release notes for 9.2.0

Pull request from Samuel ESRF

.gitignore

@@ -1,11 +1,8 @@
 .cproject
 .project
-bin/
 .settings
 *.aux
 *.log
 *.out
 *.toc
-build
-docs/
-RELEASE.txt
+

.travis.yml

@@ -1,45 +0,0 @@
-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: developer
-

CMakeLists.txt

@@ -1,57 +0,0 @@
-cmake_minimum_required(VERSION 2.8)
-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 "${CMAKE_CXX_FLAGS} -Wall -std=c++98")
-endif ()
-
-find_package(Qt4)
-find_package(Qwt 6)
-find_package(CBF)
-find_package(Doxygen)
-# find_package(PNG REQUIRED)
-
-if (USE_HDF5)
-	find_package(HDF5 1.10 COMPONENTS CXX)
-endif (USE_HDF5)
-
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-
-set(CMAKE_INSTALL_RPATH "$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(CALIBRATE)

Makefile

@@ -1,235 +0,0 @@
-# do not change below this line#
-
-# Include common definitions
-include Makefile.include
-
-INSTALLROOT	?=	$(PWD)
-BINDIR	?=	$(INSTALLROOT)/bin
-DOCDIR	?=	$(INSTALLROOT)/manual/docs
-LIBDIR	?=	$(INSTALLROOT)/bin
-INCDIR	?=	$(INSTALLROOT)/include
-DETAILDOC	?=	$(INSTALLROOT)/docs
- 
-WD				=	$(shell pwd)
-LIBRARYDIR		=	$(WD)/slsDetectorSoftware
-LIBRARYRXRDIR 		= 	$(WD)/slsReceiverSoftware
-CLIENTDIR		=	$(LIBRARYDIR)/slsDetectorClient
-GUIDIR			=	$(WD)/slsDetectorGui
-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$(LIBRARYDIR)/threadFiles -I$(LIBRARYDIR)/sharedMemory -I$(ASM)
-
-INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM) 
-#LIBFLAGRXR += 
-
-$(info )
-$(info #######################################)
-$(info #   In slsDetectorsPackage Makefile   #)
-$(info #######################################)
-$(info )
-
-
-.PHONY: all nonstatic static lib libreceiver textclient receiver gui stextclient sreceiver
-
-#all: lib textclient  receiver gui 
-all: textclient  receiver gui 
-
-nonstatic: lib libreceiver textclient receiver  gui 
-
-static: lib  libreceiver stextclient sreceiver gui 
-
-
-lib:
-	cd $(LIBRARYDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
-
-libreceiver:
-	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)' 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='$(BINDIR)'  LIBS='$(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)
-
-
-
-gui: slsDetectorGUI
-
-
-doc:
-	$(shell test -d $(DOCDIR) || mkdir -p $(DOCDIR))
-	cd manual && make all DESTDIR=$(DOCDIR)
-
-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:
-	cd $(BINDIR) && rm -rf sls_detector_* slsDetectorGui slsReceiver angularCalibrationWizard energyCalibrationWizard 
-	cd $(LIBDIR) && rm -rf libSlsDetector.so libSlsDetector.a libSlsReceiver.so libSlsReceiver.a 
-	cd $(LIBRARYDIR) && $(MAKE) clean 
-	cd $(LIBRARYRXRDIR) && $(MAKE) clean 
-	cd $(CLIENTDIR) && $(MAKE) clean
-	cd $(GUIDIR) && $(MAKE) 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: 
-#	cd $(LIBRARYDIR) && $(MAKE) install DESTDIR=$(LIBDIR) INCLUDES=$(INCLUDES)
-#	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR)
-
-mythen_virtual:
-	cd $(LIBRARYDIR) && $(MAKE) mythenVirtualServer DESTDIR=$(BINDIR)
-
-
-gotthard_virtual:
-	cd $(LIBRARYDIR) && $(MAKE) gotthardVirtualServer DESTDIR=$(BINDIR)
-
-
-install_client: textclient slsReceiver
-
-install_gui: gui
-
-confinstall:
-	make conf;\
-	make install
-
-install_lib: 
-	make lib;\
-	make libreceiver; \
-	make textclient; \
-	make slsReceiver; \
-	make doc; \
-	make htmldoc; \
-	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR); \
-	cd $(LIBRARYRXRDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);
-
-install: 
-	make install_lib; \
-	make gui; \
-	make calWiz; \
-	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);\
-	cd $(LIBRARYRXRDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);
-
-conf:
-	set -e; \
-	. ./configure; \
-	@echo "INSTALLROOT is $(INSTALLROOT)"
-	@echo "BINDIR is $(BINDIR)"
-	@echo "LIBDIR is $(LIBDIR)"
-	@echo "INCDIR is $(INCDIR)"
-	@echo "DOCDIR is $(DOCDIR)"
-
-
-help:
-	@echo "Targets:"
-	@echo "make all 		compile library,  text clients, data reciever"
-	@echo "make lib 		compile library"
-	@echo "make libreceiver 		compile receiver library"
-	@echo "make textclient		compile the slsDetectorClient dynamically linking the libraries"
-	@echo "make stextclient 		compile slsDetectorClient statically linking the libraries"
-	@echo "make receiver		compile the slsReciever dynamically linking the libraries"
-	@echo "make sreceiver		compile the slsReciever statically linking the libraries"
-	@echo "make gui			compile slsDetectorGUI - requires a working Qt4 and Qwt installation"
-	@echo "make calWiz 		compile the calibration wizards - requires a working Root installation"
-	@echo "make doc			compile pdf documentation"
-	@echo "make htmldoc		compile html (and pdf) documentation"
-	@echo "make install_lib         installs the libraries, the text clients, the documentation and the includes for the API"
-	@echo "make install             installs all software, including the gui, the cal wizards and the includes for the API"
-	@echo "make confinstall         installs all software, including the gui, the cal wizards and the includes for the API, prompting for the install paths"
-	@echo "make clean              	remove object files and executables"
-	@echo "make help               	lists possible targets"
-	@echo ""
-	@echo ""
-	@echo "Makefile variables"
-	@echo "DEBUG=1,2		 set debug level to 1 (VERBOSE) or 2 (VERYVERBOSE)"
-	@echo ""
-	@echo ""
-	@echo "Variables -  to change them run <source configure> :"
-	@echo "INSTALLROOT=<yourdir>:    installation root di	r, default $PWD"
-	@echo "BINDIR=<yourbin>:         binary installation dir below INSTALLROOT, default bin"
-	@echo "LIBDIR=<yourlib>:         library installation dir below INSTALLROOT, default lib"
-	@echo "INCDIR=<yourincludes>:    header installation dir below INSTALLROOT, default include"
-	@echo "DOCDIR=<yourdoc>:         documentation installation dir below INSTALLROOT, default doc"

