboot. 
-        Therefore, one can use other half modules of the detector.
-
-    Receiver
-    --------
-
-    1.  Zmq
-        The static library and the zmq.h is no longer provided with package.
-        One must install ZeroMQ version 4.
-        ZmqSocket.h API has changed, especially in parsing receiving JSON header.
-        One must pick up needed parameters  from exposed struct zmqHeader in 
-        ZmqSocket.h.
-
-    2.  Metadata
-        Detector dependant metadata has been added to the master files.
-
-    3.  Shared Memory
-        Almost all receiver parameters have been removed from client shared memory.
-        Therefore the receiver process needs to be alive to access any receiver
-        parameter as they are now fetched directly from the receiver.
-
-    4.  UDP IP
-        Since all the parameters are fetched from receiver or detector directly 
-        (not shared memory), the udp desintation ip (previously rx_udpip) is safer 
-        to be specified before setting rx_hostname. Setting it before has the
-        advantage that the detector is updated first before the receiver is
-        requested for the udp mac. This helps when changing pc and the receiver
-        cannot find the udp ip to get the udp mac.
-
-    5.  (Eiger) Header packet
-        The header packets of Eiger are not sent in this firmware version. So, 
-        custom receivers should handle accordingly.
-
-    Gui
-    ---
-    
-    1.  Zmq high water mark
-        When opening the Gui, the zmq send and receiver high water mark is set to 2
-        instead of default (1000 for zmq library version 4). This is to ensure
-        fast and large detectors can still see latest data on the gui at the cost of
-        losing images in between.
-        When using a different processor or client data call back to handle zmq data, 
-        please ensure this is set back to default to get every zmq packet. Setting it to 
-        -1 sets it to library defaults.
-
-    
-    
-
-3. Resolved Issues
-==================
-
-    Detector Server
-    ---------------
-
-    1.  (Eiger) Blocked Server
-        Very rarely, Eiger control or stop server would block and would require a restart
-        of server. This is due to both servers accessing the same link to get to FEB
-        registers. Locking has been implemented in server shared memory to resolve.
-
-
-
-4. Known Issues
-===============
-
-    1.  (Eiger) Extra 8 byte Packets
-        When stopping detector acquisition while acquiring for more than 128 frames,
-        the next acquisition sends out first an 8 byte packet. This is discarded
-        by the slsReceiver/slsMultiReceiver. Please handle this in custom receivers.
-
-
-
-5. Firmware Requirements
+4. Firmware Requirements
 ========================
-        
-        Eiger
-        =====  
-        Compatible version : 08.09.2020 (v27)
-        
-        Jungfrau
-        ========       
-        Compatible version : 24.07.2020 (v1.1, PCB v1.0) 
-                           : 21.07.2020 (v2.1, PCB v2.0)
-
-        Gotthard
-        ========   
-        Compatible version : 08.02.2018 (50um and 25um Master)
-                           : 09.02.2018 (25 um Slave) 
-
-        Mythen3
-        =======
-        Compatible version : 25.09.2020 (development)
-
-        Gotthard2
-        =========
-        Compatible version : 25.09.2020 (development)
-
-        Moench
-        ======
-        Compatible version : 05.10.2020 (v1.0)
-
-        Ctb
-        ===
-        Compatible version : 05.10.2020 (v1.0)
-
-        Detector Upgrade
-        ================
-
-        The following can be upgraded remotely:
-        Eiger      via bit files
-        Jungfrau   via command <.pof>
-        Mythen3    via command <.rbf>
-        Gotthard2  via command <.rbf> 
-        Moench     via command <.pof>
-        Ctb        via command <.pof>
-
-        The following cannot be upgraded remotely:
-        Gotthard   
-
-        Instructions available at
-            https://slsdetectorgroup.github.io/devdoc/firmware.html
-        and
-            https://slsdetectorgroup.github.io/devdoc/serverupgrade.html
-
     
+
+
+5. Known Issues
+===============
+
+    No updates from 5.0.0
+
+
+
 6. Download, Documentation & Support
 ====================================
 

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

@@ -13,8 +13,9 @@ cmake .. \
       -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/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
@@ -94,6 +106,13 @@ 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.*

docs/src/consuming.rst

@@ -9,7 +9,7 @@ CMake approaches.
 One can test with :ref:`detector simulators<Virtual Detector Servers>` before testing the API with a real detector or when a real detector is not at hand.
 
