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

@@ -1,10 +1,13 @@
+### Documentation
+Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
+
 ### Binaries
-Documentation to obtain the binaries via the conda package is available [here.](https://github.com/slsdetectorgroup/sls_detector_software)
+Documentation to obtain the binaries via the conda package is available for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
 
 ### Source code
 One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
 ```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 3.0.1
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Setup dependencies 
@@ -16,7 +19,7 @@ Requirements: Qt 4.8 and Qwt 6.0
 ```
 If either of them does not exist, the GUI client will not be built.
 
-* Calibration wizards<br>
+* Advanced user Calibration wizards<br>
 Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
@@ -40,6 +43,10 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
  * -r: Build/Rebuilds only receiver<br>
  * -g: Build/Rebuilds only gui<br>
  * -j: Number of threads to compile through<br>
+ * -e: Debug mode
+ 
+Basic Option:
+./cmk.sh -b
  
 For only make:
 ./cmk.sh
@@ -80,5 +87,5 @@ After compiling, the libraries and executables will be found at `bin` directory
 ```
     $ ls bin/
     gui_client  libSlsDetector.a  libSlsDetector.so  libSlsReceiver.a  libSlsReceiver.so
-    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver
+    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver slsMultiReceiver
 ```

RELEASE.txt

@@ -1,350 +1,508 @@
-SLS Detector Package 3.0.1 released on 2018-02-12
+SLS Detector Package 4.0.0 released on 27.09.2018
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.0.0 and 3.0.1 release.
+	This document describes the differences between 4.0.0 and 3.1.4 releases.
 
-The conda package of the binaries can be downloaded from
+	Download
+	--------
 	
-	https://github.com/erikfrojdh/sls_detector_software.git
+	The Source Code (Default C++ API):
+		 https://github.com/slsdetectorgroup/slsDetectorPackage
 		 
-The conda package of the python API wrap-around to the software package is at 
+	The Conda Lib Package:
+		https://github.com/slsdetectorgroup/sls_detector_lib
 		
-	https://github.com/slsdetectorgroup/sls_detector.git
+	The Conda GUI Package:
+		https://github.com/slsdetectorgroup/sls_detector_gui	
 		
-Manual (both HTML and pdf versions) are provided in
+	The Python Interface (including the package):
+    	https://github.com/slsdetectorgroup/sls_detector
 	
-	manual/docs/
 	
-Documentation from Source Code can be found for the Command Line and C++ API in
+	Documentation
+	-------------
 	
-	html:
+	Manual (HTML & PDF):
+		https://www.psi.ch/detectors/documentation
+		slsDetectorPackage/manual/docs/
+		
+	Command Line Documentation:
 		manual/docs/html/slsDetectorClientDocs/index.html
-		manual/docs/html/slsDetectorUsersDocs/index.html
-	pdf:
 		manual/docs/pdf/slsDetectorClientDocs.pdf
+		
+	C++ API Documentation:
+		manual/docs/html/slsDetectorUsersDocs/index.html
 		manual/docs/pdf/slsDetectorUsersDocs.pdf
 		
-Documentation to the python API is available at
+	C++ API Example:
+		manual/manual-api/mainClient.cpp
+		manual/manual-api/mainReceiver.cpp
 		
+	Python API Documentation:
 		https://slsdetectorgroup.github.io/sls_detector/
 		
-Example including binaries for detector and receiver user classes can be found in 
-
-	manual/manual-api
-	
-User documentation can also be accessed directly at this location:
-
+	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
-=====================
+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.
 		
-	Gotthard
-	========   
-    Minimum compatible version	: old one
-    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				: 21
-        
-    -Can be upgraded remotely via bit files.
-    
-        
-    Jungfrau
-    ========       
-    Minimum compatible version	: 13.11.2017
-    Latest version				: 13.11.2017
-
-    -Can be upgraded remotely via sls_detector_put programfpga <pof>.
-	 
-
-
-Changes in User Interface
-========================= 
-	
+2. Changes in User Interface
+============================
 	
 	Client
 	------
-	1.	Additional functions added for advanced users in users class:
-		(setSpeed, setClockDivider, setReadOutFlags, setDac, getADC, 
-		setAllTrimbits, startReceiver, stopReceiver,
-		startAcquisition non blocking, setReceiverSilentMode, setHighVoltage,
-		enableDataStreamingToClient, enableDataStreamingFromReceiver, 
-		setReceiverDataStreamingOutPort, setClientDataStreamingInPort)
 	
-	2.	Zmq set up for client and receiver are separated.
-		zmqport for client and rx_zmqport for receiver. By default, they are the
-		same for the slsDetectorGui to work.
+	1.	Shared Memory:
 	
-	3. 	Users example also works without config file, where detector already
-		configured in shared memory.
+		POSIX shared memory has been implemented and they are typically created in
+		/dev/shm/ folder.
 		
-	4. 	Use "sls_detector_get busy 0" to clear acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
+		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]
 		 	
-	5. 	Set bit, clear bit, read register and write register cannot give -1 for
-		inconsistent values from multiple detectors. One has to check error from 
-		API or read the values individually.
+		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.
 		
-	6. 	multiSlsDetector::char* getSettingsFile() function signature has been 
-		changed to string getSettingsFile().
+		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
 	--------
-	7.	Modified the help manaual/main-api/mainReceiver.cpp to make it more
-		robust (handling child process exit) and flexible to determine upon 
-		start up the number of receivers (child processes), the start TCP port 
-		and whether to call back data.
 	
-		detReceiver is now executed with [start tcp port] [number of receivers]
-		[1 for call back, 0 for none] as arguments. 
-		By default, start tcp port is 1954, number of receivers	is 1, and call
-		back is initiated.
+	1.	Reciever Header Structure in file writing and call back:
 	
-	8.	rx_datastream to enable/disable data streaming in receiver. Using the GUI
-		or registering data call back in client automatically enables zmq in 
-		receiver and client. "externalgui" is removed from the command line. Use
-		this command instead.
+		sls_receiver_header structure added to sls_receiver_defs.h for image headers 
+		in file writing. 
 		
-	9.	Rx_tcpport argument to the slsReceiver can be given using -t. 
-		Eg. slsReceiver -t1955
+		#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.
 		
 		
-New Features
-============
+	2.	ZmqSocket class:
+	
+		If one uses ZmqSocket.h, then the json header has to be parsed outside 
+		the class to allow the user to remove the restriction in extracting all data
+		from the json header.
 
 
-	Package
-	-------
-	1.	In addition to the C++ API, the Python API is also now provided.
+	3.	Receiver Call back with modified size:
 	
-	2. 	CMAKE now with debug flag and rpath, show warnings, compile only certain 
-		components (such as receiver or gui)
+		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.
 
-	3. 	One repository for entire package and made available at github.
+		This also means that the call back is now called before writing to file.
 
-	4. 	One can do --version or -v to all the binaries to find out the release
-		version of the particular executable.
 
-	5. 	All the software version numbers have only date in format YYMMDD.
 
+3. New/Modified Commands 
+========================
 	
 	Client
 	------
-	6. 	Parallelized more commands to detector. Beneficial for large detectors.
-		(setTimer, setFileIndex, setOnline, setReceiverOnline, getReceiverStatus,
-		resetFramesCaught, setFrameIndex, setFileName, getFramesCaughtByReceiver,
-		setDynamicRange, setRateCorrection)
 
-		Option to also use "sls_detector_put threaded 0" to improve speed by 
-		eliminating progress display during acquisition. Effective only for 
-		large detectors.
+	1.	add (modified): 
+		appends detector to end of multi detector list.
 
+	2.	replace: 
+		sets hostname/ip address for a single detector.
 
-	Detector Server
-	---------------
-	7.	(Eiger) Virtual class to execute on pc.
+	3.	user: 
+		get user details from shared memory.
 
