Merge branch 'main-rc' into b4.2.0

Pull request from Samuel ESRF

.clang-format

@@ -0,0 +1,6 @@
+BasedOnStyle: LLVM
+IndentWidth: 4
+
+UseTab: Never
+ColumnLimit: 0
+AlignConsecutiveAssignments: false 

.clang-tidy

@@ -0,0 +1,7 @@
+---
+Checks:          '*, -google-runtime-references, -hicpp-no-array-decay, -cppcoreguidelines-pro-bounds-array-to-pointer-decay, -cppcoreguidelines-pro-bounds-pointer-arithmetic, -fuchsia*,-readability-else-after-return,-readability-avoid-const-params-in-decls,-hicpp-signed-bitwise,-cppcoreguidelines-pro-bounds-constant-array-index,-llvm-header-guard,-readability-static-accessed-through-instance,-google-readability-todo'
+WarningsAsErrors: '*'
+HeaderFilterRegex: '.*'
+AnalyzeTemporaryDtors: false
+FormatStyle:     none
+...

.gitignore

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

.travis.yml

@@ -0,0 +1,44 @@
+sudo: false
+
+language: cpp
+
+matrix:
+  include:
+    - os: linux
+      env: CONDA_PY=3.6
+
+dist: trusty
+
+install:
+  - sudo apt-get update
+  - ldd --version
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - rm -f miniconda.sh
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda config --add channels conda-forge
+  - conda config --add channels slsdetectorgroup
+  - conda update conda
+  - conda update --all
+  - conda install conda-build anaconda-client
+
+  # Useful for debugging any issues with conda
+  - conda info -a
+
+
+  # Replace dep1 dep2 ... with your dependencies
+  - conda create -q -n test-environment python=$CONDA_PY
+  - source activate test-environment
+  - conda-build .
+
+script:
+ - echo "No test scripts to be run!"
+
+
+deploy:
+  provider: script
+  script: find $HOME/miniconda/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  on:
+    branch: 4.2.0

CMakeLists.txt

@@ -1,27 +1,71 @@
 cmake_minimum_required(VERSION 2.8)
-set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
-set (REST OFF)
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
 set (CALIBRATE OFF)
-option (USE_HDF5 "HDF5 File format" OFF)
+
+# Check if project is being used directly or via add_subdirectory
+set(SLS_MASTER_PROJECT OFF)
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+	set(SLS_MASTER_PROJECT ON)
+endif()
+
+option (SLS_USE_HDF5 "HDF5 File format" OFF)
+option (SLS_USE_TEXTCLIENT "Text Client" OFF)
+option (SLS_USE_RECEIVER "Receiver" OFF)
+option (SLS_USE_GUI "GUI" OFF)
+
+
+#Flags to always be used
+# -Wno-unused-parameter should eventually be removes
+# -Wno-overloaded-virtual TODO! remove warnings in refactor
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-overloaded-virtual -Wno-unused-parameter -std=c++98")
+
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    # clang does not support -Wno-misleading-indentation 
+    # add any special clang flags
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+        set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wno-misleading-indentation")
+    endif ()
+endif()
 
 
 find_package(Qt4)
 find_package(Qwt 6)
 find_package(CBF)
 find_package(Doxygen)
-if (USE_HDF5)
+# find_package(PNG REQUIRED)
+
+if (SLS_USE_HDF5)
 	find_package(HDF5 1.10 COMPONENTS CXX)
-endif (USE_HDF5)
+endif (SLS_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 (SLS_USE_TEXTCLIENT)
+       add_subdirectory(slsDetectorSoftware)
+endif (SLS_USE_TEXTCLIENT)
+
+if (SLS_USE_RECEIVER)
+       add_subdirectory(slsReceiverSoftware)
+       add_subdirectory(manual/manual-api)    
+endif (SLS_USE_RECEIVER)
+               
+               
+if (SLS_USE_GUI)   
+       if (QT4_FOUND AND QWT_FOUND)
+       add_subdirectory(slsDetectorGui)
+       endif()
+endif (SLS_USE_GUI)
+
+if (SLS_MASTER_PROJECT)
+	# Set targets export name (otherwise set by upstream project)
+	set(TARGETS_EXPORT_NAME "slsdetector-targets")
+endif (SLS_MASTER_PROJECT)
+
 if (CALIBRATE)
     if (DEFINED ENV{ROOTSYS})
         find_package(ROOT)

