Merge branch 'main-rc' into b4.0.0

* 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).

.travis.yml

@@ -0,0 +1,45 @@
+sudo: false
+
+language: cpp
+
+matrix:
+  include:
+    - os: linux
+      env: CONDA_PY=3.6
+
+dist: trusty
+
+install:
+  - sudo apt-get update
+  - ldd --version
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - rm -f miniconda.sh
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda config --add channels conda-forge
+  - conda config --add channels slsdetectorgroup
+  - conda update conda
+  - conda update --all
+  - conda install conda-build anaconda-client
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+
+  # Replace dep1 dep2 ... with your dependencies
+  - conda create -q -n test-environment python=$CONDA_PY
+  - source activate test-environment
+  - conda-build .
+
+script:
+ - echo "No test scripts to be run!"
+
+
+deploy:
+  provider: script
+  script: find $HOME/miniconda/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  on:
+    branch: 4.0.0
+

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

@@ -2,12 +2,12 @@
 Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
 
 ### Binaries
-Documentation to obtain the binaries via the conda package is available [here.](https://github.com/slsdetectorgroup/sls_detector_software)
+Documentation to obtain the binaries via the conda package is available for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
 
 ### Source code
 One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
 ```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 3.1.0
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Setup dependencies 
@@ -19,7 +19,7 @@ Requirements: Qt 4.8 and Qwt 6.0
 ```
 If either of them does not exist, the GUI client will not be built.
 
-* Calibration wizards<br>
+* Advanced user Calibration wizards<br>
 Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
@@ -43,6 +43,10 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
  * -r: Build/Rebuilds only receiver<br>
  * -g: Build/Rebuilds only gui<br>
  * -j: Number of threads to compile through<br>
+ * -e: Debug mode
+ 
+Basic Option:
+./cmk.sh -b
  
 For only make:
 ./cmk.sh
@@ -83,5 +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

@@ -1,26 +1,508 @@
-SLS Detector Package 3.1.3 released on 2018-06-28
+SLS Detector Package 4.0.0 released on 27.09.2018
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.1.3 into 3.1.2 releases.
+	This document describes the differences between 4.0.0 and 3.1.4 releases.
+
+	Download
+	--------
+	
+	The Source Code (Default C++ API):
+		 https://github.com/slsdetectorgroup/slsDetectorPackage
+		 
+	The Conda Lib Package:
+		https://github.com/slsdetectorgroup/sls_detector_lib
+		
+	The Conda GUI Package:
+		https://github.com/slsdetectorgroup/sls_detector_gui	
+		
+	The Python Interface (including the package):
+    	https://github.com/slsdetectorgroup/sls_detector
+	
+	
+	Documentation
+	-------------
+	
+	Manual (HTML & PDF):
+		https://www.psi.ch/detectors/documentation
+		slsDetectorPackage/manual/docs/
+		
+	Command Line Documentation:
+		manual/docs/html/slsDetectorClientDocs/index.html
+		manual/docs/pdf/slsDetectorClientDocs.pdf
+		
+	C++ API Documentation:
+		manual/docs/html/slsDetectorUsersDocs/index.html
+		manual/docs/pdf/slsDetectorUsersDocs.pdf
+		
+	C++ API Example:
+		manual/manual-api/mainClient.cpp
+		manual/manual-api/mainReceiver.cpp
+		
+	Python API Documentation:
+		https://slsdetectorgroup.github.io/sls_detector/
+		
+	Further Documentation:
+		https://www.psi.ch/detectors/users-support
+		
+	
+	Support
+	-------
+
+	General Software related:
+		dhanya.thattil@psi.ch
+		anna.bergamaschi@psi.ch
+		
+	Python related:
+		erik.frojdh@psi.ch
 
 
-Topics Concerning
-==================
-	Using delay after trigger for Jungfrau
+
+CONTENTS
+
+	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
 
