docu update

Docu/chapters/part01-use.tex

@@ -7,31 +7,34 @@
 
 \section{start}
 \Grafik[H]{1}{Kapture.png}
-Currently the Startup of the system needs some manual workaround. Before turning on the PC put the 3 switches in the state shown in the Picture.
-Then Boot the PC when the Lockin screen is visible turn the HighFlex of and on with the big switch on the Highflex. Then reboot the PC. 
+The left Ethernet connector is configured for the KARA office network. The right one can be used for other networks.
 
-The two switches are to powerdown the inputstage of the KAPTURE Modules. To power them up first turn on the switch 1 and than the switch 2! (if there is a longer period without measurement one can turn them back of to reduce termal stress.)
+Currently the Start-up of the system needs some manual workaround. Before turning on the PC put the 3 switches in the state shown in the Picture.
+Then Boot the PC when the Lock-in screen is visible turn the HighFlex of and on with the big switch on the Highflex. Then reboot the PC. 
+
+\Grafik[H]{0.5}{switch.jpg}
+The two switches are to power down the input stage of the KAPTURE Modules. To power them up first turn on the switch 1 and than the switch 2! (if there is a longer period without measurement one can turn them back of to reduce thermal stress.)
 
 Now you are good to go ;)
 
-After starting the PC, start the gui and hit 'Prepare Board' and you are ready to Measure at 500\,MHz with 125\,MHz as reference. To reset the Board one can just use Prepare Board. (Soft Reset and Board Off are not necessary for KAPTURE-2). After that DataFlow, Master Controll and Data Check should be green. Also take a look on the LEDs of the HighFlex. The 3 inside the red circle indicate that the PCI is working (if one of them is not on - turn the HighFlex off and on and reboot). The 2 inside the blue circle indicate that both PLL are locked. If one is of, redo the prepare Board.
+After starting the PC, start the GUI and hit 'Prepare Board' and you are ready to Measure at 500\,MHz with 125\,MHz as reference. To reset the Board one can just use Prepare Board. (Soft Reset and Board Off are not necessary for KAPTURE-2). After that DataFlow, Master Control and Data Check should be green. Also take a look on the LEDs of the HighFlex. The 3 inside the red circle indicate that the PCI is working (if one of them is not on - turn the HighFlex off and on and reboot). The 2 inside the blue circle indicate that both PLL are locked. If one is of, redo the prepare Board.
 
-It can be also done maualy. For example if the 500\,MHz is used as imputclock. Than first \textit{Board Reset}, now the correct \textit{PLL init} then \textit{PLL Sync}, then \textit{ADC Calib} and \textit{ADC Autosync}.
+It can be also done manually. For example if the 500\,MHz is used as input clock. Than first \textit{Board Reset}, now the correct \textit{PLL init} then \textit{PLL Sync}, then \textit{ADC Calib} and \textit{ADC Autosync}.
 
 On the MultiView Page one can find all the controls. 
 
 \subsection{Basic Settings}
 \subsubsection{Configfile}
 In 'home/user/.kcg2' are two config files. One for the general and one specific for epics.
-The Configfile is more or less self explaining. 
-If the file does not exist a window opens where the config can also be edited. 
+The Configfile is more or less self explaining. The newest option is the "Working Channels" config. It can be used to define which channels are used. It does not affect the RAW-file but it ins used for displaying in some cases.
+If the file does not exist a window opens where the config can also be edited.  
 
 The epics config is best to edit only via the epicsWidget.
 
 After a change, the GUI needs to be restarted.
 
 \subsubsection{file/settings}
-This is a small Settings window to set at runtime the Save Location and the Subdirectory.
+This is a small Settings window to set at runtime the Save Location and the Sub-directory.
 
 
 
@@ -44,10 +47,10 @@ This is a small Settings window to set at runtime the Save Location and the Subd
 25ps global Delay with 24 possible steps\\
 3ps channel independent Delay with 32 steps\\
 
-In addition the second KAPTURE Module can be delayed with the 25ps in the \textit{T/H FMC2} column. The Default is 4! So for example value of 3 means that the second board wir sample 25\,ps earlier.
+In addition the second KAPTURE Module can be delayed with the 25ps in the \textit{T/H FMC2} column. The Default is 4! So for example value of 3 means that the second board will sample 25\,ps earlier.
 
