after merging with developer

* not done. The 'setsockopt(SO_RECVBUF)' system call cannot set the socket buffer
  size lager than the specified in net.core.rmem_max. The requested value
  was 2 GB (commit 3b0e2e6), which is far too large for this application,
  so it was restored to the acceptable 100 MB value.

* The syscall does not fail if the requested buffer size is larger than
  net.core.rmem_max. Use 'setsockopt(SO_RECVBUFFORCE)' to actually force a
  value larger than the system limit, which can be done if run in a
  privileged context (capability CAP_NET_ADMIN set).

* The real value is read with 'getsockopt(SO_RECVBUF)'. If it
  corresponds to twice the requested value (see 'man 7 socket'), it is
  printed in green, otherwise it is signalled in red.

* The 'setsockopt(SO_RECVBUFFORCE)' syscall removes the need to write to
  /proc/sys/net/core/rmem_max, so this was was suppressed in the
  'UDPStandardImplementation' constructor.

* The test on EIGER detectors before setting the system
  buffers was removed. Was there for 9m/2m eiger, but one can take care of
  memory requirements using a customizable max socket buffer size(only with
  permissions). to be implmented later.

* The file /proc/sys/net/core/netdev_max_backlog is first read by the
  receiver to check is the current value is OK. If it is not, the receiver
  directly writes the good value into the file (instead of delegating to
  the system shell), printing a red error message if there is an access
  error (non-privileged user).

CMakeLists.txt

@@ -1,5 +1,5 @@
 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)
@@ -7,13 +7,18 @@ option (USE_TEXTCLIENT "Text Client" OFF)
 option (USE_RECEIVER "Receiver" OFF)
 option (USE_GUI "GUI" OFF)
 
-set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wno-misleading-indentation")
+
+if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+	set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -std=c++98 -Wno-misleading-indentation")
+else ()
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -std=c++98")
+endif ()
 
 find_package(Qt4)
 find_package(Qwt 6)
 find_package(CBF)
 find_package(Doxygen)
-find_package(PNG REQUIRED)
+# find_package(PNG REQUIRED)
 
 if (USE_HDF5)
 	find_package(HDF5 1.10 COMPONENTS CXX)
@@ -31,8 +36,10 @@ endif (USE_TEXTCLIENT)
 
 if (USE_RECEIVER)
        add_subdirectory(slsReceiverSoftware)
+       add_subdirectory(manual/manual-api)    
 endif (USE_RECEIVER)
                
+               
 if (USE_GUI)   
        if (QT4_FOUND AND QWT_FOUND)
        add_subdirectory(slsDetectorGui)

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

@@ -1,10 +1,13 @@
+### Documentation
+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 3.0.1
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Setup dependencies 
@@ -16,7 +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
@@ -40,6 +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
@@ -80,5 +87,5 @@ 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

@@ -1,350 +1,508 @@
-SLS Detector Package 3.0.1 released on 2018-02-12
+SLS Detector Package 4.0.0 released on 27.09.2018
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.0.0 and 3.0.1 release.
+	This document describes the differences between 4.0.0 and 3.1.4 releases.
 
-The conda package of the binaries can be downloaded from
+	Download
+	--------
 	
-	https://github.com/erikfrojdh/sls_detector_software.git
+	The Source Code (Default C++ API):
+		 https://github.com/slsdetectorgroup/slsDetectorPackage
 		 
-The conda package of the python API wrap-around to the software package is at 
+	The Conda Lib Package:
+		https://github.com/slsdetectorgroup/sls_detector_lib
 		
-	https://github.com/slsdetectorgroup/sls_detector.git
+	The Conda GUI Package:
+		https://github.com/slsdetectorgroup/sls_detector_gui	
 		
-Manual (both HTML and pdf versions) are provided in
+	The Python Interface (including the package):
+    	https://github.com/slsdetectorgroup/sls_detector
 	
-	manual/docs/
 	
-Documentation from Source Code can be found for the Command Line and C++ API in
+	Documentation
+	-------------
 	
-	html:
+	Manual (HTML & PDF):
+		https://www.psi.ch/detectors/documentation
+		slsDetectorPackage/manual/docs/
+		
+	Command Line Documentation:
 		manual/docs/html/slsDetectorClientDocs/index.html
-		manual/docs/html/slsDetectorUsersDocs/index.html
-	pdf:
 		manual/docs/pdf/slsDetectorClientDocs.pdf
+		
+	C++ API Documentation:
+		manual/docs/html/slsDetectorUsersDocs/index.html
 		manual/docs/pdf/slsDetectorUsersDocs.pdf
 		
-Documentation to the python API is available at
+	C++ API Example:
+		manual/manual-api/mainClient.cpp
+		manual/manual-api/mainReceiver.cpp
 		
+	Python API Documentation:
 		https://slsdetectorgroup.github.io/sls_detector/
 		
-Example including binaries for detector and receiver user classes can be found in 
+	Further Documentation:
-
-	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:
 	
+	Support
+	-------
+
+	General Software related:
 		dhanya.thattil@psi.ch
 		anna.bergamaschi@psi.ch
 		
-If you have any python related questions or comments, please send them to:
+	Python related:
-	
 		erik.frojdh@psi.ch
 
 
+
 CONTENTS
 
-- Firmware Requirements
+	1.	Firmware Requirements
-- Changes in User Interface
+	2.	Changes in User Interface
-- New Features
+	3.	New/Modified Commands
-- Resolved Issues
+	4.	Other New Features
-- Known Issues
+	5.	Resolved Issues
+	6.	Known Issues
+	7.	Next Major Release Plans
 
 
 
-Firmware Requirements
+1. Firmware Requirements
-=====================
+========================
-
-Please refer to the link below for more details on the firmware versions.
-	https://www.psi.ch/detectors/firmware.
 
     	Gotthard
     	========   
-    Minimum compatible version	: old one
+    	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
+    	Minimum compatible version  : 22
-    Latest version				: 21
+    	Latest version              : 22
-        
-    -Can be upgraded remotely via bit files.
-    
         
     	Jungfrau
     	========       
-    Minimum compatible version	: 13.11.2017
+    	Minimum compatible version  : 15.06.2018
-    Latest version				: 13.11.2017
+    	Latest version              : 15.06.2018
 
-    -Can be upgraded remotely via sls_detector_put programfpga <pof>.
+    	
+    	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://www.psi.ch/detectors/installation-instructions
+    	under Detector Upgrade -> [Detector Type] -> Firmware. 
+    	
+    	 
+	Please refer to the link below for more details on the firmware versions.
+	https://www.psi.ch/detectors/firmware.
 		
 
 
-Changes in User Interface
+2. Changes in User Interface
-========================= 
+============================
-	
 	
 	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)
 	
-	2.	Zmq set up for client and receiver are separated.
+	1.	Shared Memory:
-		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
+		POSIX shared memory has been implemented and they are typically created in
-		configured in shared memory.
+		/dev/shm/ folder.
 		
-	4. 	Use "sls_detector_get busy 0" to clear acquiring flag in shared memory
+		A multiSlsDetector object will create a shared memory segment with naming style:
-		caused due to an earlier interrupted acquisition from Ctrl+C"
+		slsDetectorPackage_x_[_z]
+		and an slsDetector object will create a shared memory segment with naming style:
+		slsDetectorPackage_x_sls_y[_z]
 		 	
-	5. 	Set bit, clear bit, read register and write register cannot give -1 for
+		where
-		inconsistent values from multiple detectors. One has to check error from 
+		x is the multi detector id
-		API or read the values individually.
+		y is the sls detector id
+		z is the environment variable SLSDETNAME, if set.
+		They can be deleted directly.
 		
-	6. 	multiSlsDetector::char* getSettingsFile() function signature has been 
+		Environment variable SLSDETNAME included for user-friendliness
-		changed to string getSettingsFile().
+		of using 2 different detectors from the same client pc. One needn't use
+		different multi detector id if the SLSDETNAME is different for both consoles.
 		
+		Constructor will fail if shared memory size is different (different package
+		releases/detectors). Loading config file cleans shared memory.
+
+
+	2.	Exceptions in constructors:
+	
+		All constructors that have an error throws an exception. For this release,
+		this is caught within the package and interfaced as error codes or messages
+		to the users using command line or API.
+		
+		As a result:
+		- slsDetectorsUsers constructor signature now includes a success flag.
+		- If one uses multiSlsDetector, slsDetector, ZmqSocket classes directly, 
+		  catch exceptions from constructors.
+		- In future releases, the exception will be thrown 
+		  outside the package for the users to handle it.
+		  
+		  
+	3.	API Compatibility:
+	
+		Client now checks API version of Detector Server - Client and Receiver - Client
+		when connecting for the first time to detector server or receiver server
+		and the online flags have not been set in shm. 
+		
+		Upon failure, error messages will ensue and further commands will not 
+		be executed. Detector servers referred to are only for Eiger, Jungfrau and Gotthard.
+		
+		Previously, the detector server would exit on mismatched Firmware-Detector
+		server mismatch. They now wait for client to ask for compatibility check,
+		which is done the first time client connects to the detector and the
+		online flag in shm has not been set.
+		
+		
+	4.	Commands "type", "id" and "replace" are removed.
 		  
 		  
 	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.
 	
-		detReceiver is now executed with [start tcp port] [number of receivers]
+	1.	Reciever Header Structure in file writing and call back:
-		[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
+		sls_receiver_header structure added to sls_receiver_defs.h for image headers 
-		or registering data call back in client automatically enables zmq in 
+		in file writing. 
-		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. 
+		#define MAX_NUM_PACKETS	512
-		Eg. slsReceiver -t1955
+		typedef std::bitset<MAX_NUM_PACKETS> sls_bitset;
+		typedef struct {
+			sls_detector_header detHeader;	/**< is the detector header */
+			sls_bitset packetsMask;			/**< is the packets caught bit mask */
+		} sls_receiver_header;
+		
+		It includes the detector header structure + bitmask of 512 bits, 
+		where each bit represents a packet caught. This is useful in saving time 
+		in writing to file by not padding missing packets and still retaining useful data.
+		
+		The binary and HDF5 writer version number changed from 1.0 to 2.0. 
+		The detector header version remains as 1.0.
+		
+		registerCallBackRawDataReady modified to give this structure pointer,
+		instead of individual structure member pointers.
 		
 		
-New Features
+	2.	ZmqSocket class:
-============
+	
+		If one uses ZmqSocket.h, then the json header has to be parsed outside 
+		the class to allow the user to remove the restriction in extracting all data
+		from the json header.
 
 
-	Package
+	3.	Receiver Call back with modified size:
-	-------
-	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 
+		registerCallBackRawDataModifyReady call back that is similar to the receiver 
-		components (such as receiver or gui)
+		registerCallBackRawDataReady has been added to allow the call back to 
+		specify an updated size of image after call back. This is in view to process
+		an image in call back (including extract only a region of the image) and 
+		provide this updated size in callback. This new resized/processed image
+		will be written to file or streamed out via zmq. This is useful in ROI
+		selection in the receiver.
 
-	3. 	One repository for entire package and made available at github.
+		This also means that the call back is now called before writing to file.
 
-	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.
 
+3. New/Modified Commands 
+========================
 	
 	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 
+	1.	add (modified): 
-		eliminating progress display during acquisition. Effective only for 
+		appends detector to end of multi detector list.
-		large detectors.
 
+	2.	replace: 
+		sets hostname/ip address for a single detector.
 
-	Detector Server
+	3.	user: 
-	---------------
+		get user details from shared memory.
-	7.	(Eiger) Virtual class to execute on pc.
 
-	8. 	One can now read temperatures during acquisition. It goes via the stop
+	4.	checkdetversion: 
-		server.
+		checks client version compatibility with detector server.
 
-	9.	(Jungfrau) One can start server in "debug" mode and then program the
+	5.	checkrecversion: 
-		new firmware via software command "sls_detector_put programfpga xx.pof".
+		checks client version compatibility with receiver server.
-		
-	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 include minimum exposure time is 186 ns and
-		minimum period is 1278 ns + current exposure time.
 		
 	
 	Receiver
 	--------
-	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. 
+	1.	rx_zmqip:	
-		It might be beneficial for max frame rate applications.
+		sets/gets the zmq (TCP) ip of the receiver from where data is streamed 
+		out from. (Eg. to the gui or intermediate process). By default, it is 
+		the same as the zmqip.
 	
-	16.	Receiver print out can handle black or white backgrounds.
+	2.	zmqip: 
+		sets/gets the zmq (TCP) ip, where client listens to, to reconstuct images. 
+		(Eg. from receiver or intermediate process). By default, it is the same 
+		as rx_zmqip.
 	  		 	
-	17.	zmq package included updated to v4.0.8.
+	3.	rx_jsonaddheader:
+		sets/gets additional json header to be streamed out with the zmq from 
+		receiver. Default is empty. Eg. p rx_jsonaddheader \"what\":\"nothing\"
 		
-	18.	Zmq streaming from receiver also sends file index in json header.
+	4.	r_discardpolicy:
+		sets/gets the frame discard policy in the receiver. 
+		nodiscard - no discard (default), 
+		discardempty - discard only empty frames, 
+		discardpartial - discard any partial frame(fastest)
+		
+	5.	r_padding:
+		sets/gets the frame padding in the receiver. 
+		0 does not pad partial frames(fastest), 
+		1 (default) pads partial frames.
+		One can look at bitmask in the sls_receiver_header to process the unpadded
+		partial	frames later.
+		
+	6.	activate (modified):
+		Extra option added to pad or unpad images in receivers when deactivated.
+		activate i [padding option], where i is activate/deactivate	and padding 
+		option is "padding" (default) or "nopadding".
+		
+	7.	rx_udpsocksize:
+		sets/gets the UDP socket buffer size. Already attempts to set by default 
+		to 100mb, 2gb for Jungfrau. Does not remember custom values	in client 
+		shared memory, so must be initialized each time after setting receiver 
+		hostname in config file.
+		
+	8.	rx_realudpsocksize:
+		gets the actual UDP socket buffer size. Usually double the set udp socket 
+		buffer size due to kernel bookkeeping.
+	
+	9.	r_framesperfile:
+		sets/gets the frames per file in receiver. 0 means infinite or all frames 
+		in a single file. Default of Eiger changed from 2k to 10k.
+		
+
+	Eiger Specific
+	--------------
+	
+	1.	status trigger:
+		To trigger internally via software, one can use "status trigger".
+		
+	2.	subdeadtime:
+		sets/gets sub frame dead time in s in 32 bit mode. Subperiod is	set in 
+		the detector by subexptime + subdeadtime. This value is	normally a 
+		constant set by an expert catered to individual detector modules in the 
+		config file. Receiver files writes master file metadata subperiod 
+		instead of subdeadtime.
+		
+	3.	gappixels:
+		enables/disables gap pixels in system (detector & receiver). 1 sets, 
+		0 unsets. In Receiver, 4 bit gap pixels mode is not implemented, but is 
+		implemented in client data call back. Gap pixels are at module level 
+		and not at multi module level.
+				
+	4.	measuredperiod:
+		gets the measured frame period (time between last frame and the	previous 
+		one) in s. Makes sense only for acquisitions of more than 1 frame.
+		
+	5.	measuredsubperiod:
+		gets the measured subframe period (time between last subframe and the 
+		previous one) in s in 32 bit mode.
+
+	6.	flags(modified):
+		extra flags "nooverflow" (default) and "overflow" for sub images in	32 
+		bit mode. If set to overflow, it will set MSB of pixel data high if 
+		there was any saturation in any of the sub images 32 bit mode.
+		
+				
+	Jungfrau Specific
+	-----------------
+	
+	1.	storagecells:
+		sets/gets number of additional storage cells per acquisition. For very 
+		advanced users only. Range: 0-15. Default: 0. 
+		The #images = #frames * #cycles * (#storagecells +1).
+		
+	2.	storage_start:
+		sets/gets the storage cell that stores the first acquisition of the	series. 
+		For very advanced users only. Range: 0-15. Default: 15(0xf).  
+
+
+
+4. Other New Features
+=====================
+
+	Client
+	------
+	
+	1.	(Jungfrau & Gotthard) Settingsdir and caldir is removed from config file.
+		Default dacs are stored in detector server. Hence, these folders
+		are also removed from slsDetectorPackage/settingsdir. Eiger and Mythen 
+		continue to have them.
+		
+	2.	Depending on 1d position of detectors and detsizechan in config file,
+		row and column (previously xcoord and ycoord) are given to detector 
+		servers (Eiger and Jungfrau) to encode into the udp header.
+		
+	3.	(Eiger) Setting threshold energy changes such as CAL dac is irrelevant 
+		when interpolating between two energies and VRS dac is interpolated, not copied.
+		
+	4.	Users API updated with the following functions:
+		-	setReceiverFramesDiscardPolicy
+		-	setReceiverPartialFramesPadding
+		-	setReceiverFramesPerFile
+		-	sendSoftwareTrigger
+		-	setSubFrameExposureDeadTime
+		-	setSubFrameExposureTime
+		-	enableGapPixels
+		-	getMeasuredPeriod
+		-	getMeasuredSubFramePeriod
+		-	setOverflowMode
+		-	setNumberOfStorageCells
+		-	setStoragecellStart
+		-	setThresholdEnergy (overloaded)
+		-	resetFramesCaughtInReceiver
+		-	setReceiverFifoDepth
+		-	setFlowControl10G
+		-	setTenGigabitEthernet
+		-	getNMods
+		-	setReceiverDataStreamingOutIP
+		-	setClientDataStreamingInIP
+		
+	SlsReceiver
+	-----------
+	
+	1.	slsMultiReceiver executable added that creates multiple receiver child processes.
+		./slsMultiReceiver [start_tcp_port] [num_receivers] [1 for call back, 0 for none]
+		
+	2.	Default row and column (previously xcoord and ycoord) are hardcoded 
+		for missing packets. (Eiger and Jungfrau)
 		
 
 	Gui
 	---
-	18.	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
+	1.	(Jungfrau) Gain plot included. Option under 2D options in Plot tab.
-		doesnt hang forever. This is used only for very fast detectors like 
+	
-		Moench.
+	2.	Option to maintain aspect ratio
+	
+	3.	Start and Stop separated to prevent multiple click syndrome.
+	
+
+	Detector Server
+	---------------
+	
+	1. 	(Jungfrau) To use programfpga command, one must start server with -update
+		mode and then restart server without -update mode.
+	
+	2.	(Jungfrau) ASIC Timer configured at server start up and changed a few
+		startup values for firmware v0.7 such as adc phase, ADC_PORT_INVERT_VAL
+		and ADC offset half speed value.
+		
+	3.	(Jungfrau) Minimum exposure time of 50 us was implemented.
+	
+	4. 	(Eiger and Jungfrau) They can be configured to have x and y coord values
+		of the detector in their udp header.
 