 CMake: slsDetectorPackage as submodule in your project
----------------------------------------
+---------------------------------------------------------------
 
 If you are using CMake to build your integration and want to build everything
 in one go, we support adding slsDetectorPackage as a subfolder in your cmake project. 

docs/src/firmware.rst

@@ -12,32 +12,7 @@ Download
 
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- bit files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
-
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - 
-         - 08.09.2020
-         - `v27 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v27/>`__
-         - 
-       * - v4.0.0 - v4.2.0
-         - 
-         - 30.07.2019
-         - `v24 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v24/>`__
-         - 
-       * - v3.1.0 - v3.1.5
-         - 
-         - 17.08.2017
-         - `v20 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/eiger/v20/>`__
-         -
-
+- `bit files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
 Upgrade
 ^^^^^^^^
@@ -116,37 +91,7 @@ Download
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- pof files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
-
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - 2.0
-         - 21.07.2020
-         - `v2.1 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v2_1/jungfrau_v2_1.pof>`__
-         - 
-       * - v5.0.0-rcx
-         - 1.0
-         - 24.07.2020
-         - `v1.1 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v1_1/jungfrau_v1_1.pof>`__
-         - 
-       * - v4.0.1 - v4.2.0
-         - 1.0
-         - 06.12.2018
-         - `v0.7 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v0_7/jungfrau_v0_7.pof>`__
-         - 
-       * - v3.1.0 - v3.1.5
-         - 1.0
-         - 13.11.2017
-         - `v0.6 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/jungfrau/v0_6/jungfrau_v0_6.pof>`__
-         -
-
+- `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
 
 Upgrade (from v4.x.x)
@@ -156,7 +101,7 @@ Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you
 
 #. Tftp must be installed on pc.
 
-#. Update client package to the latest (5.0.0-rc1).
+#. Update client package to the latest (5.x.x).
 
 #. Disable server respawning or kill old server
     .. code-block:: bash
@@ -204,7 +149,7 @@ Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you
         jungfrauDetectorServervxxx --stop-server 1953
 
 
-Upgrade (from v5.0.0-rcx)
+Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
@@ -230,31 +175,8 @@ Download
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- pof files
-    .. list-table:: 
-       :widths: 15 15 15 15 5
-       :header-rows: 1
+- `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - All versions
-         - 50um
-         - 08.02.2018
-         - `50um <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/50um/gotthard_I_50um.pof>`__
-         - 
-       * - All versions
-         - 25um (master)
-         - 08.02.2018
-         - `25um (master) <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/25um/master/gotthard_I_25um_master.pof>`__
-         - 
-       * - All versions
-         - 25um (slave)
-         - 09.02.2018
-         - `25um (slave) <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/gotthard_I/25um/slave/gotthard_I_25um_slave.pof>`__
-         - 
 
 .. _firmware upgrade using blaster for blackfin:
 
@@ -294,24 +216,10 @@ Download
 
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- rbf files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
-
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - 
-         - 25.09.2020
-         - 
-         - development
+- rbf files (in developement)
 
 
-Upgrade (from v5.0.0-rcx)
+Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 #. Program from console
@@ -337,23 +245,10 @@ Download
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- rbf files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
+- rbf files (in development)
 
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - 
-         - 25.09.2020
-         - 
-         - development
 
-Upgrade (from v5.0.0-rcx)
+Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 #. Program from console
@@ -375,28 +270,10 @@ Download
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- pof files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
+- `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - EPCQ128
-         - 05.10.2020
-         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/moench/EPCQ128/v1_0/moench_v1_0_201005.pof>`__
-         - 
-       * - v5.0.0-rcx
-         - EPCS128
-         - 05.10.2020
-         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/moench/EPCS128/v1_0/moench_v1_0_201005.pof>`__
-         - 
 