-	8. 	One can now read temperatures during acquisition. It goes via the stop
-		server.
+	4.	checkdetversion: 
+		checks client version compatibility with detector server.
 
-	9.	(Jungfrau) One can start server in "debug" mode and then program the
-		new firmware via software command "sls_detector_put programfpga xx.pof".
-		
-	10.	(Jungfrau) Server can exit on start up if either the firmware or the 
-		server is incompatible with each other.
-	
-	11.	(Jungfrau) One is able to set transmission delay (ms) of image for each
-		individual detector using "txndelay_frame" command. Beneficial for 
-		large detectors.
-		
-	12.	(Jungfrau) One can set a threshold temperature (temp_threshold) and 
-		enable the temperature control feature (temp_control). When the 
-		temperature (temp_fpga) overshoots the threshold temperature, it will
-		set the temperature event (temp_event) and power off the chip. One must
-		then switch off the detector and check cooling. Switching back on starts
-		with defaults.
-		
-	13.	(25um Gotthard) Added start acquisition delay to master module.
-	
-	14. (Gotthard) New constraints include minimum exposure time is 186 ns and
-		minimum period is 1278 ns + current exposure time.
+	5.	checkrecversion: 
+		checks client version compatibility with receiver server.
 		
 	
 	Receiver
 	--------
-	14. The detectorip and rx_udpip does not have to be in the same subnet anymore.
-		Add the following commands after rx_hostname in config file to overwrite
-		mac configuration:
-		rx_udpmac [router mac]
-		configuremac 0 
 	
-	15.	Added silent mode to receiver using command r_silent [i] from client. 
-		It might be beneficial for max frame rate applications.
+	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.
 	
-	16.	Receiver print out can handle black or white backgrounds.
+	2.	zmqip: 
+		sets/gets the zmq (TCP) ip, where client listens to, to reconstuct images. 
+		(Eg. from receiver or intermediate process). By default, it is the same 
+		as rx_zmqip.
 	  		 	
-	17.	zmq package included updated to v4.0.8.
+	3.	rx_jsonaddheader:
+		sets/gets additional json header to be streamed out with the zmq from 
+		receiver. Default is empty. Eg. p rx_jsonaddheader \"what\":\"nothing\"
 		
-	18.	Zmq streaming from receiver also sends file index in json header.
+	4.	r_discardpolicy:
+		sets/gets the frame discard policy in the receiver. 
+		nodiscard - no discard (default), 
+		discardempty - discard only empty frames, 
+		discardpartial - discard any partial frame(fastest)
+		
+	5.	r_padding:
+		sets/gets the frame padding in the receiver. 
+		0 does not pad partial frames(fastest), 
+		1 (default) pads partial frames.
+		One can look at bitmask in the sls_receiver_header to process the unpadded
+		partial	frames later.
+		
+	6.	activate (modified):
+		Extra option added to pad or unpad images in receivers when deactivated.
+		activate i [padding option], where i is activate/deactivate	and padding 
+		option is "padding" (default) or "nopadding".
+		
+	7.	rx_udpsocksize:
+		sets/gets the UDP socket buffer size. Already attempts to set by default 
+		to 100mb, 2gb for Jungfrau. Does not remember custom values	in client 
+		shared memory, so must be initialized each time after setting receiver 
+		hostname in config file.
+		
+	8.	rx_realudpsocksize:
+		gets the actual UDP socket buffer size. Usually double the set udp socket 
+		buffer size due to kernel bookkeeping.
+	
+	9.	r_framesperfile:
+		sets/gets the frames per file in receiver. 0 means infinite or all frames 
+		in a single file. Default of Eiger changed from 2k to 10k.
+		
+
+	Eiger Specific
+	--------------
+	
+	1.	status trigger:
+		To trigger internally via software, one can use "status trigger".
+		
+	2.	subdeadtime:
+		sets/gets sub frame dead time in s in 32 bit mode. Subperiod is	set in 
+		the detector by subexptime + subdeadtime. This value is	normally a 
+		constant set by an expert catered to individual detector modules in the 
+		config file. Receiver files writes master file metadata subperiod 
+		instead of subdeadtime.
+		
+	3.	gappixels:
+		enables/disables gap pixels in system (detector & receiver). 1 sets, 
+		0 unsets. In Receiver, 4 bit gap pixels mode is not implemented, but is 
+		implemented in client data call back. Gap pixels are at module level 
+		and not at multi module level.
+				
+	4.	measuredperiod:
+		gets the measured frame period (time between last frame and the	previous 
+		one) in s. Makes sense only for acquisitions of more than 1 frame.
+		
+	5.	measuredsubperiod:
+		gets the measured subframe period (time between last subframe and the 
+		previous one) in s in 32 bit mode.
+
+	6.	flags(modified):
+		extra flags "nooverflow" (default) and "overflow" for sub images in	32 
+		bit mode. If set to overflow, it will set MSB of pixel data high if 
+		there was any saturation in any of the sub images 32 bit mode.
+		
+				
+	Jungfrau Specific
+	-----------------
+	
+	1.	storagecells:
+		sets/gets number of additional storage cells per acquisition. For very 
+		advanced users only. Range: 0-15. Default: 0. 
+		The #images = #frames * #cycles * (#storagecells +1).
+		
+	2.	storage_start:
+		sets/gets the storage cell that stores the first acquisition of the	series. 
+		For very advanced users only. Range: 0-15. Default: 15(0xf).  
+
+
+
+4. Other New Features
+=====================
+
+	Client
+	------
+	
+	1.	(Jungfrau & Gotthard) Settingsdir and caldir is removed from config file.
+		Default dacs are stored in detector server. Hence, these folders
+		are also removed from slsDetectorPackage/settingsdir. Eiger and Mythen 
+		continue to have them.
+		
+	2.	Depending on 1d position of detectors and detsizechan in config file,
+		row and column (previously xcoord and ycoord) are given to detector 
+		servers (Eiger and Jungfrau) to encode into the udp header.
+		
+	3.	(Eiger) Setting threshold energy changes such as CAL dac is irrelevant 
+		when interpolating between two energies and VRS dac is interpolated, not copied.
+		
+	4.	Users API updated with the following functions:
+		-	setReceiverFramesDiscardPolicy
+		-	setReceiverPartialFramesPadding
+		-	setReceiverFramesPerFile
+		-	sendSoftwareTrigger
+		-	setSubFrameExposureDeadTime
+		-	setSubFrameExposureTime
+		-	enableGapPixels
+		-	getMeasuredPeriod
+		-	getMeasuredSubFramePeriod
+		-	setOverflowMode
+		-	setNumberOfStorageCells
+		-	setStoragecellStart
+		-	setThresholdEnergy (overloaded)
+		-	resetFramesCaughtInReceiver
+		-	setReceiverFifoDepth
+		-	setFlowControl10G
+		-	setTenGigabitEthernet
+		-	getNMods
+		-	setReceiverDataStreamingOutIP
+		-	setClientDataStreamingInIP
+		
+	SlsReceiver
+	-----------
+	
+	1.	slsMultiReceiver executable added that creates multiple receiver child processes.
+		./slsMultiReceiver [start_tcp_port] [num_receivers] [1 for call back, 0 for none]
+		
+	2.	Default row and column (previously xcoord and ycoord) are hardcoded 
+		for missing packets. (Eiger and Jungfrau)
 		
 
 	Gui
 	---
-	18.	If acquisition is done, but "stop dummy packet" to the gui was lost in 
-		the network, stop acquisition command will restream it so that the gui
-		doesnt hang forever. This is used only for very fast detectors like 
-		Moench.
+	
+	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 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.
 
