Merge branch 'main-rc' into b3.1.2

among other fixes, this fixes the tmpnam warning

.gitignore

@@ -8,3 +8,4 @@ bin/
 *.toc
 build
 docs/
+RELEASE.txt

CMakeLists.txt

@@ -1,25 +1,43 @@
 cmake_minimum_required(VERSION 2.8)
 set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
-set (REST OFF)
 set (CALIBRATE OFF)
-option (USE_HDF5 "HDF5 File format" OFF)
 
+option (USE_HDF5 "HDF5 File format" OFF)
+option (USE_TEXTCLIENT "Text Client" OFF)
+option (USE_RECEIVER "Receiver" OFF)
+option (USE_GUI "GUI" OFF)
+
+set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wall -Wno-misleading-indentation")
 
 find_package(Qt4)
 find_package(Qwt 6)
 find_package(CBF)
 find_package(Doxygen)
+find_package(PNG REQUIRED)
+
 if (USE_HDF5)
 	find_package(HDF5 1.10 COMPONENTS CXX)
 endif (USE_HDF5)
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-add_subdirectory(slsDetectorSoftware)
-add_subdirectory(slsReceiverSoftware)
-if (QT4_FOUND AND QWT_FOUND)
-    add_subdirectory(slsDetectorGui)
-endif()
+set(CMAKE_INSTALL_RPATH "$ORIGIN")
+set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+
+
+if (USE_TEXTCLIENT)
+       add_subdirectory(slsDetectorSoftware)
+endif (USE_TEXTCLIENT)
+
+if (USE_RECEIVER)
+       add_subdirectory(slsReceiverSoftware)
+endif (USE_RECEIVER)
+               
+if (USE_GUI)   
+       if (QT4_FOUND AND QWT_FOUND)
+       add_subdirectory(slsDetectorGui)
+       endif()
+endif (USE_GUI)
 
 
 if (CALIBRATE)

Makefile

@@ -221,7 +221,6 @@ help:
 	@echo ""
 	@echo ""
 	@echo "Makefile variables"
-	@echo "REST=yes		 compile REST-aware Receiver (POCO and JsonBox libraries required)"
 	@echo "DEBUG=1,2		 set debug level to 1 (VERBOSE) or 2 (VERYVERBOSE)"
 	@echo ""
 	@echo ""

Makefile.include

@@ -33,26 +33,6 @@ ifeq ($(HDF5),yes)
 endif	
 
 
-##############################################################
-# EigerSLS specific. Set this to yes, if you want to compile
-# EigerSLS code: in this case, you need also POCO and JsonBox 
-# libraries
-##############################################################   
-
-REST = no
-
-
-POCODIR = /afs/psi.ch/user/s/sala/public/poco
-JSONBOXDIR = /opt/JsonBox-0.5
-
-RESTFLAGS = -L$(POCODIR)/lib -Wl,-rpath=$(POCODIR)/lib  -L$(JSONBOXDIR) -Wl,-rpath=$(JSONBOXDIR)  -lPocoNet -lPocoFoundation -lJsonBox
-
-ifeq ($(REST),yes)
-     LDFLAGRXR = -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsReceiver $(RESTFLAGS) -DREST
-     INCLUDESRXR = $(EIGERFLAGS) -I$(POCODIR)/include -I$(JSONBOXDIR)/include
-endif
-
-
 ##############################################################
 # ROOTSLS specific. Set this to yes, if you want to compile
 # ROOTSLS code: in this case, you need also root libraries

README.md

@@ -1,46 +1,85 @@
-# slsDetector package
+### Documentation
+Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
 
+### Binaries
+Documentation to obtain the binaries via the conda package is available [here.](https://github.com/slsdetectorgroup/sls_detector_software)
 
-## Installation
-
-### Get source
-The source code is organised into several submodules, and the top level module is
-sls_detectors_package.
+### Source code
+One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
+```
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 3.1.0
 
 ```
-    $ git clone git@git.psi.ch:sls_detectors_software/sls_detectors_package.git
-    $ cd sls_detectors_package
-    $ ./checkout.sh
-```
-
-### Setup dependencies
-The GUI client requires Qt 4.8 and Qwt 6.0
+#### Setup dependencies 
+* Gui Client <br>
+Requirements: Qt 4.8 and Qwt 6.0
 ```
     export QTDIR=/usr/local/Trolltech/
     export QWTDIR=/usr/local/qwt-6.0.1/
 ```
 If either of them does not exist, the GUI client will not be built.
 
-The calibration wizards require ROOT
+* Calibration wizards<br>
+Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
 ```
 
-### Compile
-Use cmake to create out-of-source builds, by creating an build folder parallel to source directory.
+#### Compilation 
+
+Compiling can be done in two ways.
+
+**1. Compile using script cmk.sh**<br>
+
+After compiling, the libraries and executables will be found in `slsDetectorPackage/build/bin` directory<br>
+
+Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
+ * -[no option]: only make<br>
+ * -c: Clean<br>
+ * -b: Builds/Rebuilds CMake files normal mode<br>
+ * -h: Builds/Rebuilds Cmake files with HDF5 package<br>
+ * -d: HDF5 Custom Directory<br>
+ * -t: Build/Rebuilds only text client<br>
+ * -r: Build/Rebuilds only receiver<br>
+ * -g: Build/Rebuilds only gui<br>
+ * -j: Number of threads to compile through<br>
+ 
+For only make:
+./cmk.sh
+
+For make clean;make:
+./cmk.sh -c
+
+For using hdf5 without custom dir /blabla:
+./cmk.sh -h -d /blabla
+
+For rebuilding cmake without hdf5 
+./cmk.sh -b
+
+For using multiple cores to compile faster:
+./cmk.sh -j9<br>
+
+
+For rebuilding only certain sections<br>
+./cmk.sh -tg #only text client and gui<br>
+./cmk.sh -r #only receiver<br>
+
+
+**2. Compile without script**<br>
+Use cmake to create out-of-source builds, by creating a build folder parallel to source directory.
 ```
     $ cd ..
-    $ mkdir sls_detectors_package-build
-    $ cd sls_detectors_package-build
-    $ cmake ../sls_detectors_package
+    $ mkdir slsDetectorPackage-build
+    $ cd slsDetectorPackage-build
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=OFF 
     $ make
 ```
 
