version

CMakeLists.txt

@@ -157,37 +157,8 @@ 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()

RELEASE.txt

@@ -1,13 +1,14 @@
-SLS Detector Package 5.X.X released on XX.XX.2021 (Minor Release)
+SLS Detector Package 5.1.0 released on xx.xx.2020 (Minor Release)
 ===================================================================
 
-This document describes the differences between X and Y releases.   
+This document describes the differences between 5.1.0 and 5.x.x releases.   
 
 
 
     CONTENTS
     --------
-    1.  New Features
+    1.  Topics Concerning
+    2.  New Features
     2.  Resolved Issues
     3.  Known Issues
     4.  Firmware Requirements
@@ -15,15 +16,58 @@ This document describes the differences between X and Y releases.
 
 
 
+1. Topics Concerning
+====================
 
-1. New Features
+    - potentital memory leak in receiver
+    - scanParameters in Python
+    - cmk.sh refactored
+    - m3 settings and threshold
+
+
+2. New Features
 ===============
 
-    Setting Mythen3 gain from command line
+    Client
+    ------
+
+    1. Aded settings and threshold features for Mythen3.
+    2. Internal modification of acquire for Mythen3.
+    3. Added getMaster functio for M3
+
+
+    Mythen3 server
+    -----------------
+
+    1. Setting timing to auto, sets timing to trigger for slaves
+    
+
+3. Resolved Issues
+==================
+
+
+    Receiver
+    --------
+
+    1.  Current code only calls Implementation::setDetectorType from constructor, 
+	    but potential memory leak if called out of constructor context. Fixed.
+
+    Client
+    ------
+
+    1.  Fixed missing scanParameters class in Python 
+
+    2.  cmk.sh refactored to have better option handling
+
+
+
+
 
 4. Firmware Requirements
 ========================
         
+    No updates from 5.0.0
+
 
 
 5. Known Issues

cmake/FindZeroMQ.cmake

@@ -0,0 +1,112 @@
+
+# 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

@@ -25,12 +25,6 @@ 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

@@ -12,21 +12,8 @@ include(CMakeFindDependencyMacro)
 
 set(SLS_USE_HDF5 "@SLS_USE_HDF5@")
 
-
-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
+find_dependency(Threads)
 if (SLS_USE_HDF5)
     find_dependency(HDF5)
 endif ()

conda-recepie/build.sh

@@ -13,9 +13,8 @@ cmake .. \
       -DCMAKE_BUILD_TYPE=Release \
       -DSLS_USE_HDF5=OFF\
      
-NCORES=$(getconf _NPROCESSORS_ONLN)
+
-echo "Building using: ${NCORES} cores"
+cmake --build . -- -j10
-cmake --build . -- -j${NCORES}
 cmake --build . --target install
 
 CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2

conda-recepie/copy_gui.sh

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

conda-recepie/copy_lib.sh

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

conda-recepie/meta.yaml

@@ -59,16 +59,6 @@ outputs:
     script: copy_lib.sh
 
     requirements:
-      build:
-        - {{ compiler('c') }}
-        - {{compiler('cxx')}}
-        - libstdcxx-ng
-        - libgcc-ng
-        - zeromq
-
-      host:
-        - zeromq
-
       run: 
         - libstdcxx-ng
         - libgcc-ng
@@ -88,8 +78,6 @@ outputs:
 
       host:
         - python
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
-
 
       run:
         - libstdcxx-ng
@@ -106,13 +94,6 @@ 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.*

libzmq-pkg-config/FindZeroMQ.cmake

@@ -1,27 +0,0 @@
-#From: https://github.com/zeromq/cppzmq/
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH ON)
-find_package(PkgConfig)
-pkg_check_modules(PC_LIBZMQ QUIET libzmq)
-
-set(ZeroMQ_VERSION ${PC_LIBZMQ_VERSION})
-find_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/scripts/compile_servers.py

@@ -1,80 +0,0 @@
-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

@@ -11,8 +11,6 @@ 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(',')
@@ -51,11 +49,7 @@ def extract_enums(lines):
 def generate_enum_string(enums):
     data = []
     for key, value in enums.items():
-        if key in allow_bitwise_op:
+        data.append(f'py::enum_<slsDetectorDefs::{key}>(Defs, "{key}")\n')
-            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')

python/slsdet/enums.py

@@ -15,4 +15,3 @@ readoutMode = _slsdet.slsDetectorDefs.readoutMode
 masterFlags = _slsdet.slsDetectorDefs.masterFlags
 burstMode = _slsdet.slsDetectorDefs.burstMode
 timingSourceType = _slsdet.slsDetectorDefs.timingSourceType
-M3_GainCaps = _slsdet.slsDetectorDefs.M3_GainCaps

python/src/detector.cpp

@@ -1136,16 +1136,6 @@ void init_det(py::module &m) {
              (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,

python/src/enums.cpp

@@ -277,14 +277,4 @@ 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();
 }

slsDetectorCalibration/circularFifo.h

@@ -1,156 +0,0 @@
-#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

@@ -1,238 +0,0 @@
-#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

@@ -14,8 +14,6 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
   const int nSamples;
   const int offset;
 
-
-
   double ghost[200][25];
   double xtalk;
 
@@ -31,22 +29,17 @@ 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=2*2): slsDetectorData<uint16_t>(400, 400, ns*32*2+oo), nSamples(ns), offset(oo), 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) {
-    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;
@@ -57,11 +50,11 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
     int i;
     int adc4(0);
   
-    //for (int ip=0; ip<npackets; ip++) {
+    for (int ip=0; ip<npackets; ip++) {
-    // for (int is=0; is<128; is++) {
+      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++) {
@@ -77,7 +70,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	  }
 	}
       }
-  // }
+    }
 
     
     int ii=0;

slsDetectorCalibration/energyCalibration.cpp

@@ -1,798 +0,0 @@
-#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

@@ -98,8 +98,6 @@ 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
@@ -155,8 +153,6 @@ 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
@@ -289,8 +285,6 @@ 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
@@ -321,8 +315,16 @@ 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);
-  TF1 *fitSpectrumKb(TH1 *h1, Double_t *mypar, Double_t *emypar);
+
-  TF1 *fitSpectrumKaDoublet(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);
 
 
   /**
@@ -397,8 +399,6 @@ class energyCalibration  {
 */
   
   void initFitFunction(TF1 *fun, TH1 *h1);
-  void initFitFunctionKb(TF1 *fun, TH1 *h1);
-  void initFitFunctionKaDoublet(TF1 *fun, TH1 *h1);
 
 
   /**
@@ -410,8 +410,6 @@ 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
 
@@ -425,16 +423,11 @@ 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

@@ -1,47 +0,0 @@
-#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~

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

slsDetectorCalibration/jungfrauExecutables/Makefile.zmq

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

slsDetectorCalibration/jungfrauExecutables/jungfrauClusterFinder.cpp

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

slsDetectorCalibration/jungfrauExecutables/jungfrauClusterFinder.cpp~

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

slsDetectorCalibration/jungfrauExecutables/jungfrauInterpolation.cpp

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

slsDetectorCalibration/jungfrauExecutables/jungfrauPhotonCounter.cpp

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

slsDetectorCalibration/moenchExecutables/CMakeLists.txt

@@ -3,11 +3,11 @@ find_package(TIFF REQUIRED)
 
 #Moench ZMQ
 add_executable(moenchZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
-target_compile_definitions(moenchZmqProcess PRIVATE NEWZMQ INTERP)
+add_compile_definitions(moenchZmqProcess NEWZMQ INTERP)
 
 #Moench04 ZMQ
 add_executable(moench04ZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
-target_compile_definitions(moench04ZmqProcess PRIVATE NEWZMQ INTERP MOENCH04)
+add_compile_definitions(moenchZmqProcess NEWZMQ INTERP MOENCH04)
 
 
 #Both executables should have the same includes and output dirs

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

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

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -17,7 +17,7 @@
 #include <pthread.h>
 
 #include "analogDetector.h"
-#include "circularFifo.h"
+#include "sls/CircularFifo.h"
 #include <unistd.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -123,7 +123,7 @@ public:
      return fifoFree->pop(ptr);
    }
 
-   virtual int isBusy() {if (fifoData->isEmpty() && busy==0) return 0; return 1;}
+   virtual int isBusy() {if (fifoData->isEmpty() && busy==0) return 0; else return 1;}
    
    //protected:
    /** Implement this method in your subclass with the code you want your thread to run. */

slsDetectorGui/CMakeLists.txt

@@ -91,6 +91,7 @@ target_include_directories(slsDetectorGui PUBLIC
 
 target_link_libraries(slsDetectorGui PUBLIC
     slsProjectOptions 
+    slsProjectWarnings
     slsDetectorStatic
     ${QT_QTCORE_LIBRARIES}
     ${QT_QTGUI_LIBRARIES}
@@ -100,9 +101,6 @@ target_link_libraries(slsDetectorGui PUBLIC
     Qt4::QtOpenGL
     Qt4::QtSvg
     expat
-    
-    PRIVATE
-    slsProjectWarnings
 )
 
 set_target_properties(slsDetectorGui PROPERTIES
@@ -113,7 +111,7 @@ if(SLS_LTO_AVAILABLE)
 endif()
 
 install(TARGETS slsDetectorGui
-    # EXPORT "${TARGETS_EXPORT_NAME}" #do not export gui
+    EXPORT "${TARGETS_EXPORT_NAME}"
     RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
     LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
     ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}

slsDetectorServers/eigerDetectorServer/FebControl.c

@@ -1395,7 +1395,7 @@ int Feb_Control_SetMaster(enum MASTERINDEX ind) {
 int Feb_Control_SetQuad(int val) {
     LOG(logINFO, ("Setting Quad to %d in Feb\n", val));
     // only setting on the right feb if quad
-    return Feb_Control_SetTop(val == 0 ? TOP_HARDWARE : OW_BOTTOM, 0, 1);
+    return Feb_Control_SetTop(val == 0 ? TOP_HARDWARE : OW_TOP, 0, 1);
 }
 