Makefile.include

@@ -1,58 +0,0 @@
-##############################################################
-# Generic 
-##############################################################
-
-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
-# -DVERBOSE 
-
-# Setting up the verbose flags
-ifeq ($(DEBUG),1)
-     FLAGS = -Wall -DVERBOSE
-endif
-ifeq ($(DEBUG),2)
-     FLAGS = -Wall -DVERYVERBOSE
-endif
-
-##############################################################
-# HDF5 specific. Set this to yes, if you want to compile
-# HDF5 code: in this case, you need HDF5 libraries
-##############################################################   
-
-HDF5 = no
-HDF5_DIR = /opt/hdf5v1.10.0
-
-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	
-
-
-##############################################################
-# ROOTSLS specific. Set this to yes, if you want to compile
-# ROOTSLS code: in this case, you need also root libraries
-##############################################################   
-
-ROOTSLS = no
-
-ROOTFLAGS = $(shell root-config --cflags --glibs) -DMYROOT1   #-DALLFILE_DEBUG #-DMYROOT1 
-
-ifeq ($(ROOTSLS),yes)
-     LDFLAGRXR = -L$(LIBDIR) -lSlsReceiver $(ROOTFLAGS) -DROOTSLS
-endif
-
-
-define colorecho
-      @tput setaf 6
-      @echo $1
-      @tput sgr0
-endef
-
-
-
-

README.md

@@ -1,91 +0,0 @@
-### 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)
-
-### 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
-
-```
-#### 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.
-
-* Advanced user Calibration wizards<br>
-Requirements: ROOT
-```
-    export ROOTSYS=/usr/local/root-5.34
-```
-
-#### 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 slsDetectorPackage-build
-    $ cd slsDetectorPackage-build
-    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=OFF 
-    $ make
-```
-
-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 slsMultiReceiver
-```

cleansharedmemory.sh

@@ -1 +0,0 @@
-rm /dev/shm/slsDetectorPackage*;

cmake/FindCBF.cmake

@@ -1,11 +0,0 @@
-FIND_PATH (CBF_INCLUDE_DIR
-    ${CBF_DIR}/include
-    ${CBF_DIR}/include/cbflib
-)
-FIND_LIBRARY (CBF_LIBRARY
-    NAMES cbf
-    HINTS ${CBF_DIR}/lib
-)
-INCLUDE ( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS (CBF DEFAULT_MSG CBF_LIBRARY CBF_INCLUDE_DIR )
-