 Use the following as an example to compile statically and using specific hdf5 folder
 ```
-    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake -DHDF5_USE_STATIC_LIBRARIES=TRUE ../slsDetectorsPackage
+    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=ON
  ```  
-The libraries and executables will be found at `bin` directory
+After compiling, the libraries and executables will be found at `bin` directory
 ```
     $ ls bin/
     gui_client  libSlsDetector.a  libSlsDetector.so  libSlsReceiver.a  libSlsReceiver.so

RELEASE.txt

@@ -1,229 +1,26 @@
-SLS Detector Package 3.0.0 released on 2017-08-25
-================================================================================
+SLS Detector Package 3.1.2 released on 2018-06-12
+=================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between previous versions and 3.0.0 releases.
-
-Manual (both HTML and pdf versions) are provided in
-	manual/docs/
-
-Documentation from Source Code can be found for the Command Line and for the API in
-	html:
-		manual/docs/html/slsDetectorClientDocs/index.html
-		manual/docs/html/slsDetectorUsersDocs/index.html
-	pdf:
-		manual/docs/pdf/slsDetectorClientDocs.pdf
-		manual/docs/pdf/slsDetectorUsersDocs.pdf
-
-Example including binaries for detector and receiver user classes can be found in 
-
-	manual/manual-api
-	
-User documentation can also be accessed directly at this location:
-
-    https://www.psi.ch/detectors/users-support
-
-If you have any software related questions or comments, please send them to:
-
-    dhanya.thattil@psi.ch
-    anna.bergamaschi@psi.ch
+This document describes the differences between 3.1.2 into 3.1.1 releases.
 
 
-CONTENTS
-
-- Changes in User Interface
-- New Features
-- Resolved Issues
-- Known Issues
-
-
-
-Changes in User Interface
-=========================
-This release has no changes in user interface from the previous 2.3 version.
-However, receiver data call backs have been redefined for the 
-standard image header.
-
-Reiterating, both 2.3 and 3.0 supports the following features:
-  	
-	Receiver
-	--------
-	1.	The files will be written in this format in the binary mode:
-		* 1 ASCII file per measurement: header with measurement parameters
-		* binary files: series of images, each preceded by a 
-		  	  Standard Image Header (header described below)
-	
-	2. 	Standard 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.
-		
-		* Frame Number       : 8 bytes 	# Image Number
-		* Exposure Length    : 4 bytes  # Sub frame number in 32 bit mode (Eiger)
-		  		       					  Real time exposre time in 100ns (Others) 
-		* Packet Number      : 4 bytes	# Number of packets caught in the image
-		* Bunch ID           : 8 bytes  # Bunch Id in beamline (Jungfrau) 
-		* Timestamp          : 8 bytes  # Not implemened. 
-										  Time stamp with 10MHz clock
-		* Module Id          : 2 bytes  # Not implemented. Unique module ID.
-		* X Coordinate       : 2 bytes  # Currently as Id of part of detector in 1D
-										  (Future Releases) as X coordinate 
-										  in complete detector system
-		* Y Coordinate       : 2 bytes  # Not implemented 
-										  Y coordinate in complete detector system
-		* Z Coordinate       : 2 bytes  # Not implemented
-										  Z coordinate in complete detector system
-		* Debug              : 4 bytes  # Not implemented
-										  For debugging purposes
-		* Round Robin Number : 2 bytes  # Not implemented
-										  Round Robin Number
-		* Detector Type      : 1 byte   # Detector type defined by enum
-				                          detectorType in slsReceiverSoftware
-						                  /include/sls_receiver_defs.h
-		* Header Version     : 1 byte   # 1.0 currently
-		
-	3.	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).
-		
-	4.	Multiple Receivers have to be started as different processes, instead of threads
-		due to static variables being used. Please refer example code provided in the 
-		slsDetectorsPackage/manual/manual-api folder (mainReceiver.cpp).
-		
-
-
-New Features
-============
-	Package
-	-------
-	1.	One can compile using cmake or the ./cmk.sh script(also uses cmake)
-	  	Run ./cmk.sh -help to get more info. This method does not touch the 
-	  	source files. Please start off with ./cmk.sh -bj9, where (9 is #cores+1)
-	  
-	2.	One can compile the normal way using Makefile (editing Makefile.include
-	  	for the hdf5 options), but this will modify other gitInfo files.
-	
-	
-	General
-	-------
-	3.	UDP Packets from all the detectors will contain the standard sls detector header. 
-		Jungfrau will have an extra 6 bytes preceding the standard header in the udp packets
-		only. X, Y and Z Coordinates define the position of the detector in 3d. These values
-		are not filled in the udp header at the moment, but will be in the files and receiver
-		call backs with only x in 1d at the moment.
-	  	
-	4.	When acquire has started, one can use sls_detector_get busy to check the status
-		of the acquire. 1 is running 0 is idle. This way one can start acqusition with &,
-		poll the busy command ( or framescaught or frameindex to get status from receiver).
-	  	
-	  	
-	Receiver
-	--------
-	4.	One can choose the file format using the command "fileformat binary/hdf5" from 
-	  	the client, but one must compile with the options as defined in README.md
-	
-	5.	Virtual HDF5 file maps all the files into a single file.
-	
-	6.	Gotthard, Propix and Moench also save data in the same way as Jungfrau and Eiger,
-	  	as described above (ie. without any packet headers, only standard image headers 
-	  	for each image data)
-	
-	7.	(Eiger) The ascii part of the file (file header with acquisition parameters) moved to 
-	  	a separate file called the master file. So one master file per acquisition.
-	  
-	  
-   	Client
-	------
-	8.	(Eiger) Can now set Threshold without uploading Trimbits.
-	
-	9. 	(Eiger)	Setting high voltage returns -999 for only slave and on the multi level gives
-		the value of the master only.
-		
-	10.	StartAcquisition (or sls_detector_put status start) parallelized.
-	
-	
-	Gui
-	---
-	10.	Set the data streaming port (individually/ a single one that calculates for the other
-	  	receiver streamer threads) via the command line
-	
-		
-	Users-API
-	-----
-	11.	manual-api example forks new child processes for every extra receiver object.
-
+Topics Concerning
+==================
+	Memory Leak in Client API
 
 
 Resolved Issues
 ===============
+
 	Client
 	------
-	1.	 Memory Leak fixed when setting receiver parameters such as udp port or detector 
-	  	network parameter. The signature in slsDetector.cpp and corresponding files have 
-	  	changed, but does not change the slsDetectorUser API.
-	  
-	2.	Bug Fix: Has been made more threadsafe (strtok). Removed bug of configuring MAC 
-	  	correctly even in multiple thread mode.
-	  
-	3.	Bug Fix: Client crashing when rx_hostname is IP instead of a hostname has been fixed.
+	1. 	Memory Leak for every multi threading command in client
+		when using API in multi detector mode. This is fixed now.
 	
-	
-	
-	Server
-	------
-	4.	(Eiger/Jungfrau) Bug Fix: Client crashing should not crash the server as SIGPIPE 
-	  	signal is caught.
-	  
-	5.	(Eiger) Bug Fix: Front End Temperature read out conversion fixed.
-	
-	6.	(Eiger) Bug Fix: sls_detector_get trimval(get all trimbits) would return only the first pixel 
-		value. Now it returns -1 if all the pixels are different.
-	  
-	  
-	Receiver
-	--------	  
-	6.	Bug Fix: Ctrl+C kills the receiver properly calling the appropriate destructors.
-	
-	7.	Acquire & Unblocking acquire (receiver start, status start, receiver stop) can work
-	  	also when switching from gui to command line and vice versa.
-	  
-	8.	Bug Fix: sls_detector_get frameindex was always returning 0.
-	
-	9.	Bug Fix: In the rare chance that the shut down socket is still processing in 
-		the genericsocket class, but the object is being deleted. 
-		
-	10.	(Eiger): When running independent(not slsReceiver) receiver, one needn't do receiver start
-		to prepare acquisition. Prepare Acquisition has been moved to StartAcqusition and
-		StartAndReadAll. 
-	
-	11.	(Gotthard): 639 pixels in first packet and 641 pixels in second packet. The first pixel in second 
-		packet was unaccounted for. This is fixed now.
-
-
-
-Known Issues
-============
-	Server
-	------
-	1.	(Eiger) The hardware mac of the detector is used (not relayed back to the client). 
-	  	For 1 GbE, the hardware IP of the detector is used (also not relayed back to the 
-	  	client). 
-	  	
-	2.	Standard header fills x-coord in 1D. y-coord and z-coord is not implemented (3D).
-	
-	
-	3. HDF5 compression and filters are not implemented yet.
-
-
 
 
 

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

cmk.sh

@@ -3,6 +3,10 @@ BUILDDIR="build"
 HDF5DIR="/opt/hdf5v1.10.0"
 HDF5=0
 COMPILERTHREADS=0
+TEXTCLIENT=0
+RECEIVER=0
+GUI=0
+
 
 CLEAN=0
 REBUILD=0
@@ -16,6 +20,9 @@ Usage: $0 [-c] [-b] [-h] [-d <HDF5 directory>] [-j]
  -b: Builds/Rebuilds CMake files normal mode
  -h: Builds/Rebuilds Cmake files with HDF5 package
