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

@@ -2,7 +2,7 @@
 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.
@@ -19,7 +19,7 @@ Requirements: Qt 4.8 and Qwt 6.0
 ```
 If either of them does not exist, the GUI client will not be built.
 
-* Calibration wizards<br>
+* Advanced user Calibration wizards<br>
 Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
@@ -43,6 +43,7 @@ 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
@@ -86,5 +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

@@ -1,113 +1,508 @@
-SLS Detector Package 3.1.1 released on 2018-03-12
+SLS Detector Package 4.0.0 released on 27.09.2018
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.1.0 and 3.1.0 releases.
+	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/slsdetectorgroup/sls_detector_software.git
+	The Source Code (Default C++ API):
+		 https://github.com/slsdetectorgroup/slsDetectorPackage
 		 
-The Python interface to the software package (including the 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
-	manual/docs/
+	The Python Interface (including the package):
+    	https://github.com/slsdetectorgroup/sls_detector
 	
-Documentation from Source Code can be found for the Command Line and for the API in
-	html:
+	
+	Documentation
+	-------------
+	
+	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
 		
-Example including binaries for detector and receiver user classes can be found in 
+	C++ API Example:
+		manual/manual-api/mainClient.cpp
+		manual/manual-api/mainReceiver.cpp
 		
-	manual/manual-api
-	
-User documentation can also be accessed directly at this location:
+	Python API Documentation:
+		https://slsdetectorgroup.github.io/sls_detector/
 		
+	Further Documentation:
 		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
-- Changes in User Interface
-- New Features
-- Resolved Issues
-- Known Issues
+	1.	Firmware Requirements
+	2.	Changes in User Interface
+	3.	New/Modified Commands
+	4.	Other New Features
+	5.	Resolved Issues
+	6.	Known Issues
+	7.	Next Major Release Plans
 
 
 
-Firmware Requirements
-=====================
-
-	Please refer to the link below for more details on the firmware versions.
-		https://www.psi.ch/detectors/firmware.
+1. Firmware Requirements
+========================
 
     	Gotthard
     	========   
     	Minimum compatible version  : 11.01.2013
     	Latest version              : 08.02.2018 (50um and 25um Master)
                                       09.02.2018 (25 um Slave) 
-
-   	-Can not be upgraded remotely.
-    
-    
     	Eiger
     	=====  
-    	Minimum compatible version  : 16
-    	Latest version              : 20
-        
-    	-Can be upgraded remotely via bit files.
-    
+    	Minimum compatible version  : 22
+    	Latest version              : 22
         
     	Jungfrau
     	========       
-    	Minimum compatible version  : 13.11.2017
-    	Latest version              : 13.11.2017
+    	Minimum compatible version  : 15.06.2018
+    	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.	Shared Memory:
+	
+		POSIX shared memory has been implemented and they are typically created in
+		/dev/shm/ folder.
+		
+		A multiSlsDetector object will create a shared memory segment with naming style:
+		slsDetectorPackage_x_[_z]
+		and an slsDetector object will create a shared memory segment with naming style:
+		slsDetectorPackage_x_sls_y[_z]
+		 	
+		where
+		x is the multi detector id
+		y is the sls detector id
+		z is the environment variable SLSDETNAME, if set.
+		They can be deleted directly.
+		
+		Environment variable SLSDETNAME included for user-friendliness
+		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
+	--------
+	
+	1.	Reciever Header Structure in file writing and call back:
+	
+		sls_receiver_header structure added to sls_receiver_defs.h for image headers 
+		in file writing. 
+		
+		#define MAX_NUM_PACKETS	512
+		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.
+		
+		
+	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.
+
+
+	3.	Receiver Call back with modified size:
+	
+		registerCallBackRawDataModifyReady call back that is similar to the receiver 
+		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.
+
+		This also means that the call back is now called before writing to file.
+
+
+
+3. New/Modified Commands 
+========================
+	
+	Client
+	------
+
+	1.	add (modified): 
+		appends detector to end of multi detector list.
+
+	2.	replace: 
+		sets hostname/ip address for a single detector.
+
+	3.	user: 
+		get user details from shared memory.
+
+	4.	checkdetversion: 
+		checks client version compatibility with detector server.
+
+	5.	checkrecversion: 
+		checks client version compatibility with receiver server.
+		
+	
+	Receiver
+	--------
+	
+	1.	rx_zmqip:	
+		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.
+	
+	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.
+	  		 	
+	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\"
+		
+	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
+	---
+	
+	1.	(Jungfrau) Gain plot included. Option under 2D options in Plot tab.
+	
+	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.
 
 
 
 
-New Features
-============
+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
+	---------------
 	
-Resolved Issues
+	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
+	--------
 	
-Known Issues
-============
-
-	
+	1. 	HDF5 compression and filters are not implemented yet.
+	
+	
+	Detector Server
+	---------------
+	
+	1.	(Eiger) Registers mapped differently between firmware v20 and v22.
+		So, please ensure correct on-board server before switching between
+		firmware versions. Else one cannot ping it anymore. Will need to flash firmware
+		again to recover.
+		
+	2.	(Gotthard) To switch back to all ADC from single ADC ROI, one must take
+		even number of images for the receiver to understand complete images.
+		This will be fixed in the next firmware upgrade.
 	
 	
 	
+7. Next Major Release Plans
+===========================
+
+	Client
+	------
+	
+	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
-timing auto
+#extsig:0 trigger_in_rising_edge
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/moench03_T1_lab.config

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+
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+patword 0148 870c599f000e50ba
+patword 0149 870c599f000850ba
+patword 014a 870c599f000e50ba
+patword 014b 870c599f000850ba
+patword 014c 870c599f000e50ba
+patword 014d 870c599f000850ba
+patword 014e 870c599f000e50ba
+patword 014f 870c599f000850ba
+patword 0150 870c599f000e50ba
+patword 0151 870c599f000850ba
+patword 0152 870c599f000e50ba
+patword 0153 870c599f000850ba
+patword 0154 870c599f200e50ba
+patword 0155 870c599f000850ba
+patword 0156 870c599f000e50ba
+patword 0157 870c599f000850ba
+patword 0158 870c599f000e50ba
+patword 0159 870c599f000850ba
+patword 015a 870c599f000e50ba
+patword 015b 870c599f000850ba
+patword 015c 870c599f000e50ba
+patword 015d 870c599f000850ba
+patword 015e 870c599f000e50ba
+patword 015f 870c599f000850ba
+patword 0160 870c599f000e50ba
+patword 0161 870c599f000850ba
+patword 0162 870c599f000e50ba
+patword 0163 870c599f000850ba
+patword 0164 870c599f000e50ba
+patword 0165 870c599f000850ba
+patword 0166 870c599f000e50ba
+patword 0167 870c599f000850ba
+patword 0168 870c599f000e50ba
+patword 0169 870c599f000850ba
+patword 016a 870c599f000e50ba
+patword 016b 870c599f000850ba
+patword 016c 070c599f000850ba
+patword 016d 070c599f000850ba
+patword 016e 000c599f000850ba
+patword 016f 000c599f000850ba
+patword 0170 0008599f200e503a
+patword 0171 0008599f0008503a
+patword 0172 0008599f200e503a
+patword 0173 0008599f0008503a
+patword 0174 0008599f0008503a
+patword 0175 0008599f0008503a
+patword 0176 0008599f0008503a
+patword 0177 0008599f0008503a
+patword 0178 0008599f0008503a
+patword 0179 0008599f0008503a
+patword 017a 0008599f0008503a
+patword 017b 0008599f0008503a
+patword 017c 0008599f0008503a
+patword 017d 0008599f0008503a
+patword 017e 0008599f0008503a
+patword 017f 0008599f0008503a
+patword 0180 0008599f0008503a
+patword 0181 0008599f0008503a
+patword 0182 0008599f0008503a
+patword 0183 0008599f0008503a
+patword 0184 0008599f0008503a
+patword 0185 0008599f0008503a
+patword 0186 0008599f0008503a
+patword 0187 0008599f0008503a
+patword 0188 0008599f0008503a
+patword 0189 0008599f0008503a
+patword 018a 0008599f0008503a
+patword 018b 0008599f0008503a
+patword 018c 0008599f0008503a
+patword 018d 0008599f0008503a
+patioctrl 8f0effff6dbffdbf
+patclkctrl 0000000000000000
+patlimits 0000 018c
+patloop0 013a 016b
+patnloop0 199
+patloop1 0400 0400
+patnloop1 0
+patloop2 0400 0400
+patnloop2 0
+patwait0 00aa
+patwaittime0 40000
+patwait1 0400
+patwaittime1 0
+patwait2 0400
+patwaittime2 0
+
+
+
+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/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$(PKGDIR)/slsDetectorSoftware/slsDetector 
 SRC_DET		= 	mainClient.cpp 	
 SRC_REC		=   mainReceiver.cpp
-LIBDIR		=   .
-LDFLAG_DET 	=	-I. -L$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread -lrt -L. -lzmq
-LDFLAG_REC 	=	-I. -L$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread -lrt -L. -lzmq
+ZMQLIBDIR	= 	$(PKGDIR)/slsReceiverSoftware/include
+LDFLAG_DET 	=	-I. -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread -lrt -L$(ZMQLIBDIR) -Wl,-rpath=$(ZMQLIBDIR) -lzmq
+LDFLAG_REC 	=	-I. -L$(LIBDIR) -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/ansi.h

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

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) */
@@ -71,10 +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 */
@@ -93,7 +94,7 @@ int main(int argc,  char **argv) {
 
 	/** - start measurement */
 	pDetector->startMeasurement();
-	std::cout << "measurement finished" << std::endl;	usleep(1*1000*1000);
+	std::cout << "measurement finished" << std::endl;
 
 	/** - returning when acquisition is finished or data are avilable */
 

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 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 metadata sls_receiver_header metadata
  * @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,
-		uint16_t modId, uint16_t xCoord, uint16_t yCoord, uint16_t zCoord, uint32_t debug, uint16_t roundRNumber, uint8_t detType, uint8_t version,
-		char* datapointer, uint32_t datasize, void* p){
+void GetData(char* metadata, char* datapointer, uint32_t datasize, void* p){
+	slsReceiverDefs::sls_receiver_header* header = (slsReceiverDefs::sls_receiver_header*)metadata;
+	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"
-			"xCoord: %u\t\tyCoord: %u\t\tzCoord: %u\t\tdebug: %u\t\troundRNumber: %u\t\tdetType: %u\t\t"
-			"version: %u\t\tfirstbytedata: 0x%x\t\tdatsize: %u\n\n",
-			xCoord, frameNumber, expLength, packetNumber, bunchId, timestamp, modId,
-			xCoord, yCoord, zCoord, debug, roundRNumber, detType, version,
+			"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)))), 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/sls_receiver_defs.h

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

manual/manual-api/sls_receiver_funcs.h

@@ -1 +0,0 @@
-../../slsReceiverSoftware/include/sls_receiver_funcs.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$10~Gb/s transceivers to optionally, receive data at high rate.
+\item 2$\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. 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-threshold energy_in_eV
+sls_detector_put 0-settings standard 
+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.\\ 
-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/}\\ 
+%\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:
-\begin{itemize}
+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{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}
-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}
+\end{enumerate}
 
 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. 
-The number of images that can be stored on memories are listed in table~\ref{timgs}:
+ 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}.
 \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\\
-\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\\
+4 & 2 & \tiny {parallel} & 11.2 & 5.4 & 197& 197.01 & 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\\
-\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\\
+8 & 2 & \tiny {parallel} & 11.2 &  2.9 &  342 & 342.01 & 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\\
-\hline
-\hline
-32 & 2 & parallel &  11 & 2&  & &\\
-\hline
-32 & 2 & nonparallel & 504 & $<2$&  & &\\
+16 & 2 & \tiny {nonparallel} & 505 & 1.8  & 555 & 555.01& infinite\\
 \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{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{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{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{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. 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.  {\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.  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 10Gb/s physical link is signaled by the second most external LED next to the 1Gb/s one (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). 
 \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
-Dynamic Range      : 16
+Version                    : 2.0
+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:
-\begin{verbatim}
-cbfMaker [filename] [pixels x] [pixels y] ([singlemodulelongside_x] [start det])
-\end{verbatim}
+To use it any geometry:\\
+{\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]}}\\
 eg.
-{\tt cbfMaker /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 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. 
+{\tt cbfMaker /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 2 ``Eiger'' 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]
-bcfMaker9M [file_name_with_dir]
+cbfMaker1.5M [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}
-   GapPixelsBetweenChips_x = 2;
-   GapPixelsBetweenChips_y = 2;
-   GapPixelsBetweenModules_x = 8;
-   GapPixelsBetweenModules_y = 36;
- \end{verbatim}
+\subsubsection{hdf5}
+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.
+
+To choose HDF5, with ZLIB implementation, open {\tt{slsImageReconstruction/src/main\_csaxs.cpp}} and make sure that 
+\begin{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/slsDetectorInstall.tex

@@ -61,6 +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.
@@ -110,13 +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)
-conda install sls_detector_software=3.1.0
+#Install specific release
+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_3.1.0
 \end{verbatim}
  \item The package including Python interface
 \begin{verbatim}
@@ -127,11 +132,9 @@ conda config --add channels sls_detector
 #Install latest version
 conda install sls_detector
 
-#Install specific release (GLIBC2.14)
-conda install sls_detector=3.1.0
+#Install specific release 
+conda install sls_detector=4.0.0
 
-#Scientific Linux 6 version (GLIBC2.12)
-conda install sls_detector=SL6_3.1.0
 \end{verbatim}
 \end{itemize}
 
@@ -148,13 +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
-3.1.0
+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
-3.1.0
+4.0.0
 \end{verbatim}
 \end{itemize}
 
@@ -437,14 +440,11 @@ 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 use the following commands to clean the shared memory
-segments one by one.
-\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}
+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}
 
@@ -544,14 +544,14 @@ detector board the programming files and/or software package provided by
 the SLS Detectors group.
 
 \subsubsection{GOTTHARD Firmware}
-\textit{For SLS Detector Package v3.1.0} \\
+\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 and 25um Master) \\
+\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.
 
@@ -636,9 +636,9 @@ detector board the programming files and/or software package provided by
 the SLS Detectors group.
