Merge branch 'main-rc' into b4.2.0

Pull request from Samuel ESRF

.clang-format

@@ -0,0 +1,6 @@
+BasedOnStyle: LLVM
+IndentWidth: 4
+
+UseTab: Never
+ColumnLimit: 0
+AlignConsecutiveAssignments: false 

.clang-tidy

@@ -0,0 +1,7 @@
+---
+Checks:          '*, -google-runtime-references, -hicpp-no-array-decay, -cppcoreguidelines-pro-bounds-array-to-pointer-decay, -cppcoreguidelines-pro-bounds-pointer-arithmetic, -fuchsia*,-readability-else-after-return,-readability-avoid-const-params-in-decls,-hicpp-signed-bitwise,-cppcoreguidelines-pro-bounds-constant-array-index,-llvm-header-guard,-readability-static-accessed-through-instance,-google-readability-todo'
+WarningsAsErrors: '*'
+HeaderFilterRegex: '.*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+...

.travis.yml

@@ -0,0 +1,44 @@
+sudo: false
+
+language: cpp
+
+matrix:
+  include:
+    - os: linux
+      env: CONDA_PY=3.6
+
+dist: trusty
+
+install:
+  - sudo apt-get update
+  - ldd --version
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - rm -f miniconda.sh
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda config --add channels conda-forge
+  - conda config --add channels slsdetectorgroup
+  - conda update conda
+  - conda update --all
+  - conda install conda-build anaconda-client
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+
+  # Replace dep1 dep2 ... with your dependencies
+  - conda create -q -n test-environment python=$CONDA_PY
+  - source activate test-environment
+  - conda-build .
+
+script:
+ - echo "No test scripts to be run!"
+
+
+deploy:
+  provider: script
+  script: find $HOME/miniconda/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  on:
+    branch: 4.2.0

CMakeLists.txt

@@ -1,23 +1,43 @@
 cmake_minimum_required(VERSION 2.8)
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 set (CALIBRATE OFF)
 
-option (USE_HDF5 "HDF5 File format" OFF)
-option (USE_TEXTCLIENT "Text Client" OFF)
-option (USE_RECEIVER "Receiver" OFF)
-option (USE_GUI "GUI" OFF)
+# Check if project is being used directly or via add_subdirectory
+set(SLS_MASTER_PROJECT OFF)
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+	set(SLS_MASTER_PROJECT ON)
+endif()
+
+option (SLS_USE_HDF5 "HDF5 File format" OFF)
+option (SLS_USE_TEXTCLIENT "Text Client" OFF)
+option (SLS_USE_RECEIVER "Receiver" OFF)
+option (SLS_USE_GUI "GUI" OFF)
+
+
+#Flags to always be used
+# -Wno-unused-parameter should eventually be removes
+# -Wno-overloaded-virtual TODO! remove warnings in refactor
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-overloaded-virtual -Wno-unused-parameter -std=c++98")
+
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    # clang does not support -Wno-misleading-indentation 
+    # add any special clang flags
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+        set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wno-misleading-indentation")
+    endif ()
+endif()
 
-set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wno-misleading-indentation")
 
 find_package(Qt4)
 find_package(Qwt 6)
 find_package(CBF)
 find_package(Doxygen)
-find_package(PNG REQUIRED)
+# find_package(PNG REQUIRED)
 
-if (USE_HDF5)
+if (SLS_USE_HDF5)
 	find_package(HDF5 1.10 COMPONENTS CXX)
-endif (USE_HDF5)
+endif (SLS_USE_HDF5)
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
@@ -25,20 +45,26 @@ set(CMAKE_INSTALL_RPATH "$ORIGIN")
 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 
 
-if (USE_TEXTCLIENT)
+if (SLS_USE_TEXTCLIENT)
        add_subdirectory(slsDetectorSoftware)
-endif (USE_TEXTCLIENT)
+endif (SLS_USE_TEXTCLIENT)
 
-if (USE_RECEIVER)
+if (SLS_USE_RECEIVER)
        add_subdirectory(slsReceiverSoftware)
-endif (USE_RECEIVER)
+       add_subdirectory(manual/manual-api)    
+endif (SLS_USE_RECEIVER)
                
-if (USE_GUI)   
+               
+if (SLS_USE_GUI)   
        if (QT4_FOUND AND QWT_FOUND)
        add_subdirectory(slsDetectorGui)
        endif()
-endif (USE_GUI)
+endif (SLS_USE_GUI)
 
+if (SLS_MASTER_PROJECT)
+	# Set targets export name (otherwise set by upstream project)
+	set(TARGETS_EXPORT_NAME "slsdetector-targets")
+endif (SLS_MASTER_PROJECT)
 
 if (CALIBRATE)
     if (DEFINED ENV{ROOTSYS})

Makefile

@@ -19,11 +19,12 @@ RECEIVERDIR		=	$(LIBRARYRXRDIR)
 CALWIZDIR		=	$(WD)/calibrationWizards
 MANDIR			=	$(WD)/manual
 CALIBDIR		=	$(WD)/slsDetectorCalibration
+MANAPIDIR		=	$(MANDIR)/manual-api
 
 TABSPACE		:=	"\t"
 
  
-INCLUDES=-I. -I$(LIBRARYDIR)/commonFiles -I$(LIBRARYDIR)/slsDetector -I$(LIBRARYDIR)/usersFunctions -I$(LIBRARYDIR)/multiSlsDetector -I$(LIBRARYDIR)/slsDetectorUtils -I$(LIBRARYDIR)/slsDetectorCommand -I$(LIBRARYDIR)/slsDetectorAnalysis -I$(LIBRARYDIR)/slsReceiverInterface  -I$(LIBRARYRXRDIR)/include -I$(LIBRARYDIR)/threadFiles -I$(ASM)
+INCLUDES=-I. -I$(LIBRARYDIR)/commonFiles -I$(LIBRARYDIR)/slsDetector -I$(LIBRARYDIR)/usersFunctions -I$(LIBRARYDIR)/multiSlsDetector -I$(LIBRARYDIR)/slsDetectorUtils -I$(LIBRARYDIR)/slsDetectorCommand -I$(LIBRARYDIR)/slsDetectorAnalysis -I$(LIBRARYDIR)/slsReceiverInterface  -I$(LIBRARYRXRDIR)/include -I$(LIBRARYDIR)/threadFiles -I$(LIBRARYDIR)/sharedMemory -I$(ASM)
 
 INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM) 
 #LIBFLAGRXR += 
@@ -79,6 +80,7 @@ slsReceiver_static: receiver
 receiver: #libreceiver
 #	cd  $(RECEIVERDIR) && $(MAKE) receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
 	cd  $(RECEIVERDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
+	cd  $(MANAPIDIR) && $(MAKE) slsMultiReceiver
 	@echo ""
 	@echo "#######################################"
 	@echo "# Back in slsDetectorPackage Makefile #"
@@ -151,6 +153,7 @@ clean:
 	cd $(DOCDIR) && rm -rf * 
 	rm -rf 	slsDetectorPackageDocs;
 	rm -rf $(DETAILDOC)
+	rm -rf $(MANAPIDIR)/slsMultiReceiver
 
 
 #install_lib: 

README.md

@@ -2,12 +2,12 @@
 Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
 
 ### Binaries
-Documentation to obtain the binaries via the conda package is available [here.](https://github.com/slsdetectorgroup/sls_detector_software)
+Documentation to obtain the binaries via the conda package is available for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
 
 ### Source code
 One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
 ```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 3.1.0
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Setup dependencies 
@@ -19,7 +19,7 @@ Requirements: Qt 4.8 and Qwt 6.0
 ```
 If either of them does not exist, the GUI client will not be built.
 
-* Calibration wizards<br>
+* Advanced user Calibration wizards<br>
 Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
@@ -43,6 +43,10 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
  * -r: Build/Rebuilds only receiver<br>
  * -g: Build/Rebuilds only gui<br>
  * -j: Number of threads to compile through<br>
+ * -e: Debug mode
+ 
+Basic Option:
+./cmk.sh -b
  