-The advanced settings for ADC Delay and FPGA Delay are usualy not to use. They are mainly for developement. In normal user-operation the GUI handles them automaticaly.
-\TextGrafik[h]{Timing distribution of a KAPTURE-2 Modul. The Cascade Clock output of the first Modul is used as input for the second modul}{pl:T:bahn}{0.7}{timeplan4.png}
+The advanced settings for ADC Delay and FPGA Delay are usually not to use. They are mainly for development. In normal user-operation the GUI handles them automatically.
+\TextGrafik[h]{Timing distribution of a KAPTURE-2 Module. The Cascade Clock output of the first Module is used as input for the second modul}{pl:T:bahn}{0.7}{timeplan4.png}
 
 
 
@@ -59,42 +62,44 @@ The advanced settings for ADC Delay and FPGA Delay are usualy not to use. They a
 \Grafik[H]{1}{Widgets/TimeScan.PNG}
 The Time Scan was moved to a new Widget (mostly for code simplification). A TimeScan can be used to find the delays. 
 
-Via a dropdown menu one can select how the measured data is processed.
+Via a drop down menu one can select how the measured data is processed.
 \begin{itemize}
 	\item Mean over Everything:
-	It just calculates the mean of the complete data. This is usualy not to helpfull.
+	It just calculates the mean of the complete data. This is usually not to helpful.
 	\item Threshold:
-	Calculates the mean only for datapoints with not in $2048 +$ threshold. If you have a negativ peak, enter a negativ sign. 
+	Calculates the mean only for data points with not in $2048 +$ threshold. If you have a negative peak, enter a negative sign. 
 	\item Bucket:
-	Calculates the mean of only on bucket - usualy the best way.
+	Calculates the mean of only on bucket - usually the best way.
 	\item All Buckets:
-	New Feature: It calculates the mean for all buckets individually. Therefore the resulting file is bigger but it allowes to compare the buckets.
+	New Feature: It calculates the mean for all buckets individually. Therefore the resulting file is bigger but it allows to compare the buckets.
 \end{itemize}
 
-It offers different Scan Modes. In the standard way (as it is in the Screenshot) it scanns step by step throught all delays. In this mode usualy one uses the 25\,ps Step4 Option. If it is set to Step 1 one does oversample the Signal and increases the needed Time. 
-The \textbf{Fast Mode} is primary desinged to find the region of the Signal inside the 2\,ns Bucket. In this case it sets spreads the 8 ADCs over the 100\,ps area of the 3\,ps. and then  goes over the complete 2\,ns domain with 25\,ps Step 1. It is usualy best to use with a threshold of 20.
+It offers different Scan Modes. In the standard way (as it is in the Screenshot) it scans step by step through all delays. In this mode usually one uses the 25\,ps Step4 Option. If it is set to Step 1 one does over sample the Signal and increases the needed Time. 
+The \textbf{Fast Mode} is primary designed to find the region of the Signal inside the 2\,ns Bucket. In this case it sets spreads the 8 ADCs over the 100\,ps area of the 3\,ps. and then  goes over the complete 2\,ns domain with 25\,ps Step 1. It is usually best to use with a threshold of 20.
 The \textbf{Calibration Scan} is only needed to generate the Calibration data with the analog 500\,MHz signal and will take a long time. (Details in the Calibration Section)
 
-The Scan Results are stored in the subfolder \texttt{TimeScan}. In the logfile \texttt{scan.info} will the Scan Parameters be stored. The user has the posibility to use the Identifyer entry to add any text to the Logfile. 
+The Scan Results are stored in the sub folder \texttt{TimeScan}. In the logfile \texttt{scan.info} will the Scan Parameters be stored. The user has the possibility to use the identifier entry to add any text to the Logfile. 
 
 The Plotwindow offers multiple view. In \textbf{default} the data is plotted for each Channel separately over the delay setting. The other option is the \textbf{timecorrected} where the selected ADCs are plotted in one plot over Time. In this view also the Calibration can be activated and the Error can be plotted. In Addition a Fit can be performed.
 
+For simpler positioning of the ADC Timings one can plot them inside the Timescan via \textbf{show ADC} in the timecorrected view.
+
 
 \newpage
 \section{Calibration}
 \includegraphics[width=1.5em]{Plots/Icons/calib.png} (Ctrl+U)
 \Grafik[H]{0.3}{Widgets/CalibrationWidget0.PNG}
-This offers a Calibration Routine. First a small widget opens where the TimeScan that will be used is to be selected. It is also Possible to open the Calibration directly from the Scan Results Widget. In this case this Fileselection is skipped.
+This offers a Calibration Routine. First a small widget opens where the TimeScan that will be used is to be selected. It is also Possible to open the Calibration directly from the Scan Results Widget. In this case this File selection is skipped.
 