 
 \subsubsection{EIGER Firmware}
-\textit{For SLS Detector Package v3.1.0} \\
-\indent Minimum compatible version:  16 \\
-\indent Latest version:	20  \\
+\textit{For SLS Detector Package v4.0.0} \\
+\indent Minimum compatible version:  22 \\
+\indent Latest version:	22  \\
 
 
 \begin{enumerate}
@@ -647,6 +647,20 @@ 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
@@ -715,9 +729,9 @@ detector board the programming files and/or software package provided by
 the SLS Detectors group.
 
 \subsubsection{JUNGFRAU Firmware}
-\textit{For SLS Detector Package v3.1.0} \\
-\indent Minimum compatible version: 13.11.2017 \\
-\indent Latest version: 13.11.2017 \\
+\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
@@ -733,7 +747,7 @@ 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 debug mode:
+  \item Start the on-board server in update mode:
   \begin{enumerate}
     \item Connect to the blackfin on the detector\\ 
 \verb=telnet bchipxxx=
@@ -743,10 +757,10 @@ section.
       \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
+      \item Run \verb=ps= to ensure no jungfrauDetectorServers are running
     \end{enumerate}
-    \item Start the server in debug mode using: \\
-\verb=./jungfrauDetectorServerxxx -debug= \\
+    \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 \\
@@ -759,7 +773,7 @@ script in \verb=slsDetectorPackage/cleansharedmemory.sh=
 \verb=./sls_detector_put programfpga xxx.pof= 
   \item Once the programming is done:
   \begin{enumerate}
-    \item Switch to the console that has the debug server running and kill it
+    \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 \\

serverBin/eigerDetectorServer_virtualMaster

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServer_virtualMaster

serverBin/eigerDetectorServer_virtualSlave

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServer_virtualSlave

serverBin/eigerDetectorServerv3.1.0.16.1

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.1.0.16.1

serverBin/eigerDetectorServerv3.1.0.21.0

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.1.0.21.0

serverBin/eigerDetectorServerv4.0.0.22.0

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

serverBin/gotthardDetectorServer_virtual

@@ -1 +0,0 @@
-../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServer_virtual

serverBin/gotthardDetectorServerv3.1.0.1

@@ -1 +0,0 @@
-../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv3.1.0.1

serverBin/gotthardDetectorServerv4.0.0.3

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

serverBin/jungfrauDetectorServer_virtual

@@ -1 +0,0 @@
-../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServer_virtual

serverBin/jungfrauDetectorServerv3.0.0.12

@@ -1 +0,0 @@
-../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.0.0.12

serverBin/jungfrauDetectorServerv3.1.0.2

@@ -1 +0,0 @@
-../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.1.0.2

serverBin/jungfrauDetectorServerv4.0.0.0

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

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

settingsdir/jungfrau/dynamicgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 1220
-VDAC1 3000
-VDAC2 1053
-VDAC3 1450
-VDAC4 750
-VDAC5 1000
-VDAC6 480
-VDAC7 420

settingsdir/jungfrau/dynamichg0

@@ -1 +0,0 @@
-dynamicgain

settingsdir/jungfrau/fixgain1

@@ -1 +0,0 @@
-dynamicgain

settingsdir/jungfrau/fixgain2

@@ -1 +0,0 @@
-dynamicgain

settingsdir/jungfrau/forceswitchg1

@@ -1 +0,0 @@
-dynamicgain

settingsdir/jungfrau/forceswitchg2

@@ -1 +0,0 @@
-dynamicgain

settingsdir/moench/dynamicgain/calibration.sn

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

settingsdir/moench/dynamicgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 660
-VDAC1 650
-VDAC2 1480
-VDAC3 1520
-VDAC4 1320
-VDAC5 1350
-VDAC6 887
-VDAC7 2001

settingsdir/moench/highgain/calibration.sn

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

settingsdir/moench/highgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 660
-VDAC1 650
-VDAC2 1480
-VDAC3 1520
-VDAC4 1320
-VDAC5 1350
-VDAC6 887
-VDAC7 2001

settingsdir/moench/lowgain/calibration.sn

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

settingsdir/moench/lowgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 660
-VDAC1 650
-VDAC2 1480
-VDAC3 1520
-VDAC4 1320
-VDAC5 1350
-VDAC6 887
-VDAC7 2001

settingsdir/moench/mediumgain/calibration.sn

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

settingsdir/moench/mediumgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 660
-VDAC1 650
-VDAC2 1480
-VDAC3 1520
-VDAC4 1320
-VDAC5 1350
-VDAC6 887
-VDAC7 2001

settingsdir/moench/veryhighgain/calibration.sn

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

settingsdir/moench/veryhighgain/settings.sn

@@ -1,8 +0,0 @@
-VDAC0 660
-VDAC1 650
-VDAC2 1480
-VDAC3 1520
-VDAC4 1320
-VDAC5 1350
-VDAC6 887
-VDAC7 2001

settingsdir/propix/dynamicgain/calibration.sn

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

settingsdir/propix/dynamicgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 887
-Vib_test 2001

settingsdir/propix/highgain/calibration.sn

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

settingsdir/propix/highgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 887
-Vib_test 2001

settingsdir/propix/lowgain/calibration.sn

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

settingsdir/propix/lowgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 887
-Vib_test 2001

settingsdir/propix/mediumgain/calibration.sn

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

settingsdir/propix/mediumgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 887
-Vib_test 2001

settingsdir/propix/veryhighgain/calibration.sn

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

settingsdir/propix/veryhighgain/settings.sn

@@ -1,8 +0,0 @@
-Vref 660
-VcascN 650
-VcascP 1480
-Vout 1520
-Vcasc 1320
-Vin 1350
-Vref_comp 887
-Vib_test 2001

slsDetectorCalibration/analogDetector.h

@@ -8,8 +8,20 @@
 #include "pedestalSubtraction.h"
 #include "commonModeSubtraction.h"
 #include "tiffIO.h"
+#include "slsInterpolation.h"
 
 
+#ifdef ROOTSPECTRUM
+#include <TPaveText.h> 
+#include <TLegend.h> 
+#include <TF1.h> 
+#include <TGraphErrors.h> 
+#include <TH2F.h> 
+#include <TASImage.h> 
+#include <TImage.h> 
+#include <TFile.h> 
+#endif
+
 using namespace std;
 
 #ifndef FRAMEMODE_DEF
@@ -18,6 +30,10 @@ using namespace std;
 enum to define the flags of the data set, which are needed to seect the type of processing it should undergo: frame, pedestal, flat
 */
  enum frameMode { eFrame, ePedestal, eFlat };
+/** 
+enum to define the detector mode
+*/
+ enum detectorMode { eAnalog, ePhotonCounting, eInterpolating };
 #endif
 
 
@@ -65,12 +81,30 @@ template <class dataType> class analogDetector {
     fMode=ePedestal;
     thr=0;
     myFile=NULL;
-    fm=new pthread_mutex_t ;
+#ifdef ROOTSPECTRUM
+    hs=new TH2F("hs","hs",2000,-100,10000,nx*ny,-0.5,nx*ny-0.5);
+#ifdef ROOTCLUST
+    hs3=new TH2F("hs3","hs3",2000,-100,3*3*10000,nx*ny,-0.5,nx*ny-0.5);
+    hs5=new TH2F("hs5","hs5",2000,-100,5*5*10000,nx*ny,-0.5,nx*ny-0.5);
+    hs7=new TH2F("hs7","hs7",2000,-100,7*7*10000,nx*ny,-0.5,nx*ny-0.5);
+    hs9=new TH2F("hs9","hs9",2000,-100,9*9*10000,nx*ny,-0.5,nx*ny-0.5);
+#endif
+#endif
   };
   /**
      destructor. Deletes the pdestalSubtraction array and the image
   */
-  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat[i]; delete [] stat; delete [] image;};
+  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat[i]; delete [] stat; delete [] image;
+#ifdef ROOTSPECTRUM
+    delete hs;
+#ifdef ROOTCLUST
+    delete hs3;
+    delete hs5;
+    delete hs7;
+    delete hs9;
+#endif
+#endif
+};
 
   /**
      constructor cloning another analog detector
@@ -94,7 +128,6 @@ template <class dataType> class analogDetector {
     // nSigma=orig->nSigma;
     fMode=orig->fMode;
     myFile=orig->myFile;
-    fm=orig->fm;
     
 
     stat=new pedestalSubtraction*[ny];
@@ -111,6 +144,15 @@ template <class dataType> class analogDetector {
       }
     }
     image=new int[nx*ny];
+#ifdef ROOTSPECTRUM
+    hs=(TH2F*)(orig->hs)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5);
+#ifdef ROOTCLUST
+     hs3=(TH2F*)(orig->hs3)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5);
+     hs5=(TH2F*)(orig->hs5)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+     hs7=(TH2F*)(orig->hs7)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+     hs9=(TH2F*)(orig->hs9)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+#endif
+#endif
 
   }
 
@@ -220,6 +262,15 @@ template <class dataType> class analogDetector {
 	image[iy*nx+ix]=0;
       }
     if (cmSub) cmSub->Clear(); 
+#ifdef ROOTSPECTRUM
+    hs->Reset();
+#ifdef ROOTCLUST
+     hs3->Reset();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5);
+     hs5->Reset();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+     hs7->Reset();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+     hs9->Reset();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
+#endif
+#endif
   };  
   
   /** resets the commonModeSubtraction and increases the frame index */
@@ -253,16 +304,46 @@ template <class dataType> class analogDetector {
        \param iy pixel y coordinate
        \param cm 1 adds the value to common mod, 0 skips it. Defaults to 0. - not properly implemented
     */
-    virtual void addToPedestal(double val, int ix, int iy=0){ 
+    virtual void addToPedestal(double val, int ix, int iy=0, int cm=0){ 
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) { 
+	if (cmSub && cm>0)  { 
+	  val-=	getCommonMode(ix, iy);
+	}
 	stat[iy][ix].addToPedestal(val); 
-	if (cmSub)  {
-	  if (det) if (det->isGood(ix, iy)==0) return;
-	  cmSub->addToCommonMode(val, ix, iy);
-	};
+	/* if (cmSub && cm>0)  { */
+	/*   if (det) if (det->isGood(ix, iy)==0) return; */
+	/*   cmSub->addToCommonMode(val, ix, iy); */
+	/* }; */
       };
     }
     
+    double getCommonMode(int ix, int iy) {
+      if (cmSub) return cmSub->getCommonMode(ix, iy);
+      else return 0;
+    }
+
+
+    virtual void addToCommonMode(char *data){ 
+      if (cmSub) {
+	for (int ix=xmin; ix<xmax; ix++) {
+	  for (int iy=ymin; iy<ymax; iy++) { 
+	    // if (getNumpedestals(ix,iy)>0) 
+	    if (det->isGood(ix,iy))
+	      addToCommonMode(data, ix, iy);
+	  }
+	}
+	//cout << "cm " << getCommonMode(0,0) << " " << getCommonMode(1,0) << endl;
+      }
+    }      
+    virtual void addToCommonMode(char *data, int ix, int iy=0){ 
+      if (cmSub) {
+	if (det) if (det->isGood(ix, iy)==0) return;
+	if (getNumpedestals(ix,iy)>0){
+	    cmSub->addToCommonMode(subtractPedestal(data,ix,iy,0), ix, iy);
+	    // cout << ix << " " <<subtractPedestal(data,ix,iy,0)  << endl;
+	}
+      }
+    }      
   /**
        gets  pedestal (and common mode)
        \param ix pixel x coordinate
@@ -270,7 +351,14 @@ template <class dataType> class analogDetector {
        \param cm 0 (default) without common mode subtraction, 1 with common mode subtraction (if defined)
        \returns pedestal value
     */
-    virtual double getPedestal(int ix, int iy, int cm=0){if (ix>=0 && ix<nx && iy>=0 && iy<ny) if (cmSub && cm>0) return stat[iy][ix].getPedestal()-cmSub->getCommonMode(); else return stat[iy][ix].getPedestal(); else return -1;};
+    virtual double getPedestal(int ix, int iy, int cm=0){
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
+	if (cmSub && cm>0) 
+	  return stat[iy][ix].getPedestal()+getCommonMode(ix,iy); 
+	else return stat[iy][ix].getPedestal(); 
+      else return -1;
+    };
+
 
     /**
        gets  pedestal rms (i.e. noise)
@@ -278,9 +366,17 @@ template <class dataType> class analogDetector {
        \param iy pixel y coordinate
        \returns pedestal rms
     */
-    virtual double getPedestalRMS(int ix, int iy){if (ix>=0 && ix<nx && iy>=0 && iy<ny) return stat[iy][ix].getPedestalRMS();else return -1;};