 int Feb_Control_SetReadNLines(int value) {

slsDetectorServers/mythen3DetectorServer/CMakeLists.txt

@@ -1,6 +1,5 @@
 add_executable(mythen3DetectorServer_virtual
     slsDetectorFunctionList.c
-    mythen3.c
     ../slsDetectorServer/src/slsDetectorServer.c
     ../slsDetectorServer/src/slsDetectorServer_funcs.c
     ../slsDetectorServer/src/communication_funcs.c
@@ -12,7 +11,6 @@ add_executable(mythen3DetectorServer_virtual
     ../slsDetectorServer/src/ALTERA_PLL_CYCLONE10.c   
     ../slsDetectorServer/src/programFpgaNios.c
     ../slsDetectorServer/src/readDefaultPattern.c         
-    ../slsDetectorServer/src/loadPattern.c         
     ../slsDetectorServer/src/sharedMemory.c
 )
 

slsDetectorServers/mythen3DetectorServer/Makefile

@@ -13,7 +13,7 @@ DESTDIR		?= 	bin
 INSTMODE	= 	0777
 
 SRCS	=	slsDetectorFunctionList.c 
-SRCS	+=	$(main_src)slsDetectorServer.c $(main_src)slsDetectorServer_funcs.c $(main_src)communication_funcs.c $(main_src)nios.c $(main_src)DAC6571.c $(main_src)common.c $(main_src)LTC2620_Driver.c $(main_src)ALTERA_PLL_CYCLONE10.c $(main_src)/programFpgaNios.c $(main_src)readDefaultPattern.c $(main_src)/sharedMemory.c $(main_src)/loadPattern.c mythen3.c
+SRCS	+=	$(main_src)slsDetectorServer.c $(main_src)slsDetectorServer_funcs.c $(main_src)communication_funcs.c $(main_src)nios.c $(main_src)DAC6571.c $(main_src)common.c $(main_src)LTC2620_Driver.c $(main_src)ALTERA_PLL_CYCLONE10.c $(main_src)/programFpgaNios.c $(main_src)readDefaultPattern.c $(main_src)/sharedMemory.c
 
 OBJS 	= 	$(SRCS:.c=.o) 
  

slsDetectorServers/mythen3DetectorServer/mythen3.c

@@ -1,374 +0,0 @@
-
-#include "clogger.h"
-#include "common.h"
-#include "mythen3.h"
-#include "sls/ansi.h"
-#include "sls/sls_detector_defs.h"
-#include "slsDetectorServer_defs.h"
-
-#include <string.h>
-
-/*
-// Common C/C++ structure to handle pattern data
-typedef struct __attribute__((packed)) {
-    uint64_t word[MAX_PATTERN_LENGTH];
-    uint64_t ioctrl;
-    uint32_t limits[2];
-    // loop0 start, loop0 stop .. loop2 start, loop2 stop
-    uint32_t loop[6];
-    uint32_t nloop[3];
-    uint32_t wait[3];
-    uint64_t waittime[3];
-} patternParameters;
-*/
-
-int chipStatusRegister=0;
-
-int setBit(int ibit, int patword) { return patword |= (1 << ibit); }
-
-int clearBit(int ibit, int patword) { return patword &= ~(1 << ibit); }
-
-extern enum TLogLevel trimmingPrint ;
-
-
-int getChipStatusRegister(){
-  return chipStatusRegister;
-}
-
-int gainCapsToCsr(int caps){
-  //Translates bit representation
-  int csr = 0;
-  if (!(caps & M3_C10pre))
-    csr |= 1 << _CSR_C10pre;
-  if (caps & M3_C15sh)
-    csr |= 1 << CSR_C15sh;
-  if (caps & M3_C30sh)
-    csr |= 1 << CSR_C30sh;
-  if (caps & M3_C50sh)
-    csr |= 1 << CSR_C50sh;
-  if (caps & M3_C225ACsh)
-    csr |= 1 << CSR_C225ACsh;
-  if (!(caps & M3_C15pre))
-    csr |= 1 << _CSR_C15pre;
-
-  return csr;
-}
-
-int csrToGainCaps(int csr){
-  //Translates bit representation
-  int caps = 0;
-  if (!(csr & (1 << _CSR_C10pre)))
-    caps |= M3_C10pre;
-  if (csr & (1 << CSR_C15sh))
-    caps |= M3_C15sh;
-  if (csr & (1 << CSR_C30sh))
-    caps |= M3_C30sh;
-  if (csr & (1 << CSR_C50sh))
-    caps |= M3_C50sh;
-  if (csr & (1 << CSR_C225ACsh))
-    caps |= M3_C225ACsh;
-  if (!(csr & (1 << _CSR_C15pre)))
-    caps |= M3_C15pre;
-
-  return caps;
-}
-
-patternParameters *setChipStatusRegisterPattern(int csr) {
-  int iaddr=0;
-  int  nbits=18;
-  int error=0;
-  //int start=0, stop=MAX_PATTERN_LENGTH, loop=0;
-  int patword=0;
-  
-  patternParameters *pat = malloc(sizeof(patternParameters));
-  memset(pat, 0, sizeof(patternParameters));
-  
-  patword=setBit(SIGNAL_STATLOAD,patword);
-  for (int i=0; i<2; i++)
-    pat->word[iaddr++]=patword;
-  patword=setBit(SIGNAL_resStorage,patword);
-  patword=setBit(SIGNAL_resCounter,patword);
-  for (int i=0; i<8; i++)
-    pat->word[iaddr++]=patword;
-  patword=clearBit(SIGNAL_resStorage,patword);
-  patword=clearBit(SIGNAL_resCounter,patword);
-  for (int i=0; i<8; i++)
-    pat->word[iaddr++]=patword;
-  //#This version of the serializer pushes in the MSB first (compatible with the CSR bit numbering)
-  for (int ib=nbits-1; ib>=0; ib--) {
-    if (csr&(1<<ib))
-      patword=setBit(SIGNAL_serialIN,patword);
-    else
-      patword=clearBit(SIGNAL_serialIN,patword);
-    for (int i=0; i<4; i++)
-      pat->word[iaddr++]=patword;
-    patword=setBit(SIGNAL_CHSclk,patword);
-    pat->word[iaddr++]=patword;
-    patword=clearBit(SIGNAL_CHSclk,patword);
-    pat->word[iaddr++]=patword;
-  }
-
-  patword=clearBit(SIGNAL_serialIN,patword);
-  for (int i=0; i<2; i++)
-    pat->word[iaddr++]=patword;
-  patword=setBit(SIGNAL_STO,patword);
-  for (int i=0; i<5; i++)
-    pat->word[iaddr++]=patword;
-  patword=clearBit(SIGNAL_STO,patword);
-  for (int i=0; i<5; i++)
-    pat->word[iaddr++]=patword;
-  patword=clearBit(SIGNAL_STATLOAD,patword);
-  for (int i=0; i<5; i++)
-    pat->word[iaddr++]=patword;
-
-  if (iaddr >= MAX_PATTERN_LENGTH) {
-    LOG(logERROR, ("Addr 0x%x is past max_address_length 0x%x!\n",
-		   iaddr, MAX_PATTERN_LENGTH));
-    error = 1;
-  }
-  // set pattern wait address
-  for (int i = 0; i <= 2; i++)
-    pat->wait[i]=MAX_PATTERN_LENGTH - 1;
-  // pattern loop
-  for (int i = 0; i <= 2; i++) {
-    //int stop = MAX_PATTERN_LENGTH - 1, nloop = 0;
-    pat->loop[i * 2 + 0]=MAX_PATTERN_LENGTH - 1;
-    pat->loop[i * 2 + 1]=MAX_PATTERN_LENGTH - 1;
-    pat->nloop[i]=0;
-  }
-  
-  // pattern limits
-  {
-    pat->limits[0]=0;
-    pat->limits[1]=iaddr;
-  }
-  
-  if (error != 0) {
-    free(pat);
-    return NULL;
-  }
-  chipStatusRegister=csr;
-  return pat;
-
-}
-
-patternParameters *setInterpolation(int mask) {
-  int csr;
-  if (mask)
-    csr=chipStatusRegister|(1<< CSR_interp);
-  else
-    csr=chipStatusRegister & ~(1<< CSR_interp);
-
-  return setChipStatusRegisterPattern(csr);
-}
-
-
-
-patternParameters *setPumpProbe(int mask) {
-  int csr;
-  if (mask)
-    csr=chipStatusRegister|(1<< CSR_pumprobe);
-  else
-    csr=chipStatusRegister & ~(1<< CSR_pumprobe);
-
-  return setChipStatusRegisterPattern(csr);
-
-}
-patternParameters *setDigitalPulsing(int mask) {
-
-  int csr;
-  if (mask)
-    csr=chipStatusRegister|(1<< CSR_dpulse);
-  else
-    csr=chipStatusRegister & ~(1<< CSR_dpulse);
-
-  return setChipStatusRegisterPattern(csr);
-  
-}
-patternParameters *setAnalogPulsing(int mask){
-
-  int csr;
-  if (mask)
-    csr=chipStatusRegister|(1<< CSR_apulse);
-  else
-    csr=chipStatusRegister & ~(1<< CSR_apulse);
-
-  return setChipStatusRegisterPattern(csr);
-  
-}
-patternParameters *setNegativePolarity(int mask){
-
-  int csr;
-  if (mask)
-    csr=chipStatusRegister|(1<< CSR_invpol);
-  else
-    csr=chipStatusRegister & ~(1<< CSR_invpol);
-
-  return setChipStatusRegisterPattern(csr);
-  
-}
-
-patternParameters *setChannelRegisterChip(int ichip, int *mask, int *trimbits) {
-
-  patternParameters *pat = malloc(sizeof(patternParameters));
-  memset(pat, 0, sizeof(patternParameters));
-  
-
-    // validate
-  for (int ichan = ichip * NCHAN_1_COUNTER * NCOUNTERS; ichan < ichip * NCHAN_1_COUNTER * NCOUNTERS+NCHAN_1_COUNTER*NCOUNTERS; ichan++) {
-    if (trimbits[ichan]<0)  {
-      LOG(logERROR, ("Trimbit value (%d) for channel %d is invalid - setting it to 0\n",
-		     trimbits[ichan], ichan));
-      trimbits[ichan]=0;
-    }
-    if (trimbits[ichan] > 63) {
-      LOG(logERROR, ("Trimbit value (%d) for channel %d is invalid - settings it to 63\n",
-		     trimbits[ichan], ichan));
-      trimbits[ichan]=63;
-    }
-  }
-  LOG(logINFO, ("Trimbits validated\n"));
-  trimmingPrint = logDEBUG5;
-
-    
-  // trimming
-  int error = 0;
-  uint64_t patword = 0;
-  int iaddr = 0;
-  
-  LOG(logDEBUG1, (" Chip %d\n", ichip));
-  iaddr = 0;
-  patword = 0;
-  pat->word[iaddr++]=patword;
-  
-  // chip select
-  patword = setBit(SIGNAL_TBLoad_1 + ichip, patword);
-  pat->word[iaddr++]=patword;
-  
-  // reset trimbits
-  patword = setBit(SIGNAL_resStorage, patword);
-  patword = setBit(SIGNAL_resCounter, patword);
-  pat->word[iaddr++]=patword;
-  pat->word[iaddr++]=patword;
-  patword = clearBit(SIGNAL_resStorage, patword);
-  patword = clearBit(SIGNAL_resCounter, patword);
-  pat->word[iaddr++]=patword;
-  pat->word[iaddr++]=patword;
-  
-  // select first channel
-  patword = setBit(SIGNAL_CHSserialIN, patword);
-  pat->word[iaddr++]=patword;
-  // 1 clk pulse
-  patword = setBit(SIGNAL_CHSclk, patword);
-  pat->word[iaddr++]=patword;
-  patword = clearBit(SIGNAL_CHSclk, patword);
-  // clear 1st channel
-  pat->word[iaddr++]=patword;
-  patword = clearBit(SIGNAL_CHSserialIN, patword);
-  // 2 clk pulses
-  for (int i = 0; i < 2; i++) {
-    patword = setBit(SIGNAL_CHSclk, patword);
-    pat->word[iaddr++]=patword;
-    patword = clearBit(SIGNAL_CHSclk, patword);
-    pat->word[iaddr++]=patword;
-  }
-  
-  // for each channel (all chips)
-  for (int ich = 0; ich < NCHAN_1_COUNTER; ich++) {
-    LOG(logDEBUG1, (" Chip %d, Channel %d\n", ichip, ich));
-    int val = trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
-		       NCOUNTERS * ich] +
-      trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
-	       NCOUNTERS * ich + 1] *
-      64 +
-      trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
-	       NCOUNTERS * ich + 2] *
-      64 * 64;
-    
-    // push 6 0 bits
-    for (int i = 0; i < 3; i++) {
-      patword = clearBit(SIGNAL_serialIN, patword);
-      patword = clearBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-      patword = setBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-    }
-    
-    for (int i = 0; i < 3; i++) {
-      if (mask[i])
-	patword = setBit(SIGNAL_serialIN, patword);
-      else
-	patword = clearBit(SIGNAL_serialIN, patword);
-      patword = clearBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-      patword = setBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-    }
-    
-    // deserialize
-    for (int i = 0; i < 18; i++) {
-      if (val & (1 << i)) {
-	patword = setBit(SIGNAL_serialIN, patword);
-      } else {
-	patword = clearBit(SIGNAL_serialIN, patword);
-      }
-      patword = clearBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-      
-      patword = setBit(SIGNAL_clk, patword);
-      pat->word[iaddr++]=patword;
-    }
-    pat->word[iaddr++]=patword;
-    pat->word[iaddr++]=patword;
-    
-    // move to next channel
-    for (int i = 0; i < 3; i++) {
-      patword = setBit(SIGNAL_CHSclk, patword);
-      pat->word[iaddr++]=patword;
-      patword = clearBit(SIGNAL_CHSclk, patword);
-      pat->word[iaddr++]=patword;
-    }
-  }
-  // chip unselect
-  patword = clearBit(SIGNAL_TBLoad_1 + ichip, patword);
-  pat->word[iaddr++]=patword;
-  
-  // last iaddr check
-  if (iaddr >= MAX_PATTERN_LENGTH) {
-    LOG(logERROR, ("Addr 0x%x is past max_address_length 0x%x!\n",
-		   iaddr, MAX_PATTERN_LENGTH));
-    error = 1;
-  }
-  
-  if (iaddr >= MAX_PATTERN_LENGTH) {
-    LOG(logERROR, ("Addr 0x%x is past max_address_length 0x%x!\n",
-		   iaddr, MAX_PATTERN_LENGTH));
-    error = 1;
-  }
-  // set pattern wait address
-  for (int i = 0; i <= 2; i++)
-    pat->wait[i]=MAX_PATTERN_LENGTH - 1;
-  // pattern loop
-  for (int i = 0; i <= 2; i++) {
-    //int stop = MAX_PATTERN_LENGTH - 1, nloop = 0;
-    pat->loop[i * 2 + 0]=MAX_PATTERN_LENGTH - 1;
-    pat->loop[i * 2 + 1]=MAX_PATTERN_LENGTH - 1;
-    pat->nloop[i]=0;
-  }
-  
-  // pattern limits
-  {
-    pat->limits[0]=0;
-    pat->limits[1]=iaddr;
-  }
-  
-  trimmingPrint = logINFO;
-  if (error == 0) {
-    
-    LOG(logINFO, ("All trimbits have been loaded\n"));
-  } else {
-    free(pat);
-    return NULL;
-  }
-  return pat;
-}