 \Grafik[H]{0.8}{Widgets/CalibrationWidget.PNG}
-The main Widget. The Left plot shows the original data with no calibration applied. The Right Plot than with all calibration used. The lower Inputlines can be  used to manualy adjust the calibration. 
+The main Widget. The Left plot shows the original data with no calibration applied. The Right Plot than with all calibration used. The lower input lines can be  used to manually adjust the calibration. 
 
 The Calibration is split into two Parts
 \begin{itemize}
 	\item 500\,MHz:\\
-		This needs only to be done once. Maybe it is usefull to repeat it after one year or so. To do this one uses the 500\,MHz RF clock as Input for the Channels and does a Calibration Scan. And then in this Widget select the type to be \textit{500\,MHz}. (the other Options have no effect in this case). It will take a view minutes! It calibrates the width of the Delays.
+		This needs only to be done once. Maybe it is useful to repeat it after one year or so. To do this one uses the 500\,MHz RF clock as Input for the Channels and does a Calibration Scan. And then in this Widget select the type to be \textit{500\,MHz}. (the other Options have no effect in this case). It will take a view minutes! It calibrates the width of the Delays.
 	\item Peak:\\
-		This is the more often needed One. It should be done at least every time the Measurement setup is changed. This calibrates the Baseline, Gain and Timeoffset for the 8 Channels. To do that take a Timescan (usualy with step 4) of the Measurement Signal (as seen in the Screenshot). Now select if it is a Negative Peak or a Positive Peak. If there is a region with the Baseline in front of the Puls (like in the screenshot) one can force the system to use that for Baseline determination via \textit{use first data as Baseline}. If not or not wanted, set it to 0 (which is also the default).
+		This is the more often needed One. It should be done at least every time the Measurement setup is changed. This calibrates the Baseline, Gain and Time offset for the 8 Channels. To do that take a Timescan (usualy with step 4) of the Measurement Signal (as seen in the Screenshot). Now select if it is a Negative Peak or a Positive Peak. If there is a region with the Baseline in front of the Puls (like in the screen-shot) one can force the system to use that for Baseline determination via \textit{use first data as Baseline}. If not or not wanted, set it to 0 (which is also the default).
 \end{itemize}
 To run the Calibration hit \texttt{Run}. This does not override the old one. If the result is good use \texttt{Save} to write it into the file. The old calibration file will than be renamed.
 
@@ -102,7 +107,7 @@ To run the Calibration hit \texttt{Run}. This does not override the old one. If
 \section{Correlation Test}
 \includegraphics[width=1.5em]{Plots/Icons/correlation.png} (Ctrl+Shift+C)
 \Grafik[H]{1}{Widgets/Correlation.PNG}
-This is only needed if a PeakReconstruction is later to be done. It can also be opened from the Scan Results Widget. With this, one can test if the used distribution of the Channels will give good results. Everytime a SingeRead or a ContinuousRead is done the widget updates the distribution. To Perform the test hit \texttt{Run} and wait. On the current KAPTURE-2 System without a CUDA-GPU this is done remotely on ibpt-kapture1. If the result is pleasing one can save the Correlation Correction Parameters via \texttt{Save} so that they can be used later for the ReconstructionAlgorithm.
+This is only needed if a PeakReconstruction is later to be done. It can also be opened from the Scan Results Widget. With this, one can test if the used distribution of the Channels will give good results. Every time a SingeRead or a ContinuousRead is done the widget updates the distribution. To Perform the test hit \texttt{Run} and wait. On the current KAPTURE-2 System without a CUDA-GPU this is done remotely on ibpt-kapture1. If the result is pleasing one can save the Correlation Correction Parameters via \texttt{Save} so that they can be used later for the ReconstructionAlgorithm.
 
