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).

.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

.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

@@ -1,21 +1,57 @@
 cmake_minimum_required(VERSION 2.8)
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+set (CALIBRATE OFF)
+
+option (USE_HDF5 "HDF5 File format" OFF)
+option (USE_TEXTCLIENT "Text Client" OFF)
+option (USE_RECEIVER "Receiver" OFF)
+option (USE_GUI "GUI" OFF)
+
+
+if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+	set(CMAKE_CXX_FLAGS  "${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)
 
-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)
+       add_subdirectory(manual/manual-api)    
+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
@@ -18,23 +19,27 @@ 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 += 
 
 $(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 +47,62 @@ 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)'
+	cd  $(MANAPIDIR) && $(MAKE) slsMultiReceiver
+	@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 +119,26 @@ 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 +151,9 @@ clean:
 	cd $(CALWIZDIR) && $(MAKE) clean
 	cd manual && $(MAKE) clean
 	cd $(DOCDIR) && rm -rf * 
-
+	rm -rf 	slsDetectorPackageDocs;
+	rm -rf $(DETAILDOC)
+	rm -rf $(MANAPIDIR)/slsMultiReceiver
 
 
 #install_lib: 
@@ -174,7 +224,6 @@ 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

@@ -5,40 +5,32 @@
 CC = g++
 CXX = $(CC)
 ASM=$(shell echo "/lib/modules/`uname -r`/build/include")
+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 -DEIGER_DEBUG  -DEIGER_DEBUG3 #-DFIFO_DEBUG
+FLAGS= -Wall  -pthread  #-DEIGER_DEBUG2
 # -DVERBOSE 
 
 # Setting up the verbose flags
 ifeq ($(DEBUG),1)
-     FLAGS = -Wall -pthread -DVERBOSE
+     FLAGS = -Wall -DVERBOSE
 endif
 ifeq ($(DEBUG),2)
-     FLAGS = -Wall -pthread -DVERYVERBOSE
+     FLAGS = -Wall -DVERYVERBOSE
 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

@@ -1,44 +1,91 @@
-# 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 for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
 
-## 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
 
 ```
-    $ 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
+* Advanced user 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>
+ * -e: Debug mode
+ 
+Basic Option:
+./cmk.sh -b
+ 
+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
-    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

@@ -1,135 +1,508 @@
-SLS Detector Package 2.3.0 released on 2017-03-23
-================================================================================
-
+SLS Detector Package 4.0.0 released on 27.09.2018
+=================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between previous versions and 2.3.0 releases.
+	This document describes the differences between 4.0.0 and 3.1.4 releases.
 
-Manuals can be found under the 'manual' folder.
-
-User documentation and other help can 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
+	Download
+	--------
+	
+	The Source Code (Default C++ API):
+		 https://github.com/slsdetectorgroup/slsDetectorPackage
+		 
+	The Conda Lib Package:
+		https://github.com/slsdetectorgroup/sls_detector_lib
+		
+	The Conda GUI Package:
+		https://github.com/slsdetectorgroup/sls_detector_gui	
+		
+	The Python Interface (including the package):
+    	https://github.com/slsdetectorgroup/sls_detector
+	
+	
+	Documentation
+	-------------
+	
+	Manual (HTML & PDF):
+		https://www.psi.ch/detectors/documentation
+		slsDetectorPackage/manual/docs/
+		
+	Command Line Documentation:
+		manual/docs/html/slsDetectorClientDocs/index.html
+		manual/docs/pdf/slsDetectorClientDocs.pdf
+		
+	C++ API Documentation:
+		manual/docs/html/slsDetectorUsersDocs/index.html
+		manual/docs/pdf/slsDetectorUsersDocs.pdf
+		
+	C++ API Example:
+		manual/manual-api/mainClient.cpp
+		manual/manual-api/mainReceiver.cpp
+		
+	Python API Documentation:
+		https://slsdetectorgroup.github.io/sls_detector/
+		
+	Further Documentation:
+		https://www.psi.ch/detectors/users-support
+		
+	
+	Support
+	-------
 
+	General Software related:
+		dhanya.thattil@psi.ch
+		anna.bergamaschi@psi.ch
+		
+	Python related:
+		erik.frojdh@psi.ch
 
 
 
 CONTENTS
 
-- 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
 
 
 
+1. Firmware Requirements
+========================
 
-Changes in User Interface
-=========================
+    	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
 
-This release supports the following features:
+    	
+    	Detector Upgrade
+    	================
+    	Gotthard	Cannot be upgraded remotely. Requires programming via USB blaster
+    	Eiger		Can be upgraded remotely via bit files
+    	Jungfrau	Can be upgraded remotely using sls_detector_put programfpga <pof>
+    	
+    	Instructions available at
+    	https://www.psi.ch/detectors/installation-instructions
+    	under Detector Upgrade -> [Detector Type] -> Firmware. 