 
 
-Resolved Issues
+
+5. Resolved Issues
+==================
+
+	Client
+	------
+	memory leak for multi threading
+	
+	1.	Compiler flag -std=c++98 enforced. Debug flag removed.
+	
+	2.	If trimen gives different list from different detectors, it returns a -1.
+	
+	3.	Version format for each submodule of the package changed to just date YYMMDD.
+		Users class fixed to give correct version, instead of -1.
+		
+	4.	Getting settings in users class gave -1. Fixed now.
+
+	5.	(Jungfrau) Programming FPGA now creates the rawbin file from pof in tmp
+		rather than source file location (for permission issues).
+		
+	6.	(Gotthard) ROI segmentation fault fixed.
+		
+	Receiver
+	--------
+	
+	1.	Silent feature of receiver fixed.
+	
+	2. 	Socket descriptor misused earlier for success flag, instead exceptions
+		used that are handled inside the package.
+
+	3.	Global optind variable initialized to instantiate multiple receivers 
+		in same process. Also removed static members to enable this feature.
+		
+	4.	Socket buffer size attempts to set for each acquiistion and provide
+		warning if no capabilities. Warnings can be removed using instruction with
+		error provided. Default Jungfrau UDP socket buffer size if 2 GB, default is 
+		100 MB.
+		
+	5.	Refactored code a bit for performance and robustness, blocking push 
+		in buffer between listener and dataprocessor
+
+	
+	Detector Server
+	---------------
+	
+	1.	(Jungfrau) Stop server also mapped during a reset. Reading power status
+		instead of user input register for power.
+	
+	2.	(Eiger) Bug fix for saving trimbits to file (Advanced users).
+	
+	3.	(Gotthard 25um) config.txt is not read again after detector startup,
+		no matter the number of times the detector server is restarted. 
+
+	
+6. Known Issues
 ===============
 
+	Receiver
+	--------
 	
-	Client
+	1. 	HDF5 compression and filters are not implemented yet.
-	------
-	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.
 	
 	
 	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 
+	1.	(Eiger) Registers mapped differently between firmware v20 and v22.
-		reading status register in the front end board. Earlier, it would only 
+		So, please ensure correct on-board server before switching between
-		return idle.
+		firmware versions. Else one cannot ping it anymore. Will need to flash firmware
+		again to recover.
 		
-	6.	(Jungfrau) patch server v3.0.0.6.3
+	2.	(Gotthard) To switch back to all ADC from single ADC ROI, one must take
-		Able to set settings, high voltage now correctly reads 0 when 
+		even number of images for the receiver to understand complete images.
-		switched off, dacs are properly set.
+		This will be fixed in the next firmware upgrade.
-			
-	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
+7. Next Major Release Plans
-============
+===========================
-
 
 	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.
 	
+	1.	Exceptions thrown to the user to be handled.
 	
+	2. 	Compilation using c++11.
 	
+	3.	Support of Mythen II restricted to this major and its minor releases.
 	
+	4.	Restructuring and refactoring of client code. 
 
 
 

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
@@ -53,7 +55,7 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bchd:j:trg" opt ; do
+while getopts ":bchd:j:trge" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -91,6 +93,10 @@ while getopts ":bchd:j:trg" opt ; do
 		GUI=1
 		REBUILD=1
 		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
+		;;    
     \?)
      	echo "Invalid option: -$OPTARG" 
 		usage
@@ -145,7 +151,12 @@ 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

examples/bchip2modules.config

@@ -0,0 +1,61 @@
+detsizechan 2560 1
+
+hostname bchip074+bchip075+
+
+#replace my_installation_path 
+settingsdir /my_installation_path/slsDetectorPackage/settingsdir/gotthard
+caldir /my_installation_path/slsDetectorPackage/settingsdir/gotthard
+
+0:extsig:0 trigger_in_rising_edge
+0:rx_tcpport 1954
+0:rx_udpport 50001
+0:vhighvoltage 0
+
+1:extsig:0 trigger_in_rising_edge
+1:rx_tcpport 1955
+1:rx_udpport 50002
+#1:detectorip 10.1.1.52
+1:vhighvoltage 0
+
+##############################################################################
+#########
+######### Uncomment this part to use the gotthard25umZmq process
+#########
+##############################################################################
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#0:rx_zmqip my_receiver_hostname 
+#0:rx_zmqport 30003
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#0:zmqip my_client_hostname 
+#0:zmqport  40003
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#1:rx_zmqip my_receiver_hostname 
+#1:rx_zmqport 30004
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#1:zmqip  my_client_hostname 
+#1:zmqport  40004
+
+##############################################################################
+#########
+######### until here
+#########
+##############################################################################
+
+
+r_readfreq 1
+rx_datastream 1
+
+#replace my_receiver_hostname with the hostname of 1Gb IP of the machine where the receiver runs
+rx_hostname my_receiver_hostname
+rx_datastream 1
+outdir /tmp/
+angconv none
+threaded 1
+
+settings veryhighgain
+exptime 0.000005
+period 0.0001
+
+vhighvoltage 90

examples/bchip2modules_pc8829.config

@@ -0,0 +1,61 @@
+detsizechan 2560 1
+
+hostname bchip074+bchip075+
+
+#replace my_installation_path 
+settingsdir /my_installation_path/slsDetectorPackage/settingsdir/gotthard
+caldir /my_installation_path/slsDetectorPackage/settingsdir/gotthard
+
+0:extsig:0 trigger_in_rising_edge
+0:rx_tcpport 1954
+0:rx_udpport 50001
+0:vhighvoltage 0
+
+1:extsig:0 trigger_in_rising_edge
+1:rx_tcpport 1955
+1:rx_udpport 50002
+#1:detectorip 10.1.1.52
+1:vhighvoltage 0
+
+##############################################################################
+#########
+######### Uncomment this part to use the gotthard25umZmq process
+#########
+##############################################################################
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#0:rx_zmqip my_receiver_hostname 
+#0:rx_zmqport 30003
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#0:zmqip my_client_hostname 
+#0:zmqport  40003
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#1:rx_zmqip my_receiver_hostname 
+#1:rx_zmqport 30004
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#1:zmqip  my_client_hostname 
+#1:zmqport  40004
+
+##############################################################################
+#########
+######### until here
+#########
+##############################################################################
+
+
+r_readfreq 1
+rx_datastream 1
+
+#replace my_receiver_hostname with the hostname of 1Gb IP of the machine where the receiver runs
+rx_hostname my_receiver_hostname
+rx_datastream 1
+outdir /tmp/
+angconv none
+threaded 1
+
+settings veryhighgain
+exptime 0.000005
+period 0.0001
+
+vhighvoltage 90

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/howto_gotthatd_twomodules.txt

@@ -0,0 +1,14 @@
+Turn on the two receivers:
+slsReceiver --rx_tcpport 1954 &
+slsReceiver --rx_tcpport 1955 &
+
+Switch on the photon conversion on the receiver machine (replace my_receiver_hostname):
+gotthard25umZmq my_receiver_hostname 30003 my_receiver_hostname 40003 &
+
+Run the configuration file:
+sls_detector_put config bchip2modules.config 
+
+
+Start your measurements using the command line, the slsDetectorGui or the EPICS driver
+
+

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
+#extsig:0 trigger_in_rising_edge
-timing auto
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/moench03_T1_lab.config

@@ -0,0 +1,471 @@
+hostname bchip011
+
+patword 0000 0000000000000000
+patword 0001 0000000000000000
+patword 0002 0008000900080000
+patword 0003 0008000900080000
+patword 0004 0008000900080000
+patword 0005 0008000900080000
+patword 0006 0008000900080000
+patword 0007 0008000900080000
+patword 0008 0008000900080000
+patword 0009 0008000900080000
+patword 000a 0008000900080000
+patword 000b 0008000900080000
+patword 000c 0008000900080000
+patword 000d 0008000900080000
+patword 000e 0008000900080000
+patword 000f 0008000900080000
+patword 0010 0008000900080000
+patword 0011 0008000900080000
+patword 0012 0008000900080000
+patword 0013 0008000900080000
+patword 0014 0008000900080000
+patword 0015 0008000900080000
+patword 0016 0008400900080020
+patword 0017 0008400900080020
+patword 0018 0008599f0418503a
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+patword 001a 0108599f0418503a
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+
+
+
+0:rx_udpip 10.1.1.102
+0:detectorip 10.1.1.19
+0:rx_udpport 32410
+#0:detectormac 00:ab:bc:cd:de:ef
+#0:rx_udpmac 70:10:6f:a0:b5:b1
+
+#gui listening to
+zmqip 129.129.202.131
+zmqport 30001
+
+#data streaming out of
+rx_zmqip 10.1.2.103
+rx_zmqport 30003
+
+#turn on datastream from commandline
+rx_datastream 1
+
+r_readfreq 1
+
+0:rx_hostname mpc2011
+#0:configuremac -1
+rx_datastream 1
+
+r_readfreq 1
+
+
+dac:6 800
+dac:0 1300
+dac:4 1428
+dac:1 1000
+dac:7 900
+dac:3 680
+dac:2 1400
+dac:5 1200
+adcinvert 4a342593
+samples 5000
+adcphase 90
+adcpipeline 15
+adcreg 14 40
+powerchip 1
+vhighvoltage 90
+period 0.005
+
+
+
+
+
+
+frames 100
+period 0.1
+outdir /scratch/
+enablefwrite 0
+

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/slsDetectors-FAQ/WARNINGS

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manual/docs/html/slsDetectors-FAQ/footnode.html

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-
-<!--Converted with LaTeX2HTML 2008 (1.71)
-original version by:  Nikos Drakos, CBLU, University of Leeds
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-* with significant contributions from:
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-
-<DL>
-<DT><A NAME="foot1316">... tab&nbsp;</A><A
- HREF="MYTHEN.html#tex2html20"><SUP>3.1</SUP></A></DT>
-<DD>The default name of the calibrated trimfiles is <I>trimbits/beamline/</I><I>settings</I><I>/noise.snxxx</I> where  <I>settings</I> is the chosen settings. You  can change it in <I>src/qDetector.h</I> and then recompile the acquisition program as described in&nbsp;<A HREF="#sec:installation"><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
- SRC="file:/usr/share/latex2html/icons/crossref.png"></A>.
-
-<PRE>.
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-<DT><A NAME="foot1317">....snxxx&nbsp;</A><A
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-<DD>The default name of the calibration file <I>calibration/</I><I>settings</I><I>.snxxx</I> where  <I>settings</I> is the chosen settings. You  can change it in <I>src/qDetector.h</I> and then recompile the acquisition program.
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manual/docs/html/slsDetectors-FAQ/index.html

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-
-<!--Converted with LaTeX2HTML 2008 (1.71)
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-* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
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-<HTML>
-<HEAD>
-<TITLE>SLS Detectors
-Frequently Asked Questions</TITLE>
-<META NAME="description" CONTENT="SLS Detectors
-Frequently Asked Questions">
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-
-<P>
-
-<H1 ALIGN=CENTER>SLS Detectors
-<BR>
-Frequently Asked Questions</H1>
-<P ALIGN=CENTER><STRONG>Anna Bergamaschi</STRONG>
-</P>
-<BR><P ALIGN=CENTER><B>Date:</B> February 27, 2018</P>
-
-<HR>
-
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-
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@@ -1,30 +0,0 @@
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manual/docs/html/slsDetectors-FAQ/slsDetectors-FAQ.html

@@ -1,41 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-
-<!--Converted with LaTeX2HTML 2008 (1.71)
-original version by:  Nikos Drakos, CBLU, University of Leeds
-* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
-  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>SLS Detectors
-Frequently Asked Questions</TITLE>
-<META NAME="description" CONTENT="SLS Detectors
-Frequently Asked Questions">
-<META NAME="keywords" CONTENT="slsDetectors-FAQ">
-<META NAME="resource-type" CONTENT="document">
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-
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-
-<BODY >
-
-<P>
-
-<H1 ALIGN=CENTER>SLS Detectors
-<BR>
-Frequently Asked Questions</H1>
-<P ALIGN=CENTER><STRONG>Anna Bergamaschi</STRONG>
-</P>
-<BR><P ALIGN=CENTER><B>Date:</B> February 27, 2018</P>
-
-<HR>
-
-<BR><HR>
-
-</BODY>
-</HTML>

manual/manual-api/CMakeLists.txt

@@ -0,0 +1,35 @@
+set(SOURCES
+    mainReceiver.cpp
+)
+
+include_directories(
+    ../../slsReceiverSoftware/include
+    ../../slsDetectorSoftware/slsDetectorAnalysis 
+    ../../build/bin 
+    ../../slsdetectorSoftware/slsDetector 
+)
+
+add_executable(slsMultiReceiver
+    ${SOURCES}
+)
+
+target_link_libraries(slsMultiReceiver
+    slsReceiverShared
+    pthread
+    zmq
+    rt
+    ${HDF5_LIBRARIES}
+)
+
+if (HDF5_FOUND)
+    target_link_libraries(slsMultiReceiver 
+    ${HDF5_LIBRARIES}
+    )
+endif ()
+
+
+set_target_properties(slsMultiReceiver PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+)
+
+install(TARGETS slsMultiReceiver DESTINATION bin)

manual/manual-api/Makefile

@@ -1,18 +1,26 @@
-INCLUDES	=   -I . 
+PKGDIR		=	../..
+LIBDIR		=   $(PKGDIR)/build/bin
+INCLUDES	=   -I . -I$(PKGDIR)/slsReceiverSoftware/include -I$(PKGDIR)/slsDetectorSoftware/slsDetectorAnalysis -I$(LIBDIR) -I$(PKGDIR)/slsDetectorSoftware/slsDetector 
 SRC_DET		= 	mainClient.cpp 	
 SRC_REC		=   mainReceiver.cpp
-LIBDIR		=   .
+ZMQLIBDIR	= 	$(PKGDIR)/slsReceiverSoftware/include
-LDFLAG_DET 	=	-I. -L$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread -lrt -L. -lzmq
+LDFLAG_DET 	=	-I. -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread -lrt -L$(ZMQLIBDIR) -Wl,-rpath=$(ZMQLIBDIR) -lzmq
-LDFLAG_REC 	=	-I. -L$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread -lrt -L. -lzmq
+LDFLAG_REC 	=	-I. -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread -lrt -L$(ZMQLIBDIR) -Wl,-rpath=$(ZMQLIBDIR) -lzmq
 DESTDIR		?=	../docs
 
+HDF5 		?=	no
+HDF5_DIR 	?=	/opt/hdf5v1.10.0
 
-all: docs detUser detReceiver 
+ifeq ($(HDF5),yes)
+	LDFLAG_REC += -L$(HDF5_DIR)/lib  -Wl,-rpath=$(HDF5_DIR)/lib -lhdf5 -lhdf5_cpp -lsz -lz -DHDF5C 
+endif
+
+all: docs detUser slsMultiReceiver 
 #all: docs
 
 docs: createdocs docspdf docshtml removedocs
 
-createdocs: slsDetectorUsers.doxy slsDetectorUsers.h detectorData.h slsReceiverUsers.h mainClient.cpp mainReceiver.cpp
+createdocs: slsDetectorUsers.doxy mainClient.cpp mainReceiver.cpp
 	doxygen slsDetectorUsers.doxy	
 
 docspdf: 
@@ -35,18 +43,20 @@ detUser:$(SRC_DET)
 	mkdir -p bin
 	g++ -o bin/detUser $(SRC_DET) $(INCLUDES) $(LDFLAG_DET) -lm -lstdc++
 
-detReceiver:$(SRC_REC)
+slsMultiReceiver:$(SRC_REC)
 	echo "creating receiver"
+	echo $LDFLAG_REC
 	mkdir -p bin
-	g++ -o bin/detReceiver $(SRC_REC) $(INCLUDES) $(LDFLAG_REC) -lm -lstdc++
+	g++ -o bin/slsMultiReceiver $(SRC_REC) $(INCLUDES) $(LDFLAG_REC) -lm -lstdc++
-	
+	cp bin/slsMultiReceiver $(LIBDIR)
 	
 clean:
 	echo "cleaning for manual-api"
-	rm -rf bin/detUser bin/detReceiver slsDetectorUsersDocs
+	rm -rf bin/detUser bin/slsMultiReceiver bin/detReceiver slsDetectorUsersDocs
 	rm -rf slsDetectorUsersDocs
 	rm -rf $(DESTDIR)/html/slsDetectorUsersDocs
 	rm -rf $(DESTDIR)/pdf/slsDetectorUsersDocs.pdf
+	rm -rf $(LIBDIR)/slsMultiReceiver
 	
 
 

manual/manual-api/detectorData.h

@@ -1 +0,0 @@
-../../slsDetectorSoftware/slsDetectorAnalysis/detectorData.h

manual/manual-api/libSlsDetector.so

@@ -1 +0,0 @@
-../../build/bin/libSlsDetector.so

manual/manual-api/libSlsReceiver.so

@@ -1 +0,0 @@
-../../build/bin/libSlsReceiver.so

manual/manual-api/libzmq.a

@@ -1 +0,0 @@
-../../slsReceiverSoftware/include/libzmq.a

manual/manual-api/mainClient.cpp

@@ -54,7 +54,12 @@ int main(int argc,  char **argv) {
 
 
 	/** - slsDetectorUsers Object is instantiated with appropriate ID */
-	slsDetectorUsers *pDetector = new  slsDetectorUsers (id);
+	int ret = 1;
+	slsDetectorUsers *pDetector = new slsDetectorUsers (ret, id);
+	if (ret == 1) {
+		std::cout << "Error: Could not instantiate slsDetectorUsers" << std::endl;
+		return EXIT_FAILURE;
+	}
 
 
 	/** - if specified, load configuration file (necessary at least the first time it is called to properly configure advanced settings in the shared memory) */
@@ -71,11 +76,6 @@ int main(int argc,  char **argv) {
 