-
+    virtual double getPedestalRMS(int ix, int iy){
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
+	return stat[iy][ix].getPedestalRMS();
+      else return -1;
+    };
 
+     virtual int getNumpedestals(int ix, int iy){
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
+	return stat[iy][ix].getNumpedestals();
+      else return -1;
+    };
     /**
        gets  pedestal (and common mode)
        \param ix pixel x coordinate
@@ -294,6 +390,7 @@ template <class dataType> class analogDetector {
       for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
 	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
+	  //cout << ped[iy*nx+ix] << " " ;
 	}
       }
       return ped;
@@ -328,7 +425,6 @@ template <class dataType> class analogDetector {
 
 
     
-    
     /**
        sets  pedestal
        \param ix pixel x coordinate
@@ -396,17 +492,45 @@ template <class dataType> class analogDetector {
   virtual void *writeImage(const char * imgname) {
     float *gm=NULL;
     void *ret;
+#ifdef ROOTSPECTRUM
+
+      TH2F *hmap=new TH2F("hmap","hmap",nx, -0.5,nx-0.5, ny, -0.5, ny-0.5);
+
+#endif
       gm=new float[nx*ny];
       for (int ix=0; ix<nx; ix++) {
 	for (int iy=0; iy<ny; iy++) {
 	    gm[iy*nx+ix]=image[iy*nx+ix];
+#ifdef ROOTSPECTRUM
+	    hmap->SetBinContent(ix+1, iy+1,image[iy*nx+ix]);
+#endif
 	}
       }
       ret=WriteToTiff(gm, imgname, ny, nx);   
       delete [] gm;
+#ifdef ROOTSPECTRUM
+      char rootfn[10000];
+      sprintf(rootfn,"%s.root",imgname);
+      TFile *f=new TFile(rootfn,"RECREATE");
+      hs->Write("hs");
+#ifdef ROOTCLUST
+      hs3->Write("hs3");
+      hs5->Write("hs5");
+      hs7->Write("hs7");
+      hs9->Write("hs9");
+#endif    
+      hmap->Write("hmap");
+      
+
+      f->Close();
+      delete f;
+      delete hmap;
+#endif
       return ret;
   }
-   
+#ifdef ROOTSPECTRUM
+  TH2F *getSpectrum(){return hs;};
+#endif
        /**
        write 32bit tiff file containing the pedestals
        \param imgname file name to be written
@@ -417,16 +541,41 @@ template <class dataType> class analogDetector {
     float *gm=NULL;
     void *ret;
     gm=new float[nx*ny];
+#ifdef ROOTSPECTRUM
+
+      TH2F *hmap=new TH2F("hmap","hmap",nx, -0.5,nx-0.5, ny, -0.5, ny-0.5);
+
+#endif
     for (int ix=0; ix<nx; ix++) {
       for (int iy=0; iy<ny; iy++) {
-	  if (cmSub) 
-	    gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode();
-	  else
+	/* if (cmSub)  */
+	/*     gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode(); */
+	/* else */
 	  gm[iy*nx+ix]=stat[iy][ix].getPedestal();
+#ifdef ROOTSPECTRUM
+	  hmap->SetBinContent(ix+1, iy+1,gm[iy*nx+ix]);
+#endif
       }
     }
     ret=WriteToTiff(gm, imgname, ny, nx);   
     delete [] gm;
+    
+#ifdef ROOTSPECTRUM
+    char rootfn[10000];
+    sprintf(rootfn,"%s.root",imgname);
+    TFile *f=new TFile(rootfn,"RECREATE");
+    hs->Write("hs");
+#ifdef ROOTCLUST
+    hs3->Write("hs3");
+    hs5->Write("hs5");
+    hs7->Write("hs7");
+    hs9->Write("hs9");
+#endif
+    hmap->Write("hmap");
+    f->Close();
+    delete f;
+    delete hmap;
+#endif
     return ret;
   }
   
@@ -538,18 +687,28 @@ template <class dataType> class analogDetector {
        \param data pointer to the data
     */
 
-    virtual void addToPedestal(char *data) {
     
+    virtual void addToPedestal(char *data, int cm=0) {
       
+      //    cout << "add to pedestal " << endl;
       newFrame();
       
+      if (cmSub) {
+	addToCommonMode(data);
+      }
             
+      //cout << xmin << " " << xmax << endl;
+      // cout << ymin << " " << ymax << endl;
       for (int ix=xmin; ix<xmax; ix++) {
 	for (int iy=ymin; iy<ymax; iy++) {
-	  
-	  
-	  addToPedestal(data,ix,iy);
-	  
+	  if (det->isGood(ix,iy)) {
+	    addToPedestal(data,ix,iy,1);
+	  //if (ix==10 && iy==10) 
+	  // cout <<ix << " " << iy << " " << getPedestal(ix,iy)<< endl;
+#ifdef ROOTSPECTRUM 
+	    subtractPedestal(data,ix,iy,cm); 
+ #endif 
+	  }
 	  
 	}
       }
@@ -559,6 +718,7 @@ template <class dataType> class analogDetector {
 
 
 
+
   /**
      Sets region of interest in which data should be processed
        \param xmi minimum x. if -1 or out of range remains unchanged
@@ -585,6 +745,20 @@ template <class dataType> class analogDetector {
       }
       
 
+#ifdef ROOTSPECTRUM
+      delete hs;
+      hs=new TH2F("hs","hs",2000,-100,10000,(xmax-xmin)*(ymax-ymin),-0.5,(xmax-xmin)*(ymax-ymin)-0.5);
+#ifdef ROOTCLUST
+      delete hs3;
+      hs3=new TH2F("hs3","hs3",2000,-100,3*3*10000,(xmax-xmin)*(ymax-ymin),-0.5,(xmax-xmin)*(ymax-ymin)-0.5);
+      delete hs5;
+      hs5=new TH2F("hs5","hs5",2000,-100,5*5*10000,(xmax-xmin)*(ymax-ymin),-0.5,(xmax-xmin)*(ymax-ymin)-0.5);
+      delete hs7;
+      hs7=new TH2F("hs7","hs7",2000,-100,7*7*10000,(xmax-xmin)*(ymax-ymin),-0.5,(xmax-xmin)*(ymax-ymin)-0.5);
+      delete hs9;
+      hs9=new TH2F("hs9","hs9",2000,-100,9*9*10000,(xmax-xmin)*(ymax-ymin),-0.5,(xmax-xmin)*(ymax-ymin)-0.5);
+#endif
+#endif
 
     };
       /**
@@ -608,7 +782,7 @@ template <class dataType> class analogDetector {
     */
 
 
-    virtual void addToPedestal(char *data, int ix, int iy=0) {
+    virtual void addToPedestal(char *data, int ix, int iy=0, int cm=0) {
       
       
       double val;
@@ -619,7 +793,15 @@ template <class dataType> class analogDetector {
 	else
 	  val=((double*)data)[iy*nx+ix];
 	
+	 /* if (ix==10 && iy==10)  */
+	 /*     cout << ix << " " << iy << " " << val ;  */
+	  /* if (ix==100 && iy==100) */
+	  /*   cout << ix << " " << iy << " " << val; */
 	addToPedestal(val,ix,iy);
+	  /* if (ix==10 && iy==10)  */
+	  /*   cout <<" " << getPedestal(ix,iy)<< endl; */
+	  /* if (ix==100 && iy==100) */
+	  /*   cout << " " << getPedestal(ix,iy)<< endl; */
       }
       return  ;
       
@@ -632,18 +814,19 @@ template <class dataType> class analogDetector {
        \param val pointer where the pedestal subtracted data should be added. If NULL, the internal image is used
        \returns pointer to the pedestal subtracted data
     */ 
+  // virtual  int *subtractPedestal(char *data, int *val=NULL) {
       
-        
-   virtual  double *subtractPedestal(char *data, double *val=NULL) {
+    virtual  int *subtractPedestal(char *data, int *val=NULL, int cm=0) {
       
       newFrame();
       
       if (val==NULL)
-	val=new double[nx*ny];
+	val=image;//new double[nx*ny];
       
       for (int ix=xmin; ix<xmax; ix++) {
 	for (int iy=ymin; iy<ymax; iy++) {
-	  val[iy*nx+ix]+=subtractPedestal(data, ix, iy);
+	    if (det->isGood(ix,iy))
+	      val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
 	}
       }
       return  val;
@@ -662,8 +845,9 @@ template <class dataType> class analogDetector {
 
 
 
-   virtual  double subtractPedestal(char *data, int ix, int iy=0) {
+   virtual  double subtractPedestal(char *data, int ix, int iy=0, int cm=0) {
      double g=1.;
+     double val;
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
 	if (gmap) {
 	  g=gmap[iy*nx+ix];
@@ -671,9 +855,40 @@ template <class dataType> class analogDetector {
 	}
 
 	if (det)
-	  return (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy))/g;
+	  val= (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,cm))/g;
 	else
-	  return (((double*)data)[iy*nx+ix]-getPedestal(ix,iy))/g;
+	  val= (((double*)data)[iy*nx+ix]-getPedestal(ix,iy))/g;
+    
+#ifdef ROOTSPECTRUM
+	hs->Fill(val,(iy-ymin)*(xmax-xmin)+(ix-xmin));
+#ifdef ROOTCLUST
+	double v3=0,v5=0,v7=0,v9=0;
+	for (int iix=-4; iix<5; iix++)
+	  for (int iiy=-4; iiy<5; iiy++) {
+	    if (det)
+	      val= (dataSign*det->getValue(data, ix+iix, iy+iiy)-getPedestal(ix+iix,iy+iiy,cm))/g;
+	    else
+	      val= (((double*)data)[(iy+iiy)*nx+ix+iix]-getPedestal(ix+iix,iy+iiy,cm))/g;
+	    
+	    if (iix>-4 && iiy>-4 && iix<4 && iiy<4) {
+	      if (iix>-3 && iiy>-3 && iix<3 && iiy<3){
+		if (iix>-2 && iiy>-2 && iix<2 && iiy<2){
+		  v3+=val;
+		}
+		v5+=val;
+	      }
+	      v7+=val;
+	    }
+	    v9+=val;
+	  }
+	hs3->Fill(v3,(iy-ymin)*(xmax-xmin)+(ix-xmin));
+	hs5->Fill(v5,(iy-ymin)*(xmax-xmin)+(ix-xmin));
+	hs7->Fill(v7,(iy-ymin)*(xmax-xmin)+(ix-xmin));
+	hs9->Fill(v9,(iy-ymin)*(xmax-xmin)+(ix-xmin));
+
+#endif
+#endif
+	return val;
       }	  
    };
       
@@ -703,11 +918,19 @@ template <class dataType> class analogDetector {
      double v;
      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
        v=subtractPedestal(data,ix,iy);
+
+/*        // cout << v << " " ; */
+/* #ifdef ROOTSPECTRUM */
+/*        // cout << (iy-ymin)*(xmax-xmin)+(ix-xmin) << endl; */
+/*        hs->Fill(v,(iy-ymin)*(xmax-xmin)+(ix-xmin)); */
+/* #endif */
        if (thr>0) {
 	 v+=0.5*thr;
 	 nph=v/thr;
+	 if (nph>0)
 	   return nph;
-       } else
+	 return 0;
+       } 
        return v;
      }
      return 0;  
@@ -725,8 +948,12 @@ template <class dataType> class analogDetector {
        if (nph==NULL)
 	 nph=image;
        newFrame();
+
+       addToCommonMode(data);
+
        for (int ix=xmin; ix<xmax; ix++) {
 	 for (int iy=ymin; iy<ymax; iy++) {
+	   if (det->isGood(ix,iy))
 	     nph[iy*nx+ix]+=getNPhotons(data, ix, iy);
 	 }
        }
@@ -744,6 +971,23 @@ template <class dataType> class analogDetector {
 	 image[iy*nx+ix]=0;
        }
      }
+#ifdef ROOTSPECTRUM
+     //cout << "reset histogram " << endl;
+     if (hs)
+       hs->Reset();
+#ifdef ROOTCLUST
+
+     if (hs3)
+       hs3->Reset();
+     if (hs5)
+       hs5->Reset();
+     if (hs7)
+       hs7->Reset();
+     if (hs9)
+       hs9->Reset();
+#endif
+     //cout << "done " << endl;
+#endif
    };
 
     /** sets/gets number of samples for moving average pedestal calculation
@@ -788,8 +1032,11 @@ template <class dataType> class analogDetector {
       
       for (int ix=xmi; ix<xma; ix++)
 	for (int iy=ymi; iy<yma; iy++)
+	  if (det->isGood(ix,iy)) {
 	    if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
 	      val+=getNPhotons(data, ix, iy);
+	  }
+
       return val;
       
     };
@@ -806,14 +1053,17 @@ template <class dataType> class analogDetector {
     virtual void processData(char *data,int *val=NULL) {
       switch(fMode) {
       case ePedestal:
+	//cout << "analog ped " << endl;
 	addToPedestal(data);
 	break;
       default:
-	getNPhotons(data,val);
+	//	cout << "analog " << endl;
+	//subtractPedestal(data);
+	getNPhotons(data);
       }
     };
 
-    virtual char *getInterpolation(){return NULL;};
+    //  virtual char *getInterpolation(){return NULL;};
 
  /** sets the current frame mode for the detector
      \param f frame mode to be set
@@ -827,17 +1077,57 @@ template <class dataType> class analogDetector {
     */
     frameMode getFrameMode() {return fMode;};
     
+
+
+    //enum detectorMode { eAnalog, ePhotonCounting, eInterpolating };
+ /** sets the current detector mode for the detector
+     \param f detector mode to be set
+     \returns current detector mode
+    */
+    detectorMode setDetectorMode(detectorMode f) {dMode=f; return dMode;};
+    
+ /** gets the current detector mode for the detector
+     \returns current detector mode
+    */
+    detectorMode getDetectorMode() {return dMode;};
+  
+
 /** sets file pointer where to write the clusters to 
     \param f file pointer
     \returns current file pointer
 */
-    FILE *setFilePointer(FILE *f){myFile=f; return myFile;};
+FILE *setFilePointer(FILE *f){myFile=f; return myFile;};
 
 /** gets file pointer where to write the clusters to 
     \returns current file pointer
 */
-    FILE *getFilePointer(){return myFile;};
-    void setMutex(pthread_mutex_t *m){fm=m;};
+FILE *getFilePointer(){return myFile;};
+
+
+
+
+
+
+
+    virtual slsInterpolation *getInterpolation(){
+      return NULL;
+    };
+    
+    virtual slsInterpolation *setInterpolation(slsInterpolation *ii){return NULL;}
+
+
+
+    