+    	
+    	 
+	Please refer to the link below for more details on the firmware versions.
+	https://www.psi.ch/detectors/firmware.
+		
 
-  	
+
+2. Changes in User Interface
+============================
+	
+	Client
+	------
+	
+	1.	Shared Memory:
+	
+		POSIX shared memory has been implemented and they are typically created in
+		/dev/shm/ folder.
+		
+		A multiSlsDetector object will create a shared memory segment with naming style:
+		slsDetectorPackage_x_[_z]
+		and an slsDetector object will create a shared memory segment with naming style:
+		slsDetectorPackage_x_sls_y[_z]
+		 	
+		where
+		x is the multi detector id
+		y is the sls detector id
+		z is the environment variable SLSDETNAME, if set.
+		They can be deleted directly.
+		
+		Environment variable SLSDETNAME included for user-friendliness
+		of using 2 different detectors from the same client pc. One needn't use
+		different multi detector id if the SLSDETNAME is different for both consoles.
+		
+		Constructor will fail if shared memory size is different (different package
+		releases/detectors). Loading config file cleans shared memory.
+
+
+	2.	Exceptions in constructors:
+	
+		All constructors that have an error throws an exception. For this release,
+		this is caught within the package and interfaced as error codes or messages
+		to the users using command line or API.
+		
+		As a result:
+		- slsDetectorsUsers constructor signature now includes a success flag.
+		- If one uses multiSlsDetector, slsDetector, ZmqSocket classes directly, 
+		  catch exceptions from constructors.
+		- In future releases, the exception will be thrown 
+		  outside the package for the users to handle it.
+		  
+		  
+	3.	API Compatibility:
+	
+		Client now checks API version of Detector Server - Client and Receiver - Client
+		when connecting for the first time to detector server or receiver server
+		and the online flags have not been set in shm. 
+		
+		Upon failure, error messages will ensue and further commands will not 
+		be executed. Detector servers referred to are only for Eiger, Jungfrau and Gotthard.
+		
+		Previously, the detector server would exit on mismatched Firmware-Detector
+		server mismatch. They now wait for client to ask for compatibility check,
+		which is done the first time client connects to the detector and the
+		online flag in shm has not been set.
+		
+		
+	4.	Commands "type", "id" and "replace" are removed.
+		  
+		  
 	Receiver
-    	--------
-	- The files will be written in this format in the default mode:
-		* ASCII file header of 1024 bytes (only for EIGER detectors)
-		* series of images, each preceded by a Standard Header image 
-		(header described below)
+	--------
 	
-
-	- Stanard Header image header in file and call back
-	arguments defined. It is in the following format defined as 
-	sls_detector_header defined in 
-	slsReceiverSoftware/include/sls_receiver_defs.h
-	Mostly 0 if not applicatble or implemented, but updated in next release 
-	from firmware.
+	1.	Reciever Header Structure in file writing and call back:
+	
+		sls_receiver_header structure added to sls_receiver_defs.h for image headers 
+		in file writing. 