 
-Resolved Issues
-===============
+
+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) 
+    	Eiger
+    	=====  
+    	Minimum compatible version  : 22
+    	Latest version              : 22
+        
+    	Jungfrau
+    	========       
+    	Minimum compatible version  : 15.06.2018
+    	Latest version              : 15.06.2018
+
+    	
+    	Detector Upgrade
+    	================
+    	Gotthard	Cannot be upgraded remotely. Requires programming via USB blaster
+    	Eiger		Can be upgraded remotely via bit files
+    	Jungfrau	Can be upgraded remotely using sls_detector_put programfpga <pof>
+    	
+    	Instructions available at
+    	https://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.
+		
+
+
+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.	Delay after trigger was always set to 5 seconds. This is fixed now.
-	3.	Get delay left after trigger is not available for this version.
 	
+	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 ns was implemented.
+	
+	4. 	(Eiger and Jungfrau) They can be configured to have x and y coord values
+		of the detector in their udp header.
+
+
+
+
+5. Resolved Issues
+==================
+
+	Client
+	------
+	memory leak for multi threading
+	
+	1.	Compiler flag -std=c++98 enforced. Debug flag removed.
+	
+	2.	If trimen gives different list from different detectors, it returns a -1.
+	
+	3.	Version format for each submodule of the package changed to just date YYMMDD.
+		Users class fixed to give correct version, instead of -1.
+		
+	4.	Getting settings in users class gave -1. Fixed now.
+
+	5.	(Jungfrau) Programming FPGA now creates the rawbin file from pof in tmp
+		rather than source file location (for permission issues).
+		
+	6.	(Gotthard) ROI segmentation fault fixed.
+		
+	Receiver
+	--------
+	
+	1.	Silent feature of receiver fixed.
+	
+	2. 	Socket descriptor misused earlier for success flag, instead exceptions
+		used that are handled inside the package.
+
+	3.	Global optind variable initialized to instantiate multiple receivers 
+		in same process. Also removed static members to enable this feature.
+		
+	4.	Socket buffer size attempts to set for each acquiistion and provide
+		warning if no capabilities. Warnings can be removed using instruction with
+		error provided. Default Jungfrau UDP socket buffer size if 2 GB, default is 
+		100 MB.
+		
+	5.	Refactored code a bit for performance and robustness, blocking push 
+		in buffer between listener and dataprocessor
+
+	
+	Detector Server
+	---------------
+	
+	1.	(Jungfrau) Stop server also mapped during a reset. Reading power status
+		instead of user input register for power.
+	
+	2.	(Eiger) Bug fix for saving trimbits to file (Advanced users).
+	
+	3.	(Gotthard 25um) config.txt is not read again after detector startup,
+		no matter the number of times the detector server is restarted. 
+
+	
+6. Known Issues
+===============
+
+	Receiver
+	--------
+	
+	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 $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -90,7 +92,11 @@ while getopts ":bchd:j:trg" opt ; do
 		echo "Compiling Options: GUI" 
 		GUI=1
 		REBUILD=1
-		;;      
+		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
+		;;    
     \?)
      	echo "Invalid option: -$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/gotthard.config

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

examples/jungfrau.config

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

examples/jungfrau_two.config

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

examples/two_gotthard.config

@@ -8,13 +8,11 @@ hostname bchip007+bchip009+
 #0:port 1952
 #0:stopport 1953
 #0:rx_tcpport 1956 
-0:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:angdir 1.000000
 0:moveflag 0.000000
-0:lock 0
-0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
+
 0:detectorip 10.1.1.2
 #0:detectormac 00:aa:bb:cc:dd:ee
 #0:rx_udpport 50001
@@ -28,13 +26,11 @@ hostname bchip007+bchip009+
 #1:port 1952
 #1:stopport 1953
 1:rx_tcpport 1957
-1:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:angdir 1.000000
 1:moveflag 0.000000
-1:lock 0
-1:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:ffdir /home/l_msdetect
 1:extsig:0 off
+
 1:detectorip 10.1.2.2
 #1:detectormac 00:aa:bb:cc:dd:ee
 1:rx_udpport 50004
@@ -56,4 +52,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

manual/docs/html/angularCalibrationHowTo/angularCalibrationHowTo.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
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+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

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 Output written on images.dvi (18 pages, 4432 bytes).

manual/docs/html/angularCalibrationHowTo/images.pl

@@ -1,4 +1,4 @@
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
 # Associate images original text with physical files.
 