+  virtual double setNSigma(double n) {return 0;};
+  virtual void setEnergyRange(double emi, double ema) {;};
+
+
+
+
+
+
+
+
  protected:
   
     slsDetectorData<dataType> *det; /**< slsDetectorData to be used */
@@ -858,9 +1148,17 @@ template <class dataType> class analogDetector {
     double thr; /**< threshold to be used for conversion into number of photons */
     //  int nSigma; /**< number of sigma to be used for conversion into number of photons if threshold is undefined */
     frameMode fMode; /**< current detector frame mode */
+    detectorMode dMode; /**< current detector frame mode */
     FILE *myFile; /**< file pointer to write to */
-    
-    pthread_mutex_t *fm;
+#ifdef ROOTSPECTRUM
+    TH2F *hs;
+#ifdef ROOTCLUST
+    TH2F *hs3;
+    TH2F *hs5;
+    TH2F *hs7;
+    TH2F *hs9;
+#endif
+#endif
 };
 
 #endif

slsDetectorCalibration/dataStructures/Mythen3_01_jctbData.h

@@ -43,7 +43,7 @@ class mythen3_01_jctbData : public slsDetectorData<short unsigned int> {
  }
  
 
- static short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
+ virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
     int iarg;
     int64_t word, *wp;

slsDetectorCalibration/dataStructures/Mythen3_02_jctbData.h

@@ -0,0 +1,127 @@
+#ifndef MYTHEN302JCTBDATA_H
+#define MYTHEN302JCTBDATA_H
+
+
+#include "Mythen3_01_jctbData.h"
+//class mythen3_02_jctbData : public slsDetectorData<short unsigned int> {
+class mythen3_02_jctbData : public mythen3_01_jctbData {
+
+
+ public:
+ mythen3_02_jctbData( int nch=64*3,int dr=24, int off=5): mythen3_01_jctbData( nch,dr, off)
+  //slsDetectorData<short unsigned int>(64*3,1,dr*8*nch,NULL,NULL,NULL), dynamicRange(dr), serialOffset(off), frameNumber(0), numberOfCounters(nch) 
+  {};
+
+  /* virtual void getPixel(int ip, int &x, int &y) {x=-1; y=-1;}; */
+  
+  /* virtual short unsigned int getChannel(char *data, int ix, int iy=0) { */
+  /*   int ret=-1; */
+  /*   short unsigned int *val=mythen03_frame(data,dynamicRange,numberOfCounters,serialOffset); */
+  /*   if (ix>=0 && ix<numberOfCounters) ret=val[ix]; */
+  /*   delete [] val; */
+  /*   return ret; */
+  /* }; */
+  
+ /*  virtual int getFrameNumber(char *buff) {return frameNumber;}; */
+ 
+ /*  virtual  char *findNextFrame(char *data, int &ndata, int dsize) { */
+ /*    ndata=dsize; */
+ /*    return data; */
+ /*  } */
+  
+ /* virtual char *readNextFrame(ifstream &filebin) { */
+ /*    char *data=NULL; */
+ /*    if (filebin.is_open()) { */
+ /*      data=new char[dataSize]; */
+ /*      filebin.read(data,dataSize); */
+ /*    } */
+ /*    return data; */
+ /*  } */
+ 
+ /* virtual short unsigned int **getData(char *ptr, int dsize=-1) { */
+ /*   short unsigned int **val; */
+ /*   val=new short unsigned int*[1]; */
+ /*   val[0]=mythen03_frame(ptr,dynamicRange,nx,serialOffset); */
+ /*   return val; */
+   
+ /* } */
+ 
+
+ virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
+   // off=0;
+    int iarg;
+    int64_t word, *wp;
+    short unsigned int* val=new short unsigned int[nch];
+    int bit[64];
+    int nb=2;
+    int ioff=0;
+    int idr=0;
+    int ib=0;
+    int iw=0;
+    int ii=0;
+    bit[0]=17;//19;
+    bit[1]=6;//8;
+    idr=0;
+    for (ib=0; ib<nch; ib++) {
+      val[ib]=0;
+    }
+    wp=(int64_t*)ptr;
+    
+    for (iw=0; iw<nch/nb; iw) {
+      word=*wp;;
+      if (ioff<off) {
+	ioff++;
+	 cout <<"*";
+      }  else {
+	
+	if (idr<16) {
+	  for (ib=0; ib<nb; ib++) {
+	    if (word&(1<<bit[ib]))  {
+	      cout << "+" ;
+	      val[iw+nch*(ib/nb)]|=(1<<idr);
+	    }  else { 
+	      	cout << "-" ; 
+	       } 
+	  }//end for()
+	}
+	
+	idr++;
+	
+	
+	if (idr==dr) {
+	  idr=0;
+	  //  cout << dec << " " << iw << " " << val[iw] << " " << val[iw+nch/2] << endl;
+	  cout <<dec << iw<<endl;
+	  iw++;
+	}//end if()
+
+      }//end else()
+      wp+=1;
+      ii++;
+    }//end for
+    
+    cout << "Decoded "<<ii << " samples"<< endl;
+    cout << "Should be "<< nch/nb*dr+off << " samples"<< endl;
+  
+    return val;
+ }
+
+ /* virtual int setFrameNumber(int f=0) {if (f>=0) frameNumber=f; return frameNumber; }; */
+ /* virtual int setDynamicRange(int d=-1) {if (d>0 && d<=24) dynamicRange=d; return dynamicRange;}; */
+ /* virtual int setSerialOffset(int d=-1) {if (d>=0) serialOffset=d; return serialOffset;}; */
+ /* virtual int setNumberOfCounters(int d=-1) {if (d>=0) numberOfCounters=d; return numberOfCounters;}; */
+  
+
+ /* private: */
+ 
+ /* int dynamicRange; */
+ /* int serialOffset; */
+ /* int frameNumber; */
+ /* int numberOfCounters; */
+   
+   
+
+
+};
+
+#endif

slsDetectorCalibration/dataStructures/gotthardDoubleModuleDataNew.h

@@ -34,6 +34,9 @@ public:
     
     
     
+#ifdef BCHIP074_BCHIP075
+		  cout << "This is a bchip074-bchip075 system " << endl;
+#endif
 
 
 		uint16_t **dMask;
@@ -59,6 +62,11 @@ public:
 		    dMap[0][ix] = 1280*2+2*offset+ipix*2;//dataSize-2-ix;//+2*offset;
 		  // dMap[0][ix] = 2*ipix+offset*(imod+1)+1280*2*imod; 
 		  dMask[0][ix] = 0x0;
+#ifdef BCHIP074_BCHIP075
+		  int ibad=ix/2+1280*imod;
+		  if ((ibad>=128*4 && ibad<128*5) || (ibad>=9*128 && ibad<10*128) || (ibad>=(1280+128*4) && ibad<ibad>=(1280+128*6))) 
+		    	dataROIMask[0][ix]=0; 
+#endif
 		}
 
 		setDataMap(dMap);

slsDetectorCalibration/dataStructures/jungfrau10ModuleData.h

@@ -8,6 +8,23 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
 
  private:
 
+     typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
   int iframe;
   int nadc;
   int sc_width;
@@ -25,7 +42,7 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
   */
   
 
- jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, 256*256*8*2, NULL, NULL, NULL) , iframe(0), nadc(32), sc_width(64), sc_height(256) {
+ jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, 256*256*8*2+48, NULL, NULL, NULL) , iframe(0) {
 
     
    
@@ -38,43 +55,51 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
     int ichip;
 
     // cout << sizeof(uint16_t) << endl;
-
-    for (iadc=0; iadc<nadc; iadc++) {
-      ichip=iadc/4;
-
-      for (int i=0; i<sc_width*sc_height; i++) {
-
-	if (ichip%2==0) {
-	  row=sc_height+i/sc_width;
-	  col=(ichip/2)*256+iadc%4*sc_width+(i%sc_width);
-	} else { 
-	  row=sc_height-1-i/sc_width; 
-	  col=((ichip/2)*256+iadc%4*sc_width)+sc_width-(i%sc_width)-1;
+    int ip=0;
+    for (int iy=0; iy<256*2; iy++) {
+      for (int ix=0; ix<256*4; ix++){
+	dataMap[iy][ix]=ip*2+48;
+	ip++;
+      }
     }
       
 
+    /* for (iadc=0; iadc<nadc; iadc++) { */
+    /*   ichip=iadc/4; */
 
-/* 	if (iadc<nadc/2) { */
+    /*   for (int i=0; i<sc_width*sc_height; i++) { */
+
+/* 	if (ichip%2==0) { */
 /* 	  row=sc_height+i/sc_width; */
-/* 	  col=iadc*sc_width+(i%sc_width); */
+/* 	  col=(ichip/2)*256+iadc%4*sc_width+(i%sc_width); */
 /* 	} else {  */
 /* 	  row=sc_height-1-i/sc_width;  */
-/* 	  col=(nx-1)-((iadc-16)*sc_width)-(i%sc_width); */
+/* 	  col=((ichip/2)*256+iadc%4*sc_width)+sc_width-(i%sc_width)-1; */
 /* 	} */
-	if (row<0 || row>=ny ||  col<0 || col>=nx) {
-	    cout << "Wrong row, column " << row << " " << col << " " << iadc << " " << i << endl;
-	} else
-	  dataMap[row][col]=(nadc*i+iadc)*2;
-	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
-	   cout << "Error: pointer " << dataMap[row][col] << " out of range " << row << " " << col  <<" " << iadc << " " << i << endl;
-	else {
-	  xmap[nadc*i+iadc]=col;
-	  ymap[nadc*i+iadc]=row;
 	  
-	}
-      }
 
-    }
+	
+/* /\* 	if (iadc<nadc/2) { *\/ */
+/* /\* 	  row=sc_height+i/sc_width; *\/ */
+/* /\* 	  col=iadc*sc_width+(i%sc_width); *\/ */
+/* /\* 	} else { *\/ */
+/* /\* 	  row=sc_height-1-i/sc_width; *\/ */
+/* /\* 	  col=(nx-1)-((iadc-16)*sc_width)-(i%sc_width); *\/ */
+/* /\* 	} *\/ */
+/* 	if (row<0 || row>=ny ||  col<0 || col>=nx) { */
+/* 	    cout << "Wrong row, column " << row << " " << col << " " << iadc << " " << i << endl; */
+/* 	} else */
+/* 	  dataMap[row][col]=(nadc*i+iadc)*2; */
+      /* 	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) */
+      /* 	   cout << "Error: pointer " << dataMap[row][col] << " out of range " << row << " " << col  <<" " << iadc << " " << i << endl; */
+      /* 	else { */
+      /* 	  xmap[nadc*i+iadc]=col; */
+      /* 	  ymap[nadc*i+iadc]=row; */
+
+      /* 	} */
+      /* } */
+
+    //  }
 
     
     
@@ -91,7 +116,7 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
   */
 
 
-  int getFrameNumber(char *buff){(void)buff; return iframe;};   
+  int getFrameNumber(return (sls_detector_header*)buff)->frameNumber;};   
 
   /**
 
@@ -123,28 +148,65 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
 
   */
-   char *readNextFrame(ifstream &filebin){
-      //	int afifo_length=0;  
-      uint16_t *afifo_cont; 
-      int ib=0;
-      if (filebin.is_open()) {
-	afifo_cont=new uint16_t[dataSize/2];
- 	while (filebin.read(((char*)afifo_cont)+ib,2)) {
-	  ib+=2;
-	  if (ib==dataSize) break;
-	}
-	if (ib>0) {
-	  iframe++;
-	  // cout << ib << "-" << endl;
-	  return (char*)afifo_cont;
-	} else {
-	  delete [] afifo_cont;
-	  return NULL;
-	}
-      }     
-      return NULL;
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
   };
 
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+    // char *readNextFrame(ifstream &filebin){
+      //	int afifo_length=0;  
+    /*   uint16_t *afifo_cont;  */
+    /*   int ib=0; */
+    /*   if (filebin.is_open()) { */
+    /* 	afifo_cont=new uint16_t[dataSize/2]; */
+    /* 	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+    /* 	  ib+=2; */
+    /* 	  if (ib==dataSize) break; */
+    /* 	} */
+    /* 	if (ib>0) { */
+    /* 	  iframe++; */
+    /* 	  // cout << ib << "-" << endl; */
+    /* 	  return (char*)afifo_cont; */
+    /* 	} else { */
+    /* 	  delete [] afifo_cont; */
+    /* 	  return NULL; */
+    /* 	} */
+    /*   }      */
+    /*   return NULL; */
+    /* }; */
+
+ char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
 	    
   
 

slsDetectorCalibration/dataStructures/moench02CtbData.h

@@ -31,23 +31,28 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
   */
   
 
-  moench02CtbData(int ns=6400): slsDetectorData<uint16_t>(160, 160, ns*2*32, NULL, NULL) , nadc(4), sc_width(40), sc_height(160) {
+ moench02CtbData(int ns=6400): slsDetectorData<uint16_t>(160, 160, ns*2*32, NULL, NULL) , nadc(32), sc_width(40), sc_height(160) {
 
     
-    int adc_nr[4]={120,0,80,40};
+    int adc_off[4]={40,0,120,80};
+    int adc_nr[4]={8,10,20,23};
     int row, col;
 
     int isample;
-    int iadc;
+    int iadc, iiadc;
     int ix, iy;
     maplength=this->getDataSize()/2;
+    //cout << maplength << endl;
 
+    for (iiadc=0; iiadc<4; iiadc++) {
       
-    for (iadc=0; iadc<nadc; iadc++) {
+      iadc=adc_nr[iiadc];
+      //cout << iiadc << endl;
       for (int i=0; i<sc_width*sc_height; i++) {
-	col=adc_nr[iadc]+(i%sc_width);
+	
+	col=adc_off[iiadc]+(i%sc_width);
 	row=i/sc_width;
-	dataMap[row][col]=(32*i+iadc+2)*2;
+	dataMap[row][col]=(32*i+iadc)*2;
 	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) {
 	  cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;	  
 	}
@@ -56,12 +61,17 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
     }
     
     for (int i=0; i<maplength; i++) {
+      //cout << i << endl;
       isample=i/32;
-      iadc=i%32;
+      iiadc=i%32;
+      iadc=-1;
+      for (int iii=0; iii<4; iii++) {
+	if (iiadc==adc_nr[iii]) iadc=iii;
+      }
       ix=isample%sc_width;
       iy=isample/sc_width;
-      if(iadc>1 && iadc<6){
-	xmap[i]=adc_nr[iadc-2]+ix;
+      if(iadc>=0){
+	xmap[i]=adc_off[iadc]+ix;
 	ymap[i]=iy;
       }else{
 	xmap[i]=-1;
@@ -76,10 +86,10 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
     if(ip>=0 && ip<maplength){
       x=xmap[ip]; 
       y=ymap[ip];
-    }else{
+    }/*else{
       cerr<<"WRONG ARRAY LENGTH"<<endl;
       cerr<<"Trying to access the "<<ip<<"-th element"<<endl;