 
 
-Resolved Issues
+
+5. Resolved Issues
+==================
+
+	Client
+	------
+	memory leak for multi threading
+	
+	1.	Compiler flag -std=c++98 enforced. Debug flag removed.
+	
+	2.	If trimen gives different list from different detectors, it returns a -1.
+	
+	3.	Version format for each submodule of the package changed to just date YYMMDD.
+		Users class fixed to give correct version, instead of -1.
+		
+	4.	Getting settings in users class gave -1. Fixed now.
+
+	5.	(Jungfrau) Programming FPGA now creates the rawbin file from pof in tmp
+		rather than source file location (for permission issues).
+		
+	6.	(Gotthard) ROI segmentation fault fixed.
+		
+	Receiver
+	--------
+	
+	1.	Silent feature of receiver fixed.
+	
+	2. 	Socket descriptor misused earlier for success flag, instead exceptions
+		used that are handled inside the package.
+
+	3.	Global optind variable initialized to instantiate multiple receivers 
+		in same process. Also removed static members to enable this feature.
+		
+	4.	Socket buffer size attempts to set for each acquiistion and provide
+		warning if no capabilities. Warnings can be removed using instruction with
+		error provided. Default Jungfrau UDP socket buffer size if 2 GB, default is 
+		100 MB.
+		
+	5.	Refactored code a bit for performance and robustness, blocking push 
+		in buffer between listener and dataprocessor
+
+	
+	Detector Server
+	---------------
+	
+	1.	(Jungfrau) Stop server also mapped during a reset. Reading power status
+		instead of user input register for power.
+	
+	2.	(Eiger) Bug fix for saving trimbits to file (Advanced users).
+	
+	3.	(Gotthard 25um) config.txt is not read again after detector startup,
+		no matter the number of times the detector server is restarted. 
+
+	
+6. Known Issues
 ===============
 
+	Receiver
+	--------
 	
-	Client
-	------
-	1. 	gethostbyname used in connecting to sockets was not thread safe for 
-		multiple detectors. Using getaddrinfo for stability in multi threaded
-		environment.
-	
-	2. 	Updated writing content of config and parameter dump into files.
-	
-	3. 	More locking to handle main and processing threads using the threadpool.
-		Removing unlock twice, which is undefined behavior.
+	1. 	HDF5 compression and filters are not implemented yet.
 	
 	
 	Detector Server
 	---------------
-	4. 	(Eiger) The hardware MAC of the detector is used during configuration 
-		and relayed  back to client. Similarly, hardware IP for 1 Gbe data mode.
 	
-	5. 	(Eiger) Status will return error if there was the unlikely trouble 
-		reading status register in the front end board. Earlier, it would only 
-		return idle.
+	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.
 		
-	6.	(Jungfrau) patch server v3.0.0.6.3
-		Able to set settings, high voltage now correctly reads 0 when 
-		switched off, dacs are properly set.
-			
-	7. 	(Jungfrau) FPGA reset and programming FPGA firmware via software is done
-		properly
-		
-	8. 	(Gotthard) patch server v3.0.0.5.1
-		Able to read temperature properly.
-		
-	9. 	(Gotthard) butst mode if set too fast had unwanted behavior such as 
-		sending same image continuously. Now it is handled to display error
-		and stop acquisition.
-		
-	10.	(Gotthard) completely removed the possibility to set timing modes 
-		other than auto and trigger as they are not implemented anyway. Also
-		signal index 1, 2 and 3 are reserved and hence, cannot be configured for
-		an external trigger.
-		
-	11.	Non Mythen and non Eiger detectors can also now get settings file from 
-		board.
-		
-	12. (Gotthard) Did not get first few images initially after configuring MAC
-		of detector. Fixed.
-	
-	
-	Receiver
-	--------
-	12.	Made it easier to disable the standard receiver and fixing bugs related 
-		to the use of a custom one. 
-		
-	13.	(Jungfrau) HDF5 dimensions (npixelsY) required for mapping fixed.
-	
-	14.	patch2-v3.0.0-slsReceiverSoftware.patch
-		x, y and z coordinates in the call backs and the files are hardcoded 
-		for this release. 
-		
-	15.	Rest implementation (not used by standard receiver) removed.
-
-	
-	Gui
-	---
-	16.	patch1-v3.0.0-slsDetectorGui.patch
-		(Eiger) In expert mode and in advanced tab, when trimbits 
-		loaded are different for every pixel, the gui complains and sets 
-		all trimbits to zero. This has been resolved. Now, the "Set All 
-		Trimbits" field is just set to -1.
-		
-	17.	Fixed segmentation fault of xputsn properly.
-	
-	18.	Upon clicking on "Start", clears acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
-		
-	19.	Fixed plotting twice caused due to unzooming the first time.
-	
-	20.	Removed option for compression in Gui as it is not available currently.
-	
-	21. Can also show Jungfrau multi detector in x direction in gui.
-	
-	22. Switching tabs sometimes results in delay and gates fields being incorrectly
-		enabled. Fixed.
+	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.
 	
 	
 	
-Known Issues
-============
-
+7. Next Major Release Plans
+===========================
 
 	Client
 	------
-	1.	File name prefix can only be done at multi deector level. Changing at 
-		individual detector level will not include scan or position variables.
-
-	
-	Detector Server
-	---------------
-	2.	Standard header fills x-coord in 1D. y-coord and z-coord is not 
-		implemented (3D).
-
-
-	Receiver
-	--------
-	3. 	HDF5 compression and filters are not implemented yet.
 	
+	1.	Exceptions thrown to the user to be handled.
 	
+	2. 	Compilation using c++11.
 	
+	3.	Support of Mythen II restricted to this major and its minor releases.
 	
+	4.	Restructuring and refactoring of client code. 
 
 
 

cleansharedmemory.sh

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

cmk.sh

@@ -6,6 +6,7 @@ COMPILERTHREADS=0
 TEXTCLIENT=0
 RECEIVER=0
 GUI=0
+DEBUG=0
 
 
 CLEAN=0
@@ -24,6 +25,7 @@ Usage: $0 [-c] [-b] [-h] [-d <HDF5 directory>] [-j]
  -r: Build/Rebuilds only receiver
  -g: Build/Rebuilds only gui
  -j: Number of threads to compile through
+ -e: Debug mode
  
 For only make:
 ./cmk.sh
@@ -53,7 +55,7 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bchd:j:trg" opt ; do
+while getopts ":bchd:j:trge" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -91,6 +93,10 @@ while getopts ":bchd:j:trg" opt ; do
 		GUI=1
 		REBUILD=1
 		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
+		;;    
     \?)
      	echo "Invalid option: -$OPTARG" 
 		usage
@@ -145,7 +151,12 @@ else
 	fi
 fi
 
+#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/WARNINGS

@@ -0,0 +1 @@
+No implementation found for style `graphicx'

manual/docs/html/angularCalibrationHowTo/angularCalibrationHowTo.css

@@ -0,0 +1,30 @@
+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH    { font-family: "Century Schoolbook", serif; }
+.MATH I  { font-family: "Century Schoolbook", serif; font-style: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY		{ font-size : xx-small }
+SMALL.TINY		{ font-size : x-small  }
+SMALL.SCRIPTSIZE	{ font-size : smaller  }
+SMALL.FOOTNOTESIZE	{ font-size : small    }
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+BIG.XXLARGE		{ font-size : x-large  }
+BIG.HUGE		{ font-size : larger   }
+BIG.XHUGE		{ font-size : xx-large }
+
+/* heading styles */
+H1		{  }
+H2		{  }
+H3		{  }
+H4		{  }
+H5		{  }
+
+/* mathematics styles */
+DIV.displaymath		{ }	/* math displays */
+TD.eqno			{ }	/* equation-number cells */
+
+
+/* document-specific styles come next */

manual/docs/html/angularCalibrationHowTo/angularCalibrationHowTo.html

@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Angular calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Angular calibration wizard manual">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
+
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+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html6"
+  HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A> 
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+ SRC="file:/usr/share/latex2html/icons/prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html7"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Angular calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html8"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html9"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html10"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html11"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html12"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html13"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html14"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2018-09-28
+</ADDRESS>
+</BODY>
+</HTML>