  -d: HDF5 Custom Directory
+ -t: Build/Rebuilds only text client
+ -r: Build/Rebuilds only receiver
+ -g: Build/Rebuilds only gui
  -j: Number of threads to compile through
  
 For only make:
@@ -39,10 +46,14 @@ For using multiple cores to compile faster:
 ./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:" opt ; do
+while getopts ":bchd:j:trg" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -65,6 +76,21 @@ while getopts ":bchd:j:" opt ; do
 		echo "Number of compiler threads: $OPTARG" 
 		COMPILERTHREADS=$OPTARG
 		;;
+	t) 
+    	echo "Compiling Options: Text Client" 
+		TEXTCLIENT=1
+		REBUILD=1
+		;;      
+	r) 
+		echo "Compiling Options: Receiver" 
+		RECEIVER=1
+		REBUILD=1
+		;;      
+	g) 
+		echo "Compiling Options: GUI" 
+		GUI=1
+		REBUILD=1
+		;;      
     \?)
      	echo "Invalid option: -$OPTARG" 
 		usage
@@ -83,6 +109,29 @@ 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"
@@ -96,14 +145,15 @@ else
 	fi
 fi
 
+CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
 
 #hdf5 rebuild
 if [ $HDF5 -eq 1 ]; then
 	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
-	CMAKE_POST+="-DUSE_HDF5=ON"
+	CMAKE_POST+=" -DUSE_HDF5=ON "
 #normal mode rebuild
 else
-	CMAKE_POST+="-DUSE_HDF5=OFF"
+	CMAKE_POST+=" -DUSE_HDF5=OFF "
 fi
 
 

examples/gotthard.config

@@ -10,9 +10,6 @@ hostname bchip007
 0:caldir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
 0:ffdir /home/l_maliakal_d
 0:extsig:0 off
-0:extsig:1 off
-0:extsig:2 off
-0:extsig:3 off
 #0:detectorip 129.129.202.9
 0:detectormac 00:aa:bb:cc:dd:ee
 0:rx_udpport 50004

examples/two_gotthard.config

@@ -15,9 +15,6 @@ hostname bchip007+bchip009+
 0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
-0:extsig:1 off
-0:extsig:2 off
-0:extsig:3 off
 0:detectorip 10.1.1.2
 #0:detectormac 00:aa:bb:cc:dd:ee
 #0:rx_udpport 50001
@@ -38,9 +35,6 @@ hostname bchip007+bchip009+
 1:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:ffdir /home/l_msdetect
 1:extsig:0 off
-1:extsig:1 off
-1:extsig:2 off
-1:extsig:3 off
 1:detectorip 10.1.2.2
 #1:detectormac 00:aa:bb:cc:dd:ee
 1:rx_udpport 50004

genVersionHeader.sh

@@ -21,5 +21,5 @@ echo "Updating $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 $@
-for i in sls*/; do
-     cd $i
-     echo $i
-     git $@
-     cd ..
-done

manual/Makefile

@@ -5,7 +5,7 @@ DESTDIR?=docs
 
 
 
-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-%)

manual/docs/html/angularCalibrationHowTo/angularCalibrationHowTo.html

@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/index.html

@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node1.html

@@ -180,7 +180,7 @@ These results show that  the angular calibration allows a resolution in determin
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
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manual/docs/html/angularCalibrationHowTo/node2.html

@@ -211,7 +211,7 @@ Acquisition GUI window to setup the motor position scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node3.html

@@ -180,7 +180,7 @@ After fitting all modules you can click on the <I>Write Angular Calibration</I>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node4.html

@@ -62,7 +62,7 @@ while for the GUI the file name should be specified in the configuration file (w
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node5.html

@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 angularCalibrationHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2017-08-24
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 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
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manual/docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
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manual/docs/html/energyCalibrationHowTo/index.html

@@ -44,7 +44,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node1.html

@@ -377,7 +377,7 @@ Median of the number of counts as a function of the threshold for X-rays of 12.5
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node2.html

@@ -180,7 +180,7 @@ Acquisition GUI window to setup the threshold scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node3.html

@@ -184,7 +184,7 @@ Window to calibrate the modules.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node4.html

@@ -68,7 +68,7 @@ By reloading the default detector settings, the calibration coefficients will be
 <BR><HR>
 <ADDRESS>
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-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node5.html

@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 energyCalibrationHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2017-08-24
+The translation was initiated by Thattil Dhanya on 2018-03-12
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientDocs/acquisition.html

@@ -43,10 +43,10 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <li><b>acquire</b> blocking acquisition (like calling sls_detector_acquire). Starts receiver and detector, writes and processes the data, stops detector. Only get! <code>Returns</code> (string)<code>"acquire unsuccessful"</code> if fails, else "" for MYTHEN, <code>"Acquired (int)"</code> for others, where int is number of frames caught.</li>
 </ul>
 <ul>
-<li><b>busy</b> returns <code>1</code> if the acquisition is active, <code>0</code> otherwise. Works when the acquisition is started in blocking mode. Only get! <code>Returns</code> <code></code>(int)</li>
+<li><b> busy i</b> sets/gets acquiring flag. <code>1</code> the acquisition is active, <code>0</code> otherwise. Acquire command will set this flag to 1 at the beginning and to 0 at the end. Use this to clear flag if acquisition terminated unexpectedly. <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
-<li><b> status [s] </b> starts or stops acquisition in detector in non blocking mode. <code>s:</code> [<code>start</code>, <code>stop</code>]. <code>Returns</code> the detector status: [<code>running</code>, <code>error</code>, <code>transmitting</code>, <code>finished</code>, <code>waiting</code>, <code>idle</code>]. <code>Returns</code> <code></code>(string)</li>
+<li><b> status [s] </b> starts or stops acquisition in detector in non blocking mode. When using stop acquisition and if acquisition is done, it will restream the stop packet from receiver (if data streaming in receiver is on). <code>s:</code> [<code>start</code>, <code>stop</code>]. <code>Returns</code> the detector status: [<code>running</code>, <code>error</code>, <code>transmitting</code>, <code>finished</code>, <code>waiting</code>, <code>idle</code>]. <code>Returns</code> <code></code>(string)</li>
 </ul>
 <ul>
 <li><b>data</b> gets all data from the detector (if any) processes them and writes them to file according to the preferences already setup (MYTHEN only). Only get!</li>
@@ -78,7 +78,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/actions.html

@@ -129,7 +129,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/advanced.html

@@ -54,7 +54,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/config.html

@@ -53,9 +53,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 Data Structure</a></h2>
 <p>commands to configure detector data structure</p>
 <ul>
-<li><b> externalgui </b>sets/gets external gui flag. 1 sets and enables the 0MQ data stream (0MQ threads created) from receiver to client, while 0 unsets and disables. <code>Returns</code> <code></code>(int)</li>
-</ul>
-<ul>
 <li><b>free</b> Free shared memory on the control PC</li>
 </ul>
 <ul>
@@ -144,6 +141,9 @@ Chip</a></h2>
 <li><b>led [i]</b> sets/gets the led status. 1 on, 0 off. Used for MOENCH only ?? <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
+<li><b>auto_comp_disable i </b> Currently not implemented. this mode disables the on-chip gain switching comparator automatically after 93.75% of exposure time (only for longer than 100us). 1 enables mode, 0 disables mode. By default, mode is disabled (comparator is enabled throughout). (JUNGFRAU only). <code>Returns</code> <code></code>(int)</li>
+</ul>
+<ul>
 <li><b>pulse [n] [x] [y]</b> pulses pixel at coordinates (x,y) n number of times. Used in EIGER only. Only put! <code>Returns</code> <code></code>("successful", "unsuccessful")</li>
 </ul>
 <ul>
@@ -183,7 +183,7 @@ Versions</a></h2>
 Speed</a></h2>
 <p>commands to configure speed of detector</p>
 <ul>
-<li><b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
+<li><b>clkdivider [i]</b> sets/gets the readout clock divider. EIGER, JUNGFRAU [0(fast speed), 1(half speed), 2(quarter speed)]. Jungfrau, full speed is not implemented and overwrites adcphase to recommended default. MYTHEN[???]. <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
 <li><b>setlength [i]</b> sets/gets length of set/reset signals (in clock cycles). Used in MYTHEN only. <code>Returns</code> <code></code>(int)</li>
@@ -207,7 +207,7 @@ Speed</a></h2>
 <li><b>adcclk [i]</b> sets/gets the ADC clock frequency in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
-<li><b>adcphase [i]</b> Sets/gets the ADC clock frequency in MHz. For the new chiptestboard!<code>Returns</code> <code></code>(int)</li>
