jungfrauserver adcphase fix: bug was if adcphase was same as previous value, it still shifted

README.md

@@ -1,10 +1,13 @@
+### 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)
 
 ### 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 3.0.1
+git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
 #### Setup dependencies 
@@ -41,6 +44,9 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
  * -g: Build/Rebuilds only gui<br>
  * -j: Number of threads to compile through<br>
  
+Basic Option:
+./cmk.sh -b
+ 
 For only make:
 ./cmk.sh
 

RELEASE.txt

@@ -1,37 +1,31 @@
-SLS Detector Package 3.0.1 released on 2018-02-12
+SLS Detector Package 3.1.1 released on 2018-03-12
 =================================================
 
 
 
 INTRODUCTION
 
-This document describes the differences between 3.0.0 and 3.0.1 release.
+This document describes the differences between 3.1.0 and 3.1.0 releases.
 
 The conda package of the binaries can be downloaded from
 	
-	https://github.com/erikfrojdh/sls_detector_software.git
+	https://github.com/slsdetectorgroup/sls_detector_software.git
 	
-The conda package of the python API wrap-around to the software package is at 
+The Python interface to the software package (including the package) is at 
 	
 	https://github.com/slsdetectorgroup/sls_detector.git
 	
 Manual (both HTML and pdf versions) are provided in
-	
 	manual/docs/
 
-Documentation from Source Code can be found for the Command Line and C++ API in
-	
+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
-		
-Documentation to the python API is available at
 
-	https://slsdetectorgroup.github.io/sls_detector/
-		
 Example including binaries for detector and receiver user classes can be found in 
 
 	manual/manual-api
@@ -63,284 +57,53 @@ CONTENTS
 Firmware Requirements
 =====================
 
-Please refer to the link below for more details on the firmware versions.
-	https://www.psi.ch/detectors/firmware.
+	Please refer to the link below for more details on the firmware versions.
+		https://www.psi.ch/detectors/firmware.
 
-	Gotthard
-	========   
-    Minimum compatible version	: old one
-    Latest version				: 08.02.2018 (50um and 25um Master)
-        						  09.02.2018 (25 um Slave) 
+    	Gotthard
+    	========   
+    	Minimum compatible version  : 11.01.2013
+    	Latest version              : 08.02.2018 (50um and 25um Master)
+                                      09.02.2018 (25 um Slave) 
 
    	-Can not be upgraded remotely.
     
     
-    Eiger
-	=====  
-    Minimum compatible version	: 16
-    Latest version				: 21
+    	Eiger
+    	=====  
+    	Minimum compatible version  : 16
+    	Latest version              : 20
         
-    -Can be upgraded remotely via bit files.
+    	-Can be upgraded remotely via bit files.
     
         
-    Jungfrau
-    ========       
-    Minimum compatible version	: 13.11.2017
-    Latest version				: 13.11.2017
+    	Jungfrau
+    	========       
+    	Minimum compatible version  : 13.11.2017
+    	Latest version              : 13.11.2017
 
-    -Can be upgraded remotely via sls_detector_put programfpga <pof>.
+    	-Can be upgraded remotely via sls_detector_put programfpga <pof>.
 	 
 
 
 Changes in User Interface
 ========================= 
 	
-	
-	Client
-	------
-	1.	Additional functions added for advanced users in users class:
-		(setSpeed, setClockDivider, setReadOutFlags, setDac, getADC, 
-		setAllTrimbits, startReceiver, stopReceiver,
-		startAcquisition non blocking, setReceiverSilentMode, setHighVoltage,
-		enableDataStreamingToClient, enableDataStreamingFromReceiver, 
-		setReceiverDataStreamingOutPort, setClientDataStreamingInPort)
-			
-	2.	Zmq set up for client and receiver are separated.
-		zmqport for client and rx_zmqport for receiver. By default, they are the
-		same for the slsDetectorGui to work.
-		
-	3. 	Users example also works without config file, where detector already
-		configured in shared memory.
-		
-	4. 	Use "sls_detector_get busy 0" to clear acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
-		
-	5. 	Set bit, clear bit, read register and write register cannot give -1 for
-		inconsistent values from multiple detectors. One has to check error from 
-		API or read the values individually.
-		
-	6. 	multiSlsDetector::char* getSettingsFile() function signature has been 
-		changed to string getSettingsFile().
 
-		
-		
-	Receiver
-	--------
-	7.	Modified the help manaual/main-api/mainReceiver.cpp to make it more
-		robust (handling child process exit) and flexible to determine upon 
-		start up the number of receivers (child processes), the start TCP port 
-		and whether to call back data.
-		
-		detReceiver is now executed with [start tcp port] [number of receivers]
-		[1 for call back, 0 for none] as arguments. 
-		By default, start tcp port is 1954, number of receivers	is 1, and call
-		back is initiated.
-		
-	8.	rx_datastream to enable/disable data streaming in receiver. Using the GUI
-		or registering data call back in client automatically enables zmq in 
-		receiver and client. "externalgui" is removed from the command line. Use
-		this command instead.
-		
-	9.	Rx_tcpport argument to the slsReceiver can be given using -t. 
-		Eg. slsReceiver -t1955
-		
+
 
 New Features
 ============
 
 
-	Package
-	-------
-	1.	In addition to the C++ API, the Python API is also now provided.
-	
-	2. 	CMAKE now with debug flag and rpath, show warnings, compile only certain 
-		components (such as receiver or gui)
-	
-	3. 	One repository for entire package and made available at github.
-	
-	4. 	One can do --version or -v to all the binaries to find out the release
-		version of the particular executable.
-		
-	5. 	All the software version numbers have only date in format YYMMDD.
-	
-	  
-   	Client
-	------
-	6. 	Parallelized more commands to detector. Beneficial for large detectors.
-		(setTimer, setFileIndex, setOnline, setReceiverOnline, getReceiverStatus,
-		resetFramesCaught, setFrameIndex, setFileName, getFramesCaughtByReceiver,
-		setDynamicRange, setRateCorrection)
-		
-		Option to also use "sls_detector_put threaded 0" to improve speed by 
-		eliminating progress display during acquisition. Effective only for 
-		large detectors.
-		
-	
-	Detector Server
-	---------------
-	7.	(Eiger) Virtual class to execute on pc.
-	
-	8. 	One can now read temperatures during acquisition. It goes via the stop
-		server.
-		
-	9.	(Jungfrau) One can start server in "debug" mode and then program the
-		new firmware via software command "sls_detector_put programfpga xx.pof".
-		
-	10.	(Jungfrau) Server can exit on start up if either the firmware or the 
-		server is incompatible with each other.
-	
-	11.	(Jungfrau) One is able to set transmission delay (ms) of image for each
-		individual detector using "txndelay_frame" command. Beneficial for 
-		large detectors.
-		
-	12.	(Jungfrau) One can set a threshold temperature (temp_threshold) and 
-		enable the temperature control feature (temp_control). When the 
-		temperature (temp_fpga) overshoots the threshold temperature, it will
-		set the temperature event (temp_event) and power off the chip. One must
-		then switch off the detector and check cooling. Switching back on starts
-		with defaults.
-		
-	13.	(25um Gotthard) Added start acquisition delay to master module.
-	
-	14. (Gotthard) New constraints include minimum exposure time is 186 ns and
-		minimum period is 1278 ns + current exposure time.
-	
-	
-	Receiver
-	--------
-	14. The detectorip and rx_udpip does not have to be in the same subnet anymore.
-		Add the following commands after rx_hostname in config file to overwrite
-		mac configuration:
-		rx_udpmac [router mac]
-		configuremac 0 
-		
-	15.	Added silent mode to receiver using command r_silent [i] from client. 
-		It might be beneficial for max frame rate applications.
-		
-	16.	Receiver print out can handle black or white backgrounds.
-	
-	17.	zmq package included updated to v4.0.8.
-	
-	18.	Zmq streaming from receiver also sends file index in json header.
-	
-	
-	Gui
-	---
-	18.	If acquisition is done, but "stop dummy packet" to the gui was lost in 
-		the network, stop acquisition command will restream it so that the gui
-		doesnt hang forever. This is used only for very fast detectors like 
-		Moench.
-
-
 
