Merge branch 'main-rc' into b3.1.0

among other fixes, this fixes the tmpnam warning

.gitignore

@@ -1,17 +1,11 @@
 .cproject
 .project
 bin/
-calibrationWizards/
-slsDetectorGui/
-slsDetectorSoftware/
-slsReceiverSoftware/
-slsDetectorCalibration/
-slsImageReconstruction/
 .settings
-JCTBGui/
 *.aux
 *.log
 *.out
 *.toc
 build
-tests
+docs/
+RELEASE.txt

CMakeLists.txt

@@ -1,21 +1,50 @@
 cmake_minimum_required(VERSION 2.8)
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+set (CALIBRATE OFF)
+
+option (USE_HDF5 "HDF5 File format" OFF)
+option (USE_TEXTCLIENT "Text Client" OFF)
+option (USE_RECEIVER "Receiver" OFF)
+option (USE_GUI "GUI" OFF)
+
+set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wno-misleading-indentation")
 
 find_package(Qt4)
 find_package(Qwt 6)
 find_package(CBF)
 find_package(Doxygen)
+find_package(PNG REQUIRED)
 
-add_subdirectory(slsDetectorSoftware)
-add_subdirectory(slsReceiverSoftware)
-add_subdirectory(slsImageReconstruction)
-if (QT4_FOUND AND QWT_FOUND)
-    add_subdirectory(slsDetectorGui)
-endif()
+if (USE_HDF5)
+	find_package(HDF5 1.10 COMPONENTS CXX)
+endif (USE_HDF5)
 
-if (DEFINED ENV{ROOTSYS})
-    find_package(ROOT)
-    if (ROOT_FOUND)
-        add_subdirectory(calibrationWizards)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+set(CMAKE_INSTALL_RPATH "$ORIGIN")
+set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+
+
+if (USE_TEXTCLIENT)
+       add_subdirectory(slsDetectorSoftware)
+endif (USE_TEXTCLIENT)
+
+if (USE_RECEIVER)
+       add_subdirectory(slsReceiverSoftware)
+endif (USE_RECEIVER)
+               
+if (USE_GUI)   
+       if (QT4_FOUND AND QWT_FOUND)
+       add_subdirectory(slsDetectorGui)
+       endif()
+endif (USE_GUI)
+
+
+if (CALIBRATE)
+    if (DEFINED ENV{ROOTSYS})
+        find_package(ROOT)
+        if (ROOT_FOUND)
+            add_subdirectory(calibrationWizards)
+        endif()
     endif()
-endif()
+endif(CALIBRATE)

Makefile

@@ -5,10 +5,11 @@ include Makefile.include
 
 INSTALLROOT	?=	$(PWD)
 BINDIR	?=	$(INSTALLROOT)/bin
-DOCDIR	?=	$(INSTALLROOT)/docs
+DOCDIR	?=	$(INSTALLROOT)/manual/docs
 LIBDIR	?=	$(INSTALLROOT)/bin
 INCDIR	?=	$(INSTALLROOT)/include
-
+DETAILDOC	?=	$(INSTALLROOT)/docs
+ 
 WD				=	$(shell pwd)
 LIBRARYDIR		=	$(WD)/slsDetectorSoftware
 LIBRARYRXRDIR 		= 	$(WD)/slsReceiverSoftware
@@ -19,7 +20,9 @@ CALWIZDIR		=	$(WD)/calibrationWizards
 MANDIR			=	$(WD)/manual
 CALIBDIR		=	$(WD)/slsDetectorCalibration
 
+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)
 
 INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM) 
@@ -27,14 +30,15 @@ INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM)
 
 $(info )
 $(info #######################################)
-$(info #    Compiling slsDetectorsPackage    #)
+$(info #   In slsDetectorsPackage Makefile   #)
 $(info #######################################)
 $(info )
 
 
 .PHONY: all nonstatic static lib libreceiver textclient receiver gui stextclient sreceiver
 
-all: lib textclient  receiver gui 
+#all: lib textclient  receiver gui 
+all: textclient  receiver gui 
 
 nonstatic: lib libreceiver textclient receiver  gui 
 
@@ -42,39 +46,61 @@ static: lib  libreceiver stextclient sreceiver gui
 
 
 lib:
-	cd $(LIBRARYDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' INCLUDES='$(INCLUDES)'
+	cd $(LIBRARYDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
 
 libreceiver:
-	cd $(LIBRARYRXRDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' INCLUDES='$(INCLUDESRXR)'
+	cd $(LIBRARYRXRDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
 
 
 stextclient: slsDetectorClient_static
 
 slsDetectorClient: textclient
 
-slsDetectorClient_static: lib
-	cd  $(CLIENTDIR) && $(MAKE) static_clients FLAGS='$(FLAGS)' LIBS='$(LDFLAGDET)' DESTDIR='$(BINDIR)' LIBDIR='$(LIBDIR)' INCLUDES='$(INCLUDES)'
-
-textclient: lib
-	cd  $(CLIENTDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBDIR='$(LIBDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)'
-
-
+slsDetectorClient_static: #lib
+	cd  $(CLIENTDIR) && $(MAKE) static_clients FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)' LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
+	@echo ""
+	@echo "#######################################"
+	@echo "# Back in slsDetectorPackage Makefile #"
+	@echo "#######################################"
+	@echo ""
+		
+textclient: #lib
+	cd  $(CLIENTDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
+	@echo ""
+	@echo "#######################################"
+	@echo "# Back in slsDetectorPackage Makefile #"
+	@echo "#######################################"
+	@echo ""
+	
 slsReceiver: receiver
 
 slsReceiver_static: receiver
 
-receiver: libreceiver
-	cd  $(RECEIVERDIR) && $(MAKE) receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)' LIBDIR='$(LIBDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)'
-
-sreceiver: libreceiver
-	cd  $(RECEIVERDIR) && $(MAKE)  static_receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)' LIBDIR='$(LIBDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)'
-
-
-
-slsDetectorGUI: lib
-	cd  $(GUIDIR) && $(MAKE) DESTDIR='$(BINDIR)' LIBDIR='$(LIBDIR)' INCLUDES='$(INCLUDES)' LDFLAGDET='-L$(LIBDIR) -lSlsDetector'  
-
+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)'
+	@echo ""
+	@echo "#######################################"
+	@echo "# Back in slsDetectorPackage Makefile #"
+	@echo "#######################################"
+	@echo ""
+		
+sreceiver: #libreceiver
+	cd  $(RECEIVERDIR) && $(MAKE)  static_receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
+	@echo ""
+	@echo "#######################################"
+	@echo "# Back in slsDetectorPackage Makefile #"
+	@echo "#######################################"
+	@echo ""
 