 
@@ -44,18 +44,18 @@ $cached_env_img{$key} = q|<IMG
  SRC="|."$dir".q|img9.png"
  ALT="$p=50&nbsp;\mu m$">|; 
 
-$key = q/_6;MSF=1.6;AAT/;
-$cached_env_img{$key} = q|<IMG
- WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
- SRC="|."$dir".q|img10.png"
- ALT="$_6$">|; 
-
 $key = q/C_{peak};MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
  SRC="|."$dir".q|img2.png"
  ALT="$C_{peak}$">|; 
 
+$key = q/_6;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$_6$">|; 
+
 $key = q/includegraphics[width=textwidth]{peakFit.eps};AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
@@ -74,18 +74,18 @@ $cached_env_img{$key} = q|<IMG
  SRC="|."$dir".q|img16.png"
  ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}">|; 
 
-$key = q/pm;MSF=1.6;AAT/;
-$cached_env_img{$key} = q|<IMG
- WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
- SRC="|."$dir".q|img12.png"
- ALT="$\pm$">|; 
-
 $key = q/includegraphics[width=textwidth]{angleFit.eps};AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
  SRC="|."$dir".q|img18.png"
  ALT="\includegraphics[width=\textwidth]{angleFit.eps}">|; 
 
+$key = q/pm;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$\pm$">|; 
+
 $key = q/{displaymath}Theta_e=Theta_o^i-arctanBig(frac{pcdot(C_{peak}-C_{center}^i)}{R^i}Big),{displaymath};MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
  WIDTH="291" HEIGHT="41" BORDER="0"
@@ -96,13 +96,13 @@ $cached_env_img{$key} = q|<IMG
 
 $key = q/theta;MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="|."$dir".q|img1.png"
  ALT="$\theta$">|; 
 
 $key = q/R^i;MSF=1.6;AAT/;
 $cached_env_img{$key} = q|<IMG
- WIDTH="22" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
  SRC="|."$dir".q|img8.png"
  ALT="$R^i$">|; 
 

manual/docs/html/angularCalibrationHowTo/index.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/internals.pl

@@ -1,4 +1,4 @@
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
 # Associate internals original text with physical files.
 
 

manual/docs/html/angularCalibrationHowTo/labels.pl

@@ -1,4 +1,4 @@
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+# LaTeX2HTML 2012 (1.2)
 # Associate labels original text with physical files.
 
 
@@ -29,7 +29,7 @@ $noresave{$key} = "$nosave";
 1;
 
 
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
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manual/docs/html/angularCalibrationHowTo/node1.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
@@ -55,7 +55,7 @@ Introduction</A>
 
 <P>
 In order to convert from strip number to 2<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img1.png"
  ALT="$\theta$">-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). 
 <BR>
@@ -107,7 +107,7 @@ where the parameters <IMG
  WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
  SRC="img7.png"
  ALT="$C_{center}^{i}$"> is the central channel  and <IMG
- WIDTH="22" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
  SRC="img8.png"
  ALT="$R^i$"> is the distance of the module <IMG
  WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
@@ -121,7 +121,7 @@ Finally, the global offset of the detector system is precisely determined by ref
 
 <P>
 The same function of equation&nbsp;<A HREF="#eq:angcal">1</A>, with the parameters obtained from the calibration, is used in order to convert from channel number to 2<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img1.png"
  ALT="$\theta$">-angle.
 