 Resolved Issues
 ===============
 
 
-	Client
-	------
-	1. 	gethostbyname used in connecting to sockets was not thread safe for 
-		multiple detectors. Using getaddrinfo for stability in multi threaded
-		environment.
-	
-	2. 	Updated writing content of config and parameter dump into files.
-	
-	3. 	More locking to handle main and processing threads using the threadpool.
-		Removing unlock twice, which is undefined behavior.
-			
-
-	Detector Server
-	---------------
-	4. 	(Eiger) The hardware MAC of the detector is used during configuration 
-		and relayed  back to client. Similarly, hardware IP for 1 Gbe data mode.
-		
-	5. 	(Eiger) Status will return error if there was the unlikely trouble 
-		reading status register in the front end board. Earlier, it would only 
-		return idle.
-		
-	6.	(Jungfrau) patch server v3.0.0.6.3
-		Able to set settings, high voltage now correctly reads 0 when 
-		switched off, dacs are properly set.
-			
-	7. 	(Jungfrau) FPGA reset and programming FPGA firmware via software is done
-		properly
-		
-	8. 	(Gotthard) patch server v3.0.0.5.1
-		Able to read temperature properly.
-		
-	9. 	(Gotthard) butst mode if set too fast had unwanted behavior such as 
-		sending same image continuously. Now it is handled to display error
-		and stop acquisition.
-		
-	10.	(Gotthard) completely removed the possibility to set timing modes 
-		other than auto and trigger as they are not implemented anyway. Also
-		signal index 1, 2 and 3 are reserved and hence, cannot be configured for
-		an external trigger.
-		
-	11.	Non Mythen and non Eiger detectors can also now get settings file from 
-		board.
-		
-	12. (Gotthard) Did not get first few images initially after configuring MAC
-		of detector. Fixed.
-	
-	
-	Receiver
-	--------
-	12.	Made it easier to disable the standard receiver and fixing bugs related 
-		to the use of a custom one. 
-		
-	13.	(Jungfrau) HDF5 dimensions (npixelsY) required for mapping fixed.
-	
-	14.	patch2-v3.0.0-slsReceiverSoftware.patch
-		x, y and z coordinates in the call backs and the files are hardcoded 
-		for this release. 
-		
-	15.	Rest implementation (not used by standard receiver) removed.
-
-	
-	Gui
-	---
-	16.	patch1-v3.0.0-slsDetectorGui.patch
-		(Eiger) In expert mode and in advanced tab, when trimbits 
-		loaded are different for every pixel, the gui complains and sets 
-		all trimbits to zero. This has been resolved. Now, the "Set All 
-		Trimbits" field is just set to -1.
-		
-	17.	Fixed segmentation fault of xputsn properly.
-	
-	18.	Upon clicking on "Start", clears acquiring flag in shared memory
-		caused due to an earlier interrupted acquisition from Ctrl+C"
-		
-	19.	Fixed plotting twice caused due to unzooming the first time.
-	
-	20.	Removed option for compression in Gui as it is not available currently.
-	
-	21. Can also show Jungfrau multi detector in x direction in gui.
-	
-	22. Switching tabs sometimes results in delay and gates fields being incorrectly
-		enabled. Fixed.
-
-
-	
 Known Issues
 ============
 
-
-	Client
-	------
-	1.	File name prefix can only be done at multi deector level. Changing at 
-		individual detector level will not include scan or position variables.
-
-	
-	Detector Server
-	---------------
-	2.	Standard header fills x-coord in 1D. y-coord and z-coord is not 
-		implemented (3D).
-
-
-	Receiver
-	--------
-	3. 	HDF5 compression and filters are not implemented yet.
 	
 
 	

manual/docs/html/slsDetectors-FAQ/WARNINGS

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-
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-
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manual/docs/html/slsDetectors-FAQ/footnode.html

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-
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-original version by:  Nikos Drakos, CBLU, University of Leeds
-* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
-  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>Footnotes</TITLE>
-<META NAME="description" CONTENT="Footnotes">
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-
-<DL>
-<DT><A NAME="foot1316">... tab&nbsp;</A><A
- HREF="MYTHEN.html#tex2html20"><SUP>3.1</SUP></A></DT>
-<DD>The default name of the calibrated trimfiles is <I>trimbits/beamline/</I><I>settings</I><I>/noise.snxxx</I> where  <I>settings</I> is the chosen settings. You  can change it in <I>src/qDetector.h</I> and then recompile the acquisition program as described in&nbsp;<A HREF="#sec:installation"><IMG  ALIGN="BOTTOM" BORDER="1" ALT="[*]"
- SRC="file:/usr/share/latex2html/icons/crossref.png"></A>.
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-<DT><A NAME="foot1317">....snxxx&nbsp;</A><A
- HREF="MYTHEN.html#tex2html21"><SUP>3.2</SUP></A></DT>
-<DD>The default name of the calibration file <I>calibration/</I><I>settings</I><I>.snxxx</I> where  <I>settings</I> is the chosen settings. You  can change it in <I>src/qDetector.h</I> and then recompile the acquisition program.
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manual/docs/html/slsDetectors-FAQ/index.html

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-* with significant contributions from:
-  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
-<HTML>
-<HEAD>
-<TITLE>SLS Detectors
-Frequently Asked Questions</TITLE>
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-Frequently Asked Questions">
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-
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-
-<BODY >
-
-<P>
-
-<H1 ALIGN=CENTER>SLS Detectors
-<BR>
-Frequently Asked Questions</H1>
-<P ALIGN=CENTER><STRONG>Anna Bergamaschi</STRONG>
-</P>
-<BR><P ALIGN=CENTER><B>Date:</B> February 27, 2018</P>
-
-<HR>
-
-<BR><HR>
-
-</BODY>
-</HTML>

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manual/docs/html/slsDetectors-FAQ/slsDetectors-FAQ.css