 For only make:
 ./cmk.sh
@@ -71,17 +75,17 @@ Use cmake to create out-of-source builds, by creating a build folder parallel to
     $ cd ..
     $ mkdir slsDetectorPackage-build
     $ cd slsDetectorPackage-build
-    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=OFF 
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_HDF5=OFF 
     $ make
 ```
 
 Use the following as an example to compile statically and using specific hdf5 folder
 ```
-    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=ON
+    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_HDF5=ON
  ```  
 After compiling, the libraries and executables will be found at `bin` directory
 ```
     $ ls bin/
     gui_client  libSlsDetector.a  libSlsDetector.so  libSlsReceiver.a  libSlsReceiver.so
-    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver
+    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver slsMultiReceiver
 ```

RELEASE.txt

@@ -1,31 +1,215 @@
-SLS Detector Package 3.1.1 released on 2018-03-20
-=================================================
+SLS Detector Package 4.2.0 released on 09.04.2020 (Minor Release)
+===================================================================
+
+
+This document describes the differences between 4.2.0 and 4.1.1 releases.   
+    
+    CONTENTS
+    --------
+    1.  Topics Concerning
+    2.  New Features
+    3.  Resolved Issues
+    4.  Firmware Requirements
+    5.  Download, Documentation & Support
     
 
 
-INTRODUCTION
+1. Topics Concerning
+====================
 
-This document describes the differences between 3.1.0 into 3.1.0 releases.
+    - (Eiger) Additional status: Transmitting
+    - (Eiger) Default vcal dac value
+    - (Eiger) Default readout mode
+    - (Eiger) Dynamic range change effect on clock divider
+    - (Eiger) Deactivate a module
+    - (Eiger) Setting all trimbits argument check
+    - (Receiver) performance (memory allocation and alignment, file buffering)
+    - (Receiver) Eiger: Different rx_fifodepth defaults
+    - (Receiver) rx_fifodepth has a higher range
+    - (Receiver) subperiod in master file
+    - (Package) Removed warnings including memory overlap copy
+    - (Users) Added setflippeddatax to users class
+    - (Zmq) Client data streaming fix (Client data call back)
+
+    Compared to 4.1.1, 
+        - no firmware update required for this release
+        - eiger on-board detector server update required for this release
 
 
-Topics Concerning
-==================
-	Jungfrau adcphase
-	Eiger in 10 GbE mode
 
-
-Resolved Issues
+2. New Features
 ===============
 
-	Detector Server and Client
-	--------------------------
-	1. 	(Jungfrau) Bug fix: Same adc phase given to the PLL will still shift
-		adc by one step. One can now give same adc phase repeatedly.
+    Receiver
+    --------
+    1.  Memory in receiver is now byte aligned and write to every page
+        at memory allocation to ensure complete memory allocated right
+        from start. Removed file buffering when writing to file. Replaced
+        pausing on keepRunning variable with semaphore to reduce cpu
+        load.
 
-		Updated Command Line Manual for adcphase and clkdivider.
-		
-	2.	(Eiger) Bug Fix: This bug was introduced in 3.1.0 release.
-		In 10GbE mode, if "detectorip" is before "tengiga", the detector still
-		used the 1G IP (DHCP IP). This is fixed in this release.
+    2.  (Eiger) Default rx_fifodepth for 32 bit mode is 100, but 1000
+        for other modes. Changing dynamic range will now change bit mode to 
+        their defaults.
 
 
+    Client
+    ------
+    1.  Added setflippeddatax to users class.
+
+
+    Detector Server (Eiger)
+    -----------------------
+    1.  Transmitting Status: After acquiring, if the detector is still 
+        streaming out data, then the status is Trasnmitting 
+        (command line: 'data'). Only after this process, will it become idle. 
+        Previously, sls_detector_acquire waited for end of data streaming 
+        before returning. It will continue to do so.
+
+
+
+3. Resolved Issues
+==================          
+
+    Detector Server (Eiger)
+    -----------------------
+    1.  Vcal dac set to 0 at on-board detector server start up to
+        reduce noise.
+
+    2.  Default Readout mode set to Parallel instead of Non parallel.
+
+    3.  Dynamic range  4, 8 or 16 changes the clock divider to full speed, 
+        whereas dynamic range of 32 still changes the clock divider to 
+        quarter speed. So, default is dynamic range of 16 and full speed 
+	at detector server start up.
+
+    4.  Setting activate to 0 sent to both control and stop server.
+        So, deactivate a module can be done even if FEB communication fails.
+        Restarting the server will activate the module again.
+
+    5.  Verification included for input of setting all trimbits values.
+        Valid input is 0 - 63.
+
+
+    Receiver
+    --------
+    1.  Earlier, setting rx_fifodepth to a high value would set to 
+        a lower value, printing this low value to console, 
+        but not giving an error. Memory allocated can now take in 64 bits.
+    
+    2.  Modifying subexptime now also updates subperiod in master file.
+        Also, the print for subperiod name to console is corrected.
+
+
+    Package
+    -------
+    1.  Many warnings have been fixed, including those with overlapping 
+        memory copies for source and destination. 
+
+
+    Client
+    ------
+    1.  Each time client data streaming was enabled to receive, it
+        creates zmq sockets without checking if they were already created.
+        This is fixed now.
+    
+    
+    
+4. Firmware Requirements
+========================
+        
+        Gotthard
+        ========   
+        Minimum compatible version  : 11.01.2013
+        Latest compatible version   : 08.02.2018 (50um and 25um Master)
+                                      09.02.2018 (25 um Slave) 
+        Eiger
+        =====  
+        Minimum compatible version  : 24
+        Latest compatible version   : 24
+        
+        Jungfrau
+        ========       
+        Minimum compatible version  : 26.02.2018
+        Latest compatible version   : 06.12.2018
+
+        
+        Detector Upgrade
+        ================
+        Gotthard    Cannot be upgraded remotely. Requires programming via USB blaster
+        Eiger       Can be upgraded remotely via bit files
+        Jungfrau    Can be upgraded remotely using sls_detector_put programfpga <pof>
+        
+        Instructions available at
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/GOTTHARD_Firmware.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/EIGER_Firmware.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/JUNGFRAU_Firmware.html
+
+         
+    Please refer to the link below for more details on the firmware versions.
+    https://www.psi.ch/en/detectors/firmware
+    
+    
+        
+5. Download, Documentation & Support
+====================================
+
+    Download
+    --------
+    
+    The Source Code (Default C++ API):
+         https://github.com/slsdetectorgroup/slsDetectorPackage
+         
+    The Conda Lib Package:
+        https://github.com/slsdetectorgroup/sls_detector_lib
+        
+    The Conda GUI Package:
+        https://github.com/slsdetectorgroup/sls_detector_gui    
+        
+    The Python Interface (including the package):
+        https://github.com/slsdetectorgroup/sls_detector
+    
+    
+    Documentation
+    -------------
+    
+    Manual (HTML & PDF):
+        https://www.psi.ch/en/detectors/documentation
+        slsDetectorPackage/manual/docs/
+        
+    Command Line Documentation:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorClientDocs/index.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/pdf/slsDetectorClientDocs.pdf
+
+        manual/docs/html/slsDetectorClientDocs/index.html
+        manual/docs/pdf/slsDetectorClientDocs.pdf
+        
+    C++ API Documentation:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorUsersDocs/index.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/pdf/slsDetectorUsersDocs.pdf
+
+        manual/docs/html/slsDetectorUsersDocs/index.html
+        manual/docs/pdf/slsDetectorUsersDocs.pdf