+slsDetectorGUI: #lib
+	cd  $(GUIDIR) && $(MAKE) DESTDIR='$(BINDIR)' LIBRARYDIR='$(LIBRARYDIR)' INCLUDES='$(INCLUDES)' LDFLAGDET='$(LDFLAGDETONLY)' LIBDIR='$(LIBDIR)'
+	@echo ""
+	@echo "#######################################"
+	@echo "# Back in slsDetectorPackage Makefile #"
+	@echo "#######################################"
+	@echo ""
+	
 calWiz: 
 	cd  $(CALWIZDIR) && $(MAKE)  DESTDIR=$(BINDIR) #FLAGS=$(FLAGS)  LDFLAGDET=$(LDFLAGDET) INCLUDES=$(INCLUDES)
 
@@ -91,6 +117,26 @@ htmldoc:
 	make doc
 	$(shell test -d $(DOCDIR) || mkdir -p $(DOCDIR))
 	cd manual && make html DESTDIR=$(DOCDIR)
+	
+detaildoc: createdocs docspdf docshtml removedocs
+
+createdocs: $(LIBRARYDIR)/doxy.config
+	doxygen $(LIBRARYDIR)/doxy.config	
+
+docspdf: 
+	cd slsDetectorPackageDocs/latex && make 
+	$(shell test -d $(DETAILDOC) || mkdir -p $(DETAILDOC))
+	$(shell test -d $(DETAILDOC)/pdf || mkdir -p $(DETAILDOC)/pdf)
+	mv slsDetectorPackageDocs/latex/refman.pdf $(DETAILDOC)/pdf/slsDetectorPackageDocs.pdf
+
+docshtml: 
+	$(shell test -d $(DETAILDOC) || mkdir -p $(DETAILDOC))
+	$(shell test -d $(DETAILDOC)/html || mkdir -p $(DETAILDOC)/html)
+	$(shell test -d $(DETAILDOC)/html/slsDetectorPackageDocs && rm -r $(DETAILDOC)/html/slsDetectorPackageDocs)
+	mv slsDetectorPackageDocs/html $(DETAILDOC)/html/slsDetectorPackageDocs
+	
+removedocs:
+	rm -rf 	slsDetectorPackageDocs;
 
 
 clean:
@@ -103,7 +149,8 @@ clean:
 	cd $(CALWIZDIR) && $(MAKE) clean
 	cd manual && $(MAKE) clean
 	cd $(DOCDIR) && rm -rf * 
-
+	rm -rf 	slsDetectorPackageDocs;
+	rm -rf $(DETAILDOC)
 
 
 #install_lib: 
@@ -174,7 +221,6 @@ help:
 	@echo ""
 	@echo ""
 	@echo "Makefile variables"
-	@echo "REST=yes		 compile REST-aware Receiver (POCO and JsonBox libraries required)"
 	@echo "DEBUG=1,2		 set debug level to 1 (VERBOSE) or 2 (VERYVERBOSE)"
 	@echo ""
 	@echo ""

Makefile.include

@@ -5,9 +5,10 @@
 CC = g++
 CXX = $(CC)
 ASM=$(shell echo "/lib/modules/`uname -r`/build/include")
-LDFLAGDET = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -lpthread
-LDFLAGRXR = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -lpthread
-FLAGS= -Wall  #-DEIGER_DEBUG2 -DEIGER_DEBUG  -DEIGER_DEBUG3 #-DFIFO_DEBUG
+LDFLAGDETONLY = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsDetector 
+LDFLAGDET = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread
+LDFLAGRXR = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread
+FLAGS= -Wall  -pthread  #-DEIGER_DEBUG2
 # -DVERBOSE 
 
 # Setting up the verbose flags
@@ -19,26 +20,17 @@ ifeq ($(DEBUG),2)
 endif
 
 ##############################################################
-# EigerSLS specific. Set this to yes, if you want to compile
-# EigerSLS code: in this case, you need also POCO and JsonBox 
-# libraries
+# HDF5 specific. Set this to yes, if you want to compile
+# HDF5 code: in this case, you need HDF5 libraries
 ##############################################################   
 
-REST = no
+HDF5 = no
+HDF5_DIR = /opt/hdf5v1.10.0
 
-#POCODIR = /afs/psi.ch/user/s/sala/public/poco-slp_5.7-32bit
-#JSONBOXDIR = /afs/psi.ch/user/s/sala/public/JsonBox-slp_5.7-32bit
-POCODIR = /afs/psi.ch/user/s/sala/public/poco-slp_6.4-64bit
-JSONBOXDIR = /afs/psi.ch/user/s/sala/public/JsonBox-slp_6.4-64bit
-#POCODIR = /home/sala/Programs/poco-ubuntu_13.10-64bit
-#JSONBOXDIR = /home/sala/Programs/JsonBox-ubuntu_13.10-64bit
-
-RESTFLAGS = -L$(POCODIR)/lib -Wl,-rpath=$(POCODIR)/lib  -L$(JSONBOXDIR) -Wl,-rpath=$(JSONBOXDIR)/lib  -lPocoNet -lPocoFoundation -lJsonBox
-
-ifeq ($(REST),yes)
-     LDFLAGRXR = -L$(LIBDIR) -lSlsReceiver $(RESTFLAGS) -DREST
-     INCLUDESRXR = $(EIGERFLAGS) -I$(POCODIR)/include -I$(JSONBOXDIR)/include
-endif
+ifeq ($(HDF5),yes)
+	LDFLAGRXR = -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L$(HDF5_DIR)/lib  -Wl,-rpath=$(HDF5_DIR)/lib -lhdf5 -lhdf5_cpp -lsz -lz -DHDF5C -L/usr/lib64/ -pthread
+	INCLUDESRXR = -I$(HDF5_DIR)/include
+endif	
 
 
 ##############################################################
@@ -55,6 +47,11 @@ ifeq ($(ROOTSLS),yes)
 endif
 
 
+define colorecho
+      @tput setaf 6
+      @echo $1
+      @tput sgr0
+endef
 
 
 

README.md

@@ -1,42 +1,85 @@
-# slsDetector package
+### 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)
 
-## Installation
-
-### Get source
-The source code is organised into several submodules, and the top level module is
-sls_detectors_package.
+### Source code
+One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
+```
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 3.1.0
 
 ```
-    $ git clone git@git.psi.ch:sls_detectors_software/sls_detectors_package.git
-    $ cd sls_detectors_package
-    $ ./checkout.sh
-```
-
-### Setup dependencies
-The GUI client requires Qt 4.8 and Qwt 6.0
+#### Setup dependencies 
+* Gui Client <br>
+Requirements: Qt 4.8 and Qwt 6.0
 ```
     export QTDIR=/usr/local/Trolltech/
     export QWTDIR=/usr/local/qwt-6.0.1/
 ```
 If either of them does not exist, the GUI client will not be built.
 
-The calibration wizards require ROOT
+* Calibration wizards<br>
+Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
 ```
 