Makefile

@@ -19,11 +19,12 @@ RECEIVERDIR		=	$(LIBRARYRXRDIR)
 CALWIZDIR		=	$(WD)/calibrationWizards
 MANDIR			=	$(WD)/manual
 CALIBDIR		=	$(WD)/slsDetectorCalibration
+MANAPIDIR		=	$(MANDIR)/manual-api
 
 TABSPACE		:=	"\t"
 
  
-INCLUDES=-I. -I$(LIBRARYDIR)/commonFiles -I$(LIBRARYDIR)/slsDetector -I$(LIBRARYDIR)/usersFunctions -I$(LIBRARYDIR)/multiSlsDetector -I$(LIBRARYDIR)/slsDetectorUtils -I$(LIBRARYDIR)/slsDetectorCommand -I$(LIBRARYDIR)/slsDetectorAnalysis -I$(LIBRARYDIR)/slsReceiverInterface  -I$(LIBRARYRXRDIR)/include -I$(LIBRARYDIR)/threadFiles -I$(ASM)
+INCLUDES=-I. -I$(LIBRARYDIR)/commonFiles -I$(LIBRARYDIR)/slsDetector -I$(LIBRARYDIR)/usersFunctions -I$(LIBRARYDIR)/multiSlsDetector -I$(LIBRARYDIR)/slsDetectorUtils -I$(LIBRARYDIR)/slsDetectorCommand -I$(LIBRARYDIR)/slsDetectorAnalysis -I$(LIBRARYDIR)/slsReceiverInterface  -I$(LIBRARYRXRDIR)/include -I$(LIBRARYDIR)/threadFiles -I$(LIBRARYDIR)/sharedMemory -I$(ASM)
 
 INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM) 
 #LIBFLAGRXR += 
@@ -79,6 +80,7 @@ slsReceiver_static: receiver
 receiver: #libreceiver
 #	cd  $(RECEIVERDIR) && $(MAKE) receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
 	cd  $(RECEIVERDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
+	cd  $(MANAPIDIR) && $(MAKE) slsMultiReceiver
 	@echo ""
 	@echo "#######################################"
 	@echo "# Back in slsDetectorPackage Makefile #"
@@ -151,6 +153,7 @@ clean:
 	cd $(DOCDIR) && rm -rf * 
 	rm -rf 	slsDetectorPackageDocs;
 	rm -rf $(DETAILDOC)
+	rm -rf $(MANAPIDIR)/slsMultiReceiver
 
 
 #install_lib: 
@@ -221,7 +224,6 @@ help:
 	@echo ""
 	@echo ""
 	@echo "Makefile variables"
-	@echo "REST=yes		 compile REST-aware Receiver (POCO and JsonBox libraries required)"
 	@echo "DEBUG=1,2		 set debug level to 1 (VERBOSE) or 2 (VERYVERBOSE)"
 	@echo ""
 	@echo ""

Makefile.include

@@ -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

@@ -1,48 +1,91 @@
-# slsDetector package
+### Documentation
+Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
 
+### Binaries
+Documentation to obtain the binaries via the conda package is available for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
 
-## Installation
-
-### Get source
-The source code is organised into several submodules, and the top level module is
-sls_detectors_package.
+### Source code
+One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
+```
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
-    $ git clone git@git.psi.ch:sls_detectors_software/sls_detectors_package.git
-    $ cd sls_detectors_package
-    $ ./checkout.sh
-```
-
-### Setup dependencies
-The GUI client requires Qt 4.8 and Qwt 6.0
+#### Setup dependencies 
+* Gui Client <br>
+Requirements: Qt 4.8 and Qwt 6.0
 ```
     export QTDIR=/usr/local/Trolltech/
     export QWTDIR=/usr/local/qwt-6.0.1/
 ```
 If either of them does not exist, the GUI client will not be built.
 