@@ -1,30 +0,0 @@
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-.MATH    { font-family: "Century Schoolbook", serif; }
-.MATH I  { font-family: "Century Schoolbook", serif; font-style: italic }
-.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
-
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-SMALL.TINY		{ font-size : x-small  }
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-
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-
-/* mathematics styles */
-DIV.displaymath		{ }	/* math displays */
-TD.eqno			{ }	/* equation-number cells */
-
-
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manual/docs/html/slsDetectors-FAQ/slsDetectors-FAQ.html

@@ -1,41 +0,0 @@
-<!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>SLS Detectors
-Frequently Asked Questions</TITLE>
-<META NAME="description" CONTENT="SLS Detectors
-Frequently Asked Questions">
-<META NAME="keywords" CONTENT="slsDetectors-FAQ">
-<META NAME="resource-type" CONTENT="document">
-<META NAME="distribution" CONTENT="global">
-
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-<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
-
-<LINK REL="STYLESHEET" HREF="slsDetectors-FAQ.css">
-
-</HEAD>
-
-<BODY >
-
-<P>
-
-<H1 ALIGN=CENTER>SLS Detectors
-<BR>
-Frequently Asked Questions</H1>
-<P ALIGN=CENTER><STRONG>Anna Bergamaschi</STRONG>
-</P>
-<BR><P ALIGN=CENTER><B>Date:</B> February 27, 2018</P>
-
-<HR>
-
-<BR><HR>
-
-</BODY>
-</HTML>

manual/manual-api/mainClient.cpp

@@ -77,7 +77,6 @@ int main(int argc,  char **argv) {
 	pDetector->enableDataStreamingToClient(1);
 
 
-
 	/** - ensuring detector status is idle before starting acquisition. exiting if not idle */
 	int status = pDetector->getDetectorStatus();
 	if (status  !=  0){
@@ -94,7 +93,7 @@ int main(int argc,  char **argv) {
 
 	/** - start measurement */
 	pDetector->startMeasurement();
-	std::cout << "measurement finished" << std::endl;
+	std::cout << "measurement finished" << std::endl;	usleep(1*1000*1000);
 
 	/** - returning when acquisition is finished or data are avilable */
 

manual/manual-main/Makefile

@@ -4,31 +4,46 @@ DESTDIR=../docs
 TEX=latex
 
 
-MAINTEXS= slsDetectorInstall.tex slsDetectors-FAQ.tex 
+MAINTEXS2= slsDetectorInstall.tex 
+MAINTEXS=slsDetectors-FAQ.tex 
 
 TEXS=slsDetector-softFAQ.tex singlePhotonCounting-FAQ.tex angConv-FAQ.tex generalDet-FAQ.tex 
 
 DVIS = $(MAINTEXS:.tex=.dvi)
 PSS = $(MAINTEXS:.tex=.ps)
 PDFS = $(MAINTEXS:.tex=.pdf)
+PDFS2 = $(MAINTEXS2:.tex=.pdf)
 HTMLS = $(MAINTEXS:%.tex=%)
+HTMLS2 = $(MAINTEXS2:%.tex=%)
 
 
 
 all: pdf html
 	echo $(PWD)
 	echo $(PDFS)
+	echo $(PDFS2)
 	echo $(HTMLS)
+	echo $(HTMLS2)
 
-pdf: $(PDFS)
+pdf: $(PDFS) $(PDFS2)
 	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
 	$(shell test -d $(DESTDIR)/pdf || mkdir -p $(DESTDIR)/pdf)
-	mv $(PDFS) $(DESTDIR)/pdf	
+	mv $(PDFS) $(DESTDIR)/pdf
+	mv $(PDFS2) $(DESTDIR)/pdf	
 
-html: $(HTMLS)
+html: $(HTMLS) $(HTMLS2)
 
 
 $(HTMLS): $(TEXS) $(MAINTEXS)
+	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
+	$(shell test -d $(DESTDIR)/html || mkdir -p $(DESTDIR)/html)
+	$(shell test -d $(DESTDIR)/html/$@ && rm -fr $(DESTDIR)/html/$@)
+	echo "*****************************  $@"
+	latex $@.tex
+	latex2html $@.tex
+	mv $@ $(DESTDIR)/html
+	
+$(HTMLS2): $(MAINTEXS2)
 	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
 	$(shell test -d $(DESTDIR)/html || mkdir -p $(DESTDIR)/html)
 	$(shell test -d $(DESTDIR)/html/$@ && rm -fr $(DESTDIR)/html/$@)
@@ -53,7 +68,7 @@ $(HTMLS): $(TEXS) $(MAINTEXS)
 
 
 clean:
-	rm -rf *.aux *.log *.toc *.out $(DVIS) $(PSS) $(PDFS) $(HTMLS)
+	rm -rf *.aux *.log *.toc *.out $(DVIS) $(PSS) $(PDFS) $(PDFS2) $(HTMLS) $(HTMLS2)
 	rm -rf $(DESTDIR)/html/slsDetectors-FAQ
 	rm -rf $(DESTDIR)/html/slsDetectorInstall
 	rm -rf $(DESTDIR)/pdf/slsDetectors-FAQ.pdf

manual/manual-main/slsDetectorInstall.tex

@@ -28,9 +28,10 @@
 The SLS detectors software is intended to control the detectors developed by
 the SLS Detectors group. The detectors currently supported are:
 
-MYTHEN, GOTTHARD, EIGER and JUNGFRAU.\bigskip
+\indent MYTHEN, GOTTHARD, EIGER and JUNGFRAU.
 
-\noindent The package provides software for the distributed system that comprises of
+
+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
@@ -78,18 +79,28 @@ However, only control commands work, not the data acquisition itself.
 \section{Install Binaries via Conda}
 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.\bigskip
+sections to download source code and compile them.
 
-\noindent One can download and install Miniconda via 
 
-\url{https://conda.io/miniconda.html} \bigskip
+One can download and install Miniconda via 
 
-\noindent The conda package uses Travis CI for continuous integration with
+\url{https://conda.io/miniconda.html}
+
+
+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. \bigskip
+package including the python interface.
 
-\noindent After the installation, the binaries will be available in your path.
 
+After the installation, the binaries will be available in your path.
+
+Please remember to clear shared memory after installation.
+\begin{verbatim}
+#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]
+\end{verbatim}
 
 \begin{itemize}
  \item Only the package
@@ -102,10 +113,10 @@ conda config --add channels slsdetectorgroup
 conda install sls_detector_software
 
 #Install specific release (GLIBC2.14)
-conda install sls_detector_software=3.0.1
+conda install sls_detector_software=3.1.0
 
 #Scientific Linux 6 version (GLIBC2.12)
-conda install sls_detector_software=SL6_3.0.1
+conda install sls_detector_software=SL6_3.1.0
 \end{verbatim}
  \item The package including Python interface
 \begin{verbatim}
@@ -117,10 +128,10 @@ conda config --add channels sls_detector
 conda install sls_detector
 
 #Install specific release (GLIBC2.14)
-conda install sls_detector=3.0.1
+conda install sls_detector=3.1.0
 
 #Scientific Linux 6 version (GLIBC2.12)
-conda install sls_detector=SL6_3.0.1
+conda install sls_detector=SL6_3.1.0
 \end{verbatim}
 \end{itemize}
 