+        
+    C++ API Example:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/exampleCode/slsDetectorUsersExample/index.html
+
+        manual/manual-api/mainClient.cpp
+        manual/manual-api/mainReceiver.cpp
+        
+    Python API Documentation:
+        https://slsdetectorgroup.github.io/sls_detector/
+
+    TroubleShotting:
+        https://www.psi.ch/en/detectors/troubleshooting
+        
+    Further Documentation:
+        https://www.psi.ch/en/detectors/users-support
+        
+    
+    Support
+    -------
+
+        dhanya.thattil@psi.ch
+        erik.frojdh@psi.ch
+        anna.bergamaschi@psi.ch

cleansharedmemory.sh

@@ -1 +1 @@
-for i in seq `ipcs -m | cut -d ' ' -f1`; do ipcrm -M $i; done;
+rm /dev/shm/slsDetectorPackage*;

cmk.sh

@@ -6,6 +6,7 @@ COMPILERTHREADS=0
 TEXTCLIENT=0
 RECEIVER=0
 GUI=0
+DEBUG=0
 
 
 CLEAN=0
@@ -24,6 +25,7 @@ Usage: $0 [-c] [-b] [-h] [-d <HDF5 directory>] [-j]
  -r: Build/Rebuilds only receiver
  -g: Build/Rebuilds only gui
  -j: Number of threads to compile through
+ -e: Debug mode
  
 For only make:
 ./cmk.sh
@@ -53,11 +55,12 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bchd:j:trg" opt ; do
+while getopts ":bchd:j:trge" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
 		REBUILD=1
+		CLEAN=1
 		;;
 	c) 
 		echo "Clean Required"
@@ -67,6 +70,7 @@ while getopts ":bchd:j:trg" opt ; do
 		echo "Building of CMake files with HDF5 option Required"
 		HDF5=1
 		REBUILD=1
+		CLEAN=1
 		;;
 	d) 
 		echo "New HDF5 directory: $OPTARG" 
@@ -80,16 +84,23 @@ while getopts ":bchd:j:trg" opt ; do
     	echo "Compiling Options: Text Client" 
 		TEXTCLIENT=1
 		REBUILD=1
+		CLEAN=1
 		;;      
 	r) 
 		echo "Compiling Options: Receiver" 
 		RECEIVER=1
 		REBUILD=1
+		CLEAN=1
 		;;      
 	g) 
 		echo "Compiling Options: GUI" 
 		GUI=1
 		REBUILD=1
+		CLEAN=1
+		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
 		;;    
     \?)
      	echo "Invalid option: -$OPTARG" 
@@ -110,20 +121,20 @@ done
 
 
 if [ $TEXTCLIENT -eq 0 ] && [ $RECEIVER -eq 0 ]  && [ $GUI -eq 0 ]; then
-       CMAKE_POST+=" -DUSE_TEXTCLIENT=ON -DUSE_RECEIVER=ON -DUSE_GUI=ON "
+       CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=ON -DSLS_USE_GUI=ON "
        echo "Compile Option: TextClient, Receiver and GUI"
 else 
        if [ $TEXTCLIENT -eq 1 ]; then
-              CMAKE_POST+=" -DUSE_TEXTCLIENT=ON "
+              CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON "
                echo "Compile Option: TextClient"
        fi
        if [ $RECEIVER -eq 1 ]; then
-               CMAKE_POST+=" -DUSE_RECEIVER=ON "
+               CMAKE_POST+=" -DSLS_USE_RECEIVER=ON "
                echo "Compile Option: Receiver"
        fi
                                
        if [ $GUI -eq 1 ]; then
-               CMAKE_POST+=" -DUSE_GUI=ON "
+               CMAKE_POST+=" -DSLS_USE_GUI=ON "
                echo "Compile Option: GUI"
        fi
 fi
@@ -145,15 +156,20 @@ else
 	fi
 fi
 
-CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+#Debug
+if [ $DEBUG -eq 1 ]; then
+	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+	echo "Debug Option enabled"
+fi 
+
 
 #hdf5 rebuild
 if [ $HDF5 -eq 1 ]; then
 	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
-	CMAKE_POST+=" -DUSE_HDF5=ON "
+	CMAKE_POST+=" -DSLS_USE_HDF5=ON "
 #normal mode rebuild
 else
-	CMAKE_POST+=" -DUSE_HDF5=OFF "
+	CMAKE_POST+=" -DSLS_USE_HDF5=OFF "
 fi
 
 

examples/gotthard.config

@@ -3,12 +3,8 @@ hostname bchip007
 #0:port 1952
 #0:stopport 1953
 #0:rx_tcpport 1956 must also have this in receiver config file
-0:settingsdir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
 0:angdir 1.000000
 0:moveflag 0.000000
-0:lock 0
-0:caldir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
-0:ffdir /home/l_maliakal_d
 0:extsig:0 off
 #0:detectorip 129.129.202.9
 0:detectormac 00:aa:bb:cc:dd:ee
@@ -20,7 +16,6 @@ hostname bchip007
 master -1
 sync none
 outdir /bigRAID/datadir_gotthard/rec_test_data
-ffdir /home/l_maliakal_d
 headerbefore none
 headerafter none
 headerbeforepar none
@@ -29,4 +24,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

examples/jungfrau.config

@@ -1,18 +1,15 @@
 hostname bchip038+
 
-settingsdir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-caldir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-lock 0
-
 0:rx_udpport 50004
 0:rx_udpip 10.1.1.100
 0:detectorip 10.1.1.10
-
 rx_hostname pcmoench01
 
 powerchip 1
-timing auto
+
+#extsig:0 trigger_in_rising_edge
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/jungfrau_two.config

@@ -1,11 +1,6 @@
 detsizechan 1024 1024
 hostname bchip048+bchip052+
 
-settingsdir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-caldir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-lock 0
-
-
 0:rx_udpport 50004
 0:rx_udpip 10.1.1.100
 0:rx_udpmac F4:52:14:2F:32:00
@@ -22,9 +17,9 @@ lock 0
 rx_hostname pcmoench01
 
 powerchip 1
-extsig:0 trigger_in_rising_edge
-timing auto
+#extsig:0 trigger_in_rising_edge
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/two_gotthard.config

@@ -8,13 +8,11 @@ hostname bchip007+bchip009+
 #0:port 1952
 #0:stopport 1953
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-0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
+
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 #0:detectormac 00:aa:bb:cc:dd:ee
 #0:rx_udpport 50001
@@ -28,13 +26,11 @@ hostname bchip007+bchip009+
 #1:port 1952
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@@ -56,4 +52,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
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 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
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 Thattil Dhanya
-2018-03-12
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+$key = q/_6;MSF=1.6;AAT/;
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-$key = q/pm;MSF=1.6;AAT/;
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+$key = q/pm;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$\pm$">|; 
+
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manual/docs/html/angularCalibrationHowTo/index.html

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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/internals.pl

@@ -1,4 +1,4 @@
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manual/docs/html/angularCalibrationHowTo/labels.pl

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manual/docs/html/angularCalibrationHowTo/node1.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -55,7 +55,7 @@ Introduction</A>
 
 <P>
 In order to convert from strip number to 2<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img1.png"
  ALT="$\theta$">-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). 
 <BR>
@@ -107,7 +107,7 @@ where the parameters <IMG
  WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
  SRC="img7.png"
  ALT="$C_{center}^{i}$"> is the central channel  and <IMG
- WIDTH="22" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
  SRC="img8.png"
  ALT="$R^i$"> is the distance of the module <IMG
  WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
@@ -121,7 +121,7 @@ Finally, the global offset of the detector system is precisely determined by ref
 
 <P>
 The same function of equation&nbsp;<A HREF="#eq:angcal">1</A>, with the parameters obtained from the calibration, is used in order to convert from channel number to 2<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img1.png"
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@@ -180,7 +180,7 @@ These results show that  the angular calibration allows a resolution in determin
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -211,7 +211,7 @@ Acquisition GUI window to setup the motor position scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
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@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -180,7 +180,7 @@ After fitting all modules you can click on the <I>Write Angular Calibration</I>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node4.html

@@ -1,6 +1,6 @@
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@@ -62,7 +62,7 @@ while for the GUI the file name should be specified in the configuration file (w