slsDetectorServers/mythen3DetectorServer/mythen3.h

@@ -1,68 +0,0 @@
-#ifndef MYTHEN3_H
-#define MYTHEN3_H
-
-#include "Pattern.h"
-
-/** Signal Definitions */
-#define SIGNAL_TBLoad_1    (0)
-#define SIGNAL_TBLoad_2    (1)
-#define SIGNAL_TBLoad_3    (2)
-#define SIGNAL_TBLoad_4    (3)
-#define SIGNAL_TBLoad_5    (4)
-#define SIGNAL_TBLoad_6    (5)
-#define SIGNAL_TBLoad_7    (6)
-#define SIGNAL_TBLoad_8    (7)
-#define SIGNAL_TBLoad_9    (8)
-#define SIGNAL_TBLoad_10   (9)
-#define SIGNAL_AnaMode     (10)
-#define SIGNAL_CHSserialIN (11)
-#define SIGNAL_READOUT     (12)
-#define SIGNAL_pulse       (13)
-#define SIGNAL_EN1         (14)
-#define SIGNAL_EN2         (15)
-#define SIGNAL_EN3         (16)
-#define SIGNAL_clk         (17)
-#define SIGNAL_SRmode      (18)
-#define SIGNAL_serialIN    (19)
-#define SIGNAL_STO         (20)
-#define SIGNAL_STATLOAD    (21)
-#define SIGNAL_resStorage  (22)
-#define SIGNAL_resCounter  (23)
-#define SIGNAL_CHSclk      (24)
-#define SIGNAL_exposing    (25)
-
-
-//CHIP STARTUS REGISTER BITS
-#define CSR_spypads  0
-#define CSR_invpol  4
-#define CSR_dpulse  5
-#define CSR_interp  6
-#define _CSR_C10pre  7 //#default, negative polarity
-#define CSR_pumprobe  8
-#define CSR_apulse  9
-#define CSR_C15sh  10 
-#define CSR_C30sh  11 //#default
-#define CSR_C50sh  12
-#define CSR_C225ACsh  13 // Connects 225fF SHAPER AC cap (1: 225 to shaper, 225 to GND. 0: 450 to shaper) 
-#define _CSR_C15pre  14 // negative polarity
-
-#define CSR_default  (1<<_CSR_C10pre )|(1<< CSR_C30sh)
-
-#define GAIN_MASK ((1 << _CSR_C10pre) | ( 1 << CSR_C15sh) | (1 << CSR_C30sh) | (1 << CSR_C50sh) | (1 << CSR_C225ACsh) | ( 1 << _CSR_C15pre))
-
-
-int setBit(int ibit, int patword);
-int clearBit(int ibit, int patword);
-int getChipStatusRegister();
-int gainCapsToCsr(int caps);
-int csrToGainCaps(int csr);
-
-patternParameters *setChipStatusRegisterPattern(int csr);
-patternParameters *setChannelRegisterChip(int ichip, int *mask, int *trimbits);
-patternParameters *setInterpolation(int mask);
-patternParameters *setPumpProbe(int mask);
-patternParameters *setDigitalPulsing(int mask);
-patternParameters *setAnalogPulsing(int mask);
-patternParameters *setNegativePolarity(int mask);
-
-#endif

slsDetectorServers/mythen3DetectorServer/slsDetectorFunctionList.c

@@ -5,8 +5,6 @@
 #include "RegisterDefs.h"
 #include "clogger.h"
 #include "common.h"
-#include "mythen3.h"
-#include "loadPattern.h"
 #include "sharedMemory.h"
 #include "sls/versionAPI.h"
 #ifdef VIRTUAL
@@ -21,6 +19,8 @@
 #include <time.h>
 #endif
 
+/// NOT the right place to put it!
+int setChipStatusRegister(int csr);
 