@@ -137,13 +148,13 @@ acquisition system, or if one wants to download the source code and compile.
 \begin{verbatim}
 #Clone source code with specific release
 git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch
-3.0.1
+3.1.0
 \end{verbatim}
  \item The package including Python interface
 \begin{verbatim}
 #Clone source code with specific release
 git clone https://github.com/slsdetectorgroup/sls_detector.git --branch
-3.0.1
+3.1.0
 \end{verbatim}
 \end{itemize}
 
@@ -194,9 +205,10 @@ required. One can install it:
  \item via download from:\\
 \url{
 https://download.qt.io/archive/qt/4.8/4.8.2/qt-everywhere-opensource-src-4.8.2.t
-ar.gz} \bigskip
+ar.gz} 
 
-\noindent To install:
+
+To install:
 \begin{verbatim}
 > gunzip qt-everywhere-opensource-src-4.8.2.tar.gz
 > tar xvf qt-everywhere-opensource-src-4.8.2.tar
@@ -207,14 +219,17 @@ ar.gz} \bigskip
 By default Qt4 will be installed in /usr/local/Trolltech/Qt-4.8.2/. 
 \end{itemize}
 
-\noindent \textbf{Setup Environment} 
 
-\noindent One has to ensure that \verb=PATH= and \verb=LD_LIBRARY_PATH= have
+\textbf{Setup Environment} 
+
+
+One has to ensure that \verb=PATH= and \verb=LD_LIBRARY_PATH= have
 been updated to include Qt4 install path, binaries and libraries.
 Confirm by executing \verb=qmake -v= and ensuring the result points to Qt4 (not
-Qt3 or Qt5). \bigskip
+Qt3 or Qt5). 
 
-\noindent If the environment is not set up, one can add the libraries and
+
+If the environment is not set up, one can add the libraries and
 executables to the .bashrc by adding
 \verb=LD_LIBRARY_PATH= and \verb=PATH=:
 \begin{verbatim}
@@ -228,9 +243,10 @@ export LD_LIBRARY_PATH=$QTDIR/lib:$LD_LIBRARY_PATH
 Before installing Qwt, one must install Qt
 and ensure that \verb=QTDIR=, \verb=LD_LIBRARY_PATH= and \verb=PATH= point to
 the correct Qt4
-version. \bigskip
+version.
 
-\noindent A Qwt version equal or higher than 6 is required. One can
+
+A Qwt version equal or higher than 6 is required. One can
 install it:
 \begin{itemize}
  \item via YUM:
@@ -240,9 +256,9 @@ install it:
  \item via download from:\\
 \url{
 https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download}
-\bigskip
 
-\noindent To install:
+
+To install:
 \begin{verbatim}
 > cd qwt-6.0.0
 > qmake
@@ -252,12 +268,14 @@ https://sourceforge.net/projects/qwt/files/qwt/6.0.0/qwt-6.0.0.zip/download}
 By default Qwt will be installed int /usr/local/qwt-6.0.0 
 \end{itemize}
 
-\noindent \textbf{Setup Environment} 
+\textbf{Setup Environment} 
 
-\noindent One has to ensure that \verb=QWTDIR= and \verb=LD_LIBRARY_PATH= have
-been updated to include Qwt install path and libraries. \bigskip
 
-\noindent If the environment is not set up, one can add the libraries to the
+One has to ensure that \verb=QWTDIR= and \verb=LD_LIBRARY_PATH= have
+been updated to include Qwt install path and libraries.
+
+
+If the environment is not set up, one can add the libraries to the
 .bashrc by adding \verb=LD_LIBRARY_PATH=:
 \begin{verbatim}
 export QWTDIR=/usr/local/qwt-6.0.0/
@@ -324,6 +342,8 @@ Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]
 
 Some example options for compilation:
 
+Most basic option: \verb=./cmk.sh -b=
+
 For only make: \verb=./cmk.sh=
 
 For make clean;make: \verb=./cmk.sh -c=
@@ -367,10 +387,69 @@ sls_detector_help sls_detector_put  slsReceiver
 
 
 
+
+\subsection{Setting environment variables}
+One can set up the environment variables in the following ways.
+
+\subsubsection{Using .bashrc file}
+\begin{enumerate}
+ \item \verb=emacs ~/.bashrc=
+ \item Add the following function \verb=setup_slsdet= and replace \verb=path=
+with absolute path of installed directory
+\begin{verbatim}
+function setup_slsdet
+{ 
+export PKGPATH=[path]
+export LD_LIBRARY_PATH=$PKGPATH/slsDetectorPackage/build/bin:$LD_LIBRARY_PATH
+export PATH=$PKGPATH/slsDetectorPackage/build/bin:$PATH
+cd $PKGPATH/slsDetectorPackage/build/bin
+} 
+\end{verbatim}
+  \item \verb=source ~/.bashrc=
+  \item Next time, just run \verb=setup_slsdet= to load the environment
+variables.
+\end{enumerate}
+
+
+One can also add the GUI environment variables if installed locally by adding
+the following in the function \verb=setup_sldet= \\
+\begin{verbatim}
+export QTDIR=/path-where-it-is/Qt-4.8.2
+export QWTDIR=/path-where-it-is/qwt-6.0.1
+export QWT3D=/path-where-it-is/qwtplot3d
+export QMAKESPEC=$QTDIR/mkspecs/linux-g++
+export LD_LIBRARY_PATH=$QTDIR/lib:$QWTDIR/lib:$QWT3D/lib:$LD_LIBRARY _PATH
+export PATH=$QTDIR/bin:$PATH
+\end{verbatim}
+
+\subsubsection{Without .bashrc file}
+Go to binaries folder slsDetectorPackage/build/bin and execute the following:
+\begin{verbatim}
+export LD_LIBRARY_PATH=$PWD:$LD_LIBRARY_PATH
+export PATH=$PWD:$PATH
+\end{verbatim}
+
+
+\subsection{Clean Shared Memory}
+It is very crucial to clean the shared memory, before using a new version of
+the SLS Detector Package or a different detector type.
+
+One can use the \verb=cleansharedmemory.sh= script available under the
+slsDetector Package.
+
+One can also just use the following commands to clean the shared memory
+segments one by one.
+\begin{verbatim}
+#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]
+\end{verbatim}
+
 \section{Software Upgrade}
 
 The upgrade of the package could require an upgrade of the on-board detector
-server and/or firmware running on the detector as well. 
+server and/or firmware running on the detector as well.
 
 
 \subsection{MYTHEN}
@@ -379,7 +458,7 @@ 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.
 
-\subsubsection{Firmware}
+\subsubsection{MYTHEN Firmware}
 
 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
@@ -389,9 +468,10 @@ from: \\
 
 \noindent Normally, installation of the software and of the driver for the
 USB-Blaster (provided together with the MYTHEN detector) are simpler under
-Windows. \bigskip
+Windows. 
 