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
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@@ -1,6 +1,6 @@
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 </H1>
  <STRONG>Angular calibration wizard manual</STRONG><P>
 This document was generated using the
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 Copyright &#169; 1993, 1994, 1995, 1996,
 <A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>, 
@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
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 <P>
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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
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manual/docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

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 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
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 <BR><HR>
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 Thattil Dhanya
-2018-03-12
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manual/docs/html/energyCalibrationHowTo/images.pl

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manual/docs/html/energyCalibrationHowTo/index.html

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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/energyCalibrationHowTo/internals.pl

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manual/docs/html/energyCalibrationHowTo/labels.pl

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manual/docs/html/energyCalibrationHowTo/node1.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -78,21 +78,21 @@ The thick solid line represents the physical curve which also takes into account
 
 <P>
 The intrinsic noise on the electronic signal  is defined by the Equivalent Noise Charge (<IMG
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  SRC="img3.png"
  ALT="$ENC$"> describes noise in terms of the charge at the detector input needed to create the same output at the end of the analog chain and is normally expressed in electrons. For silicon sensors, it can be converted into energy units by considering 1&nbsp;<IMG
  WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
  SRC="img12.png"
  ALT="$e^-$">=3.6&nbsp;eV.
 The value of the <IMG
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+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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 The resulting electronic signal spectrum is then  given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
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  SRC="img3.png"
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 The S-curve for a monochromatic radiation beam is well described by a Gaussian cumulative distribution <IMG
@@ -204,10 +204,10 @@ Moreover, setting the threshold too close to the energy of the fluorescent light
 The comparator threshold is given by a global level which can be set on a module basis and adds to a component which is individually adjustable for each channel. In order to optimize the uniformity of the detector response it is important to properly adjust the threshold for all channels. 
 <BR>
 Since both the signal amplification stages and the comparator  are linear, it is necessary to calibrate the detector offset <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img25.png"
  ALT="$O$"> and gain <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img26.png"
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  WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
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  WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
  SRC="img2.png"
  ALT="$N_0$">=10000 is the number of photons absorbed by the detector during the acquisition time. The dashed line represents the curve in an ideal case without electronic noise and charge sharing, the solid thin line with noise  <IMG
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+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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  ALT="$ENC$">=1&nbsp;keV but without charge sharing and the solid thick line is the physical case with noise and <IMG
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+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img4.png"
  ALT="$CS=$">22&nbsp;% charge sharing. <IMG
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@@ -377,7 +377,7 @@ Median of the number of counts as a function of the threshold for X-rays of 12.5
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
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@@ -180,7 +180,7 @@ Acquisition GUI window to setup the threshold scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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 </HTML>

manual/docs/html/energyCalibrationHowTo/node3.html

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@@ -107,7 +107,7 @@ Once you have uploaded at least 2 energies, you will be allowed to  <I>proceed t
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 7:</STRONG>
 Window to add energies to the calibration.</CAPTION>
 <TR><TD><IMG
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+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
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@@ -153,7 +153,7 @@ The button <I>Finished</I> will be enebled only once the calibration files have
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 8:</STRONG>
 Window to calibrate the modules.</CAPTION>
 <TR><TD><IMG
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+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
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 </TABLE>
@@ -184,7 +184,7 @@ Window to calibrate the modules.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node4.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
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 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -68,7 +68,7 @@ By reloading the default detector settings, the calibration coefficients will be
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node5.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -48,7 +48,7 @@ About this document ...</A>
 </H1>
  <STRONG>Energy calibration wizard manual</STRONG><P>
 This document was generated using the
-<A HREF="http://www.latex2html.org/"><STRONG>LaTeX</STRONG>2<tt>HTML</tt></A> translator Version 2008 (1.71)
+<A HREF="http://www.latex2html.org/"><STRONG>LaTeX</STRONG>2<tt>HTML</tt></A> translator Version 2012 (1.2)
 <P>
 Copyright &#169; 1993, 1994, 1995, 1996,
 <A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>, 
@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 energyCalibrationHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2018-03-12
+The translation was initiated by Thattil Dhanya on 2018-09-28
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientDocs/acquisition.html

@@ -1,85 +1,98 @@
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-
-
-<h1><a class="anchor" id="acquisition">Acquition commands </a></h1><p>Commands to control the acquisition</p>
-<ul>
-<li><b>acquire</b> blocking acquisition (like calling sls_detector_acquire). Starts receiver and detector, writes and processes the data, stops detector. Only get! <code>Returns</code> (string)<code>"acquire unsuccessful"</code> if fails, else "" for MYTHEN, <code>"Acquired (int)"</code> for others, where int is number of frames caught.</li>
-</ul>
-<ul>
-<li><b> busy i</b> sets/gets acquiring flag. <code>1</code> the acquisition is active, <code>0</code> otherwise. Acquire command will set this flag to 1 at the beginning and to 0 at the end. Use this to clear flag if acquisition terminated unexpectedly. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
-<li><b> status [s] </b> starts or stops acquisition in detector in non blocking mode. When using stop acquisition and if acquisition is done, it will restream the stop packet from receiver (if data streaming in receiver is on). <code>s:</code> [<code>start</code>, <code>stop</code>]. <code>Returns</code> the detector status: [<code>running</code>, <code>error</code>, <code>transmitting</code>, <code>finished</code>, <code>waiting</code>, <code>idle</code>]. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>data</b> gets all data from the detector (if any) processes them and writes them to file according to the preferences already setup (MYTHEN only). Only get!</li>