 // Global variable from slsDetectorServer_funcs
 extern int debugflag;
@@ -47,12 +47,11 @@ enum detectorSettings thisSettings;
 sls_detector_module *detectorModules = NULL;
 int *detectorChans = NULL;
 int *detectorDacs = NULL;
-int *channelMask=NULL;
 
+enum TLogLevel trimmingPrint = logINFO;
 int32_t clkPhase[NUM_CLOCKS] = {};
 uint32_t clkDivider[NUM_CLOCKS] = {};
 
-enum TLogLevel trimmingPrint = logINFO;
 int highvoltage = 0;
 int detPos[2] = {};
 int64_t exptimeReg[NCOUNTERS] = {0, 0, 0};
@@ -375,11 +374,7 @@ void allocateDetectorStructureMemory() {
     // Allocation of memory
     detectorModules = malloc(sizeof(sls_detector_module));
     detectorChans = malloc(NCHIP * NCHAN * sizeof(int));
-    channelMask = malloc(NCHIP * NCHAN * sizeof(char));
-    memset(channelMask, 0, NCHIP * NCHAN * sizeof(char));
     detectorDacs = malloc(NDAC * sizeof(int));
-
-    
     LOG(logDEBUG1,
         ("modules from 0x%x to 0x%x\n", detectorModules, detectorModules));
     LOG(logDEBUG1, ("chans from 0x%x to 0x%x\n", detectorChans, detectorChans));
@@ -517,11 +512,11 @@ void setupDetector() {
     }
 
     powerChip(1);
-
+    if (initError != FAIL) {
-    if (!initError) {
+      initError = setChipStatusRegister(CSR_default);
-      setChipStatusRegister(CSR_default);
+      //loadDefaultPattern(DEFAULT_PATTERN_FILE, initErrorMessage);
+      //startStateMachine(); //this was missing in previous code! runs the default pattern
     }
-
     setAllTrimbits(DEFAULT_TRIMBIT_VALUE);
 }
 
@@ -1057,44 +1052,72 @@ int64_t getMeasurementTime() {
 
 /* parameters - module, speed, readout */
 
-int setDACS(int* dacs){
+int setModule(sls_detector_module myMod, char *mess) {
+
+    LOG(logINFO, ("Setting module\n"));
+
+    // settings
+    if (myMod.reg >= 0) {
+        setSettings((enum detectorSettings)myMod.reg);
+        if (getSettings() != (enum detectorSettings)myMod.reg) {
+            sprintf(
+                mess,
+                "Could not set module. Could not set settings to %d, read %d\n",
+                myMod.reg, (int)getSettings());
+            LOG(logERROR, (mess));
+            return FAIL;
+        }
+        detectorModules->reg = myMod.reg;
+    }
+    // custom trimbit file
+    else {
+        // changed for setsettings (direct),
+        // custom trimbit file (setmodule with myMod.reg as -1),
+        // change of dac (direct)
+        for (int i = 0; i < NCOUNTERS; ++i) {
+            setThresholdEnergy(i, -1);
+        }
+    }
+
+    // dacs
     for (int i = 0; i < NDAC; ++i) {
-        if (dacs[i] != -1) {
+        // ignore dacs with -1
-            setDAC((enum DACINDEX)i, dacs[i], 0);
+        if (myMod.dacs[i] != -1) {
-            if (dacs[i] != detectorDacs[i]) {
+            setDAC((enum DACINDEX)i, myMod.dacs[i], 0);
+            if (myMod.dacs[i] != detectorDacs[i]) {
                 // dont complain if that counter was disabled
                 if ((i == M_VTH1 || i == M_VTH2 || i == M_VTH3) &&
                     (detectorDacs[i] == DEFAULT_COUNTER_DISABLED_VTH_VAL)) {
                     continue;
                 }
+                sprintf(mess,
+                        "Could not set module. Could not set dac %d, wrote %d, "
+                        "read %d\n",
+                        i, myMod.dacs[i], detectorDacs[i]);
+                LOG(logERROR, (mess));
                 return FAIL;
             }
         }
     }
-    return OK;
-}
 
-
+    // if settings given and cannot be validated (after setting dacs), return
-int setModule(sls_detector_module myMod, char *mess) {
+    // error
-    LOG(logINFO, ("Setting module\n"));
+    if (myMod.reg >= 0) {
-
+        if (getSettings() != (enum detectorSettings)myMod.reg) {
-    if (setChipStatusRegister(myMod.reg)){
+            sprintf(
-        sprintf(mess, "Could not CSR from module\n");
+                mess,
-        LOG(logERROR, (mess));
+                "Could not set module. The dacs in file do not correspond to "
-        return FAIL;
+                "settings %d\n",
-    }
+                myMod.reg);
-
+            LOG(logERROR, (mess));
-    if (setDACS(myMod.dacs)){
+            return FAIL;
-        sprintf(mess, "Could not set dacs\n");
+        }
-        LOG(logERROR, (mess));
-        return FAIL;
     }
 
+    // threshold
     for (int i = 0; i < NCOUNTERS; ++i) {
         if (myMod.eV[i] >= 0) {
             setThresholdEnergy(i, myMod.eV[i]);
-        }else{
-            setThresholdEnergy(i, -1);
         }
     }
 
@@ -1113,31 +1136,155 @@ int setModule(sls_detector_module myMod, char *mess) {
     return OK;
 }
 
+int setBit(int ibit, int patword) { return patword |= (1 << ibit); }
+
+int clearBit(int ibit, int patword) { return patword &= ~(1 << ibit); }
+
 int setTrimbits(int *trimbits) {
+    LOG(logINFOBLUE, ("Setting trimbits\n"));
+
+    // validate
+    for (int ichan = 0; ichan < ((detectorModules)->nchan); ++ichan) {
+        if (trimbits[ichan] < 0 || trimbits[ichan] > 63) {
+            LOG(logERROR, ("Trimbit value (%d) for channel %d is invalid\n",
+                           trimbits[ichan], ichan));
+            return FAIL;
+        }
+    }
+    LOG(logINFO, ("Trimbits validated\n"));
+    trimmingPrint = logDEBUG5;
+
     // remember previous run clock
     uint32_t prevRunClk = clkDivider[SYSTEM_C0];
-    patternParameters *pat = NULL;
+
-    int error = 0;
     // set to trimming clock
     if (setClockDivider(SYSTEM_C0, DEFAULT_TRIMMING_RUN_CLKDIV) == FAIL) {
         LOG(logERROR,
             ("Could not start trimming. Could not set to trimming clock\n"));
         return FAIL;
     }
-    /////////////////////////////////////////////////////////////////
-    for (int ichip = 0; ichip < NCHIP; ichip++) {
 
-        pat = setChannelRegisterChip(ichip, channelMask,
+    // trimming
-                                     trimbits); // change here!!!
+    int error = 0;
-        if (pat) {
+    uint64_t patword = 0;
-            error |= loadPattern(pat);
+    int iaddr = 0;
-            if (error == 0)
+    for (int ichip = 0; ichip < NCHIP; ichip++) {
-                startPattern();
+        if (error != 0) {
-            free(pat);
+            break;
-        } else
+        }
+        LOG(logDEBUG1, (" Chip %d\n", ichip));
+        iaddr = 0;
+        patword = 0;
+        writePatternWord(iaddr++, patword);
+
+        // chip select
+        patword = setBit(SIGNAL_TBLoad_1 + ichip, patword);
+        writePatternWord(iaddr++, patword);
+
+        // reset trimbits
+        patword = setBit(SIGNAL_resStorage, patword);
+        patword = setBit(SIGNAL_resCounter, patword);
+        writePatternWord(iaddr++, patword);
+        writePatternWord(iaddr++, patword);
+        patword = clearBit(SIGNAL_resStorage, patword);
+        patword = clearBit(SIGNAL_resCounter, patword);
+        writePatternWord(iaddr++, patword);
+        writePatternWord(iaddr++, patword);
+
+        // select first channel
+        patword = setBit(SIGNAL_CHSserialIN, patword);
+        writePatternWord(iaddr++, patword);
+        // 1 clk pulse
+        patword = setBit(SIGNAL_CHSclk, patword);
+        writePatternWord(iaddr++, patword);
+        patword = clearBit(SIGNAL_CHSclk, patword);
+        // clear 1st channel
+        writePatternWord(iaddr++, patword);
+        patword = clearBit(SIGNAL_CHSserialIN, patword);
+        // 2 clk pulses
+        for (int i = 0; i < 2; i++) {
+            patword = setBit(SIGNAL_CHSclk, patword);
+            writePatternWord(iaddr++, patword);
+            patword = clearBit(SIGNAL_CHSclk, patword);
+            writePatternWord(iaddr++, patword);
+        }
+
+        // for each channel (all chips)
+        for (int ich = 0; ich < NCHAN_1_COUNTER; ich++) {
+            LOG(logDEBUG1, (" Chip %d, Channel %d\n", ichip, ich));
+            int val = trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
+                               NCOUNTERS * ich] +
+                      trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
+                               NCOUNTERS * ich + 1] *
+                          64 +
+                      trimbits[ichip * NCHAN_1_COUNTER * NCOUNTERS +
+                               NCOUNTERS * ich + 2] *
+                          64 * 64;
+
+            // push 6 0 bits
+            for (int i = 0; i < 6; i++) {
+                patword = clearBit(SIGNAL_serialIN, patword);
+                patword = clearBit(SIGNAL_clk, patword);
+                writePatternWord(iaddr++, patword);
+                patword = setBit(SIGNAL_clk, patword);
+                writePatternWord(iaddr++, patword);
+            }
+
+            // deserialize
+            for (int i = 0; i < 18; i++) {
+                if (val & (1 << i)) {
+                    patword = setBit(SIGNAL_serialIN, patword);
+                } else {
+                    patword = clearBit(SIGNAL_serialIN, patword);
+                }
+                patword = clearBit(SIGNAL_clk, patword);
+                writePatternWord(iaddr++, patword);
+
+                patword = setBit(SIGNAL_clk, patword);
+                writePatternWord(iaddr++, patword);
+            }
+            writePatternWord(iaddr++, patword);
+            writePatternWord(iaddr++, patword);
+
+            // move to next channel
+            for (int i = 0; i < 3; i++) {
+                patword = setBit(SIGNAL_CHSclk, patword);
+                writePatternWord(iaddr++, patword);
+                patword = clearBit(SIGNAL_CHSclk, patword);
+                writePatternWord(iaddr++, patword);
+            }
+        }
+        // chip unselect
+        patword = clearBit(SIGNAL_TBLoad_1 + ichip, patword);
+        writePatternWord(iaddr++, patword);
+
+        // last iaddr check
+        if (iaddr >= MAX_PATTERN_LENGTH) {
+            LOG(logERROR, ("Addr 0x%x is past max_address_length 0x%x!\n",
+                           iaddr, MAX_PATTERN_LENGTH));
             error = 1;
+            break;
+        }
+
+        // set pattern wait address
+        for (int i = 0; i <= 2; i++)
+            setPatternWaitAddress(i, MAX_PATTERN_LENGTH - 1);
+
+        // pattern loop
+        for (int i = 0; i <= 2; i++) {
+            int stop = MAX_PATTERN_LENGTH - 1, nloop = 0;
+            setPatternLoop(i, &stop, &stop, &nloop);
+        }
+
+        // pattern limits
+        {
+            int start = 0, nloop = 0;
+            setPatternLoop(-1, &start, &iaddr, &nloop);
+        }
+        // send pattern to the chips
+        startPattern();
     }
-    /////////////////////////////////////////////////////////////////
+
     if (error == 0) {
         // copy trimbits locally
         for (int ichan = 0; ichan < ((detectorModules)->nchan); ++ichan) {
@@ -1145,6 +1292,7 @@ int setTrimbits(int *trimbits) {
         }
         LOG(logINFO, ("All trimbits have been loaded\n"));
     }
+
     trimmingPrint = logINFO;
     // set back to previous clock
     if (setClockDivider(SYSTEM_C0, prevRunClk) == FAIL) {
@@ -1155,6 +1303,7 @@ int setTrimbits(int *trimbits) {
     if (error != 0) {
         return FAIL;
     }
+
     return OK;
 }
 