-\noindent Under Windows, the first time that you connect the USB-Blaster to one
+
+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:
 \verb=C:\altera\80sp1\qprogrammer\drivers\usb-blasterp= (where 
@@ -414,7 +494,7 @@ your cable (pin1 corresponds) and that you have selected the correct programming
 connector.
 \end{enumerate}
 
-\subsubsection{On-board Software}
+\subsubsection{MYTHEN On-board Software}
 \begin{enumerate}
  \item Connect to the board using telnet:
 \begin{verbatim}
@@ -454,6 +534,297 @@ acqusition program correctly start.
 \end{enumerate}
 
 
+
+
+\subsection{GOTTHARD}
+
+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.
+
+\subsubsection{GOTTHARD Firmware}
+\textit{For SLS Detector Package v3.1.0} \\
+\indent Minimum compatible version: \\
+\indent \indent 11.01.2013 \\
+\indent Latest version:	\\
+\indent \indent 08.02.2018 (50um and 25um Master) \\
+\indent \indent 09.02.2018 (25 um Slave) \\
+
+
+Normally, the firmware will be upgraded by us as it requires programming the
+FPGA via the USB-Blaster.
+
+
+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: \\
+\url{https://www.altera.com/download/programming/quartus2/pq2-index.jsp}
+
+
+Normally, installation of the software and of the driver for the
+USB-Blaster (provided together with the MYTHEN detector) are simpler under
+Windows.
+
+
+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:
+\verb=C:\altera\80sp1\qprogrammer\drivers\usb-blasterp= (where 
+\verb=C:\altera\80sp1\qprogrammer\= is assumed to be ther path where your
+Quartus version is installed).
+\begin{enumerate}
+\item After starting the Quartus programmer, click on Hardware Setup and in the
+"Currently selected hardware" window select USB-Blaster.
+\item In the Mode combo box select "Active Serial Programming".
+\item 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.
+\item Click on add file and from select the programming file provided when
+the upgrade has been reccomended.
+\item Check "Program/Configure" and "Verify".
+\item Push the start button and wait until the programming process is
+finished (progress bar top left).
+\item 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.
+\end{enumerate}
+
+\subsubsection{GOTTHARD On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+\begin{enumerate}
+  \item Install tftp if the pc does not have it.
+  \item Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+  \item Copy the server to the detector by:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/gotthardDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no gotthardDetectorServers are running
+    \end{enumerate}
+    \item Copy new on-board server from pc to the blackfin using: \\
+\verb=tftp pcxxx -r gotthardDetectorServerxxx -g= 
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/gotthardDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=gotthardDetectorServerxxx= \\
+\verb=gotthardDetectorServerxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+\end{enumerate}
+
+
+
+\subsection{EIGER}
+
+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.
+
+\subsubsection{EIGER Firmware}
+\textit{For SLS Detector Package v3.1.0} \\
+\indent Minimum compatible version:  16 \\
+\indent Latest version:	20  \\
+
+
+\begin{enumerate}
+  \item One must get the latest package's corresponding bit files from the SLS
+Detector Group.
+  \item 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.
+  \item Run the following to update firmware
+\begin{verbatim}
+ #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
+\end{verbatim}
+Please update bit files with great caution as it could make your board
+inaccessible, if done incorrectly.
+\end{enumerate}
+
+
+
+\subsubsection{EIGER On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+
+Update the on-board software without connecting to the detector
+\begin{verbatim}
+#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
+\end{verbatim}
+
+
+\bigskip One can connect to the detector by:
+\begin{verbatim}
+ssh root@bebxxx
+password: root
+\end{verbatim}
+
+
+The on-board server is in ~/executables folder and respawned at startup in \\
+\verb=/etc/rc5.d/S50board_com.sh= 
+
+
+
+
+
+\subsection{JUNGFRAU}
+
+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.
+
+\subsubsection{JUNGFRAU Firmware}
+\textit{For SLS Detector Package v3.1.0} \\
+\indent Minimum compatible version: 13.11.2017 \\
+\indent Latest version: 13.11.2017 \\
+
+
+At times, one has to update the firmware, which then also requires updating the
+on-board software. 
+
+
+\textbf{\textit{Jungfrau firmware can be upgraded via the SLS Detector Package
+binaries from the command line.}}
+
+\begin{enumerate}
+  \item One must get the latest package's corresponding POF file from the SLS
+Detector Group.
+  \item Update the latest SLS Detector package installed.
+  \item Update the on-board software as per the instructions in the next
+section.
+  \item Start the on-board server in debug mode:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no gotthardDetectorServers are running
+    \end{enumerate}
+    \item Start the server in debug mode using: \\
+\verb=./jungfrauDetectorServerxxx -debug= \\
+    Leave this console on to come back to it later.
+  \end{enumerate}
+  \item From the command line of the pc, clear shared memory \\
+\verb=./sls_detector_get free= \\
+  If one gets shmget error, please clean the shared memory properly using the
+script in \verb=slsDetectorPackage/cleansharedmemory.sh=
+  \item Add the detector to shared memory using \\
+\verb=./sls_detector_put hostname bchipxxx=
+  \item Program the FPGA using \\
+\verb=./sls_detector_put programfpga xxx.pof= 
+  \item Once the programming is done:
+  \begin{enumerate}
+    \item Switch to the console that has the debug server running and kill it
+using Ctrl+C and ensure no jungfrauDetectorServers are
+running
+    \item Restart the new server to see if it runs with the new firmware \\
+\verb=./jungfrauDetectorServerxxx= \\
+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.
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=jungfrauDetectorServervxxx= \\
+\verb=jungfrauDetectorServervxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+
+\end{enumerate}
+
+
+
+\subsubsection{JUNGFRAU On-board Software}
+Every SLS Detector package release will have its coresponding matching on-board
+server under \textbf{slsDetectorPackage/serverBin}.
+
+
+\begin{enumerate}
+  \item Install tftp if the pc does not have it.
+  \item Copy the server from serverBin folder to /tftpboot (or equivalent tftp
+folder) of the pc
+  \item Copy the server to the detector by:
+  \begin{enumerate}
+    \item Connect to the blackfin on the detector\\ 
+\verb=telnet bchipxxx=
+    \item Prevent existing on-board server from respawning by:
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Comment out the line
+\verb=#ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure no gotthardDetectorServers are running
+    \end{enumerate}
+    \item Copy new on-board server from pc to the blackfin using: \\
+\verb=tftp pcxxx -r jungfrauDetectorServervxxx -g= 
+    \item Respawn the new server (server starts at detector statup): 
+    \begin{enumerate}
+      \item Edit \verb=/etc/inittab= 
+      \item Uncomment out the line
+\verb=ttyS0::respawn:/jungfrauDetectorServervxxx= 
+      \item Reboot blackfin using \verb=reboot=
+      \item Run \verb=ps= to ensure that both the gotthardDetectorServers are
+running.\\
+\verb=jungfrauDetectorServervxxx= \\
+\verb=jungfrauDetectorServervxxx 1953=
+    \end{enumerate}
+  \end{enumerate}
+\end{enumerate}
+
+
+
+
+
+
 \begin{comment}
 \section{Detector system architecture}
 

serverBin/eigerDetectorServer_virtualMaster

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServer_virtualMaster

serverBin/eigerDetectorServer_virtualSlave

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServer_virtualSlave

serverBin/eigerDetectorServerv3.0.0.16.10

@@ -1 +0,0 @@
-../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.0.0.16.10