-Upgrade (from v5.0.0-rcx)
+Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
@@ -419,28 +296,10 @@ Download
 ^^^^^^^^^^^^^
 - detector server corresponding to package in slsDetectorPackage/serverBin
 
-- pof files
-    .. list-table:: 
-       :widths: 25 10 30 25 10
-       :header-rows: 1
+- `pof files <https://github.com/slsdetectorgroup/slsDetectorFirmware>`__
 
-       * - Software
-         - Hardware
-         - Firmware Date
-         - Firmware Link
-         - Comments
-       * - v5.0.0-rcx
-         - EPCQ128
-         - 05.10.2020
-         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/ctb/EPCQ128/v1_0/ctb_v1_0_201005.pof>`__
-         - 
-       * - v5.0.0-rcx
-         - EPCS128
-         - 05.10.2020
-         - `v1.0 <https://github.com/slsdetectorgroup/slsDetectorFirmware/blob/master/binaries/ctb/EPCS128/v1_0/ctb_v1_0_201005.pof>`__
-         - 
 
-Upgrade (from v5.0.0-rcx)
+Upgrade (from v5.0.0)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you run into issues while programming firmware.
@@ -462,11 +321,12 @@ Check :ref:`firmware troubleshooting <blackfin firmware troubleshooting>` if you
 Firmware Troubleshooting with blackfin
 ----------------------------------------
 
-#. v4.x.x client after programming will most likely reboot the blackfin processor, regardless of error.
+1. v4.x.x client after programming will most likely reboot the blackfin processor, regardless of error.
 
-#. v5.x.x-rcx client after programming will not reboot the blackfin processor, if error occurred.
+2. v5.x.x-rcx client after programming will not reboot the blackfin processor, if error occurred.
+
+3. If a reboot occured with an incomplete firmware in flash, the blackfin will most likely not find the mtd3 drive. To see if this drive exists:
 
-#. If a reboot occured with an incomplete firmware in flash, the blackfin will most likely not find the mtd3 drive. To see if this drive exists:
   .. code-block:: bash
     
     # connect to the board
@@ -482,7 +342,7 @@ Firmware Troubleshooting with blackfin
 
 4. If one can see the mtd3 drive, one can already try to flash again using the **programfpga** command (without rebooting blackfin or detector). 
 
-#. If one can't list it, read the next section to try to get the blackfin to list it.
+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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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})

python/CMakeLists.txt

@@ -1,19 +1,16 @@
 
-# find_package (Python COMPONENTS Interpreter Development)
-
 pybind11_add_module(_slsdet 
     src/main.cpp 
     src/enums.cpp
     src/detector.cpp
     src/network.cpp
+    src/pattern.cpp
+    src/scan.cpp
 )
 
 target_link_libraries(_slsdet PUBLIC 
-                        slsDetectorShared
-                        slsReceiverShared
-                        slsSupportShared
-                        ${ZeroMQ_LIBRARIES}
-                        )  
+                      slsDetectorStatic
+)  
 
 
 
@@ -33,6 +30,7 @@ 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_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 +1,19 @@
+
+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)
+
+
+

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

@@ -11,6 +11,8 @@ import subprocess
 
 from parse import remove_comments
 
+allow_bitwise_op = ["M3_GainCaps"]
+
 def single_line_enum(line):
     sub = line[line.find('{')+1:line.find('}')]
     return sub.strip().split(',')
@@ -49,13 +51,17 @@ def extract_enums(lines):
 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')
         for v in value:
             data.append(f'\t.value("{v}", slsDetectorDefs::{key}::{v})\n')
         data.append('.export_values();\n\n')
     return ''.join(data)
 
-with open('../../slsSupportLib/include/sls_detector_defs.h') as f:
+with open('../../slsSupportLib/include/sls/sls_detector_defs.h') as f:
     data = f.read()
 
 data = remove_comments(data)

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 +20,4 @@ from .enums import *
 
