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

@@ -1,353 +1,215 @@
-SLS Detector Package 3.1.0 released on 2018-03-12
-=================================================
+SLS Detector Package 4.2.0 released on 09.04.2020 (Minor Release)
+===================================================================
 
 
-
-INTRODUCTION
-
-This document describes the differences between 3.1.0 and 3.0.0 releases.
-
-The conda package of the binaries can be downloaded from
-	
-	https://github.com/slsdetectorgroup/sls_detector_software.git
-	
-The Python interface to the software package (including the package) is at 
-	
-	https://github.com/slsdetectorgroup/sls_detector.git
-	
-Manual (both HTML and pdf versions) are provided in
-	
-	manual/docs/
-
-Documentation from Source Code can be found for the Command Line and C++ API in
-	
-	html:
-		manual/docs/html/slsDetectorClientDocs/index.html
-		manual/docs/html/slsDetectorUsersDocs/index.html
-	pdf:
-		manual/docs/pdf/slsDetectorClientDocs.pdf
-		manual/docs/pdf/slsDetectorUsersDocs.pdf
-		
-Documentation to the python API is available at
-
-	https://slsdetectorgroup.github.io/sls_detector/
-		
-Example including binaries for detector and receiver user classes can be found in 
-
-	manual/manual-api
-	
-User documentation can also be accessed directly at this location:
-
-    https://www.psi.ch/detectors/users-support
-
-If you have any software related questions or comments, please send them to:
-
-    dhanya.thattil@psi.ch
-    anna.bergamaschi@psi.ch
-    
-If you have any python related questions or comments, please send them to:
-	
-	erik.frojdh@psi.ch
-
+This document describes the differences between 4.2.0 and 4.1.1 releases.   
     
     CONTENTS
-
-- Firmware Requirements
-- Changes in User Interface
-- New Features
-- Resolved Issues
-- Known Issues
+    --------
+    1.  Topics Concerning
+    2.  New Features
+    3.  Resolved Issues
+    4.  Firmware Requirements
+    5.  Download, Documentation & Support
     
 
 
-Firmware Requirements
-=====================
+1. Topics Concerning
+====================
 
-	Please refer to the link below for more details on the firmware versions.
-		https://www.psi.ch/detectors/firmware.
+    - (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)
 
-    	Gotthard
-    	========   
-    	Minimum compatible version  : 11.01.2013
-    	Latest version              : 08.02.2018 (50um and 25um Master)
-                                      09.02.2018 (25 um Slave) 
-
-   	-Can not be upgraded remotely.
-    
-    
-    	Eiger
-    	=====  
-    	Minimum compatible version  : 16
-    	Latest version              : 20
-        
-    	-Can be upgraded remotely via bit files.
-    
-        
-    	Jungfrau
-    	========       
-    	Minimum compatible version  : 13.11.2017
-    	Latest version              : 13.11.2017
-
-    	-Can be upgraded remotely via sls_detector_put programfpga <pof>.
+    Compared to 4.1.1, 
+        - no firmware update required for this release
+        - eiger on-board detector server update required for this release
 
 
 
-Changes in User Interface
-========================= 
+2. New Features
+===============
+
+    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.
+
+    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.	Additional functions added for advanced users in users class:
-		(setSpeed, setClockDivider, setReadOutFlags, setDac, getADC, 
-		setAllTrimbits, startReceiver, stopReceiver,
-		startAcquisition non blocking, setReceiverSilentMode, setHighVoltage,
-		enableDataStreamingToClient, enableDataStreamingFromReceiver, 
-		setReceiverDataStreamingOutPort, setClientDataStreamingInPort)
+    1.  Added setflippeddatax to users class.
 
-	2.	Zmq set up for client and receiver are separated.
-		zmqport for client and rx_zmqport for receiver. By default, they are the
-		same for the slsDetectorGui to work.
 
-	3. 	Users example also works without config file, where detector already
-		configured in shared memory.
+    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.
 
-	4. 	Use "sls_detector_get busy 0" to clear acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
 
-	5. 	Set bit, clear bit, read register and write register cannot give -1 for
-		inconsistent values from multiple detectors. One has to check error from 
-		API or read the values individually.
 
-	6. 	multiSlsDetector::char* getSettingsFile() function signature has been 
-		changed to string getSettingsFile().
+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
     --------
-	7.	Modified the help manaual/main-api/mainReceiver.cpp to make it more
-		robust (handling child process exit) and flexible to determine upon 
-		start up the number of receivers (child processes), the start TCP port 
-		and whether to call back data.
+    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.
     