 		
-		* Frame Number       : 8 bytes 	# Image Number
-		* Exposure Length    : 4 bytes  # sub frame number in 32 bit mode
-		  		       Eiger. 
-		* Packet Number      : 4 bytes	# Number of packets in an image
-		* Bunch ID           : 8 bytes  # Bunch Id in beamline for jungfrau. 
-		* Timestamp          : 8 bytes  # Not implemened
-		* Module Id          : 2 bytes  # Not implemented
-		* X Coordinate       : 2 bytes  # Id of part of detector in 1D
-		* Y Coordinate       : 2 bytes  # Not implemented
-		* Z Coordinate       : 2 bytes  # Not implemented
-		* Debug              : 4 bytes  # Not implemented
-		* Round Robin Number : 2 bytes  # Not implemented
-		* Detector Type      : 1 byte   # Detector type defined by enum
-				                  detectorType in slsReceiverSoftware
-						  /include/sls_receiver_defs.h
-		* Header Version     : 1 byte   # 1
-	
-
-	
-	- The call back value for Start Acquisition Call back is insignificant at the 
-	moment and left for future use. Instead, the following rules apply:
-		* If file write is enabled from the client, we will write the files.
-		* If callbacks are registered, they will be called.
-	For example, the user prefers to write the data himself, one must disable
-	file write (so we dont write) and register the callbacks (so the user gets 
-	the data).
+		#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
-============
-	Eiger
-    	-----
-	- Tau is moved to settings file, Gain and offset are removed from calibration
-	file. Put settings only sets client variable, whereas putting threshold loads 
-	settings files to the server.
+	2.	ZmqSocket class:
 	
-	- Mode argument in starting up receiver is removed. FlippedData command is used
-	in config file to specify bottom.
+		If one uses ZmqSocket.h, then the json header has to be parsed outside 
+		the class to allow the user to remove the restriction in extracting all data
+		from the json header.
+
+
+	3.	Receiver Call back with modified size:
 	
+		registerCallBackRawDataModifyReady call back that is similar to the receiver 
+		registerCallBackRawDataReady has been added to allow the call back to 
+		specify an updated size of image after call back. This is in view to process
+		an image in call back (including extract only a region of the image) and 
+		provide this updated size in callback. This new resized/processed image
+		will be written to file or streamed out via zmq. This is useful in ROI
+		selection in the receiver.
+
+		This also means that the call back is now called before writing to file.
+
+
+
+3. New/Modified Commands 
+========================
+	
+	Client
+	------
+
+	1.	add (modified): 
+		appends detector to end of multi detector list.
+
+	2.	replace: 
+		sets hostname/ip address for a single detector.
+
+	3.	user: 
+		get user details from shared memory.
+
+	4.	checkdetversion: 
+		checks client version compatibility with detector server.
+
+	5.	checkrecversion: 
+		checks client version compatibility with receiver server.
+		
 	
 	Receiver
-    	--------
-	- Image Reconstruction from the files are different as packet headers are not
-	stored and a standard image header is used.
+	--------
+	
+	1.	rx_zmqip:	
+		sets/gets the zmq (TCP) ip of the receiver from where data is streamed 
+		out from. (Eg. to the gui or intermediate process). By default, it is 
+		the same as the zmqip.
+	
+	2.	zmqip: 
+		sets/gets the zmq (TCP) ip, where client listens to, to reconstuct images. 
+		(Eg. from receiver or intermediate process). By default, it is the same 
+		as rx_zmqip.
+	  		 	
+	3.	rx_jsonaddheader:
+		sets/gets additional json header to be streamed out with the zmq from 
+		receiver. Default is empty. Eg. p rx_jsonaddheader \"what\":\"nothing\"
+		
+	4.	r_discardpolicy:
+		sets/gets the frame discard policy in the receiver. 
+		nodiscard - no discard (default), 
+		discardempty - discard only empty frames, 
+		discardpartial - discard any partial frame(fastest)
+		
+	5.	r_padding:
+		sets/gets the frame padding in the receiver. 