serverBin/eigerDetectorServerv3.1.0.16.1

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.1.0.16.1

serverBin/eigerDetectorServerv3.1.0.21.0

@@ -0,0 +1 @@
+../slsDetectorSoftware/eigerDetectorServer/bin/eigerDetectorServerv3.1.0.21.0

serverBin/gotthardDetectorServer_virtual

@@ -0,0 +1 @@
+../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServer_virtual

serverBin/gotthardDetectorServerv3.0.0.6

@@ -1 +0,0 @@
-../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv3.0.0.6

serverBin/gotthardDetectorServerv3.1.0.1

@@ -0,0 +1 @@
+../slsDetectorSoftware/gotthardDetectorServer/gotthardDetectorServerv3.1.0.1

serverBin/jungfrauDetectorServer_virtual

@@ -0,0 +1 @@
+../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServer_virtual

serverBin/jungfrauDetectorServerv3.0.0.12

@@ -0,0 +1 @@
+../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.0.0.12

serverBin/jungfrauDetectorServerv3.0.0.6.3

@@ -1 +0,0 @@
-../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.0.0.6.3

serverBin/jungfrauDetectorServerv3.1.0.2

@@ -0,0 +1 @@
+../slsDetectorSoftware/jungfrauDetectorServer/bin/jungfrauDetectorServerv3.1.0.2

serverBin/moenchDetectorServerv2.0.3

@@ -1 +0,0 @@
-../slsDetectorSoftware/moenchDetectorServer/moenchDetectorServerv2.0.3

slsDetectorCalibration/IntMap.h

@@ -1,113 +0,0 @@
-#ifndef INTMAP_H
-#define INTMAP_H
-#define N 60
-#include <stdio.h>
-#include <math.h>
-
-
-
-
-class IntMap{
-
-
- public:
-
-  IntMap(){};
-
-  ~IntMap(){};
-
-  void Init(){
-    //lookup table of the output intensity for IR laser
-    //measurements performed by Dominic april 2014
-    //intensity[59]=intensity with 0 Optical Density
-    //intensity[0]=intensity with 5.9 Optical Density
-    intensity[0]=29;//5.9
-    intensity[1]=21;//5.8
-    intensity[2]=31;//5.7
-    intensity[3]=43;//5.6
-    intensity[4]=60;//5.5
-    intensity[5]=91;//5.4
-    intensity[6]=69;//5.3
-    intensity[7]=102;//5.2
-    intensity[8]=136;//5.1
-    intensity[9]=196;//5.0
-    intensity[10]=425;//4.9
-    intensity[11]=311;//4.8
-    intensity[12]=462;//4.7
-    intensity[13]=653;//4.6
-    intensity[14]=926;//4.5
-    intensity[15]=1423;//4.4
-    intensity[16]=1072;//4.3
-    intensity[17]=1592;//4.2
-    intensity[18]=2142;//4.1
-    intensity[19]=3085;//4.0
-    intensity[20]=729;//3.9
-    intensity[21]=533;//3.8
-    intensity[22]=793;//3.7
-    intensity[23]=1121;//3.6
-    intensity[24]=1588;//3.5
-    intensity[25]=2439;//3.4
-    intensity[26]=1842;//3.3
-    intensity[27]=2730;//3.2
-    intensity[28]=3663;//3.1
-    intensity[29]=5271;//3.0
-    intensity[30]=8102;//2.9
-    intensity[31]=5933;//2.8
-    intensity[32]=8789;//2.7
-    intensity[33]=12350;//2.6
-    intensity[34]=17358;//2.5
-    intensity[35]=26300;//2.4
-    intensity[36]=20029;//2.3
-    intensity[37]=29414;//2.2
-    intensity[38]=39202;//2.1
-    intensity[39]=55724;//2.0
-    intensity[40]=15697;//1.9
-    intensity[41]=11541;//1.8
-    intensity[42]=16976;//1.7
-    intensity[43]=23866;//1.6
-    intensity[44]=33478;//1.5
-    intensity[45]=50567;//1.4
-    intensity[46]=38552;//1.3
-    intensity[47]=56394;//1.2
-    intensity[48]=74897;//1.1
-    intensity[49]=106023;//1.0
-    intensity[50]=157384;//0.9
-    intensity[51]=117677;//0.8
-    intensity[52]=171101;//0.7
-    intensity[53]=236386;//0.6
-    intensity[54]=327248;//0.5
-    intensity[55]=492781;//0.4
-    intensity[56]=379641;//0.3
-    intensity[57]=546927;//0.2
-    intensity[58]=717203;//0.1
-    intensity[59]=1000000;//0.
-    return;
-  };
-    //_od is the total Optical Density
-  int getIntensity(float _od){
-    int _int(-1);
-
-    //these lines are to take into account rounding errors with floats
-    float hun_od = 100.*_od;
-    int Ihun_od = (int)round(hun_od); 
-    float R_od =(float) Ihun_od/10.;
-    int I_od = (int)R_od;
-
-    if(I_od >-1 && I_od <60){
-      int index=59-I_od;
-      cerr<<index<<endl;
-      _int=intensity[index];
-    }else{
-      cerr<<"Optical density out of range!"<<endl;
-    }
-    return _int;
-  };
-
-
- private:
-
-  int intensity[N];
-
-};
-
-#endif

slsDetectorCalibration/MovingStat.h

@@ -29,28 +29,41 @@ class MovingStat
 	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
 	*/
-        void Set(double val, double rms=0)
+        void Set(double val, double rms=0, int m=-1)
         {
-	  m_n = n; 
-	  m_newM=val*n; 
-	  if (rms<=0)
-	    m_newM2=val*val*n;
-	  else
-	    m_newM2=(n*rms*rms+m_newM*m_newM/n);
+	  if (m>=0) m_n = m;  else m_n = n; 
+	  m_newM=val*m_n; 
+	  SetRMS(rms);
+        }
+		/**
+	   clears the moving average number of samples parameter, mean and standard deviation
+	*/
+        void SetRMS(double rms)
+        {
+	  if (rms<=0) {
+	    m_newM2=m_newM*m_newM/n;
+	    m_n=0;
+	  } else {
+	    if (m_n>0)
+	      m_newM2=(m_n*rms*rms+m_newM*m_newM/m_n);
+	    else {
+	      m_newM2=(m_n*rms*rms+m_newM*m_newM/n);
+	      m_n=0;
+	    }
+	  }
         }
-	
 	
 	/** sets number of samples parameter
 	    \param i number of samples  parameter to be set 
 	*/
 	
-	void SetN(int i) {if (i>=1) n=i;};
+	int SetN(int i) {if (i>=1) n=i; return n;};
 	
 	/** 
 	    gets number of samples  parameter
 	    \returns actual number of samples   parameter
 	*/
-	int GetN() {return n;};
+	int GetN() {return m_n;};
 		