-    }
+      }*/
 
   };
   
@@ -137,7 +147,9 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
 	}
 	if (ib>0) {
 	  iframe++;
-	  //cout << ib << "-" << endl;
+	  //cout << ib/2 << "-" << endl;
+	  //for (int i=0; i<ib/2; i++)
+	  //cout << i << " " << afifo_cont[i] << endl;
 	  return (char*)afifo_cont;
 	} else {
 	  delete [] afifo_cont;

slsDetectorCalibration/dataStructures/moench02CtbDataDGS.h

@@ -0,0 +1,187 @@
+#ifndef MOENCH02CTBDATADGS_H
+#define  MOENCH02CTBDATADGS_H
+#include "slsDetectorData.h"
+
+
+
+class moench02CtbData : public slsDetectorData<uint16_t> {
+
+ private:
+  
+  int iframe;
+  // int *xmap, *ymap;
+  //int nadc;
+  int sc_width;
+  int sc_height;
+
+  int maplength;
+
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  
+
+ moench02CtbDataDGS(int ns=6400): slsDetectorData<uint16_t>(160, 160, ns*(2*32+8), NULL, NULL) ,  sc_width(40), sc_height(160) {
+
+    
+    int adc_off[4]={40,0,120,80};
+    int adc_nr[4]={8,10,20,23};
+    int row, col;
+
+    int isample;
+    int iadc, iiadc;
+    int ix, iy;
+    maplength=this->getDataSize()/2;
+    //cout << maplength << endl;
+
+    for (iiadc=0; iiadc<4; iiadc++) {
+      
+      iadc=adc_nr[iiadc];
+      //cout << iiadc << endl;
+      for (int i=0; i<sc_width*sc_height; i++) {
+	col=adc_off[iiadc]+(i%sc_width);
+	row=i/sc_width;
+	dataMap[row][col]=(32*i+iadc)*2;
+	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) {
+	  cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;	  
+	}
+	  
+      }
+    }
+    
+    for (int i=0; i<maplength; i++) {
+      //cout << i << endl;
+      isample=i/32;
+      iiadc=i%32;
+      iadc=-1;
+      for (int iii=0; iii<4; iii++) {
+	if (iiadc==adc_nr[iii]) iadc=iii;
+      }
+      ix=isample%sc_width;
+      iy=isample/sc_width;
+      if(iadc>=0){
+	xmap[i]=adc_off[iadc]+ix;
+	ymap[i]=iy;
+      }else{
+	xmap[i]=-1;
+	ymap[i]=-1;
+      }
+    }
+    iframe=0;
+    cout << "data struct created" << endl;
+  };
+  
+  void getPixel(int ip, int &x, int &y) {
+    if(ip>=0 && ip<maplength){
+      x=xmap[ip]; 
+      y=ymap[ip];
+    }/*else{
+      cerr<<"WRONG ARRAY LENGTH"<<endl;
+      cerr<<"Trying to access the "<<ip<<"-th element"<<endl;
+      }*/
+
+  };
+  
+  /**
+     Returns the gain for the selected pixel (at the moemnt only 3rd supercolumn)
+     \param buff pointer to the dataset
+     \param ix x coordinate 
+     \param iy y coordinate
+     \returns gain value
+   */
+
+  int getGain(char *buff, int ix, int iy) {
+    int isample=iy*sc_width+iy;
+    if (ix<sc_width) return 0; //first supercolumn no gain switching - could return the static gain if wished
+    if (ix<2*sc_width) return 0; //second supercolumn no gain switching  - could return the static gain if wished
+    if (ix<3*sc_width){ 
+      if(*((long*)(buff+(32*2*isample+8*(isample-1)))&(1>>31)) return 1;
+      return 0;
+    }
+    return 0; //not yet implemented for 4th supercolumn
+  }
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+
+    virtual  int getFrameNumber(char *buff){(void)buff; return iframe;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+  virtual int getPacketNumber(char *buff)=0;
+
+  */
+
+   /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+
+  */
+    virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
+
+
+   /**
+
+     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
+     \param filebin input file stream (binary)
+     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
+
+  */
+    virtual char *readNextFrame(ifstream &filebin){
+      //	int afifo_length=0;  
+      uint16_t *afifo_cont; 
+      int ib=0;
+      if (filebin.is_open()) {
+	afifo_cont=new uint16_t[dataSize/2];
+ 	while (filebin.read(((char*)afifo_cont)+ib,2)) {
+	  ib+=2;
+	  if (ib==dataSize) break;
+	}
+	if (ib>0) {
+	  iframe++;
+	  //cout << ib/2 << "-" << endl;
+	  //for (int i=0; i<ib/2; i++)
+	  //cout << i << " " << afifo_cont[i] << endl;
+	  return (char*)afifo_cont;
+	} else {
+	  delete [] afifo_cont;
+	  return NULL;
+	}
+      }     
+      return NULL;
+    };
+
+
+  
+
+};
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03Ctb10GbT1Data.h

@@ -121,6 +121,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
 
+  // int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;}; 
    int getFrameNumber(char *buff){return *((int*)(buff+5))&0xffffff;};   
 
   /**
@@ -199,7 +200,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	  int  nd;
 	  int fnum = -1;
 	  np=0;
-	  int  pn;
+	  int  pn, po=0;
 	  char aa[8224];
 	  char *packet=(char *)aa;
 	  //  cout << packetSize*nPackets << endl;
@@ -219,13 +220,14 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	      
 	      //   cout << "fn: " << fnum << "\t pn: " << pn << endl;
 	      if (fnum>=0) {
-		if (getFrameNumber(packet) !=fnum) { 
+		if (getFrameNumber(packet) !=fnum || pn<po) { 
 		  
 		  if (np==0){
 		    // delete [] data;
 		    return NULL;
 		  } else
 		    filebin.seekg(-8208,ios_base::cur);
+		  po =pn;
 		    return data;
 		}
 		if (pn>nPackets) {
@@ -234,6 +236,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 		memcpy(data+(pn-1)*packetSize, packet, packetSize);
 		np++;
+		po =pn;
 
 		if (np==nPackets)
 		  break;

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNewRect.h

@@ -0,0 +1,321 @@
+#ifndef MOENCH03T1RECDATANEWRECT_H
+#define  MOENCH03T1RECDATANEWRECT_H
+#include "slsDetectorData.h"
+
+#define VERT 1
+
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
+
+
+class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+#ifdef HOR
+    moench03T1ReceiverDataNew(int ns=5000): slsDetectorData<uint16_t>(800, 200, ns*2*32+sizeof(sls_detector_header)), nSamples(ns) {
+#endif
+#ifdef VERT
+    moench03T1ReceiverDataNew(int ns=5000): slsDetectorData<uint16_t>(200, 800, ns*2*32+sizeof(sls_detector_header)), nSamples(ns) {
+#endif
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+    int pix;
+
+
+    int off=0;
+#ifdef OFF_1
+    off=1;
+#endif
+    cout << "This is a MOENCH with rectangular pixels!" << endl;
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    pix=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (pix<0 || pix>=nSamples*2*32+sizeof(sls_detector_header))
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    ix=col;
+	    iy=row;
+#ifdef HOR
+	    if (row%2==off) {
+	      ix=2*col;
+	      iy=row/2;
+	    } else {
+	      ix=2*col+1;
+	      iy=row/2;
+	    }
+#endif
+
+#ifdef VERT
+	    if (col%2==off) {
+	      ix=col/2;
+	      iy=row*2+1;
+	    } else {
+	      ix=col/2;
+	      iy=row*2;
+	    }
+#endif
+	    dataMap[iy][ix]=pix;
+	  }
+	}
+      }
+    }
+
+    /* int ipacket; */
+    /* int ibyte; */
+    /* int ii=0; */
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/gotthardDoubleModuleCommonModeSubtractionNew.h

@@ -0,0 +1,30 @@
+#ifndef GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
+#define GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
+
+
+#include "commonModeSubtractionNew.h"
+
+class gotthardDoubleModuleCommonModeSubtraction : public commonModeSubtraction {
+
+  /** @short class to calculate the common mode of the pedestals based on an approximated moving average*/ 
+
+ public:
+  
+  /** constructor
+      \param nn number of samples for the moving average to calculate the average common mode
+      \param iroi number of regions on which one can calculate the common mode separately. Defaults to 1 i.e. whole detector
+
+  */
+ gotthardDoubleModuleCommonModeSubtraction(int ns=3) : commonModeSubtraction(2, ns) {};
+
+    /** 
+	gets the common mode ROI for pixel ix, iy 
+     */
+  virtual int getROI(int ix, int iy){return ix%2;};
+
+
+};
+
+
+
+#endif

slsDetectorCalibration/gotthardExecutables/gotthard25umOnTheFlyAnalysis.C

@@ -1,215 +0,0 @@
-#include <vector>
-#include <string>
-#include <sstream>
-#include <iomanip>
-#include <fstream>
-#include <stdio.h>
-//#include <deque>
-//#include <list>
-//#include <queue>
-#include <fstream>
-#include <cstring>
-
-#include "gotthardModuleDataNew.h"
-#include "gotthardDoubleModuleDataNew.h"
-
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-//#include "linearInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-
-#include <ctime>
-
-#define NC 1280
-#define NR 1
-
-#include "tiffIO.h"
-
-
-void *gotthardProcessFrame() {
-
-
-
-
-
-	if (argc < 3 ) {
-		cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n");
-		return EXIT_FAILURE;
-	}
-
-	// receive parameters
-	bool send = false;
-	  char* socketip=argv[1];
-	uint32_t portnum = atoi(argv[2]);
-	int size = 32*2*5000;//atoi(argv[3]);
-
-	// send parameters if any
-	char* socketip2 = 0;
-	uint32_t portnum2 = 0;
-	if (argc > 3) {
-		send = true;
-		socketip2 = argv[3];
-		portnum2 = atoi(argv[4]);
-	}
-	cout << "\nrx socket ip : " << socketip <<
-	  "\nrx port num  : " <<  portnum ;
-	if (send) {
-	  cout << "\nsd socket ip : " << socketip2 <<
-	    "\nsd port num  : " <<  portnum2;
-	}
-	cout << endl;
-  
-
-
-	
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  char fname0[10000], fname1[10000];
-  char fformat[10000];
-  int fifosize=1000;
-  strcpy(fformat,"/external_pool/gotthard_data/datadir_gotthardI/bchip074075/20170731/Xray/xray_15kV_200uA_5us_d%d_f000000000000_0.raw");
-  sprintf(fname0,fformat,0,0);
-  sprintf(fname1,fformat,1,1);
-  
-  
-  int nthreads=3;
-  
-  int nph, nph1;
-  //  single_photon_hit clusters[NR*NC];
-  // cout << "hits "<< endl;
-  int etabins=550;
-  double etamin=-1, etamax=2;
-  int nsubpix=1;
-  float *etah=new float[etabins*etabins];
-  // cout << "etah "<< endl;
-  cout << "image size "<< nsubpix*nsubpix*NC*NR << endl;
- 
-  int *heta, *himage;
-
-    gotthardModuleDataNew *decoder=new   gotthardModuleDataNew();
-    gotthardDoubleModuleDataNew *det=new   gotthardDoubleModuleDataNew();
-  // cout << "decoder "<< endl;
-  // etaInterpolationPosXY *interp=new etaInterpolationPosXY(NC, NR, nsubpix, etabins, etamin, etamax);
-  // cout << "interp "<< endl;
-    //   linearInterpolation *interp=new linearInterpolation(NC, NR, nsubpix);
-  //noInterpolation *interp=new noInterpolation(NC, NR, nsubpix);
-    // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
-    // interpolatingDetector *filter0=new interpolatingDetector(decoder,interp, 5, 1, 0, 1000, 10);
-    // interpolatingDetector *filter1=new interpolatingDetector(decoder,interp, 5, 1, 0, 1000, 10);
-  //filter->readPedestals("/scratch/ped_100.tiff");
-  //cout << "filter "<< endl;
-  
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 200);
-
-  filter->setFrameMode(eFrame);
-  
-  char *buff;//[2*(48+1280*2)];
-
-
-  char *buff0;
-  char *buff1;
-
-
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  mt->setFrameMode(eFrame);
-  mt->StartThreads();
-  mt->popFree(buff);
-  buff0=buff;
-  buff1=buff+48+1280*2;
-
-
-  int photons[1280*2];
-
-  int nf=0;
-  int ok=0;
-  ifstream filebin0,filebin1;
-  std::time_t end_time;
-  int16_t dout[1280*2];
-  int iFrame=-1;
-  int np=-1;
-
-  nph=0;
-  nph1=0;
-  //int np;
-  int iph;
-  int data_ready=1;
-  int *image;
-
-  // filter->setROI(0,512,0,1);
-
-    filebin0.open((const char *)(fname0), ios::in | ios::binary);
-    filebin1.open((const char *)(fname1), ios::in | ios::binary);
-    if (filebin0.is_open() && filebin1.is_open()) {
-      cout << "Opened file " << fname0<< endl;
-      cout << "Opened file " << fname1<< endl;
-	//	mt->setFrameMode(eFrame);
-  // 	mt->prepareInterpolation(ok);
-  // mt->StartThreads();
-  // mt->popFree(buff);
-      nf=0;
-      iFrame=-1;
-      while ((decoder->readNextFrame(filebin0, iFrame, np, buff0)) && (decoder->readNextFrame(filebin1, iFrame, np, buff1))) {
-	//filter->processData(buff, photons);
-	//	cout << nf << " " << decoder->getFrameNumber(buff0) << " " << decoder->getFrameNumber(buff1) << " " << filter->getPhFrame() << " " << filter->getPhTot() << endl; 