-The calibration wizards require ROOT
+* Advanced user Calibration wizards<br>
+Requirements: ROOT
 ```
     export ROOTSYS=/usr/local/root-5.34
 ```
 
-### Compile
-Use cmake to create out-of-source builds, by creating an build folder parallel to source directory.
+#### Compilation 
+
+Compiling can be done in two ways.
+
+**1. Compile using script cmk.sh**<br>
+
+After compiling, the libraries and executables will be found in `slsDetectorPackage/build/bin` directory<br>
+
+Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
+ * -[no option]: only make<br>
+ * -c: Clean<br>
+ * -b: Builds/Rebuilds CMake files normal mode<br>
+ * -h: Builds/Rebuilds Cmake files with HDF5 package<br>
+ * -d: HDF5 Custom Directory<br>
+ * -t: Build/Rebuilds only text client<br>
+ * -r: Build/Rebuilds only receiver<br>
+ * -g: Build/Rebuilds only gui<br>
+ * -j: Number of threads to compile through<br>
+ * -e: Debug mode
+ 
+Basic Option:
+./cmk.sh -b
+ 
+For only make:
+./cmk.sh
+
+For make clean;make:
+./cmk.sh -c
+
+For using hdf5 without custom dir /blabla:
+./cmk.sh -h -d /blabla
+
+For rebuilding cmake without hdf5 
+./cmk.sh -b
+
+For using multiple cores to compile faster:
+./cmk.sh -j9<br>
+
+
+For rebuilding only certain sections<br>
+./cmk.sh -tg #only text client and gui<br>
+./cmk.sh -r #only receiver<br>
+
+
+**2. Compile without script**<br>
+Use cmake to create out-of-source builds, by creating a build folder parallel to source directory.
 ```
     $ cd ..
-    $ mkdir sls_detectors_package-build
-    $ cd sls_detectors_package-build
-    $ cmake ../sls_detectors_package
+    $ mkdir slsDetectorPackage-build
+    $ cd slsDetectorPackage-build
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_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 -DSLS_USE_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
-    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver
+    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver slsMultiReceiver
 ```

RELEASE.txt

@@ -1,229 +1,215 @@
-SLS Detector Package 3.0.0 released on 2017-08-25
-================================================================================
+SLS Detector Package 4.2.0 released on 09.04.2020 (Minor Release)
+===================================================================
+
+
+This document describes the differences between 4.2.0 and 4.1.1 releases.   
+    
+    CONTENTS
+    --------
+    1.  Topics Concerning
+    2.  New Features
+    3.  Resolved Issues
+    4.  Firmware Requirements
+    5.  Download, Documentation & Support
+    
+
+
+1. Topics Concerning
+====================
+
+    - (Eiger) Additional status: Transmitting
+    - (Eiger) Default vcal dac value
+    - (Eiger) Default readout mode
+    - (Eiger) Dynamic range change effect on clock divider
+    - (Eiger) Deactivate a module
+    - (Eiger) Setting all trimbits argument check
+    - (Receiver) performance (memory allocation and alignment, file buffering)
+    - (Receiver) Eiger: Different rx_fifodepth defaults
+    - (Receiver) rx_fifodepth has a higher range
+    - (Receiver) subperiod in master file
+    - (Package) Removed warnings including memory overlap copy
+    - (Users) Added setflippeddatax to users class
+    - (Zmq) Client data streaming fix (Client data call back)
+
+    Compared to 4.1.1, 
+        - no firmware update required for this release
+        - eiger on-board detector server update required for this release
 
 
 
-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
-
-
-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.
-
-
-
-Resolved Issues
+2. New Features
 ===============
-	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.
-	
-	
-	
-	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.
+
+    Receiver
+    --------
+    1.  Memory in receiver is now byte aligned and write to every page
+        at memory allocation to ensure complete memory allocated right
+        from start. Removed file buffering when writing to file. Replaced
+        pausing on keepRunning variable with semaphore to reduce cpu
+        load.
+
+    2.  (Eiger) Default rx_fifodepth for 32 bit mode is 100, but 1000
+        for other modes. Changing dynamic range will now change bit mode to 
+        their defaults.
+
+
+    Client
+    ------
+    1.  Added setflippeddatax to users class.
+
+
+    Detector Server (Eiger)
+    -----------------------
+    1.  Transmitting Status: After acquiring, if the detector is still 
+        streaming out data, then the status is Trasnmitting 
+        (command line: 'data'). Only after this process, will it become idle. 
+        Previously, sls_detector_acquire waited for end of data streaming 
+        before returning. It will continue to do so.
 