 	/** - registering data callback */
 	pDetector->registerDataCallback(&dataCallback, NULL);
-	/** - if receiver exists, enable data streaming from receiver to get the data */
-	pDetector->enableDataStreamingFromReceiver(1);
-	/** - create zmq sockets in client to enable data streaming in of data from receiver/different process */
-	pDetector->enableDataStreamingToClient(1);
-
 
 
 	/** - ensuring detector status is idle before starting acquisition. exiting if not idle */

manual/manual-api/mainReceiver.cpp

@@ -54,7 +54,7 @@ void sigInterruptHandler(int p){
  */
 void printHelp() {
 	cprintf(RESET, "Usage:\n"
-			"./detReceiver [start_tcp_port] [num_receivers] [1 for call back, 0 for none]\n\n");
+			"./slsMultiReceiver(detReceiver) [start_tcp_port] [num_receivers] [1 for call back, 0 for none]\n\n");
 	exit(EXIT_FAILURE);
 }
 
@@ -71,7 +71,7 @@ void printHelp() {
  */
 int StartAcq(char* filepath, char* filename, uint64_t fileindex, uint32_t datasize, void*p){
 	cprintf(BLUE, "#### StartAcq:  filepath:%s  filename:%s fileindex:%llu  datasize:%u ####\n",
-			filepath, filename, fileindex, datasize);
+			filepath, filename, (long long unsigned int)fileindex, datasize);
 
 	cprintf(BLUE, "--StartAcq: returning 0\n");
 	return 0;
@@ -83,45 +83,80 @@ int StartAcq(char* filepath, char* filename, uint64_t fileindex, uint32_t datasi
  * @param p pointer to object
  */
 void AcquisitionFinished(uint64_t frames, void*p){
-	cprintf(BLUE, "#### AcquisitionFinished: frames:%llu ####\n",frames);
+	cprintf(BLUE, "#### AcquisitionFinished: frames:%llu ####\n",(long long unsigned int)frames);
 }
 
+
 /**
  * Get Receiver Data Call back
  * Prints in different colors(for each receiver process) the different headers for each image call back.
- * @param frameNumber frame number
+ * @param metadata sls_receiver_header metadata
- * @param expLength real time exposure length (in 100ns) or sub frame number (Eiger 32 bit mode only)
- * @param packetNumber number of packets caught for this frame
- * @param bunchId bunch id from beamline
- * @param timestamp time stamp  in 10MHz clock (not implemented for most)
- * @param modId module id	(not implemented for most)
- * @param xCoord x coordinates (detector id in 1D)
- * @param yCoord y coordinates (not implemented)
- * @param zCoord z coordinates (not implemented)
- * @param debug debug values if any
- * @param roundRNumber (not implemented)
- * @param detType detector type see :: detectorType
- * @param version version of standard header (structure format)
  * @param datapointer pointer to data
- * @param datasize data size in bytes
+ * @param datasize data size in bytes.
  * @param p pointer to object
  */
-void GetData(uint64_t frameNumber, uint32_t expLength, uint32_t packetNumber, uint64_t bunchId, uint64_t timestamp,
+void GetData(char* metadata, char* datapointer, uint32_t datasize, void* p){
-		uint16_t modId, uint16_t xCoord, uint16_t yCoord, uint16_t zCoord, uint32_t debug, uint16_t roundRNumber, uint8_t detType, uint8_t version,
+	slsReceiverDefs::sls_receiver_header* header = (slsReceiverDefs::sls_receiver_header*)metadata;
-		char* datapointer, uint32_t datasize, void* p){
+	slsReceiverDefs::sls_detector_header detectorHeader = header->detHeader;
 
-	PRINT_IN_COLOR (modId?modId:xCoord,
+	PRINT_IN_COLOR (detectorHeader.modId?detectorHeader.modId:detectorHeader.row,
 			"#### %d GetData: ####\n"
-			"frameNumber: %llu\t\texpLength: %u\t\tpacketNumber: %u\t\tbunchId: %llu\t\ttimestamp: %llu\t\tmodId: %u\t\t"
+			"frameNumber: %llu\t\texpLength: %u\t\tpacketNumber: %u\t\tbunchId: %llu"
-			"xCoord: %u\t\tyCoord: %u\t\tzCoord: %u\t\tdebug: %u\t\troundRNumber: %u\t\tdetType: %u\t\t"
+			"\t\ttimestamp: %llu\t\tmodId: %u\t\t"
-			"version: %u\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
+			"row: %u\t\tcolumn: %u\t\treserved: %u\t\tdebug: %u"
-			xCoord, frameNumber, expLength, packetNumber, bunchId, timestamp, modId,
+			"\t\troundRNumber: %u\t\tdetType: %u\t\tversion: %u"
-			xCoord, yCoord, zCoord, debug, roundRNumber, detType, version,
+			//"\t\tpacketsMask:%s"
+			"\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
+			detectorHeader.row, (long long unsigned int)detectorHeader.frameNumber,
+			detectorHeader.expLength, detectorHeader.packetNumber, (long long unsigned int)detectorHeader.bunchId,
+			(long long unsigned int)detectorHeader.timestamp, detectorHeader.modId,
+			detectorHeader.row, detectorHeader.column, detectorHeader.reserved,
+			detectorHeader.debug, detectorHeader.roundRNumber,
+			detectorHeader.detType, detectorHeader.version,
+			//header->packetsMask.to_string().c_str(),
             ((uint8_t)(*((uint8_t*)(datapointer)))), datasize);
 }
 
 
 
+/**
+ * Get Receiver Data Call back (modified)
+ * Prints in different colors(for each receiver process) the different headers for each image call back.
+ * @param metadata sls_receiver_header metadata
+ * @param datapointer pointer to data
+ * @param datasize data size in bytes.
+ * @param revDatasize new data size in bytes after the callback.
+ * This will be the size written/streamed. (only smaller value is allowed).
+ * @param p pointer to object
+ */
+void GetData(char* metadata, char* datapointer, uint32_t &revDatasize, void* p){
+	slsReceiverDefs::sls_receiver_header* header = (slsReceiverDefs::sls_receiver_header*)metadata;
+	slsReceiverDefs::sls_detector_header detectorHeader = header->detHeader;
+
+	PRINT_IN_COLOR (detectorHeader.modId?detectorHeader.modId:detectorHeader.row,
+			"#### %d GetData: ####\n"
+			"frameNumber: %llu\t\texpLength: %u\t\tpacketNumber: %u\t\tbunchId: %llu"
+			"\t\ttimestamp: %llu\t\tmodId: %u\t\t"
+			"row: %u\t\tcolumn: %u\t\treserved: %u\t\tdebug: %u"
+			"\t\troundRNumber: %u\t\tdetType: %u\t\tversion: %u"
+			//"\t\tpacketsMask:%s"
+			"\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
+			detectorHeader.row, (long long unsigned int)detectorHeader.frameNumber,
+			detectorHeader.expLength, detectorHeader.packetNumber, (long long unsigned int)detectorHeader.bunchId,
+			(long long unsigned int)detectorHeader.timestamp, detectorHeader.modId,
+			detectorHeader.row, detectorHeader.column, detectorHeader.reserved,
+			detectorHeader.debug, detectorHeader.roundRNumber,
+			detectorHeader.detType, detectorHeader.version,
+			//header->packetsMask.to_string().c_str(),
+			((uint8_t)(*((uint8_t*)(datapointer)))), revDatasize);
+
+	// if data is modified, eg ROI and size is reduced
+	revDatasize = 26000;
+}
+
+
+
+
 /**
  * Example of main program using the slsReceiverUsers class
  *
@@ -209,7 +244,8 @@ int main(int argc, char *argv[]) {
 
 				/* 	- Call back for raw data */
 				cprintf(BLUE, "Registering     GetData() \n");
-				receiver->registerCallBackRawDataReady(GetData,NULL);
+				if (withCallback == 1) receiver->registerCallBackRawDataReady(GetData,NULL);
+				else if (withCallback == 2) receiver->registerCallBackRawDataModifyReady(GetData,NULL);
 			}
 
 

manual/manual-api/slsDetectorUsers.doxy

@@ -82,6 +82,10 @@ SOURCE_BROWSER	= YES
 
 PREDEFINED           = __cplusplus
  
-INPUT            = slsDetectorUsers.h detectorData.h slsReceiverUsers.h mainClient.cpp mainReceiver.cpp
+INPUT            = 		../../slsDetectorSoftware/slsDetector/slsDetectorUsers.h		\
+					 	../../slDetectorSoftware/slsDetectorAnalysis/detectorData.h 	\
+					 	../../slsReceiverSoftware/include/slsReceiverUsers.h 			\
+					 	mainClient.cpp 													\
+					 	mainReceiver.cpp
 
 OUTPUT_DIRECTORY = slsDetectorUsersDocs

manual/manual-api/slsDetectorUsers.h

@@ -1 +0,0 @@
-../../slsDetectorSoftware/slsDetector/slsDetectorUsers.h

manual/manual-api/slsReceiverUsers.h

@@ -1 +0,0 @@
-../../slsReceiverSoftware/include/slsReceiverUsers.h

manual/manual-api/zmq.h

@@ -1 +0,0 @@
-../../slsReceiverSoftware/include/zmq.h

manual/manual-client/Eiger_short.tex

@@ -18,17 +18,26 @@
 \tableofcontents
 
 \section{Usage}
+\subsection{Short description}
+Figure ~\ref{boards} show the readout board basic components on an Eiger half module. An half module can read up to 4 readout chips.  
+\begin{figure}[t]
+\begin{center}
+\includegraphics[width=1\textwidth]{Boards}
+\end{center}
+\caption{Picture with most relevant components of the EIGER readout system. The readout system starts with the Front End Boards (FEB) which performs data descrambling (also converts the packets from 12 $\to$ 16 bits) and rate correction. The BackEndBoard (BEB) has 2x2GB DDR2 memories and can perform data buffering (storing images on board) and data summation (16 bit $\to$ 32 bits). The controls to the detector are passed through the 1Gb, while in most installations, the data are sent out through the 10GB ethernet connection.} 
+\label{boards}
+\end{figure}
 
 \subsection{Mandatory setup - Hardware}
 An EIGER single module (500~kpixels) needs:
 \begin{itemize}
-\item A chilled (water+alcohol) at approximately 21~$^{\circ}$C, which needs to dissipate 85~W. For the 9M, a special cooling liquid is required: 2/3 deionized water and 1/3 ESA Type 48.
+\item A chilled (water+alcohol) at 21~$^{\circ}$C for a single module (500k pixels), which needs to dissipate 85~W (every module, i.e. for two half boards). For the 9M, 1.5M, a special cooling liquid is required: 2/3 deionized water and 1/3 ESA Type 48. This is important as the high temperature generated by the boards accelerate the corrosion due to Cu/Al reaction and the blockage of the small channels where the liquid flows, in particular near the face of the detector and if it is a parallel flow and not a single loop. The 9M and 1.5M run at 19~$^{\circ}$C.  
 \item A power supply (12~V, 8~A). For the 9~M, a special cpu is give to remotely switch on and off the detector: see section~\ref{bchip100}. 
-\item 2$\times$1~Gb/s Ethernet connectors to control the detector and, optionally, receive data at low rate. A DHCP server that gives IPs to the 1~Gb/s connectors of the detector is needed. Note that flow control has to be enabled on the switch you are using.
+\item 2$\times$1~Gb/s Ethernet connectors to control the detector and, optionally, receive data at low rate. A DHCP server that gives IPs to the 1~Gb/s connectors of the detector is needed. Note that flow control has to be enabled on the switch you are using, if you plan to read the data out from there. If not, you need to implement delays in the sending out of the data.
-\item 2$\times$10~Gb/s transceivers to optionally, receive data at high rate.
+\item 2$\times$10~Gb/s transceivers to optionally, receive data at high rate. The 10Gb/s transceiver need to match the wavelength (long/short range) of the fibers chosen by the beamline infrastructure.
 \end{itemize}
 The equipment scales linearly with the number of modules.
-Figure~\ref{fig:1} shows the relationship between the \textbf{Client} (which sits on a beamline control PC), the \textbf{Receiver} (which can run in multiple instances on one or more PCs which receive data from the detector. The receiver(s) does not necessary have to be running on the same PC as the client.) It is important that the receiver is closely connected to the detector (they have to be on the same network). Note that if you implement the 1Gb/s readout only: client, receiver and detector have to be all three in the same network. If you implement the 10Gb/s readout, then client, the 1~GbE of the detector and the receiver have to stay on the 1GbE. But the receiver data receiving device and the 10GbE detector can be on their private network, minimizing the missing packets.  
+Figure~\ref{fig:1} shows the relationship between the \textbf{Client} (which sits on a beamline control PC), the \textbf{Receiver} (which can run in multiple instances on one or more PCs which receive data from the detector. The receiver(s) does not necessary have to be running on the same PC as the client.) The username under which the receiver runs is the owner of the data files, if using our implementation. It is important that the receiver is closely connected to the detector (they have to be on the same network). Note that if you implement the 1Gb/s readout only: client, receiver and detector have to be all three in the same network. If you implement the 10Gb/s readout, then client, the 1~GbE of the detector and the receiver have to stay on the 1GbE. But the receiver data receiving device and the 10GbE detector can be on their private network, minimizing the missing packets.  
 
 \begin{figure}[t]
 \begin{center}
@@ -41,7 +50,7 @@ Figure~\ref{fig:1} shows the relationship between the \textbf{Client} (which sit
 The Client talks to control over 1~Gb Ethernet connection using TCP/IP to the detector and to the receiver. The detector sends data in UDP packets to the receiver. This data sending can be done over 1~Gb/s or 10~Gb/s. 
  
 \begin{itemize}
-\item \textbf{Switch on the detector only after having started the chiller: the 500k single module and the 1.5M at cSAXS have a hardware temperature sensor, which will power off the boards if the temperature is too high. Note that the detector will be power on again as soon as the temperature has been lowered. The 9M will not boot up without the correct waterflow and temperature has it has an integrated flowmeter.} 
+\item \textbf{Switch on the detector only after having started the chiller: the 500k single module and the 1.5M at cSAXS/OMNY have a hardware temperature sensor, which will power off the boards if the temperature is too high. Note that the detector will be power on again as soon as the temperature has been lowered. The 9M will not boot up without the correct waterflow and temperature has it has an integrated flowmeter.} 
 \item \textbf{Switch on the detector only after having connected all the cables and network. EIGER is unable to get IP address after it has been switched on without a proper network set up. In that case switch off and on the detector again.}
 \end{itemize}
 
@@ -73,28 +82,26 @@ You can also Check temperatures and water flow in a browser (from the same subne
 
 \subsection{Mandatory setup - Receiver}
 
-The receiver is a process run on a PC closely connected to the detector. Open one receiver for every half module board (remember, a module has two receivers!!!) . Go to {\tt{slsDetectorsPackage/bin/}}, \textbf{slsReceiver} should be started on the machine expected to receive the data from the detector.
+The receiver is a process run on a PC closely connected to the detector. Open one receiver for every half module board (remember, a module has two receivers!!!) . Go to {\tt{slsDetectorsPackage/build/bin/}}, \textbf{slsReceiver} should be started on the machine expected to receive the data from the detector.
 
 \begin{itemize}
 \item {\tt{./slsReceiver --rx\_tcpport xxxx}} 
 \item {\tt{./slsReceiver --rx\_tcpport yyyy}}
 \end{itemize}
-where xxxx, yyyy are the tcp port numbers. Use 1955 and 1956 for example. Note that in older version of the software {\tt{--mode 1}} was used only for the ``bottom'' half module. Now, the receiver for the bottom is open without arguments anymore, but still in the configuration file one needs to write {\tt{n:flippeddatax 1}}, where {\tt{n}} indicated the half module number, 1 if it is a module.
+where xxxx, yyyy are the tcp port numbers. Use 1955 and 1956 for example. The receiver for the bottom is open without arguments but still in the configuration file one needs to write {\tt{n:flippeddatax 1}}, where {\tt{2n+1}} indicated the half module number, 1 if it is a module.
 \\ Open as many receiver as half module boards. A single module has two half module boards.
 
-From the software version 3.0.1, one can decide weather start a zmq callback from the receiver to the client (for example to visualize data in the slsDetectorGui or another gui). If the zmq steam is not required (cased of the command line for example, one can switch off the streaming with {\tt{./sls\_detector\_put rx\_datastream 0}}, enable it with {\tt{./sls\_detector\_put rx\_datastream 1}}. In the case of inizialising the stream to use the slsDetectorGui, nothing needs to be taken care of by the user. If instead you want to stream the streaming on different channels, the zmq port of the client can be set stealing from the slsDetectorGui stream having {\tt{./sls\_detector\_put n:zmqport 300y}}, where n is each half module independently, matching the receiver stream {\tt{./sls\_detector\_put n:rx\_zmqport 300y}}.
+From the software version 3.0.1, one can decide weather start a zmq callback from the receiver to the client (for example to visualize data in the slsDetectorGui or another gui). If the zmq steam is not required (cased of the command line for example, one can switch off the streaming with {\tt{./sls\_detector\_put rx\_datastream 0}}, enable it with {\tt{./sls\_detector\_put rx\_datastream 1}}. In the case of initializing the stream to use the slsDetectorGui, nothing needs to be taken care of by the user. If instead you want to stream the streaming on different channels, the zmq port of the client can be set stealing from the slsDetectorGui stream having {\tt{./sls\_detector\_put zmqport 300y}}. Note that if this is done globally (not for every half module n independently, then the client automatically takes into account that for every half module, there are 2 zmq stream. The receiver stream {\tt{./sls\_detector\_put rx\_zmqport 300y}} has to match such that the GUI can work. 
+If one desires to set the zmqport manually, he offset has to be taken into account: {\tt{./sls\_detector\_put 0:rx\_zmqport 300y}}, {\tt{./sls\_detector\_put 1:rx\_zmqport 300y+2}} and so on..
 