+<li><b>adcphase [i]</b> Sets/gets phase of the sampling clock. For JUNGFRAU, setting speed (clkdivider) overwrites adcphase to its default recommended value. (Not for EIGER) <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
 <li><b>adcpipeline [i]</b> Sets/gets the pipeline of the ADC. For the new chiptestbaord!<code>Returns</code> <code></code>(int)</li>
@@ -251,7 +251,7 @@ Detector Parameters</a></h2>
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/ctb.html

@@ -114,7 +114,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/data.html

@@ -99,7 +99,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
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 </body>

manual/docs/html/slsDetectorClientDocs/index.html

@@ -83,7 +83,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/network.html

@@ -73,7 +73,13 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <li><b>flowcontrol_10g [delay]</b> Enables/disables 10 GbE flow control. 1 enables, 0 disables. Used for EIGER only. <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
-<li><b>zmqport [port]</b> sets/gets the 0MQ (TCP) port of the receiver from where data is streamed to the client. Use single-detector command to set individually or multi-detector command to calculate based on <code>port</code> for the rest. <code>Returns</code> <code></code>(int)</li>
+<li><b>zmqport [port]</b> sets/gets the 0MQ (TCP) port of the client to where final data is streamed to (eg. for GUI). Use single-detector command to set individually or multi-detector command to calculate based on <code>port</code> for the rest. Must restart zmq client streaming in gui/external gui <code>Returns</code> <code></code>(int)</li>
+</ul>
+<ul>
+<li><b>rx_zmqport [port]</b> sets/gets the 0MQ (TCP) port of the receiver from where data is streamed from (eg. to GUI or another process for further processing). Use single-detector command to set individually or multi-detector command to calculate based on <code>port</code> for the rest. put restarts streaming in receiver with new port. <code>Returns</code> <code></code>(int)</li>
+</ul>
+<ul>
+<li><b> rx_datastream </b>enables/disables data streaming from receiver. 1 enables 0MQ data stream from receiver (creates streamer threads), while 0 disables (destroys streamer threads). <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
 <li><b>configuremac [i]</b> configures the MAC of the detector with these parameters: detectorip, detectormac, rx_udpip, rx_udpmac, rx_udpport, rx_udpport2 (if applicable). This command is already included in <code>rx_hsotname</code>. Only put!. <code>Returns</code> <code></code>(int)</li>
@@ -108,7 +114,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/output.html

@@ -75,7 +75,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/pages.html

@@ -77,7 +77,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/receiver.html

@@ -67,7 +67,10 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <li><b>r_readfreq [i]</b> sets/gets the stream frequency of data from receiver to client. i &gt; 0 is the nth frame being streamed. 0 sets frequency to a default timer (200ms). <code>Returns</code> <code></code>(int)</li>
 </ul>
 <ul>
-<li><b>rx_fifodepth [i]</b> sets/gets receiver fifo (between Listener and Writer Threads) depth to i number of frames. Can improve listener packet loss (loss due to packet processing time in Listener threads), not if limited by writing. <code>Returns</code> <code></code>(int) </li>
+<li><b>rx_fifodepth [i]</b> sets/gets receiver fifo (between Listener and Writer Threads) depth to i number of frames. Can improve listener packet loss (loss due to packet processing time in Listener threads), not if limited by writing. <code>Returns</code> <code></code>(int)</li>
+</ul>
+<ul>
+<li><b>r_silent [i]</b> sets/gets receiver in silent mode, ie. it will not print anything during real time acquisition. 1 sets, 0 unsets. <code>Returns</code> <code></code>(int) </li>
 </ul>
 </div>
 <!--- window showing the filter options -->
@@ -84,7 +87,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
+<hr size="1"/><address style="text-align: right;"><small>Generated on 20 Mar 2018 by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.6.1 </small></address>
 </body>

manual/docs/html/slsDetectorClientDocs/settings.html

@@ -44,6 +44,7 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <li><a class="el" href="settings.html#settingssett">Settings and Threshold</a>: commands to configure settings and threshold of detector</li>
 <li><a class="el" href="settings.html#settingsdacs">DACs</a>: commands to configure DACs of detector</li>
 <li><a class="el" href="settings.html#settingsadcs">ADCs</a>: commands to readout ADCs of detector</li>
+<li><a class="el" href="settings.html#settingstmp">Temp Control</a>: commands to monitor and handle temperature overshoot (only JUNGFRAU)</li>
 </ul>
 <h2><a class="anchor" id="settingsdir">
 Settings, trim &amp; cal Directories</a></h2>
@@ -287,7 +288,19 @@ ADCs</a></h2>
 <li><b>vm_d</b> Gets the measured voltage of the power supply d on the new chiptest board <code>Returns</code> <code></code>(int"mV")</li>
 </ul>
 <ul>
-<li><b>vm_io</b> Gets the measured voltage of the power supply io on the new chiptest board <code>Returns</code> <code></code>(int"mV") </li>
+<li><b>vm_io</b> Gets the measured voltage of the power supply io on the new chiptest board <code>Returns</code> <code></code>(int"mV")</li>
+</ul>
+<h2><a class="anchor" id="settingstmp">
+Temp Control</a></h2>
+<p>commands to monitor and handle temperature overshoot (only JUNGFRAU)</p>
+<ul>
+<li><b>temp_threshold</b> Sets/gets the threshold temperature. JUNGFRAU ONLY. <code>Returns</code> <code></code>(double"°C")</li>
+</ul>
+<ul>
+<li><b>temp_control</b> Enables/Disables the temperature control. 1 enables, 0 disables. JUNGFRAU ONLY. <code>Returns</code> <code>int</code> </li>
+</ul>
+<ul>
+<li><b>temp_event</b> Resets/gets over-temperative event. Put only with option 0 to clear event. Gets 1 if temperature went over threshold and control is enabled, else 0. /Disables the temperature control. JUNGFRAU ONLY. <code>Returns</code> <code>int</code> </li>
 </ul>
 </div>
 <!--- window showing the filter options -->
@@ -304,7 +317,7 @@ ADCs</a></h2>
 </iframe>
 </div>
 
-<hr size="1"/><address style="text-align: right;"><small>Generated on 24 Aug 2017 by&nbsp;
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manual/docs/html/slsDetectorClientDocs/test.html

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manual/docs/html/slsDetectorClientDocs/timing.html

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manual/docs/html/slsDetectorClientHowTo/index.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">SLS Detector text clients manual</H1>
 <DIV>
 
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 20, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -148,7 +148,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-20
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 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientHowTo/node1.html

@@ -123,7 +123,7 @@ For additional questions concerning the indexing of the detector, please refer t
 <!--End of Navigation Panel-->
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-2017-08-24
+2018-03-20
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 </HTML>

manual/docs/html/slsDetectorClientHowTo/node2.html

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manual/docs/html/slsDetectorClientHowTo/node3.html

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manual/docs/html/slsDetectorClientHowTo/node4.html

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manual/docs/html/slsDetectorClientHowTo/node5.html

@@ -160,7 +160,7 @@ sls_detector_put ratecorr -1
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-2017-08-24
+2018-03-20
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manual/docs/html/slsDetectorClientHowTo/node6.html

@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 slsDetectorClientHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2017-08-24
+The translation was initiated by Thattil Dhanya on 2018-03-20
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorClientHowTo/slsDetectorClientHowTo.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">SLS Detector text clients manual</H1>
 <DIV>
 
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 20, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -148,7 +148,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-20
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/index.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">Mythen v3.0 manual</H1>
 <DIV>
 
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -113,7 +113,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node1.html

@@ -82,7 +82,7 @@ Here you can find in brief the main things you need to know in order to start wo
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node10.html