 
 
-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.
+3. Resolved Issues
+==================          
+
+    Detector Server (Eiger)
+    -----------------------
+    1.  Vcal dac set to 0 at on-board detector server start up to
+        reduce noise.
+
+    2.  Default Readout mode set to Parallel instead of Non parallel.
+
+    3.  Dynamic range  4, 8 or 16 changes the clock divider to full speed, 
+        whereas dynamic range of 32 still changes the clock divider to 
+        quarter speed. So, default is dynamic range of 16 and full speed 
+	at detector server start up.
+
+    4.  Setting activate to 0 sent to both control and stop server.
+        So, deactivate a module can be done even if FEB communication fails.
+        Restarting the server will activate the module again.
+
+    5.  Verification included for input of setting all trimbits values.
+        Valid input is 0 - 63.
 
 
+    Receiver
+    --------
+    1.  Earlier, setting rx_fifodepth to a high value would set to 
+        a lower value, printing this low value to console, 
+        but not giving an error. Memory allocated can now take in 64 bits.
+    
+    2.  Modifying subexptime now also updates subperiod in master file.
+        Also, the print for subperiod name to console is corrected.
 
 
+    Package
+    -------
+    1.  Many warnings have been fixed, including those with overlapping 
+        memory copies for source and destination. 
 
+
+    Client
+    ------
+    1.  Each time client data streaming was enabled to receive, it
+        creates zmq sockets without checking if they were already created.
+        This is fixed now.
+    
+    
+    
+4. Firmware Requirements
+========================
+        
+        Gotthard
+        ========   
+        Minimum compatible version  : 11.01.2013
+        Latest compatible version   : 08.02.2018 (50um and 25um Master)
+                                      09.02.2018 (25 um Slave) 
+        Eiger
+        =====  
+        Minimum compatible version  : 24
+        Latest compatible version   : 24
+        
+        Jungfrau
+        ========       
+        Minimum compatible version  : 26.02.2018
+        Latest compatible version   : 06.12.2018
+
+        
+        Detector Upgrade
+        ================
+        Gotthard    Cannot be upgraded remotely. Requires programming via USB blaster
+        Eiger       Can be upgraded remotely via bit files
+        Jungfrau    Can be upgraded remotely using sls_detector_put programfpga <pof>
+        
+        Instructions available at
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/GOTTHARD_Firmware.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/EIGER_Firmware.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorInstall/JUNGFRAU_Firmware.html
+
+         
+    Please refer to the link below for more details on the firmware versions.
+    https://www.psi.ch/en/detectors/firmware
+    
+    
+        
+5. Download, Documentation & Support
+====================================
+
+    Download
+    --------
+    
+    The Source Code (Default C++ API):
+         https://github.com/slsdetectorgroup/slsDetectorPackage
+         
+    The Conda Lib Package:
+        https://github.com/slsdetectorgroup/sls_detector_lib
+        
+    The Conda GUI Package:
+        https://github.com/slsdetectorgroup/sls_detector_gui    
+        
+    The Python Interface (including the package):
+        https://github.com/slsdetectorgroup/sls_detector
+    
+    
+    Documentation
+    -------------
+    
+    Manual (HTML & PDF):
+        https://www.psi.ch/en/detectors/documentation
+        slsDetectorPackage/manual/docs/
+        
+    Command Line Documentation:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorClientDocs/index.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/pdf/slsDetectorClientDocs.pdf
+
+        manual/docs/html/slsDetectorClientDocs/index.html
+        manual/docs/pdf/slsDetectorClientDocs.pdf
+        
+    C++ API Documentation:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/html/slsDetectorUsersDocs/index.html
+        https://slsdetectorgroup.github.io/slsDetectorPackage/docs/pdf/slsDetectorUsersDocs.pdf
+
+        manual/docs/html/slsDetectorUsersDocs/index.html
+        manual/docs/pdf/slsDetectorUsersDocs.pdf
+        
+    C++ API Example:
+        https://slsdetectorgroup.github.io/slsDetectorPackage/exampleCode/slsDetectorUsersExample/index.html
+
+        manual/manual-api/mainClient.cpp
+        manual/manual-api/mainReceiver.cpp
+        
+    Python API Documentation:
+        https://slsdetectorgroup.github.io/sls_detector/
+
+    TroubleShotting:
+        https://www.psi.ch/en/detectors/troubleshooting
+        
+    Further Documentation:
+        https://www.psi.ch/en/detectors/users-support
+        
+    
+    Support
+    -------
+
+        dhanya.thattil@psi.ch
+        erik.frojdh@psi.ch
+        anna.bergamaschi@psi.ch