 
-There is an example code that can be compiled in {\tt{manual/manual-api/mainReceiver.cpp}} and gives the executable {\tt{./detReceiver}}, use it with two or more receivers to open all receivers in one single terminal: {\tt{./detReceiver startTCPPort numReceivers withCallback}}, where startTCPPort assumes the other ports are consecutively increased.
+{\tt{slsMultiReceiver}} uses two or more receivers in one single terminal: {\tt{./slsMultiReceiver startTCPPort numReceivers withCallback}}, where startTCPPort assumes the other ports are consecutively increased.
-
 
+The command {\tt{r\_framesperfile}} sets the number of frames written in the same file. By default now it is 10000. It can be changes. It needs to be lowered particularly if one wants to parallelize the following conversion of the files. 
 
 
 \subsection{Mandatory setup - Client}
 
-\underline{In the case of cSAXS, the detector software is installed on:}\\
-\underline{/sls/X12SA/data/x12saop/EigerPackage/slsDetectorsPackage}
-
 The command line interface consists in these main functions:
 \begin{description}
 \item[sls\_detector\_acquire] to acquire data from the detector
@@ -166,15 +173,15 @@ Other important settings that are configured in the {\tt{setup.det}} file are:
 \begin{itemize}
 \item {\tt{tengiga 0/1}}, which sets whether the detector is enabled to send data through the 1~or the 10~Gb Ethernet.
 \item {\tt{flags parallel/nonparallel}}, which sets whether the detector is set in parallel acquisition and readout or in sequential mode. This changes the readout time of the chip and affects the frame rate capability (faster is {\tt{parallel}}, with higher noise but needed when the frame rate is $>2$~kHz. 
-\item {\tt{dr 32/16}} sets the detector in autosumming mode (32 bit counter or not autosumming, 12 bit out of the chip). This is strictly connected to what is required for the readout clock of chip. See next point.
+\item {\tt{dr 32/16/8/4}} sets the detector in autosumming mode (32 bit counter or not autosumming, 12 bit out of the chip). This is strictly connected to what is required for the readout clock of chip. See next point.
 \item {\tt{clkdivider 0/1/2}}. Changes the readout clock: 200, 100, 50~MHz (also referred to as full, half, quarter speed). Note that autosumming mode ({\tt{dr 32}} only works at {clkdivider 2}=quarter speed). By selecting Refer to readout timing specifications in~section\ref{timing} for how to set the detector. 
-\item {\tt{flags continuous/storeinram}}. Allows to take frame continuously or storing them on memory. Normally {\tt{continuous}} should be used. Enabling the  {\tt{stroreinram}} mode allows you to obtain the maximum frame rate, but at the expenses to have to receive the data all at the end of the acquisition. Refer to readout timing specifications in section~\ref{timing} for how to set the detector.
+\item {\tt{flags continuous/storeinram}}. Allows to take frame continuously or storing them on memory. Users should use the {\tt{continuous}} flags. Enabling the {\tt{stroreinram}} flag makes the data to be sent out all at the end of the acquisition. Refer to readout timing specifications in section~\ref{timing} for how to set the detector. Examples will be given in section~\ref{}.
 \end{itemize}
 
 One should notice that, by default, by choosing the option {\tt{dr 32}}, then the software automatically sets the detector to  {\tt{clkdivider 2}}. By choosing the option {\tt{dr 16}}, the software automatically sets the detector to  {\tt{clkdivider 1}}. One needs to choose {\tt{clkdivider 0}} after setting the {\tt{dr 16}} option to have the fastest frame rate. 
 We would recommend expert users (beamline people) to write their parameters file for the users. 
 
-\section{API versioning}
+\section{API versioning} \label{api}
 The eigerDetectorServer running on the boards has a versioning API scheme that will make it crash if used with a wrong firmware.
 You can also check your versioning by hand with the code:
 \begin{verbatim}
@@ -194,12 +201,18 @@ Killing and starting the server on the boards allows you to check the firmware v
 \section{Setting up the threshold}
 \begin{verbatim}
 sls_detector_put 0-trimen N xxxx yyyy zzzz
-sls_detector_put 0-settings standard #[veryhighgain/highgain/lowgain/verylowgain] also possible
+sls_detector_put 0-settings standard 
-sls_detector_put 0-threshold energy_in_eV
+sls_detector_put 0-threshold energy_in_eV standard
 \end{verbatim}
 The first line requires to specify how many ({\tt{N}}) and at which energies in eV {\{tt{xxxx}}, {\tt{yyyy}}, {\tt{zzzz}} and so on) trimmed files were generated (to allow for an interpolation). This line should normally be included into the {\tt{mydetector.config}} file and should be set for you by one of the detector group.
 NORMALLY, in this new calibration scheme, only {\tt{settings standard}} will be provided to you, unless specific cases to be discussed.
-The threshold at 6000 eV , for example would be set as:{\tt{sls\_detector\_put 0-threshold 6000}}.
+The threshold at 6000 eV , for example would be set as:{\tt{sls\_detector\_put 0-threshold 6000 standard}}.
+
+For \E, at the moment normally only {\tt{standard}} settings are possible.
+ {\tt{lowgain}}, {\tt{verylowgain}}, {\tt{veryhighgain}} and {\tt{highgain}} are theoretically possible, but we never calibrate like this. They could be implemented later if needed. 
+
+Notice that setting the threshold actually loads the trimbit files (and interpolate them between the closest calibration energies) so it is time consuming. 
+The threshold is expressed in (eV) as the proper threshold setting, i.e. normally is set to 50\% of the beam energy.  
 
 We have added a special command, {\tt{thresholdnotb}}, which allows to scan the threshold energy without reloading the trimbits at every stage. One can either keep the trimbits at a specific value (es.32 if the range of energies to scan is large) or use the trimbits from a specific energy (like a central energy).
 \begin{verbatim}
@@ -216,12 +229,7 @@ sls_detector_put 0-period 0[time_is_s]
 \end{verbatim}
 In this acquisition 10 consecutive 1~s frames will be acquired. Note that {\tt{period}} defines the sum of the acquisition time and the desired dead time before the next frame. If {\tt{period}} is set to 0, then the next frame will start as soon as the detector is ready to take another acquisition. \\
 
-For \E, at the moment 5 settings are possible: {\tt{standard}}, {\tt{lowgain}}, {\tt{verylowgain}}, {\tt{veryhighgain}} and {\tt{highgain}}. According to the setting chosen, one can reach different requirements (low noise or high rate). Refer to the settings requirements for your detector.\\ 
+%\underline{At cSAXS, the {\tt{settingsdir}} and {\tt{caldir}} are in}\\\underline{/sls/X12SA/data/x12saop/EigerPackage/calibrations/}\\ 
-Notice that the option {\tt{settings standard/highgain/lowgain/veryhighgain/verylowgain}} actually loads the trimbit files so it is time consuming. Only setting the {\tt{threshold}} does not load trimbit files.  
-
-The threshold is expressed in (eV) as the proper threshold setting, i.e. normally is set to 50\% of the beam energy.  
-
-\underline{At cSAXS, the {\tt{settingsdir}} and {\tt{caldir}} are in}\\\underline{/sls/X12SA/data/x12saop/EigerPackage/calibrations/}\\ 
 
 You need to setup where the files will be written to
 \begin{verbatim}
@@ -247,23 +255,28 @@ sls_detector_get receiver
 \end{verbatim}
 
 There is a more complex way of performing an acquisition, that is useful for debugging and in case one wants a non blocking behavior: 
-\begin{itemize}
+
+You can then reset to zero the number of frames caught, then  start the receiver and the detector:
+\begin{enumerate}
+\item {\tt{sls\_detector\_put 0-resetframescaught 0}} 
 \item {\tt{sls\_detector\_put 0-receiver start}} 
 \item {\tt{sls\_detector\_put 0-status start}} 
-\end{itemize}
+\end{enumerate}
 
 You can poll the detector status using:
 \begin{verbatim}
 sls_detector_get 0-status 
 \end{verbatim}
-When the detector is {\tt{idle}}, then you need to stop the receiver doing:
+When the detector is {\tt{idle}}, then the acquisition is done but the receiver could still be receiving data. If you want, you can check if the receiver is finished receiving as many frames as you were expecting (this is optional but required for many many frames acquisition or when using some delays to send data at very high frame rate.
-\begin{itemize}
+\begin{enumerate}
+\setcounter{enumi}{3}
+\item {\tt{sls\_detector\_get framescaught}} 
+\end{enumerate}
+Then you can stop the receiver as well now:
+\begin{enumerate}
+\setcounter{enumi}{4}
 \item {\tt{sls\_detector\_put 0-receiver stop}} 
-\end{itemize}
+\end{enumerate}
-You can then reset to zero the number of frames caught, if you desire:
-\begin{itemize}
-\item {\tt{sls\_detector\_put 0-resetframescaught 0}} 
-\end{itemize}
 
 The detector will not accept other commands while acquiring. If an acquisition wishes to be properly aborted, then:
 \begin{itemize}
@@ -271,11 +284,44 @@ The detector will not accept other commands while acquiring. If an acquisition w
 \end{itemize}
 this same command can be used after a non proper abortion of the acquisition to reset to normal status the detector.
 
+\section{Gap pixels inside a module}
+A module is composed of 2$\times$4 chips. Each chip is of dimension 256$\times$256 pixels. There is no dead area in a module, as a single sensor covers the 8 chips. The physical pixels at the border of the chips in the sensor are double in size, to allow not to loose photons in the gaps between the chip alignment. They count double what the other normal pixels would count. In the corner between chips, the pixels are 4-times the normal size. See figure~\ref{fgappix} to check the geometry.
+
+\begin{figure}[t]
+\begin{center}
+\includegraphics[width=0.9\textwidth]{GapPixels}
+\end{center}
+\caption{Geometry of gap pixels between a module.}
+\label{fgappix}
+\end{figure}
+
+It is possible to interpolated the value on the larger pixels by splitting the events (or properly interpolating) introducing a virtual pixel for every double pixel, or 3 virtual pixels for every corner. In this way the counts of a single large pixel can be shared among the correct amount of pixels of the normal dimension.     
+
+The gap pixels can be added for the slsDetectorGui, from the datacall back or stealing the zmq port from the GUI (see later). The detector size can be added in the configuration file as first thing. 
+
+Putting the long side of the module first always as a convection for the code, WITHOUT GAP PIXELS an EIGER module is:
+\begin{verbatim}
+detsizechan 1024 512 
+\end{verbatim}
+and the client needs to be set {\tt{sls\_detector\_put  gappixels 0}}, which is the default behavior.\\
+If you want to have GAP PIXELS included: 
+\begin{verbatim}
+detsizechan 1030 514 
+\end{verbatim}
+and the client needs to be set {\tt{sls\_detector\_put  gappixels 1}}.
+
+The size of the gap pixels between modules to insert is 
+\begin{verbatim}
+   GapPixelsBetweenModules_x = 8
+   GapPixelsBetweenModules_y = 36
+\end{verbatim}
+where the {\tt{GapPixelsBetweenModules\_x}} are the one on the short side of the module, while {\tt{GapPixelsBetweenModules\_y}} are the ones on the long side of the module (where the wirebonds take physical space).
+  
 \section{Readout timing- maximum frame rate}\label{timing}
 IMPORTANT: to have faster readout and smaller dead time, one can configure {\tt{clkdivider}}, i.e. the speed at which the data are read, i.e. 200/100/50~MHz for {\tt{clkdivider 0/1/2}} and the dead time between frames through {\tt{flags parallel}}, i.e. acquire and read at the same time or acquire and then read out.
 The configuration of this timing variables allows to achieve different frame rates. NOTE THAT IN EIGER, WHATEVER YOU DO, THE FRAME RATE LIMITATIONS COME FROM THE NETWORK BOTTLENECK AS THE HARDWARE GOES FASTER THAN THE DATA OUT.
 
-In the case of REAL CONTINUOUS readout, i.e. continuous acquire and readout from the boards (independent on how the chip is set), the continuous frame rates are listed in table~\ref{tcont}:
+In the case of REAL CONTINUOUS readout, i.e. continuous acquire and readout from the boards (independent on how the chip is set), the continuous frame rates are listed in table~\ref{tcont}.
 \begin{table} 
 \begin{tabular}{|c|c|c|c|}
 \hline
@@ -294,10 +340,9 @@ GbE & dynamic range & continuos maximum frame rate(Hz) & minimum period ($\mu$s)
 10 & 4 & \textbf{10240} & 98\\
 \hline
 \end{tabular}
-\caption{Frame rate limits for the CONTINUOS streaming out of images.} 
+\caption{Frame rate limits for the CONTINUOS streaming out of images, i.e. the data rate out is just below 1Gb/s or 10Gb/s.} 
 \label{tcont}\end{table}
-Note that in the {\tt{continuous}} flag mode, some buffering is still done on the memories, so a higher frame rate than the proper real continuous one can be achieved. Still, this extra buffering is possible till the memories are not saturated. 
+ Note that in the {\tt{continuous}} flag mode, some buffering is still done on the memories, so a higher frame rate than the proper real continuous one can be achieved. Still, this extra buffering is possible till the memories are not saturated. The number of images that can be stored on the DDR2 on board memories are listed in table~\ref{timgs}.
-The number of images that can be stored on memories are listed in table~\ref{timgs}:
 \begin{table}
 \begin{tabular}{|c|c|}
 \hline
@@ -314,72 +359,194 @@ dynamic range & images\\
 \label{timgs}
 \end{table}
 
-The maximum frame rate achievable with 10~GbE, {\tt{dr 16}}, {\tt{flags continuous}}, {\tt{flags parallel}},{\tt{clkdivider 0}}, \textbf{6.1~kHz}. This is currently limited by the connection between the Front End Board and the Backend board. We expect the 32 bit mode limit to be \textbf{2~kHz} ({\tt{clkdivider 2}}).
+The maximum frame rate achievable with 10~GbE, {\tt{dr 16}}, {\tt{flags continuous}}, {\tt{flags parallel}},{\tt{clkdivider 0}}, \textbf{6.1~kHz}. This is currently limited by the connection between the Front End Board and the Backend board. We expect the 32 bit mode limit, internally, to be \textbf{2~kHz} ({\tt{clkdivider 2}}).
  In dynamic range {\tt{dr 8}} the frame rate is \textbf{11~kHz} and for{\tt{dr 4}} is \textbf{22~kHz}. For 4 and 8 bit mode the frame rate are directly limited by the speed of the detector chip and not by the readout boards.    
 