cmake/FindQwt.cmake

@@ -1,118 +0,0 @@
-# Qt Widgets for Technical Applications
-# available at http://www.http://qwt.sourceforge.net/
-#
-# The module defines the following variables:
-#  QWT_FOUND - the system has Qwt
-#  QWT_INCLUDE_DIR - where to find qwt_plot.h
-#  QWT_INCLUDE_DIRS - qwt includes
-#  QWT_LIBRARY - where to find the Qwt library
-#  QWT_LIBRARIES - aditional libraries
-#  QWT_MAJOR_VERSION - major version
-#  QWT_MINOR_VERSION - minor version
-#  QWT_PATCH_VERSION - patch version
-#  QWT_VERSION_STRING - version (ex. 5.2.1)
-#  QWT_ROOT_DIR - root dir (ex. /usr/local)
-
-#=============================================================================
-# Copyright 2010-2013, Julien Schueller
-# All rights reserved.
-# 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met: 
-# 
-# 1. Redistributions of source code must retain the above copyright notice, this
-#    list of conditions and the following disclaimer. 
-# 2. Redistributions in binary form must reproduce the above copyright notice,
-#    this list of conditions and the following disclaimer in the documentation
-#    and/or other materials provided with the distribution. 
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
-# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-# The views and conclusions contained in the software and documentation are those
-# of the authors and should not be interpreted as representing official policies, 
-# either expressed or implied, of the FreeBSD Project.
-#=============================================================================
-
-
-find_path ( QWT_INCLUDE_DIR
-  NAMES qwt_plot.h
-  HINTS $ENV{QWTDIR} $ENV{QWTDIR}/src ${QT_INCLUDE_DIR}
-  PATH_SUFFIXES qwt qwt-qt3 qwt-qt4 qwt-qt5
-)
-
-set ( QWT_INCLUDE_DIRS ${QWT_INCLUDE_DIR} )
-
-# version
-set ( _VERSION_FILE ${QWT_INCLUDE_DIR}/qwt_global.h )
-if ( EXISTS ${_VERSION_FILE} )
-  file ( STRINGS ${_VERSION_FILE} _VERSION_LINE REGEX "define[ ]+QWT_VERSION_STR" )
-  if ( _VERSION_LINE )
-    string ( REGEX REPLACE ".*define[ ]+QWT_VERSION_STR[ ]+\"(.*)\".*" "\\1" QWT_VERSION_STRING "${_VERSION_LINE}" )
-    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\1" QWT_MAJOR_VERSION "${QWT_VERSION_STRING}" )
-    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\2" QWT_MINOR_VERSION "${QWT_VERSION_STRING}" )
-    string ( REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)" "\\3" QWT_PATCH_VERSION "${QWT_VERSION_STRING}" )
-  endif ()
-endif ()
-
-
-# check version
-set ( _QWT_VERSION_MATCH TRUE )
-if ( Qwt_FIND_VERSION AND QWT_VERSION_STRING )
-  if ( Qwt_FIND_VERSION_EXACT )
-    if ( NOT Qwt_FIND_VERSION VERSION_EQUAL QWT_VERSION_STRING )
-      set ( _QWT_VERSION_MATCH FALSE )
-    endif ()
-  else ()
-    if ( QWT_VERSION_STRING VERSION_LESS Qwt_FIND_VERSION )
-      set ( _QWT_VERSION_MATCH FALSE )
-    endif ()
-  endif ()
-endif ()
-
-
-find_library ( QWT_LIBRARY
-  NAMES qwt qwt-qt3 qwt-qt4 qwt-qt5
-  HINTS $ENV{QWTDIR}/lib ${QT_LIBRARY_DIR}
-)
-
-set ( QWT_LIBRARIES ${QWT_LIBRARY} )
-
-
-# try to guess root dir from include dir
-if ( QWT_INCLUDE_DIR )
-  string ( REGEX REPLACE "(.*)/include.*" "\\1" QWT_ROOT_DIR ${QWT_INCLUDE_DIR} )
-# try to guess root dir from library dir
-elseif ( QWT_LIBRARY )
-  string ( REGEX REPLACE "(.*)/lib[/|32|64].*" "\\1" QWT_ROOT_DIR ${QWT_LIBRARY} )
-endif ()
-
-
-# handle the QUIETLY and REQUIRED arguments
-include ( FindPackageHandleStandardArgs )
-if ( CMAKE_VERSION LESS 2.8.3 )
-  find_package_handle_standard_args( Qwt DEFAULT_MSG QWT_LIBRARY QWT_INCLUDE_DIR _QWT_VERSION_MATCH )
-else ()
-  find_package_handle_standard_args( Qwt REQUIRED_VARS QWT_LIBRARY QWT_INCLUDE_DIR _QWT_VERSION_MATCH VERSION_VAR QWT_VERSION_STRING )
-endif ()
-
-
-mark_as_advanced (
-  QWT_LIBRARY 
-  QWT_LIBRARIES
-  QWT_INCLUDE_DIR
-  QWT_INCLUDE_DIRS
-  QWT_MAJOR_VERSION
-  QWT_MINOR_VERSION
-  QWT_PATCH_VERSION
-  QWT_VERSION_STRING
-  QWT_ROOT_DIR
-)