 	/** calculates the moving average i.e. adds if number of elements is lower than number of samples parameter, pushes otherwise
 	   \param x value to calculate the moving average

slsDetectorCalibration/PlotGifs.C

@@ -1,194 +0,0 @@
-#include "moench03ReadData.C"
-
-
-
-/************************************************************************/
-TH2F *readExactImage(char *fname, int iframe=0, int frperfile,TH2F *hped=NULL) {
-  ifstream filebin;
-  filebin.open((const char *)(fname), ios::in | ios::binary);
-  TH2F *h2=new TH2F("h2","",400,0,400,400,0,400);
-  int framen(0);
-  moench03CtbData *decoder=new moench03CtbData();
-  char *buff=decoder->readNextFrame(filebin);
-  framen=decoder->getFrameNumber(buff);
-
-  int counter(0);
-
-  while(framen<iframe && counter<frperfile){
-   buff=decoder->readNextFrame(filebin);
-   framen=decoder->getFrameNumber(buff);
-   cerr<<"...";
-   if(framen%1000==0) cerr<<framen;
-   counter++;
-  }
-  if(counter<frperfile){
-    h2->SetName(Form("frame_%d",framen));
-    h2->SetTitle(Form("frame_%d",framen));
-    cout << "==" << endl;
-    for (int ix=0; ix<400; ix++) {
-      for (int iy=0; iy<400; iy++) {
-	//	cout <<  decoder->getDataSize() << " " << decoder->getValue(buff,ix,iy)<< endl;
-	h2->SetBinContent(ix+1,iy+1,decoder->getValue(buff,ix,iy));
-	//	h1->SetBinContent(++ip,decoder->getValue(buff,ix,iy));
-      }
-    }
-    if (hped) h2->Add(hped,-1);
-
-  }else{
-    cerr<<"frame number not found"<<endl;
-  }
-
-  return h2;
-
-
-}
-
-/************************************************************/
-//fnamein filename: ..._f0_%d.raw
-//runmin, runmax to calculate pedestals
-//framen0, framen1 first and last frame you want to add to the gif
-//frperfile number of frames per file
-void PlotRawFrameGif(char * fnamein, int runmin, int runmax, int framen0,int framen1, int frperfile){
-  cerr<<"/***********************************/"<<endl;
-  cerr<<"calculating pedestals"<<endl;
-
-  TH2F * hp = calcPedestal(fnamein,runmin,runmax);
-  int filen = (int)(framen0/frperfile);
-  char  fname[1000];
-  sprintf(fname,fnamein,filen);
-  cerr<<"/***********************************/"<<endl;
-  cerr<<"retrieving frame from"<<fname<<endl;
-  
-  int fileframe0 = framen0%frperfile;
-  int fileframe1 = framen1%frperfile;
-
-  TImage * img = NULL;
-  TH2F * hf = NULL;
-  TCanvas * c1 =NULL; 
-  for(int fileframe=fileframe0; fileframe<fileframe1; fileframe++){
-    hf=readExactImage(fname, fileframe,frperfile,hp);
-    delete img;
-    delete c1;
-    c1 = new TCanvas("c1","",800,600); 
-    c1->cd();
-    
-    hf->SetTitle(Form("Frame_%d",fileframe+framen0));
-    hf->SetName(Form("Frame_%d",fileframe+framen0));
-    hf->GetXaxis()->SetRangeUser(0,50);
-    hf->GetXaxis()->SetTitle("Column");
-    hf->GetYaxis()->SetRangeUser(240,290);
-    hf->GetYaxis()->SetTitle("Row");
-    hf->GetZaxis()->SetRangeUser(-50.,1300.);
-    hf->SetStats(kFALSE);
-    // c1->SetLogz();
-    hf->Draw("colz");
-    c1->Print(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Raw3_%d.png",fileframe));
-    img = TImage::Open(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Raw3_%d.png",fileframe));
-    if(fileframe<fileframe1-1){
-      img->WriteImage(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Raw3_%d.gif+200",fileframe1-fileframe0));
-    }else{
-      img->WriteImage(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Raw3_%d.gif++200++",fileframe1-fileframe0));
-    }
-  }
-  return;
-
-}
-/*********************************************************************/
-TProfile2D * GetHitMap(TTree * treein, int framen,double zlow, double zup){
-  TProfile2D* map = new TProfile2D("map","",400,-0.5,399.5,400,-0.5,399.5,zlow,zup);
-
-
-  int x, y, iFrame;
-  double data[9];
-
-  TBranch * b_x = (TBranch*)treein->GetBranch("x");
-  TBranch * b_y = (TBranch*)treein->GetBranch("y");
-  TBranch * b_data = (TBranch*)treein->GetBranch("data");
-  TBranch * b_iFrame = (TBranch*)treein->GetBranch("iFrame");
-
-  b_x->SetAddress(&x);
-  b_y->SetAddress(&y);
-  b_data->SetAddress(data);
-  b_iFrame->SetAddress(&iFrame);
-
-  Int_t nEnt=treein->GetEntries();
-
-  for(Int_t i=0; i<nEnt; i++){
-    b_iFrame->GetEntry(i);
-    if(iFrame==framen){
-      b_x->GetEntry(i);
-      b_y->GetEntry(i);
-      b_data->GetEntry(i);
-      map->SetBinEntries(map->FindFixBin(x-1,y-1),1); 
-      map->SetBinEntries(map->FindFixBin(x,y-1),1); 
-      map->SetBinEntries(map->FindFixBin(x+1,y-1),1); 
-
-      map->SetBinEntries(map->FindFixBin(x-1,y),1); 
-      map->SetBinEntries(map->FindFixBin(x,y),1);
-      map->SetBinEntries(map->FindFixBin(x+1,y),1); 
-
-      map->SetBinEntries(map->FindFixBin(x-1,y+1),1); 
-      map->SetBinEntries(map->FindFixBin(x,y+1),1); 
-      map->SetBinEntries(map->FindFixBin(x+1,y+1),1);
-
-
-      map->SetBinContent(map->FindFixBin(x-1,y-1),data[0]); 
-      map->SetBinContent(map->FindFixBin(x,y-1),data[1]); 
-      map->SetBinContent(map->FindFixBin(x+1,y-1),data[2]);
- 
-      map->SetBinContent(map->FindFixBin(x-1,y),data[3]); 
-      map->SetBinContent(map->FindFixBin(x,y),data[4]);
-      map->SetBinContent(map->FindFixBin(x+1,y),data[5]); 
-
-      map->SetBinContent(map->FindFixBin(x-1,y+1),data[6]); 
-      map->SetBinContent(map->FindFixBin(x,y+1),data[7]); 
-      map->SetBinContent(map->FindFixBin(x+1,y+1),data[8]);
-    }
-  }
-
-
-  return map;
-
-
-}
-
-/*********************************************************/
-/** creates an infinitely looping gif from clustered data
- **/
-void PlotClusterHitMapGif(std::string filename, std::string treename,int framen0,int framen1){
-
-  TFile * fin = new TFile(filename.c_str(),"read");
-  TTree * treein = (TTree*)fin->Get(treename.c_str());
-
-  TCanvas * c1 = NULL;
-
-
-  TProfile2D* hmap = NULL;
-  TImage * img = NULL;
-  for(int framen=framen0; framen<framen1; framen++){
-    delete c1;
-    c1 = new TCanvas("c1","",800,600);
-    c1->cd();
-    // c1->SetLogz();
-    hmap=GetHitMap(treein,framen,-50.,1300.);
-    hmap->SetName(Form("Frame_%d",framen));
-    hmap->SetTitle(Form("Frame_%d",framen));
-    hmap->GetXaxis()->SetRangeUser(0,50);
-    hmap->GetXaxis()->SetTitle("Column");
-    hmap->GetYaxis()->SetRangeUser(240,290);
-    hmap->GetYaxis()->SetTitle("Row");
-    hmap->GetZaxis()->SetRangeUser(-50.,1300.);
-    hmap->SetStats(kFALSE);
-    hmap->Draw("colz");
-    c1->Print(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Cluster3_%d.png",framen));
-    img = TImage::Open(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Cluster3_%d.png",framen));
-    if(framen<framen1-1){
-      img->WriteImage(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Cluster3_%d.gif+200",framen1-framen0));
-    }else{
-      img->WriteImage(Form("/afs/psi/project/mythen/Marco/Pics/Fe_Cluster3_%d.gif++200++",framen1-framen0));
-    }
-  }
-  return;
-
-
-}