checkout.sh

@@ -1,17 +0,0 @@
-#git clone $1@git.psi.ch:sls_det_software/sls_detectors_package.git slsDetectorsPackage
-
-#cd slsDetectorsPackage
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_software.git slsDetectorSoftware
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_gui.git slsDetectorGui
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_receiver_software.git slsReceiverSoftware
-
-git clone $1@git.psi.ch:sls_detectors_software/sls_detector_calibration.git slsDetectorCalibration
-
-#git clone $1@git.psi.ch:sls_detectors_software/sls_image_reconstruction.git slsImageReconstruction
-
-git clone $1@git.psi.ch:sls_detectors_software/calibration_wizards.git calibrationWizards
-
-#git clone git@git.psi.ch:sls_detectors_software/tests.git tests

cleansharedmemory.sh

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

cmk.sh

@@ -3,6 +3,11 @@ BUILDDIR="build"
 HDF5DIR="/opt/hdf5v1.10.0"
 HDF5=0
 COMPILERTHREADS=0
+TEXTCLIENT=0
+RECEIVER=0
+GUI=0
+DEBUG=0
+
 
 CLEAN=0
 REBUILD=0
@@ -16,7 +21,11 @@ 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
+ -e: Debug mode
  
 For only make:
 ./cmk.sh
@@ -39,14 +48,19 @@ 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:trge" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
 		REBUILD=1
+		CLEAN=1
 		;;
 	c) 
 		echo "Clean Required"
@@ -56,6 +70,7 @@ while getopts ":bchd:j:" opt ; do
 		echo "Building of CMake files with HDF5 option Required"
 		HDF5=1
 		REBUILD=1
+		CLEAN=1
 		;;
 	d) 
 		echo "New HDF5 directory: $OPTARG" 
@@ -65,6 +80,28 @@ while getopts ":bchd:j:" opt ; do
 		echo "Number of compiler threads: $OPTARG" 
 		COMPILERTHREADS=$OPTARG
 		;;
+	t) 
+    	echo "Compiling Options: Text Client" 
+		TEXTCLIENT=1
+		REBUILD=1
+		CLEAN=1
+		;;      
+	r) 
+		echo "Compiling Options: Receiver" 
+		RECEIVER=1
+		REBUILD=1
+		CLEAN=1
+		;;      
+	g) 
+		echo "Compiling Options: GUI" 
+		GUI=1
+		REBUILD=1
+		CLEAN=1
+		;;  
+	e)
+		echo "Compiling Options: Debug" 
+		DEBUG=1
+		;;    
     \?)
      	echo "Invalid option: -$OPTARG" 
 		usage
@@ -83,6 +120,29 @@ done
 
 
 