-</ul>
-<ul>
-<li><b>frame</b> gets a single frame from the detector (if any) processes it and writes it to file according to the preferences already setup (MYTHEN only). Only get!</li>
-</ul>
-<ul>
-<li><b>readctr </b> Reads the counters from the detector memory (analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
-</ul>
-<ul>
-<li><b>resetctr i </b> Resets counter in detector, restarts acquisition if i=1(analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
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-<ul>
-<li><b>resmat i </b> sets/resets counter bit in detector.gets the counter bit in detector ???? </li>
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+<div class="textblock"><p>Commands to control the acquisition</p>
+<ul>
+<li><b>acquire</b> blocking acquisition (like calling sls_detector_acquire). Starts receiver and detector, writes and processes the data, stops detector. Only get! <code>Returns</code> (string)<code>"acquire unsuccessful"</code> if fails, else "" for MYTHEN, <code>"Acquired (int)"</code> for others, where int is number of frames caught.</li>
+<li><b> busy i</b> sets/gets acquiring flag. <code>1</code> the acquisition is active, <code>0</code> otherwise. Acquire command will set this flag to 1 at the beginning and to 0 at the end. Use this to clear flag if acquisition terminated unexpectedly. <code>Returns</code> <code></code>(int)</li>
+<li><b> status [s] </b> starts or stops acquisition in detector in non blocking mode. When using stop acquisition and if acquisition is done, it will restream the stop packet from receiver (if data streaming in receiver is on). Eiger can also provide an internal software trigger. <code>s:</code> [<code>start</code>, <code>stop</code>, <code>trigger(EIGER only)</code>]. <code>Returns</code> the detector status: [<code>running</code>, <code>error</code>, <code>transmitting</code>, <code>finished</code>, <code>waiting</code>, <code>idle</code>]. <code>Returns</code> <code></code>(string)</li>
+<li><b>data</b> gets all data from the detector (if any) processes them and writes them to file according to the preferences already setup (MYTHEN only). Only get!</li>
+<li><b>frame</b> gets a single frame from the detector (if any) processes it and writes it to file according to the preferences already setup (MYTHEN only). Only get!</li>
+<li><b>readctr </b> Reads the counters from the detector memory (analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
+<li><b>resetctr i </b> Resets counter in detector, restarts acquisition if i=1(analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
+<li><b>resmat i </b> sets/resets counter bit in detector.gets the counter bit in detector ???? </li>
+</ul>
+</div></div><!-- contents -->
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manual/docs/html/slsDetectorClientDocs/actions.html

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-</div>
-<div class="contents">
-
-
-<h1><a class="anchor" id="actions">Actions </a></h1><p>Commands to define scripts to be executed during the acquisition flow</p>
-<ul>
-<li><b>positions [n [p0..pn-1]]</b> sets/gets number of angular position and positions to be acquired.. <code>Returns</code> <code></code>(int int..) n [p0..pn-1]</li>
-</ul>
-<ul>
-<li><b>startscript [s]</b> sets/gets the script to be executed at the beginning of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>startscriptpar [s]</b> sets/gets a string to be passed as a parameter to the startscript. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>stopscript [s]</b> sets/gets the script to be executed at the end of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>stopscriptpar [s]</b> sets/gets a string to be passed as a parameter to the stopscript. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptbefore [s]</b> sets/gets the script to be executed before starting the detector every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptbeforepar [s]</b> sets/gets a string to be passed as a parameter to the scriptbefore. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptafter [s]</b> sets/gets the script to be executed after the detector has finished every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptafterpar [s]</b> sets/gets a string to be passed as a parameter to the scriptafter. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerafter [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerbefore [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerbeforepar [s]</b> sets/gets a string to be passed as a parameter to the headerbefore script. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerafterpar [s]</b> sets/gets a string to be passed as a parameter to the headerafter script. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>enacallog [i]</b> enables/disables logging of the parameters necessary for the energy calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
-<li><b>angcallog [i]</b> enables/disables logging of the parameters necessary for the angular calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
-<li><b>scan0script [s]</b> sets/gets the script to be executed for the scan 0 level. <code>none</code> unsets.</li>
-</ul>
-<ul>
-<li><b>scan0par [s]</b> sets/gets a string to be passed as a parameter to the scan0script</li>
-</ul>
-<ul>
-<li><b>scan0prec [i]</b> sets/gets number of digits to be used for the scan0 variable in the file name.</li>
-</ul>
-<ul>
-<li><b>scan0steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan0 level and their values (float).</li>
-</ul>
-<ul>
-<li><b>scan0range [smin smax sstep]</b> sets scan0 min, max and step, returns the number of steps and their values as scan0steps.</li>
-</ul>
-<ul>
-<li><b>scan1script [s]</b> sets/gets the script to be executed for the scan1 level. <code>none</code> unsets.</li>
-</ul>
-<ul>
-<li><b>scan1par [s]</b> sets/gets a string to be passed as a parameter to the scan1script</li>
-</ul>
-<ul>
-<li><b>scan1prec [i]</b> sets/gets number of digits to be used for the scan1 variable in the file name.</li>
-</ul>
-<ul>
-<li><b>scan1steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan1 level and their values (float).</li>
-</ul>
-<ul>
-<li><b>scan1range [smin smax sstep]</b> sets scan1 min, max and step, returns the number of steps and their values as scan1steps. </li>
-</ul>
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-<!--- window showing the filter options -->
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+<div class="textblock"><p>Commands to define scripts to be executed during the acquisition flow</p>
+<ul>
+<li><b>positions [n [p0..pn-1]]</b> sets/gets number of angular position and positions to be acquired.. <code>Returns</code> <code></code>(int int..) n [p0..pn-1]</li>
+<li><b>startscript [s]</b> sets/gets the script to be executed at the beginning of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>startscriptpar [s]</b> sets/gets a string to be passed as a parameter to the startscript. <code>Returns</code> <code></code>(string)</li>
+<li><b>stopscript [s]</b> sets/gets the script to be executed at the end of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>stopscriptpar [s]</b> sets/gets a string to be passed as a parameter to the stopscript. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptbefore [s]</b> sets/gets the script to be executed before starting the detector every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptbeforepar [s]</b> sets/gets a string to be passed as a parameter to the scriptbefore. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptafter [s]</b> sets/gets the script to be executed after the detector has finished every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptafterpar [s]</b> sets/gets a string to be passed as a parameter to the scriptafter. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerafter [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerbefore [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerbeforepar [s]</b> sets/gets a string to be passed as a parameter to the headerbefore script. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerafterpar [s]</b> sets/gets a string to be passed as a parameter to the headerafter script. <code>Returns</code> <code></code>(string)</li>