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manual/docs/html/angularCalibrationHowTo/images.tex

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+\batchmode
+\documentclass{article}
+\RequirePackage{ifthen}
+
+
+\usepackage{amssymb}
+\usepackage[dvips]{graphicx}
+\usepackage{verbatim}
+
+
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+
+
+\pagecolor[gray]{.7}
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+
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+{\newpage\clearpage
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+{\newpage\clearpage
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+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline106}%
+$_6$%
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+\lthtmlpictureA{tex2html_wrap344}%
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+\lthtmlpictureA{tex2html_wrap348}%
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+\stepcounter{section}
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manual/docs/html/angularCalibrationHowTo/index.html

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+
+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Angular calibration wizard manual</TITLE>
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+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
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+  HREF="node1.html">
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+ SRC="file:/usr/share/latex2html/icons/prev_g.png">   
+<BR>
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+<P>
+
+<H1 ALIGN="CENTER">Angular calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html8"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html9"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html10"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html11"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html12"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html13"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html14"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2018-09-28
+</ADDRESS>
+</BODY>
+</HTML>

manual/docs/html/angularCalibrationHowTo/internals.pl

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+
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+
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+
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+

manual/docs/html/angularCalibrationHowTo/labels.pl

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+# LaTeX2HTML 2012 (1.2)
+# Associate labels original text with physical files.
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+
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+
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+1;
+