-	// for (int i=0; i<1280*2; i++) {
-	//   filter->addToPedestal(buff,i,0);
-	//   dout[i]=filter->subtractPedestal(buff,i,0);
-	//   if (nf>10 && i<512)
-	//     if (i%2)
-	//       cout << nf << " " << i << " " << filter->getPedestal(i,0) << " " << det->getValue(buff,i,0) << " " << decoder->getValue(buff1,1280-1-i/2,0)<< " " << dout[i] << endl;
-	//     else
-	//       cout << nf << " " << i << " " << filter->getPedestal(i,0) << " " << det->getValue(buff,i,0) << " " << decoder->getValue(buff0,i/2,0)<< " " << dout[i] << endl;
-	
-	// }
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
-	  buff0=buff;
-	  buff1=buff+48+1280*2;
-	  
-	nf++;
-	
-	//	cout << id << " " << nf << endl;
-	if (nf%10000==0) {
-	  while (mt->isBusy()) {;}
-	  image=filter->getImage();
-	  if (image) {
-	    cout << nf << "*****************" << endl;
-	    for (int i=0; i<512; i++) {
-	      cout << image[i] << "\t";
-	    }
-	    cout << endl;
-	  }
-	  filter->clearImage();
-	  std::time(&end_time);
-	  cout << std::ctime(&end_time) << " " << nf <<   endl;
-	}
-	iFrame=-1;
-      }
-      
-      filebin0.close();
-      filebin1.close();
-    }
-    else
-      cout << "Could not open file " << fname0<< " or " << fname1 <<  endl;
-  return NULL;
-}
-  
-int main(int argc, char *argv[]){
-
-   gotthardProcessFrame();
-
-}

slsDetectorCalibration/gotthardExecutables/gotthard25umZmqAnalysis.C

@@ -14,8 +14,11 @@
 #include <fstream>
 #include <cstring>
 
+//#define BCHIP074_BCHIP075
+
 #include "gotthardModuleDataNew.h"
 #include "gotthardDoubleModuleDataNew.h"
+#include "gotthardDoubleModuleCommonModeSubtractionNew.h"
 
 #include "singlePhotonDetector.h"
 //#include "interpolatingDetector.h"
@@ -27,8 +30,7 @@
 #define NC 1280
 #define NR 1
 
-#include "tiffIO.h"
-
+//#include "tiffIO.h"
 
 
 
@@ -40,19 +42,6 @@ int main(int argc, char *argv[]){
 
 
 
-	
-
-
-
-
-
-
-
-
-
-
-
-
   int fifosize=1000;
   int nthreads=1;
   int nph, nph1;
@@ -69,16 +58,22 @@ int main(int argc, char *argv[]){
   offset=48;
   #endif
  
+  //commonModeSubtraction *cm=NULL;
 
+  gotthardDoubleModuleCommonModeSubtraction *cm=new gotthardDoubleModuleCommonModeSubtraction();
   gotthardModuleDataNew *decoder=new   gotthardModuleDataNew();
   gotthardDoubleModuleDataNew *det=new   gotthardDoubleModuleDataNew(offset);
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 100);
+  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, cm, 1000, 100);
+  // analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det, 1, cm, 1000);
+  // analogDetector<uint16_t> *filter_nocm=new analogDetector<uint16_t>(det, 1, NULL, 1000);
   filter->setROI(0,2560,0,1);
   char *buff;//[2*(48+1280*2)];
   char *buff0;
   char *buff1;
   multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
   mt->setFrameMode(eFrame);
+  // mt->setFrameMode(eFrame);
+  // mt->setFrameMode(ePedestal);
   mt->StartThreads();
   mt->popFree(buff);
   buff0=buff;
@@ -210,7 +205,8 @@ int main(int argc, char *argv[]){
 	string filename0 = "";
 
 
-
+	int eoa0=0;
+	int eoa1=0;
 
 
 
@@ -230,7 +226,9 @@ int main(int argc, char *argv[]){
 
 
 	char ofname[10000];
+	char fn0[10000], fn1[10000];
 	FILE *fout=NULL;
+	FILE *fclust=NULL;
 	for (int i=0; i<nnx; i++)
 	  dout[i]=0;
 	char fname0[10000], fname1[10000];
@@ -279,89 +277,204 @@ int main(int argc, char *argv[]){
 	int end_of_acquisition;
 	while(1) {
 	  end_of_acquisition=0;
+	  eoa0=0;
+	  eoa1=0;
+	  
 	  //  cout << "Receive header " << nf << endl;
 	  if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
 	    
-	    cout << "************************************************************************** packet0!*****************************"<< endl;
-
+	    //   cout << "************************************************************************** packet0!*****************************"<< endl;
+	    eoa0=1;
 	    end_of_acquisition++;
 	  } 
 	  if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-	    cout << "************************************************************************** packet1!*****************************"<< endl;
-
+	    //cout << "************************************************************************** packet1!*****************************"<< endl;
+	    eoa1=1;
 	    end_of_acquisition++;
 	  }
 
+
+
+
+
 	  //	  if ((!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) && (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1))){
-	  if (end_of_acquisition) {
-	    cout << "************************************************************************** END OF FRAME" << end_of_acquisition << " !*****************************"<< endl;
-	    //  return 0;
+	  if (end_of_acquisition==0) {
 	    
-	    while (mt->isBusy()) {;}
-	    image=filter->getImage();
-	    if (image) {
-	      //fout=fopen(ofname,"w");
-	     cout << nf << "*****************" << endl;
-	      for (int i=0; i<2560; i++) {
-	      // // 	fprintf(fout,"%d %d\n",i,image[i]);
-	      	dout[i]=image[i];
-	      }
-	      // // fclose(fout);;
-	    }
-
-
-	    if (send) {
-		strcpy(fname0,filename0.c_str());
-		strcpy(fname1,filename1.c_str());
-		//  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
-		zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-		zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-		
-		zmqsocket2->SendData((char*)dout,size/2);
-		zmqsocket3->SendData(((char*)dout)+size/2,size/2);
-		//	cprintf(GREEN, "Sent Data\n");
-
-
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-
-	      cprintf(RED, "Received %d frames\n", nf);
-
-	    }
-
-	    
-	    filter->clearImage();
-	    // std::time(&end_time);
-	    // cout << std::ctime(&end_time) << " " << nf <<   endl;
-
-
-	
-
-	    continue; 
-	  }
 	    if (acqIndex0!=acqIndex1)
 	      cout << "different acquisition indexes " << acqIndex0 << " and " << acqIndex1 << endl;
 	    if (frameIndex0!=frameIndex1)
 	      cout << "different frame indexes " << frameIndex0 << " and " << frameIndex1 << endl;
 	    
 	    
+	    while (frameIndex0<frameIndex1) {
+	      cout << "aligning det 0 " << endl; 
+	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
+	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
+		end_of_acquisition++;
+		eoa0=1;
+		break;
+	      } 
+	    }
+	    
+	    while (frameIndex1<frameIndex0) {
+	      cout << "aligning det 1 " << endl; 
+	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
+	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
+		end_of_acquisition++;
+		eoa1=1;
+		break;
+	      } 
+	    }
+	  }
+
+
+
+	  if (eoa0!=eoa1) {
+
+	    while (eoa0<1) {
+	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
+	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
+		end_of_acquisition++;
+		eoa0=1;
+	      }
+	    }
+
+
+	    while (eoa1<1) {
+	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
+	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
+		end_of_acquisition++;
+		eoa1=1;
+	      }
+	    }
+	  }
+
+	  
+
+
+
+	  
+	  if (end_of_acquisition) {
+	    // cout << "************************************************************************** END OF FRAME" << end_of_acquisition << " !*****************************"<< endl;
+	    //  return 0;
+	    
+	    sprintf(ofname,"%s_%d.ph",fn0,irun);
+	    while (mt->isBusy()) {;}
+	    image=filter->getImage();
+	    if (image) {
+	      fout=fopen(ofname,"w");
+	      cout << nf << "*****************" << endl;
+	      for (int i=0; i<2560; i++) {
+		fprintf(fout,"%d %d\n",i,image[i]);
+		dout[i]=image[i];
+		if (dout[i]<0)
+		   dout[i]=0;
+	      }
+	      fclose(fout);
+	    }
+	    
+
+	    if (send) {
+	      
+	      zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
+	      zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
+	      
+	      zmqsocket2->SendData((char*)dout,size/2);
+	      zmqsocket3->SendData(((char*)dout)+size/2,size/2);
+	      //    	//	cprintf(GREEN, "Sent Data\n");
+
+	      
+	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	      zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	    }
+	    
+	    
+	    //mt->setFrameMode(eFrame);
+	    filter->clearImage();
+	    // std::time(&end_time);
+	    // cout << std::ctime(&end_time) << " " << nf <<   endl;
+	    fclose(fclust);
+	    fclust=NULL;
+	    
+	    
+	    
+	    continue; 
+	  }
+	  
+	  if (fclust==NULL) {
+
+	    strcpy(fn0,filename0.c_str());
+	    strcpy(fn1,filename1.c_str());
+	    sprintf(ofname,"%s_%d.clust",fn0,irun);
+	    fclust=fopen(ofname,"w");
+	    while (mt->isBusy()) {;}
+	    mt->setFilePointer(fclust);
+	  }
+
+	  // strcpy(fn0,filename0.c_str());
+	  // strcpy(fn1,filename1.c_str());
+	  
 	  //	  cout << "Receive data " << nf << endl;
 	  length = zmqsocket0->ReceiveData(0, buff0, size/2);
 	  length += zmqsocket1->ReceiveData(0, buff1, size/2);  
 	  
 	  irun=fileindex0;
-	  sprintf(ofname,"%s_%d.ph",filename0.c_str(),fileindex0);
+	  
+	  
+	    
+	    // //  if (nf>100)
+	    // //  mt->setFrameMode(eFrame);
+	    // //filter->clearImage();
+
 
 #endif
 
 
-
 	mt->pushData(buff);
 	mt->nextThread();
+	// cout << "==" << nf << endl;
+
+	    // while (mt->isBusy()) {;}
+	    // image=filter->getImage();
+	    // if (image) {
+	    //   for (int i=0; i<2560; i++) {
+	    // 	//	if (i<512)
+	
+	    // 	//  	fprintf(fout,"%d %d\n",i,image[i]);
+	    //   	dout[i]=filter->subtractPedestal(buff,i,0,1);//image[i];//filter->getPedestal(i,0);//
+	    // 	if (dout[i]<0)
+	    // 	   dout[i]=0;
+	    // 	//	cout << i << " " << image[i] << " " << dout[i] << endl;
+	    //   }
+	    // }
+
+
+	    // if (send) {
+	    // 	strcpy(fname0,filename0.c_str());
+	    // 	strcpy(fname1,filename1.c_str());
+	    // 	//  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
+	    // 	zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
+	    // 	zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
+		
+	    // 	zmqsocket2->SendData((char*)dout,size/2);
+	    // 	zmqsocket3->SendData(((char*)dout)+size/2,size/2);
+	    // 	//	cprintf(GREEN, "Sent Data\n");
+
+
+	    // 	// zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	    // 	// zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+
+	    // 	//	cprintf(RED, "Received %d frames\n", nf);
+
+	    // }
+	    
+
 	mt->popFree(buff);
 	buff0=buff;
 	buff1=buff+offset*2+1280*2;
 	  
+
+
 	nf++;
 	
 
@@ -370,6 +483,8 @@ int main(int argc, char *argv[]){
 #ifndef ZMQ
 
 
+	 
+
 	  while (mt->isBusy()) {;}
 	  image=filter->getImage();
 	  if (image) {
@@ -378,7 +493,7 @@ int main(int argc, char *argv[]){
 	      for (int i=0; i<512; i++) {
 		fprintf(fout,"%d %d\n",i,image[i]);
 	      }
-	      fclose(fout);;
+	      fclose(fout);
 	  }
 	  filter->clearImage();
       

slsDetectorCalibration/interpolatingDetector.h

@@ -6,7 +6,7 @@
 
 #include "slsInterpolation.h"
 
-#define M015
+//#define M015
 
 #ifdef MYROOT1
 #include <TTree.h>
@@ -17,10 +17,7 @@
 #include <iostream>
 
 using namespace std;
-#define XMIN 350/2
-#define XMAX 600/2
-#define YMIN 0
-#define YMAX 400
+
 
 class interpolatingDetector : public singlePhotonDetector {
 
@@ -50,21 +47,23 @@ class interpolatingDetector : public singlePhotonDetector {
 		       commonModeSubtraction *cm=NULL,
 		       int nped=1000, 
 		       int nd=100, int nnx=-1, int nny=-1) : 
-  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny) , interp(inte), id(0), xmin(XMIN), xmax(XMAX), ymin(YMIN), ymax(YMAX)  {
-    cout << "**"<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
+  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny) , interp(inte), id(0)  {
+    //cout << "**"<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
+    fi=new pthread_mutex_t ;
 
 };
   
   
   
  interpolatingDetector(interpolatingDetector *orig) : singlePhotonDetector(orig) {
-    interp=(orig->interp)->Clone();
-    id=orig->id;
-    xmin=orig->xmin;
-    xmax=orig->xmax;
-    ymin=orig->ymin;