@@ -180,7 +180,7 @@ These results show that  the angular calibration allows a resolution in determin
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
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manual/docs/html/angularCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
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@@ -211,7 +211,7 @@ Acquisition GUI window to setup the motor position scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
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@@ -180,7 +180,7 @@ After fitting all modules you can click on the <I>Write Angular Calibration</I>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node4.html

@@ -1,6 +1,6 @@
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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node5.html

@@ -1,6 +1,6 @@
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 Copyright &#169; 1993, 1994, 1995, 1996,
 <A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>, 
@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
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 <P>
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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
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manual/docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

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

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manual/docs/html/energyCalibrationHowTo/index.html

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

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manual/docs/html/energyCalibrationHowTo/node1.html

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@@ -78,21 +78,21 @@ The thick solid line represents the physical curve which also takes into account
 
 <P>
 The intrinsic noise on the electronic signal  is defined by the Equivalent Noise Charge (<IMG
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  SRC="img12.png"
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- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$"> normally depends on the shaping settings of the analog chain and increases with shorter shaping times. 
 The resulting electronic signal spectrum is then  given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$">.  
 The S-curve for a monochromatic radiation beam is well described by a Gaussian cumulative distribution <IMG
@@ -204,10 +204,10 @@ Moreover, setting the threshold too close to the energy of the fluorescent light
 The comparator threshold is given by a global level which can be set on a module basis and adds to a component which is individually adjustable for each channel. In order to optimize the uniformity of the detector response it is important to properly adjust the threshold for all channels. 
 <BR>
 Since both the signal amplification stages and the comparator  are linear, it is necessary to calibrate the detector offset <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img25.png"
  ALT="$O$"> and gain <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img26.png"
  ALT="$G$"> in order to correctly set its comparator threshold <IMG
  WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
@@ -258,10 +258,10 @@ Expected counts as a function of a threshold energy for a monochromatic beam of
  WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
  SRC="img2.png"
  ALT="$N_0$">=10000 is the number of photons absorbed by the detector during the acquisition time. The dashed line represents the curve in an ideal case without electronic noise and charge sharing, the solid thin line with noise  <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$">=1&nbsp;keV but without charge sharing and the solid thick line is the physical case with noise and <IMG
- WIDTH="45" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img4.png"
  ALT="$CS=$">22&nbsp;% charge sharing. <IMG
  WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
@@ -377,7 +377,7 @@ Median of the number of counts as a function of the threshold for X-rays of 12.5
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
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+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -180,7 +180,7 @@ Acquisition GUI window to setup the threshold scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -107,7 +107,7 @@ Once you have uploaded at least 2 energies, you will be allowed to  <I>proceed t
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 7:</STRONG>
 Window to add energies to the calibration.</CAPTION>
 <TR><TD><IMG
- WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
  SRC="img39.png"
  ALT="\includegraphics[width=\textwidth]{addEnergy.eps}"></TD></TR>
 </TABLE>
@@ -153,7 +153,7 @@ The button <I>Finished</I> will be enebled only once the calibration files have
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 8:</STRONG>
 Window to calibrate the modules.</CAPTION>
 <TR><TD><IMG
- WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
  SRC="img40.png"
  ALT="\includegraphics[width=\textwidth]{calibrateModule.eps}"></TD></TR>
 </TABLE>
@@ -184,7 +184,7 @@ Window to calibrate the modules.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node4.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
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 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -68,7 +68,7 @@ By reloading the default detector settings, the calibration coefficients will be
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2018-03-12
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node5.html