@@ -61,7 +61,7 @@ the detector is started and the data are acquired, postprocessed and written to
 <BR><HR>
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-2017-08-24
+2018-03-12
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 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node11.html

@@ -263,7 +263,7 @@ is used to configure the detector parameter var
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node12.html

@@ -294,7 +294,7 @@ is used to retrieve the detector parameter var
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node13.html

@@ -216,7 +216,7 @@ The configuration of the detector can either be set when startin the GUI using t
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node14.html

@@ -64,7 +64,7 @@ Please don't be too nervous clicking on start and/or stop since this is one of t
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node15.html

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manual/docs/html/slsDetectorGuiHowTo/node16.html

@@ -115,7 +115,7 @@ Chose ``Add calibration step'' and select the file created prevously. The settin
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+2018-03-12
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 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node17.html

@@ -61,11 +61,11 @@ Mathematics Department, Macquarie University, Sydney.
 The command line arguments were: <BR>
  <STRONG>latex2html</STRONG> <TT>-split 4 slsDetectorGuiHowTo.tex</TT>
 <P>
-The translation was initiated by Thattil Dhanya on 2017-08-24
+The translation was initiated by Thattil Dhanya on 2018-03-12
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node2.html

@@ -72,7 +72,7 @@ The complete software package is composed of several programs which can be insta
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manual/docs/html/slsDetectorGuiHowTo/node3.html

@@ -60,7 +60,7 @@ For installing the slsDetector shared and static libraries and the slsDetectorCl
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 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node4.html

@@ -74,7 +74,7 @@ To be able to run the slsDetectorClient commands, add their location to your pat
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manual/docs/html/slsDetectorGuiHowTo/node5.html

@@ -96,7 +96,7 @@ To build you can:
 <BR><HR>
 <ADDRESS>
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-2017-08-24
+2018-03-12
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 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node6.html

@@ -128,7 +128,7 @@ After pressing reset on the board, the board should reboot and the acqusition pr
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node7.html

@@ -93,7 +93,7 @@ The default calibration files for each file will be stored in the directory acco
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+2018-03-12
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manual/docs/html/slsDetectorGuiHowTo/node8.html

@@ -94,7 +94,7 @@ slsDetectorClient</A>
 <BR><HR>
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-2017-08-24
+2018-03-12
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 </BODY>
 </HTML>

manual/docs/html/slsDetectorGuiHowTo/node9.html

@@ -106,7 +106,7 @@ There are different ways for communicationg with your detector(s).
 <!--End of Navigation Panel-->
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 </HTML>

manual/docs/html/slsDetectorGuiHowTo/slsDetectorGuiHowTo.html

@@ -43,7 +43,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <H1 ALIGN="CENTER">Mythen v3.0 manual</H1>
 <DIV>
 
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>March 12, 2018</STRONG></P>
 </DIV>
 
 <P>
@@ -113,7 +113,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-03-12
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/slsDetectorInstall/Binaries.html

@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Binaries</TITLE>
+<META NAME="description" CONTENT="Binaries">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00021000000000000000">
+Binaries</A>
+</H2>
+The complete software package is composed of several programs which
+can be installed (or locally compiled) depending on one's requirements:
+
+<P>
+
+<UL>
+<LI><FONT COLOR="#0000ff">libSlsDetector.so, libSlsReceiver.so</FONT>:
+<BR>
+The <I>slsDetector shared and static libraries</I>, which are
+necessary for all user interfaces. The <I>C++ API</I> via the class
+<I>slsDetectorUsers</I> (installed with the default package) or the
+<I>Python API</I> via the class <I>sls_detector</I> (installed with the
+package including Python API), which can be used from the user's acquisition
+software to control the detectors and the data receivers.
+
+<P>
+</LI>
+<LI><FONT COLOR="#0000ff">sls_detector_put, sls_detector_get,
+sls_detector_acquire, sls_detector_help</FONT>: 
+<BR>
+The <I>command line interfaces</I>, which are provided to communicate with the
+detectors and data receivers using the command line.
+
+<P>
+</LI>
+<LI><FONT COLOR="#0000ff">slsReceiver</FONT>: 
+<BR>
+The <I>data receiver</I>, which can be run on a different machine than the
+client, receives the data from the detector and processes it. The receiver can
+be configured, controlled and monitored by the client.
+
+<P>
+</LI>
+<LI><FONT COLOR="#0000ff">slsDetectorGUI</FONT>: 
+<BR>
+The <I>graphical user interface</I>, which provides a user friendly way
+of operating the detectors and data receivers with online data preview.
+
+<P>
+</LI>
+<LI><FONT COLOR="#0000ff">energyCalibrationWizard,angularCalibrationWizard</FONT>: 
+<BR>
+The <I>calibration wizards</I> to analyze the data and produce the energy or
+angular calibration files.
+
+<P>
+</LI>
+<LI>The <I>virtual Detector servers</I> to simulate the detectors behavior.
+However, only control commands work, not the data acquisition itself.
+</LI>
+</UL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Clean_Shared_Memory.html

@@ -0,0 +1,49 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Clean Shared Memory</TITLE>
+<META NAME="description" CONTENT="Clean Shared Memory">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00045000000000000000">
+Clean Shared Memory</A>
+</H2>
+It is very crucial to clean the shared memory, before using a new version of
+the SLS Detector Package or a different detector type.
+
+<P>
+One can use the <code>cleansharedmemory.sh</code> script available under the
+slsDetector Package.
+
+<P>
+One can also just use the following commands to clean the shared memory
+segments one by one.
+<PRE>
+#displays list of shared memeory segments 
+ipcs -m
+#remove segments that have nattach equal to zero. They key is the first column
+ipcrm -M [key]
+</PRE>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Compilation.html

@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Compilation</TITLE>
+<META NAME="description" CONTENT="Compilation">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00043000000000000000">
+Compilation</A>
+</H2>
+One requires <code>cmake</code> to compile and can be done in two ways:
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Contents.html

@@ -0,0 +1,74 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Contents</TITLE>
+<META NAME="description" CONTENT="Contents">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+<BR>
+
+<H2><A NAME="SECTION00010000000000000000">
+Contents</A>
+</H2>
+<!--Table of Contents-->
+
+<UL>
+<LI><A NAME="tex2html20"
+  HREF="Software_Package.html">The Software Package</A>
+<UL>
+<LI><A NAME="tex2html21"
+  HREF="Binaries.html">Binaries</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html22"
+  HREF="Install_Binaries_via_Conda.html">Install Binaries via Conda</A>
+<LI><A NAME="tex2html23"
+  HREF="Install_via_Source_Code.html">Install via Source Code</A>
+<UL>
+<LI><A NAME="tex2html24"
+  HREF="Download_Source_Code.html">Download Source Code</A>
+<LI><A NAME="tex2html25"
+  HREF="Requirements.html">Requirements</A>
+<LI><A NAME="tex2html26"
+  HREF="Compilation.html">Compilation</A>
+<LI><A NAME="tex2html27"
+  HREF="Setting_environment_variabl.html">Setting environment variables</A>
+<LI><A NAME="tex2html28"
+  HREF="Clean_Shared_Memory.html">Clean Shared Memory</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html29"
+  HREF="Software_Upgrade.html">Software Upgrade</A>
+<UL>
+<LI><A NAME="tex2html30"
+  HREF="MYTHEN.html">MYTHEN</A>
+<LI><A NAME="tex2html31"
+  HREF="GOTTHARD.html">GOTTHARD</A>
+<LI><A NAME="tex2html32"
+  HREF="EIGER.html">EIGER</A>
+<LI><A NAME="tex2html33"
+  HREF="JUNGFRAU.html">JUNGFRAU</A>
+</UL></UL>
+<!--End of Table of Contents-->
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Directly_using_cmake.html

@@ -0,0 +1,61 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Directly using cmake</TITLE>
+<META NAME="description" CONTENT="Directly using cmake">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00043200000000000000">
+Directly using cmake</A>
+</H3>
+
+<P>
+Use cmake to create out-of-source builds, by creating a build folder parallel to
+source directory. 
+<PRE>
+ $ cd ..
+ $ mkdir slsDetectorPackage-build