-### Compile
-Use cmake to create out-of-source builds, by creating an build folder parallel to source directory.
+#### Compilation 
+
+Compiling can be done in two ways.
+
+**1. Compile using script cmk.sh**<br>
+
+After compiling, the libraries and executables will be found in `slsDetectorPackage/build/bin` directory<br>
+
+Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
+ * -[no option]: only make<br>
+ * -c: Clean<br>
+ * -b: Builds/Rebuilds CMake files normal mode<br>
+ * -h: Builds/Rebuilds Cmake files with HDF5 package<br>
+ * -d: HDF5 Custom Directory<br>
+ * -t: Build/Rebuilds only text client<br>
+ * -r: Build/Rebuilds only receiver<br>
+ * -g: Build/Rebuilds only gui<br>
+ * -j: Number of threads to compile through<br>
+ 
+For only make:
+./cmk.sh
+
+For make clean;make:
+./cmk.sh -c
+
+For using hdf5 without custom dir /blabla:
+./cmk.sh -h -d /blabla
+
+For rebuilding cmake without hdf5 
+./cmk.sh -b
+
+For using multiple cores to compile faster:
+./cmk.sh -j9<br>
+
+
+For rebuilding only certain sections<br>
+./cmk.sh -tg #only text client and gui<br>
+./cmk.sh -r #only receiver<br>
+
+
+**2. Compile without script**<br>
+Use cmake to create out-of-source builds, by creating a build folder parallel to source directory.
 ```
     $ cd ..
-    $ mkdir sls_detectors_package-build
-    $ cd sls_detectors_package-build
-    $ cmake ../sls_detectors_package
+    $ mkdir slsDetectorPackage-build
+    $ cd slsDetectorPackage-build
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=OFF 
     $ make
 ```
 
-The libraries and executables will be found at `bin` directory
+Use the following as an example to compile statically and using specific hdf5 folder
+```
+    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=ON
+ ```  
+After compiling, the libraries and executables will be found at `bin` directory
 ```
     $ ls bin/
     gui_client  libSlsDetector.a  libSlsDetector.so  libSlsReceiver.a  libSlsReceiver.so

RELEASE.txt

@@ -0,0 +1,353 @@
+SLS Detector Package 3.1.0 released on 2018-03-12
+=================================================
+
+
+
+INTRODUCTION
+
+This document describes the differences between 3.1.0 and 3.0.0 releases.
+
+The conda package of the binaries can be downloaded from
+	
+	https://github.com/slsdetectorgroup/sls_detector_software.git
+	
+The Python interface to the software package (including the package) is at 
+	
+	https://github.com/slsdetectorgroup/sls_detector.git
+	
+Manual (both HTML and pdf versions) are provided in
+	
+	manual/docs/
+
+Documentation from Source Code can be found for the Command Line and C++ API in
+	
+	html:
+		manual/docs/html/slsDetectorClientDocs/index.html
+		manual/docs/html/slsDetectorUsersDocs/index.html
+	pdf:
+		manual/docs/pdf/slsDetectorClientDocs.pdf
+		manual/docs/pdf/slsDetectorUsersDocs.pdf
+		
+Documentation to the python API is available at
+
+	https://slsdetectorgroup.github.io/sls_detector/
+		
+Example including binaries for detector and receiver user classes can be found in 
+
+	manual/manual-api
+	
+User documentation can also be accessed directly at this location:
+
+    https://www.psi.ch/detectors/users-support
+
+If you have any software related questions or comments, please send them to:
+
+    dhanya.thattil@psi.ch
+    anna.bergamaschi@psi.ch
+    
+If you have any python related questions or comments, please send them to:
+	
+	erik.frojdh@psi.ch
+
+
+CONTENTS
+
+- Firmware Requirements
+- Changes in User Interface
+- New Features
+- Resolved Issues
+- Known Issues
+
+
+
+Firmware Requirements
+=====================
+
+	Please refer to the link below for more details on the firmware versions.
+		https://www.psi.ch/detectors/firmware.
+
+    	Gotthard
+    	========   
+    	Minimum compatible version  : 11.01.2013
+    	Latest version              : 08.02.2018 (50um and 25um Master)
+                                      09.02.2018 (25 um Slave) 
+
+   	-Can not be upgraded remotely.
+    
+    
+    	Eiger
+    	=====  
+    	Minimum compatible version  : 16
+    	Latest version              : 20
+        
+    	-Can be upgraded remotely via bit files.
+    
+        
+    	Jungfrau
+    	========       
+    	Minimum compatible version  : 13.11.2017
+    	Latest version              : 13.11.2017
+
+    	-Can be upgraded remotely via sls_detector_put programfpga <pof>.
+	 
+
+
+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.
+		
+	3. 	Users example also works without config file, where detector already
+		configured in shared memory.
+		
+	4. 	Use "sls_detector_get busy 0" to clear acquiring flag in shared memory
+		caused due to an earlier interrupted acquisition from Ctrl+C"
+		
+	5. 	Set bit, clear bit, read register and write register cannot give -1 for
+		inconsistent values from multiple detectors. One has to check error from 
+		API or read the values individually.
+		
+	6. 	multiSlsDetector::char* getSettingsFile() function signature has been 
+		changed to string getSettingsFile().
+
+		
+		
+	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.
+		
+	8.	rx_datastream to enable/disable data streaming in receiver. Using the GUI
+		or registering data call back in client automatically enables zmq in 
+		receiver and client. "externalgui" is removed from the command line. Use
+		this command instead.
+		
+	9.	Rx_tcpport argument to the slsReceiver can be given using -t. 
+		Eg. slsReceiver -t1955
+		
+
+New Features
+============
+
+
+	Package
+	-------
+	1.	In addition to the C++ API, the Python API is also now provided.
+	
+	2. 	CMAKE now with debug flag and rpath, show warnings, compile only certain 
+		components (such as receiver or gui)
+	
+	3. 	One repository for entire package and made available at github.
+	
+	4. 	One can do --version or -v to all the binaries to find out the release
+		version of the particular executable.
+		
+	5. 	All the software version numbers have only date in format YYMMDD.
+	
+	  
+   	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.
+		
+	
+	Detector Server
+	---------------
+	7.	(Eiger) Virtual class to execute on pc.
+	
+	8. 	One can now read temperatures during acquisition. It goes via the stop
+		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 for firmware dated 08.02.2018 and 09.02.2018 
+		(25 um Slave) include minimum exposure time is 186 ns and minimum 
+		period is 1278 ns + current exposure time.
+	
+	
+	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.
+		
+	16.	Receiver print out can handle black or white backgrounds.
+	
+	17.	zmq package included updated to v4.0.8.
+	
+	18.	Zmq streaming from receiver also sends file index in json header.
+	
+	
+	Gui
+	---
+	19.	If acquisition is done, but "stop dummy packet" to the gui was lost in 
+		the network, stop acquisition command will restream it so that the gui
+		doesnt hang forever. This is used only for very fast detectors like 
+		Moench.
+
+
+
+Resolved Issues
+===============
+
+
+	Client
+	------
+	1. 	gethostbyname used in connecting to sockets was not thread safe for 
+		multiple detectors. Using getaddrinfo for stability in multi threaded
+		environment.
+	
+	2. 	Updated writing content of config and parameter dump into files.
+	
+	3. 	More locking to handle main and processing threads using the threadpool.
+		Removing unlock twice, which is undefined behavior.
+		
+	4.	(Jungfrau) adcphase returns the correct value, instead of -1.
+			
+
+	Detector Server
+	---------------
+	4. 	(Eiger) The hardware MAC of the detector is used during configuration 
+		and relayed  back to client. Similarly, hardware IP for 1 Gbe data mode.
+		
+	5. 	(Eiger) Status will return error if there was the unlikely trouble 
+		reading status register in the front end board. Earlier, it would only 
+		return idle.
+		
+	6.	(Jungfrau) patch server v3.0.0.6.3
+		Able to set settings, high voltage now correctly reads 0 when 
+		switched off, dacs are properly set.
+			
+	7. 	(Jungfrau) FPGA reset and programming FPGA firmware via software is done
+		properly
+		
+	8. 	(Gotthard) patch server v3.0.0.5.1
+		Able to read temperature properly.
+		
+	9. 	(Gotthard) butst mode if set too fast had unwanted behavior such as 
+		sending same image continuously. Now it is handled to display error
+		and stop acquisition.
+		
+	10.	(Gotthard) completely removed the possibility to set timing modes 
+		other than auto and trigger as they are not implemented anyway. Also
+		signal index 1, 2 and 3 are reserved and hence, cannot be configured for
+		an external trigger.
+		
+	11.	Non Mythen and non Eiger detectors can also now get settings file from 
+		board.
+		
+	12. 	(Gotthard) Did not get first few images initially after configuring MAC
+		of detector. Fixed.
+	
+	
+	Receiver
+	--------
+	12.	Made it easier to disable the standard receiver and fixing bugs related 
+		to the use of a custom one. 
+		
+	13.	(Jungfrau) HDF5 dimensions (npixelsY) required for mapping fixed.
+	
+	14.	patch2-v3.0.0-slsReceiverSoftware.patch
+		x, y and z coordinates in the call backs and the files are hardcoded 
+		for this release. 
+		
+	15.	Rest implementation (not used by standard receiver) removed.
+
+	
+	Gui
+	---
+	16.	patch1-v3.0.0-slsDetectorGui.patch
+		(Eiger) In expert mode and in advanced tab, when trimbits 
+		loaded are different for every pixel, the gui complains and sets 
+		all trimbits to zero. This has been resolved. Now, the "Set All 
+		Trimbits" field is just set to -1.
+		
+	17.	Fixed segmentation fault of xputsn properly.
+	
+	18.	Upon clicking on "Start", clears acquiring flag in shared memory
+		caused due to an earlier interrupted acquisition from Ctrl+C"
+		
+	19.	Fixed plotting twice caused due to unzooming the first time.
+	
+	20.	Removed option for compression in Gui as it is not available currently.
+	
+	21. 	Can also show Jungfrau multi detector in x direction in gui.
+	
+	22. 	Switching tabs sometimes results in delay and gates fields being incorrectly
+		enabled. Fixed.
+
+
+	
+Known Issues
+============
+
+
+	Client
+	------
+	1.	File name prefix can only be done at multi deector level. Changing at 
+		individual detector level will not include scan or position variables.
+
+	
+	Detector Server
+	---------------
+	2.	Standard header fills x-coord in 1D. y-coord and z-coord is not 
+		implemented (3D).
+
+
+	Receiver
+	--------
+	3. 	HDF5 compression and filters are not implemented yet.
+	
+
+	
+
+
+
+