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

manual/docs/html/slsDetectorClientDocs/acquisition.html

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

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+</script>
+  <div id="navrow1" class="tabs">
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-</div>
-<div class="contents">
-
-
-<h1><a class="anchor" id="actions">Actions </a></h1><p>Commands to define scripts to be executed during the acquisition flow</p>
-<ul>
-<li><b>positions [n [p0..pn-1]]</b> sets/gets number of angular position and positions to be acquired.. <code>Returns</code> <code></code>(int int..) n [p0..pn-1]</li>
-</ul>
-<ul>
-<li><b>startscript [s]</b> sets/gets the script to be executed at the beginning of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>startscriptpar [s]</b> sets/gets a string to be passed as a parameter to the startscript. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>stopscript [s]</b> sets/gets the script to be executed at the end of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>stopscriptpar [s]</b> sets/gets a string to be passed as a parameter to the stopscript. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptbefore [s]</b> sets/gets the script to be executed before starting the detector every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptbeforepar [s]</b> sets/gets a string to be passed as a parameter to the scriptbefore. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptafter [s]</b> sets/gets the script to be executed after the detector has finished every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>scriptafterpar [s]</b> sets/gets a string to be passed as a parameter to the scriptafter. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerafter [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerbefore [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerbeforepar [s]</b> sets/gets a string to be passed as a parameter to the headerbefore script. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>headerafterpar [s]</b> sets/gets a string to be passed as a parameter to the headerafter script. <code>Returns</code> <code></code>(string)</li>
-</ul>
-<ul>
-<li><b>enacallog [i]</b> enables/disables logging of the parameters necessary for the energy calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
-<li><b>angcallog [i]</b> enables/disables logging of the parameters necessary for the angular calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
-<li><b>scan0script [s]</b> sets/gets the script to be executed for the scan 0 level. <code>none</code> unsets.</li>
-</ul>
-<ul>
-<li><b>scan0par [s]</b> sets/gets a string to be passed as a parameter to the scan0script</li>
-</ul>
-<ul>
-<li><b>scan0prec [i]</b> sets/gets number of digits to be used for the scan0 variable in the file name.</li>
-</ul>
-<ul>
-<li><b>scan0steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan0 level and their values (float).</li>
-</ul>
-<ul>
-<li><b>scan0range [smin smax sstep]</b> sets scan0 min, max and step, returns the number of steps and their values as scan0steps.</li>
-</ul>
-<ul>
-<li><b>scan1script [s]</b> sets/gets the script to be executed for the scan1 level. <code>none</code> unsets.</li>
-</ul>
-<ul>
-<li><b>scan1par [s]</b> sets/gets a string to be passed as a parameter to the scan1script</li>
-</ul>
-<ul>
-<li><b>scan1prec [i]</b> sets/gets number of digits to be used for the scan1 variable in the file name.</li>
-</ul>
-<ul>
-<li><b>scan1steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan1 level and their values (float).</li>
-</ul>
-<ul>
-<li><b>scan1range [smin smax sstep]</b> sets scan1 min, max and step, returns the number of steps and their values as scan1steps. </li>
-</ul>
-</div>
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+  <div class="headertitle">