cmake/FindROOT.cmake

@@ -1,167 +0,0 @@
-# - Finds ROOT instalation
-# This module sets up ROOT information 
-# It defines:
-# ROOT_FOUND          If the ROOT is found
-# ROOT_INCLUDE_DIR    PATH to the include directory
-# ROOT_LIBRARIES      Most common libraries
-# ROOT_GUI_LIBRARIES  Most common libraries + GUI
-# ROOT_LIBRARY_DIR    PATH to the library directory 
-
-
-find_program(ROOT_CONFIG_EXECUTABLE root-config
-  PATHS $ENV{ROOTSYS}/bin)
-
-if(NOT ROOT_CONFIG_EXECUTABLE)
-  set(ROOT_FOUND FALSE)
-else()    
-  set(ROOT_FOUND TRUE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --prefix 
-    OUTPUT_VARIABLE ROOTSYS 
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --version 
-    OUTPUT_VARIABLE ROOT_VERSION
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --incdir
-    OUTPUT_VARIABLE ROOT_INCLUDE_DIR
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --libs
-    OUTPUT_VARIABLE ROOT_LIBRARIES
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --glibs
-    OUTPUT_VARIABLE ROOT_GUI_LIBRARIES
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lThread -lMinuit -lHtml -lVMC -lEG -lGeom -lTreePlayer -lXMLIO -lProof)
-  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lProofPlayer -lMLP -lSpectrum -lEve -lRGL -lGed -lXMLParser -lPhysics)
-  set(ROOT_LIBRARY_DIR ${ROOTSYS}/lib)
-
-  # Make variables changeble to the advanced user
-  mark_as_advanced(ROOT_CONFIG_EXECUTABLE)
-
-  if(NOT ROOT_FIND_QUIETLY)
-    message(STATUS "Found ROOT ${ROOT_VERSION} in ${ROOTSYS}")
-  endif()
-endif()
-
-
-include(CMakeParseArguments)
-find_program(ROOTCINT_EXECUTABLE rootcint PATHS $ENV{ROOTSYS}/bin)
-find_program(GENREFLEX_EXECUTABLE genreflex PATHS $ENV{ROOTSYS}/bin)
-find_package(GCCXML)
-
-#----------------------------------------------------------------------------
-# function ROOT_GENERATE_DICTIONARY( dictionary   
-#                                    header1 header2 ... 
-#                                    LINKDEF linkdef1 ... 
-#                                    OPTIONS opt1...)
-function(ROOT_GENERATE_DICTIONARY dictionary)
-  CMAKE_PARSE_ARGUMENTS(ARG "" "" "LINKDEF;OPTIONS" "" ${ARGN})
-  #---Get the list of header files-------------------------
-  set(headerfiles)
-  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
-    file(GLOB files ${fp})
-    if(files)
-      foreach(f ${files})
-        if(NOT f MATCHES LinkDef)
-          set(headerfiles ${headerfiles} ${f})
-        endif()
-      endforeach()
-    else()
-      set(headerfiles ${headerfiles} ${fp})
-    endif()
-  endforeach()
-  #---Get the list of include directories------------------
-  get_directory_property(incdirs INCLUDE_DIRECTORIES)
-  set(includedirs) 
-  foreach( d ${incdirs})    
-   set(includedirs ${includedirs} -I${d})
-  endforeach()
-  #---Get LinkDef.h file------------------------------------
-  set(linkdefs)
-  foreach( f ${ARG_LINKDEF})
-    if( IS_ABSOLUTE ${f})
-      set(linkdefs ${linkdefs} ${f})
-    else() 
-      if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
-        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
-      else()
-        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/${f})
-      endif()
-    endif()
-  endforeach()
-  #---call rootcint------------------------------------------
-  add_custom_command(OUTPUT ${dictionary}.cxx ${dictionary}.h
-                     COMMAND ${ROOTCINT_EXECUTABLE} -cint -f  ${dictionary}.cxx 
-                                          -c ${ARG_OPTIONS} ${includedirs} ${headerfiles} ${linkdefs} 
-                     DEPENDS ${headerfiles} ${linkdefs})
-endfunction()
-
-#----------------------------------------------------------------------------
-# function REFLEX_GENERATE_DICTIONARY(dictionary   
-#                                     header1 header2 ... 
-#                                     SELECTION selectionfile ... 
-#                                     OPTIONS opt1...)
-function(REFLEX_GENERATE_DICTIONARY dictionary)  
-  CMAKE_PARSE_ARGUMENTS(ARG "" "" "SELECTION;OPTIONS" "" ${ARGN})
-  #---Get the list of header files-------------------------
-  set(headerfiles)
-  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
-    file(GLOB files ${fp})
-    if(files)
-      foreach(f ${files})
-        set(headerfiles ${headerfiles} ${f})
-      endforeach()
-    else()
-      set(headerfiles ${headerfiles} ${fp})
-    endif()
-  endforeach()
-  #---Get Selection file------------------------------------
-  if(IS_ABSOLUTE ${ARG_SELECTION})
-    set(selectionfile ${ARG_SELECTION})
-  else() 
-    set(selectionfile ${CMAKE_CURRENT_SOURCE_DIR}/${ARG_SELECTION})
-  endif()
-  #---Get the list of include directories------------------
-  get_directory_property(incdirs INCLUDE_DIRECTORIES)
-  set(includedirs) 
-  foreach( d ${incdirs})    
-    set(includedirs ${includedirs} -I${d})
-  endforeach()
-  #---Get preprocessor definitions--------------------------
-  get_directory_property(defs COMPILE_DEFINITIONS)
-  foreach( d ${defs})    
-   set(definitions ${definitions} -D${d})
-  endforeach()
-  #---Nanes and others---------------------------------------
-  set(gensrcdict ${dictionary}.cpp)
-  if(MSVC)
-    set(gccxmlopts "--gccxmlopt=\"--gccxml-compiler cl\"")
-  else()
-    #set(gccxmlopts "--gccxmlopt=\'--gccxml-cxxflags -m64 \'")
-    set(gccxmlopts)
-  endif()  
-  #set(rootmapname ${dictionary}Dict.rootmap)
-  #set(rootmapopts --rootmap=${rootmapname} --rootmap-lib=${libprefix}${dictionary}Dict)
-  #---Check GCCXML and get path-----------------------------
-  if(GCCXML)
-    get_filename_component(gccxmlpath ${GCCXML} PATH)
-  else()
-    message(WARNING "GCCXML not found. Install and setup your environment to find 'gccxml' executable")
-  endif()
-  #---Actual command----------------------------------------
-  add_custom_command(OUTPUT ${gensrcdict} ${rootmapname}     
-                     COMMAND ${GENREFLEX_EXECUTABLE} ${headerfiles} -o ${gensrcdict} ${gccxmlopts} ${rootmapopts} --select=${selectionfile}
-                             --gccxmlpath=${gccxmlpath} ${ARG_OPTIONS} ${includedirs} ${definitions}
-                     DEPENDS ${headerfiles} ${selectionfile})
-endfunction()
-  