 IpAddr = _slsdet.IpAddr
 MacAddr = _slsdet.MacAddr
+scanParameters = _slsdet.scanParameters

python/slsdet/detector.py

@@ -349,7 +349,7 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def nframes(self):
+    def framecounter(self):
         """
         [Jungfrau][Mythen3][Gotthard2][Moench][CTB] Number of frames from start run control.
         Note
@@ -1009,6 +1009,32 @@ class Detector(CppDetectorApi):
         ip = ut.make_ip(ip) #Convert from int or string to IpAddr
         ut.set_using_dict(self.setClientZmqIp, ip)
 
+
+    @property
+    def zmqhwm(self):
+        """
+        Client's zmq receive high water mark. Default is the zmq library's default (1000), can also be set here using -1. 
+        This is a high number and can be set to 2 for gui purposes. 
+        One must also set the receiver's send high water mark to similar value. Final effect is sum of them.
+	    Setting it via command line is useful only before zmq enabled (before opening gui).
+        """
+        return self.getClientZmqHwm()
+
+    @zmqhwm.setter
+    def zmqhwm(self, n_frames):
+        self.setClientZmqHwm(n_frames)
+
+    @property
+    def rx_zmqhwm(self):
+        """
+        Receiver's zmq send high water mark. Default is the zmq library's default (1000). This is a high number and can be set to 2 for gui purposes. One must also set the client's receive high water mark to similar value. Final effect is sum of them. Also restarts receiver zmq streaming if enabled. Can set to -1 to set default value.
+        """
+        return self.getRxZmqHwm()
+
+    @rx_zmqhwm.setter
+    def rx_zmqhwm(self, n_frames):
+        self.setRxZmqHwm(n_frames)
+
     @property
     @element
     def udp_dstip(self):
@@ -1499,7 +1525,7 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def timestamp(self):
+    def frametime(self):
         """[Jungfrau][Mythen3][Gotthard2][Moench][CTB] Timestamp at a frame start.
         Note
         ----
@@ -1670,6 +1696,8 @@ 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
@@ -1965,7 +1993,7 @@ class Detector(CppDetectorApi):
 
     @property
     @element
-    def now(self):
+    def runtime(self):
         """[Jungfrau][Mythen3][Gotthard2][Moench][CTB] Time from detector start up.
         Note
         -----
@@ -3079,6 +3107,14 @@ class Detector(CppDetectorApi):
         """
         return ClkFreqProxy(self)
 
+
+    def readout(self):
+        """
+        Mythen3] Starts detector readout. Status changes to TRANSMITTING and automatically returns to idle at the end of readout.
+        """
+        self.startDetectorReadout()
+    
+
     """
     ---------------------------<<<Debug>>>---------------------------
     """

python/slsdet/enums.py

@@ -14,4 +14,5 @@ clockIndex = _slsdet.slsDetectorDefs.clockIndex
 readoutMode = _slsdet.slsDetectorDefs.readoutMode
 masterFlags = _slsdet.slsDetectorDefs.masterFlags
 burstMode = _slsdet.slsDetectorDefs.burstMode
-timingSourceType = _slsdet.slsDetectorDefs.timingSourceType
+timingSourceType = _slsdet.slsDetectorDefs.timingSourceType
+M3_GainCaps = _slsdet.slsDetectorDefs.M3_GainCaps