+<div class="title">Actions </div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><p>Commands to define scripts to be executed during the acquisition flow</p>
+<ul>
+<li><b>positions [n [p0..pn-1]]</b> sets/gets number of angular position and positions to be acquired.. <code>Returns</code> <code></code>(int int..) n [p0..pn-1]</li>
+<li><b>startscript [s]</b> sets/gets the script to be executed at the beginning of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>startscriptpar [s]</b> sets/gets a string to be passed as a parameter to the startscript. <code>Returns</code> <code></code>(string)</li>
+<li><b>stopscript [s]</b> sets/gets the script to be executed at the end of the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>stopscriptpar [s]</b> sets/gets a string to be passed as a parameter to the stopscript. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptbefore [s]</b> sets/gets the script to be executed before starting the detector every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptbeforepar [s]</b> sets/gets a string to be passed as a parameter to the scriptbefore. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptafter [s]</b> sets/gets the script to be executed after the detector has finished every time in the acquisition. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>scriptafterpar [s]</b> sets/gets a string to be passed as a parameter to the scriptafter. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerafter [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerbefore [s]</b> sets/gets the script to be executed for logging the detector parameters. <code>none</code> unsets. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerbeforepar [s]</b> sets/gets a string to be passed as a parameter to the headerbefore script. <code>Returns</code> <code></code>(string)</li>
+<li><b>headerafterpar [s]</b> sets/gets a string to be passed as a parameter to the headerafter script. <code>Returns</code> <code></code>(string)</li>
+<li><b>enacallog [i]</b> enables/disables logging of the parameters necessary for the energy calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
+<li><b>angcallog [i]</b> enables/disables logging of the parameters necessary for the angular calibration. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int)</li>
+<li><b>scan0script [s]</b> sets/gets the script to be executed for the scan 0 level. <code>none</code> unsets.</li>
+<li><b>scan0par [s]</b> sets/gets a string to be passed as a parameter to the scan0script</li>
+<li><b>scan0prec [i]</b> sets/gets number of digits to be used for the scan0 variable in the file name.</li>
+<li><b>scan0steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan0 level and their values (float).</li>
+<li><b>scan0range [smin smax sstep]</b> sets scan0 min, max and step, returns the number of steps and their values as scan0steps.</li>
+<li><b>scan1script [s]</b> sets/gets the script to be executed for the scan1 level. <code>none</code> unsets.</li>
+<li><b>scan1par [s]</b> sets/gets a string to be passed as a parameter to the scan1script</li>
+<li><b>scan1prec [i]</b> sets/gets number of digits to be used for the scan1 variable in the file name.</li>
+<li><b>scan1steps [i [s0..sn-1]]</b> sets/gets number of steps (int) of the scan1 level and their values (float).</li>
+<li><b>scan1range [smin smax sstep]</b> sets scan1 min, max and step, returns the number of steps and their values as scan1steps. </li>
+</ul>
+</div></div><!-- contents -->
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+Generated by &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/>
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+</small></address>
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manual/docs/html/slsDetectorClientDocs/advanced.html