-In table~\ref{tframes} is a list of all the readout times in the different configurations:
+\subsection{Minimum time between frames and Maximum frame rate}
+
+We need to leave enough time between an exposure and the following. This time is a combination of the time required by the chip, by the readout boards and eventually extra time to reduce some appearance of cross talk noise between the digital and analog parts of the chip. 
+\textbf{It is essential to set the {\tt{period}} of the detector, defined as the {\tt{exptime}} plus an extra time, that needs to be at least the chip/board readout time. If this is set wrong (it is $<$ {\tt{exptime}} plus chip/board readout time), then the detector takes the minimum time it can, but you are in a not controlled frame rate situation.} 
+
+The expected time difference between frames given by the pure chip readout time is in Table~\ref{tchipro}.    
+\begin{tiny}
+\begin{table}
+\begin{flushleft}
+\begin{tabular}{|c|c|c|c|}
+\hline
+\tiny{dr} & \tiny{clkdivider} & \tiny{expected chip readout t($\mu$s)} & \tiny{measured chip readout t($\mu$s)}\\
+\hline
+4 & 0 & 41 & 40\\
+4 & 1 & 82 & 84\\
+4 & 2 & 123 & 172\\
+\hline
+\hline
+8 & 0 & 82 & 82\\
+8 & 1 & 164 & 167\\
+8 & 2 & 328 & 336\\
+\hline
+\hline
+12 & 0 & 123 &122\\
+12 & 1 & 246 & 251\\
+12 & 2 & 491 & 500\\
+\hline
+\end{tabular}
+\caption{Readout time required from the chip to readout the pixels. The numbers are obtained using equation~\ref{dtnonparallel}.}
+\label{tchipro}
+\end{flushleft}
+\end{table}
+\end{tiny}
+
+The {\tt{period}} is s is defined as:
+\begin{equation} \label{period}
+\textrm{period}  = \textrm{exptime} + \textrm{minimum time between frames}
+\end{equation}
+where the 'minimum time between frames' and the minimum period will be discussed in Table~\ref{tframes}.
 \begin{tiny}
 \begin{table}
 \begin{flushleft}
 \begin{tabular}{|c|c|c|c|c|c|c|c|}
 \hline
-\tiny{dr} & \tiny{clkdivider} & \tiny{flags} & \tiny{readout t($\mu$s)} & \tiny{max frame rate (kHz)} & \tiny{max exptime ($\mu$s)} & \tiny{min period ($\mu$s)} & \tiny{max imgs (nominal/our network)}\\
+\tiny{dr} & \tiny{clkdivider} & \tiny{flags} & \tiny{$\Delta$t frames($\mu$s) } &  \tiny{max FR (kHz)} & \tiny{min period ($\mu$s)} & \tiny{meas. period ($\mu$s)} & \tiny{max imgs (nominal/our network)}\\
 \hline
-4 & 0 & parallel & 3.4 & 22 &  40 & 44 & 30k/50k\\
+4 & 0 & \tiny {parallel} & 3.4 & 22  & 44 & 44.01 & 30k/50k\\
 \hline
-4 & 0 & nonparallel & 44 & 21 &  3 & 49 & 30k/50k\\
+4 & 1 & \tiny {parallel} & 6 & 10.5 & 92 & 92.02 & 30k/100k\\
 \hline
-4 & 1 & parallel & 6 & 10.5 &  85 & 92 & 30k/100k\\
+4 & 2 & \tiny {parallel} & 11.2 & 5.4 & 197& 197.01 & infinite\\
-\hline
-4 & 1 & nonparallel & 88.7 & 10.5 & 3 & 93 & 30k/100k\\
-\hline
-4 & 2 & parallel & 11.2 & 5.4 &  185 & 197 & infinite\\
-\hline
-4 & 2 & nonparallel & 176.5 & 5.4 &  3 & 180 & infinite\\
 \hline
 \hline
-8 & 0 & parallel & 3.4 & 11.1 &  85 & 89 & 15k/24k\\
+8 & 0 & \tiny {parallel} & 3.4 & 11.1 & 89 & 89.01 & 15k/24k\\
 \hline
-8 & 0 & nonparallel & 85.7 & 11.1 & 3 & 91 & 15k/24k\\
+8 & 1 & \tiny {parallel} & 6.1 & 5.7 & 181 & 181.01 & 15k/52k\\
 \hline
-8 & 1 & parallel & 6.1 & 5.7 &  174 & 181 & 15k/52k\\
+8 & 2 & \tiny {parallel} & 11.2 &  2.9 &  342 & 342.01 & infinite\\
-\hline
-8 & 1 & nonparallel & 170.5 & 5.7 &  3 & 175 & 15k/52k\\
-\hline
-8 & 2 & parallel & 11.2 &  2.9 &  330 & 342 & infinite\\
-\hline
-8 & 2 & nonparallel & 340.3 &  2.9 &  3 & 344 & infinite\\
 \hline
 \hline
-16 & 0 & parallel & 3.4 & 6 & 164 & 168 & 8k/12k\\
+16 & 0 & \tiny {parallel} & 3.4 & 6.1 & (126+38)* =164 & 164.02 & 8k/12k\\
 \hline
-16 & 0 & nonparallel &  126 & 3.4& 164 & 295 & 8k/23k\\
+16 & 0 & \tiny {nonparallel} &  127 & 5.6 & (126+52)*= 179 & 179.01& 8k/23k\\
 \hline
-16 & 1 & parallel &  6.1 & 2.9&  339 & 346 & 8k/28k\\
+16 & 1 & \tiny {parallel} &  6.1 & 3.9 &  257 & 257.01 & 8k/28k\\
 \hline
-16 & 1 & nonparallel & 255 & 1.7&  339 & 592 & infinite\\
+16 & 1 & \tiny {nonparallel} & 255 & 3.3 &  303 & 303.01 & infinite\\
 \hline
-16 & 2 & parallel &  11 & 1.5& 66 & 78 & infinite \\
+16 & 2 & \tiny {parallel} &  11.2 & 1.9 & 526 & 526.2 & infinite \\
 \hline
-16 & 2 & nonparallel & 504 & 0.85 & 7 & 512 & infinite\\
+16 & 2 & \tiny {nonparallel} & 505 & 1.8  & 555 & 555.01& infinite\\
-\hline
-\hline
-32 & 2 & parallel &  11 & 2&  & &\\
-\hline
-32 & 2 & nonparallel & 504 & $<2$&  & &\\
 \hline
+%32 & 2 & parallel &  11 & 2&  & &\\
+%\hline
+%32 & 2 & nonparallel & 504 & $<2$&  & &\\
+%\hline
 \end{tabular}
-\caption{Readout settings. The {\tiny{min exptime}} possible is 5$-$10~$\mu$s. This is due to the time to pass the pixel enable signal in the whole chip.}
+\caption{Readout settings. The {\tiny{min exptime}} possible is 5$-$10~$\mu$s. This is due to the time to pass the pixel enable signal in the whole chip. The time between frames ($\Delta$t) has been measured with the oscilloscope and the maximum frames rate (max FR) has been tested with an external gating from a pulse generator at known frequency. The minimum period is obtained as 1/$\textrm{max frame rate}$.}
 \label{tframes}
 \end{flushleft}
 \end{table}
 \end{tiny}
-\textbf{As if you run too fast, the detector could become noisier, it is important to match the detector settings to your frame rate. This can be done having more parameters files and load the one suitable with your experiment.} We experienced that {\tt{highgain}} settings could not be used at 6~kHz.
+
-\textbf{We recommend to use the detector in 32 bit mode with {\tt{clkdivider 2}}, {\tt{flags parallel}}. We recommend to use the detector in 16 bit mode with {\tt{clkdivider 1}}, {\tt{flags parallel}}}. In general, choose first the desired dead time: this will tell you if you want to run in parallel or non parallel mode. Then, choose the maximum frame rate you want to aim, not exceeding what you aim for not to increase the noise.
+\textbf{From software version 4.0.0, there is a very useful function {\tt{sls\_detector\_get measuredperiod}} which return the measured period AFTER the acquisition. This is important to check that the settings to obtain the targeted frame rate was correct.} 
+
+\textbf{If you run too fast, the detector could become noisier (see problem shooting), it is important to match the detector settings to your frame rate. This can be done having more parameters files and load the one suitable with your experiment.} We experienced that with low energy settings could not reach 6~kHz and no noise.
+
+In 16 bit mode, it could make sense, in case of noise and low threshold to either reduce the frame rate:
+\begin{equation} 
+\textrm{new period}  = \textrm{exptime} + \textrm{minimum time between frames} + (\textrm{10$-$20 }\mu \textrm{s})
+\end{equation}
+to let the signal settle  or,  if the frame rate is important, leave the {\tt{period}} at the same value but reduce the {\tt{exptime}}:
+\begin{equation} 
+\textrm{new exptime}  = \textrm{old exptime} - (\textrm{10$-$20 }\mu \textrm{s})
+\end{equation}
+
+In general, choose first the desired dead time: this will tell you if you want to run in parallel or non parallel mode, although most likely it is parallel mode. Then, choose the maximum frame rate you want to aim, not exceeding what you aim for not to increase the noise. In 4 and 8 bit modes it makes no sense to run nonparallel as the exposure time is too small compared to the readout time. 
+
+\subsubsection{4 and 8 bit mode}
+In {\tt{parallel}} mode, the minimum time between frames is due to the time required to latch the values of the counter with capacitors. These values are determined in firmware and they can be estimated as:
+
+\begin{equation} \label{dtparallel}
+\textrm{time between frames, parallel} = 4 \mu s \cdot (clkdivider+1)
+\end{equation}
+
+This time is independent on the {\tt{dr}}.
+
+In {\tt{nonparallel}} mode, it is easily possible to calculate the required asic readout time. 
+Indeed a block of (8*256) pixels are readout, the bits pixel are the {\tt{dr}} and the speed of readout is 5ns/bit *({\tt{clkdivider}}+1) : 
+
+\begin{equation}\label{dtnonparallel}
+\textrm{asics readout time} = 5ns/bit \cdot 2^{(clkdivider+1)} \cdot dr \cdot (8*256) + 4 \mu s \cdot (clkdivider+1)
+\end{equation}
+
+While we expose the next frame, we still need to readout the previous frame, so we need to guarantee that the period is large enough at least to readout the frame. So the maximum frame rate has to be $1/(\textrm{asic readout time})$. The minimum period has to be equal to the asic readout time. 
+
+\subsubsection{16 bit mode}
+
+A similar situation happens in 16 bit mode, where this is more complicated because of three things:
+\begin{enumerate}
+\item The chip actual {\tt{dr}} is 12 bit
+\item The chip is readout as 12-bit/pixel, but the FEB inflates the pixel values to 16-bits when it passes to the BEB. This means that effectively the FEB to BEB connection limits the data throughput in the same way as if the {\tt{dr}} of the chip would really be 16 bits.
+\item While in 4 and 8 bit mode it makes no sense to run in {\tt{nonparallel}} mode as the exptime/dead time ratio would be not advantageous, in 16 bit mode, one can choose how to run more freely.
+\end{enumerate}
+
+If we are in parallel mode, the dead time between frames, is also here described by equation~\ref{dtparallel}. If we are in {\tt{nonparallel}} mode, the dead time between frames is defined by \ref{dtnonparallel} ONLY for {\tt{clkdivider}} 1 and 2. So the maximum frame rate has to be $1/(\textrm{chip readout time})$ in this case. Only for {\tt{clkdivider}} 0 we hit some limitation in the bandwidth of The FEB $\to$ BEB connection. In this case, the maximum frame rate is lowered compared to what expected.
+
+\subsubsection{32 bit mode}
+The autosumming mode of Eiger is the intended for long exposure times (frame rate of order of 100Hz, PILATUS like). A single acquisition is broken down into many smaller 12-bit acquisitions, each of a {\tt{subexptime}} of 2.621440~ms by default. Normally, this is a good default value to sustain an intensity of $10^6$ photons/pixel/s with no saturation. To change the value of {\tt{subexptime}} see section~\ref{advanced}. 
+
+The time between 12-bit subframes are listed in table~\ref{t32bitframe}.  
+\begin{tiny}
+\begin{table}
+\begin{flushleft}
+\begin{tabular}{|c|c|c|c|c|c|}
+\hline
+\tiny{dr} & \tiny{clkdivider} & \tiny{flags} & \tiny{t difference between subframes($\mu$s)} & \tiny{max internal subframe rate (kHz)} & \tiny{maximum frame rate (Hz)}\\
+\hline
+32 & 2 & parallel & 12 & 2 & 170\\
+\hline
+32 & 2 & nonparallel & 504 & $<2$ & 160\\
+\hline
+\end{tabular}
+\caption{Timing for the 32bit case. The maximum frame rate has been computed assuming 2 subframes of default {\tt{subexptime}} of 2.62144 ms.}
+\label{t32bitframe}
+\end{flushleft}
+\end{table}
+\end{tiny}
+
+\textbf{The exposure time brokend up rounding up to the full next complete subframe that can be started.}
+The number of subframes composing a single 32bit acquisition can be calculated as:
+\begin{equation}
+\textrm{\# subframes}= (int) (\frac{\textrm{exptime (s)}}{\textrm{subexptime (s) + difference between frames (s)}}+0.5)
+%\label{esubframes}
+\end{equation}
+This also means that {\tt{exptime}}$<${\tt{subexptime}} will be rounded to{\tt{subexptime}}. If you want shorter acquisitions, either reduce the {\tt{subexptime}} or switch two 16-bit mode (you can always sum offline if needed).   
+
+From release 4.0.0, an extra {\tt{flag overflow/nooverflow}} is added, with {\tt{nooverflow}} default:
+\begin{itemize}
+\item {\tt{nooverflow}}: the internal 12-bit result is summed, even if there was saturation of the 12-bit counter (4095) in any of the subframes. Note that if there is saturation for every subframe, you might get as a result a value of the counter equal to (4095$\times$~number~of~subframes), which you need to correctly identify. On the other hand if the saturation occurred only one time, you will get something "close'' to the real number.
+\item {\tt{overflow}}: In this case, even if a pixel saturate only 1 time in a subframe, you will be returned as a value of the counter for that pixel: $2^{32}-1$, i.e. 4294967295.  
+\end{itemize}
+
+The UDP header will contain, after you receive the data, the effective number of subframe per image (see section~\ref{UDP}) as  "SubFrame Num or Exp Time", i.e. the number of subframes recorded  (32 bit eiger).
+The effective time the detector has recorded data can be computed as:
+\begin{equation}
+\textrm{effective exptime}=(\textrm{subexptime})\cdot (\textrm{\# subframes})
+%\label{esubframes}
+\end{equation}
+
+ From release 4.0.0, a configurable extra time difference between subframes can be introduced for the parallel mode, so that some noise appearing in detectors at low threshold can be removed. This is obtained through the {\tt{subdeadtime}}. You need to add values specific for your detector (ask the detector group). Typically, values between 15-40~$\mu$s should be used (for the 9M it is currently 200~$\mu$s due to a noisier module).
 
 
-\section{External triggering options}
+
-The detector can be setup such to receive external triggers. Connect a LEMO signal to the TRIGGER IN connector in the Power Distribution Board. The logic 0 for the board is passed by low level 0$-$0.7~V, the logic 1 is passed to the board with a signal between 1.2$-$5~V. Eiger is 50~$\Omega$ terminated. By default the positive polarity is used (negative should not be passed to the board).  
+\section{External triggering options}\label{triggering}
+The detector can be setup such to receive external triggers. Connect a LEMO signal to the TRIGGER IN connector in the Power Distribution Board (see Fig.). The logic 0 for the board is passed by low level 0$-$0.7~V, the logic 1 is passed to the board with a signal between 1.2$-$5~V. Eiger is 50~$\Omega$ terminated. By default the positive polarity is used (negative should not be passed to the board).
+
+\begin{figure}[t]
+\begin{center}
+\includegraphics[width=.4\textwidth]{tiggerIN}
+\end{center}
+\caption{\textbf{Trigger INPUT} (looking at a single module from the back, top) is the \textbf{rightmost, down}.}
+\label{triggerIN}
+\end{figure}
+
 \begin{verbatim}
 sls_detector_put 0-timing [auto/trigger/burst_trigger/gating]
 sls_detector_put 0-frames x
@@ -390,17 +557,17 @@ No timeout is expected between the start of the acquisition and the arrival of t
 
 Here are the implemented options so far:
 \begin{itemize}
-\item {\tt{auto}} is the software controlled acquisition, where {\tt{exptime}} and {\tt{period}} have to be set.
+\item {\tt{auto}} is the software controlled acquisition (does not use triggers), where {\tt{exptime}} and {\tt{period}} have to be set. Set number of cycles (i.e. triggers) to 1 using {\tt{cycles}}. Set number of frames using {\tt{frames}}.
-\item {\tt{trigger}} 1 frame taken for 1 trigger. You {\tt{frames}} needs to be  1 always, {\tt{cycles}} can be changed and defines how many triggers are considered. In the GUI this is called trigger exposure series. 
+\item {\tt{trigger}} 1 frame taken for 1 trigger. Your {\tt{frames}} needs to be  1 always, {\tt{cycles}} can be changed and defines how many triggers are considered.  {\tt{exptime}} needs to be set. In the GUI this is called trigger exposure series.  
-\item {\tt{burst\_trigger}} gets only 1 trigger, but allows to take many frames. With {\tt{frames}} one can change the number of frames. {\tt{cycles}} needs to be 1. In the gui it is called trigger readout.
+\item {\tt{burst\_trigger}} gets only 1 trigger, but allows to take many frames. With {\tt{frames}} one can change the number of frames. {\tt{cycles}} needs to be 1.  {\tt{exptime}} and {\tt{period}} have to be set. In the gui it is called trigger readout.
-\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{cycles}} allows to select how many gates to consider. 
+\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{cycles}} allows to select how many gates to consider.  Set number of frames to 1 using {\tt{frames}}.
 \end{itemize}
 
 Hardware-wise, the ENABLE OUT signal outputs when the chips are really acquiring. This means that the single subframes will be output in 32 bit mode. The TRIGGER OUT outputs the sum-up-signal at the moment (which is useless). This will be changed in the future to output the envelop of the enable signal. 
 
 We are planning to change some functionality, i.e. unify the {\tt{trigger}} and {\tt{burst}} trigger modes and make both {\tt{frames}} and {\tt{cycles}} configurable at the same time.
 
-\section{Autosumming and rate corrections}
+\section{Autosumming and rate corrections} \label{advanced}
 
 In the case of autosumming mode, i.e, {\tt{dr 32}}, the acquisition time ({\tt{exptime}} is broken in as many subframes as they fit into the acquisition time minus all the subframes readout times. By default the {\tt{subexptime}} is set to 2.621440~ms. This implies that 12 bit counter of \E will saturate when the rate is above or equal to 1.57~MHz/pixel. The minimum value is of order of 10~ns (although as explained values smaller than 500~$\mu$s do not make sense). The maximum value is 5.2~s.
 
@@ -417,7 +584,7 @@ In the EIGER on board server, this look-up table is generated assuming that the
 n_d= n_i \cdot exp(-n_i \cdot \tau),
 \label{rate}
 \end{equation}
-where $\tau$ represents an effective parameter for the dead time and the loss in efficiency. The look-up table is necessary as we are interested to obtain $c_i(c_d)$ and equation~\ref{rate} is not invertible. One needs to notice that the paralizable counter model to create a look-up tables applies only if photons arrive with a continuous pattern (like at the SLS). If photons are structured in fewer but intenser bunches, deviations may arise. This is the case for some operation modes at the ESRF. For those cases we are studying how to correct, probably from a simulated correction tables if an analytical curve cannot be found.  
+where $\tau$ represents an effective parameter for the dead time and the loss in efficiency. The look-up table is necessary as we are interested to obtain $c_i(c_d)$ and equation~\ref{rate} is not invertible. One needs to notice that the paralyzable counter model to create a look-up tables applies only if photons arrive with a continuous pattern (like at the SLS). If photons are structured in fewer but intenser bunches, deviations may arise. This is the case for some operation modes at the ESRF. For those cases we are studying how to correct, probably from a simulated correction tables if an analytical curve cannot be found.  
 \textbf{In the new calibration scheme, $\tau$ is given as a function of the energy. It is loaded from the trimbit files and interpolation between two trimbit files are performed.} One needs to make sure the appropriate $\tau$ value is written in the trimbit files, then need to load the appropriate {\tt{settings}} and {\tt{vthreshold}} before.
 