cmk.sh

@@ -1,204 +0,0 @@
-#!/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
-
-
-
-
-
-

commitVersions.sh

@@ -1,15 +0,0 @@
-sh updateSvnVersion.sh
-
-cd slsDetectorGui
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ../slsDetectorSoftware
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ../slsReceiverSoftware
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ..

configure

@@ -1,58 +0,0 @@
-##!/bin/bash
-
-: ${INSTALLROOT=$PWD}
-read -p "Installation directory [default:\"$INSTALLROOT\"]:" -e t3
-if [ -z "$t3" ]
-then
-echo
-else
-	INSTALLROOT=$t3
-fi
-echo "INSTALLROOT will be  \"$INSTALLROOT\""	
-export INSTALLROOT
-
-: ${BINDIR="bin"}
-read -p "Binaries directory [default:\"$BINDIR\"]:" -e t4
-if [ -z "$t4" ]
-then
-	BINDIR=$INSTALLROOT/$BINDIR
-else
-	BINDIR=$INSTALLROOT/$t4
-fi
-echo "BINDIR will be  \"$BINDIR\""	
-export BINDIR
-
-: ${LIBDIR="bin"}
-read -p "Libraries directory [default:\"$LIBDIR\"]:" -e t5
-if [ -z "$t5" ]
-then
-	LIBDIR=$INSTALLROOT/$LIBDIR
-else
-	LIBDIR=$INSTALLROOT/$t5
-fi	
-echo "LIBDIR will be  \"$LIBDIR\""	
-export LIBDIR
-
-:  ${INCDIR="include"}
-read -p "Includes directory [default:\"$INCDIR\"]:" -e t6
-if [ -z "$t6" ]
-then
-	INCDIR=$INSTALLROOT/$INCDIR
-else
-	INCDIR=$INSTALLROOT/$t6
-fi	
-echo "INCDIR will be  \"$INCDIR\""	
-export INCDIR
-
-:  ${DOCDIR="doc"}
-read -p "Documentation directory [default:\"$DOCDIR\"]:" -e t7
-if [ -z "$t7" ]
-then
-	DOCDIR=$INSTALLROOT/$DOCDIR
-else	
-	DOCDIR=$INSTALLROOT/$t7
-fi
-echo "DOCDIR will be  \"$DOCDIR\""
-export DOCDIR
-
-

docs/html/angularCalibrationHowTo/WARNINGS

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

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 */

docs/html/angularCalibrationHowTo/angularCalibrationHowTo.html

@@ -0,0 +1,81 @@
+<!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="next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="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>April 8, 2019</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
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/angularCalibrationHowTo/images.pl

@@ -0,0 +1,116 @@
+# LaTeX2HTML 2012 (1.2)
+# Associate images original text with physical files.
+
+
+$key = q/Theta_e;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$\Theta_e$">|; 
+
+$key = q/C_{center}^{i};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$C_{center}^{i}$">|; 
+
+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="$i$">|; 
+
+$key = q/mu;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\mu$">|; 
+
+$key = q/Theta_o^i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$\Theta_o^i$">|; 
+
+$key = q/includegraphics[width=textwidth]{enable_angcal.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="\includegraphics[width=\textwidth]{enable_angcal.eps}">|; 
+
+$key = q/p=50~mum;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="79" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$p=50&nbsp;\mu m$">|; 
+
+$key = q/C_{peak};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$C_{peak}$">|; 
+
+$key = q/_6;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$_6$">|; 
+
+$key = q/includegraphics[width=textwidth]{peakFit.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="\includegraphics[width=\textwidth]{peakFit.eps}">|; 
+
+$key = q/pslashR^i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="38" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$p/R^i$">|; 
+
+$key = q/includegraphics[width=textwidth]{setupAngcal.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{angleFit.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img18.png"
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+

docs/html/angularCalibrationHowTo/images.tex

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docs/html/angularCalibrationHowTo/index.html

@@ -0,0 +1,81 @@
+<!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="next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="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>April 8, 2019</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
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/angularCalibrationHowTo/internals.pl