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+<div class="title">Advanced Usage </div>  </div>
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manual/docs/html/slsDetectorClientDocs/config.html

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

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-<div class="contents">
-
-
-<h1><a class="anchor" id="ctb">Chiptest board </a></h1><p>Commands specific for the new chiptest board as pattern generator</p>
-<ul>
-<li><b>adcinvert [mask]</b> Sets/gets ADC inversion mask (8 digits hex format)</li>
-</ul>
-<ul>
-<li><b>adcdisable [mask]</b> Sets/gets ADC disable mask (8 digits hex format)</li>
-</ul>
-<ul>
-<li><b>pattern fn</b> loads binary pattern file fn</li>
-</ul>
-<ul>
-<li><b>patword addr [word]</b> sets/gets 64 bit word at address addr of pattern memory. Both address and word in hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patioctrl [word]</b> sets/gets 64 bit mask defining input (0) and output (1) signals. hex format.</li>
-</ul>
-<ul>
-<li><b>patclkctrl [word]</b> sets/gets 64 bit mask defining if output signal is a clock and runs. hex format. Unused at the moment.</li>
-</ul>
-<ul>
-<li><b>patlimits [addr1 addr2]</b> sets/gets the start and stop limits of the pattern to be executed. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patloop0 [addr1 addr2]</b> sets/gets the start and stop limits of the level 0 loop. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patnloop0 [n]</b> sets/gets the number of cyclesof the level 0 loop (int).</li>
-</ul>
-<ul>
-<li><b>patwait0 [addr]</b> sets/gets the address of the level 0 wait point. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patwaittime0 [n]</b> sets/gets the duration of the witing of the 0 waiting point in clock cycles (int).</li>
-</ul>
-<ul>
-<li><b>patloop1 [addr1 addr2]</b> sets/gets the start and stop limits of the level 1 loop. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patnloop1 [n]</b> sets/gets the number of cyclesof the level 1 loop (int).</li>
-</ul>
-<ul>
-<li><b>patwait1 [addr]</b> sets/gets the address of the level 1 wait point. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patwaittime1 [n]</b> sets/gets the duration of the witing of the 1 waiting point in clock cycles (int).</li>
-</ul>
-<ul>
-<li><b>patloop2 [addr1 addr2]</b> sets/gets the start and stop limits of the level 2 loop. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patnloop2 [n]</b> sets/gets the number of cyclesof the level 2 loop (int).</li>
-</ul>
-<ul>
-<li><b>patwait2 [addr]</b> sets/gets the address of the level 2 wait point. hex format. Advanced!</li>
-</ul>
-<ul>
-<li><b>patwaittime2 [n]</b> sets/gets the duration of the waiting of the 2 waiting point in clock cycles (int).</li>
-</ul>
-<ul>
-<li><b>dut_clk [i]</b> sets/gets the signal to be used as a clock for the digital data coming from the device under test. Advanced! </li>
-</ul>
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+<div class="title">Chiptest board </div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><p>Commands specific for the new chiptest board as pattern generator</p>
+<ul>
+<li><b>adcinvert [mask]</b> Sets/gets ADC inversion mask (8 digits hex format)</li>
+<li><b>adcdisable [mask]</b> Sets/gets ADC disable mask (8 digits hex format)</li>
+<li><b>pattern fn</b> loads binary pattern file fn</li>
+<li><b>patword addr [word]</b> sets/gets 64 bit word at address addr of pattern memory. Both address and word in hex format. Advanced!</li>
+<li><b>patioctrl [word]</b> sets/gets 64 bit mask defining input (0) and output (1) signals. hex format.</li>
+<li><b>patclkctrl [word]</b> sets/gets 64 bit mask defining if output signal is a clock and runs. hex format. Unused at the moment.</li>
+<li><b>patlimits [addr1 addr2]</b> sets/gets the start and stop limits of the pattern to be executed. hex format. Advanced!</li>
+<li><b>patloop0 [addr1 addr2]</b> sets/gets the start and stop limits of the level 0 loop. hex format. Advanced!</li>
+<li><b>patnloop0 [n]</b> sets/gets the number of cyclesof the level 0 loop (int).</li>
+<li><b>patwait0 [addr]</b> sets/gets the address of the level 0 wait point. hex format. Advanced!</li>
+<li><b>patwaittime0 [n]</b> sets/gets the duration of the witing of the 0 waiting point in clock cycles (int).</li>
+<li><b>patloop1 [addr1 addr2]</b> sets/gets the start and stop limits of the level 1 loop. hex format. Advanced!</li>
+<li><b>patnloop1 [n]</b> sets/gets the number of cyclesof the level 1 loop (int).</li>
+<li><b>patwait1 [addr]</b> sets/gets the address of the level 1 wait point. hex format. Advanced!</li>
+<li><b>patwaittime1 [n]</b> sets/gets the duration of the witing of the 1 waiting point in clock cycles (int).</li>
+<li><b>patloop2 [addr1 addr2]</b> sets/gets the start and stop limits of the level 2 loop. hex format. Advanced!</li>
+<li><b>patnloop2 [n]</b> sets/gets the number of cyclesof the level 2 loop (int).</li>
+<li><b>patwait2 [addr]</b> sets/gets the address of the level 2 wait point. hex format. Advanced!</li>
+<li><b>patwaittime2 [n]</b> sets/gets the duration of the waiting of the 2 waiting point in clock cycles (int).</li>
+<li><b>dut_clk [i]</b> sets/gets the signal to be used as a clock for the digital data coming from the device under test. Advanced! </li>
+</ul>
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manual/docs/html/slsDetectorClientDocs/data.html