manual/docs/html/angularCalibrationHowTo/node1.html

@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
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+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+In order to convert from strip number to 2<IMG
+ 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>
+<P>
+For this purpose, a series of patterns of a powder standard with symmetric peaks (e.g. silicon) must acquired while shifting the detector by an angular step of the order of about 2% of the module size. During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position.
+<BR>
+<P>
+In a first step, the   peak is fitted with a Gaussian in order to determine its position <IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$C_{peak}$"> in channel number for each of the acquired patterns.
+<BR>
+In a second step, for each module <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$">, the encoder position  <IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img4.png"
+ ALT="$\Theta_e$"> is fitted as a function of the peak position  <IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$C_{peak}$"> according to:
+<BR>
+<DIV ALIGN="RIGHT">
+
+<!-- MATH
+ \begin{equation}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
+\end{equation}
+ -->
+<TABLE WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE"><TD ALIGN="CENTER" NOWRAP><A NAME="eq:angcal"></A><IMG
+ WIDTH="291" HEIGHT="41" BORDER="0"
+ SRC="img5.png"
+ ALT="\begin{displaymath}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
+\end{displaymath}"></TD>
+<TD WIDTH=10 ALIGN="RIGHT">
+(1)</TD></TR>
+</TABLE>
+<BR CLEAR="ALL"></DIV><P></P>
+where the parameters <IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$\Theta_o^i$"> is the angular offset with respect to the diffractometer zero position, <!-- MATH
+ $C_{center}^{i}$
+ -->
+<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="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"
+ SRC="img3.png"
+ ALT="$i$"> from the diffractometer center while <IMG
+ WIDTH="79" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img9.png"
+ ALT="$p=50~\mu m$"> is the strip pitch of the detector. 
+<BR>
+Finally, the global offset of the detector system is precisely determined by refining a silicon pattern at a well-defined energy (i.e., knowing the position of the peak).
+
+<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="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$\theta$">-angle.
+
+<P>
+The parallax at the borders of the modules due to the thickness of the silicon sensor is a function of the X-ray energy (higher energy X-rays are absorbed deeper inside the sensor) and is of the order of 0.2&nbsp;mdeg at 12&nbsp;keV and 0.5&nbsp;mdeg at 30&nbsp;keV. 
+<BR>
+The differences in pixel size due to the different portion of solid angle covered by the strips on the border of the modules and  the higher efficiency due to the longer path of the X-rays in the sensor are removed by the flat field correction. This also normalizes additional differences in pixel size between channels which are also present because of mismatches in the strip sensor fabrication and in fluctuations of the channels threshold level.
+
+<P>
+Patterns acquired at different detector positions are generally merged together  in order to fill the gaps between the modules and correct possibly bad functioning channels. In this procedure the data from different positions which are closer than 4&nbsp;mdeg (the average pixel size) are averaged and the new position is set to the mean of the positions of the original points.
+
+<P>
+The position and width of the peaks results from a fit over several detector channels. Geometrical distortions might disturb this determination mainly because of errors in the angular calibration, fluctuations in the encoder position, variations between channels and parallax effects.
+<BR>
+The resolution in locating the peak center and determining its width and integrated intensity has been estimated by acquiring several patterns of a LaB<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$_6$"> sample in a 300&nbsp;<IMG
+ WIDTH="14" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img11.png"
+ ALT="$\mu$">m capillary with the detector shifted in 5&nbsp;mdeg steps between 30.4 and 36.5 degrees. The 16&nbsp;peaks acquired have been fitted with a Gaussian function plus background and the fluctuations on the fitted parameters have been calculated. The resulting average resolutions are  0.63<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">0.06&nbsp;mdeg for the peak center and 0.22<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">0.05&nbsp;mdeg for the peak Full-Width at Half-Maximum (FWHM) for an average peak FWHM of 27.0<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">2.5&nbsp;mdeg. 
+<BR>
+These results show that  the angular calibration allows a resolution in determining the peaks position and width which is appropriate for structural determination.
+
+<P>
+<HR>
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
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+  HREF="node1.html">Introduction</A>
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+<BR>
+<!--End of Navigation Panel-->
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+
+<UL>
+<LI><A NAME="tex2html35"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+
+<H1><A NAME="SECTION00020000000000000000">
+Data acquisition</A>
+</H1>
+
+<P>
+The angular calibration consists in acquiring a set of diffraction patterns of a well known powder standard (e.g. Silicon) at different encoder positions.  In order to facilitate the procedure, the sample should not emit fluorescent light and should present relatively symmetric peaks. 
+<BR>
+During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position. In general the highest peak will be used for the calibration, but this is not necessary in case there would be e.g. geometrical limitations for shifting the detector. 
+<BR><B>Do not forget to properly position the beam stopper if the detector is scanned in front of the direct beam.</B>
+<BR>
+The detector should be shifted of an angular step of the order of about 2% of the module size, such that about 50 patterns can contribute to the fitting of the 3 parameters necessary for the angular calibration.
+<BR>
+<P>
+All the angular calibration procedure should be acquired using a trimmed detector with the threshold set at half of the X-ray energy (Assuming no fluorescent element in the standard). A flat field should also be acquired in order to precisely correct the data, while the X-ray intensity should be kept lower than about 100&nbsp;kHz per strip in order to avoid the need for rate corrections.
+
+<P>
+A rough angular conversion file starting from a previous calibration or from the geometric characteristics of the mechanics is an advantage. The angular conversion file should contain a line for each module of the detector with its module number <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$">, center  <!-- MATH
+ $C_{center}^{i}$
+ -->
+<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$C_{center}^{i}$"> and error, conversion radius <IMG
+ WIDTH="38" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img13.png"
+ ALT="$p/R^i$"> and error, offset <IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$\Theta_o^i$"> and error:
+<PRE>
+module 0 center 639.5 +- 0 conversion 6.56E-05 +- 0 offset 0 +- 0
+</PRE>
+Also the <I>global offset</I> value of the beamline should be approximately known i.e. the angular position of channel 0 of module 0 when the motor is set at 0. 
+<BR>
+All the documentation assumes that the detector is oriented in the same direction as the encoder position i.e. large channel number at higher angles (both per module and absolute). If this is not the case, the <I>angular direction</I> should be set to -1. 
+
+<P>
+
+<H2><A NAME="SECTION00021000000000000000">
+Software</A>
+</H2>
+
+<P>
+For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.
+<BR>
+<P>
+Please make sure that you have edited the 
+<BR><I>slsDetectorSoftware/usersFunctions/angleFunction.h</I> 
+<BR>
+in order to match the angular conversion for your geometry and 
+<BR><I>slsDetectorSoftware/usersFunctions/usersFunctions.cpp</I> 
+<BR>
+in order to be able to move the detector and read out its position by using the slsDetector software.
+
+<P>
+In the following the command to acquire a dataset for the angular calibration with an exposure time of 1&nbsp;s, and position shift 
+<PRE>
+#setup angular calibration log mode
+&gt; sls_detector_put angcallog 1 
+#set exposure time to 1s
+&gt; sls_detector_put exptime 1. 
+#setup threshold scan
+&gt; sls_detector_put scan0script position 
+#setup the precision for the scan variable in the file name
+&gt; sls_detector_put scan0prec 2 
+#set scan range between 20deg and -60deg, step of -0.1deg
+# (at 12.4 keV the Si(111) peak is at approx 19deg
+&gt; sls_detector_put scan0range 20 -60 -0.1 
+#acquire the data
+&gt; sls_detector_acquire
+#unset angular calibration log mode
+&gt; sls_detector_put angcallog 0
+</PRE>
+
+<P>
+With the GUI you can obtain the same results by clicking on the <I>Angular calibration</I> log button in the advanced tab (see figure&nbsp;<A HREF="#fig:guiangcallog">1</A>) and setting up the motor position scan in the Actions tab (see figure&nbsp;<A HREF="#fig:guiposscan">2</A>). The exposure time should also be set in the measurement tab.
+
+<P>
+Additional to the data files, the acquisition will produce a .angcal file containing an header and, for each step of the acquisition, the exect value of the motor position and the file name. 
+<BR>
+In case you forgot to enable the angcallog flag in the software, you can produce the file with the syntax as follows, assuming that you know the exact values of your encoder for each frame:
+<PRE>
+type Mythen
+maxmod 32
+nmod 32
+angconv /scratch/angcal20120422/ang.off
+globaloff 5.088
+fineoff 0.0
+angdir 1
+ffdir /scratch/angcal20120422/
+flatfield flatfield_E12keV_T6keV_0.raw
+badchannels /scratch/cal/bad.chans
+19.99998 angcal_S20.00_0
+19.90001 angcal_S19.90_0
+19.79999 angcal_S19.80_0
+19.70002 angcal_S19.70_0
+......
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiangcallog"></A><A NAME="46"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 1:</STRONG>
+Acquisition GUI window to enable the angular calibration log.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img14.png"
+ ALT="\includegraphics[width=\textwidth]{enable_angcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiposscan"></A><A NAME="51"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 2:</STRONG>
+Acquisition GUI window to setup the motor position scan.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img15.png"
+ ALT="\includegraphics[width=\textwidth]{position_scan.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
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+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
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+  HREF="node2.html">Data acquisition</A>
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+<BR>
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+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
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+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+
+<H1><A NAME="SECTION00030000000000000000">
+Data analysis</A>
+</H1>
+
+<P>
+The data analysis consists in fitting with a gaussian the selected peak of the powder pattern for each position in order to determine its position is channel number as a function of the encoder position. 
+<BR>
+In a second step, for each module, the channel vs. encoder curve is fitted in order to extrapolate the three parameters necessary for the angular conversion and the result is written to file
+
+<P>
+
+<H2><A NAME="SECTION00031000000000000000">
+Software</A>
+</H2>
+
+<P>
+The software used for the angular calibration data analysis is based on root (see http://root.cern.ch).
+<BR>
+This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
+
+<P>
+To start the data analysis simply launch:
+<PRE>
+&gt; ./angularCalibrationWizard
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:setangcal"></A><A NAME="60"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 3:</STRONG>
+Overview of the nagular calibration dataset.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img16.png"
+ ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+To setup the angular calibration dataset, the .angcal file should be selected (or digited) and the load button should be pressed to confirm. The parameters of the angular calibration are then read to the file and the data loaded for a quick overview (see figure&nbsp;<A HREF="#fig:setangcal">3</A>).
+<BR>
+The software assumes that the data files (.raw) and the .encal file are in the same directory.
+<BR>
+A 2D color plot will show a rebinned overview of the dataset. The peak to be fitted should be visible as a high intensity diagonal line passing through all the channels.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:peakfit"></A><A NAME="66"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 4:</STRONG>
+Preview of the fitting of the Si(111) peak for one of the detector positions.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img17.png"
+ ALT="\includegraphics[width=\textwidth]{peakFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+For a more detailed view of the data, one can select an angular calibration step from the combo box, select the plot mode (raw data or processed data as a function of channel number, processed angular converted data, flat field data, or again an overview of the whole dataset). 
+<BR>
+By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.
+<BR>
+<P>
+If the bad channel list, angular conversion file or flat field file are changed compared to the acquisition, they can be reloaded by editing the correspondent text entries and pressing enter.
+
+<P>
+In particular, the angular converted data should be checked in order to view the position of the selected peak. In this case, the plot will be zoomed to the angular region slected in the minimum and maximum angle entries. By pressing fit, the fit of the peak in the selected angular range will be shown (see figure&nbsp;<A HREF="#fig:peakfit">4</A>).  It is useful to check that it works properly in several positions such that then the sequential fitting on all steps can give good results.
+
+<P>
+To automatically fit all positions simply press <I>Proceed to Modules Calibration</I> and wait until all steps are fitted. This can take sometime, depending on the number of steps.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:anglefit"></A><A NAME="73"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 5:</STRONG>
+Window for fitting the angular calibration parameters of a module.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img18.png"
+ ALT="\includegraphics[width=\textwidth]{angleFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+In the module calibration window (see figure&nbsp;<A HREF="#fig:anglefit">5</A>), you will be able to fit the channel number to encoder position curve to estimate the three angular calibration parameters for each module.
+<BR>
+The entries show the angular calibration parameters used for approximate angular conversion in the previous step of the calibration. These can be edited and will be used as start parameters for the fit.
+By clicking on the check box next to the parameters, the selected parameter will be set and fixed during the fit. Often the center is used as a fix parameter.
+<BR>
+It is possible to navigate between modules by using the Previous and Next module buttons. To refit the current module (e.g. after changing one of the parameters) simply re-click on the module number.
+
+<P>
+After fitting all modules you can click on the <I>Write Angular Calibration</I> button, select the file name to write to and save the calibration angulat calibration data. Please note that the offset of module 0 will always be 0 and the other values will be rescaled to its value. Therefore the global offset of the steup will always need to be specified for a proper angular conversion unless the home of the encoder will not be redifined.
+
+<P>
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+<!--End of Navigation Panel-->
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+<H1><A NAME="SECTION00040000000000000000">
+Setup calibration files</A>
+</H1>
+
+<P>
+To use the generated angular calibration files, using the text client:
+<PRE>
+sls_detector_put angconv /scratch/ang_new.off
+</PRE>
+while for the GUI the file name should be specified in the configuration file (works also for the text client).
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2018-09-28
+</ADDRESS>
+</BODY>
+</HTML>

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+</H1>
+ <STRONG>Angular 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 2012 (1.2)
+<P>
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+<BR>
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+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html11"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html12"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html13"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
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+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
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+  HREF="node3.html#SECTION00031000000000000000">Software</A>
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+  HREF="node5.html">About this document ...</A>
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+Thattil Dhanya
+2018-09-28
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+</BODY>
+</HTML>

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manual/docs/html/energyCalibrationHowTo/images.pl

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+ SRC="|."$dir".q|img32.png"
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+$key = q/O;MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img18.png"
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+$key = q/includegraphics[width=textwidth]{GUI_ThresholdScan.eps};AAT/;
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manual/docs/html/energyCalibrationHowTo/images.tex

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manual/docs/html/energyCalibrationHowTo/index.html