-		detReceiver is now executed with [start tcp port] [number of receivers]
-		[1 for call back, 0 for none] as arguments. 
-		By default, start tcp port is 1954, number of receivers	is 1, and call
-		back is initiated.
-		
-	8.	rx_datastream to enable/disable data streaming in receiver. Using the GUI
-		or registering data call back in client automatically enables zmq in 
-		receiver and client. "externalgui" is removed from the command line. Use
-		this command instead.
-		
-	9.	Rx_tcpport argument to the slsReceiver can be given using -t. 
-		Eg. slsReceiver -t1955
-		
-
-New Features
-============
+    2.  Modifying subexptime now also updates subperiod in master file.
+        Also, the print for subperiod name to console is corrected.
 
 
     Package
     -------
-	1.	In addition to the C++ API, the Python API is also now provided.
-	
-	2. 	CMAKE now with debug flag and rpath, show warnings, compile only certain 
-		components (such as receiver or gui)
-	
-	3. 	One repository for entire package and made available at github.
-	
-	4. 	One can do --version or -v to all the binaries to find out the release
-		version of the particular executable.
-		
-	5. 	All the software version numbers have only date in format YYMMDD.
+    1.  Many warnings have been fixed, including those with overlapping 
+        memory copies for source and destination. 
 
 
     Client
     ------
-	6. 	Parallelized more commands to detector. Beneficial for large detectors.
-		(setTimer, setFileIndex, setOnline, setReceiverOnline, getReceiverStatus,
-		resetFramesCaught, setFrameIndex, setFileName, getFramesCaughtByReceiver,
-		setDynamicRange, setRateCorrection)
-		
-		Option to also use "sls_detector_put threaded 0" to improve speed by 
-		eliminating progress display during acquisition. Effective only for 
-		large detectors.
+    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.
     
     
-	Detector Server
-	---------------
-	7.	(Eiger) Virtual class to execute on pc.
     
-	8. 	One can now read temperatures during acquisition. It goes via the stop
-		server.
+4. Firmware Requirements
+========================
         
-	9.	(Jungfrau) One can start server in "debug" mode and then program the
-		new firmware via software command "sls_detector_put programfpga xx.pof".
+        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
         
-	10.	(Jungfrau) Server can exit on start up if either the firmware or the 
-		server is incompatible with each other.
-	
-	11.	(Jungfrau) One is able to set transmission delay (ms) of image for each
-		individual detector using "txndelay_frame" command. Beneficial for 
-		large detectors.
-		
-	12.	(Jungfrau) One can set a threshold temperature (temp_threshold) and 
-		enable the temperature control feature (temp_control). When the 
-		temperature (temp_fpga) overshoots the threshold temperature, it will
-		set the temperature event (temp_event) and power off the chip. One must
-		then switch off the detector and check cooling. Switching back on starts
-		with defaults.
-		
-	13.	(25um Gotthard) Added start acquisition delay to master module.
-	
-	14. 	(Gotthard) New constraints for firmware dated 08.02.2018 and 09.02.2018 
-		(25 um Slave) include minimum exposure time is 186 ns and minimum 
-		period is 1278 ns + current exposure time.
+        Jungfrau
+        ========       
+        Minimum compatible version  : 26.02.2018
+        Latest compatible version   : 06.12.2018
 
         
-	Receiver
+        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
     --------
-	14. 	The detectorip and rx_udpip does not have to be in the same subnet anymore.
-		Add the following commands after rx_hostname in config file to overwrite
-		mac configuration:
-		rx_udpmac [router mac]
-		configuremac 0 
     
-	15.	Added silent mode to receiver using command r_silent [i] from client. 
-		It might be beneficial for max frame rate applications.
+    The Source Code (Default C++ API):
+         https://github.com/slsdetectorgroup/slsDetectorPackage
          