+		0 does not pad partial frames(fastest), 
+		1 (default) pads partial frames.
+		One can look at bitmask in the sls_receiver_header to process the unpadded
+		partial	frames later.
+		
+	6.	activate (modified):
+		Extra option added to pad or unpad images in receivers when deactivated.
+		activate i [padding option], where i is activate/deactivate	and padding 
+		option is "padding" (default) or "nopadding".
+		
+	7.	rx_udpsocksize:
+		sets/gets the UDP socket buffer size. Already attempts to set by default 
+		to 100mb, 2gb for Jungfrau. Does not remember custom values	in client 
+		shared memory, so must be initialized each time after setting receiver 
+		hostname in config file.
+		
+	8.	rx_realudpsocksize:
+		gets the actual UDP socket buffer size. Usually double the set udp socket 
+		buffer size due to kernel bookkeeping.
+	
+	9.	r_framesperfile:
+		sets/gets the frames per file in receiver. 0 means infinite or all frames 
+		in a single file. Default of Eiger changed from 2k to 10k.
+		
 
+	Eiger Specific
+	--------------
 	
-	General
-    	-------
-	
-	- Users folder that gives an example on how to user the slsDetectorUsers and
-	slsReceiverUsers class.
-	
-	- Data is streamed from Receiver to Gui via ZMQ if gui call back defined.
+	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).  
 
 
 
-Resolved Issues
+4. Other New Features
+=====================
+
+	Client
+	------
+	
+	1.	(Jungfrau & Gotthard) Settingsdir and caldir is removed from config file.
+		Default dacs are stored in detector server. Hence, these folders
+		are also removed from slsDetectorPackage/settingsdir. Eiger and Mythen 
+		continue to have them.
+		
+	2.	Depending on 1d position of detectors and detsizechan in config file,
+		row and column (previously xcoord and ycoord) are given to detector 
+		servers (Eiger and Jungfrau) to encode into the udp header.
+		
+	3.	(Eiger) Setting threshold energy changes such as CAL dac is irrelevant 
+		when interpolating between two energies and VRS dac is interpolated, not copied.
+		
+	4.	Users API updated with the following functions:
+		-	setReceiverFramesDiscardPolicy
+		-	setReceiverPartialFramesPadding
+		-	setReceiverFramesPerFile
+		-	sendSoftwareTrigger
+		-	setSubFrameExposureDeadTime
+		-	setSubFrameExposureTime
+		-	enableGapPixels
+		-	getMeasuredPeriod
+		-	getMeasuredSubFramePeriod
+		-	setOverflowMode
+		-	setNumberOfStorageCells
+		-	setStoragecellStart
+		-	setThresholdEnergy (overloaded)
+		-	resetFramesCaughtInReceiver
+		-	setReceiverFifoDepth
+		-	setFlowControl10G
+		-	setTenGigabitEthernet
+		-	getNMods
+		-	setReceiverDataStreamingOutIP
+		-	setClientDataStreamingInIP
+		
+	SlsReceiver
+	-----------
+	
+	1.	slsMultiReceiver executable added that creates multiple receiver child processes.
+		./slsMultiReceiver [start_tcp_port] [num_receivers] [1 for call back, 0 for none]
+		
+	2.	Default row and column (previously xcoord and ycoord) are hardcoded 
+		for missing packets. (Eiger and Jungfrau)
+		
+
+	Gui
+	---
+	
+	1.	(Jungfrau) Gain plot included. Option under 2D options in Plot tab.
+	
+	2.	Option to maintain aspect ratio
+	
+	3.	Start and Stop separated to prevent multiple click syndrome.
+	
+
+	Detector Server
+	---------------
+	
+	1. 	(Jungfrau) To use programfpga command, one must start server with -update
+		mode and then restart server without -update mode.
+	
+	2.	(Jungfrau) ASIC Timer configured at server start up and changed a few
+		startup values for firmware v0.7 such as adc phase, ADC_PORT_INVERT_VAL
+		and ADC offset half speed value.