checkout.sh

@@ -1,15 +0,0 @@
-#git clone $1@git.psi.ch:sls_det_software/sls_detectors_package.git slsDetectorsPackage
-
-#cd slsDetectorsPackage
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_software.git slsDetectorSoftware
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_gui.git slsDetectorGui
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_receiver_software.git slsReceiverSoftware
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_calibration.git slsDetectorCalibration
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_image_reconstruction.git slsImageReconstruction
-
-git clone $1@git.psi.ch:sls_detectors_software/calibration_wizards.git calibrationWizards

cmk.sh

@@ -0,0 +1,193 @@
+#!/bin/bash
+BUILDDIR="build"
+HDF5DIR="/opt/hdf5v1.10.0"
+HDF5=0
+COMPILERTHREADS=0
+TEXTCLIENT=0
+RECEIVER=0
+GUI=0
+
+
+CLEAN=0
+REBUILD=0
+CMAKE_PRE=""
+CMAKE_POST=""
+
+usage() { echo -e "
+Usage: $0 [-c] [-b] [-h] [-d <HDF5 directory>] [-j]
+ -[no option]: only make
+ -c: Clean
+ -b: Builds/Rebuilds CMake files normal mode
+ -h: Builds/Rebuilds Cmake files with HDF5 package
+ -d: HDF5 Custom Directory
+ -t: Build/Rebuilds only text client
+ -r: Build/Rebuilds only receiver
+ -g: Build/Rebuilds only gui
+ -j: Number of threads to compile through
+ 
+For only make:
+./cmk.sh
+
+For make clean;make:
+./cmk.sh -c
+
+For using hdf5 without default dir /opt/hdf5v1.10.0:
+./cmk.sh -h
+
+For using hdf5 without custom dir /blabla:
+./cmk.sh -h -d /blabla
+
+For rebuilding cmake without hdf5 (Use this if you had previously run with hdf5 and now you dont want it)
+./cmk.sh -b
+
+For using multiple cores to compile faster:
+(all these options work)
+./cmk.sh -j9
+./cmk.sh -cj9 #with clean
+./cmk.sh -hj9 #with hdf5
+./cmk.sh -j9 -h #with hdf
+
+For rebuilding only certain sections
+./cmk.sh -tg #only text client and gui
+./cmk.sh -r #only receiver
+ 
+ " ; exit 1; }
+
+while getopts ":bchd:j:trg" opt ; do
+	case $opt in
+	b) 
+		echo "Building of CMake files Required"
+		REBUILD=1
+		;;
+	c) 
+		echo "Clean Required"
+		CLEAN=1
+		;;
+	h) 
+		echo "Building of CMake files with HDF5 option Required"
+		HDF5=1
+		REBUILD=1
+		;;
+	d) 
+		echo "New HDF5 directory: $OPTARG" 
+		HDF5DIR=$OPTARG
+		;;
+	j) 
+		echo "Number of compiler threads: $OPTARG" 
+		COMPILERTHREADS=$OPTARG
+		;;
+	t) 
+    	echo "Compiling Options: Text Client" 
+		TEXTCLIENT=1
+		REBUILD=1
+		;;      
+	r) 
+		echo "Compiling Options: Receiver" 
+		RECEIVER=1
+		REBUILD=1
+		;;      
+	g) 
+		echo "Compiling Options: GUI" 
+		GUI=1
+		REBUILD=1
+		;;      
+    \?)
+     	echo "Invalid option: -$OPTARG" 
+		usage
+      	exit 1
+      	;;
+    :)
+      	echo "Option -$OPTARG requires an argument."
+		usage
+      	exit 1
+      	;;	
+	esac
+done
+
+
+
+
+
+
+if [ $TEXTCLIENT -eq 0 ] && [ $RECEIVER -eq 0 ]  && [ $GUI -eq 0 ]; then
+       CMAKE_POST+=" -DUSE_TEXTCLIENT=ON -DUSE_RECEIVER=ON -DUSE_GUI=ON "
+       echo "Compile Option: TextClient, Receiver and GUI"
+else 
+       if [ $TEXTCLIENT -eq 1 ]; then
+              CMAKE_POST+=" -DUSE_TEXTCLIENT=ON "
+               echo "Compile Option: TextClient"
+       fi
+       if [ $RECEIVER -eq 1 ]; then
+               CMAKE_POST+=" -DUSE_RECEIVER=ON "
+               echo "Compile Option: Receiver"
+       fi
+                               
+       if [ $GUI -eq 1 ]; then
+               CMAKE_POST+=" -DUSE_GUI=ON "
+               echo "Compile Option: GUI"
+       fi
+fi
+
+
+
+
+
+#build dir doesnt exist
+if [ ! -d "$BUILDDIR" ] ; then
+	echo "No Build Directory. Building of Cmake files required"
+	mkdir $BUILDDIR;
+	REBUILD=1
+else
+	#rebuild not requested, but no makefile
+	if [ $REBUILD -eq 0 ] && [ ! -f "$BUILDDIR/Makefile" ] ; then
+		echo "No Makefile. Building of Cmake files required"
+		REBUILD=1
+	fi
+fi
+
+CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+
+#hdf5 rebuild
+if [ $HDF5 -eq 1 ]; then
+	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
+	CMAKE_POST+=" -DUSE_HDF5=ON "
+#normal mode rebuild
+else
+	CMAKE_POST+=" -DUSE_HDF5=OFF "
+fi
+
+
+#enter build dir
+cd $BUILDDIR;
+echo "in "$PWD
+
+
+
+#cmake
+if [ $REBUILD -eq 1 ]; then
+	rm -f CMakeCache.txt
+	BUILDCOMMAND="$CMAKE_PRE cmake $CMAKE_POST .."
+	echo $BUILDCOMMAND
+	eval $BUILDCOMMAND
+fi
+
+#make clean
+if [ $CLEAN -eq 1 ]; then
+	make clean;
+fi
+
+
+#make
+if [ $COMPILERTHREADS -gt 0 ]; then
+	BUILDCOMMAND="make -j$COMPILERTHREADS"
+	echo $BUILDCOMMAND
+	eval $BUILDCOMMAND
+else
+	make
+fi
+
+
+
+
+
+