@@ -0,0 +1,84 @@
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+
+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Energy calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Energy calibration wizard manual">
+<META NAME="keywords" CONTENT="energyCalibrationHowTo">
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+
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+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html9"
+  HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html10"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html11"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html12"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html13"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html15"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html17"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2018-09-28
+</ADDRESS>
+</BODY>
+</HTML>

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manual/docs/html/energyCalibrationHowTo/node1.html

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+<!--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:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
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+<BR>
+<BR>
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+
+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+The choice of the level of the comparator threshold plays a very important role in counting systems since it influences the efficiency of the detector as well as its spatial resolution (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668).
+
+<P>
+Single-photon-counting detectors are sensitive to single photons and the only limitation on the fluctuations of the number of counts is given by the Poisson-like statistics of the X-ray quanta. 
+The digitized signal does not carry any information concerning the energy of the X-rays and all photons with an energy larger than the threshold are counted as one bit. This means that the choice of the correct comparator threshold level is critical in order to obtain good-quality data.
+<BR>
+Figure&nbsp;<A HREF="#fig:thrscanexpl">1</A> shows the expected number of counts as a function of the threshold energy for <IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$N_0$"> monochromatic X-rays of energy <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img1.png"
+ ALT="$E_0$">. This is often denominated  S-curve and can be interpreted as the integral of the signal spectrum between the threshold level and infinity.
+The dashed curve represents the behavior of an ideal counting system: nothing is counted for thresholds larger than the photon energy and all the <IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$N_0$"> X-rays are counted for thresholds lower than <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img1.png"
+ ALT="$E_0$">.
+The thick solid line represents the physical curve which also takes into account the electronic noise and the charge sharing between channels.
+
+<P>
+The intrinsic noise on the electronic signal  is defined by the Equivalent Noise Charge (<IMG
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$ENC$">). The <IMG
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$ENC$"> describes noise in terms of the charge at the detector input needed to create the same output at the end of the analog chain and is normally expressed in electrons. For silicon sensors, it can be converted into energy units by considering 1&nbsp;<IMG
+ WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
+ SRC="img12.png"
+ ALT="$e^-$">=3.6&nbsp;eV.
+The value of the <IMG
+ 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="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
+ WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="img13.png"
+ ALT="$D$"> with an additional increase at low threshold due to the baseline noise, as shown by the solid thin line. 
+
+<P>
+Moreover, when a photon is absorbed in the region between two strips of the sensor, the generated charge is partially collected by the two nearest electronic channels. For this reason the physical S-curve is not flat but can be modeled by a decreasing straight line. The number of shared photons  <IMG
+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img5.png"
+ ALT="$N_S$"> is given by the difference between the number of counts and the number of X-rays whose charge is completely collected by the strip (shown by the dotted line).
+
+<P>
+The number of counts in the physical case is equal to that in the ideal case for a threshold set at half the photon energy. This defines the optimal threshold level <IMG
+ WIDTH="78" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="img14.png"
+ ALT="$E_t=E_0/2$">.
+<BR>
+The detector response <IMG
+ WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="img15.png"
+ ALT="$N$"> as a function of the threshold energy <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$E_t$"> is given by the sum of the noise counts  <IMG
+ WIDTH="26" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="$N_n$"> and the counts originating from photons <IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img17.png"
+ ALT="$N_\gamma$">:
+<BR>
+<DIV ALIGN="RIGHT">
+
+<!-- MATH
+ \begin{equation}
+N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big),
+\end{equation}
+ -->
+<TABLE WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE"><TD ALIGN="CENTER" NOWRAP><A NAME="eq:thrscan"></A><IMG
+ WIDTH="335" HEIGHT="41" BORDER="0"
+ SRC="img18.png"
+ ALT="\begin{displaymath}
+N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big),
+\end{displaymath}"></TD>
+<TD WIDTH=10 ALIGN="RIGHT">
+(1)</TD></TR>
+</TABLE>
+<BR CLEAR="ALL"></DIV><P></P>
+where <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img19.png"
+ ALT="$C_s$"> is the fraction of photons which produce a charge cloud which is shared between neighboring strips (<IMG
+ WIDTH="83" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img20.png"
+ ALT="$N_s=C_s N_0$">).
+<BR>
+By assuming a noise of Gaussian type, and considering its bandwidth limited by the shaping time  <IMG
+ WIDTH="18" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="$\tau_s$">, the number of noise counts in the acquisition time <IMG
+ WIDTH="16" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="img22.png"
+ ALT="$T$"> can be approximated as:
+<BR>
+<DIV ALIGN="RIGHT">
+
+<!-- MATH
+ \begin{equation}
+N_n(E_t) \sim \frac{T}{\tau_s}  D \Big(\frac{-E_t}{ENC} \Big).
+\end{equation}
+ -->
+<TABLE WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE"><TD ALIGN="CENTER" NOWRAP><A NAME="eq:noisescan"></A><IMG
+ WIDTH="169" HEIGHT="41" BORDER="0"
+ SRC="img23.png"
+ ALT="\begin{displaymath}
+N_n(E_t) \sim \frac{T}{\tau_s} D \Big(\frac{-E_t}{ENC} \Big).
+\end{displaymath}"></TD>
+<TD WIDTH=10 ALIGN="RIGHT">
+(2)</TD></TR>
+</TABLE>
+<BR CLEAR="ALL"></DIV><P></P> 
+
+<P>
+The choice of the comparator threshold level <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$E_t$"> influences not only the counting efficiency and noise performances, but also the spatial resolution and the counting statistics of the detector. 
+If the threshold is set at values higher than the ideal value <IMG
+ WIDTH="78" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="img14.png"
+ ALT="$E_t=E_0/2$">, a fraction of the photons absorbed in the sensor in the region between two strips is not counted thus reducing the detector efficiency but improving its spatial resolution (narrower strip size). On the other hand, if the threshold is set at values lower than <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$E_t$">, part of the X-rays absorbed in the region between two strips are counted by both of them, resulting in a deterioration of the spatial resolution of the detector and of the fluctuations on the number of photons because of the increased multiplicity. 
+
+<P>
+Furthermore, the threshold uniformity is particularly critical with regards to fluorescent radiation emitted by the sample under investigation. Since the emission of fluorescent light is isotropic, the data quality will be improved by setting the threshold high enough in order to discard the fluorescence background (see figure&nbsp;<A HREF="#fig:thrscanfluo">3</A>). 
+<BR>
+Moreover, setting the threshold too close to the energy of the fluorescent light gives rise to large fluctuations between channels in the number of counts since the threshold sits on the steepest part of the threshold scan curve for the fluorescent background. These differences cannot be corrected by using a flat-field normalization  since the fluorescent component is not present in the reference image. For this reason, it is extremely important that the threshold uniformity over the whole detector is optimized. The threshold level must be set at least <IMG
+ WIDTH="88" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img24.png"
+ ALT="$\Sigma&gt;3\,ENC$"> away from both the fluorescent energy level and the X-ray energy in order to remove the fluorescence background while efficiently count the diffracted photons. 
+
+<P>
+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="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img25.png"
+ ALT="$O$"> and gain <IMG
+ 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"
+ SRC="img27.png"
+ ALT="$V_t$"> at the desired energy <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$E_t$">:
+<BR>
+<DIV ALIGN="RIGHT">
+
+<!-- MATH
+ \begin{equation}
+V_{t}=O+G \cdot E_t.
+\end{equation}
+ -->
+<TABLE WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE"><TD ALIGN="CENTER" NOWRAP><A NAME="eq:encal"></A><IMG
+ WIDTH="111" HEIGHT="26" BORDER="0"
+ SRC="img28.png"
+ ALT="\begin{displaymath}
+V_{t}=O+G \cdot E_t.
+\end{displaymath}"></TD>
+<TD WIDTH=10 ALIGN="RIGHT">
+(3)</TD></TR>
+</TABLE>
+<BR CLEAR="ALL"></DIV><P></P>
+This is initially performed by acquiring measurements while scanning the global threshold using different X-ray energies and calculating the median of the counts at each threshold value for each module <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img29.png"
+ ALT="$i$">. The curves obtained for one of the detector modules at three energies are shown in figure&nbsp;<A HREF="#fig:modulecalibration">4</A>. The experimental data are then fitted according to equation&nbsp;<A HREF="#eq:thrscan">1</A> and for each module a linear relation is found between the X-ray energy and the estimated inflection point, as shown in the inset of figure&nbsp;<A HREF="#fig:modulecalibration">4</A>. The resulting offset  <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="$O_i$"> and  gain <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img31.png"
+ ALT="$G_i$"> are used as a conversion factor between the threshold level and the energy. 
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:thrscanexpl"></A><A NAME="116"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 1:</STRONG>
+Expected counts as a function of a threshold energy for a monochromatic beam of energy <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img1.png"
+ ALT="$E_0$">=12&nbsp;keV. <IMG
+ 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="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="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img4.png"
+ ALT="$CS=$">22&nbsp;% charge sharing. <IMG
+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img5.png"
+ ALT="$N_S$"> is the number of photons whose charge is shared between neighbouring strips (<!-- MATH
+ $CS=\frac{N_S}{N_0}$
+ -->
+<IMG
+ WIDTH="71" HEIGHT="38" ALIGN="MIDDLE" BORDER="0"
+ SRC="img32.png"
+ ALT="$CS=\frac{N_S}{N_0}$">). The dotted line represents the number of photons whose charge is completely collected by a single strip.</CAPTION>
+<TR><TD><IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="img33.png"
+ ALT="\includegraphics[width=\textwidth]{fig4.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:expthrscan"></A><A NAME="117"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 2:</STRONG>
+Measured threshold scan at 12.5&nbsp;keV with the three different settings. In the inset the fit of the experimental data with the expected curve as in function&nbsp;<A HREF="#eq:thrscan">1</A> is shown in the region of the inflection point.</CAPTION>
+<TR><TD><IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="img34.png"
+ ALT="\includegraphics[width=\textwidth]{fig5.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:thrscanfluo"></A><A NAME="53"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 3:</STRONG>
+Number of counts as a function of the threshold measured from a sample containing iron (<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$E_f$">=5.9&nbsp;keV) when using X-rays of energy <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img1.png"
+ ALT="$E_0$">=12&nbsp;keV. In this case, setting the threshold at <IMG