+		
+	3.	(Jungfrau) Minimum exposure time of 50 ns was implemented.
+	
+	4. 	(Eiger and Jungfrau) They can be configured to have x and y coord values
+		of the detector in their udp header.
+
+
+
+
+5. Resolved Issues
+==================
+
+	Client
+	------
+	memory leak for multi threading
+	
+	1.	Compiler flag -std=c++98 enforced. Debug flag removed.
+	
+	2.	If trimen gives different list from different detectors, it returns a -1.
+	
+	3.	Version format for each submodule of the package changed to just date YYMMDD.
+		Users class fixed to give correct version, instead of -1.
+		
+	4.	Getting settings in users class gave -1. Fixed now.
+
+	5.	(Jungfrau) Programming FPGA now creates the rawbin file from pof in tmp
+		rather than source file location (for permission issues).
+		
+	6.	(Gotthard) ROI segmentation fault fixed.
+		
+	Receiver
+	--------
+	
+	1.	Silent feature of receiver fixed.
+	
+	2. 	Socket descriptor misused earlier for success flag, instead exceptions
+		used that are handled inside the package.
+
+	3.	Global optind variable initialized to instantiate multiple receivers 
+		in same process. Also removed static members to enable this feature.
+		
+	4.	Socket buffer size attempts to set for each acquiistion and provide
+		warning if no capabilities. Warnings can be removed using instruction with
+		error provided. Default Jungfrau UDP socket buffer size if 2 GB, default is 
+		100 MB.
+		
+	5.	Refactored code a bit for performance and robustness, blocking push 
+		in buffer between listener and dataprocessor
+
+	
+	Detector Server
+	---------------
+	
+	1.	(Jungfrau) Stop server also mapped during a reset. Reading power status
+		instead of user input register for power.
+	
+	2.	(Eiger) Bug fix for saving trimbits to file (Advanced users).
+	
+	3.	(Gotthard 25um) config.txt is not read again after detector startup,
+		no matter the number of times the detector server is restarted. 
+
+	
+6. Known Issues
 ===============
 
-	Eiger
-    	-----
-	- Frame and packet counters in server to check delays were buggy.
-
-
-Known Issues
-============
-	- X, Y and Z Coordinates do not exactly define the position of the
-	detector in 3d. This will be defined in the next release. Other header
-	parameters will be complete in the next release.
+	Receiver
+	--------
 	
-	- Too many split files per detector especially for Eiger. Next Release will
-	have a HDF5 version, with virtual file mapping all the split files in an
-	acquisition.
+	1. 	HDF5 compression and filters are not implemented yet.
 	
-	- This version is tested only for Eiger and Jungfrau.
+	
+	Detector Server
+	---------------
+	
+	1.	(Eiger) Registers mapped differently between firmware v20 and v22.
+		So, please ensure correct on-board server before switching between
+		firmware versions. Else one cannot ping it anymore. Will need to flash firmware
+		again to recover.
+		
+	2.	(Gotthard) To switch back to all ADC from single ADC ROI, one must take
+		even number of images for the receiver to understand complete images.
+		This will be fixed in the next firmware upgrade.
+	
+	
+	
+7. Next Major Release Plans
+===========================
+
+	Client
+	------
+	
+	1.	Exceptions thrown to the user to be handled.
+	
+	2. 	Compilation using c++11.
+	
+	3.	Support of Mythen II restricted to this major and its minor releases.
+	
+	4.	Restructuring and refactoring of client code. 