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-<h1><a class="anchor" id="data">Data processing commands </a></h1><p>Commands to setup the data processing (mainly MYTHEN related)</p>
-<ul>
-<li><b>flatfield [fn]</b> <code>put</code> sets flatfield file to <code>fn</code> (relative to <code>ffdir</code>).  returns the flatfield file name relative to <code>ffdir</code> (string). If</li>
-</ul>
-<ul>
-<li><b>ffdir [d]</b> Sets/gets the directory in which the flat field file is located. <code>Returns</code> <code></code>(string) ffdir</li>
-</ul>
-<ul>
-<li><b>ratecorr [ns]</b> Returns the dead time used for rate correections in ns (int). <code>put</code> sets the deadtime correction constant in ns, -1 will set it to default tau of settings (0 unset). <code>Returns</code> <code></code>(double with 9 decimal digit precision)</li>
-</ul>
-<ul>
-<li><b>badchannels [fn]</b> <code>put</code> sets the badchannels file to <code>fn</code> .  returns the bad channels file name. If</li>
-</ul>
-<ul>
-<li><b>angconv [fn]</b> <code>put</code> sets the angular conversion file to <code>fn</code> .  returns the angular conversion file name. If</li>
-</ul>
-<ul>
-<li><b>globaloff [f]</b> Sets/gets the beamline angular global offset (float).</li>
-</ul>
-<ul>
-<li><b>fineoff [f]</b> Sets/gets the angular fine offset of the measurement (float).</li>
-</ul>
-<ul>
-<li><b>binsize [f]</b> Sets/gets the bin size used for the angular conversion (float).</li>
-</ul>
-<ul>
-<li><b>angdir [i]</b> Sets/gets the angular direction. 1 means increasing channels number as increasing angle, -1 increasing channel number decreasing angle.</li>
-</ul>
-<ul>
-<li><b>moveflag [i]</b> Sets/gets the flag for physically moving the detector during the acquisition of several positions. 1 sets (moves), 0 unsets.</li>
-</ul>
-<ul>
-<li><b>samplex [f]</b> Sets/gets the sample displacement in th direction parallel to the beam in um. Unused!</li>
-</ul>
-<ul>
-<li><b>sampley [f]</b> Sets/gets the sample displacement in th direction orthogonal to the beam in um. Unused!</li>
-</ul>
-<ul>
-<li><b>threaded [i]</b> Sets/gets the data processing threaded flag. 1 is threaded, 0 unthreaded.</li>
-</ul>
-<ul>
-<li><b>darkimage fn</b> Loads the dark image to the detector from file fn (pedestal image). Cannot get.</li>
-</ul>
-<ul>
-<li><b>gainimage fn</b> Loads the gain image to the detector from file fn (gain map for translation into number of photons of an analog detector). Cannot get. </li>
-</ul>
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-<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
-<a href="http://www.doxygen.org/index.html">
-<img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
+</div><!-- top -->
+<div class="header">
+  <div class="headertitle">
+<div class="title">Data processing commands </div>  </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><p>Commands to setup the data processing (mainly MYTHEN related)</p>
+<ul>
+<li><b>flatfield [fn]</b> <code>put</code> sets flatfield file to <code>fn</code> (relative to <code>ffdir</code>).  returns the flatfield file name relative to <code>ffdir</code> (string). If</li>
+<li><b>ffdir [d]</b> Sets/gets the directory in which the flat field file is located. <code>Returns</code> <code></code>(string) ffdir</li>
+<li><b>ratecorr [ns]</b> Returns the dead time used for rate correections in ns (int). <code>put</code> sets the deadtime correction constant in ns, -1 will set it to default tau of settings (0 unset). <code>Returns</code> <code></code>(double with 9 decimal digit precision)</li>
+<li><b>badchannels [fn]</b> <code>put</code> sets the badchannels file to <code>fn</code> .  returns the bad channels file name. If</li>
+<li><b>angconv [fn]</b> <code>put</code> sets the angular conversion file to <code>fn</code> .  returns the angular conversion file name. If</li>
+<li><b>globaloff [f]</b> Sets/gets the beamline angular global offset (float).</li>
+<li><b>fineoff [f]</b> Sets/gets the angular fine offset of the measurement (float).</li>
+<li><b>binsize [f]</b> Sets/gets the bin size used for the angular conversion (float).</li>
+<li><b>angdir [i]</b> Sets/gets the angular direction. 1 means increasing channels number as increasing angle, -1 increasing channel number decreasing angle.</li>
+<li><b>moveflag [i]</b> Sets/gets the flag for physically moving the detector during the acquisition of several positions. 1 sets (moves), 0 unsets.</li>
+<li><b>samplex [f]</b> Sets/gets the sample displacement in th direction parallel to the beam in um. Unused!</li>
+<li><b>sampley [f]</b> Sets/gets the sample displacement in th direction orthogonal to the beam in um. Unused!</li>
+<li><b>threaded [i]</b> Sets/gets the data processing threaded flag. 1 is threaded, 0 unthreaded.</li>
+<li><b>darkimage fn</b> Loads the dark image to the detector from file fn (pedestal image). Cannot get.</li>
+<li><b>gainimage fn</b> Loads the gain image to the detector from file fn (gain map for translation into number of photons of an analog detector). Cannot get. </li>
+</ul>
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