@@ -2631,51 +2780,76 @@ int getNumberOfDACs() { return NDAC; }
 int getNumberOfChannelsPerChip() { return NCHAN; }
 
 int setChipStatusRegister(int csr) {
-    uint32_t prevRunClk = clkDivider[SYSTEM_C0];
+  int iaddr=0;
-    patternParameters *pat = NULL;
+  int  nbits=18;
+  int error=0;
+  //int start=0, stop=MAX_PATTERN_LENGTH, loop=0;
+  int patword=0;
+  patword=setBit(SIGNAL_STATLOAD,patword);
+  for (int i=0; i<2; i++)
+    writePatternWord(iaddr++, patword);
+  patword=setBit(SIGNAL_resStorage,patword);
+  patword=setBit(SIGNAL_resCounter,patword);
+  for (int i=0; i<8; i++)
+    writePatternWord(iaddr++, patword);
+  patword=clearBit(SIGNAL_resStorage,patword);
+  patword=clearBit(SIGNAL_resCounter,patword);
+  for (int i=0; i<8; i++)
+    writePatternWord(iaddr++, patword);
+  //#This version of the serializer pushes in the MSB first (compatible with the CSR bit numbering)
+  for (int ib=nbits-1; ib>=0; ib--) {
+    if (csr&(1<<ib))
+      patword=setBit(SIGNAL_serialIN,patword);
+    else
+      patword=clearBit(SIGNAL_serialIN,patword);
+    for (int i=0; i<4; i++)
+      writePatternWord(iaddr++, patword);
+    patword=setBit(SIGNAL_CHSclk,patword);
+    writePatternWord(iaddr++, patword);
+    patword=clearBit(SIGNAL_CHSclk,patword);
+    writePatternWord(iaddr++, patword);
+  }
 
-    int error = 0;
+  patword=clearBit(SIGNAL_serialIN,patword);
-    if (setClockDivider(SYSTEM_C0, DEFAULT_TRIMMING_RUN_CLKDIV) == FAIL) {
+  for (int i=0; i<2; i++)
-        LOG(logERROR,
+      writePatternWord(iaddr++, patword);
-            ("Could not set to trimming clock in order to change CSR\n"));
+  patword=setBit(SIGNAL_STO,patword);
-        return FAIL;
+  for (int i=0; i<5; i++)
-    }
+      writePatternWord(iaddr++, patword);
-    pat = setChipStatusRegisterPattern(csr);
+  patword=clearBit(SIGNAL_STO,patword);
+  for (int i=0; i<5; i++)
+    writePatternWord(iaddr++, patword);
+  patword=clearBit(SIGNAL_STATLOAD,patword);
+  for (int i=0; i<5; i++)
+    writePatternWord(iaddr++, patword);
 
-    if (pat) {
+  if (iaddr >= MAX_PATTERN_LENGTH) {
-        error |= loadPattern(pat);
+    LOG(logERROR, ("Addr 0x%x is past max_address_length 0x%x!\n",
-        if (!error)
+		   iaddr, MAX_PATTERN_LENGTH));
-            startPattern();
+    error = 1;
-        free(pat);
+  }
-    } else {
+  // set pattern wait address
-        error = 1;
+  for (int i = 0; i <= 2; i++)
-    }
+    setPatternWaitAddress(i, MAX_PATTERN_LENGTH - 1);
   
-    if (!error) {
+  // pattern loop
-        LOG(logINFO, ("CSR is now: 0x%x\n", csr));
+  for (int i = 0; i <= 2; i++) {
-    }
+    int stop = MAX_PATTERN_LENGTH - 1, nloop = 0;
+    setPatternLoop(i, &stop, &stop, &nloop);
+  }
+  
+  // pattern limits
+  {
+    int start = 0, nloop = 0;
+    setPatternLoop(-1, &start, &iaddr, &nloop);
+  }
+  // send pattern to the chips
+  startPattern();
+  
+  if (error != 0) {
+    return FAIL;
+  }
+  
+  return OK;
 
-    if (setClockDivider(SYSTEM_C0, prevRunClk) == FAIL) {
-        LOG(logERROR,
-            ("Could not set to previous run clock after changing CSR\n"));
-        return FAIL;
-    }
-    return OK;
-}
-
-int setGainCaps(int caps){
-    // Update only gain caps, leave the rest of the CSR unchanged
-    int csr = getChipStatusRegister();
-    csr &= ~GAIN_MASK;
-
-    caps = gainCapsToCsr(caps);
-    // caps &= GAIN_MASK;
-    csr |= caps;
-    return setChipStatusRegister(csr);
-}
-
-int getGainCaps(){
-    int csr = getChipStatusRegister();
-    int caps = csrToGainCaps(csr);
-    return caps; 
 }

slsDetectorServers/mythen3DetectorServer/slsDetectorServer_defs.h

@@ -47,7 +47,7 @@
 #define DEFAULT_HIGHGAIN_VRPREAMP (1300)
 #define DEFAULT_STANDARD_VRSHAPER (1280)
 #define DEFAULT_FAST_VRSHAPER     (1500)
-#define DEFAULT_HIGHGAIN_VRSHAPER (1100)
+#define DEFAULT_HIGHGAIN_VRSHAPER (900)
 
 #define DEFAULT_READOUT_C0 (10) //(100000000) // rdo_clk, 100 MHz
 #define DEFAULT_READOUT_C1 (10) //(100000000) // smp sample clk (x2), 100 MHz
@@ -158,3 +158,47 @@ typedef struct udp_header_struct {
 #define UDP_IP_HEADER_LENGTH_BYTES (28)
 #define PACKETS_PER_FRAME_10G      (2)
 #define PACKETS_PER_FRAME_1G       (20)
+
+/** Signal Definitions */
+#define SIGNAL_TBLoad_1    (0)
+#define SIGNAL_TBLoad_2    (1)
+#define SIGNAL_TBLoad_3    (2)
+#define SIGNAL_TBLoad_4    (3)
+#define SIGNAL_TBLoad_5    (4)
+#define SIGNAL_TBLoad_6    (5)
+#define SIGNAL_TBLoad_7    (6)
+#define SIGNAL_TBLoad_8    (7)
+#define SIGNAL_TBLoad_9    (8)
+#define SIGNAL_TBLoad_10   (9)
+#define SIGNAL_AnaMode     (10)
+#define SIGNAL_CHSserialIN (11)
+#define SIGNAL_READOUT     (12)
+#define SIGNAL_pulse       (13)
+#define SIGNAL_EN1         (14)
+#define SIGNAL_EN2         (15)
+#define SIGNAL_EN3         (16)
+#define SIGNAL_clk         (17)
+#define SIGNAL_SRmode      (18)
+#define SIGNAL_serialIN    (19)
+#define SIGNAL_STO         (20)
+#define SIGNAL_STATLOAD    (21)
+#define SIGNAL_resStorage  (22)
+#define SIGNAL_resCounter  (23)
+#define SIGNAL_CHSclk      (24)
+#define SIGNAL_exposing    (25)
+
+//CHIP STARTUS REGISTER BITS
+#define CSR_spypads  0
+#define CSR_invpol  4
+#define CSR_dpulse  5
+#define CSR_interp  6
+#define CSR_C10pre  7 //#default
+#define CSR_pumprobe  8
+#define CSR_apulse  9
+#define CSR_C15sh  10 
+#define CSR_C30sh  11 //#default
+#define CSR_C50sh  12
+#define CSR_C225ACsh  13 // Connects 225fF SHAPER AC cap (1: 225 to shaper, 225 to GND. 0: 450 to shaper) 
+#define CSR_C15pre  14 
+
+#define CSR_default  (1<<CSR_C10pre )|(1<< CSR_C30sh)