+
 
 

checkout.sh

@@ -1,17 +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
-
-#git clone git@git.psi.ch:sls_detectors_software/tests.git tests

cleansharedmemory.sh

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

cmk.sh

@@ -0,0 +1,204 @@
+#!/bin/bash
+BUILDDIR="build"
+HDF5DIR="/opt/hdf5v1.10.0"
+HDF5=0
+COMPILERTHREADS=0
+TEXTCLIENT=0
+RECEIVER=0
+GUI=0
+DEBUG=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
+ -e: Debug mode
+ 
+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:trge" 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
+		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=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
+
+#Debug
+if [ $DEBUG -eq 1 ]; then
+	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+	echo "Debug Option enabled"
+fi 
+
+
+#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

@@ -1,18 +1,11 @@
-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
-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: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
@@ -23,7 +16,6 @@ type Gotthard+
 master -1
 sync none
 outdir /bigRAID/datadir_gotthard/rec_test_data
-ffdir /home/l_maliakal_d
 headerbefore none
 headerafter none
 headerbeforepar none
@@ -32,4 +24,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

examples/jungfrau.config

@@ -0,0 +1,15 @@
+hostname bchip038+
+
+0:rx_udpport 50004
+0:rx_udpip 10.1.1.100
+0:detectorip 10.1.1.10
+rx_hostname pcmoench01
+
+powerchip 1
+
+#extsig:0 trigger_in_rising_edge
+#timing trigger
+
+outdir /external_pool/jungfrau_data/softwaretest
+
+

examples/jungfrau_two.config

@@ -0,0 +1,25 @@
+detsizechan 1024 1024
+hostname bchip048+bchip052+
+
+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 trigger
+
+outdir /external_pool/jungfrau_data/softwaretest
+
+

examples/two_gotthard.config

@@ -2,23 +2,17 @@
 
 detsizechan 2560 1
 
-#type Gotthard+
 hostname bchip007+bchip009+
 
 #0:hostname bchip007
 #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: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
@@ -32,16 +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: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
@@ -63,4 +52,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

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		{  }
+
+/* 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">
+
+<LINK REL="next" HREF="node1.html">
+</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> 
+<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="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.pl

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+$key = q/mu;MSF=1.6;AAT/;
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+$key = q/Theta_o^i;MSF=1.6;AAT/;
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+$key = q/p=50~mum;MSF=1.6;AAT/;
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+$key = q/includegraphics[width=textwidth]{angleFit.eps};AAT/;
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+ SRC="|."$dir".q|img18.png"
+ ALT="\includegraphics[width=\textwidth]{angleFit.eps}">|; 
+
+$key = q/pm;MSF=1.6;AAT/;
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+ WIDTH="291" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="\begin{displaymath}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
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+$key = q/theta;MSF=1.6;AAT/;
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+1;
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manual/docs/html/angularCalibrationHowTo/images.tex

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+\batchmode
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+\RequirePackage{ifthen}
+
+
+\usepackage{amssymb}
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+\usepackage{verbatim}
+
+
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+
+
+\pagecolor[gray]{.7}
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+
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+\def\lthtmlsetmath{\hbox{\vrule width.1em\kern-.05em\vtop{\vbox{%
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+  \ifdim\dp\sizebox>0pt\kern.1em\fi \kern0.8 pt%
+  \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\centerinlinemath{%
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+
+\def\lthtmlcheckvsize{\ifdim\ht\sizebox<\vsize 
+  \ifdim\wd\sizebox<\hsize\expandafter\hfill\fi \expandafter\vfill
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+
+
+\begin{document}
+\pagestyle{empty}\thispagestyle{empty}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hsize=\the\hsize}\lthtmltypeout{}%
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+\setcounter{page}{1}
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+
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+
+\stepcounter{section}
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+\lthtmlinlinemathA{tex2html_wrap_inline84}%
+$\theta$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
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+$C_{peak}$%
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+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline88}%
+$i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline90}%
+$\Theta_e$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath18}%
+\begin{displaymath}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
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+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline94}%
+$\Theta_o^i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
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+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline96}%
+$C_{center}^{i}$%
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+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline98}%
+$R^i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline102}%
+$p=50~\mu m$%
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+\lthtmlcheckvsize\clearpage}
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+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline106}%
+$_6$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
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+\lthtmlinlinemathA{tex2html_wrap_inline108}%
+$\mu$%
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+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline110}%
+$\pm$%
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+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline120}%
+$p/R^i$%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap330}%
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+\lthtmlcheckvsize\clearpage}
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+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap334}%
+\includegraphics[width=\textwidth]{position_scan.eps}%
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+
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap340}%
+\includegraphics[width=\textwidth]{setupAngcal.eps}%
+\lthtmlpictureZ
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+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap344}%
+\includegraphics[width=\textwidth]{peakFit.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
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+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap348}%
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+\stepcounter{section}
+
+\end{document}

manual/docs/html/angularCalibrationHowTo/index.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">
+
+<LINK REL="next" HREF="node1.html">
+</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> 
+<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="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>

manual/docs/html/angularCalibrationHowTo/internals.pl

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+# LaTeX2HTML 2012 (1.2)
+# Associate internals original text with physical files.