+if [ $TEXTCLIENT -eq 0 ] && [ $RECEIVER -eq 0 ]  && [ $GUI -eq 0 ]; then
+       CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=ON -DSLS_USE_GUI=ON "
+       echo "Compile Option: TextClient, Receiver and GUI"
+else 
+       if [ $TEXTCLIENT -eq 1 ]; then
+              CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON "
+               echo "Compile Option: TextClient"
+       fi
+       if [ $RECEIVER -eq 1 ]; then
+               CMAKE_POST+=" -DSLS_USE_RECEIVER=ON "
+               echo "Compile Option: Receiver"
+       fi
+                               
+       if [ $GUI -eq 1 ]; then
+               CMAKE_POST+=" -DSLS_USE_GUI=ON "
+               echo "Compile Option: GUI"
+       fi
+fi
+
+
+
+
+
 #build dir doesnt exist
 if [ ! -d "$BUILDDIR" ] ; then
 	echo "No Build Directory. Building of Cmake files required"
@@ -96,14 +156,20 @@ else
 	fi
 fi
 
+#Debug
+if [ $DEBUG -eq 1 ]; then
+	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+	echo "Debug Option enabled"
+fi 
+
 
 #hdf5 rebuild
 if [ $HDF5 -eq 1 ]; then
 	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
-	CMAKE_POST+="-DUSE_HDF5=ON"
+	CMAKE_POST+=" -DSLS_USE_HDF5=ON "
 #normal mode rebuild
 else
-	CMAKE_POST+="-DUSE_HDF5=OFF"
+	CMAKE_POST+=" -DSLS_USE_HDF5=OFF "
 fi
 
 

examples/gotthard.config

@@ -3,16 +3,9 @@ hostname bchip007
 #0:port 1952
 #0:stopport 1953
 #0:rx_tcpport 1956 must also have this in receiver config file
-0:settingsdir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
 0:angdir 1.000000
 0:moveflag 0.000000
-0:lock 0
-0:caldir /home/l_maliakal_d/mySoft/newMythenSoftware/settingsdir/gotthard
-0:ffdir /home/l_maliakal_d
 0:extsig:0 off
-0:extsig:1 off
-0:extsig:2 off
-0:extsig:3 off
 #0:detectorip 129.129.202.9
 0:detectormac 00:aa:bb:cc:dd:ee
 0:rx_udpport 50004
@@ -23,7 +16,6 @@ hostname bchip007
 master -1
 sync none
 outdir /bigRAID/datadir_gotthard/rec_test_data
-ffdir /home/l_maliakal_d
 headerbefore none
 headerafter none
 headerbeforepar none
@@ -32,4 +24,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

examples/jungfrau.config

@@ -1,18 +1,15 @@
 hostname bchip038+
 
-settingsdir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-caldir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-lock 0
-
 0:rx_udpport 50004
 0:rx_udpip 10.1.1.100
 0:detectorip 10.1.1.10
-
 rx_hostname pcmoench01
 
 powerchip 1
-timing auto
+
+#extsig:0 trigger_in_rising_edge
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/jungfrau_two.config

@@ -1,11 +1,6 @@
 detsizechan 1024 1024
 hostname bchip048+bchip052+
 
-settingsdir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-caldir /home/mySoft/slsDetectorsPackage/settingsdir/jungfrau
-lock 0
-
-
 0:rx_udpport 50004
 0:rx_udpip 10.1.1.100
 0:rx_udpmac F4:52:14:2F:32:00
@@ -22,9 +17,9 @@ lock 0
 rx_hostname pcmoench01
 
 powerchip 1
-extsig:0 trigger_in_rising_edge
-timing auto
+#extsig:0 trigger_in_rising_edge
+#timing trigger
 