slsDetectorServers/slsDetectorServer/include/loadPattern.h

@@ -1,6 +0,0 @@
-#ifndef LOADPATTERN_H
-#define LOADPATTERN_H
-#include "Pattern.h"
-
-int loadPattern(patternParameters *pat);
-#endif

slsDetectorServers/slsDetectorServer/include/slsDetectorFunctionList.h

@@ -25,10 +25,6 @@
 #include "blackfin.h"
 #endif
 
-#if defined(MYTHEN3D) 
-#include "mythen3.h"
-#endif
-
 #include <stdio.h> // FILE
 #include <stdlib.h>
 #include <sys/types.h>
@@ -357,10 +353,6 @@ enum timingMode getTiming();
 #ifdef MYTHEN3D
 void setInitialExtSignals();
 int isMaster();
-int setGainCaps(int caps);
-int getGainCaps();
-int setChipStatusRegister(int csr);
-int setDACS(int* dacs);
 #endif
 #if defined(GOTTHARDD) || defined(MYTHEN3D)
 void setExtSignal(int signalIndex, enum externalSignalFlag mode);

slsDetectorServers/slsDetectorServer/include/slsDetectorServer_funcs.h

@@ -247,6 +247,3 @@ int get_pattern(int);
 int load_default_pattern(int);
 int get_all_threshold_energy(int);
 int get_master(int);
-int get_csr();
-int set_gain_caps(int);
-int get_gain_caps(int);

slsDetectorServers/slsDetectorServer/src/loadPattern.c

@@ -1,105 +0,0 @@
-#include "readDefaultPattern.h"
-#include "loadPattern.h"
-#include "clogger.h"
-#include "common.h"
-#include "sls/ansi.h"
-#include "sls/sls_detector_defs.h"
-#include "slsDetectorServer_defs.h"
-
-#if defined(CHIPTESTBOARDD) || defined(MOENCHD) || defined(MYTHEN3D)
-#include "Pattern.h"
-#endif
-
-#include <string.h>
-#include <unistd.h>
-
-extern char initErrorMessage[MAX_STR_LENGTH];
-
-#ifndef MYTHEN3D
-extern uint64_t writePatternIOControl(uint64_t word);
-#endif
-extern uint64_t writePatternWord(int addr, uint64_t word);
-extern int setPatternWaitAddress(int level, int addr);
-extern uint64_t setPatternWaitTime(int level, uint64_t t);
-extern void setPatternLoop(int level, int *startAddr, int *stopAddr,
-                           int *nLoop);
-
-int loadPattern(patternParameters *pat) {
-
-  int ret=OK;
-
-  for (int i = 0; i < MAX_PATTERN_LENGTH; ++i) {
-    if ((i % 10 == 0) && pat->word[i] != 0) {
-      LOG(logINFO, ("Setting Pattern Word (addr:0x%x, word:0x%llx)\n",
-		    i, (long long int)pat->word[i]));
-    }
-    writePatternWord(i, pat->word[i]);
-  }
-#ifndef MYTHEN3D 
-   if (ret == OK) { 
-     uint64_t retval64 = writePatternIOControl(pat->ioctrl); 
-     //validate64(pat->ioctrl, retval64, "set pattern IO Control", HEX); 
-   } 
-#endif 
-        if (ret == OK) {
-            int numLoops = -1;
-            int retval0 = pat->limits[0];
-            int retval1 = pat->limits[1];
-            setPatternLoop(-1, &retval0, &retval1, &numLoops);
-            //validate(pat->limits[0], retval0,
-	    // "set pattern Limits start address", HEX);
-	//validate(pat->limits[1], retval1,
-	    //       "set pattern Limits start address", HEX);
-        }
-	uint64_t retval64;
-        if (ret == OK) {
-            for (int i = 0; i <= 2; ++i) {
-                char msg[128];
-                int retval0 = -1, retval1 = -1, numLoops = -1;
-
-                // patloop
-                retval0 = pat->loop[i * 2 + 0];
-                retval1 = pat->loop[i * 2 + 1];
-                numLoops = pat->nloop[i];
-                setPatternLoop(i, &retval0, &retval1, &numLoops);
-                memset(msg, 0, sizeof(msg));
-                sprintf(msg, "set pattern Loop %d start address", i);
-                //validate(pat->loop[i * 2 + 0], retval0, msg, HEX);
-                if (ret == FAIL) {
-                    break;
-                }
-                memset(msg, 0, sizeof(msg));
-                sprintf(msg, "set pattern Loop %d stop address", i);
-                //validate(pat->loop[i * 2 + 1], retval1, msg, HEX);
-                if (ret == FAIL) {
-                    break;
-                }
-                memset(msg, 0, sizeof(msg));
-                sprintf(msg, "set pattern Loop %d num loops", i);
-                //validate(pat->nloop[i], numLoops, msg, HEX);
-                if (ret == FAIL) {
-                    break;
-                }
-                // patwait
-                memset(msg, 0, sizeof(msg));
-                sprintf(msg, "set pattern Loop %d wait address", i);
-                retval0 = setPatternWaitAddress(i, pat->wait[i]);
-                //validate(pat->wait[i], retval0, msg, HEX);
-                if (ret == FAIL) {
-                    break;
-                }
-
-                // patwaittime
-                memset(msg, 0, sizeof(msg));
-                sprintf(msg, "set pattern Loop %d wait time", i);
-                retval64 = setPatternWaitTime(i, pat->waittime[i]);
-                //validate64(pat->waittime[i], retval64, msg, HEX);
-                if (retval64 == FAIL) {
-                    break;
-                }
-	    }
-	}
-	return ret;
-}
-
-

slsDetectorServers/slsDetectorServer/src/readDefaultPattern.c

@@ -1,5 +1,4 @@
 #include "readDefaultPattern.h"
-#include "loadPattern.h"
 #include "clogger.h"
 #include "common.h"
 #include "sls/ansi.h"

slsDetectorServers/slsDetectorServer/src/slsDetectorServer_funcs.c

@@ -369,9 +369,6 @@ void function_table() {
     flist[F_LOAD_DEFAULT_PATTERN] = &load_default_pattern;
     flist[F_GET_ALL_THRESHOLD_ENERGY] = &get_all_threshold_energy;
     flist[F_GET_MASTER] = &get_master;
-    flist[F_GET_CSR] = &get_csr;
-    flist[F_SET_GAIN_CAPS] = &set_gain_caps;
-    flist[F_GET_GAIN_CAPS] = &get_gain_caps;
 
     // check
     if (NUM_DET_FUNCTIONS >= RECEIVER_ENUM_START) {
@@ -1550,11 +1547,18 @@ int set_module(int file_des) {
     // only set
     else if (Server_VerifyLock() == OK) {
         // check index
-
-#if !(defined(EIGERD) || defined(MYTHEN3D))
-//TODO! Check if this is used for any detector
         switch (module.reg) {
-#ifdef JUNGFRAUD
+#ifdef EIGERD
+        case STANDARD:
+        case HIGHGAIN:
+        case LOWGAIN:
+        case VERYHIGHGAIN:
+        case VERYLOWGAIN:
+#elif MYTHEN3D
+        case STANDARD:
+        case FAST:
+        case HIGHGAIN:
+#elif JUNGFRAUD
         case DYNAMICGAIN:
         case DYNAMICHG0:
         case FIXGAIN1:
@@ -1573,12 +1577,10 @@ int set_module(int file_des) {
             modeNotImplemented("Settings", (int)module.reg);
             break;
         }
-#endif
+
         ret = setModule(module, mess);
         enum detectorSettings retval = getSettings();
-#if !(defined(EIGERD) || defined(MYTHEN3D))
         validate(module.reg, (int)retval, "set module (settings)", DEC);
-#endif
         LOG(logDEBUG1, ("Settings: %d\n", retval));
     }
     free(myChan);
@@ -7576,7 +7578,8 @@ int set_pattern(int file_des) {
 
     patternParameters *pat = malloc(sizeof(patternParameters));
     memset(pat, 0, sizeof(patternParameters));
-      // ignoring endianness for eiger
+
+    // ignoring endianness for eiger
     if (receiveData(file_des, pat, sizeof(patternParameters), INT32) < 0) {
         if (pat != NULL)
             free(pat);
@@ -7587,11 +7590,6 @@ int set_pattern(int file_des) {
         LOG(logINFO, ("Setting Pattern from structure\n"));
         LOG(logINFO,
             ("Setting Pattern Word (printing every 10 words that are not 0\n"));
-	/****************************************************************************************************************/
-	/* I SUGGEST TO VALIDATE THE VALUES HERE AND THEN WRITE THE PATTERN IN A SEPARATE FUNCTION WHICH COULD BE REUSED*/
-	/* added loadPattern.c/h - the same func could be reused also in readDefaultPattern                                  */
-	/***************************************************************************************************************/
-
         for (int i = 0; i < MAX_PATTERN_LENGTH; ++i) {
             if ((i % 10 == 0) && pat->word[i] != 0) {
                 LOG(logINFO, ("Setting Pattern Word (addr:0x%x, word:0x%llx)\n",
@@ -7664,7 +7662,6 @@ int set_pattern(int file_des) {
                 }
             }
         }
-	/******* DOWN TO HERE ***********/
     }
     if (pat != NULL)
         free(pat);
@@ -8386,63 +8383,3 @@ int get_master(int file_des){
 #endif
     return Server_SendResult(file_des, INT32, &retval, sizeof(retval));
 }
-
-int get_csr(int file_des){
-    ret = OK;
-    memset(mess, 0, sizeof(mess));
-    int retval = -1;
-
-    LOG(logDEBUG1, ("Getting csr\n"));
-
-#ifndef MYTHEN3D
-    functionNotImplemented();
-#else
-    retval = getChipStatusRegister();
-#endif
-    return Server_SendResult(file_des, INT32, &retval, sizeof(retval));
-}
-
-int set_gain_caps(int file_des){
-    ret = OK;
-    memset(mess, 0, sizeof(mess));
-    int arg = 0;
-
-    if (receiveData(file_des, &arg, sizeof(arg), INT32) < 0)
-        return printSocketReadError();
-    LOG(logINFO, ("Setting gain caps to: %u\n", arg));
-
-    int retval = -1;
-
-#ifndef MYTHEN3D
-    functionNotImplemented();
-#else
-    if (Server_VerifyLock() == OK) {
-        setGainCaps(arg);
-        retval = getChipStatusRegister(); //TODO! fix 
-        LOG(logDEBUG1, ("gain caps retval: %u\n", retval));
-    }
-#endif
-    return Server_SendResult(file_des, INT32, &retval, sizeof(retval));
-}
-
-int get_gain_caps(int file_des){
-    ret = OK;
-    memset(mess, 0, sizeof(mess));
-    // int arg = 0;
-
-    // if (receiveData(file_des, &arg, sizeof(arg), INT32) < 0)
-    //     return printSocketReadError();
-    LOG(logINFO, ("Getting gain caps\n"));
-
-    int retval = -1;
-
-#ifndef MYTHEN3D
-    functionNotImplemented();
-#else
-    if (Server_VerifyLock() == OK) {
-        retval = getGainCaps();
-        LOG(logDEBUG1, ("Gain caps: %u\n", retval));
-    }
-#endif
-    return Server_SendResult(file_des, INT32, &retval, sizeof(retval));
-}