+
+
+$key = q/fig:guiangcallog/;
+$ref_files{$key} = "$dir".q|node2.html|; 
+$noresave{$key} = "$nosave";
+
+$key = q/fig:guiposscan/;
+$ref_files{$key} = "$dir".q|node2.html|; 
+$noresave{$key} = "$nosave";
+
+$key = q/fig:peakfit/;
+$ref_files{$key} = "$dir".q|node3.html|; 
+$noresave{$key} = "$nosave";
+
+$key = q/eq:angcal/;
+$ref_files{$key} = "$dir".q|node1.html|; 
+$noresave{$key} = "$nosave";
+
+$key = q/fig:setangcal/;
+$ref_files{$key} = "$dir".q|node3.html|; 
+$noresave{$key} = "$nosave";
+
+$key = q/fig:anglefit/;
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+
+
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+
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+
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+
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+
+$key = q/fig:setangcal/;
+$external_labels{$key} = "$URL/" . q|node3.html|; 
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+
+$key = q/fig:anglefit/;
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+
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+

manual/docs/html/angularCalibrationHowTo/node1.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
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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>
+<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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+* with significant contributions from:
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+
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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>
+
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+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
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+  HREF="node2.html">Data acquisition</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html46"
+  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>
+<HR>
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+2018-09-28
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+<!--End of Navigation Panel-->
+
+<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><A NAME="SECTION00050000000000000000">
+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 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>
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manual/docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

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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>
+<BR>
+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html15"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
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+<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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+
+! Missing } inserted.
+<inserted text> 
+                }
+l.170 $CS={\begingroupN_S\endgroup
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+I've inserted something that you may have forgotten.
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+With luck, this will get me unwedged. But if you
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+
+! Missing } inserted.
+<inserted text> 
+                }
+l.170 $CS={\begingroupN_S\endgroup
+                                  \over N_0}$%
+I've inserted something that you may have forgotten.
+(See the <inserted text> above.)
+With luck, this will get me unwedged. But if you
+really didn't forget anything, try typing `2' now; then
+my insertion and my current dilemma will both disappear.
+
+! Extra \endgroup.
+<recently read> \endgroup 
+                          
+l.170 $CS={\begingroupN_S\endgroup
+                                  \over N_0}$%
+Things are pretty mixed up, but I think the worst is over.
+
+! Missing $ inserted.
+<inserted text> 
+                $
+l.170 $CS={\begingroupN_S\endgroup\over
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+I've inserted a begin-math/end-math symbol since I think
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+
+! Extra }, or forgotten $.
+l.170 $CS={\begingroupN_S\endgroup\over N_0}
+                                            $%
+I've deleted a group-closing symbol because it seems to be
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+
+! Too many }'s.
+\lthtmlinlinemathZ ->\egroup 
+                             \expandafter \ifdim \dp \sizebox >0pt \expandaf...
+l.171 \lthtmlinlinemathZ
+                        
+You've closed more groups than you opened.
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+
+l2hSize :tex2html_wrap_inline474:0.0pt::0.0pt::0.0pt.