 Online rate corrections can be activated for {\tt{dr=32}}. They are particularly useful in the autosumming mode as  every single subframe is corrected before summing it. To correct for rate, the subframe duration has to be known to the correction algorithm. Rate corrections for {\tt{dr=16}} will be activated as well in the next firmware release.     
@@ -454,20 +621,37 @@ Here is a list of limits that should be checked:
 If \textbf{dr} is 32 and \textbf{clkdivider} is not 2, whatever the detector gets out is wrong (the boards cannot properly keep up) 
 \item If the variable \textbf{frames} is greater than what the memory can store (table~\ref{timgs}) and the frame rate exceed the continuos streaming (table~\ref{tcont}), limits on the maximum number of images need to be implemented if the period is lower than the one listed in table~\ref{tcont}. Check table~\ref{tframes} to see the different cases.
 \item Running at a speed that does not support the frame rate you are asking: see table~\ref{tframes} to check if the frame rate (\textbf{period}) you are asking is compatible with the \textbf{clkdivider} you are asking.
-\item Running at a redout time that does not support the frame rate you are asking. Check table~\ref{tframes} to check if the frame rate (\textbf{period}) you are asking is compatible with the \textbf{flags} you are asking.
+\item Running at a readout time that does not support the frame rate you are asking. Check table~\ref{tframes} to check if the frame rate (\textbf{period}) you are asking is compatible with the \textbf{flags} you are asking.
 \item The minimum allowed value for \textbf{exptime} should be 10~$\mu$s. 
 \item By default the {\textbf{subexptime}} is set to 2.621440~ms. Values smaller than 500~$\mu$s do not make sense. The maximum value is 5.2~s. This limits should be checked.
 \end{enumerate}
 
+Here is a list of parameters that should be reset:
+\begin{enumerate}
+\item  \textbf{resetframescaught} should be reset to zero after every acquisition taken with {\tt{receiver start}},{\tt{status start}},{\tt{receiver stop}}. If the acquisition is taken with {\tt{sls\_detector\_acquire}}, there is no need to reset this.
+\item After changing the {\tt{timing}} mode of the detector, one should reset to '1' the unused value, in that specific timing mode, between \textbf{frames} and \textbf{cycles}. See section~\ref{triggering} for how to use the timing. At the present moment the detector will acquire more frames than planned if the variable not used between \textbf{frames} and \textbf{cycles} is not reset. In future releases, the unused variable will be ignored. Still resetting is a good practice.
+      
+\end{enumerate}
 
 \section{1Gb/s, 10Gb/s links}
 \subsection{Checking the 1Gb/s, 10Gb/s physical links}\label{led}
 LEDs on the backpanel board at the back of each half module signal:
 \begin{itemize}
-\item  the 1Gb/s physical link is signaled by the most external LED (should be green) 
+\item  the 1Gb/s physical link is signaled by the most external LED (should be green). For top half modules is at the extreme left. For bottom half modules is at the extreme right.  
-\item the 10Gb/s physical link is signaled by the second most external LED next to the 1Gb/s one (should be green) 
+\item the 10Gb/s physical link is signaled by the second most external LED next to the 1Gb/s one (should be green). 
 \end{itemize}
 
+\begin{figure}[t]
+\begin{center}
+\includegraphics[width=.7\textwidth]{LEDSim}
+\end{center}
+\caption{1 and 10GB LEDs position.}
+\label{fLEDs}
+\end{figure}
+
+
+
+
 \subsection{Delays in sending for 1Gb/s, 10Gb/s, 10Gb flow control, receiver fifo}
 
 Extremely advanced options allow to:
@@ -486,10 +670,10 @@ Extremely advanced options allow to:
 \end{verbatim}
 As example:
 \begin{verbatim}
-for X in \$(seq 0 4); do ./sls_detector_put \$X:txndelay_left \$((X*100000)); done
+for X in $(seq 0 4); do ./sls_detector_put $X:txndelay_left $((X*100000)); done
  \end{verbatim}
 \begin{verbatim}
-./sls_detector_put \$X:txndelay_right \$((X*100000)); X=\$((X+1)); done
+./sls_detector_put $X:txndelay_right $((X*100000)); X=$((X+1)); done
 \end{verbatim}
 
 \item Set transmission delay of the entire frame. This is required as you want to finish sending the first frame to all receivers before starting sending the second frame to the receivers with shorter delay time.  This value has to be greater than the maximum of the transmission delays of each port.      
@@ -539,9 +723,15 @@ Very important is to activate the flow control in 10Gb (in 1Gb it is on by defau
 \end{verbatim}
 Set the transmission delays as explained in the manual.
 
+It can help to increase the fifo size of the receiver to {\tt{rx\_fifodepth}} to 1000 images
+\begin{verbatim}
+./sls_detector_put rx_fifodepth 1000
+\end{verbatim}
+One needs to keep into account that in 16 bit mode for 1 image we expect each slsReceiver  to allocate 0.5MB. So for 1000 images, we expect  500MB memory for each receiver. This can be monitored in Linux with "top" or "free -m".
+
 \section{Offline processing and monitoring}
 
-\subsection{Data out of the detector: UDP packets}
+\subsection{Data out of the detector: UDP packets}\label{UDP}
 
 The current UDP header format is described in figure~\ref{UDPheader}.
 \begin{figure}[t]
@@ -573,25 +763,27 @@ white the option {\tt{n:flippeddatax 1}}, which flips in vertical the content of
 \subsection{``raw'' files}
 If you use the option of writing raw files, you will have a raw file for each UDP port (meaning most likely 2 chips), 4 files per module. In addition to the raw files, you will get also a ``master'' file, containing in ascii some detector general parameters and the explanation of how to interpret the data from the raw files.
    
-The master file is named: {\tt{filename\_master\_0.raw}} and for version ``3.0'' of the slsDetectorSoftware looks like:
+The master file is named: {\tt{filename\_master\_0.raw}} and for version ``4.0.0'' of the slsDetectorSoftware looks like:
  
 \begin{verbatim}
-Version            : 1.0
+Version                    : 2.0
-Dynamic Range      : 16
+Dynamic Range              : 32
 Ten Giga                   : 1
-Image Size         : 262144 bytes
+Image Size                 : 524288 bytes
 x                          : 512 pixels
 y                          : 256 pixels
+Max. Frames Per File       : 10000
 Total Frames               : 1
 Exptime (ns)               : 1000000000
 SubExptime (ns)            : 2621440
+SubPeriod(ns)              : 2621440
 Period (ns)                : 1000000000
-Timestamp          : Thu Aug 17 10:55:19 2017
+Timestamp                  : Mon Sep  3 09:07:05 2018
 
 
 #Frame Header
 Frame Number               : 8 bytes
-SubFrame Number    : 4 bytes
+SubFrame Number/ExpLength  : 4 bytes
 Packet Number              : 4 bytes
 Bunch ID                   : 8 bytes
 Timestamp                  : 8 bytes
@@ -603,14 +795,21 @@ Debug              : 4 bytes
 Round Robin Number         : 2 bytes
 Detector Type              : 1 byte
 Header Version             : 1 byte
+Packets Caught Mask        : 64 bytes
 \end{verbatim}
 
 Note that if one wants to  reconstruct the real time the detector was acquiring in 32 bit (autosumming mode), one would have to multiply the SubExptime (ns) for the SubFrame Number. 
 
 \subsection{Offline image reconstruction}
-The offline image reconstruction is in {\tt{slsDetectorsPackage/slsImageReconstruction}}.
+The offline image reconstruction{\tt{slsImageReconstruction}} is not part of the package anymore. The code is still available doing \\
+{\tt{git clone git@git.psi.ch:sls\_detectors\_software/sls\_image\_reconstruction.git slsImageReconstruction}}.
+Checkout the {\tt{developer}} branch if in a 3.1.X release or the {\tt{v4.0.0}} branch if in 4.0.X release of the {\tt{slsDetector}} code.
 
-The detector writes a raw file per receiver. An offline image reconstruction executable has been written to collate the possible files together and produce cbf files. The executable uses the CBFlib-0.9.5 library (downloaded from the web as it download some architecture dependent packages at installation).\\
+Three possible conversions are possible: into \textbf{cbf}, \textbf{hdf5} and \textbf{root} format. The detector writes 4 raw files per receiver. An offline image reconstruction executable has been written to collate the possible files together and produce output files. By default an interpolation between the values of the large pixels is performed. Gap pixels between modules are also inserted.
+
+
+\subsubsection{cbf}
+The cbf executable executable uses the CBFlib-0.9.5 library (downloaded from the web as it download some architecture dependent packages at installation).Edit the Makefile to correclty point at it.\\
 \underline{At cSAXS, the CBFlib-0.9.5 has been compiled -such that the required packages are}\\\underline{ downloaded in /sls/X12SA/data/x12saop/EigerPackage/CBFlib-0.9.5.}\\ 
 
 To use it for a single module:
@@ -620,29 +819,90 @@ cbfMaker [filename with dir]
 eg.
 {\tt{cbfMaker /scratch/run\_63\_d1\_f000000000000\_3.raw}}\\
 
-To use it for a 1.5 multi modules:
+To use it any geometry:\\
-\begin{verbatim}
+{\tt{cbfMaker [filename] [pixels x, def=1024] [pixels y, def=512] [singlemodulelongside\_x, def=1] [fillgaps, def=Interpolate Big Pixels] [hdf5datasetname, def="Eiger"] [start det,def=0]}}\\
-cbfMaker [filename] [pixels x] [pixels y] ([singlemodulelongside_x] [start det])
-\end{verbatim}
 eg.
-{\tt cbfMaker /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 0}.\\
+{\tt cbfMaker /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 2 ``Eiger'' 0}.\\
-The {\tt{[singlemodulelongside\_x]}} and {\tt{[start det]}} param are optional. Defaults are ``1'', the detector long side is on the x coordinate and start to reconstruct from module 0. 
+
+The {\tt{[singlemodulelongside\_x]}} {\tt{[option to interpolate gap pixels]}} param are optional. Defaults are ``1'', the detector long side is on the x coordinate and to start to reconstruct from module 0.
+The interpolation scheme fro the gap pixels between chips is by default ``interpolate large big pixels'', =2;
+If you want to change interpolation scheme, use:\\
+\begin{tabular}{|c|c|}
+\hline
+interpolation scheme & argument\\
+\hline
+insert gap pixels and assign value only to the first one  & 0\\
+\hline
+equally divide the value of the counter bettern the two pixels & 1\\
+\hline
+interpolate large pixel value & 2\\
+\hline
+mask the value of the two gap pixels & 3\\
+\hline
+\end{tabular}
+\ \\
+\ \\ 
 The executables: 
 \begin{verbatim}
-bcfMaker1.5M [file_name_with_dir]
+cbfMaker1.5M [file_name_with_dir]
-bcfMaker9M [file_name_with_dir]
+cbfMakerOMNY [file_name_with_dir]
+cbfMaker9M [file_name_with_dir]
 \end{verbatim}
-contain the hardcoded geometry for the 1.5M (3 modules horizontal on the long side) and for the 9M at cSAXS: 6(short side)$\times$3 (long side) modules.\\ 
+contain the hardcoded geometry for the 1.5M (3 modules horizontal on the long side), the 1.5M OMNY geometry (3 modules next to each other on the long side) and for the 9M at cSAXS: 6(short side)$\times$3 (long side) modules.\\ 
 Missing packets in a frame and border pixels ($\times 2$ and $\times 4$ are given with value $-1$ at the present time.
 
-It is important to know, that the pixels at the edge between 2 chips count more as double size. We can virtually introduced 1 virtual pixel per double larger pixel, so to have an even number of counts everywhere. Virtual pixels (not filled ) between module gaps are also inserted.
+Make sure the following options are uncommented in the {\tt{slsImageReconstruction/src/main\_csaxs.cpp}} file. 
+\begin{verbatim}
+#define MYCBF
+##following line only if you need to process with 
+##BUBBLE (Material Science / uXAS beamlines).
+#define MSHeader 
+\end{verbatim}
+Compile it with: 
+\begin{verbatim}
+make cbfMaker; make cbfMakerOMNY;
+\end{verbatim}
 
- \begin{verbatim}
+\subsubsection{hdf5}
-   GapPixelsBetweenChips_x = 2;
+In case of HDF5 output file, we rely on having the HDF5 1.10.1 library installed. Edit the Makefile to correclty point at it. Different compression methods are being tried so different external filters might be to be installed. This work is not finished yet.
-   GapPixelsBetweenChips_y = 2;
+
-   GapPixelsBetweenModules_x = 8;
+To choose HDF5, with ZLIB implementation, open {\tt{slsImageReconstruction/src/main\_csaxs.cpp}} and make sure that 
-   GapPixelsBetweenModules_y = 36;
+\begin{verbatim}
- \end{verbatim}
+#define HDF5f
+#define ZLIB
+\end{verbatim}
+are not commented out. All other options need to be commented out. Copile the code with 
+\begin{verbatim}
+make hdf5Maker; make hdf5MakerOMNY;
+\end{verbatim}
+
+If you are at cSAXS. all images collected will be written in a single file. If you are not at CSAXS, most likely you want to have all the images written in a single raw file into an HDF5 file. The multiple HDF5 files are then linked in a master file, with many subdatasets (can be read by albula) or by a virtual file with a single dataset. If you want a mster o virtual file, uncomment this option:
+\begin{verbatim}
+#define MASTERVIRTUAL
+\end{verbatim}
+and recompile.
+To use it for a single module:
+\begin{verbatim}
+hdf5Maker [filename with dir]
+\end{verbatim}
+eg.
+{\tt{hdf5Maker /scratch/run\_63\_d1\_f000000000000\_3.raw}}\\
+
+To use it any geometry:\\
+{\tt{hdf5Maker [filename] [pixels x, def=1024] [pixels y, def=512] [singlemodulelongside\_x, def=1] [fillgaps, def=Interpolate Big Pixels] [hdf5datasetname, def="Eiger"] [start det,def=0]}}\\
+eg.
+{\tt hdf5Maker /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 2 ``Eiger'' 0}.\\
+
+\subsubsection{root}
+The data will be written as TH2D in root format. Edit the {\tt{Makefile}} to point to the correct ROOT library location. Compile the executable as:
+\begin{verbatim}
+make image 
+\end{verbatim}
+There is no program other executable that alredy keeps into account the geometry for it.
+To use it any geometry:\\
+{\tt{image [filename] [pixels x, def=1024] [pixels y, def=512] [singlemodulelongside\_x, def=1] [fillgaps, def=Interpolate Big Pixels] [hdf5datasetname, def="Eiger"] [start det,def=0]}}\\
+eg.
+{\tt image /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 2 ``Eiger'' 0}.\\
 
 \subsection{Read temperatures/HV from boards}
 
@@ -694,10 +954,28 @@ Start the server again:
 \begin{verbatim}
 ./eigerDetectorServer &
 \end{verbatim}
+\textbf{Note that the server appropriate for the software version used is located inside the package: {\tt{slsDetectorsPackage/serverBin/eigerDetectorServerxx.yy.}}}.
 
+To copy the detector server on many boards, a script can be implemented on the lines of:
+\begin{verbatim}
+for i in beb111 beb070; 
+do ssh root@$i killall eigerDetectorServer; 
+scp eigerDetectorServer root@$i:~/executables/eigerDetectorServer ; 
+ssh root@$i sync; done
+\end{verbatim}
 
 \section{Loading firmware bitfiles}
 
+\textbf{As a new procedure, the first thing to do is to kill the server on the boards, copy the new one there without starting it.} Note taht failure to do this step before may cause the linux on the baords to crash and not being able to ping it (this if the registers between the old and new firmware change).
+
+This is teh procedure from a terminal;
+\begin{verbatim}
+for i in beb111 beb070; 
+do ssh root@$i killall eigerDetectorServer; 
+scp eigerDetectorServer root@$i:~/executables/eigerDetectorServer ; 
+ssh root@$i sync; done
+\end{verbatim}
+
 A \textbf{bcp} executable (which needs \textbf{tftp} installed on the PC, is needed. 
 \begin{enumerate}
 \item Manual way: you need to press something on the detector. To program bitfiles (firmware files), do a hard reset with a pin/thin stuff in the holes at the very back of the module. They are between the top 7 LED and the bottom 1 and opposite for the other side. Push hard till all LEDs are alternating green and red.
@@ -708,7 +986,7 @@ cd executables
 ./boot_recovery 
  \end{verbatim} 
 \end{enumerate}
-In both case, after booting, only the central one should be on green and red alternating. 
+In both case, after booting, only the central LED should be on green and red alternating. 
 
 From a terminal, do:
 \begin{verbatim}
@@ -756,7 +1034,7 @@ for j in $(seq 0 255) ; do
 sls_detector_put pulsenmove N 0 1;
 done;
 done;
-sls_detector_p resmat 0
+sls_detector_put resmat 0
 sls_detector_acquire
 \end{verbatim}
 You read {\tt{N}} in every pixel if you are setup correctly. 
@@ -769,17 +1047,9 @@ To load the special noise file look at {\tt{settingsdir/eiger/standard/eigernois
 sls_detector_put trimbits ../settingsdir/eiger/standard/eigernoise
 \end{verbatim}
 
-\section{Running the (9M at cSAXS. For now)}
-\begin{itemize}
-\item login as {\tt{x12saop@xbl-daq-27}}
-\item {\tt{setup\_eiger}} \#loads environmental variables and brings you to the right directory to execute commands
-\item slsReceiverScript3 1991 36 \# from one shell.. opens 36 receivers
-\item p config ../../eiger\_9m\_10gb\_xbl-daq-27\_withbottom.config
-\end{itemize}
-
 \section{Troubleshooting}
 \subsection{Cannot successfully finish an acquisition}
-\subsubsection{only master module return from acquisition}
+\subsubsection{Only master module return from acquisition}
 When no packets are received AND detector states in 'running status'. Widest list of causes. 
 Query the status of each half module till the maximum number {\tt{N}},  {\tt{for i in \$(seq\ 0\ N); do sls\_detector\_get \$i:status; done}}, to check if there are half modules that are still running.
 
@@ -790,7 +1060,7 @@ If only the master modules return but ALL the other half modules do not:
 \item It can be that the synchronization cable is not connected or the termination board at the synchronization does not work. Check.
 \end{itemize}
 
-\subsubsection{a few modules do not return from acquisition}
+\subsubsection{A few modules do not return from acquisition}
 If only a few modules are still running but the others return, it is a real problem with a backend board or a synchronization bug.
 If you can, ssh into the board, kill and start the eigerDetectorServer again (see Section~\ref{server} for how to do this). Keep the terminal with the output from the  eigerDetectorServer and repeat the acquisition. 
 \begin{itemize}
@@ -800,11 +1070,33 @@ If you can, ssh into the board, kill and start the eigerDetectorServer again (se
 
 \subsection{No packets (or very little) are received} 
 In both cases running \textbf{wireshark} set to receive UDP packets on the ethernet interface of the receiver (filter the UDPport$>=$xxxx, where xxxx is written in the configuration file) can help you understanding if NO packets are seen or some packets are seen. You have to set the buffer size of the receiving device in wireshark to 100Mbyte minimum. If no packets are received, check that your receiving interface and detector UDPIPs are correct (if in 10Gb). Most of the time in this case it is a basic configuration problem.
-If some packets are received, but not all, then it is an optimization problem:
+It can help looking at the receiver output, shown in an example here:
+\begin{verbatim}
+Missing Packets         : 224064
+Complete Frames         : 3499
+Last Frame Caught       : 3499
+\end{verbatim}
+
+The {\tt{Last Frame Caught}}, meaning the packet from the last frame that was sent out by the detector, can help in understanding the problem: 
+\begin{enumerate}
+\item If some packets are received, but not all, it could be a network optimization problem. In this case, the {\tt{Last Frame Caught}} will be a value close to the expected number of frames with missing frames distributed over the whole frame range. In this case: 
  \begin{itemize}
 \item For receiving data over 1Gb, the switch must have FLOW CONTROL enabled 
 \item If using 10GbE, check that the 10Gb link is active on the backpanel board. Then refer to Section~\ref{10g} to see how to configure the 10Gb ports on the receiving machine correctly. 
 \end{itemize}
+\item If the {\tt{Last Frame Caught}} value is much lower than the expected frames and you are missing a bunch of frames from a point onwards, and you are using {\tt{receiver start, status start}}: then it can be that you are stopping the receiver too early. In particular when you are using {\tt{delay}} it might be that there is some time between when the detector is already done and in {\tt{idle}} state but the receiver is still receiving data. Check with {\tt{./sls\_detector\_get framescaught}} if the receiver is already done before doing {\tt{./sls\_detector\_put receiver stop}}.   
+\item If the {\tt{Last Frame Caught}} value is much lower than the expected frames and you are missing a bunch of frames from a point onwards and you are running at a higher frame rate than the continuous framerate (see table~\ref{tcont}) with more images than the size of the memory (see table~\ref{timgs}). It might be that you are running out of memory to store images. There is no protection for this. see point~\ref{outmemory}
+ \end{enumerate}
+
+\subsection{'Got Frame Number Zero from Firmware'}\label{outmemory}
+In this case, you have run out of memory size (see table~\ref{timgs} for the size) on the boards so you are trying to store on the DDR2 memories more images that they can contain and the network is not fast enough to send everything out from the 10GbE.
+So if you see:
+\begin{verbatim}
+Got Frame Number Zero from Firmware. Discarding Packet
+\end{verbatim}
+it means that you run out of memory at the previous acquisition. The  cure is taking 2 or 3 SINGLE images in a raw to clear out the memories.
+ 
+
 
 \subsection{The module seems dead, no lights on BEBs, no IP addresses}
 \begin{itemize}
@@ -820,7 +1112,7 @@ If the 1G LED (see Section~\ref{led}) on the backpanel board is not green:
 \item The IP address is assigned only at booting up of the boards. Try to reboot in case the board booted before it could have an IP address. 
 \item Check that you did not run out of IP addresses 
 \end{itemize}
- Check that the board is not in recovery mode (i.e. the central LED on the back is stable green). In this case reboot the board with the soft reset or power cycle it.
+ Check that the board is not in recovery mode (i.e. the central LED on the back is stable green, see Fig~\ref{fLEDs}). In this case reboot the board with the soft reset or power cycle it.
 