slsDetectorSoftware/include/sls/Detector.h

@@ -498,7 +498,7 @@ class Detector {
 
     /** Non blocking: Abort detector acquisition. Status changes to IDLE or
      * STOPPED. Goes to stop server. */
-    void stopDetector(Positions pos = {});
+    void stopDetector();
 
     /** IDLE, ERROR, WAITING, RUN_FINISHED, TRANSMITTING, RUNNING, STOPPED \n
      * Goes to stop server */
@@ -1308,14 +1308,6 @@ class Detector {
 
     Result<bool> getMaster(Positions pos = {}) const;
 
-
-    //TODO! check if we really want to expose this !!!!!
-    Result<int> getChipStatusRegister(Positions pos = {}) const;
-
-    void setGainCaps(int caps, Positions pos = {});
-
-    Result<int> getGainCaps(Positions pos = {});
-
     ///@{
 
     /** @name CTB / Moench Specific */

slsDetectorSoftware/src/CmdParser.cpp

@@ -55,12 +55,6 @@ void CmdParser::Parse(const std::string &s) {
         command_ = arguments_[0];
         arguments_.erase(begin(arguments_));
     }
-    //allow comma sep
-    for (auto& arg : arguments_){
-        if (arg.back() == ',')
-            arg.pop_back();
-    }
-
     DecodeIdAndPosition(command_.c_str());
 }
 

slsDetectorSoftware/src/CmdProxy.cpp

@@ -54,7 +54,7 @@ bool CmdProxy::ReplaceIfDepreciated(std::string &command) {
     if (d_it != depreciated_functions.end()) {
         LOG(logWARNING)
             << command
-            << " is deprecated and will be removed. Please migrate to: "
+            << " is depreciated and will be removed. Please migrate to: "
             << d_it->second;
         // insert old command into arguments (for dacs)
         if (d_it->second == "dac") {
@@ -1981,43 +1981,6 @@ std::string CmdProxy::GateDelay(int action) {
     return os.str();
 }
 
-
-std::string CmdProxy::GainCaps(int action){
-    std::ostringstream os;
-    os << cmd << ' ';
-    if (action == defs::HELP_ACTION) {
-        os << "[cap1, cap2, ...]\n\t[Mythen3] gain, options: C10pre, C15sh, C30sh, C50sh, C225ACsh, C15pre"
-           << '\n';
-    } else if (action == defs::GET_ACTION) {
-        if (!args.empty())
-            WrongNumberOfParameters(0);
-
-        auto tmp = det->getGainCaps();
-        sls::Result<defs::M3_GainCaps> csr;
-        for (auto val : tmp){
-            if (val)
-                csr.push_back(static_cast<defs::M3_GainCaps>(val));
-        }
-            
-        os << OutString(csr) << '\n';
-    } else if (action == defs::PUT_ACTION) {
-        if (args.size() < 1) {
-            WrongNumberOfParameters(1);
-        }
-        int caps = 0;
-        for (const auto& arg:args){
-            if (arg != "0")
-                caps |= sls::StringTo<defs::M3_GainCaps>(arg);
-        }
-            
-        det->setGainCaps(caps);
-        os << OutString(args) << '\n';
-    } else {
-        throw sls::RuntimeError("Unknown action");
-    }
-    return os.str();
-}
-
 /* CTB / Moench Specific */
 
 std::string CmdProxy::Samples(int action) {

slsDetectorSoftware/src/CmdProxy.h

@@ -571,6 +571,19 @@ class CmdProxy {
         return ToString(value, unit);
     }
 
+    // inline unsigned int stoiHex(const std::string& s) {
+    //     unsigned long lresult = stoul(s, nullptr, 16);
+    //     unsigned int result = lresult;
+    //     if (result != lresult) {
+    //         throw std::out_of_range("cannot convert to unsigned int");
+    //     }
+    //     return result;
+    // }
+
+    // inline unsigned long int stoulHex(const std::string& s) {
+    //     unsigned long result = stoul(s, nullptr, 16);
+    //     return result;
+    // }
 
     using FunctionMap = std::map<std::string, std::string (CmdProxy::*)(int)>;
     using StringMap = std::map<std::string, std::string>;
@@ -957,7 +970,6 @@ class CmdProxy {
         {"gatedelay1", &CmdProxy::GateDelay},
         {"gatedelay2", &CmdProxy::GateDelay},
         {"gatedelay3", &CmdProxy::GateDelay},
-        {"gaincaps", &CmdProxy::GainCaps},
 
         /* CTB/ Moench Specific */
         {"samples", &CmdProxy::Samples},
@@ -1125,7 +1137,6 @@ class CmdProxy {
     /* Mythen3 Specific */
     std::string Counters(int action);
     std::string GateDelay(int action);
-    std::string GainCaps(int action);
     /* CTB/ Moench Specific */
     std::string Samples(int action);
     /* CTB Specific */
@@ -1444,7 +1455,7 @@ class CmdProxy {
         "\n\t[Mythen3] Starts detector readout. Status changes to TRANSMITTING "
         "and automatically returns to idle at the end of readout.");
 
-    EXECUTE_SET_COMMAND(stop, stopDetector,
+    EXECUTE_SET_COMMAND_NOID(stop, stopDetector,
                              "\n\tAbort detector acquisition. Status changes "
                              "to IDLE or STOPPED. Goes to stop server.");
 

slsDetectorSoftware/src/Detector.cpp

@@ -697,7 +697,7 @@ void Detector::startDetectorReadout() {
     pimpl->Parallel(&Module::startReadout, {});
 }
 
-void Detector::stopDetector(Positions pos) { pimpl->Parallel(&Module::stopAcquisition, pos); }
+void Detector::stopDetector() { pimpl->Parallel(&Module::stopAcquisition, {}); }
 
 Result<defs::runStatus> Detector::getDetectorStatus(Positions pos) const {
     return pimpl->Parallel(&Module::getRunStatus, pos);
@@ -1615,18 +1615,6 @@ Result<bool> Detector::getMaster(Positions pos) const{
     return pimpl->Parallel(&Module::isMaster, pos);
 }
 
-Result<int> Detector::getChipStatusRegister(Positions pos) const{
-    return pimpl->Parallel(&Module::getChipStatusRegister, pos);
-}
-
-void Detector::setGainCaps(int caps, Positions pos){
-    return pimpl->Parallel(&Module::setGainCaps, pos, caps);
-}
-
-Result<int> Detector::getGainCaps(Positions pos){
-    return pimpl->Parallel(&Module::getGainCaps, pos);
-}
-
 
 // CTB/ Moench Specific
 

slsDetectorSoftware/src/Module.cpp

@@ -412,7 +412,7 @@ void Module::loadSettingsFile(const std::string &fname) {
         if (shm()->myDetectorType == MYTHEN3) {
             serialNumberWidth = 4;
         }
-        if ((fname.find(".sn") == std::string::npos) && (fname.find(".trim") == std::string::npos)) {
+        if (fname.find(".sn") == std::string::npos) {
             ostfn << ".sn" << std::setfill('0') << std::setw(serialNumberWidth)
                   << std::dec << getSerialNumber();
         }
@@ -1998,18 +1998,6 @@ bool Module::isMaster() const{
     return sendToDetector<int>(F_GET_MASTER);
 }
 
-int Module::getChipStatusRegister() const{
-    return sendToDetector<int>(F_GET_CSR);
-}
-
-void Module::setGainCaps(int caps){
-    sendToDetector<int>(F_SET_GAIN_CAPS, caps);
-}
-
-int Module::getGainCaps(){
-    return sendToDetector<int>(F_GET_GAIN_CAPS);
-}
-
 // CTB / Moench Specific
 int Module::getNumberOfAnalogSamples() const {
     return sendToDetector<int>(F_GET_NUM_ANALOG_SAMPLES);
@@ -3207,9 +3195,6 @@ sls_detector_module Module::readSettingsFile(const std::string &fname,
         throw RuntimeError("Could not open settings file: " + fname);
     }
 
-    auto file_size = getFileSize(infile);
-
-
     // eiger
     if (shm()->myDetectorType == EIGER) {
         infile.read(reinterpret_cast<char *>(myMod.dacs),
@@ -3235,16 +3220,6 @@ sls_detector_module Module::readSettingsFile(const std::string &fname,
 