 outdir /external_pool/jungfrau_data/softwaretest
-threaded 1
+
 

examples/two_gotthard.config

@@ -8,16 +8,11 @@ hostname bchip007+bchip009+
 #0:port 1952
 #0:stopport 1953
 #0:rx_tcpport 1956 
-0:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:angdir 1.000000
 0:moveflag 0.000000
-0:lock 0
-0:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 0:ffdir /home/l_msdetect
 0:extsig:0 off
-0: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
@@ -31,16 +26,11 @@ hostname bchip007+bchip009+
 #1:port 1952
 #1:stopport 1953
 1:rx_tcpport 1957
-1:settingsdir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:angdir 1.000000
 1:moveflag 0.000000
-1:lock 0
-1:caldir /home/l_msdetect/dhanya/slsDetectorsPackage/settingsdir/gotthard
 1:ffdir /home/l_msdetect
 1:extsig:0 off
-1:extsig:1 off
-1:extsig:2 off
-1:extsig:3 off
+
 1:detectorip 10.1.2.2
 #1:detectormac 00:aa:bb:cc:dd:ee
 1:rx_udpport 50004
@@ -62,4 +52,4 @@ badchannels none
 angconv none
 globaloff 0.000000
 binsize 0.001000
-threaded 1
+

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

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
 <META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
 
 <LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
@@ -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>September 28, 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
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

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 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
-<P ALIGN="CENTER"><STRONG>August 24, 2017</STRONG></P>
+<P ALIGN="CENTER"><STRONG>September 28, 2018</STRONG></P>
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 <P>
@@ -78,7 +78,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-09-28
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@@ -55,7 +55,7 @@ Introduction</A>
 
 <P>
 In order to convert from strip number to 2<IMG
- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
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  ALT="$\theta$">-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). 
 <BR>
@@ -107,7 +107,7 @@ where the parameters <IMG
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  SRC="img7.png"
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@@ -121,7 +121,7 @@ Finally, the global offset of the detector system is precisely determined by ref
 
 <P>
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- WIDTH="12" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
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@@ -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
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/angularCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -211,7 +211,7 @@ Acquisition GUI window to setup the motor position scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-09-28
 </ADDRESS>
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manual/docs/html/angularCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
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-<!--Converted with LaTeX2HTML 2008 (1.71)
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@@ -180,7 +180,7 @@ After fitting all modules you can click on the <I>Write Angular Calibration</I>
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 Thattil Dhanya
-2017-08-24
+2018-09-28
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 Thattil Dhanya
-2017-08-24
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 Copyright &#169; 1993, 1994, 1995, 1996,
 <A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>, 
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 <BR><HR>
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 Thattil Dhanya
-2017-08-24
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 <DIV>
 
 <P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
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 Thattil Dhanya
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+! Missing } inserted.
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+                }
+l.170 $CS={\begingroupN_S\endgroup
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+I've inserted something that you may have forgotten.
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+
+! Extra \endgroup.
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+l.170 $CS={\begingroupN_S\endgroup
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+                        
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+Output written on images.dvi (40 pages, 9712 bytes).

manual/docs/html/energyCalibrationHowTo/images.pl

@@ -1,4 +1,4 @@
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 $key = q/O;MSF=1.6;AAT/;
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- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
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  ALT="$O$">|; 
 
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 $key = q/ENC;MSF=1.6;AAT/;
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manual/docs/html/energyCalibrationHowTo/index.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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@@ -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>September 28, 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
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/internals.pl

@@ -1,4 +1,4 @@
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
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+$key = q/fig:addenergy/;
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+
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 $noresave{$key} = "$nosave";

manual/docs/html/energyCalibrationHowTo/labels.pl

@@ -1,4 +1,4 @@
-# LaTeX2HTML 2008 (1.71)
+# LaTeX2HTML 2012 (1.2)
 # Associate labels original text with physical files.
 
 
@@ -34,14 +34,14 @@ $key = q/fig:guiencallog/;
 $external_labels{$key} = "$URL/" . q|node2.html|; 
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-$key = q/fig:addenergy/;
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+$key = q/fig:addenergy/;
+$external_labels{$key} = "$URL/" . q|node3.html|; 
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+
 $key = q/fig:expthrscan/;
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 1;
 
 
-# LaTeX2HTML 2008 (1.71)
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+$external_latex_labels{$key} = q|7|; 
+$noresave{$key} = "$nosave";
+
 $key = q/fig:expthrscan/;
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 $noresave{$key} = "$nosave";

manual/docs/html/energyCalibrationHowTo/node1.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
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 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -78,21 +78,21 @@ The thick solid line represents the physical curve which also takes into account
 