+ $ cd slsDetectorPackage-build
+ $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=OFF 
+ $ make
+</PRE>
+
+<P>
+Use the following as an example to compile statically and using specific hdf5
+folder 
+<PRE>
+ $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage
+-DCMAKE_BUILD_TYPE=Debug -DUSE_HDF5=ON
+</PRE>
+
+<P>
+After compiling, the libraries and executables will be found at `bin` directory 
+<PRE>
+ $ 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
+</PRE>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Download_Source_Code.html

@@ -0,0 +1,52 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Download Source Code</TITLE>
+<META NAME="description" CONTENT="Download Source Code">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00041000000000000000">
+Download Source Code</A>
+</H2>
+
+<P>
+
+<UL>
+<LI>Only the package
+<PRE>
+#Clone source code with specific release
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch
+3.1.0
+</PRE>
+</LI>
+<LI>The package including Python interface
+<PRE>
+#Clone source code with specific release
+git clone https://github.com/slsdetectorgroup/sls_detector.git --branch
+3.1.0
+</PRE>
+</LI>
+</UL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/EIGER.html

@@ -0,0 +1,39 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>EIGER</TITLE>
+<META NAME="description" CONTENT="EIGER">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00053000000000000000">
+EIGER</A>
+</H2>
+
+<P>
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/EIGER_Firmware.html

@@ -0,0 +1,67 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>EIGER Firmware</TITLE>
+<META NAME="description" CONTENT="EIGER Firmware">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00053100000000000000">
+EIGER Firmware</A>
+</H3>
+<I>For SLS Detector Package v3.1.0</I> 
+<BR>
+Minimum compatible version:  16 
+<BR>
+Latest version:	20  
+<BR>
+<P>
+
+<OL>
+<LI>One must get the latest package's corresponding bit files from the SLS
+Detector Group.
+</LI>
+<LI>If one does not have the bcp script, that should also be obtained from
+the SLS Detector Group. It is required to program the bit files and requires
+that tftp be installed on the pc.
+</LI>
+<LI>Run the following to update firmware
+<PRE>
+ #update back end fpga
+bcp download.bit bebxxx:/fw0
+
+ #update front left fpga
+bcp download.bit bebxxx:/febl
+
+ #update front right fpga
+bcp download.bit bebxxx:/febr
+
+ #update kernel
+bcp download.bit bebxxx:/kernel
+</PRE>
+Please update bit files with great caution as it could make your board
+inaccessible, if done incorrectly.
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/EIGER_On_board_Software.html

@@ -0,0 +1,70 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>EIGER On-board Software</TITLE>
+<META NAME="description" CONTENT="EIGER On-board Software">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00053200000000000000">
+EIGER On-board Software</A>
+</H3>
+Every SLS Detector package release will have its coresponding matching on-board
+server under <B>slsDetectorPackage/serverBin</B>.
+
+<P>
+Update the on-board software without connecting to the detector
+<PRE>
+#password for the boards: root
+
+#Kill existing servers that are running on the detector
+ssh root@beb031 killall eigerDetectorServer;
+
+#Copy on-board server to detector inside executables folder
+scp ~/path-where-it-is/eigerDetectorServerxxx root@bebxxx:~/executables;
+
+#Overwrite the actual eigerDetectorServer on board
+scp ~/path-where-it-is/eigerDetectorServerxxx
+root@bebxxx:~/executables/eigerDetectorServer;
+
+#sync
+ssh root@bebxxx sync; 
+
+#reboot the eiger board
+</PRE>
+
+<P>
+
+<P><P>
+<BR>
+One can connect to the detector by:
+<PRE>
+ssh root@bebxxx
+password: root
+</PRE>
+
+<P>
+The on-board server is in&nbsp;/executables folder and respawned at startup in 
+<BR><code>/etc/rc5.d/S50board_com.sh</code> 
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/GOTTHARD.html

@@ -0,0 +1,39 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>GOTTHARD</TITLE>
+<META NAME="description" CONTENT="GOTTHARD">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00052000000000000000">
+GOTTHARD</A>
+</H2>
+
+<P>
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/GOTTHARD_Firmware.html

@@ -0,0 +1,91 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>GOTTHARD Firmware</TITLE>
+<META NAME="description" CONTENT="GOTTHARD Firmware">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00052100000000000000">
+GOTTHARD Firmware</A>
+</H3>
+<I>For SLS Detector Package v3.1.0</I> 
+<BR>
+Minimum compatible version: 
+<BR>
+11.01.2013 
+<BR>
+Latest version:	
+<BR>
+08.02.2018 (50um and 25um Master) 
+<BR>
+09.02.2018 (25 um Slave) 
+<BR>
+<P>
+Normally, the firmware will be upgraded by us as it requires programming the
+FPGA via the USB-Blaster.
+
+<P>
+To upgrade the firmware you need either a working version of the Altera
+Quartus software or of the Quartus programmer, which can easily be downloaded
+from: 
+<BR><TT><A NAME="tex2html5"
+  HREF="https://www.altera.com/download/programming/quartus2/pq2-index.jsp">https://www.altera.com/download/programming/quartus2/pq2-index.jsp</A></TT>
+<P>
+Normally, installation of the software and of the driver for the
+USB-Blaster (provided together with the MYTHEN detector) are simpler under
+Windows.
+
+<P>
+Under Windows, the first time that you connect the USB-Blaster to one
+of your USB ports, you will be asked to install new hardware. Set the path to
+search for the driver to:
+<code>C:\altera\80sp1\qprogrammer\drivers\usb-blasterp</code> (where 
+<code>C:\altera\80sp1\qprogrammer\</code> is assumed to be ther path where your
+Quartus version is installed).
+
+<OL>
+<LI>After starting the Quartus programmer, click on Hardware Setup and in the
+"Currently selected hardware" window select USB-Blaster.
+</LI>
+<LI>In the Mode combo box select "Active Serial Programming".
+</LI>
+<LI>Plug the end of your USB-Blaster WITH THE ADAPTER PROVIDED in the
+connector ASMI on the MCS board taking care that pin1 corresponds to the one
+indexed and with the rectangualr pad.
+</LI>
+<LI>Click on add file and from select the programming file provided when
+the upgrade has been reccomended.
+</LI>
+<LI>Check "Program/Configure" and "Verify".
+</LI>
+<LI>Push the start button and wait until the programming process is
+finished (progress bar top left).
+</LI>
+<LI>In case the programmer gives you error messages, check the polarity of
+your cable (pin1 corresponds) and that you have selected the correct programming
+connector.
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/GOTTHARD_On_board_Software.html

@@ -0,0 +1,89 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>GOTTHARD On-board Software</TITLE>
+<META NAME="description" CONTENT="GOTTHARD On-board Software">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00052200000000000000">
+GOTTHARD On-board Software</A>
+</H3>
+Every SLS Detector package release will have its coresponding matching on-board
+server under <B>slsDetectorPackage/serverBin</B>.
+
+<P>
+
+<OL>
+<LI>Install tftp if the pc does not have it.
+</LI>
+<LI>Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+</LI>
+<LI>Copy the server to the detector by:
+  
+<OL>
+<LI>Connect to the blackfin on the detector
+<BR><code>telnet bchipxxx</code>
+</LI>
+<LI>Prevent existing on-board server from respawning by:
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Comment out the line
+<code>#ttyS0::respawn:/gotthardDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure no gotthardDetectorServers are running
+    
+</LI>
+</OL>
+</LI>
+<LI>Copy new on-board server from pc to the blackfin using: 
+<BR><code>tftp pcxxx -r gotthardDetectorServerxxx -g</code> 
+</LI>
+<LI>Respawn the new server (server starts at detector statup): 
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Uncomment out the line
+<code>ttyS0::respawn:/gotthardDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure that both the gotthardDetectorServers are
+running.
+<BR><code>gotthardDetectorServerxxx</code> 
+<BR><code>gotthardDetectorServerxxx 1953</code>
+    
+</LI>
+</OL>
+</LI>
+</OL>
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Install_Binaries_via_Conda.html

@@ -0,0 +1,97 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Install Binaries via Conda</TITLE>
+<META NAME="description" CONTENT="Install Binaries via Conda">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H1><A NAME="SECTION00030000000000000000">
+Install Binaries via Conda</A>
+</H1>
+This section is useful only if one wants to download only the binaries for
+specific distribution and use the package via command line. Please refer later
+sections to download source code and compile them.
+
+<P>
+One can download and install Miniconda via 
+
+<P>
+<TT><A NAME="tex2html1"
+  HREF="https://conda.io/miniconda.html">https://conda.io/miniconda.html</A></TT>
+<P>
+The conda package uses Travis CI for continuous integration with
+automatic deployment to Anaconda Cloud. One can download only the package or the