     // mythen3 (dacs, trimbits)
     else if (shm()->myDetectorType == MYTHEN3) {
-        int expected_size =
-            sizeof(int) * myMod.ndac + sizeof(int) * myMod.nchan + sizeof(myMod.reg);
-        if (file_size != expected_size) {
-            throw RuntimeError("The size of the settings file: " + fname +
-                               " differs from the expected size, " +
-                               std::to_string(file_size) + " instead of " +
-                               std::to_string(expected_size) + " bytes");
-        }
-        infile.read(reinterpret_cast<char *>(&myMod.reg),
-                    sizeof(myMod.reg));
         infile.read(reinterpret_cast<char *>(myMod.dacs),
                     sizeof(int) * (myMod.ndac));
         for (int i = 0; i < myMod.ndac; ++i) {

slsDetectorSoftware/src/Module.h

@@ -426,9 +426,6 @@ class Module : public virtual slsDetectorDefs {
     void setGateDelay(int gateIndex, int64_t value);
     std::array<time::ns, 3> getGateDelayForAllGates() const;
     bool isMaster() const;
-    int getChipStatusRegister() const;
-    void setGainCaps(int caps);
-    int getGainCaps();
 
     /**************************************************
      *                                                *

slsSupportLib/CMakeLists.txt

@@ -57,12 +57,14 @@ target_include_directories(slsSupportObject
   PUBLIC
     "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
     "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
+  PRIVATE
+    ${ZeroMQ_INCLUDE_DIRS}
 )
 
 target_link_libraries(slsSupportObject 
   PUBLIC
     slsProjectOptions 
-    libzmq
+    ${ZeroMQ_LIBRARIES}
     rapidjson
   PRIVATE
     slsProjectWarnings     
@@ -74,6 +76,7 @@ endif(SLS_USE_TESTS)
 
 # Add shared library version of the support lib
 add_library(slsSupportShared SHARED $<TARGET_OBJECTS:slsSupportObject>)
+
 target_link_libraries(slsSupportShared PUBLIC slsSupportObject)
 
 set_target_properties(slsSupportShared PROPERTIES
@@ -105,4 +108,3 @@ install(TARGETS slsSupportShared slsSupportStatic slsSupportObject
     PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/sls
 )
 
-

slsSupportLib/include/sls/ToString.h

@@ -36,7 +36,6 @@ std::string ToString(const defs::dacIndex s);
 std::string ToString(const std::vector<defs::dacIndex> &vec);
 std::string ToString(const defs::burstMode s);
 std::string ToString(const defs::timingSourceType s);
-std::string ToString(const defs::M3_GainCaps s);
 
 std::string ToString(const slsDetectorDefs::xy &coord);
 std::ostream &operator<<(std::ostream &os, const slsDetectorDefs::xy &coord);
@@ -298,7 +297,6 @@ template <> defs::readoutMode StringTo(const std::string &s);
 template <> defs::dacIndex StringTo(const std::string &s);
 template <> defs::burstMode StringTo(const std::string &s);
 template <> defs::timingSourceType StringTo(const std::string &s);
-template <> defs::M3_GainCaps StringTo(const std::string &s);
 
 template <> uint32_t StringTo(const std::string &s);
 template <> uint64_t StringTo(const std::string &s);

slsSupportLib/include/sls/file_utils.h

@@ -48,7 +48,3 @@ int writeDataFile(std::string fname, int nch, short int *data);
 
 // mkdir -p path implemented by recursive calls
 void mkdir_p(const std::string &path, std::string dir = "");
-
-namespace sls {
-int getFileSize(std::ifstream &ifs);
-}

slsSupportLib/include/sls/sls_detector_defs.h

@@ -394,16 +394,6 @@ typedef struct {
      */
     enum timingSourceType { TIMING_INTERNAL, TIMING_EXTERNAL };
 
-    //gain caps Mythen3
-    enum M3_GainCaps {
-        M3_C10pre= 1<<7, 
-        M3_C15sh = 1<<10, 
-        M3_C30sh = 1<<11,
-        M3_C50sh = 1<<12,
-        M3_C225ACsh = 1<<13,
-        M3_C15pre = 1<<14, 
-    };
-
 #ifdef __cplusplus
 
     /** scan structure */
@@ -635,10 +625,6 @@ typedef struct {
 #endif
 
 #ifdef __cplusplus
-
-
-
-
 // TODO! discuss this
 #include <vector> //hmm... but currently no way around
 namespace sls {

slsSupportLib/include/sls/sls_detector_funcs.h

@@ -221,9 +221,6 @@ enum detFuncs {
     F_LOAD_DEFAULT_PATTERN,
     F_GET_ALL_THRESHOLD_ENERGY,
     F_GET_MASTER,
-    F_GET_CSR,
-    F_SET_GAIN_CAPS,
-    F_GET_GAIN_CAPS,
 
     NUM_DET_FUNCTIONS,
     RECEIVER_ENUM_START = 256, /**< detector function should not exceed this

slsSupportLib/include/sls/versionAPI.h

@@ -1,5 +1,5 @@
 /** API versions */
-#define GITBRANCH    "developer"
+#define GITBRANCH    "5.1.0.rc2"
 #define APICTB 0x210225
 #define APIGOTTHARD 0x210225
 #define APIGOTTHARD2 0x210225

slsSupportLib/src/ToString.cpp

@@ -859,44 +859,6 @@ template <> defs::timingSourceType StringTo(const std::string &s) {
     throw sls::RuntimeError("Unknown timing source type " + s);
 }
 
-template <> defs::M3_GainCaps StringTo(const std::string &s){
-    if (s == "C10pre")
-        return defs::M3_C10pre;
-    if (s == "C15sh")
-        return defs::M3_C15sh;
-    if (s == "C30sh")
-        return defs::M3_C30sh;
-    if (s == "C50sh")
-        return defs::M3_C50sh;
-    if (s == "C225ACsh")
-        return defs::M3_C225ACsh;
-    if (s == "C15pre")
-        return defs::M3_C15pre;
-    throw sls::RuntimeError("Unknown gain cap " + s);
-    
-}
-
-
-std::string ToString(defs::M3_GainCaps s){
-    std::ostringstream os; 
-    if (s & defs::M3_C10pre)
-        os << "C10pre, ";
-    if (s & defs::M3_C15sh)
-        os << "C15sh, ";
-    if (s & defs::M3_C30sh)
-        os << "C30sh, ";
-    if (s & defs::M3_C50sh)
-        os << "C50sh, ";
-    if (s & defs::M3_C225ACsh)
-        os << "C225ACsh, ";
-    if (s & defs::M3_C15pre)
-        os << "C15pre, ";
-    auto rs = os.str();
-    rs.erase(rs.end()-2);
-    return rs;
-    
-}
-
 template <> uint32_t StringTo(const std::string &s) {
     int base = s.find("0x") != std::string::npos ? 16 : 10;
     return std::stoul(s, nullptr, base);

slsSupportLib/src/file_utils.cpp

@@ -3,7 +3,6 @@
 #include "sls/sls_detector_exceptions.h"
 
 #include <errno.h>
-#include <ios>
 #include <iostream>
 #include <sstream>
 #include <sys/stat.h>
@@ -93,13 +92,3 @@ void mkdir_p(const std::string &path, std::string dir) {
     if (i + 1 < path.length())
         mkdir_p(path.substr(i + 1), dir);
 }
-
-namespace sls {
-int getFileSize(std::ifstream &ifs) {
-    auto current_pos = ifs.tellg();
-    ifs.seekg(0, std::ios::end);
-    int file_size = ifs.tellg();
-    ifs.seekg(current_pos);
-    return file_size;
-}
-} // namespace sls

slsSupportLib/tests/CMakeLists.txt

@@ -1,6 +1,5 @@
 target_sources(tests PRIVATE 
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-bit_utils.cpp
-                ${CMAKE_CURRENT_SOURCE_DIR}/test-file_utils.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-container_utils.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-network_utils.cpp
                 ${CMAKE_CURRENT_SOURCE_DIR}/test-string_utils.cpp

slsSupportLib/tests/test-file_utils.cpp

@@ -1,28 +0,0 @@
-#include "catch.hpp"
-#include "sls/file_utils.h"
-#include <stdio.h>
-#include <unistd.h>
-#include <iostream>
-#include <vector>
-
-TEST_CASE("Get size of empty file") {
-    char fname[] = "temfile_XXXXXX";
-    int fh = mkstemp(fname);
-    std::ifstream ifs(fname);
-    auto size = sls::getFileSize(ifs);
-    REQUIRE(size == 0);
-}
-
-TEST_CASE("Get size of file with data") {
-    constexpr size_t n_bytes = 137;
-    std::vector<char> data(n_bytes);
-    char fname[] = "temfile_XXXXXX";
-    int fh = mkstemp(fname);
-    write(fh, data.data(), n_bytes);
-
-    std::ifstream ifs(fname);
-    auto size = sls::getFileSize(ifs);
-    REQUIRE(size == n_bytes);
-    REQUIRE(ifs.tellg() == 0); //getting size resets pos!
-}
-

tests/CMakeLists.txt

@@ -19,23 +19,21 @@ set_target_properties(testserver PROPERTIES
     
 add_executable(tests ${SLS_TEST_SOURCES})
 target_link_libraries(tests 
-    PUBLIC 
+    slsProjectOptions
-      slsProjectOptions
+    slsProjectWarnings
-      slsSupportShared
+    slsSupportShared
-      pthread
+    pthread
-      rt
+    rt
-    PRIVATE
-      slsProjectWarnings
 )  
 
 if (SLS_USE_TEXTCLIENT)
-    target_link_libraries(tests PUBLIC
+    target_link_libraries(tests
         slsDetectorShared
     )
 endif (SLS_USE_TEXTCLIENT)
 
 if (SLS_USE_RECEIVER)
-    target_link_libraries(tests PUBLIC
+    target_link_libraries(tests
         slsReceiverShared
     )
 endif (SLS_USE_RECEIVER)