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+

docs/html/angularCalibrationHowTo/labels.pl

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+# LaTeX2HTML 2012 (1.2)
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+

docs/html/angularCalibrationHowTo/node1.html

@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2012 (1.2)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
+<META NAME="description" CONTENT="Introduction">
+<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">
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+<LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
+
+<LINK REL="next" HREF="node2.html">
+<LINK REL="previous" HREF="angularCalibrationHowTo.html">
+<LINK REL="up" HREF="angularCalibrationHowTo.html">
+<LINK REL="next" HREF="node2.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html23"
+  HREF="node2.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
+<A NAME="tex2html21"
+  HREF="angularCalibrationHowTo.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A> 
+<A NAME="tex2html15"
+  HREF="angularCalibrationHowTo.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>   
+<BR>
+<B> Next:</B> <A NAME="tex2html24"
+  HREF="node2.html">Data acquisition</A>
+<B> Up:</B> <A NAME="tex2html22"
+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
+<B> Previous:</B> <A NAME="tex2html16"
+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+In order to convert from strip number to 2<IMG
+ WIDTH="12" HEIGHT="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>
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+<H1><A NAME="SECTION00020000000000000000">
+Data acquisition</A>
+</H1>
+
+<P>
+The angular calibration consists in acquiring a set of diffraction patterns of a well known powder standard (e.g. Silicon) at different encoder positions.  In order to facilitate the procedure, the sample should not emit fluorescent light and should present relatively symmetric peaks. 
+<BR>
+During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position. In general the highest peak will be used for the calibration, but this is not necessary in case there would be e.g. geometrical limitations for shifting the detector. 
+<BR><B>Do not forget to properly position the beam stopper if the detector is scanned in front of the direct beam.</B>
+<BR>
+The detector should be shifted of an angular step of the order of about 2% of the module size, such that about 50 patterns can contribute to the fitting of the 3 parameters necessary for the angular calibration.
+<BR>
+<P>
+All the angular calibration procedure should be acquired using a trimmed detector with the threshold set at half of the X-ray energy (Assuming no fluorescent element in the standard). A flat field should also be acquired in order to precisely correct the data, while the X-ray intensity should be kept lower than about 100&nbsp;kHz per strip in order to avoid the need for rate corrections.
+
+<P>
+A rough angular conversion file starting from a previous calibration or from the geometric characteristics of the mechanics is an advantage. The angular conversion file should contain a line for each module of the detector with its module number <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$">, center  <!-- MATH
+ $C_{center}^{i}$
+ -->
+<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$C_{center}^{i}$"> and error, conversion radius <IMG
+ WIDTH="38" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img13.png"
+ ALT="$p/R^i$"> and error, offset <IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$\Theta_o^i$"> and error:
+<PRE>
+module 0 center 639.5 +- 0 conversion 6.56E-05 +- 0 offset 0 +- 0
+</PRE>
+Also the <I>global offset</I> value of the beamline should be approximately known i.e. the angular position of channel 0 of module 0 when the motor is set at 0. 
+<BR>
+All the documentation assumes that the detector is oriented in the same direction as the encoder position i.e. large channel number at higher angles (both per module and absolute). If this is not the case, the <I>angular direction</I> should be set to -1. 
+
+<P>
+
+<H2><A NAME="SECTION00021000000000000000">
+Software</A>
+</H2>
+
+<P>
+For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.
+<BR>
+<P>
+Please make sure that you have edited the 
+<BR><I>slsDetectorSoftware/usersFunctions/angleFunction.h</I> 
+<BR>
+in order to match the angular conversion for your geometry and 
+<BR><I>slsDetectorSoftware/usersFunctions/usersFunctions.cpp</I> 
+<BR>
+in order to be able to move the detector and read out its position by using the slsDetector software.
+
+<P>
+In the following the command to acquire a dataset for the angular calibration with an exposure time of 1&nbsp;s, and position shift 
+<PRE>
+#setup angular calibration log mode
+&gt; sls_detector_put angcallog 1 
+#set exposure time to 1s
+&gt; sls_detector_put exptime 1. 
+#setup threshold scan
+&gt; sls_detector_put scan0script position 
+#setup the precision for the scan variable in the file name
+&gt; sls_detector_put scan0prec 2 
+#set scan range between 20deg and -60deg, step of -0.1deg
+# (at 12.4 keV the Si(111) peak is at approx 19deg
+&gt; sls_detector_put scan0range 20 -60 -0.1 
+#acquire the data
+&gt; sls_detector_acquire
+#unset angular calibration log mode
+&gt; sls_detector_put angcallog 0
+</PRE>
+
+<P>
+With the GUI you can obtain the same results by clicking on the <I>Angular calibration</I> log button in the advanced tab (see figure&nbsp;<A HREF="#fig:guiangcallog">1</A>) and setting up the motor position scan in the Actions tab (see figure&nbsp;<A HREF="#fig:guiposscan">2</A>). The exposure time should also be set in the measurement tab.
+
+<P>
+Additional to the data files, the acquisition will produce a .angcal file containing an header and, for each step of the acquisition, the exect value of the motor position and the file name. 
+<BR>
+In case you forgot to enable the angcallog flag in the software, you can produce the file with the syntax as follows, assuming that you know the exact values of your encoder for each frame:
+<PRE>
+type Mythen
+maxmod 32
+nmod 32
+angconv /scratch/angcal20120422/ang.off
+globaloff 5.088
+fineoff 0.0
+angdir 1
+ffdir /scratch/angcal20120422/
+flatfield flatfield_E12keV_T6keV_0.raw
+badchannels /scratch/cal/bad.chans
+19.99998 angcal_S20.00_0
+19.90001 angcal_S19.90_0
+19.79999 angcal_S19.80_0
+19.70002 angcal_S19.70_0
+......