 If the 1Gb LED on the backpanel board is green (see Section~\ref{led}):
 \begin{itemize}
@@ -835,6 +1127,14 @@ It is connected to the TCPport which the receiver uses:
 %%%#To display only open UDP ports try the following command: netstat -vaun
  \end{itemize}
 
+\subsection{The client ignores the commands}
+Make sure that in the configuration file you do not have {\tt{lock 1}} activated, as this will let only one username from one IP address talk to the detector. 
+To deactivate it, you need to run {\tt{lock 0}} from the client session where you locked it. 
+
+\subsection{Zmq socket is blocked}
+It is connected to the TCPport which is used. In rare cases, it might be that the TCP port crashes. To find out which process uses the TCPPOrt do: \textbf{netstat -nlp | grep xxxx}, where xxxx is the tcpport number. To display open ports and established TCP connections, enter: \textbf{netstat -vatn}. Kill the process.
+
+
 \subsection{Client has \textbf{shmget error}}
 Note that occasionally if there is a shared memory of a different size (from an older software version), it will return also a line like this:
 \begin{verbatim}
@@ -842,15 +1142,23 @@ Note that occasionally if there is a shared memory of a different size (from an
 \end{verbatim}
 This needs to be cleaned with {\tt{ipcs -m}} and then {\tt{ipcrm -M xxx}}, where xxx are the keys with nattch 0. Alternative in the main slsDetectorFolder there is a script that can be used as {\tt{sh cleansharedmemory.sh}}. Note that you need to run the script with the account of the client user, as the shared memory belongs to the client. It is good procedure to implement an automatic cleanup of the shared memory if the client user changes often.   
 
+\subsection{Client has shared memory iusses}
+The shared memory from software version 4.0.0 creates shared memory segments in /dev/shm/. You can look at them and cancel them directly. Note that this is still user dependent.
+Environment variable SLSDETNAME can be set for using 2 different detectors from the same client pc. One needs a different multi detector id if the SLSDETNAME is different for both consoles.
+
 \subsection{Measure the HV}
-For every system but not the 9M: 
+For every system: 
 \begin{itemize}
 \item Software-wise measure it (now the software returns the measured value), with {\tt{sls\_detector\_get vhighvoltage}}. The returned value is the HV (for proper Eiger setting is approximately 150~V) if it is correctly set. If two master modules are presents (multi systems), the average is returned (still to be tested). If one asks for the individual $n$ half module bias voltage through {\tt{sls\_detector\_get n:vhighvoltage}}, if the $n$ module is a master, the actual voltage will be returned. If it is a slave, -999 will be returned. 
-\item Hardware-wise measure value of HV on C14 on the power distribution board. Check also that the small HV connector cable is really connected. 
+\item Hardware-wise (opening the detector) measure value of HV on C14 on the power distribution board. Check also that the small HV connector cable is really connected. 
  \end{itemize}
 
+The 2M system at ESRF has a HV enable signal that needs to be shortcut in order to overwrite vacuum protections (when not in vacuum). 
+The 1.5M for OMNY has a relay system that enables HV only when the vacuum is good. 
+For both systems, it makes sense not to set the HV while running the configuration file but set it at a later stage when sure about the vacuum. 
+
 \subsection{The image now has a vertical line}
-Check if the vertical line has a length of 256 pixels and a width of 8 columns. In this case it is a dataline beeing bad. It can be either a wirebond problem or a frontend board problem. try to read the FEB temperature (see Section~\ref{}) and report the problem to the SLSDetector group. Most likely it will be a long term fix by checking the hardware.
+Check if the vertical line has a length of 256 pixels and a width of 8 columns. In this case it is a dataline being bad. It can be either a wirebond problem or a frontend board problem. try to read the FEB temperature (see Section~\ref{}) and report the problem to the SLSDetector group. Most likely it will be a long term fix by checking the hardware.
 
 \subsection{The image now has more vertical lines}
 
@@ -860,7 +1168,7 @@ If you see strange lines in vertical occurring at period patterns, it is a memor
 Depending on your network setup,  to speed up the ssh to the boards from a pc with internal dhcp server running: \textbf{iptables -t nat -A POSTROUTING -o eth1 -j MASQUERADE; echo "1" > /proc/sys/net/ipv4/ip\_forward}, where eth1 has to be the 1Gb network device on the pc
 
 \subsection{Check firmware version installed on BEB}
-Follow some steps described in Section~\label{server}. 
+You can either ask in the client as described in section~\ref{api}, or login to the boards directly. Follow some steps described in Section~\ref{server}. 
 \begin{verbatim}
 ssh root@bebxxx #password is root
 killall eigerDetectorServer # kill server and stopserver
@@ -870,7 +1178,7 @@ cd executables/
 Scroll up in the terminal till you find {\tt{Firmware Version: xx}}
 
 \subsection{Check if half-module is a master, a slave, a top or a bottom}
-Follow some steps described in Section~\label{server}.
+Follow some steps described in Section~\ref{server}.
 \begin{verbatim}
 ssh root@bebxxx #password is root
 killall eigerDetectorServer # kill server and stopserver
@@ -882,8 +1190,32 @@ Scroll up in the terminal till you find:\\
 *************** MASTER/SLAVE ***************\\
 *************** NORMAL/SPECIAL ***************\\
 
+\subsection{'Cannot connect to socket'}
+This error is typically due to the detector server not running. For why, see section~\ref{servernot}.
 
+\subsection{Detector server is not running}\label{servernot}
+The detector server could not be running: either the detector was powered off, or it powered off itself due to too high temperature or, in the case of the 9M, if the waterflow sensor detected no flux and powered it off (the chiller stops occasionally as cSAXS).
 
+If the powering and the temperature are OK, instead, it can be that the firmware version is incompatible to the server version and/or the client software version. So check the consistency of firmware/software/server versions.
+
+\subsection{'Acquire has already started' error message}
+If you see the client returning the following error message:\\ 
+``Acquire has already started. If previous acquisition terminated unexpectedly, reset busy flag to restart.(sls\_detector\_put busy 0)''\\
+ You need to run the command:
+\begin{verbatim}
+./sls_detector_put busy 0
+\end{verbatim}
+
+\subsection{There is noise running the detector in 32-bit}
+If you are running the detector in 32-bit (autosumming), there might be some noise, particularly at lower thereshold energies. This is due to the fact that the analog part of the chips require some latency time to settle which is larger than the readout time. It is possible to run the detector only in {\tt{parallel}} or {\tt{nonparallel}} mode, respectively with readout times between frames of 12~$\mu$s and 504~$\mu$s. If you switch {\tt{flags}} to non {\tt{nonparallel}} mode you will give enough time for the signals to settle. From release 4.0.0, there is a configurable delay that can be set through the {\tt{subdeadtime}} variable, such that you can remain with the {\tt{parallel}} flag, but can obtain a configurable dead time between frames. Ask the SLS detector group for an appropriate dead time for your detector, but typically a dead time of 20-50~$\mu$s should be enough. Note that this {\tt{subdeadtime}} need to include the 12~$\mu$s minimum readout time, so it has to be larger than 12~$\mu$s to do anything.  
+ 
+\subsection{There is noise running the detector at high frame rate(4,8,16 bit)}
+If are running in {\tt{parallel}} mode, in particular at low thereshold energies, you might encounter some noise. The reason is that the analog part of the chips require some latency time to settle which is larger than the readout time. 
+\begin{enumerate}
+\item You can lower the frame rate and relax requirements on period: 
+At low frame rate, you normally leave enough time between the end of the acquisition and the starting of the next, so you should not see this effect. In any case setting a {\tt{period}}={\tt{exptime}}+readout time from Table~\ref{tchipro} +extra 20$\mu$s cures the problem. The 20$\mu$s could also be 10~$\mu$s, they are very hardware dependent.
+\item The frame rate requirement are stringent (as for time resolved measurements): the only option here is to reduce the {\tt{exptime}} to let the extra 20~$\mu$s (or 10)~$\mu$s. The {\tt{period}} remains the same.
+\end{enumerate} 
  
 \section{Client checks - command line}
 
@@ -1025,7 +1357,74 @@ where  {\tt{number}} is a string that should be interpreted as an int for 0/1 me
 
 \end{enumerate}
 
+\section{Complete data out rate tables}
 
+In table~\ref{tframescomplete} is a list of all the readout times in the different configurations.
+\begin{tiny}
+\begin{table}
+\begin{flushleft}
+\begin{tabular}{|c|c|c|c|c|c|c|}
+\hline
+\tiny{dr} & \tiny{clkdivider} & \tiny{flags} & \tiny{readout t($\mu$s)} & \tiny{max frame rate (kHz)} & \tiny{min period ($\mu$s)} & \tiny{max imgs (nominal/our network)}\\
+\hline
+4 & 0 & parallel & 3.4 & 22 &  44 & 30k/50k\\
+\hline
+4 & 0 & nonparallel & 44 & 21 & 49 & 30k/50k\\
+\hline
+4 & 1 & parallel & 6 & 10.5 &  92 & 30k/100k\\
+\hline
+4 & 1 & nonparallel & 88.7 & 10.5 & 93 & 30k/100k\\
+\hline
+4 & 2 & parallel & 11.2 & 5.4 & 197 & infinite\\
+\hline
+4 & 2 & nonparallel & 176.5 & 5.4 & 180 & infinite\\
+\hline
+\hline
+8 & 0 & parallel & 3.4 & 11.1 & 89 & 15k/24k\\
+\hline
+8 & 0 & nonparallel & 85.7 & 11.1 & 91 & 15k/24k\\
+\hline
+8 & 1 & parallel & 6.1 & 5.7 & 181 & 15k/52k\\
+\hline
+8 & 1 & nonparallel & 170.5 & 5.7 & 175 & 15k/52k\\
+\hline
+8 & 2 & parallel & 11.2 &  2.9 &  342 & infinite\\
+\hline
+8 & 2 & nonparallel & 340.3 &  2.9 &  344 & infinite\\
+\hline
+\hline
+16 & 0 & parallel & 3.4 & 6.1 & 164 & 8k/12k\\
+\hline
+16 & 0 & nonparallel &  126 & 5.6& 179 & 8k/23k\\
+\hline
+16 & 1 & parallel &  6.1 & 3.9&  257 & 8k/28k\\
+\hline
+16 & 1 & nonparallel & 255 & 3.3&  303 & infinite\\
+\hline
+16 & 2 & parallel &  11 & 1.9  & 526 &infinite \\
+\hline
+16 & 2 & nonparallel & 504 & 1.8 & 555 & infinite\\
+\hline
+\hline
+32 & 2 & parallel &  11 & 2  & &\\
+\hline
+32 & 2 & nonparallel & 504 & $<2$  & &\\
+\hline
+\end{tabular}
+\caption{Readout settings. The {\tiny{min exptime}} possible is 5$-$10~$\mu$s. This is due to the time to pass the pixel enable signal in the whole chip.}
+\label{tframescomplete}
+\end{flushleft}
+\end{table}
+\end{tiny}
+
+Table~\ref{tx} shows the bandwidth of data transferring between the FEB and BEB and of the DDR2 memory access. the GTX lanes are only capable of 25.6~Gbit/s. This limits the 12/16 bit frame rate. The 2$\times$DDR2 memories have a bandwidth or 2$\cdot$25.6~Gb/s=51.2~Gb/s. Due to this memory access bandwidth, the 32 bit autosumming mode can only run in {\tt{clkdivider}} 2.   
+\begin{figure}[t]
+\begin{center}
+\includegraphics[width=1.\textwidth]{TansmissionRates}
+\end{center}
+\caption{Transmission bandwidth for the FEB $\to$BEB transfer (second column) and the DDR2 memories (fourth column). }
+\label{tx}
+\end{figure}
 
 \end{document}
 

manual/manual-main/Makefile

@@ -4,31 +4,46 @@ DESTDIR=../docs
 TEX=latex
 
 
-MAINTEXS= slsDetectorInstall.tex slsDetectors-FAQ.tex 
+MAINTEXS2= slsDetectorInstall.tex 
+MAINTEXS=slsDetectors-FAQ.tex 
 
 TEXS=slsDetector-softFAQ.tex singlePhotonCounting-FAQ.tex angConv-FAQ.tex generalDet-FAQ.tex 
 
 DVIS = $(MAINTEXS:.tex=.dvi)
 PSS = $(MAINTEXS:.tex=.ps)
 PDFS = $(MAINTEXS:.tex=.pdf)
+PDFS2 = $(MAINTEXS2:.tex=.pdf)
 HTMLS = $(MAINTEXS:%.tex=%)
+HTMLS2 = $(MAINTEXS2:%.tex=%)
 
 
 
 all: pdf html
 	echo $(PWD)
 	echo $(PDFS)
+	echo $(PDFS2)
 	echo $(HTMLS)
+	echo $(HTMLS2)
 
-pdf: $(PDFS)
+pdf: $(PDFS) $(PDFS2)
 	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
 	$(shell test -d $(DESTDIR)/pdf || mkdir -p $(DESTDIR)/pdf)
 	mv $(PDFS) $(DESTDIR)/pdf
+	mv $(PDFS2) $(DESTDIR)/pdf	
 
-html: $(HTMLS)
+html: $(HTMLS) $(HTMLS2)
 
 
 $(HTMLS): $(TEXS) $(MAINTEXS)
+	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
+	$(shell test -d $(DESTDIR)/html || mkdir -p $(DESTDIR)/html)
+	$(shell test -d $(DESTDIR)/html/$@ && rm -fr $(DESTDIR)/html/$@)
+	echo "*****************************  $@"
+	latex $@.tex
+	latex2html $@.tex
+	mv $@ $(DESTDIR)/html
+	
+$(HTMLS2): $(MAINTEXS2)
 	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
 	$(shell test -d $(DESTDIR)/html || mkdir -p $(DESTDIR)/html)
 	$(shell test -d $(DESTDIR)/html/$@ && rm -fr $(DESTDIR)/html/$@)
@@ -53,7 +68,7 @@ $(HTMLS): $(TEXS) $(MAINTEXS)
 
 
 clean:
-	rm -rf *.aux *.log *.toc *.out $(DVIS) $(PSS) $(PDFS) $(HTMLS)
+	rm -rf *.aux *.log *.toc *.out $(DVIS) $(PSS) $(PDFS) $(PDFS2) $(HTMLS) $(HTMLS2)
 	rm -rf $(DESTDIR)/html/slsDetectors-FAQ
 	rm -rf $(DESTDIR)/html/slsDetectorInstall
 	rm -rf $(DESTDIR)/pdf/slsDetectors-FAQ.pdf

manual/manual-main/slsDetectorInstall.tex

@@ -28,9 +28,10 @@
 The SLS detectors software is intended to control the detectors developed by
 the SLS Detectors group. The detectors currently supported are:
 
-MYTHEN, GOTTHARD, EIGER and JUNGFRAU.\bigskip
+\indent MYTHEN, GOTTHARD, EIGER and JUNGFRAU.
 
-\noindent The package provides software for the distributed system that comprises of
+
+The package provides software for the distributed system that comprises of
 detectors, data receivers (to process detector data), and the client (to control
 or monitor the system). The client and data receivers can be embedded in
 the user's acquisitions system. Furthermore, the package also provides some
@@ -60,6 +61,11 @@ The \textit{data receiver}, which can be run on a different machine than the
 client, receives the data from the detector and processes it. The receiver can
 be configured, controlled and monitored by the client.
 
+\item \textcolor{blue}{slsMultiReceiver}: \\
+It is the same as the \textit{slsReceiver}, but that it is a single process 
+for many multiple slsReceiver child processes. One can configure the start TCP port,
+number of slsReceiver processes and if call back should be enabled or not.
+
 \item \textcolor{blue}{slsDetectorGUI}: \\
 The \textit{graphical user interface}, which provides a user friendly way
 of operating the detectors and data receivers with online data preview.
@@ -78,18 +84,28 @@ However, only control commands work, not the data acquisition itself.
 \section{Install Binaries via Conda}
 This section is useful only if one wants to download only the binaries for
 specific distribution and use the package via command line. Please refer later
-sections to download source code and compile them.\bigskip
+sections to download source code and compile them.
 