-    ymax=orig->ymax;
+    // if (orig->interp)
+    //  interp=(orig->interp)->Clone();
+    // else
     
+    interp=orig->interp;
+    
+    id=orig->id;
+    fi=orig->fi;
   }
 
 
@@ -72,29 +71,50 @@ class interpolatingDetector : public singlePhotonDetector {
     return new interpolatingDetector(this);
   }
 
-  virtual int setId(int i) {id=i; interp->setId(id); return id;};
+  virtual int setId(int i) {
+    id=i; 
+    //  interp->setId(id); 
+    return id;
+  };
 
   virtual void prepareInterpolation(int &ok) {
-    cout << "*"<< endl;
-#ifdef SAVE_ALL
-    char tit[1000];
-    sprintf(tit,"/scratch/ped_%d.tiff",id);
-    writePedestals(tit);
-    sprintf(tit,"/scratch/ped_rms_%d.tiff",id);
-    writePedestalRMS(tit);
-    if (gmap) {
-      sprintf(tit,"/scratch/gmap_%d.tiff",id);
-      writeGainMap(tit);
-    }
-#endif
-    if (interp)
+   /*  cout << "*"<< endl; */
+/* #ifdef SAVE_ALL */
+/*     char tit[1000]; */
+/*     sprintf(tit,"/scratch/ped_%d.tiff",id); */
+/*     writePedestals(tit); */
+/*     sprintf(tit,"/scratch/ped_rms_%d.tiff",id); */
+/*     writePedestalRMS(tit); */
+/*     if (gmap) { */
+/*       sprintf(tit,"/scratch/gmap_%d.tiff",id); */
+/*       writeGainMap(tit); */
+/*     } */
+/* #endif */ 
+    if (interp){
+      pthread_mutex_lock(fi);
       interp->prepareInterpolation(ok);
+      pthread_mutex_unlock(fi); 
+    }
   } 
 
 
-  void clearImage() {if (interp) interp->clearInterpolatedImage(); else singlePhotonDetector::clearImage();};
+  void clearImage() {
+    if (interp) {
+      pthread_mutex_lock(fi);
+      interp->clearInterpolatedImage(); 
+      pthread_mutex_unlock(fi); 
+    } else 
+      singlePhotonDetector::clearImage();
+  };
+
+  int getImageSize(int &nnx, int &nny, int &ns) {
+    if (interp) 
+      return interp->getImageSize(nnx, nny, ns); 
+    else 
+      return analogDetector<uint16_t>::getImageSize(nnx, nny, ns);
+  };
+
 
-  int getImageSize(int &nnx, int &nny, int &ns) {if (interp) return interp->getImageSize(nnx, nny, ns); else return analogDetector<uint16_t>::getImageSize(nnx, nny, ns);};
   #ifdef MYROOT1
   virtual TH2F *getImage()
 #endif
@@ -107,7 +127,6 @@ class interpolatingDetector : public singlePhotonDetector {
      return interp->getInterpolatedImage();
    else 
      return analogDetector<uint16_t>::getImage();
-   //cout << "null " << endl;
  }
 
 #ifdef MYROOT1
@@ -149,505 +168,104 @@ class interpolatingDetector : public singlePhotonDetector {
      return NULL;
    }
   
+
+
 int addFrame(char *data,  int *ph=NULL, int ff=0) {	    
   
- 
+  singlePhotonDetector::processData(data,ph);
   int nph=0;
-  double val[ny][nx];
-  int cy=(clusterSizeY+1)/2;
-  int cs=(clusterSize+1)/2;
-  int ir, ic;
-  
-    double int_x,int_y, eta_x, eta_y;
-  double max=0, tl=0, tr=0, bl=0,br=0, *v, vv;
-
-  if (ph==NULL)
-    ph=image;
-
-  if (iframe<nDark) {
-    addToPedestal(data);
-    return 0;
-  }
-  newFrame();
-  for (int ix=xmin; ix<xmax; ix++) {
-    for (int iy=ymin; iy<ymax; iy++) {
-      
-      max=0;
-      tl=0;
-      tr=0;
-      bl=0;
-      br=0;
-      tot=0;
-      quadTot=0;
-      quad=UNDEFINED_QUADRANT;
-
-     
-
-      eventMask[iy][ix]=PEDESTAL;
-      
-	
-      (clusters+nph)->rms=getPedestalRMS(ix,iy);
-      
-      
-      
-      for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-	  
-	  if ((iy+ir)>=iy && (iy+ir)<ny && (ix+ic)>=ix && (ix+ic)<nx) {
-	    val[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir);
-	  }
-	  
-	  v=&(val[iy+ir][ix+ic]);
-	  tot+=*v;
-	  if (ir<=0 && ic<=0)
-	    bl+=*v;
-	  if (ir<=0 && ic>=0)
-	    br+=*v;
-	  if (ir>=0 && ic<=0)
-	    tl+=*v;
-	  if (ir>=0 && ic>=0)
-	    tr+=*v;
-	  if (*v>max) {
-	    max=*v;
-	  }
-	  
-	  
-	  if (ir==0 && ic==0) {
-	    if (*v<-nSigma*cluster->rms)
-	      eventMask[iy][ix]=NEGATIVE_PEDESTAL;
-	  }
-	  
-	}
-      }
-      
-      if (bl>=br && bl>=tl && bl>=tr) {
-	(clusters+nph)->quad=BOTTOM_LEFT;
-	(clusters+nph)->quadTot=bl;
-      } else if (br>=bl && br>=tl && br>=tr) {
-	(clusters+nph)->quad=BOTTOM_RIGHT;
-	(clusters+nph)->quadTot=br;
-      } else if (tl>=br && tl>=bl && tl>=tr) {
-	(clusters+nph)->quad=TOP_LEFT;
-	(clusters+nph)->quadTot=tl;
-      } else if   (tr>=bl && tr>=tl && tr>=br) {
-	(clusters+nph)->quad=TOP_RIGHT;
-	(clusters+nph)->quadTot=tr;
-      }
-      
-      if (max>nSigma*cluster->rms || tot>sqrt(clusterSizeY*clusterSize)*nSigma*cluster->rms || ((clusters+nph)->quadTot)>sqrt(cy*cs)*nSigma*cluster->rms) {
-	if (val[iy][ix]>=max) {
-	  eventMask[iy][ix]=PHOTON_MAX;
-	  (clusters+nph)->tot=tot;
-	  (clusters+nph)->x=ix;
-	  (clusters+nph)->y=iy;
-	  (clusters+nph)->iframe=det->getFrameNumber(data);
-	  (clusters+nph)->ped=getPedestal(ix,iy,0);
-	  for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	    for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-	      (clusters+nph)->set_data(val[iy+ir][ix+ic],ic,ir);
-	    }
-	  }
-
-
-
 
+  double int_x, int_y;
+  double eta_x, eta_y;
   if (interp) {
+  cout << "int" << endl;
+  pthread_mutex_lock(fi); 
+    for (nph=0; nph<nphFrame; nph++) {
       if (ff) {
 	interp->addToFlatField((clusters+nph)->quadTot,(clusters+nph)->quad,(clusters+nph)->get_cluster(),eta_x, eta_y);
       } else {
-		interp->getInterpolatedPosition(ix, iy, (clusters+nph)->quadTot,(clusters+nph)->quad,(clusters+nph)->get_cluster(),int_x, int_y);
+	interp->getInterpolatedPosition((clusters+nph)->x, (clusters+nph)->y, (clusters+nph)->quadTot,(clusters+nph)->quad,(clusters+nph)->get_cluster(),int_x, int_y);
 	interp->addToImage(int_x, int_y);
       }
-	    }  else 
-	      image[ix+nx*iy]++;    
-
-
-
-
-
-
-
-
-
-
-	  nph++;
-	  image[iy*nx+ix]++;
-
-	  } else {
-	    eventMask[iy][ix]=PHOTON;
     } 
-      } else if (eventMask[iy][ix]==PEDESTAL) {
-	addToPedestal(data,ix,iy);
+    pthread_mutex_unlock(fi);  
   }
-
-
-    }
-  }
-  nphFrame=nph;
-  nphTot+=nph;
-  //cout << nphFrame << endl;
-  // cout <<"**********************************"<< endl;
-  writeClusters();
   return  nphFrame;
   
 };
   
-   /*********************************************************
-  int addFrame(char *data, int ff=0) {
-    
-    double g=1;
-    
-    single_photon_hit *cl;
-    single_photon_hit clust;
-    if (clusters)
-      cl=clusters;
-    else
-      cl=&clust;
-
-    
-      int ccs=clusterSize;
-      int ccy=clusterSizeY;
-
-    double int_x,int_y, eta_x, eta_y;
-    int nph=0;
-    double rest[ny][nx];
-    int cy=(clusterSizeY+1)/2;
-    int cs=(clusterSize+1)/2;
-    int ir, ic;
-    double cc[2][2];
-    double max=0, tl=0, tr=0, bl=0,br=0, v, vv;
-    int xoff,yoff;
-    int skip=0;
-    //  cout <<"fr"<< endl;
-    double tthr;
-    if (iframe<nDark) {
-      //cout << iframe << "+"<< nDark <<endl;
-      addToPedestal(data);
-      return 0;
-    }
-
-    newFrame();
-
-
-
-
-    //  cout << xmin << " " << xmax << " " << ymin << " " << ymax << endl;
-	for (int ix=xmin; ix<xmax; ix++) {
-	  for (int iy=ymin; iy<ymax; iy++) {
-	    //  for (int ix=clusterSize/2; ix<clusterSize/2-1; ix++) {
-	    // for (int iy=clusterSizeY/2; iy<ny-clusterSizeY/2; iy++) {
-
-	    //	    cout << ix << " " << iy << endl;
-	    eventMask[iy][ix]=PEDESTAL;
-	    
-	    
-	      tthr=nSigma*getPedestalRMS(ix,iy)/g;
-	      if (ix==xmin || iy==ymin)
-		rest[iy][ix]=subtractPedestal(data,ix,iy);
-	     
-	    
-	    max=0;
-	    tl=0;
-	    tr=0;
-	    bl=0;
-	    br=0;
-	    tot=0;
-	    quadTot=0;
-
-	    for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	      for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-		if ((iy+ir)>=ymin && (iy+ir)<ymax && (ix+ic)>=xmin && (ix+ic)<xmax) {
-		  //cluster->set_data(rest[iy+ir][ix+ic], ic, ir);
-		  
-		  if (ir>=0 && ic>=0 ) 
-		    rest[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir);
-		  
-		  v=rest[iy+ir][ix+ic];//cluster->get_data(ic,ir);
-		  tot+=v;
-		  
-		  if (ir<=0 && ic<=0)
-		    bl+=v;
-		  if (ir<=0 && ic>=0)
-		    br+=v;
-		  if (ir>=0 && ic<=0)
-		    tl+=v;
-		  if (ir>=0 && ic>=0)
-		    tr+=v;
-		  
-		  if (v>max) {
-		    max=v;
-		  }
-		  // if (ir==0 && ic==0) {
-		    if (v>tthr) {
-		      eventMask[iy][ix]=NEIGHBOUR;
-		    }
-		    //}
-		}
-	      }
-	    }
-	    if (rest[iy][ix]<=-tthr) {
-	      eventMask[iy][ix]=NEGATIVE_PEDESTAL;
-	      //if (cluster->get_data(0,0)>=max) {
-	    } else  if (max>tthr || tot>sqrt(ccy*ccs)*tthr || quadTot>sqrt(cy*cs)*tthr) {
-	      if (rest[iy][ix]>=max) { 
-		if (bl>=br && bl>=tl && bl>=tr) {
-		  cl->quad=BOTTOM_LEFT;
-		cl->quadTot=bl;
-		} else if (br>=bl && br>=tl && br>=tr) {
-		  cl->quad=BOTTOM_RIGHT;
-		cl->quadTot=br;
-	      } else if (tl>=br && tl>=bl && tl>=tr) {
-		cl->quad=TOP_LEFT;
-		cl->quadTot=tl;
-	      } else if   (tr>=bl && tr>=tl && tr>=br) {
-		cl->quad=TOP_RIGHT;
-		cl->quadTot=tr;
-	      }
-	     
-	
-		eventMask[iy][ix]=PHOTON_MAX;
-		cl->tot=tot;
-		cl->x=ix;
-		cl->y=iy;
-		cl->ped=getPedestal(ix,iy, 0);
-		cl->rms=getPedestalRMS(ix,iy);
-	    
-	    for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	      for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-		if ((iy+ir)>=ymin && (iy+ir)<ymax && (ix+ic)>=xmin && (ix+ic)<xmax) {
-		  cl->set_data(rest[iy+ir][ix+ic],ic,ir);
-		}
-	      }
-	    }
-	    
-	    
-	    if (interp) {
-	      if (ff) {
-#ifdef M015
-		if (iy>100)
-#endif
-		  interp->addToFlatField(cl->quadTot,cl->quad,cl->get_cluster(),eta_x, eta_y);
-		// if ((eta_x<0.1 || eta_x>0.9)&&(eta_y<0.1 || eta_y>0.9))
-		//  cout << ix << " " << iy << " " << eta_x <<" " << eta_y << endl;  
-		
-	      } else {
-		interp->getInterpolatedPosition(ix, iy, cl->quadTot,cl->quad,cl->get_cluster(),int_x, int_y);
-		interp->addToImage(int_x, int_y);
-	      }
-	      
-	    }  else 
-	      image[ix+nx*iy]++;    
-
-	    nph++;
-	    
-	    if (clusters) cl=(clusters+nph);	  
-	  
-
-		// rest[iy][ix]-=tthr;
-	      } else 
-		eventMask[iy][ix]=PHOTON;
-	      //else if (thr<=0 ) {
-		//addToPedestal(data,ix,iy);
-	      // }
-	    }
-	    if (eventMask[iy][ix]==PEDESTAL) {
-	      addToPedestal(data,ix,iy);
-	    }
-	  }
-	}
-	return nph;
-  }
-      
-   ******************************************/
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  /*   for (int ix=0; ix<nx; ix++) { */
-  /*     for (int iy=0; iy<ny; iy++) { */
-  /* 	skip=0; */
-  /* 	max=0; */
-  /* 	tl=0; */
-  /* 	tr=0; */
-  /* 	bl=0; */
-  /* 	br=0; */
-  /* 	tot=0; */
-  /* 	quadTot=0; */
-  /* 	quad=UNDEFINED_QUADRANT; */
-      
-      
-      
-      
-  /* 	cl->rms=getPedestalRMS(ix,iy); */
-  /* 	//(clusters+nph)->rms=getPedestalRMS(ix,iy); */
-
-  /* 	//	cout << iframe << " " << nph << " " << ix << " " << iy << endl; */
-  /* 	if (ix==0 || iy==0) */
-  /* 	   val[iy][ix]=subtractPedestal(data,ix,iy); */
-
-  /* 	if (val[iy][ix]<-nSigma*cl->rms) { */
-  /* 	  eventMask[iy][ix]=NEGATIVE_PEDESTAL; */
-  /* 		//	cout << "neg ped" << endl; */
-  /* 	} else { */
-  /* 	  for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) { */
-  /* 	    for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) { */
-	  
-
-  /* 	    if ((iy+ir)>=0 && (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx) { */
-	    
-  /* 	  if (ir>=0 && ic>=0) { */
-  /* 	    val[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir); */
-  /* 	    eventMask[iy+ir][ix+ic]=PEDESTAL;  */
-  /* 	  } */
-	  
-  /* 	  //   cout << ir << " " << ic << " " << val[iy+ir][ix+ic] << endl; */
-  /* 	    v=&(val[iy+ir][ix+ic]); */
-  /* 	    // if (skip==0) { */
-  /* 	      tot+=*v; */
-  /* 	      if (ir<=0 && ic<=0) */
-  /* 		bl+=*v; */
-  /* 	      if (ir<=0 && ic>=0) */
-  /* 		br+=*v; */
-  /* 	      if (ir>=0 && ic<=0) */
-  /* 		tl+=*v; */
-  /* 	      if (ir>=0 && ic>=0) */
-  /* 		tr+=*v; */
-  /* 	      if (*v>max) { */
-  /* 		max=*v; */
-  /* 	      } */
-	     
-  /* 	} */
-  /*     } */
-  /* 	  } */