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiangcallog"></A><A NAME="46"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 1:</STRONG>
+Acquisition GUI window to enable the angular calibration log.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img14.png"
+ ALT="\includegraphics[width=\textwidth]{enable_angcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiposscan"></A><A NAME="51"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 2:</STRONG>
+Acquisition GUI window to setup the motor position scan.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img15.png"
+ ALT="\includegraphics[width=\textwidth]{position_scan.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
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+<H1><A NAME="SECTION00030000000000000000">
+Data analysis</A>
+</H1>
+
+<P>
+The data analysis consists in fitting with a gaussian the selected peak of the powder pattern for each position in order to determine its position is channel number as a function of the encoder position. 
+<BR>
+In a second step, for each module, the channel vs. encoder curve is fitted in order to extrapolate the three parameters necessary for the angular conversion and the result is written to file
+
+<P>
+
+<H2><A NAME="SECTION00031000000000000000">
+Software</A>
+</H2>
+
+<P>
+The software used for the angular calibration data analysis is based on root (see http://root.cern.ch).
+<BR>
+This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
+
+<P>
+To start the data analysis simply launch:
+<PRE>
+&gt; ./angularCalibrationWizard
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:setangcal"></A><A NAME="60"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 3:</STRONG>
+Overview of the nagular calibration dataset.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img16.png"
+ ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+To setup the angular calibration dataset, the .angcal file should be selected (or digited) and the load button should be pressed to confirm. The parameters of the angular calibration are then read to the file and the data loaded for a quick overview (see figure&nbsp;<A HREF="#fig:setangcal">3</A>).
+<BR>
+The software assumes that the data files (.raw) and the .encal file are in the same directory.
+<BR>
+A 2D color plot will show a rebinned overview of the dataset. The peak to be fitted should be visible as a high intensity diagonal line passing through all the channels.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:peakfit"></A><A NAME="66"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 4:</STRONG>
+Preview of the fitting of the Si(111) peak for one of the detector positions.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img17.png"
+ ALT="\includegraphics[width=\textwidth]{peakFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+For a more detailed view of the data, one can select an angular calibration step from the combo box, select the plot mode (raw data or processed data as a function of channel number, processed angular converted data, flat field data, or again an overview of the whole dataset). 
+<BR>
+By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.
+<BR>
+<P>
+If the bad channel list, angular conversion file or flat field file are changed compared to the acquisition, they can be reloaded by editing the correspondent text entries and pressing enter.
+
+<P>
+In particular, the angular converted data should be checked in order to view the position of the selected peak. In this case, the plot will be zoomed to the angular region slected in the minimum and maximum angle entries. By pressing fit, the fit of the peak in the selected angular range will be shown (see figure&nbsp;<A HREF="#fig:peakfit">4</A>).  It is useful to check that it works properly in several positions such that then the sequential fitting on all steps can give good results.
+
+<P>
+To automatically fit all positions simply press <I>Proceed to Modules Calibration</I> and wait until all steps are fitted. This can take sometime, depending on the number of steps.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:anglefit"></A><A NAME="73"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 5:</STRONG>
+Window for fitting the angular calibration parameters of a module.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img18.png"
+ ALT="\includegraphics[width=\textwidth]{angleFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+In the module calibration window (see figure&nbsp;<A HREF="#fig:anglefit">5</A>), you will be able to fit the channel number to encoder position curve to estimate the three angular calibration parameters for each module.
+<BR>
+The entries show the angular calibration parameters used for approximate angular conversion in the previous step of the calibration. These can be edited and will be used as start parameters for the fit.
+By clicking on the check box next to the parameters, the selected parameter will be set and fixed during the fit. Often the center is used as a fix parameter.
+<BR>
+It is possible to navigate between modules by using the Previous and Next module buttons. To refit the current module (e.g. after changing one of the parameters) simply re-click on the module number.
+
+<P>
+After fitting all modules you can click on the <I>Write Angular Calibration</I> button, select the file name to write to and save the calibration angulat calibration data. Please note that the offset of module 0 will always be 0 and the other values will be rescaled to its value. Therefore the global offset of the steup will always need to be specified for a proper angular conversion unless the home of the encoder will not be redifined.
+
+<P>
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+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
+<A NAME="tex2html53"
+  HREF="angularCalibrationHowTo.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A> 
+<A NAME="tex2html47"
+  HREF="node3.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>   
+<BR>
+<B> Next:</B> <A NAME="tex2html56"
+  HREF="node5.html">About this document ...</A>
+<B> Up:</B> <A NAME="tex2html54"
+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
+<B> Previous:</B> <A NAME="tex2html48"
+  HREF="node3.html">Data analysis</A>
+<BR>
+<BR>
+<!--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
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/angularCalibrationHowTo/node5.html