-\noindent One can download and install Miniconda via 
 
-\url{https://conda.io/miniconda.html} \bigskip
+One can download and install Miniconda via 
 
-\noindent The conda package uses Travis CI for continuous integration with
+\url{https://conda.io/miniconda.html}
+
+
+The conda package uses Travis CI for continuous integration with
 automatic deployment to Anaconda Cloud. One can download only the package or the
-package including the python interface. \bigskip
+package including the python interface.
 
-\noindent After the installation, the binaries will be available in your path.
 
+After the installation, the binaries will be available in your path.
+
+Please remember to clear shared memory after installation.
+\begin{verbatim}
+#displays list of shared memeory segments 
+ipcs -m
+#remove segments that have nattach equal to zero. They key is the first column
+ipcrm -M [key]
+\end{verbatim}
 
 \begin{itemize}
  \item Only the package
@@ -99,13 +115,13 @@ conda config --add channels conda-forge
 conda config --add channels slsdetectorgroup
 
 #Install latest version
-conda install sls_detector_software
+conda install sls_detector_lib
+conda install sls_detector_gui
 
-#Install specific release (GLIBC2.14)
+#Install specific release
-conda install sls_detector_software=3.0.1
+conda install sls_detector_lib=4.0.0
+conda install sls_detector_gui=4.0.0
 
-#Scientific Linux 6 version (GLIBC2.12)
-conda install sls_detector_software=SL6_3.0.1
 \end{verbatim}
  \item The package including Python interface
 \begin{verbatim}
@@ -116,11 +132,9 @@ conda config --add channels sls_detector
 #Install latest version
 conda install sls_detector
 
-#Install specific release (GLIBC2.14)
+#Install specific release 
-conda install sls_detector=3.0.1
+conda install sls_detector=4.0.0
 
-#Scientific Linux 6 version (GLIBC2.12)
-conda install sls_detector=SL6_3.0.1
 \end{verbatim}
 \end{itemize}
 
@@ -137,13 +151,13 @@ acquisition system, or if one wants to download the source code and compile.
 \begin{verbatim}
 #Clone source code with specific release
 git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch
-3.0.1
+4.0.0
 \end{verbatim}
  \item The package including Python interface
 \begin{verbatim}
 #Clone source code with specific release
 git clone https://github.com/slsdetectorgroup/sls_detector.git --branch
-3.0.1
+4.0.0
 \end{verbatim}
 \end{itemize}
 
@@ -194,9 +208,10 @@ required. One can install it:
  \item via download from:\\
 \url{
 https://download.qt.io/archive/qt/4.8/4.8.2/qt-everywhere-opensource-src-4.8.2.t
-ar.gz} \bigskip
+ar.gz} 
 
-\noindent To install:
+
+To install:
 \begin{verbatim}
 > gunzip qt-everywhere-opensource-src-4.8.2.tar.gz
 > tar xvf qt-everywhere-opensource-src-4.8.2.tar
@@ -207,14 +222,17 @@ ar.gz} \bigskip
 By default Qt4 will be installed in /usr/local/Trolltech/Qt-4.8.2/. 
 \end{itemize}
 
-\noindent \textbf{Setup Environment} 
 
-\noindent One has to ensure that \verb=PATH= and \verb=LD_LIBRARY_PATH= have
+\textbf{Setup Environment} 
+
+
+One has to ensure that \verb=PATH= and \verb=LD_LIBRARY_PATH= have
 been updated to include Qt4 install path, binaries and libraries.
 Confirm by executing \verb=qmake -v= and ensuring the result points to Qt4 (not
-Qt3 or Qt5). \bigskip
+Qt3 or Qt5). 
 
-\noindent If the environment is not set up, one can add the libraries and
+
+If the environment is not set up, one can add the libraries and
 executables to the .bashrc by adding
 \verb=LD_LIBRARY_PATH= and \verb=PATH=:
 \begin{verbatim}
@@ -228,9 +246,10 @@ export LD_LIBRARY_PATH=$QTDIR/lib:$LD_LIBRARY_PATH
 Before installing Qwt, one must install Qt
 and ensure that \verb=QTDIR=, \verb=LD_LIBRARY_PATH= and \verb=PATH= point to
 the correct Qt4
-version. \bigskip
+version.
 
-\noindent A Qwt version equal or higher than 6 is required. One can
+
+A Qwt version equal or higher than 6 is required. One can
 install it:
 \begin{itemize}
  \item via YUM:
@@ -240,9 +259,9 @@ install it:
  \item via download from:\\
 \url{
 https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download}
-\bigskip
 
-\noindent To install:
+
+To install:
 \begin{verbatim}
 > cd qwt-6.0.0
 > qmake
@@ -252,12 +271,14 @@ https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download}
 By default Qwt will be installed int /usr/local/qwt-6.0.0 
 \end{itemize}
 
-\noindent \textbf{Setup Environment} 
+\textbf{Setup Environment} 
 
-\noindent One has to ensure that \verb=QWTDIR= and \verb=LD_LIBRARY_PATH= have
-been updated to include Qwt install path and libraries. \bigskip
 
-\noindent If the environment is not set up, one can add the libraries to the
+One has to ensure that \verb=QWTDIR= and \verb=LD_LIBRARY_PATH= have
+been updated to include Qwt install path and libraries.
+
+
+If the environment is not set up, one can add the libraries to the
 .bashrc by adding \verb=LD_LIBRARY_PATH=:
 \begin{verbatim}
 export QWTDIR=/usr/local/qwt-6.0.0/
@@ -324,6 +345,8 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]
 
 Some example options for compilation:
 
+Most basic option: \verb=./cmk.sh -b=
+
 For only make: \verb=./cmk.sh=
 
 For make clean;make: \verb=./cmk.sh -c=
@@ -367,6 +390,62 @@ sls_detector_help sls_detector_put  slsReceiver
 
 
 
+
+\subsection{Setting environment variables}
+One can set up the environment variables in the following ways.
+
+\subsubsection{Using .bashrc file}
+\begin{enumerate}
+ \item \verb=emacs ~/.bashrc=
+ \item Add the following function \verb=setup_slsdet= and replace \verb=path=
+with absolute path of installed directory
+\begin{verbatim}
+function setup_slsdet
+{ 
+export PKGPATH=[path]
+export LD_LIBRARY_PATH=$PKGPATH/slsDetectorPackage/build/bin:$LD_LIBRARY_PATH
+export PATH=$PKGPATH/slsDetectorPackage/build/bin:$PATH
+cd $PKGPATH/slsDetectorPackage/build/bin
+} 
+\end{verbatim}
+  \item \verb=source ~/.bashrc=
+  \item Next time, just run \verb=setup_slsdet= to load the environment
+variables.
+\end{enumerate}
+
+
+One can also add the GUI environment variables if installed locally by adding
+the following in the function \verb=setup_sldet= \\
+\begin{verbatim}
+export QTDIR=/path-where-it-is/Qt-4.8.2
+export QWTDIR=/path-where-it-is/qwt-6.0.1
+export QWT3D=/path-where-it-is/qwtplot3d
+export QMAKESPEC=$QTDIR/mkspecs/linux-g++
+export LD_LIBRARY_PATH=$QTDIR/lib:$QWTDIR/lib:$QWT3D/lib:$LD_LIBRARY _PATH
+export PATH=$QTDIR/bin:$PATH
+\end{verbatim}
+
+\subsubsection{Without .bashrc file}
+Go to binaries folder slsDetectorPackage/build/bin and execute the following:
+\begin{verbatim}
+export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH
+export PATH=$PWD:$PATH
+\end{verbatim}
+
+
+\subsection{Clean Shared Memory}
+It is very crucial to clean the shared memory, before using a new version of
+the SLS Detector Package or a different detector type.
+
+One can use the \verb=cleansharedmemory.sh= script available under the
+slsDetector Package.
+
+One can also just delete the files that are typically located under /dev/shm/ folder
+and starts with slsDetectorPackage.
+
+One no longer has to delete segments using ipcs.
+
+
 \section{Software Upgrade}
 
 The upgrade of the package could require an upgrade of the on-board detector
@@ -379,7 +458,7 @@ themselves (which would require dedicated softwares) but only to download on the
 detector board the programming files and/or software package provided by
 the SLS Detectors group.
 
-\subsubsection{Firmware}
+\subsubsection{MYTHEN Firmware}
 
 To upgrade the firmware you need either a working version of the Altera
 Quartus software or of the Quartus programmer, which can easily be downloaded
@@ -389,9 +468,10 @@ from: \\
 
 \noindent Normally, installation of the software and of the driver for the
 USB-Blaster (provided together with the MYTHEN detector) are simpler under
-Windows. \bigskip
+Windows. 
 
-\noindent Under Windows, the first time that you connect the USB-Blaster to one
+
+Under Windows, the first time that you connect the USB-Blaster to one
 of your USB ports, you will be asked to install new hardware. Set the path to
 search for the driver to:
 \verb=C:\altera\80sp1\qprogrammer\drivers\usb-blasterp= (where 
@@ -414,7 +494,7 @@ your cable (pin1 corresponds) and that you have selected the correct programming
 connector.
 \end{enumerate}
 
-\subsubsection{On-board Software}
+\subsubsection{MYTHEN On-board Software}
 \begin{enumerate}
  \item Connect to the board using telnet:
 \begin{verbatim}
@@ -454,6 +534,311 @@ acqusition program correctly start.
 \end{enumerate}
 
 
+
+
+\subsection{GOTTHARD}
+
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+\subsubsection{GOTTHARD Firmware}
+\textit{For SLS Detector Package v4.0.0} \\
+\indent Minimum compatible version: \\
+\indent \indent 11.01.2013 \\
+\indent Latest version:	\\
+\indent \indent 08.02.2018 (50um) \\
+\indent \indent 08.02.2018 (25 um Master) \\
+\indent \indent 09.02.2018 (25 um Slave) \\
+
+Normally, the firmware will be upgraded by us as it requires programming the
+FPGA via the USB-Blaster.
+
+
+To upgrade the firmware you need either a working version of the Altera
+Quartus software or of the Quartus programmer, which can easily be downloaded
+from: \\
+\url{https://www.altera.com/download/programming/quartus2/pq2-index.jsp}
+
+
+Normally, installation of the software and of the driver for the
+USB-Blaster (provided together with the MYTHEN detector) are simpler under
+Windows.
+
+
+Under Windows, the first time that you connect the USB-Blaster to one
+of your USB ports, you will be asked to install new hardware. Set the path to
+search for the driver to:
+\verb=C:\altera\80sp1\qprogrammer\drivers\usb-blasterp= (where 
+\verb=C:\altera\80sp1\qprogrammer\= is assumed to be ther path where your
+Quartus version is installed).
+\begin{enumerate}
+\item After starting the Quartus programmer, click on Hardware Setup and in the
+"Currently selected hardware" window select USB-Blaster.
+\item In the Mode combo box select "Active Serial Programming".
+\item Plug the end of your USB-Blaster WITH THE ADAPTER PROVIDED in the
+connector ASMI on the MCS board taking care that pin1 corresponds to the one
+indexed and with the rectangualr pad.
+\item Click on add file and from select the programming file provided when
+the upgrade has been reccomended.
+\item Check "Program/Configure" and "Verify".
+\item Push the start button and wait until the programming process is
+finished (progress bar top left).
+\item In case the programmer gives you error messages, check the polarity of
+your cable (pin1 corresponds) and that you have selected the correct programming
+connector.
+\end{enumerate}
+
+\subsubsection{GOTTHARD On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+\begin{enumerate}
+  \item Install tftp if the pc does not have it.
+  \item Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+  \item Copy the server to the detector by:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/gotthardDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no gotthardDetectorServers are running
+    \end{enumerate}
+    \item Copy new on-board server from pc to the blackfin using: \\
+\verb=tftp pcxxx -r gotthardDetectorServerxxx -g= 
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/gotthardDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=gotthardDetectorServerxxx= \\
+\verb=gotthardDetectorServerxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+\end{enumerate}
+
+
+
+\subsection{EIGER}
+
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+\subsubsection{EIGER Firmware}
+\textit{For SLS Detector Package v4.0.0} \\
+\indent Minimum compatible version:  22 \\
+\indent Latest version:	22  \\
+
+
+\begin{enumerate}
+  \item One must get the latest package's corresponding bit files from the SLS
+Detector Group.
+  \item If one does not have the bcp script, that should also be obtained from
+the SLS Detector Group. It is required to program the bit files and requires
+that tftp be installed on the pc.
+  \item Bring the detector into programmable mode by either of the following ways.
+Both ways end up in just the central LED blinking.
+  \begin{enumerate}
+    \item hard reset on the back panel boards resulting in blinking LEDS 
+    \item by having the following program running in the background. 
+    \begin{verbatim}
+    boot_recovery
+    \end{verbatim}
+\end{enumerate}
+  \item Start a terminal for each half module and run the following to see 
+progress.
+\begin{verbatim}
+	nc -p 3000 -u bebxxx 3000 
+\end{verbatim}
+  \item Run the following to update firmware
+\begin{verbatim}
+ #update back end fpga
+bcp download.bit bebxxx:/fw0
+
+ #update front left fpga
+bcp download.bit bebxxx:/febl
+
+ #update front right fpga
+bcp download.bit bebxxx:/febr
+
+ #update kernel
+bcp download.bit bebxxx:/kernel
+\end{verbatim}
+Please update bit files with great caution as it could make your board
+inaccessible, if done incorrectly.
+\end{enumerate}
+
+
+
+\subsubsection{EIGER On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+
+Update the on-board software without connecting to the detector
+\begin{verbatim}
+#password for the boards: root
+
+#Kill existing servers that are running on the detector
+ssh root@beb031 killall eigerDetectorServer;
+
+#Copy on-board server to detector inside executables folder
+scp ~/path-where-it-is/eigerDetectorServerxxx root@bebxxx:~/executables;
+
+#Overwrite the actual eigerDetectorServer on board
+scp ~/path-where-it-is/eigerDetectorServerxxx
+root@bebxxx:~/executables/eigerDetectorServer;
+
+#sync
+ssh root@bebxxx sync; 
+
+#reboot the eiger board
+\end{verbatim}
+
+
+\bigskip One can connect to the detector by:
+\begin{verbatim}
+ssh root@bebxxx
+password: root
+\end{verbatim}
+
+
+The on-board server is in ~/executables folder and respawned at startup in \\
+\verb=/etc/rc5.d/S50board_com.sh= 
+
+
+
+
+
+\subsection{JUNGFRAU}
+
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+\subsubsection{JUNGFRAU Firmware}
+\textit{For SLS Detector Package v4.0.0} \\
+\indent Minimum compatible version: 15.06.2018 \\
+\indent Latest version: 15.06.2018 \\
+
+
+At times, one has to update the firmware, which then also requires updating the
+on-board software. 
+
+
+\textbf{\textit{Jungfrau firmware can be upgraded via the SLS Detector Package
+binaries from the command line.}}
+
+\begin{enumerate}
+  \item One must get the latest package's corresponding POF file from the SLS
+Detector Group.
+  \item Update the latest SLS Detector package installed.
+  \item Update the on-board software as per the instructions in the next
+section.
+  \item Start the on-board server in update mode:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no jungfrauDetectorServers are running
+    \end{enumerate}
+    \item Start the server in update mode using: \\
+\verb=./jungfrauDetectorServerxxx -update= \\
+    Leave this console on to come back to it later.
+  \end{enumerate}
+  \item From the command line of the pc, clear shared memory \\
+\verb=./sls_detector_get free= \\
+  If one gets shmget error, please clean the shared memory properly using the
+script in \verb=slsDetectorPackage/cleansharedmemory.sh=
+  \item Add the detector to shared memory using \\
+\verb=./sls_detector_put hostname bchipxxx=
+  \item Program the FPGA using \\
+\verb=./sls_detector_put programfpga xxx.pof= 
+  \item Once the programming is done:
+  \begin{enumerate}
+    \item Switch to the console that has the update server running and kill it
+using Ctrl+C and ensure no jungfrauDetectorServers are
+running
+    \item Restart the new server to see if it runs with the new firmware \\
+\verb=./jungfrauDetectorServerxxx= \\
+If the server didn't start properly, please contact us with the error message
+shown when starting the server up, else continue with the following steps.
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=jungfrauDetectorServervxxx= \\
+\verb=jungfrauDetectorServervxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+
+\end{enumerate}
+
+
+
+\subsubsection{JUNGFRAU On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+
+\begin{enumerate}
+  \item Install tftp if the pc does not have it.
+  \item Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+  \item Copy the server to the detector by:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no gotthardDetectorServers are running
+    \end{enumerate}
+    \item Copy new on-board server from pc to the blackfin using: \\
+\verb=tftp pcxxx -r jungfrauDetectorServervxxx -g= 
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=jungfrauDetectorServervxxx= \\
+\verb=jungfrauDetectorServervxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+\end{enumerate}
+
+
+
+
+
+
 \begin{comment}
 \section{Detector system architecture}
 

serverBin/eigerDetectorServerv3.0.0.16.10

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.0.0.16.10

serverBin/eigerDetectorServerv4.0.0.22.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv4.0.0.22.0

serverBin/gotthardDetectorServerv3.0.0.6

@@ -1 +0,0 @@
-../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv3.0.0.6

serverBin/gotthardDetectorServerv4.0.0.3

@@ -0,0 +1 @@
+../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv4.0.0.3

serverBin/jungfrauDetectorServerv3.0.0.6.3

@@ -1 +0,0 @@
-../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.0.0.6.3

serverBin/jungfrauDetectorServerv4.0.0.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv4.0.0.0

serverBin/moenchDetectorServerv2.0.3

@@ -1 +0,0 @@
-../slsDetectorSoftware/moenchDetectorServer/moenchDetectorServerv2.0.3

settingsdir/gotthard/dynamicgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6

settingsdir/gotthard/dynamicgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 350
-Vib_test 2001

settingsdir/gotthard/highgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6

settingsdir/gotthard/highgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 350
-Vib_test 2001

settingsdir/gotthard/lowgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6

settingsdir/gotthard/lowgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 350
-Vib_test 2001

settingsdir/gotthard/mediumgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6

settingsdir/gotthard/mediumgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 350
-Vib_test 2001

settingsdir/gotthard/veryhighgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6

settingsdir/gotthard/veryhighgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 350
-Vib_test 2001

settingsdir/jungfrau/dynamicgain/calibration.sn

@@ -1 +0,0 @@
-227 5.6