-	
-  /* 	if (bl>=br && bl>=tl && bl>=tr) { */
-  /* 	  cl->quad=BOTTOM_LEFT; */
-  /* 	  cl->quadTot=bl; */
-  /* 	} else if (br>=bl && br>=tl && br>=tr) { */
-  /* 	  cl->quad=BOTTOM_RIGHT; */
-  /* 	  cl->quadTot=br; */
-  /* 	} else if (tl>=br && tl>=bl && tl>=tr) { */
-  /* 	  cl->quad=TOP_LEFT; */
-  /* 	  cl->quadTot=tl; */
-  /* 	} else if   (tr>=bl && tr>=tl && tr>=br) { */
-  /* 	  cl->quad=TOP_RIGHT; */
-  /* 	  cl->quadTot=tr; */
-  /* 	}  */
-	
-  /* 	if (max>nSigma*cl->rms || tot>sqrt(clusterSizeY*clusterSize)*nSigma*cl->rms || (cl->quadTot)>sqrt(cy*cs)*nSigma*cl->rms) { */
-  /* 	  if (val[iy][ix]>=max) { */
-  /* 	    eventMask[iy][ix]=PHOTON_MAX; */
-  /* 	    cl->tot=tot; */
-  /* 	    cl->x=ix; */
-  /* 	    cl->y=iy; */
-  /* 	    cl->ped=getPedestal(ix,iy, 0); */
-	      
-  /* 	      if (interp) { */
-  /* 		if (ff) { */
-  /* 		  interp->addToFlatField(cl->quadTot,cl->quad,cl->get_cluster(),eta_x, eta_y); */
-  /* 		  // if ((eta_x<0.1 || eta_x>0.9)&&(eta_y<0.1 || eta_y>0.9)) */
-  /* 		  //  cout << ix << " " << iy << " " << eta_x <<" " << eta_y << endl;   */
-  /* 		} else { */
-  /* 		  interp->getInterpolatedPosition(ix, iy, cl->quadTot,cl->quad,cl->get_cluster(),int_x, int_y); */
-  /* 		  interp->addToImage(int_x, int_y); */
-  /* 		} */
-  /* 	      }  else  */
-  /* 		image[ix+nx*iy]++;     */
-
-  /* 	      if (clusters) cl=(clusters+nph);	   */
-	  
-  /* 	      nph++; */
-
-  /* 	  } else { */
-  /* 	    eventMask[iy][ix]=PHOTON; */
-  /* 	  } */
-  /* 	} else if (eventMask[iy][ix]==PEDESTAL) { */
-  /* 	  addToPedestal(data,ix,iy); */
-  /* 	} */
-	  
-  /* 	} */
-  /*     } */
-  /*     } */
-  /*     return  nph; */
-    
-  /* }; */
-  
-
-
-
-
-
-
-
-  
     virtual void processData(char *data, int *val=NULL) {
-      if (interp){
+	switch (dMode) {
+	case eAnalog:
+	  // cout << "an" << endl;
+	  analogDetector<uint16_t>::processData(data,val);
+	  break;
+	case ePhotonCounting:
+	  // cout << "spc" << endl;
+	  singlePhotonDetector::processData(data,val);
+	  break;
+	default:
+	  //cout << "int" << endl;
 	    switch(fMode) {
 	    case ePedestal:
 	      addToPedestal(data);
 	      break;
 	    case eFlat:
+	      if (interp)
 		addFrame(data,val,1);
+	      else
+		singlePhotonDetector::processData(data,val);
 	      break;
 	    default:
+	      if (interp)
 		addFrame(data,val,0);
-	}
-      } else
+	      else
 		singlePhotonDetector::processData(data,val);
-      
+	    }
+	}
 	
     };
 
-    virtual char *getInterpolation(){return (char*)interp;};
+
+
+    virtual slsInterpolation *getInterpolation(){
+      return interp;
+    };
+    
+    virtual slsInterpolation *setInterpolation(slsInterpolation *ii){
+      int ok; 
+      interp=ii; 
+      /*  pthread_mutex_lock(fi);
+      if (interp)
+	interp->prepareInterpolation(ok);
+	pthread_mutex_unlock(fi);  */
+      cout << "det" << endl;
+      return interp;
+    };
+  
+    virtual void resetFlatField() { if (interp) {
+	pthread_mutex_lock(fi); 
+	interp->resetFlatField(); 
+	pthread_mutex_unlock(fi);  
+      }
+    }
+
+    virtual int getNSubPixels(){ if (interp) return interp->getNSubPixels(); else return 1;}
+    virtual int setNSubPixels(int ns)  { 
+      if (interp) {
+	pthread_mutex_lock(fi); 
+	interp->getNSubPixels(); 
+	pthread_mutex_unlock(fi);  
+      }
+      return getNSubPixels();
+    }
 
  protected:
   
   
   slsInterpolation *interp;
   int id;
-  //should put it to analogDetector
-  int xmin, xmax, ymin, ymax;
+  pthread_mutex_t *fi;
 };
 
 

slsDetectorCalibration/interpolations/eta2InterpolationBase.h

@@ -0,0 +1,434 @@
+#ifndef ETA2_INTERPOLATION_BASE_H
+#define ETA2_INTERPOLATION_BASE_H
+
+#ifdef MYROOT1
+#include <TObject.h>
+#include <TTree.h>
+#include <TH2D.h>
+#include <TH2F.h>
+#endif
+
+#include "etaInterpolationBase.h"
+
+class eta2InterpolationBase : public virtual etaInterpolationBase {
+  
+ public:
+ eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nb, emin, emax) {
+    // cout << "e2ib " << nb << " " << emin << " " << emax << endl; 
+
+    /* if (nbeta<=0) { */
+    /*   nbeta=nSubPixels*10;  */
+    /* } */
+    if (etamin>=etamax) {
+      etamin=-1;
+      etamax=2; 
+      //  cout << ":" <<endl;
+    }
+    etastep=(etamax-etamin)/nbeta;
+#ifdef MYROOT1
+    delete heta;
+    delete hhx;
+    delete hhy;
+    heta=new TH2D("heta","heta",nbeta,etamin,etamax,nbeta,etamin,etamax);
+    hhx=new TH2D("hhx","hhx",nbeta,etamin,etamax,nbeta,etamin,etamax);
+    hhy=new TH2D("hhy","hhy",nbeta,etamin,etamax,nbeta,etamin,etamax);
+#endif
+#ifndef MYROOT1
+    /* delete [] heta; */
+    /* delete [] hhx; */
+    /* delete [] hhy; */
+    /* heta=new int[nbeta*nbeta]; */
+    /* hhx=new float[nbeta*nbeta]; */
+    /* hhy=new float[nbeta*nbeta]; */
+    
+#endif
+    
+    //   cout << nbeta << " " << etamin << " " << etamax << endl;
+  };
+  
+ eta2InterpolationBase(eta2InterpolationBase *orig): etaInterpolationBase(orig){ };
+
+/*  virtual eta2InterpolationBase* Clone()=0; {
+
+    return new eta2InterpolationBase(this);
+
+  };
+
+					   */
+ 
+  //////////////////////////////////////////////////////////////////////////////
+  //////////// /*It return position hit for the event in input */ //////////////
+  virtual void getInterpolatedPosition(int x, int y, int *data, double &int_x, double &int_y)
+  {
+    double sDum[2][2];
+    double tot, totquad;
+    double etax,etay;
+    
+    int corner;
+    corner=calcQuad(data, tot, totquad, sDum); 
+    if (nSubPixels>2) 
+      calcEta(totquad, sDum, etax, etay); 
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
+  {
+    double sDum[2][2];
+    double tot, totquad;
+    double etax,etay;
+    
+    int corner;
+    corner=calcQuad(data, tot, totquad, sDum); 
+    if (nSubPixels>2) 
+      calcEta(totquad, sDum, etax, etay); 
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+
+
+
+
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
+    
+     double cc[2][2];
+     double *cluster[3];
+     int xoff, yoff;
+     cluster[0]=cl;
+     cluster[1]=cl+3;
+     cluster[2]=cl+6;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     double etax, etay;
+     if (nSubPixels>2) { 
+       cc[0][0]=cluster[yoff][xoff];
+       cc[1][0]=cluster[yoff+1][xoff];
+       cc[0][1]=cluster[yoff][xoff+1];
+       cc[1][1]=cluster[yoff+1][xoff+1];
+       calcEta(totquad,cc,etax,etay);
+     }
+     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
+
+  }
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
+    
+     double cc[2][2];
+     int *cluster[3];
+     int xoff, yoff;
+     cluster[0]=cl;
+     cluster[1]=cl+3;
+     cluster[2]=cl+6;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     double etax, etay;
+     if (nSubPixels>2) { 
+       cc[0][0]=cluster[yoff][xoff];
+       cc[1][0]=cluster[yoff+1][xoff];
+       cc[0][1]=cluster[yoff][xoff+1];
+       cc[1][1]=cluster[yoff+1][xoff+1];
+       calcEta(totquad,cc,etax,etay);
+     }
+     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
+
+  }
+
+
+
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
+  {
+
+
+    double xpos_eta=0,ypos_eta=0;
+    double dX,dY;
+    int ex,ey;
+    switch (corner)
+      {
+      case TOP_LEFT:
+	dX=-1.;
+	dY=0;
+	break;
+      case TOP_RIGHT:
+	;
+	dX=0;
+	dY=0;
+	break;
+      case BOTTOM_LEFT:
+	dX=-1.;
+	dY=-1.;
+	break;
+      case BOTTOM_RIGHT:
+	dX=0;
+	dY=-1.;
+	break;
+      default:
+	cout << "bad quadrant" << endl;
+	dX=0.; 
+	dY=0.;
+      }
+    
+
+     if (nSubPixels>2) { 
+
+#ifdef MYROOT1
+    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
+    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
+#endif
+#ifndef MYROOT1
+    ex=(etax-etamin)/etastep;
+    ey=(etay-etamin)/etastep;
+    if (ex<0) {
+      cout << "x*"<< ex << endl;
+      ex=0;
+	} 
+    if (ex>=nbeta) {
+      cout << "x?"<< ex << endl;
+      ex=nbeta-1;
+      
+    }
+    if (ey<0) {
+      cout << "y*"<< ey << endl;
+      ey=0;
+	} 
+    if (ey>=nbeta) {
+      cout << "y?"<< ey << endl;
+      ey=nbeta-1;
+      
+    }
+    
+    
+   
+    xpos_eta=(((double)hhx[(ey*nbeta+ex)]))+dX ;///((double)nSubPixels);
+    ypos_eta=(((double)hhy[(ey*nbeta+ex)]))+dY ;///((double)nSubPixels);
+    //else
+    //return 0;
+    
+#endif
+     } else {
+       xpos_eta=0.5*dX+0.25;
+       ypos_eta=0.5*dY+0.25;
+     }
+       
+       int_x=((double)x) + xpos_eta+0.5;
+       int_y=((double)y) +  ypos_eta+0.5;
+    
+
+  }
+
+
+  
+   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
+     double cc[2][2];
+     int *cluster[3];
+     int xoff, yoff;
+     cluster[0]=cl;
+     cluster[1]=cl+3;
+     cluster[2]=cl+6;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     cc[0][0]=cluster[yoff][xoff];
+     cc[1][0]=cluster[yoff+1][xoff];
+     cc[0][1]=cluster[yoff][xoff+1];
+     cc[1][1]=cluster[yoff+1][xoff+1];
+     
+      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
+      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
+      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
+      /* cout <<"******"<<totquad << " " << quad << endl;  */
+      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
+      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
+     //calcMyEta(totquad,quad,cl,etax, etay);
+     calcEta(totquad, cc,etax, etay);
+
+     //     cout <<"******"<< etax << " " << etay << endl;
+
+
+     return addToFlatField(etax,etay);
+   }
+
+   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
+     double cc[2][2];
+     double *cluster[3];
+     int xoff, yoff;
+     cluster[0]=cl;
+     cluster[1]=cl+3;
+     cluster[2]=cl+6;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     cc[0][0]=cluster[yoff][xoff];
+     cc[1][0]=cluster[yoff+1][xoff];
+     cc[0][1]=cluster[yoff][xoff+1];
+     cc[1][1]=cluster[yoff+1][xoff+1];
+     
+      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
+      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
+      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
+      /* cout <<"******"<<totquad << " " << quad << endl;  */
+      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
+      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
+     //calcMyEta(totquad,quad,cl,etax, etay);
+     calcEta(totquad, cc,etax, etay);
+
+     //     cout <<"******"<< etax << " " << etay << endl;
+
+
+     return addToFlatField(etax,etay);
+   }
+
+
+
+  //////////////////////////////////////////////////////////////////////////////////////
+  virtual int addToFlatField(double *cluster, double &etax, double &etay){
+    double sDum[2][2];
+    double tot, totquad;
+    int corner;
+    corner=calcQuad(cluster, tot, totquad, sDum); 
+    
+    double xpos_eta,ypos_eta;
+    double dX,dY;
+  
+    
+    calcEta(totquad, sDum, etax, etay); 
+   
+    return addToFlatField(etax,etay);
+
+    };
+
+  virtual int addToFlatField(int *cluster, double &etax, double &etay){
+    double sDum[2][2];
+    double tot, totquad;
+    int corner;
+    corner=calcQuad(cluster, tot, totquad, sDum); 
+    
+    double xpos_eta,ypos_eta;
+    double dX,dY;
+  
+    
+    calcEta(totquad, sDum, etax, etay); 
+   
+    return addToFlatField(etax,etay);
+
+    };
+
+
+  virtual int addToFlatField(double etax, double etay){
+#ifdef MYROOT1
+    heta->Fill(etax,etay);
+#endif
+#ifndef MYROOT1
+    int ex,ey; 
+    ex=(etax-etamin)/etastep;
+    ey=(etay-etamin)/etastep;
+    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
+      heta[ey*nbeta+ex]++; 
+#endif
+    return 0;    
+  };
+  
+/*  protected: */
+  
+/* #ifdef MYROOT1 */
+/*   TH2D *heta; */
+/*   TH2D *hhx; */
+/*   TH2D *hhy; */
+/* #endif */
+/* #ifndef MYROOT1 */
+/*   int *heta; */
+/*   float *hhx; */
+/*   float *hhy; */
+/* #endif */
+/*   int nbeta; */
+/*   double etamin, etamax, etastep; */
+
+};
+
+#endif