evalVersionVariables.sh

@@ -0,0 +1,22 @@
+GITREPO1='git remote -v'
+GITREPO2=" | grep \"fetch\" | cut -d' ' -f1"
+BRANCH1='git branch -v'
+BRANCH2=" | grep '*' | cut -d' ' -f2"
+REPUID1='git log --pretty=format:"%H" -1'
+AUTH1_1='git log --pretty=format:"%cn" -1'
+AUTH1_2=" | cut -d' ' -f1"
+AUTH2_1='git log --pretty=format:"%cn" -1'
+AUTH2_2=" | cut -d' ' -f2"
+FOLDERREV1='git log --oneline . '   #used for all the individual server folders
+FOLDERREV2=" | wc -l"  #used for all the individual server folders
+REV1='git log --oneline  '
+REV2=" | wc -l"
+
+GITREPO=`eval $GITREPO1  $GITREPO2`
+BRANCH=`eval $BRANCH1  $BRANCH2`
+REPUID=`eval $REPUID1`
+AUTH1=`eval $AUTH1_1  $AUTH1_2`
+AUTH2=`eval $AUTH2_1  $AUTH2_2`
+REV=`eval $REV1  $REV2`
+FOLDERREV=`eval $FOLDERREV1  $FOLDERREV2`
+

examples/eiger_10Gb.config

@@ -0,0 +1,33 @@
+detsizechan 1024 512 
+#detetctor geometry, long side of the module first
+hostname beb059+beb058+ 
+#1Gb detector hostname for controls
+
+0:rx_tcpport 1991 
+#tcpport for the first halfmodule                 
+0:rx_udpport 50011 
+#udp port first quadrant, first halfmodule       
+0:rx_udpport2 50012 
+#udp port second quadrant, first halfmodule       
+0:rx_udpip 10.0.30.210 
+#udp IP of the receiver over 10Gb              
+0:detectorip 10.0.30.100 
+#first half module 10 Gb IP 
+
+1:rx_tcpport 1992 
+#tcpport for the second halfmodule                  
+1:rx_udpport 50013 
+#udp port first quadrant, second halfmodule     
+1:rx_udpport2 50014 
+#udp port second quadrant, second halfmodule  
+1:rx_udpip 10.0.40.210  
+#udp IP of the receiver over 10Gb, 
+#can be the same or different from 0:rx_udpip                                   
+1:detectorip 10.0.40.101 
+#second half module 10 Gb IP 
+
+rx_hostname x12sa-vcons 
+#1Gb receiver pc hostname
+
+outdir /sls/X12SA/data/x12saop/Data10/Eiger0.5M
+threaded 1

examples/eiger_1Gb.config

@@ -0,0 +1,24 @@
+detsizechan 1024 512 
+#detetctor geometry, long side of the module first
+hostname beb059+beb058+ 
+#1Gb detector hostname for controls
+
+0:rx_tcpport 1991 
+#tcpport for the first halfmodule                 
+0:rx_udpport 50011 
+#udp port first quadrant, first halfmodule         
+0:rx_udpport2 50012 
+#udp port second quadrant, first halfmodule       
+
+1:rx_tcpport 1992 
+#tcpport for the second halfmodule               
+1:rx_udpport 50013 
+#udp port first quadrant, second halfmodule       
+1:rx_udpport2 50014 
+#udp port second quadrant, second halfmodule  
+    
+rx_hostname x12sa-vcons 
+#1Gb receiver pc hostname
+
+outdir /sls/X12SA/data/x12saop/Data10/Eiger0.5M
+threaded 1

examples/gotthard.config

@@ -1,5 +1,5 @@
-type Gotthard+
-0:hostname bchip007
+hostname bchip007
+
 #0:port 1952
 #0:stopport 1953
 #0:rx_tcpport 1956 must also have this in receiver config file
@@ -10,9 +10,6 @@ type Gotthard+
 0:caldir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
 0:ffdir /home/l_maliakal_d
 0:extsig:0 off
-0:extsig:1 off
-0:extsig:2 off
-0:extsig:3 off
 #0:detectorip 129.129.202.9
 0:detectormac 00:aa:bb:cc:dd:ee
 0:rx_udpport 50004

examples/jungfrau.config

@@ -0,0 +1,18 @@
+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
+
+outdir /external_pool/jungfrau_data/softwaretest
+threaded 1
+