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/src/detector.cpp

@@ -102,6 +102,34 @@ 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 +142,24 @@ 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("isVirtualDetectorServer",
+             (Result<bool>(Detector::*)(sls::Positions) const) &
+                 Detector::isVirtualDetectorServer,
+             py::arg() = Positions{})
         .def("registerAcquisitionFinishedCallback",
              (void (Detector::*)(void (*)(double, int, void *), void *)) &
                  Detector::registerAcquisitionFinishedCallback,
@@ -314,6 +354,9 @@ 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("getDAC",
              (Result<int>(Detector::*)(defs::dacIndex, bool, sls::Positions)
                   const) &
@@ -356,6 +399,8 @@ void init_det(py::module &m) {
         .def("startReceiver", (void (Detector::*)()) & Detector::startReceiver)
         .def("stopReceiver", (void (Detector::*)()) & Detector::stopReceiver)
         .def("startDetector", (void (Detector::*)()) & Detector::startDetector)
+        .def("startDetectorReadout",
+             (void (Detector::*)()) & Detector::startDetectorReadout)
         .def("stopDetector", (void (Detector::*)()) & Detector::stopDetector)
         .def("getDetectorStatus",
              (Result<defs::runStatus>(Detector::*)(sls::Positions) const) &
@@ -599,15 +644,15 @@ void init_det(py::module &m) {
                  Detector::setPartialFramesPadding,
              py::arg(), py::arg() = Positions{})
         .def("getRxUDPSocketBufferSize",
-             (Result<int64_t>(Detector::*)(sls::Positions) const) &
+             (Result<int>(Detector::*)(sls::Positions) const) &
                  Detector::getRxUDPSocketBufferSize,
              py::arg() = Positions{})
         .def("setRxUDPSocketBufferSize",
-             (void (Detector::*)(int64_t, sls::Positions)) &
+             (void (Detector::*)(int, sls::Positions)) &
                  Detector::setRxUDPSocketBufferSize,
              py::arg(), py::arg() = Positions{})
         .def("getRxRealUDPSocketBufferSize",
-             (Result<int64_t>(Detector::*)(sls::Positions) const) &
+             (Result<int>(Detector::*)(sls::Positions) const) &
                  Detector::getRxRealUDPSocketBufferSize,
              py::arg() = Positions{})
         .def("getRxLock",
@@ -747,6 +792,17 @@ void init_det(py::module &m) {
              (void (Detector::*)(const sls::IpAddr, sls::Positions)) &
                  Detector::setClientZmqIp,
              py::arg(), py::arg() = Positions{})
+        .def("getClientZmqHwm",
+             (int (Detector::*)() const) & Detector::getClientZmqHwm)
+        .def("setClientZmqHwm",
+             (void (Detector::*)(const int)) & Detector::setClientZmqHwm,
+             py::arg())
+        .def("getRxZmqHwm",
+             (Result<int>(Detector::*)(sls::Positions) const) &
+                 Detector::getRxZmqHwm,
+             py::arg() = Positions{})
+        .def("setRxZmqHwm",
+             (void (Detector::*)(const int)) & Detector::setRxZmqHwm, py::arg())
         .def("getSubExptime",
              (Result<sls::ns>(Detector::*)(sls::Positions) const) &
                  Detector::getSubExptime,
@@ -763,24 +819,6 @@ 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,
@@ -796,14 +834,6 @@ void init_det(py::module &m) {
         .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,
@@ -1102,6 +1132,20 @@ 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,
@@ -1251,9 +1295,17 @@ 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) {
@@ -275,4 +277,14 @@ void init_enums(py::module &m) {
         .value("TIMING_EXTERNAL",
                slsDetectorDefs::timingSourceType::TIMING_EXTERNAL)
         .export_values();
+
+    py::enum_<slsDetectorDefs::M3_GainCaps>(Defs, "M3_GainCaps",
+                                            py::arithmetic())
+        .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();
 }

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 +19,8 @@ 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 &);
 PYBIND11_MODULE(_slsdet, m) {
     m.doc() = R"pbdoc(
         C/C++ API
@@ -33,6 +35,8 @@ PYBIND11_MODULE(_slsdet, m) {
      init_enums(m);
      init_det(m);
      init_network(m);
+     init_pattern(m);
+     init_scan(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/ctbDetectorServer_developer

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

serverBin/ctbDetectorServerv5.0.0

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

serverBin/eigerDetectorServer_developer

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

serverBin/eigerDetectorServerv5.0.0

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

serverBin/gotthard2DetectorServer_developer

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

serverBin/gotthard2DetectorServerv5.0.0

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

serverBin/gotthardDetectorServer_developer

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

serverBin/gotthardDetectorServerv5.0.0

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

serverBin/jungfrauDetectorServer_developer

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

serverBin/jungfrauDetectorServerv5.0.0

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

serverBin/moenchDetectorServer_developer

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

serverBin/moenchDetectorServerv5.0.0

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

serverBin/mythen3DetectorServer_developer

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

serverBin/mythen3DetectorServerv5.0.0

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

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/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
+
+