 <P>
 The intrinsic noise on the electronic signal  is defined by the Equivalent Noise Charge (<IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$">). The <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$"> describes noise in terms of the charge at the detector input needed to create the same output at the end of the analog chain and is normally expressed in electrons. For silicon sensors, it can be converted into energy units by considering 1&nbsp;<IMG
  WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
  SRC="img12.png"
  ALT="$e^-$">=3.6&nbsp;eV.
 The value of the <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$"> normally depends on the shaping settings of the analog chain and increases with shorter shaping times. 
 The resulting electronic signal spectrum is then  given by a convolution between the radiation spectrum and the noise i.e., a Gaussian of standard deviation <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$">.  
 The S-curve for a monochromatic radiation beam is well described by a Gaussian cumulative distribution <IMG
@@ -204,10 +204,10 @@ Moreover, setting the threshold too close to the energy of the fluorescent light
 The comparator threshold is given by a global level which can be set on a module basis and adds to a component which is individually adjustable for each channel. In order to optimize the uniformity of the detector response it is important to properly adjust the threshold for all channels. 
 <BR>
 Since both the signal amplification stages and the comparator  are linear, it is necessary to calibrate the detector offset <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img25.png"
  ALT="$O$"> and gain <IMG
- WIDTH="17" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img26.png"
  ALT="$G$"> in order to correctly set its comparator threshold <IMG
  WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
@@ -258,10 +258,10 @@ Expected counts as a function of a threshold energy for a monochromatic beam of
  WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
  SRC="img2.png"
  ALT="$N_0$">=10000 is the number of photons absorbed by the detector during the acquisition time. The dashed line represents the curve in an ideal case without electronic noise and charge sharing, the solid thin line with noise  <IMG
- WIDTH="44" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img3.png"
  ALT="$ENC$">=1&nbsp;keV but without charge sharing and the solid thick line is the physical case with noise and <IMG
- WIDTH="45" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
  SRC="img4.png"
  ALT="$CS=$">22&nbsp;% charge sharing. <IMG
  WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
@@ -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
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node2.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
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 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -180,7 +180,7 @@ Acquisition GUI window to setup the threshold scan.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node3.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
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 <META NAME="distribution" CONTENT="global">
 
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@@ -107,7 +107,7 @@ Once you have uploaded at least 2 energies, you will be allowed to  <I>proceed t
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 7:</STRONG>
 Window to add energies to the calibration.</CAPTION>
 <TR><TD><IMG
- WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
  SRC="img39.png"
  ALT="\includegraphics[width=\textwidth]{addEnergy.eps}"></TD></TR>
 </TABLE>
@@ -153,7 +153,7 @@ The button <I>Finished</I> will be enebled only once the calibration files have
 <CAPTION ALIGN="BOTTOM"><STRONG>Figure 8:</STRONG>
 Window to calibrate the modules.</CAPTION>
 <TR><TD><IMG
- WIDTH="555" HEIGHT="694" ALIGN="BOTTOM" BORDER="0"
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
  SRC="img40.png"
  ALT="\includegraphics[width=\textwidth]{calibrateModule.eps}"></TD></TR>
 </TABLE>
@@ -184,7 +184,7 @@ Window to calibrate the modules.</CAPTION>
 <!--End of Navigation Panel-->
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>

manual/docs/html/energyCalibrationHowTo/node4.html

@@ -1,6 +1,6 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
 
-<!--Converted with LaTeX2HTML 2008 (1.71)
+<!--Converted with LaTeX2HTML 2012 (1.2)
 original version by:  Nikos Drakos, CBLU, University of Leeds
 * revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
 * with significant contributions from:
@@ -13,7 +13,7 @@ original version by:  Nikos Drakos, CBLU, University of Leeds
 <META NAME="resource-type" CONTENT="document">
 <META NAME="distribution" CONTENT="global">
 
-<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
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 <LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
@@ -68,7 +68,7 @@ By reloading the default detector settings, the calibration coefficients will be
 <BR><HR>
 <ADDRESS>
 Thattil Dhanya
-2017-08-24
+2018-09-28
 </ADDRESS>
 </BODY>
 </HTML>