examples/jungfrau_two.config

@@ -0,0 +1,30 @@
+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
+0:detectorip 10.1.1.10
+0:detectormac 00:aa:bb:cc:dd:33
+
+1:rx_tcpport 1955
+1:rx_udpport 50005
+1:rx_udpip 10.1.1.100
+1:rx_udpmac F4:52:14:2F:32:00
+1:detectorip 10.1.1.11
+1:detectormac 00:aa:bb:cc:dd:33
+
+rx_hostname pcmoench01
+
+powerchip 1
+extsig:0 trigger_in_rising_edge
+timing auto
+
+outdir /external_pool/jungfrau_data/softwaretest
+threaded 1
+

examples/two_gotthard.config

@@ -2,7 +2,6 @@
 
 detsizechan 2560 1
 
-#type Gotthard+
 hostname bchip007+bchip009+
 
 #0:hostname bchip007
@@ -16,9 +15,6 @@ hostname bchip007+bchip009+
 0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
-0:extsig:1 off
-0:extsig:2 off
-0:extsig:3 off
 0:detectorip 10.1.1.2
 #0:detectormac 00:aa:bb:cc:dd:ee
 #0:rx_udpport 50001
@@ -39,9 +35,6 @@ hostname bchip007+bchip009+
 1:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:ffdir /home/l_msdetect
 1:extsig:0 off
-1:extsig:1 off
-1:extsig:2 off
-1:extsig:3 off
 1:detectorip 10.1.2.2
 #1:detectormac 00:aa:bb:cc:dd:ee
 1:rx_udpport 50004

genVersionHeader.sh

@@ -15,11 +15,11 @@ fout=$3
 
 #dat=echo "date '+%Y%m%d'"
 
-
-echo "in: $fin tmp: $ftmp out: $fout"
+echo "Updating $fout"
+#echo "in: $fin tmp: $ftmp out: $fout"
 
 #awk 'NR==FNR {if ($3=="Date:") {l[FNR]=$4; gsub("-","",l[FNR]);} else { if (match($0,"Rev")) {l[FNR]=$(NF);} else {l[FNR]="\""$(NF)"\"";};};next} {$0=$1" "$2" "l[FNR]}1' $fin $ftmp > $fout
 
 awk 'BEGIN {l[0]=0; "date +%Y%m%d" | getline l[1]; l[2]="\"/\""; l[3]="\"nobody\""; l[3]="\"nobody\""; l[4]="\"0000-0000-0000\"";} \
-NR==FNR {if (match($0,"Rev")) {l[0]="0x"$(NF);} else if (match($0,"Date")) {l[1]="0x"$4; gsub("-","",l[1]);} else if (match($0,"URL")) {l[2]="\""$(NF)"\"";} else if (match($0,"Author")) {l[3]="\""$(NF)"\"";} else if (match($0,"UUID")) {l[4]="\""$(NF)"\"";};next;} 
-{if (match($2,"REV")) {$0=$1" "$2" "l[0];} else if (match($2,"DATE")) {$0=$1" "$2" "l[1];} else if (match($2,"URL")) {$0=$1" "$2" "l[2];} else if (match($2,"AUTH")) {$0=$1" "$2" "l[3];} else if (match($2,"UUID")) {$0=$1" "$2" "l[4];}}1' $fin $ftmp > $fout
+NR==FNR {if (match($0,"Rev")) {l[0]="0x"$(NF);} else if (match($0,"Date")) {l[1]="0x"$4; gsub("-","",l[1]);} else if (match($0,"URL")) {l[2]="\""$(NF)"\"";} else if (match($0,"Author")) {l[3]="\""$(NF)"\"";} else if (match($0,"UUID")) {l[4]="\""$(NF)"\"";} else if (match($0,"Branch")) {l[5]="\""$(NF)"\"";};next;} 
+{if (match($2,"REV")) {$0=$1" "$2" "l[0];} else if (match($2,"DATE")) {$0=$1" "$2" "l[1];} else if (match($2,"URL")) {$0=$1" "$2" "l[2];} else if (match($2,"AUTH")) {$0=$1" "$2" "l[3];} else if (match($2,"UUID")) {$0=$1" "$2" "l[4];} else if (match($2,"BRANCH")) {$0=$1" "$2" "l[5];}}1' $fin $ftmp > $fout

gitall.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-git $1
-for i in sls*/; do
-	cd $i
-	echo $i
-	git $1
-	cd ..
-done

manual/Makefile

@@ -1,11 +1,11 @@
-DESTDIR?=../docs
+DESTDIR?=docs
 
 
 #manual-api manual-calwiz manual-client manual-gui manual-main
 
 
 
-MAINDIRS= manual-main 
+MAINDIRS= manual-main manual-api  manual-calwiz manual-client manual-gui
 #manual-calwiz manual-calwiz manual-gui manual-client manual-api
 CLEANDIRS=$(MAINDIRS:manual-%=clean-%)
 PDFDIRS=$(MAINDIRS:manual-%=pdf-%)
@@ -14,18 +14,18 @@ ALLDIRS=$(MAINDIRS:manual-%=all-%)
 
 
 all: $(ALLDIRS)
-	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
-	mv pdf $(DESTDIR)
-	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
-	mv html $(DESTDIR)
-
+#	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
+#	mv pdf $(DESTDIR)
+#	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
+#	mv html $(DESTDIR)
+	
 pdf: $(PDFDIRS)
-	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
-	mv pdf $(DESTDIR)
+#	$(shell test -d $(DESTDIR)/pdf && rm -fr $(DESTDIR)/pdf)
+#	mv pdf $(DESTDIR)
 
 html: $(HTMLDIRS)
-	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
-	mv html $(DESTDIR)
+#	$(shell test -d $(DESTDIR)/html && rm -fr $(DESTDIR)/html)
+#	mv html $(DESTDIR)
 
 clean: $(CLEANDIRS)
 	rm -fr $(DESTDIR)/pdf
@@ -45,7 +45,7 @@ clean-%:
 	cd  $(@:clean-%=manual-%) && make clean	
 
 
-#<23><>$(@D)<29><>    The directory part of the file name of the target, with the trailing slash removed. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@D)<29><> is dir. This value is . if <20><>$@<40><> does not contain a slash.
-#<23><>$(@F)<29><>    The file-within-directory part of the file name of the target. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@F)<29><> is foo.o. <20><>$(@F)<29><> is equivalent to <20><>$(notdir $@)<29><>.
+#<23><>$(@D)<29><>    The directory part of the file name of the target, with the trailing slash removed. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@D)<29><> is dir. This value is . if <20><>$@<40><> does not contain a slash.
+#<23><>$(@F)<29><>    The file-within-directory part of the file name of the target. If the value of <20><>$@<40><> is dir/foo.o then <20><>$(@F)<29><> is foo.o. <20><>$(@F)<29><> is equivalent to <20><>$(notdir $@)<29><>.
 