+ WIDTH="39" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="img8.png"
+ ALT="$E_0/2$">, which is very close to <IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$E_f$">, would give <IMG
+ WIDTH="35" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="img9.png"
+ ALT="$\Delta \sim $">10% counts from the fluorescense background. Therefore the threshold should be set at an intermediate level <IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$E_t$"> between the two energy components with a distance of at least <IMG
+ WIDTH="85" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img11.png"
+ ALT="$\Sigma &gt;3ENC$"> from both <IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$E_f$"> and <IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img1.png"
+ ALT="$E_0$">.</CAPTION>
+<TR><TD><IMG
+ WIDTH="556" HEIGHT="553" ALIGN="BOTTOM" BORDER="0"
+ SRC="img35.png"
+ ALT="\includegraphics[width=\textwidth]{fig7.eps}"></TD></TR>
+</TABLE>
+</DIV>
+Differences in gain and offset are present also between individual channels within a module and therefore the use of threshold equalization techniques (trimming) using the internal 6-bit DAC is needed in order to reduce the threshold dispersion.
+Since both gain and offset have variations between channels, the optimal trimming should be performed as a function of the threshold energy.
+Please not that trimming of the channels of the detector should be performed in advanced and is extremely important for a succeful energy calibration of the detector.
+
+<P>
+All energy calibration procedures should be applied to a trimmed detector and only an improvement of the existing trimbits can be performed afterwards, since it does not significatively affect the energy calibration.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:modulecalibration"></A><A NAME="118"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 4:</STRONG>
+Median of the number of counts as a function of the threshold for X-rays of 12.5, 17.5 and 25&nbsp;keV for one of the detector modules using <I>standard</I> settings. The solid line represents the fit of the experimental points with equation&nbsp;<A HREF="#eq:thrscan">1</A>. In the inset the linear fit between the X-ray energy and the position of the inflection point of the curves is shown.</CAPTION>
+<TR><TD><IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="img36.png"
+ ALT="\includegraphics[width=\textwidth]{fig8.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+<HR>
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+Thattil Dhanya
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+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
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+<BR>
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+
+<UL>
+<LI><A NAME="tex2html38"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+
+<H1><A NAME="SECTION00020000000000000000">
+Data acquisition</A>
+</H1>
+
+<P>
+The energy calibration consists in acquiring threshold scans using the detector at at least 2 (better 3) energies. A monochromatic beam is ideal in this procedure, but beam obtained from some fluorescent sample is also good.
+<BR>
+Please note that the statistic is important to succesfully analyze the data. Normally the exposure time for each step should be chosen in order to achieve at least 1000 counts per step.
+If this is not possible it is better to reduce the scan range or enlarge the scan step rather than acquiring data with a too low statics.
+
+<P>
+With a quick acquisition or threshold scan it is useful to define the range of the scan and the exposure time. It is important to start from a threshold high enough that (almost) all channels of the detector have a negligible number of counts and that the plateau of the S-curve is long enough to correctly estimate the number of photons.
+
+<P>
+
+<H2><A NAME="SECTION00021000000000000000">
+Software</A>
+</H2>
+
+<P>
+For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.
+<BR>
+<P>
+In the following the command to acquire a dataset for the energy calibration with an exposure time of 1&nbsp;s, and threshold scan range between 200 and 850 with a setp of 1 DAC unit.
+<PRE>
+&gt; sls_detector_put encallog 1 #setup energy calibration
+&gt; sls_detector_put exptime 1. #set exposure time to 1s
+&gt; sls_detector_put scan0script threshold #setup threshold scan
+&gt; sls_detector_put scan0range 200 850 1 #set scan range between 200 and 850, step of 1
+&gt; sls_detector_acquire #acquire the data
+&gt; sls_detector_put encallog 0 #unset energy calibration
+</PRE>
+
+<P>
+With the GUI you can obtain the same results by clicking on the <I>Energy Calibration</I> log button in the advanced tab (see figure&nbsp;<A HREF="#fig:guiencallog">5</A>) and setting up the threshold scan in the Actions tab (see figure&nbsp;<A HREF="#fig:guithrscan">6</A>). the exposure time should also be set in the measurement tab.
+
+<P>
+This procedure should be executed at at least 2 (better 3) energies.
+
+<P>
+Additional to the data files, the acquisition will produce a .encal file containing an header and, for each step of the acquisition, the threshold value and the file name. 
+<BR>
+In case you forgot to enable the encallog flag in the software, you can produce the file with the syntax as follows:
+<PRE>
+settings standard
+type Mythen+
+nmod 12
+modulenumber:0 000
+modulenumber:1 111
+modulenumber:2 222
+modulenumber:3 333
+modulenumber:4 444
+modulenumber:5 555
+modulenumber:6 666
+modulenumber:7 777
+modulenumber:8 888
+modulenumber:9 999
+modulenumber:10 aaa
+modulenumber:11 bbb
+450 standard_12_4keV_S450_0
+460 standard_12_4keV_S460_0
+470 standard_12_4keV_S470_0
+480 standard_12_4keV_S480_0
+490 standard_12_4keV_S490_0
+500 standard_12_4keV_S500_0
+510 standard_12_4keV_S510_0
+520 standard_12_4keV_S520_0
+...
+...
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiencallog"></A><A NAME="73"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 5:</STRONG>
+Acquisition GUI window to enable the energy calibration log.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img37.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_Advanced.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guithrscan"></A><A NAME="78"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 6:</STRONG>
+Acquisition GUI window to setup the threshold scan.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img38.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+<HR>
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+  HREF="energyCalibrationHowTo.html">Energy calibration wizard manual</A>
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+
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+
+<H1><A NAME="SECTION00030000000000000000">
+Data analysis</A>
+</H1>
+
+<P>
+The data analysis consists in fitting the S-curves obtained from the datasets acquired as above and then performing a linear fit between the energy values and the inflection points.
+
+<P>
+
+<H2><A NAME="SECTION00031000000000000000">
+Software</A>
+</H2>
+
+<P>
+The software used for the energy calibration data analysis is based on root (see http://root.cern.ch).
+<BR>
+This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
+
+<P>
+To start the data analysis simply launch:
+<PRE>
+&gt; ./energyCalibrationWizard
+</PRE>
+
+<P>
+To add anew energy write the energy value and select (or digit) the name of the .encal file corresponding to that energy (see figure&nbsp;<A HREF="#fig:addenergy">7</A>).
+<BR>
+The software assumes that the data files (.raw) and the .encal file are in the same directory.
+Press  <I>Preview</I> and a 2D color plot will be displayed, showing the channel numbers on the X-axis, the threshold on the Y-axis, and the number of counts as a color scale.
+By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.
+<BR>
+If the plot corresponds to your expectations press <I>Add to list</I>. The energy value will be shown in the combo box on top and labels will display the settings of the detector, the number of modules, the number of channels per module and the modules serial numbers.
+
+<P>
+Add then all the other energies to the calibration always by editing the energy value and .encal file name, pressing <I>preview</I> and <I>add to list</I>.
+<BR>
+If the settings, number of modules or serial numbers do not match, you will not be llowed to add the energy.
+<BR>
+By using the <I>selected energy actions</I> you can navigate in the combo box with list of energies, view the plots and eventually remove the ones you don't want to use in your calibration.
+<BR>
+Once you have uploaded at least 2 energies, you will be allowed to  <I>proceed to module calibration</I>.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:addenergy"></A><A NAME="94"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 7:</STRONG>
+Window to add energies to the calibration.</CAPTION>
+<TR><TD><IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="img39.png"
+ ALT="\includegraphics[width=\textwidth]{addEnergy.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+In the module calibration window (see figure&nbsp;<A HREF="#fig:calibratemodule">8</A>), you are still able to look at the calibration summary, and eventually return to the previous windown by pressing <I>Back to energy setup</I>.
+<BR>
+The canvas will show the plot of the S-curves relative to the median of the selected module, fitted with equation&nbsp;<A HREF="node1.html#eq:thrscan">1</A> and the linear fit between the energy values and the fitted inflection points.
+Normally the points lie on a straight line (although often not perfect), therefore it should be simple to spot if there are problems in the fitting of some of the data.
+<BR>
+If <I>Manual save</I> is unclicked, the calibration files will be saved locally, with the extension automatically generated by using the modules serial numbers, every time a linear fit is performed (i.e. if you mess up wiht the linear fit you overwrite a previous good file!). If you click the checkbox, you need to save the calibration by pressing <I>Write to file</I> for each module once you are happy with the fit.
+
+<P>
+To change the Y scale of the plot, edit the <I>Counts</I> entry. After clicking of the energy button (eventually twice) the maximum of the histogram will be set to three times the value.
+
+<P>
+To re-fit one energy with modified range or start parameters, you should press the central button with the energy value once the energy is selected. The text color tells you which curve you are referring to.
+<BR>
+<P>
+You should set the range of the fit. In particular the maximum should be limited in order to avoid to enter the noise range (and can be pretty different for the various modules).
+<BR>
+Normally the data are acquired by collecting holes from the detector and therefore the <I>Invert axis</I> check button should be ckecked. Uncheck it in case your detector collects electrons (e.g. CdTe, Si n in p)
+
+<P>
+You can change the start values of the parameters of the fits by editing the number eneries. The label nearby will show you the actual value of the fitted parameters.
+<BR>
+By checking the checkboxes you can fix the values to the ones you specify.
+<BR>
+Normally it can be useful to fix the pedestal and pedestal slope to 0, unless you have a lot of 3rd armnonics contribution, primary beam background or similar.
+<BR>
+Changing the starting value of the inflection point or of the number of counts can often help the fit to converge.
+<BR>
+Normally it is not very useful to change the starting value for the noise or charge sharing slope.
+
+<P>
+The button <I>Finished</I> will be enebled only once the calibration files have been generated for all modules.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:calibratemodule"></A><A NAME="107"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 8:</STRONG>
+Window to calibrate the modules.</CAPTION>
+<TR><TD><IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="img40.png"
+ ALT="\includegraphics[width=\textwidth]{calibrateModule.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+<HR>
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+
+<H1><A NAME="SECTION00040000000000000000">
+Setup calibration files</A>
+</H1>
+
+<P>
+To use the genrated calibration files as default ones, copy them into your default <I>caldir/settings</I> renaming them calibration.snxxx, where snxxx is the extension that the genrated files already have, which corresponds to the module serial number.
+<BR>
+Fot this scope, a script as following can be used:
+<PRE>
+for i in $(ls newcal_standard.sn* | awk -F "." '{print $2}'); do \
+mv newcal_standard.$i caldir/standard/calibration.$i; \
+done
+</PRE>
+
+<P>
+By reloading the default detector settings, the calibration coefficients will be automatically loaded.
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2018-09-28
+</ADDRESS>
+</BODY>
+</HTML>