+<li><b>enacallog [i]</b> enables/disables logging of the parameters necessary for the energy calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
+<li><b>angcallog [i]</b> enables/disables logging of the parameters necessary for the angular calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
+<li><b>scan0script [s]</b> sets/gets the script to be executed for the scan 0 level. <code>none</code> unsets.</li>
+<li><b>scan0par [s]</b> sets/gets a string to be passed as a parameter to the scan0script</li>
+<li><b>scan0prec [i]</b> sets/gets number of digits to be used for the scan0 variable in the file name.</li>
+<li><b>scan0steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan0 level and their values (float).</li>
+<li><b>scan0range [smin smax sstep]</b> sets scan0 min, max and step, returns the number of steps and their values as scan0steps.</li>
+<li><b>scan1script [s]</b> sets/gets the script to be executed for the scan1 level. <code>none</code> unsets.</li>
+<li><b>scan1par [s]</b> sets/gets a string to be passed as a parameter to the scan1script</li>
+<li><b>scan1prec [i]</b> sets/gets number of digits to be used for the scan1 variable in the file name.</li>
+<li><b>scan1steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan1 level and their values (float).</li>
+<li><b>scan1range [smin smax sstep]</b> sets scan1 min, max and step, returns the number of steps and their values as scan1steps. </li>
+</ul>
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manual/docs/html/slsDetectorClientDocs/advanced.html

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manual/docs/html/slsDetectorClientDocs/config.html

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+</div><!--header-->
 <div class="contents">
-
-
-<h1><a class="anchor" id="config">Configuration commands </a></h1><p>Commands to configure the detector. these commands are often left to the configuration file.</p>
+<div class="textblock"><p>Commands to configure the detector. these commands are often left to the configuration file.</p>
 <ul>
 <li><a class="el" href="config.html#configstructure">Data Structure</a>: commands to configure detector data structure</li>
 <li><a class="el" href="config.html#configstatus">Status</a>: commands to configure detector status</li>
@@ -49,210 +87,109 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <li><a class="el" href="config.html#configspeed">Speed</a>: commands to configure speed of detector</li>
 <li><a class="el" href="config.html#configsettings">Detector Parameters</a>: commands to configure/retrieve configuration of detector</li>
 </ul>
-<h2><a class="anchor" id="configstructure">
-Data Structure</a></h2>
+<h1><a class="anchor" id="configstructure"></a>
+Data Structure</h1>
 <p>commands to configure detector data structure</p>
 <ul>
 <li><b>free</b> Free shared memory on the control PC</li>
-</ul>
-<ul>
-<li><b>add</b> Adds a detector at the end of the multi-detector structure. <code>put</code> argument is the hostname or IP adress. Returns the chained list of detector hostnames.</li>
-</ul>
-<ul>
-<li><b>remove i</b> Removes controller <code>i</code> from the multi-detector structure. Can be used for partial readout of the detector.</li>
-</ul>
-<ul>
-<li><b>type</b> Sets/gets detector type. <code>Returns</code> <code></code>(string). Normally not used. Using hostname is enough.</li>
-</ul>
-<ul>
-<li><b>hostname</b> <code>put</code> adds the hostname (ot IP adress) at the end of the multi-detector structure. If used for a single controlled (i:) replaces the current hostname. Returns the list of the hostnames of the multi-detector structure. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>id[:i]</b> Returns the id of the detector structure. i is the detector position in a multi detector system. If used a <code>put</code>, configures the id of the detector structure. i is the detector position in a multi detector system and l is the id of the detector to be added.</li>
-</ul>
-<ul>
+<li><b>hostname</b> <code>put</code> frees shared memory and sets the hostname (or IP adress). Only allowed at multi detector level. <code>Returns</code> the list of the hostnames of the multi-detector structure. <code></code>(string)</li>
+<li><b>add</b> appends a hostname (or IP address) at the end of the multi-detector structure. Only allowed at multi detector level. Cannot get. <code>Returns</code> the current list of detector hostnames. <code></code>(string)</li>
+<li><b>replace</b> <code>Sets</code> the hostname (or IP adress) for a single detector. Only allowed at single detector level. Cannot get. <code>Returns</code> the hostnames for that detector <code></code>(string)</li>
+<li><b>user</b> <code>Returns</code> user details from shared memory. Only allowed at multi detector level. Cannot put. <code></code>(string)</li>
 <li><b>master i</b> <code>put</code> sets the position of the master of the acquisition (-1 if none). Returns the position of the master of the detector structure (-1 if none).</li>
-</ul>
-<ul>
 <li><b>sync</b> Sets/gets the synchronization mode of the detectors in the multi-detector structure. Can be: <code>none</code>, <code>gating</code>, <code>trigger</code>, <code>complementary</code>. Mainly used by MYTHEN/GOTTHARD.</li>
 </ul>
-<h2><a class="anchor" id="configstatus">
-Status</a></h2>
+<h1><a class="anchor" id="configstatus"></a>
+Status</h1>
 <p>commands to configure detector status</p>
 <ul>
 <li><b>online [i]</b> sets the detector in online (1) or offline (0) mode. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>checkonline</b> returns the hostnames of all detectors without connecting to them. <code>Returns</code> (string) "All online" or "[list of offline hostnames] : Not online".</li>
+<li><b>activate [b] [p]</b> Activates/Deactivates the detector. <code>b</code> is 1 for activate, 0 for deactivate. Deactivated detector does not send data. <code>p</code> is optional and can be padding (default) or nonpadding for receivers for deactivated detectors. Used for EIGER only. <code>Returns</code> <code></code>(int) (string)</li>
 </ul>
-<ul>
-<li><b>activate</b> Activates/Deactivates the detector. Deactivated detector does not send data. Used for EIGER only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<h2><a class="anchor" id="configsize">
-Data Size</a></h2>
+<h1><a class="anchor" id="configsize"></a>
+Data Size</h1>
 <p>commands to configure detector data size</p>
 <ul>
 <li><b>nmod [i]</b> sets/gets the number of modules of the detector. Used for MYTHEN only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>maxmod </b> Gets the maximum number of modules of the detector. Used for MYTHEN only. Cannot put! <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>dr [i]</b> sets/gets the dynamic range of detector. Mythen [4,8,16,24]. Eiger [4,8,16,32]. Others cannot put! <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>roi [i] [xmin] [xmax] [ymin] [ymax] </b> sets region of interest of the detector, where i is number of rois;i=0 to clear rois. Used for GOTTHARD only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>detsizechan [xmax] [ymax]</b> sets the maximum number of channels in each dimension for complete detector set; -1 is no limit. Use for multi-detector system as first command in config file. <code>Returns</code> <code></code>("int int")</li>
-</ul>
-<ul>
 <li><b>roimask [i]</b> ?? <code>Returns</code> <code></code>(int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>flippeddatax [i]</b> enables/disables data being flipped across x axis. 1 enables, 0 disables. Used for EIGER only. 1 for bottom half-module, 0 for top-half module. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>tengiga [i]</b> enables/disables 10GbE in system (detector &amp; receiver). 1 enabled 10GbE, 0 enables 1GbE. Used in EIGER only. <code>Returns</code> <code></code>(int)</li>