-	16.	Receiver print out can handle black or white backgrounds.
-	
-	17.	zmq package included updated to v4.0.8.
-	
-	18.	Zmq streaming from receiver also sends file index in json header.
-	
-	
-	Gui
-	---
-	19.	If acquisition is done, but "stop dummy packet" to the gui was lost in 
-		the network, stop acquisition command will restream it so that the gui
-		doesnt hang forever. This is used only for very fast detectors like 
-		Moench.
-
-
-
-Resolved Issues
-===============
-
-
-	Client
-	------
-	1. 	gethostbyname used in connecting to sockets was not thread safe for 
-		multiple detectors. Using getaddrinfo for stability in multi threaded
-		environment.
-	
-	2. 	Updated writing content of config and parameter dump into files.
-	
-	3. 	More locking to handle main and processing threads using the threadpool.
-		Removing unlock twice, which is undefined behavior.
-		
-	4.	(Jungfrau) adcphase returns the correct value, instead of -1.
-			
-
-	Detector Server
-	---------------
-	4. 	(Eiger) The hardware MAC of the detector is used during configuration 
-		and relayed  back to client. Similarly, hardware IP for 1 Gbe data mode.
-		
-	5. 	(Eiger) Status will return error if there was the unlikely trouble 
-		reading status register in the front end board. Earlier, it would only 
-		return idle.
-		
-	6.	(Jungfrau) patch server v3.0.0.6.3
-		Able to set settings, high voltage now correctly reads 0 when 
-		switched off, dacs are properly set.
-			
-	7. 	(Jungfrau) FPGA reset and programming FPGA firmware via software is done
-		properly
-		
-	8. 	(Gotthard) patch server v3.0.0.5.1
-		Able to read temperature properly.
-		
-	9. 	(Gotthard) butst mode if set too fast had unwanted behavior such as 
-		sending same image continuously. Now it is handled to display error
-		and stop acquisition.
-		
-	10.	(Gotthard) completely removed the possibility to set timing modes 
-		other than auto and trigger as they are not implemented anyway. Also
-		signal index 1, 2 and 3 are reserved and hence, cannot be configured for
-		an external trigger.
-		
-	11.	Non Mythen and non Eiger detectors can also now get settings file from 
-		board.
-		
-	12. 	(Gotthard) Did not get first few images initially after configuring MAC
-		of detector. Fixed.
-	
-	
-	Receiver
-	--------
-	12.	Made it easier to disable the standard receiver and fixing bugs related 
-		to the use of a custom one. 
-		
-	13.	(Jungfrau) HDF5 dimensions (npixelsY) required for mapping fixed.
-	
-	14.	patch2-v3.0.0-slsReceiverSoftware.patch
-		x, y and z coordinates in the call backs and the files are hardcoded 
-		for this release. 
-		
-	15.	Rest implementation (not used by standard receiver) removed.
-
-	
-	Gui
-	---
-	16.	patch1-v3.0.0-slsDetectorGui.patch
-		(Eiger) In expert mode and in advanced tab, when trimbits 
-		loaded are different for every pixel, the gui complains and sets 
-		all trimbits to zero. This has been resolved. Now, the "Set All 
-		Trimbits" field is just set to -1.
-		
-	17.	Fixed segmentation fault of xputsn properly.
-	
-	18.	Upon clicking on "Start", clears acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
-		
-	19.	Fixed plotting twice caused due to unzooming the first time.
-	
-	20.	Removed option for compression in Gui as it is not available currently.
-	
-	21. 	Can also show Jungfrau multi detector in x direction in gui.
-	
-	22. 	Switching tabs sometimes results in delay and gates fields being incorrectly
-		enabled. Fixed.
-
-
-	
-Known Issues
-============
-
-
-	Client
-	------
-	1.	File name prefix can only be done at multi deector level. Changing at 
-		individual detector level will not include scan or position variables.
-
-	
-	Detector Server
-	---------------
-	2.	Standard header fills x-coord in 1D. y-coord and z-coord is not 
-		implemented (3D).
-
-
-	Receiver
-	--------
-	3. 	HDF5 compression and filters are not implemented yet.
+    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
 
+#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
 #0:rx_tcpport 1956 
-0:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:angdir 1.000000
 0:moveflag 0.000000
-0:lock 0
-0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
+
 0:detectorip 10.1.1.2
 #0:detectormac 00:aa:bb:cc:dd:ee
 #0:rx_udpport 50001
@@ -28,13 +26,11 @@ hostname bchip007+bchip009+
 #1:port 1952
 #1:stopport 1953
 1:rx_tcpport 1957
-1:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:angdir 1.000000
 1:moveflag 0.000000
-1:lock 0
-1:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:ffdir /home/l_msdetect
 1:extsig:0 off
+
 1:detectorip 10.1.2.2
 #1:detectormac 00:aa:bb:cc:dd:ee
 1:rx_udpport 50004
@@ -56,4 +52,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

manual/docs/html/angularCalibrationHowTo/angularCalibrationHowTo.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
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
@@ -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>
 </BODY>
 </HTML>

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manual/docs/html/angularCalibrationHowTo/images.pl

@@ -1,4 +1,4 @@
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
 # Associate images original text with physical files.
 