 

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    }
+SMALL.SMALL		{  }
+BIG.LARGE		{  }
+BIG.XLARGE		{ font-size : large    }
+BIG.XXLARGE		{ font-size : x-large  }
+BIG.HUGE		{ font-size : larger   }
+BIG.XHUGE		{ font-size : xx-large }
+
+/* heading styles */
+H1		{  }
+H2		{  }
+H3		{  }
+H4		{  }
+H5		{  }
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+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
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+<META NAME="description" CONTENT="Angular calibration wizard manual">
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+
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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/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="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>March 12, 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
+2018-03-12
+</ADDRESS>
+</BODY>
+</HTML>

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manual/docs/html/angularCalibrationHowTo/index.html

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+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Angular calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Angular calibration wizard manual">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
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+ SRC="file:/usr/share/latex2html/icons/prev_g.png">   
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+  HREF="node1.html">Introduction</A>
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+<!--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>March 12, 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
+2018-03-12
+</ADDRESS>
+</BODY>
+</HTML>

manual/docs/html/angularCalibrationHowTo/internals.pl

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manual/docs/html/angularCalibrationHowTo/labels.pl

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+

manual/docs/html/angularCalibrationHowTo/node1.html

@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
+<META NAME="description" CONTENT="Introduction">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
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+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
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+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+In order to convert from strip number to 2<IMG
+ WIDTH="12" HEIGHT="14" 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="16" 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="14" 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>
+<!--Navigation Panel-->
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+2018-03-12
+</ADDRESS>
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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 -->
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+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
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+
+<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>
+<HR>
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+
+<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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+<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
+2018-03-12
+</ADDRESS>
+</BODY>
+</HTML>

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+About this document ...</A>
+</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 2008 (1.71)
+<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>
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+<META NAME="description" CONTENT="Energy calibration wizard manual">
+<META NAME="keywords" CONTENT="energyCalibrationHowTo">
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+</HEAD>
+
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+ 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>March 12, 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
+2018-03-12
+</ADDRESS>
+</BODY>
+</HTML>

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+$key = q/{displaymath}N_gamma(E_t)=frac{N_0}{2}cdotBig(1+C_sfrac{E_0-2E_t}{E_0}Big)DBig(frac{E_0-E_t}{ENC}Big),{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="335" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|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}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_ThresholdScan.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img38.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}">|; 
+
+$key = q/N_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$N_0$">|; 
+
+$key = q/N_S;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="$N_S$">|; 
+
+$key = q/O_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img30.png"
+ ALT="$O_i$">|; 
+
+$key = q/E_f;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$E_f$">|; 
+
+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img29.png"
+ ALT="$i$">|; 
+
+$key = q/G_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img31.png"
+ ALT="$G_i$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig7.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="553" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img35.png"
+ ALT="\includegraphics[width=\textwidth]{fig7.eps}">|; 
+
+$key = q/D;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$D$">|; 
+
+$key = q/N_s=C_sN_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="83" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img20.png"
+ ALT="$N_s=C_s N_0$">|; 
+
+$key = q/E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="39" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="$E_0/2$">|; 
+
+$key = q/E_t=E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="78" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="$E_t=E_0/2$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig4.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img33.png"
+ ALT="\includegraphics[width=\textwidth]{fig4.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_Advanced.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img37.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_Advanced.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{addEnergy.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img39.png"
+ ALT="\includegraphics[width=\textwidth]{addEnergy.eps}">|; 
+
+$key = q/C_s;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img19.png"
+ ALT="$C_s$">|; 
+
+$key = q/CS={begingroup{N_Sbegingroup{overN_0};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="11" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$CS={\begingroupN_S\endgroup\over N_0}$">|; 
+
+$key = q/CS=;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$CS=$">|; 
+
+$key = q/e^-;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$e^-$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig5.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img34.png"
+ ALT="\includegraphics[width=\textwidth]{fig5.eps}">|; 
+
+$key = q/{displaymath}V_{t}=O+GcdotE_t.{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="111" HEIGHT="26" BORDER="0"
+ SRC="|."$dir".q|img28.png"
+ ALT="\begin{displaymath}
+V_{t}=O+G \cdot E_t.
+\end{displaymath}">|; 
+
+$key = q/Sigma>3ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="85" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\Sigma &gt;3ENC$">|; 
+
+$key = q/N;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="$N$">|; 
+
+$key = q/Sigma>3,ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="88" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img24.png"
+ ALT="$\Sigma&gt;3 ENC$">|; 
+
+$key = q/Deltasim;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="35" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$\Delta \sim $">|; 
+
+1;
+