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+
+
+]
+! Too many }'s.
+l.172 \lthtmlcheckvsize\clearpage}
+                                  
+You've closed more groups than you opened.
+Such booboos are generally harmless, so keep going.
+
+l2hSize :tex2html_wrap_inline482:7.33331pt::7.33331pt::13.06606pt.
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+l2hSize :tex2html_wrap609:436.2459pt::0.0pt::349.0pt.
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+ 14835 string characters out of 3182224
+ 55704 words of memory out of 3000000
+ 4366 multiletter control sequences out of 15000+200000
+ 5339 words of font info for 22 fonts, out of 3000000 for 9000
+ 14 hyphenation exceptions out of 8191
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+
+Output written on images.dvi (40 pages, 9712 bytes).

manual/docs/html/energyCalibrationHowTo/images.pl

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+# LaTeX2HTML 2012 (1.2)
+# Associate images original text with physical files.
+
+
+$key = q/CS=frac{N_S}{N_0};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="71" HEIGHT="38" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img32.png"
+ ALT="$CS=\frac{N_S}{N_0}$">|; 
+
+$key = q/O;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img25.png"
+ ALT="$O$">|; 
+
+$key = q/N_gamma;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="$N_\gamma$">|; 
+
+$key = q/E_t;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$E_t$">|; 
+
+$key = q/includegraphics[width=textwidth]{calibrateModule.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img40.png"
+ ALT="\includegraphics[width=\textwidth]{calibrateModule.eps}">|; 
+
+$key = q/{displaymath}N_n(E_t)simfrac{T}{tau_s}DBig(frac{-E_t}{ENC}Big).{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="169" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img23.png"
+ ALT="\begin{displaymath}
+N_n(E_t) \sim \frac{T}{\tau_s} D \Big(\frac{-E_t}{ENC} \Big).
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+$key = q/tau_s;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img21.png"
+ ALT="$\tau_s$">|; 
+
+$key = q/V_t;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
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+$key = q/ENC;MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img36.png"
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+$key = q/T;MSF=1.6;AAT/;
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+$key = q/E_0;MSF=1.6;AAT/;
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+$key = q/G;MSF=1.6;AAT/;
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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),
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+$key = q/includegraphics[width=textwidth]{GUI_ThresholdScan.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
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+ SRC="|."$dir".q|img38.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}">|; 
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+$key = q/N_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
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+ SRC="|."$dir".q|img2.png"
+ ALT="$N_0$">|; 
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+$key = q/N_S;MSF=1.6;AAT/;
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+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img5.png"
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+$key = q/O_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
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+$key = q/E_f;MSF=1.6;AAT/;
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+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
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+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
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+$key = q/G_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img31.png"
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+$key = q/includegraphics[width=textwidth]{fig7.eps};AAT/;
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+ SRC="|."$dir".q|img35.png"
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+$key = q/D;MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img13.png"
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+$key = q/N_s=C_sN_0;MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img14.png"
+ ALT="$E_t=E_0/2$">|; 
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+$key = q/includegraphics[width=textwidth]{fig4.eps};AAT/;
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+ SRC="|."$dir".q|img33.png"
+ ALT="\includegraphics[width=\textwidth]{fig4.eps}">|; 
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+
+$key = q/includegraphics[width=textwidth]{addEnergy.eps};AAT/;
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+ SRC="|."$dir".q|img39.png"
+ ALT="\includegraphics[width=\textwidth]{addEnergy.eps}">|; 
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+$key = q/C_s;MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img19.png"
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+$key = q/CS={begingroup{N_Sbegingroup{overN_0};MSF=1.6;AAT/;
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+ SRC="|."$dir".q|img6.png"
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+
+$key = q/CS=;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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+ ALT="$CS=$">|; 
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+$key = q/e^-;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
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+ 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="|."$dir".q|img28.png"
+ ALT="\begin{displaymath}
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+$key = q/Sigma>3ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
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+ 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}