+package including the python interface.
+
+<P>
+After the installation, the binaries will be available in your path.
+
+<P>
+Please remember to clear shared memory after installation.
+<PRE>
+#displays list of shared memeory segments 
+ipcs -m
+#remove segments that have nattach equal to zero. They key is the first column
+ipcrm -M [key]
+</PRE>
+
+<P>
+
+<UL>
+<LI>Only the package
+<PRE>
+#Add conda channels
+conda config --add channels conda-forge
+conda config --add channels slsdetectorgroup
+
+#Install latest version
+conda install sls_detector_software
+
+#Install specific release (GLIBC2.14)
+conda install sls_detector_software=3.1.0
+
+#Scientific Linux 6 version (GLIBC2.12)
+conda install sls_detector_software=SL6_3.1.0
+</PRE>
+</LI>
+<LI>The package including Python interface
+<PRE>
+#Add conda channels
+conda config --add channels conda-forge
+conda config --add channels sls_detector
+
+#Install latest version
+conda install sls_detector
+
+#Install specific release (GLIBC2.14)
+conda install sls_detector=3.1.0
+
+#Scientific Linux 6 version (GLIBC2.12)
+conda install sls_detector=SL6_3.1.0
+</PRE>
+</LI>
+</UL>
+
+<P>
+
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Install_via_Source_Code.html

@@ -0,0 +1,35 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Install via Source Code</TITLE>
+<META NAME="description" CONTENT="Install via Source Code">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H1><A NAME="SECTION00040000000000000000">
+Install via Source Code</A>
+</H1>
+This section is useful if one wants to use the API and embed it in their
+acquisition system, or if one wants to download the source code and compile.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/JUNGFRAU.html

@@ -0,0 +1,39 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>JUNGFRAU</TITLE>
+<META NAME="description" CONTENT="JUNGFRAU">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00054000000000000000">
+JUNGFRAU</A>
+</H2>
+
+<P>
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/JUNGFRAU_Firmware.html

@@ -0,0 +1,135 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>JUNGFRAU Firmware</TITLE>
+<META NAME="description" CONTENT="JUNGFRAU Firmware">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00054100000000000000">
+JUNGFRAU Firmware</A>
+</H3>
+<I>For SLS Detector Package v3.1.0</I> 
+<BR>
+Minimum compatible version: 13.11.2017 
+<BR>
+Latest version: 13.11.2017 
+<BR>
+<P>
+At times, one has to update the firmware, which then also requires updating the
+on-board software. 
+
+<P>
+<B><I>Jungfrau firmware can be upgraded via the SLS Detector Package
+binaries from the command line.</I></B>
+
+<P>
+
+<OL>
+<LI>One must get the latest package's corresponding POF file from the SLS
+Detector Group.
+</LI>
+<LI>Update the latest SLS Detector package installed.
+</LI>
+<LI>Update the on-board software as per the instructions in the next
+section.
+</LI>
+<LI>Start the on-board server in debug mode:
+  
+<OL>
+<LI>Connect to the blackfin on the detector
+<BR><code>telnet bchipxxx</code>
+</LI>
+<LI>Prevent existing on-board server from respawning by:
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Comment out the line
+<code>#ttyS0::respawn:/jungfrauDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure no gotthardDetectorServers are running
+    
+</LI>
+</OL>
+</LI>
+<LI>Start the server in debug mode using: 
+<BR><code>./jungfrauDetectorServerxxx -debug</code> 
+<BR>
+Leave this console on to come back to it later.
+  
+</LI>
+</OL>
+</LI>
+<LI>From the command line of the pc, clear shared memory 
+<BR><code>./sls_detector_get free</code> 
+<BR>
+If one gets shmget error, please clean the shared memory properly using the
+script in <code>slsDetectorPackage/cleansharedmemory.sh</code>
+</LI>
+<LI>Add the detector to shared memory using 
+<BR><code>./sls_detector_put hostname bchipxxx</code>
+</LI>
+<LI>Program the FPGA using 
+<BR><code>./sls_detector_put programfpga xxx.pof</code> 
+</LI>
+<LI>Once the programming is done:
+  
+<OL>
+<LI>Switch to the console that has the debug server running and kill it
+using Ctrl+C and ensure no jungfrauDetectorServers are
+running
+</LI>
+<LI>Restart the new server to see if it runs with the new firmware 
+<BR><code>./jungfrauDetectorServerxxx</code> 
+<BR>
+If the server didn't start properly, please contact us with the error message
+shown when starting the server up, else continue with the following steps.
+</LI>
+<LI>Respawn the new server (server starts at detector statup): 
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Uncomment out the line
+<code>ttyS0::respawn:/jungfrauDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure that both the gotthardDetectorServers are
+running.
+<BR><code>jungfrauDetectorServervxxx</code> 
+<BR><code>jungfrauDetectorServervxxx 1953</code>
+    
+</LI>
+</OL>
+</LI>
+</OL>
+
+<P>
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/JUNGFRAU_On_board_Software.html

@@ -0,0 +1,89 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>JUNGFRAU On-board Software</TITLE>
+<META NAME="description" CONTENT="JUNGFRAU On-board Software">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00054200000000000000">
+JUNGFRAU On-board Software</A>
+</H3>
+Every SLS Detector package release will have its coresponding matching on-board
+server under <B>slsDetectorPackage/serverBin</B>.
+
+<P>
+
+<OL>
+<LI>Install tftp if the pc does not have it.
+</LI>
+<LI>Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+</LI>
+<LI>Copy the server to the detector by:
+  
+<OL>
+<LI>Connect to the blackfin on the detector
+<BR><code>telnet bchipxxx</code>
+</LI>
+<LI>Prevent existing on-board server from respawning by:
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Comment out the line
+<code>#ttyS0::respawn:/jungfrauDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure no gotthardDetectorServers are running
+    
+</LI>
+</OL>
+</LI>
+<LI>Copy new on-board server from pc to the blackfin using: 
+<BR><code>tftp pcxxx -r jungfrauDetectorServervxxx -g</code> 
+</LI>
+<LI>Respawn the new server (server starts at detector statup): 
+    
+<OL>
+<LI>Edit <code>/etc/inittab</code> 
+</LI>
+<LI>Uncomment out the line
+<code>ttyS0::respawn:/jungfrauDetectorServervxxx</code> 
+</LI>
+<LI>Reboot blackfin using <code>reboot</code>
+</LI>
+<LI>Run <code>ps</code> to ensure that both the gotthardDetectorServers are
+running.
+<BR><code>jungfrauDetectorServervxxx</code> 
+<BR><code>jungfrauDetectorServervxxx 1953</code>
+    
+</LI>
+</OL>
+</LI>
+</OL>
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/MYTHEN.html

@@ -0,0 +1,37 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>MYTHEN</TITLE>
+<META NAME="description" CONTENT="MYTHEN">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00051000000000000000">
+MYTHEN</A>
+</H2>
+In such cases, the users are not expected to compile the software
+themselves (which would require dedicated softwares) but only to download on the
+detector board the programming files and/or software package provided by
+the SLS Detectors group.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/MYTHEN_Firmware.html

@@ -0,0 +1,79 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>MYTHEN Firmware</TITLE>
+<META NAME="description" CONTENT="MYTHEN Firmware">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00051100000000000000">
+MYTHEN Firmware</A>
+</H3>
+
+<P>
+To upgrade the firmware you need either a working version of the Altera
+Quartus software or of the Quartus programmer, which can easily be downloaded
+from: 
+<BR><TT><A NAME="tex2html4"
+  HREF="https://www.altera.com/download/programming/quartus2/pq2-index.jsp">https://www.altera.com/download/programming/quartus2/pq2-index.jsp</A></TT>
+<P>
+<BR>
+
+<P>
+Normally, installation of the software and of the driver for the
+USB-Blaster (provided together with the MYTHEN detector) are simpler under
+Windows. 
+
+<P>
+Under Windows, the first time that you connect the USB-Blaster to one
+of your USB ports, you will be asked to install new hardware. Set the path to
+search for the driver to:
+<code>C:\altera\80sp1\qprogrammer\drivers\usb-blasterp</code> (where 
+<code>C:\altera\80sp1\qprogrammer\</code> is assumed to be ther path where your
+Quartus version is installed).
+
+<OL>
+<LI>After starting the Quartus programmer, click on Hardware Setup and in the
+"Currently selected hardware" window select USB-Blaster.
+</LI>
+<LI>In the Mode combo box select "Active Serial Programming".
+</LI>
+<LI>Plug the end of your USB-Blaster WITH THE ADAPTER PROVIDED in the
+connector ASMI on the MCS board taking care that pin1 corresponds to the one
+indexed and with the rectangualr pad.
+</LI>
+<LI>Click on add file and from select the programming file provided when
+the upgrade has been reccomended.
+</LI>
+<LI>Check "Program/Configure" and "Verify".
+</LI>
+<LI>Push the start button and wait until the programming process is
+finished (progress bar top left).
+</LI>
+<LI>In case the programmer gives you error messages, check the polarity of