 
 
@@ -111,9 +116,11 @@ This is only needed if a PeakReconstruction is later to be done. It can also be
 \includegraphics[width=1.5em]{Plots/Icons/wrench.png} (Ctrl+A)
 \Grafik[H]{0.4}{Widgets/AcquireSetting.PNG}
 
-The first to parameters define each acquisition, with the number of turns to observe and the number to skip. Be aware, that the turns to observe the skipped turns include. (e.g. If observe is 1000 and skip is 1, the file contains 500 datapoints). 
+The first to parameters define each acquisition, with the number of turns to observe and the number to skip. Be aware, that the turns to observe the skipped turns include. (e.g. If observe is 1000 and skip is 1, the file contains 500 data points). 
+
+The option \textit{shift FMC2} can be used if there is a shift between ADC1-4 and ADC5-8 witch is with the current firmware usually the case. It does not change anything in the raw file!
+The shift can change when the 330\,ps is changed.
 
-The option \textit{shift FMC2} can be used if there is a shift between ADC1-4 and ADC5-8 witch is with the currend firmware usualy the case. It does not change anything in the raw file!
 Currently also KAPTURE-2 is most stable without external revolution clock. Therefore \textit{Simulate Pilot Bunch} needs to be checked.
 
 
@@ -124,24 +131,31 @@ Currently also KAPTURE-2 is most stable without external revolution clock. There
 
 \section{EPICS}
 \includegraphics[width=1.5em]{Plots/Icons/EPICS_Logo.png} (Ctrl+E)
-The epics widget allows to read out parameters of KARA to store them in the Logfile for every acquisition. To change the known PVs open the PV List. Here you can edit the displayname and the PV name as well as make them available for the Log and show them in the Monitor. To remove one entry use the garbage can icon. A new PV can be added in the last line of the table. 
-Changes will only be done in the config file by \textit{apply + save}. With \textit{apply} the changes will be only temporarly.
+The epics widget allows to read out parameters of KARA to store them in the Logfile for every acquisition. To change the known PVs open the PV List. Here you can edit the display name and the PV name as well as make them available for the Log and show them in the Monitor. To remove one entry use the garbage can icon. A new PV can be added in the last line of the table. 
+Changes will only be done in the config file by \textit{apply + save}. With \textit{apply} the changes will be only temporally.
 \Grafik[H]{0.3}{Widgets/Epics1.PNG}
 \Grafik[H]{0.8}{Widgets/Epics2.PNG}
 
 
 \chapter{Important notes for measurements}
 \begin{itemize}
-	\item startup procedure: Boot PC, switch HighFlex off and on, reboot PC
+	\item start-up procedure: Boot PC, switch HighFlex off and on, reboot PC
 	\item Prepare Board can always be used to reset the board
 	\item check that PLL lock LEDs are on
 	\item use internal pilot bunch
 	\item activate HEADER
 	\item T/H FMC2 25ps to 4 is no offset
 	
-	
-
-
+	\item Using 500\,MHz reference
+	\begin{enumerate}	
+		\item connect the 125\,MHz 
+		\item do normal init with 125\,MHz reference
+		\item connect the 500\,MHz
+		\item run \textit{PLL swap 125 to 500}, \textit{PLL Synch}, \textit{ADC Synch}
+		\item now it should be working. If log is missing redo step 4. 
+		\item do not run \textit{Board Reset} or other \textit{PLL Init}! Then you would need to redo from beginning.
+		\item If a DMA error etc happens try \textit{soft reset}
+	\end{enumerate}	
 \end{itemize}
 
 

Docu/chapters/part02-develope.tex

@@ -15,9 +15,9 @@
 
 \section{misc}
 \label{ch:dev:misc}
-The Code is written to be working on both Python2 and Python3. At the moment this guide mostly only provides infos for the modules I devloped or changed.
+The Code is written to be working on both Python2 and Python3. At the moment this guide mostly only provides infos for the modules I developed or changed.
 
-Before the Idea of KAPTURE2 came to live there was the idea to put multiple Kapture1 boards in on PC. So to the GUI a multi Kapture support was added. Unfortunately not in a perfect OOP fashion and therefore the code is now a little bit inconsistent. The new changes for KAPTURE2 mostly ingnore things from the multi kapture implementation and therefore the current GUI version does not realy support multi KAPTURE anymore - sry. 
+Before the Idea of KAPTURE2 came to live there was the idea to put multiple Kapture1 boards in on PC. So to the GUI a multi Kapture support was added. Unfortunately not in a perfect OOP fashion and therefore the code is now a little bit inconsistent. The new changes for KAPTURE2 mostly ignore things from the multi kapture implementation and therefore the current GUI version does not really support multi KAPTURE anymore - sry. 
 
 Also it should work also on the old KAPTURE-1 System but it has not been tested.
 