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+<H1><A NAME="SECTION00050000000000000000">
+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 2012 (1.2)
+<P>
+Copyright &#169; 1993, 1994, 1995, 1996,
+<A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>, 
+Computer Based Learning Unit, University of Leeds.
+<BR>
+Copyright &#169; 1997, 1998, 1999,
+<A HREF="http://www.maths.mq.edu.au/~ross/">Ross Moore</A>, 
+Mathematics Department, Macquarie University, Sydney.
+<P>
+The command line arguments were: <BR>
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+<div class="title">Acquition commands </div>  </div>
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+<div class="textblock"><p>Commands to control the acquisition</p>
+<ul>
+<li><b>acquire</b> blocking acquisition (like calling sls_detector_acquire). Starts receiver and detector, writes and processes the data, stops detector. Only get! <code>Returns</code> (string)<code>"acquire unsuccessful"</code> if fails, else "" for MYTHEN, <code>"Acquired (int)"</code> for others, where int is number of frames caught.</li>
+<li><b> busy i</b> sets/gets acquiring flag. <code>1</code> the acquisition is active, <code>0</code> otherwise. Acquire command will set this flag to 1 at the beginning and to 0 at the end. Use this to clear flag if acquisition terminated unexpectedly. <code>Returns</code> <code></code>(int)</li>
+<li><b> status [s] </b> starts or stops acquisition in detector in non blocking mode. When using stop acquisition and if acquisition is done, it will restream the stop packet from receiver (if data streaming in receiver is on). Eiger can also provide an internal software trigger. <code>s:</code> [<code>start</code>, <code>stop</code>, <code>trigger(EIGER only)</code>]. <code>Returns</code> the detector status: [<code>running</code>, <code>error</code>, <code>transmitting</code>, <code>finished</code>, <code>waiting</code>, <code>idle</code>]. <code>Returns</code> <code></code>(string)</li>
+<li><b>data</b> gets all data from the detector (if any) processes them and writes them to file according to the preferences already setup (MYTHEN only). Only get!</li>
+<li><b>frame</b> gets a single frame from the detector (if any) processes it and writes it to file according to the preferences already setup (MYTHEN only). Only get!</li>
+<li><b>readctr </b> Reads the counters from the detector memory (analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
+<li><b>resetctr i </b> Resets counter in detector, restarts acquisition if i=1(analog detector returning values translated into number of photons - only GOTTHARD). Cannot put.</li>
+<li><b>resmat i </b> sets/resets counter bit in detector.gets the counter bit in detector ???? </li>
+</ul>
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