@@ -0,0 +1,68 @@
+<!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>About this document ...</TITLE>
+<META NAME="description" CONTENT="About this document ...">
+<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="previous" HREF="node4.html">
+<LINK REL="up" HREF="angularCalibrationHowTo.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next_g.png"> 
+<A NAME="tex2html61"
+  HREF="angularCalibrationHowTo.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A> 
+<A NAME="tex2html57"
+  HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>   
+<BR>
+<B> Up:</B> <A NAME="tex2html62"
+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
+<B> Previous:</B> <A NAME="tex2html58"
+  HREF="node4.html">Setup calibration files</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<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>
+The command line arguments were: <BR>
+ <STRONG>latex2html</STRONG> <TT>-local_icons -split 4 angularCalibrationHowTo.tex</TT>
+<P>
+The translation was initiated by Thattil Dhanya on 2019-04-08
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/energyCalibrationHowTo/WARNINGS

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

docs/html/energyCalibrationHowTo/energyCalibrationHowTo.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 */

docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

@@ -0,0 +1,81 @@
+<!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>Energy calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Energy calibration wizard manual">
+<META NAME="keywords" CONTENT="energyCalibrationHowTo">
+<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="energyCalibrationHowTo.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html9"
+  HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html10"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>April 8, 2019</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html11"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html12"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html13"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html15"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html17"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/energyCalibrationHowTo/images.pl

@@ -0,0 +1,252 @@
+# 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).
+\end{displaymath}">|; 
+
+$key = q/tau_s;MSF=1.6;AAT/;
+$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{$key} = q|<IMG
+ WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img27.png"
+ ALT="$V_t$">|; 
+
+$key = q/ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="$ENC$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig8.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img36.png"
+ ALT="\includegraphics[width=\textwidth]{fig8.eps}">|; 
+
+$key = q/N_n;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="26" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="$N_n$">|; 
+
+$key = q/T;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="16" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img22.png"
+ ALT="$T$">|; 
+
+$key = q/E_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img1.png"
+ ALT="$E_0$">|; 
+
+$key = q/G;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img26.png"
+ ALT="$G$">|; 
+
+$key = q/{displaymath}N_gamma(E_t)=frac{N_0}{2}cdotBig(1+C_sfrac{E_0-2E_t}{E_0}Big)DBig(frac{E_0-E_t}{ENC}Big),{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="335" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img18.png"
+ ALT="\begin{displaymath}
+N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big),
+\end{displaymath}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_ThresholdScan.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img38.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}">|; 
+
+$key = q/N_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$N_0$">|; 
+
+$key = q/N_S;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="$N_S$">|; 
+
+$key = q/O_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img30.png"
+ ALT="$O_i$">|; 
+
+$key = q/E_f;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$E_f$">|; 
+
+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img29.png"
+ ALT="$i$">|; 
+
+$key = q/G_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img31.png"
+ ALT="$G_i$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig7.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="553" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img35.png"
+ ALT="\includegraphics[width=\textwidth]{fig7.eps}">|; 
+
+$key = q/D;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$D$">|; 
+
+$key = q/N_s=C_sN_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="83" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img20.png"
+ ALT="$N_s=C_s N_0$">|; 
+
+$key = q/E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="39" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="$E_0/2$">|; 
+
+$key = q/E_t=E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="78" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="$E_t=E_0/2$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig4.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img33.png"
+ ALT="\includegraphics[width=\textwidth]{fig4.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_Advanced.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img37.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_Advanced.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{addEnergy.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img39.png"
+ ALT="\includegraphics[width=\textwidth]{addEnergy.eps}">|; 
+
+$key = q/C_s;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img19.png"
+ ALT="$C_s$">|; 
+
+$key = q/CS={begingroup{N_Sbegingroup{overN_0};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="12" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$CS={\begingroupN_S\endgroup\over N_0}$">|; 
+
+$key = q/CS=;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$CS=$">|; 
+
+$key = q/e^-;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$e^-$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig5.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img34.png"
+ ALT="\includegraphics[width=\textwidth]{fig5.eps}">|; 
+
+$key = q/{displaymath}V_{t}=O+GcdotE_t.{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="111" HEIGHT="26" BORDER="0"
+ SRC="|."$dir".q|img28.png"
+ ALT="\begin{displaymath}
+V_{t}=O+G \cdot E_t.
+\end{displaymath}">|; 
+
+$key = q/Sigma>3ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="85" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\Sigma &gt;3ENC$">|; 
+
+$key = q/N;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="$N$">|; 
+
+$key = q/Sigma>3,ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="88" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img24.png"
+ ALT="$\Sigma&gt;3 ENC$">|; 
+
+$key = q/Deltasim;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="35" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$\Delta \sim $">|; 
+
+1;
+

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
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docs/html/energyCalibrationHowTo/index.html

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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>Energy calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Energy calibration wizard manual">
+<META NAME="keywords" CONTENT="energyCalibrationHowTo">
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+</HEAD>
+
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+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html10"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>April 8, 2019</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html11"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html12"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html13"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html15"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html17"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

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