+<li><b>gappixels [i]</b> enables/disables gap pixels in system (detector &amp; receiver). 1 sets, 0 unsets. Used in EIGER only and only in multi detector level command. <code>Returns</code> <code></code>(int)</li>
 </ul>
-<h2><a class="anchor" id="configflags">
-Flags</a></h2>
+<h1><a class="anchor" id="configflags"></a>
+Flags</h1>
 <p>commands to configure detector flags</p>
 <ul>
-<li><b>flags [flag]</b> sets/gets the readout flags to mode. Options: none, storeinram, tot, continous, parallel, nonparallel, safe, digital, analog_digital, unknown. Used for MYTHEN and EIGER only. <code>Returns</code> <code></code>(string). put takes one string and <code>returns</code> concatenation of all active flags separated by spaces.</li>
-</ul>
-<ul>
+<li><b>flags [flag]</b> sets/gets the readout flags to mode. Options: none, storeinram, tot, continous, parallel, nonparallel, safe, digital, analog_digital, overflow, nooverflow, unknown. Used for MYTHEN and EIGER only. <code>Returns</code> <code></code>(string). put takes one string and <code>returns</code> concatenation of all active flags separated by spaces.</li>
 <li><b>extsig:[i] [flag]</b> sets/gets the mode of the external signal i. Options: <code>off</code>, <code>gate_in_active_high</code>, <code>gate_in_active_low</code>, <code>trigger_in_rising_edge</code>, <code>trigger_in_falling_edge</code>, <code>ro_trigger_in_rising_edge</code>, <code>ro_trigger_in_falling_edge</code>, <code>gate_out_active_high</code>, <code>gate_out_active_low</code>, <code>trigger_out_rising_edge</code>, <code>trigger_out_falling_edge</code>, <code>ro_trigger_out_rising_edge</code>, <code>ro_trigger_out_falling_edge</code>. <br/>
  Used in MYTHEN, GOTTHARD, PROPIX only. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
 <li><b>programfpga [file]</b> programs the FPGA with file f (with .pof extension). Used for JUNGFRAU, MOENCH only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
-</ul>
-<ul>
 <li><b>resetfpga [f]</b> resets FPGA, where f can be any value. Used for JUNGFRAU only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
 </ul>
-<h2><a class="anchor" id="configchip">
-Chip</a></h2>
+<h1><a class="anchor" id="configchip"></a>
+Chip</h1>
 <p>commands to configure chip of the detector</p>
 <ul>
 <li><b>powerchip [i]</b> Powers on/off the chip. 1 powers on, 0 powers off. Can also get the power status. Used for JUNGFRAU only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>led [i]</b> sets/gets the led status. 1 on, 0 off. Used for MOENCH only ?? <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>auto_comp_disable i </b> Currently not implemented. this mode disables the on-chip gain switching comparator automatically after 93.75% of exposure time (only for longer than 100us). 1 enables mode, 0 disables mode. By default, mode is disabled (comparator is enabled throughout). (JUNGFRAU only). <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>pulse [n] [x] [y]</b> pulses pixel at coordinates (x,y) n number of times. Used in EIGER only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
-</ul>
-<ul>
 <li><b>pulsenmove [n] [x] [y]</b> pulses pixel n number of times and moves relatively by x value (x axis) and y value(y axis). Used in EIGER only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
-</ul>
-<ul>
 <li><b>pulsechip [n]</b>pulses chip n number of times, while n=-1 will reset it to normal mode. Used in EIGER only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
 </ul>
-<h2><a class="anchor" id="configversions">
-Versions</a></h2>
+<h1><a class="anchor" id="configversions"></a>
+Versions</h1>
 <p>Commands to check versions of each subsystem</p>
 <ul>
+<li><b>checkdetversion</b> Checks the version compatibility with detector server (if hostname is in shared memory). Only get! Only for Eiger, Jungfrau &amp; Gotthard. <code>Returns</code> <code></code>("compatible", "incompatible")</li>
+<li><b>checkrecversion</b> Checks the version compatibility with receiver server (if rx_hostname is in shared memory). Only get! Only for Eiger, Jungfrau &amp; Gotthard. <code>Returns</code> <code></code>("compatible", "incompatible")</li>
 <li><b>moduleversion:[i]</b> Gets the firmware version of module i. Used for MYTHEN only. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal or "undefined module number"</li>
-</ul>
-<ul>
 <li><b>detectornumber</b> Gets the serial number or MAC of detector. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>modulenumber:[i]</b> Gets the serial number of module i. Used for MYTHEN only. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal or "undefined module number"</li>
-</ul>
-<ul>
 <li><b>detectorversion</b> Gets the firmware version of detector. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>softwareversion</b> Gets the software version of detector server. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>thisversion</b> Gets the software version of this client software. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>receiverversion</b> Gets the software version of receiver. Only get! <code>Returns</code> <code></code>(long int) in hexadecimal</li>
-</ul>
-<ul>
 <li><b>framesl</b> gets number of frames left. Used in MYTHEN, GOTTHARD only. Only get! <code>Returns</code> <code></code>(double with 9 decimal digits)</li>
 </ul>
-<h2><a class="anchor" id="configspeed">
-Speed</a></h2>
+<h1><a class="anchor" id="configspeed"></a>
+Speed</h1>
 <p>commands to configure speed of detector</p>
 <ul>
 <li><b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. Jungfrau, full speed is not implemented and overwrites adcphase to recommended default. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>setlength [i]</b> sets/gets length of set/reset signals (in clock cycles). Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>waitstates [i]</b> sets/gets waitstates of the bus interface (in clock cycles). Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>totdivider [i]</b> sets/gets clock divider in tot mode. Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>totdutycycle [i]</b> sets/gets duty cycle of the tot clock. Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>phasestep [i]</b> Only put for gotthard. Moves the phase of the ADC clock.<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>oversampling [i]</b> Sets/gets the number of adcsamples per clock. For the new chiptestboard.<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>adcclk [i]</b> sets/gets the ADC clock frequency in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>adcphase [i]</b> Sets/gets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER) <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>adcpipeline [i]</b> Sets/gets the pipeline of the ADC. For the new chiptestbaord!<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>dbitclk [i]</b> Sets/gets the clock frequency of the latching of the digital bits in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>dbitphase [i]</b> Sets/gets the phase of the clock for latching of the digital bits. For the new chiptestboard!?<code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>dbitpipeline [i]</b> Sets/gets the pipeline of the latching of the digital bits. For the new chiptestbaord!<code>Returns</code> <code></code>(int)</li>
 </ul>
-<h2><a class="anchor" id="configsettings">
-Detector Parameters</a></h2>
+<h1><a class="anchor" id="configsettings"></a>
+Detector Parameters</h1>
 <p>commands to configure/retrieve configuration of detector</p>
 <ul>
 <li><b>config [fname]</b> sets/saves detector/receiver to configuration contained in fname. Same as executing sls_detector_put for every line. Normally a one time operation. <code>Returns</code> <code></code>(string) fname</li>
-</ul>
-<ul>
 <li><b>rx_printconfig</b> prints the receiver configuration. Only get! <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
 <li><b>parameters [fname]</b> sets/saves detector parameters contained in fname. Normally once per different measurement. <code>Returns</code> <code></code>(string) fname</li>
-</ul>
-<ul>
 <li><b>setup [fname]</b> sets/saves detector complete setup contained in fname (extensions automatically generated), including trimfiles, ff coefficients etc. <code>Returns</code> <code></code>(string) fname </li>
 </ul>
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