manual/docs/html/energyCalibrationHowTo/images.tex

@@ -0,0 +1,391 @@
+\batchmode
+\documentclass{article}
+\RequirePackage{ifthen}
+
+
+\usepackage{amssymb}
+\usepackage[dvips]{graphicx}
+\usepackage{verbatim}
+
+
+\usepackage[dvips]{color}
+
+
+\pagecolor[gray]{.7}
+
+\usepackage[]{inputenc}
+
+
+
+\makeatletter
+
+\makeatletter
+\count@=\the\catcode`\_ \catcode`\_=8 
+\newenvironment{tex2html_wrap}{}{}%
+\catcode`\<=12\catcode`\_=\count@
+\newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}%
+\newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}%
+  \expandafter\renewcommand\csname #1\endcsname}%
+\newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}%
+\let\newedcommand\renewedcommand
+\let\renewedenvironment\newedenvironment
+\makeatother
+\let\mathon=$
+\let\mathoff=$
+\ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi
+\newbox\sizebox
+\setlength{\hoffset}{0pt}\setlength{\voffset}{0pt}
+\addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt}
+\addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt}
+\addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt}
+\addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt}
+\setlength{\textwidth}{349pt}
+\newwrite\lthtmlwrite
+\makeatletter
+\let\realnormalsize=\normalsize
+\global\topskip=2sp
+\def\preveqno{}\let\real@float=\@float \let\realend@float=\end@float
+\def\@float{\let\@savefreelist\@freelist\real@float}
+\def\liih@math{\ifmmode$\else\bad@math\fi}
+\def\end@float{\realend@float\global\let\@freelist\@savefreelist}
+\let\real@dbflt=\@dbflt \let\end@dblfloat=\end@float
+\let\@largefloatcheck=\relax
+\let\if@boxedmulticols=\iftrue
+\def\@dbflt{\let\@savefreelist\@freelist\real@dbflt}
+\def\adjustnormalsize{\def\normalsize{\mathsurround=0pt \realnormalsize
+ \parindent=0pt\abovedisplayskip=0pt\belowdisplayskip=0pt}%
+ \def\phantompar{\csname par\endcsname}\normalsize}%
+\def\lthtmltypeout#1{{\let\protect\string \immediate\write\lthtmlwrite{#1}}}%
+\newcommand\lthtmlhboxmathA{\adjustnormalsize\setbox\sizebox=\hbox\bgroup\kern.05em }%
+\newcommand\lthtmlhboxmathB{\adjustnormalsize\setbox\sizebox=\hbox to\hsize\bgroup\hfill }%
+\newcommand\lthtmlvboxmathA{\adjustnormalsize\setbox\sizebox=\vbox\bgroup %
+ \let\ifinner=\iffalse \let\)\liih@math }%
+\newcommand\lthtmlboxmathZ{\@next\next\@currlist{}{\def\next{\voidb@x}}%
+ \expandafter\box\next\egroup}%
+\newcommand\lthtmlmathtype[1]{\gdef\lthtmlmathenv{#1}}%
+\newcommand\lthtmllogmath{\dimen0\ht\sizebox \advance\dimen0\dp\sizebox
+  \ifdim\dimen0>.95\vsize
+   \lthtmltypeout{%
+*** image for \lthtmlmathenv\space is too tall at \the\dimen0, reducing to .95 vsize ***}%
+   \ht\sizebox.95\vsize \dp\sizebox\z@ \fi
+  \lthtmltypeout{l2hSize %
+:\lthtmlmathenv:\the\ht\sizebox::\the\dp\sizebox::\the\wd\sizebox.\preveqno}}%
+\newcommand\lthtmlfigureA[1]{\let\@savefreelist\@freelist
+       \lthtmlmathtype{#1}\lthtmlvboxmathA}%
+\newcommand\lthtmlpictureA{\bgroup\catcode`\_=8 \lthtmlpictureB}%
+\newcommand\lthtmlpictureB[1]{\lthtmlmathtype{#1}\egroup
+       \let\@savefreelist\@freelist \lthtmlhboxmathB}%
+\newcommand\lthtmlpictureZ[1]{\hfill\lthtmlfigureZ}%
+\newcommand\lthtmlfigureZ{\lthtmlboxmathZ\lthtmllogmath\copy\sizebox
+       \global\let\@freelist\@savefreelist}%
+\newcommand\lthtmldisplayA{\bgroup\catcode`\_=8 \lthtmldisplayAi}%
+\newcommand\lthtmldisplayAi[1]{\lthtmlmathtype{#1}\egroup\lthtmlvboxmathA}%
+\newcommand\lthtmldisplayB[1]{\edef\preveqno{(\theequation)}%
+  \lthtmldisplayA{#1}\let\@eqnnum\relax}%
+\newcommand\lthtmldisplayZ{\lthtmlboxmathZ\lthtmllogmath\lthtmlsetmath}%
+\newcommand\lthtmlinlinemathA{\bgroup\catcode`\_=8 \lthtmlinlinemathB}
+\newcommand\lthtmlinlinemathB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA
+  \vrule height1.5ex width0pt }%
+\newcommand\lthtmlinlineA{\bgroup\catcode`\_=8 \lthtmlinlineB}%
+\newcommand\lthtmlinlineB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA}%
+\newcommand\lthtmlinlineZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+  \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetinline}
+\newcommand\lthtmlinlinemathZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+  \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetmath}
+\newcommand\lthtmlindisplaymathZ{\egroup %
+  \centerinlinemath\lthtmllogmath\lthtmlsetmath}
+\def\lthtmlsetinline{\hbox{\vrule width.1em \vtop{\vbox{%
+  \kern.1em\copy\sizebox}\ifdim\dp\sizebox>0pt\kern.1em\else\kern.3pt\fi
+  \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\lthtmlsetmath{\hbox{\vrule width.1em\kern-.05em\vtop{\vbox{%
+  \kern.1em\kern0.8 pt\hbox{\hglue.17em\copy\sizebox\hglue0.8 pt}}\kern.3pt%
+  \ifdim\dp\sizebox>0pt\kern.1em\fi \kern0.8 pt%
+  \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\centerinlinemath{%
+  \dimen1=\ifdim\ht\sizebox<\dp\sizebox \dp\sizebox\else\ht\sizebox\fi
+  \advance\dimen1by.5pt \vrule width0pt height\dimen1 depth\dimen1 
+ \dp\sizebox=\dimen1\ht\sizebox=\dimen1\relax}
+
+\def\lthtmlcheckvsize{\ifdim\ht\sizebox<\vsize 
+  \ifdim\wd\sizebox<\hsize\expandafter\hfill\fi \expandafter\vfill
+  \else\expandafter\vss\fi}%
+\providecommand{\selectlanguage}[1]{}%
+\makeatletter \tracingstats = 1 
+
+
+\begin{document}
+\pagestyle{empty}\thispagestyle{empty}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hsize=\the\hsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength vsize=\the\vsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hoffset=\the\hoffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength voffset=\the\voffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topmargin=\the\topmargin}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topskip=\the\topskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headheight=\the\headheight}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headsep=\the\headsep}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength parskip=\the\parskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength oddsidemargin=\the\oddsidemargin}\lthtmltypeout{}%
+\makeatletter
+\if@twoside\lthtmltypeout{latex2htmlLength evensidemargin=\the\evensidemargin}%
+\else\lthtmltypeout{latex2htmlLength evensidemargin=\the\oddsidemargin}\fi%
+\lthtmltypeout{}%
+\makeatother
+\setcounter{page}{1}
+\onecolumn
+
+% !!! IMAGES START HERE !!!
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline464}%
+$E_0$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline466}%
+$N_0$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline468}%
+$ENC$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline470}%
+$CS=$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline472}%
+$N_S$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline474}%
+$CS={\begingroupN_S\endgroup\over N_0}$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline482}%
+$E_f$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline486}%
+$E_0/2$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline490}%
+$\Delta \sim $%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline492}%
+$E_t$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline494}%
+$\Sigma >3ENC$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline131}%
+$e^-$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline137}%
+$D$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline141}%
+$E_t=E_0/2$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline143}%
+$N$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline147}%
+$N_n$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline149}%
+$N_\gamma$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath17}%
+\begin{displaymath}
+N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big), 
+\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline151}%
+$C_s$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline153}%
+$N_s=C_s N_0$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline155}%
+$\tau_s$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline157}%
+$T$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath26}%
+\begin{displaymath}
+N_n(E_t) \sim \frac{T}{\tau_s}  D \Big(\frac{-E_t}{ENC} \Big). 
+\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline165}%
+$\Sigma>3\,ENC$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline167}%
+$O$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline169}%
+$G$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline171}%
+$V_t$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath34}%
+\begin{displaymath}
+V_{t}=O+G \cdot E_t.
+\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline175}%
+$i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline177}%
+$O_i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline179}%
+$G_i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline191}%
+$CS=\frac{N_S}{N_0}$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap559}%
+\includegraphics[width=\textwidth]{fig4.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap563}%
+\includegraphics[width=\textwidth]{fig5.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap585}%
+\includegraphics[width=\textwidth]{fig7.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap589}%
+\includegraphics[width=\textwidth]{fig8.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap595}%
+\includegraphics[width=\textwidth]{GUI_Advanced.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap599}%
+\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap605}%
+\includegraphics[width=\textwidth]{addEnergy.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap609}%
+\includegraphics[width=\textwidth]{calibrateModule.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+
+\end{document}

manual/docs/html/energyCalibrationHowTo/index.html

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+<TITLE>Energy calibration wizard manual</TITLE>
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+<B> Next:</B> <A NAME="tex2html10"
+  HREF="node1.html">Introduction</A>
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+<P>
+
+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 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
+2018-03-12
+</ADDRESS>
+</BODY>
+</HTML>

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