+your cable (pin1 corresponds) and that you have selected the correct programming
+connector.
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/MYTHEN_On_board_Software.html

@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>MYTHEN On-board Software</TITLE>
+<META NAME="description" CONTENT="MYTHEN On-board Software">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00051200000000000000">
+MYTHEN On-board Software</A>
+</H3>
+
+<OL>
+<LI>Connect to the board using telnet:
+<PRE>
+telnet  mymcs.mydomain.com
+username: root
+password: pass
+</PRE>
+</LI>
+<LI>Kill currently running servers and ensure <code>/mnt/flash/root</code> exists.
+<PRE>
+killall mythenDetectorServer
+ls /mnt/flash/root
+#if the directory does not exist mkdir /mnt/flash/root
+</PRE>
+</LI>
+<LI>Transfer the provided software by ftp to the MCS.
+<PRE>
+ftp  mymcs.mydomain.com
+username: root
+password: pass
+cd /mnt/flash/root
+put mythenDetectorServer
+quit
+</PRE>
+
+<P>
+</LI>
+<LI>After pressing reset on the board, the board should reboot.
+
+<P>
+</LI>
+<LI>If the program does not correctly start
+ 
+<OL>
+<LI>Check by using the http interface that it is started by the inittab
+(check that the file <code>/mnt/etc/inittab</code> ends with the line 
+<BR><code>myid2:3:once:/mnt/flash/root/mythenDetectorServer</code>).  
+</LI>
+<LI>If program has not started, make the program executable by telnetting to
+the MCS and executing: 
+<BR><code>chmod a+xrw  /mnt/flash/root/mythenDetectorServer</code>
+</LI>
+<LI>After pressing reset on the board, the board should reboot and the
+acqusition program correctly start.
+ 
+</LI>
+</OL>
+</LI>
+</OL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Qt4_Installation_GUI.html

@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Qt4 Installation for GUI</TITLE>
+<META NAME="description" CONTENT="Qt4 Installation for GUI">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00042100000000000000">
+Qt4 Installation for GUI</A>
+</H3>
+It must be installed before Qwt. A Qt version equal or higher than 4.6 is
+required. One can install it:
+
+<UL>
+<LI>via YUM:
+<PRE>
+ yum install qt-devel
+</PRE>
+</LI>
+<LI>via download from:
+<BR><TT><A NAME="tex2html2"
+  HREF="
+https://download.qt.io/archive/qt/4.8/4.8.2/qt-everywhere-opensource-src-4.8.2.t
+ar.gz">https://download.qt.io/archive/qt/4.8/4.8.2/qt-everywhere-opensource-src-4.8.2.t
+ar.gz</A></TT> 
+
+<P>
+To install:
+<PRE>
+&gt; gunzip qt-everywhere-opensource-src-4.8.2.tar.gz
+&gt; tar xvf qt-everywhere-opensource-src-4.8.2.tar
+&gt; ./configure
+&gt; make
+&gt; make install
+</PRE>
+By default Qt4 will be installed in /usr/local/Trolltech/Qt-4.8.2/. 
+</LI>
+</UL>
+
+<P>
+<B>Setup Environment</B> 
+
+<P>
+One has to ensure that <code>PATH</code> and <code>LD_LIBRARY_PATH</code> have
+been updated to include Qt4 install path, binaries and libraries.
+Confirm by executing <code>qmake -v</code> and ensuring the result points to Qt4 (not
+Qt3 or Qt5). 
+
+<P>
+If the environment is not set up, one can add the libraries and
+executables to the .bashrc by adding
+<code>LD_LIBRARY_PATH</code> and <code>PATH</code>:
+<PRE>
+export QTDIR=/usr/local/Trolltech/Qt-4.8.2
+export PATH=$QTDIR/bin:$PATH
+export LD_LIBRARY_PATH=$QTDIR/lib:$LD_LIBRARY_PATH
+</PRE>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Qwt_Installation_GUI.html

@@ -0,0 +1,78 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Qwt Installation for GUI</TITLE>
+<META NAME="description" CONTENT="Qwt Installation for GUI">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00042200000000000000">
+Qwt Installation for GUI</A>
+</H3>
+Before installing Qwt, one must install Qt
+and ensure that <code>QTDIR</code>, <code>LD_LIBRARY_PATH</code> and <code>PATH</code> point to
+the correct Qt4
+version.
+
+<P>
+A Qwt version equal or higher than 6 is required. One can
+install it:
+
+<UL>
+<LI>via YUM:
+<PRE>
+ yum install qwt-devel
+</PRE>
+</LI>
+<LI>via download from:
+<BR><TT><A NAME="tex2html3"
+  HREF="
+https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download">https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download</A></TT>
+<P>
+To install:
+<PRE>
+&gt; cd qwt-6.0.0
+&gt; qmake
+&gt; make
+&gt; make install
+</PRE>
+By default Qwt will be installed int /usr/local/qwt-6.0.0 
+</LI>
+</UL>
+
+<P>
+<B>Setup Environment</B> 
+
+<P>
+One has to ensure that <code>QWTDIR</code> and <code>LD_LIBRARY_PATH</code> have
+been updated to include Qwt install path and libraries.
+
+<P>
+If the environment is not set up, one can add the libraries to the
+.bashrc by adding <code>LD_LIBRARY_PATH</code>:
+<PRE>
+export QWTDIR=/usr/local/qwt-6.0.0/
+export LD_LIBRARY_PATH=$QWTDIR/lib:$LD_LIBRARY_PATH
+</PRE>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Requirements.html

@@ -0,0 +1,82 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Requirements</TITLE>
+<META NAME="description" CONTENT="Requirements">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00042000000000000000">
+Requirements</A>
+</H2>
+These are the basic requirements to install and use the software. Fine Tuning
+the system will be discussed in other documentation provided.
+
+<UL>
+<LI><I>C/C++</I>:
+<BR>
+The software is written in C/C++. If Python API is used, it is a wrap around
+to the C++ software.  Any Linux installation with working libgcc should be
+sufficient.
+
+<P>
+</LI>
+<LI><I>Shared Memory</I>:
+<BR>
+Access to the shared memory of the control PC is required for the client.
+
+<P>
+</LI>
+<LI><I>Network</I>:
+<BR>
+The control PC communicates to the detectors and data receivers over TCP/IP.
+Therefore, the detector should receive a proper IP address (either DHCP or
+static) and no firewall should be present between the control PC and the
+detector.
+
+<P>
+</LI>
+<LI><I>Compilation</I>:
+<BR>
+cmake is required to compile. make is also possible, but is harder to find
+dependencies.
+
+<P>
+</LI>
+<LI><I>GUI</I>:
+<BR>
+To use the GUI, one requires atleast Qt4.8.2 and Qwt6.0. Installation of these
+are discussed in the next sections.
+
+<P>
+</LI>
+<LI><I>Calibration Wizards</I>:
+<BR>
+They are based on the CERN Root data analysis framework. Installation of it is
+discussed in the next sections.
+
+<P>
+</LI>
+</UL>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Root_Installation_Calibrati.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Root Installation for Calibration Wizards</TITLE>
+<META NAME="description" CONTENT="Root Installation for Calibration Wizards">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H3><A NAME="SECTION00042300000000000000">
+Root Installation for Calibration Wizards</A>
+</H3>
+The software has been developed and tested with root 5.20, but any version
+should work. One can download it from:
+<PRE>
+&gt; svn co https://root.cern.ch/svn/root/trunk root
+</PRE>
+
+<P>
+To install:
+<PRE>
+&gt; cd root
+&gt; ./configure --enable-qt
+&gt; make
+&gt; make install
+</PRE>
+
+<P>
+Edit your .bashrc to define the ROOTSYS enviroment variable and annd
+the libraries and executables to the <code>LD_LIBRARY_PATH</code> and <code>PATH</code>:
+<PRE>
+export ROOTSYS=/usr/local/root-5.34
+export PATH=$ROOTSYS/bin:$PATH
+export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
+</PRE>
+
+<P>
+You can also download the binaries, assuming that your linux and gcc versions
+match as in:
+<PRE>
+http://root.cern.ch/drupal/content/production-version-534
+</PRE>
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Setting_environment_variabl.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Setting environment variables</TITLE>
+<META NAME="description" CONTENT="Setting environment variables">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H2><A NAME="SECTION00044000000000000000">
+Setting environment variables</A>
+</H2>
+One can set up the environment variables in the following ways.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>

manual/docs/html/slsDetectorInstall/Software_Package.html

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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2008 (1.71)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>The Software Package</TITLE>
+<META NAME="description" CONTENT="The Software Package">
+<META NAME="keywords" CONTENT="slsDetectorInstall">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="slsDetectorInstall.css">
+
+</HEAD>
+
+<BODY >
+
+<H1><A NAME="SECTION00020000000000000000">
+The Software Package</A>
+</H1>
+The SLS detectors software is intended to control the detectors developed by
+the SLS Detectors group. The detectors currently supported are:
+
+<P>
+MYTHEN, GOTTHARD, EIGER and JUNGFRAU.
+
+<P>
+The package provides software for the distributed system that comprises of
+detectors, data receivers (to process detector data), and the client (to control
+or monitor the system). The client and data receivers can be embedded in
+the user's acquisitions system. Furthermore, the package also provides some
+tools for detector calibration.
+
+<P>
+<BR><HR>
+
+</BODY>
+</HTML>