 
@@ -44,18 +44,18 @@ $cached_env_img{$key} = q|<IMG
  SRC="|."$dir".q|img9.png"
  ALT="$p=50&nbsp;\mu m$">|; 
 
-$key = q/_6;MSF=1.6;AAT/;
-$cached_env_img{$key} = q|<IMG
- WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
- SRC="|."$dir".q|img10.png"
- ALT="$_6$">|; 
-
 $key = q/C_{peak};MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
  SRC="|."$dir".q|img2.png"
  ALT="$C_{peak}$">|; 
 
+$key = q/_6;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$_6$">|; 
+
 $key = q/includegraphics[width=textwidth]{peakFit.eps};AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
@@ -74,18 +74,18 @@ $cached_env_img{$key} = q|<IMG
  SRC="|."$dir".q|img16.png"
  ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}">|; 
 
-$key = q/pm;MSF=1.6;AAT/;
-$cached_env_img{$key} = q|<IMG
- WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
- SRC="|."$dir".q|img12.png"
- ALT="$\pm$">|; 
-
 $key = q/includegraphics[width=textwidth]{angleFit.eps};AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
  SRC="|."$dir".q|img18.png"
  ALT="\includegraphics[width=\textwidth]{angleFit.eps}">|; 
 
+$key = q/pm;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$\pm$">|; 
+
 $key = q/{displaymath}Theta_e=Theta_o^i-arctanBig(frac{pcdot(C_{peak}-C_{center}^i)}{R^i}Big),{displaymath};MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="291" HEIGHT="41" BORDER="0"
@@ -96,13 +96,13 @@ $cached_env_img{$key} = q|<IMG
 
 $key = q/theta;MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="|."$dir".q|img1.png"
  ALT="$\theta$">|; 
 
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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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@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
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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"
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  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
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  SRC="img7.png"
  ALT="$C_{center}^{i}$"> is the central channel  and <IMG
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@@ -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"
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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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@@ -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>
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manual/docs/html/angularCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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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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 <BR><HR>
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 Thattil Dhanya
-2018-03-12
+2018-09-28
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manual/docs/html/angularCalibrationHowTo/node5.html

@@ -1,6 +1,6 @@
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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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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
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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>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
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 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
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 Thattil Dhanya
-2018-03-12
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manual/docs/html/energyCalibrationHowTo/index.html

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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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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
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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

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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
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
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+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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  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
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  SRC="img12.png"
  ALT="$e^-$">=3.6&nbsp;eV.
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  ALT="$ENC$"> normally depends on the shaping settings of the analog chain and increases with shorter shaping times. 
 The resulting electronic signal spectrum is then  given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation <IMG
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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"
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  SRC="img25.png"
  ALT="$O$"> and gain <IMG
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+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" 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
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ 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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@@ -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>
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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)
 original version by:  Nikos Drakos, CBLU, University of Leeds
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 * with significant contributions from:
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@@ -180,7 +180,7 @@ Acquisition GUI window to setup the threshold scan.</CAPTION>
 <!--End of Navigation Panel-->
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 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
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manual/docs/html/energyCalibrationHowTo/node3.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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@@ -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
- WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
  SRC="img39.png"
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 </TABLE>
@@ -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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@@ -184,7 +184,7 @@ Window to calibrate the modules.</CAPTION>
 <!--End of Navigation Panel-->
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 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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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)
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 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>
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manual/docs/html/energyCalibrationHowTo/node5.html

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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.
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 <P>
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manual/docs/html/slsDetectorClientDocs/acquisition.html

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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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+<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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-
-
-<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>
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-</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>
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-<li><b>scan0steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan0 level and their values (float).</li>
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-<ul>
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-</ul>
-<ul>
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-<li><b>scan1par [s]</b> sets/gets a string to be passed as a parameter to the scan1script</li>
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-<ul>
-<li><b>scan1prec [i]</b> sets/gets number of digits to be used for the scan1 variable in the file name.</li>
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+</div><!-- top -->
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+  <div class="headertitle">
+<div class="title">Actions </div>  </div>
+</div><!--header-->
+<div class="contents">
+<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>
+</div></div><!-- contents -->
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+Generated by &#160;<a href="http://www.doxygen.org/index.html">
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manual/docs/html/slsDetectorClientDocs/advanced.html

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-<h1><a class="anchor" id="advanced">Advanced Usage </a></h1><p>This page is for advanced users. Make sure you have first read the introduction. </p>
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+</div><!-- top -->
+<div class="header">
+  <div class="headertitle">
+<div class="title">Advanced Usage </div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><p>This page is for advanced users. Make sure you have first read the introduction. </p>
+</div></div><!-- contents -->
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+Generated by &#160;<a href="http://www.doxygen.org/index.html">
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manual/docs/html/slsDetectorClientDocs/config.html

@@ -1,27 +1,47 @@
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-<title>Configuration commands</title>
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+<title>My Project: Configuration commands</title>
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+   <div id="projectname">My Project
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+  <div class="headertitle">
+<div class="title">Configuration commands </div>  </div>
+</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)]. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<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>
 <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 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>
 <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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