@@ -27,35 +27,35 @@ From bottom to top.
 
 \subsection{Modules}
 \subsubsection*{base/backend/board/communication}
-This contains the \code{class PCI}, witch wrapps the systemcalls for the pci communication to the FPGA.
+This contains the \code{class PCI}, witch wraps the system-calls for the pci communication to the FPGA.
 It also creates one instance of the class with the name \code{pci}. By using 
 \begin{lstlisting}
 	from .communication import pci
 \end{lstlisting}
 one can then read and write to the FPGA.
 
-There is also a dummy class wich is selected when the gui ist started with --testing parameter. It does not read or write to the hardware and can be therefore used while developing on a system without a KAPTURE board - even on a windows system.
+There is also a dummy class which is selected when the gui is started with --testing parameter. It does not read or write to the hardware and can be therefore used while developing on a system without a KAPTURE board - even on a windows system.
 
 
 \subsubsection*{base/backend/board/board\_config}
-This contains the \code{class BoardConfiguration}. It is the central control Class for all the KAPTURE settings. (Like Delay, Turns to observe ...) It uses a dictonary to stores all the settings. 
+This contains the \code{class BoardConfiguration}. It is the central control Class for all the KAPTURE settings. (Like Delay, Turns to observe ...) It uses a dictionary to stores all the settings. 
 
 It is mainly base on observers. The function \code{update(key, value)} is used to change a setting. It then calls the observers. There are 3 Types of observers
 \begin{enumerate}
 	\item observers\_write:\\ those are controlled by the class it self. They write the settings to the board.
-	\item observers\_for\_all:\\ they are called everytime one setting is changed - indipendent of the key
-	\item observers:\\ they are called when the coresponding key changes. Those are mainly used to update the GUI.
+	\item observers\_for\_all:\\ they are called every time one setting is changed - independent of the key
+	\item observers:\\ they are called when the corresponding key changes. Those are mainly used to update the GUI.
 \end{enumerate}
 
-The \code{update} function has an additional parameter \code{write=True} it controls weather the observers\_write will be called or not. By default it is set to true. This is only needed for the function \code{read\_from\_board}, wich reads the settings from the FPGA, to prevent it from unnessesary rewrite it.
+The \code{update} function has an additional parameter \code{write=True} it controls weather the observers\_write will be called or not. By default it is set to true. This is only needed for the function \code{read\_from\_board}, wich reads the settings from the FPGA, to prevent it from unnecessary rewrite it.
 
 
 In widgets one can register a observer via the function \code{observe(who, callback, key)}\\
-who is used as an identifyer when one wants to remove the observer. It can be nearly everything - Object, variable - usualy in the GUI it is the Object that will be changed (Like the lable that is updated). \\
-callback is the function that will be called and needs to have one parameter by wich the new value will be passed.\\
+who is used as an identifier when one wants to remove the observer. It can be nearly everything - Object, variable - usually in the GUI it is the Object that will be changed (Like the label that is updated). \\
+callback is the function that will be called and needs to have one parameter by which the new value will be passed.\\
 key is the setting that will be observed.
 
-When the widget will be deleted all coresponding observers need to be removed by \code{unobserve(who, key)}!
+When the widget will be deleted all corresponding observers need to be removed by \code{unobserve(who, key)}!
 
 One example from acquiresettings widget
 \begin{lstlisting}
@@ -96,13 +96,13 @@ Class to read and generate timescans files.
 \subsubsection*{base/backendinterface}
 The most messy module. It contains a vast amount of functions.
 Including:\\
-wrapperfunctions for the \code{board_control} \\
+wrapper functions for the \code{board_control} \\
 functions to run the sequences\\
 everything for data acquisition
 
 
 
-\subsubsection*{widgets/} The most of the controling is in the widgets. They can be understood as some kind of modules. To add new functionality to the gui - like advanced analytics - one can just add a new Widget.
+\subsubsection*{widgets/} The most of the controlling is in the widgets. They can be understood as some kind of modules. To add new functionality to the GUI - like advanced analytic - one can just add a new Widget.
 
 there are by now:
 \begin{itemize}
@@ -116,7 +116,7 @@ there are by now:
 	\item UpdateCalibrationWidget
 	\item CorrelationWidget
 \end{itemize}
-To activate a widget put the modulename in widgets/\_\_init\_\_.py
+To activate a widget put the module name in widgets/\_\_init\_\_.py