slsDetectorCalibration/analogDetector.h

@@ -0,0 +1,866 @@
+#ifndef ANALOGDETECTOR_H
+#define  ANALOGDETECTOR_H
+
+//#include <mutex>
+
+#include <pthread.h>
+#include "slsDetectorData.h"
+#include "pedestalSubtraction.h"
+#include "commonModeSubtraction.h"
+#include "tiffIO.h"
+
+
+using namespace std;
+
+#ifndef FRAMEMODE_DEF
+#define FRAMEMODE_DEF
+/** 
+enum to define the flags of the data set, which are needed to seect the type of processing it should undergo: frame, pedestal, flat
+*/
+ enum frameMode { eFrame, ePedestal, eFlat };
+#endif
+
+
+template <class dataType> class analogDetector {
+
+  /** @short class to perform pedestal subtraction etc. for an analog detector */
+
+ public:
+
+ 
+
+  /**
+
+     Constructor (no error checking if datasize and offsets are compatible!)
+     \param d detector data structure to be used - if null it is assumed that the data are in ordered ip=iy*nx+ix
+     \param sign is the sign of the data
+     \param nped number of samples for pedestal averaging
+     \param cm common mode subtraction algorithm, if any. Defaults to NULL i.e. none
+     \param nnx detector size in x - must be specified if no data structure is defined, otherwise defaults to the size of the data structure.
+     \param nny detector size in y - must be specified if no data structure is defined, otherwise defaults to the size of the data structure.
+     \param gm pointer to tha gain map matrix
+
+
+  */
+  
+
+ analogDetector(slsDetectorData<dataType> *d, int sign=1, 
+		commonModeSubtraction *cm=NULL, int nped=1000, int nnx=-1, int nny=-1, double *gm=NULL) : det(d), nx(nnx), ny(nny), stat(NULL), cmSub(cm),  iframe(-1), dataSign(sign), gmap(gm), id(0) {
+    
+    if (det)
+      det->getDetectorSize(nx,ny);
+    
+    stat=new pedestalSubtraction*[ny];
+    for (int i=0; i<ny; i++) {
+      stat[i]=new pedestalSubtraction[nx];
+      for (int ix=0; ix<nx; ix++) {
+	stat[i][ix].SetNPedestals(nped);
+      }
+    }
+    image=new int[nx*ny];
+    xmin=0;
+    xmax=nx;
+    ymin=0;
+    ymax=ny;
+    fMode=ePedestal;
+    thr=0;
+    myFile=NULL;
+    fm=new pthread_mutex_t ;
+  };
+  /**
+     destructor. Deletes the pdestalSubtraction array and the image
+  */
+  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat[i]; delete [] stat; delete [] image;};
+
+  /**
+     constructor cloning another analog detector
+     \param orig analog Detector structure to be cloned
+   */
+  analogDetector(analogDetector* orig) { 
+  /* copy construction from orig*/ 
+    det=orig->det;
+    nx=orig->nx;
+    ny=orig->ny;
+    dataSign=orig->dataSign;
+    iframe=orig->iframe;
+    gmap=orig->gmap;
+    cmSub=orig->cmSub;
+    id=orig->id;
+    xmin=orig->xmin;
+    xmax=orig->xmax;
+    ymin=orig->ymin;
+    ymax=orig->ymax;
+    thr=orig->thr;
+    // nSigma=orig->nSigma;
+    fMode=orig->fMode;
+    myFile=orig->myFile;
+    fm=orig->fm;
+    
+
+    stat=new pedestalSubtraction*[ny];
+    for (int i=0; i<ny; i++) {
+      stat[i]=new pedestalSubtraction[nx];
+    }
+    
+    int nped=orig->SetNPedestals();
+    //cout << nped << " " << orig->getPedestal(ix,iy) << orig->getPedestalRMS(ix,iy) << endl;
+    for (int iy=0; iy<ny; iy++) {
+      for (int ix=0; ix<nx; ix++) {
+	stat[iy][ix].SetNPedestals(nped);
+	setPedestal(ix,iy,orig->getPedestal(ix,iy),orig->getPedestalRMS(ix,iy),orig->GetNPedestals(ix,iy));
+      }
+    }
+    image=new int[nx*ny];
+    
+  }
+
+
+  /**
+     clone. Must be virtual!
+     \returns a clone of the original analog detector
+   */
+  virtual analogDetector *Clone() {
+    return new analogDetector(this);
+  }
+
+  /**
+     Gives an id to the structure. For debugging purposes in case of multithreading.
+     \param i is to be set
+     \returns current id
+   */
+  int setId(int i){id=i; return id;};
+
+  /**
+     Returns id of the structure. For debugging purposes in case of multithreading.
+     \returns current id
+   */
+  int getId() {return id; };
+ /**
+     Returns data size of the detector data structure
+     \returns data size of the detector data structurein bytes
+   */
+  int getDataSize(){return det->getDataSize();}; 
+ /**
+     Returns data size of the detector image matrix
+     \param nnx reference to image size in x
+     \param nny reference to image size in y
+     \param nns reference to number of subpixels for interpolating detector, will always be 1 in this case
+     \returns number of pixels of the detector image
+   */
+  virtual int getImageSize(int &nnx, int &nny, int &nns){nnx=nx; nny=ny; nns=1; return nx*ny;}; 
+ /**
+     Returns data size of the detector image matrix
+     \param nnx reference to pixel size in x
+     \param nny reference to pixel size in y
+     \returns number of pixels of the detector image
+   */
+  virtual int getDetectorSize(int &nnx, int &nny){nnx=nx; nny=ny; return nx*ny;}; 
+
+  /**
+     set gain map
+     \param gm pointer to gain map matrix to be set -  NULL unsets
+     \returns pointer to current gain map
+  */
+  double *setGainMap(double *gm) {gmap=gm; return gmap;};
+
+   /**
+     return gain map
+     \returns pointer to current gain map
+  */
+  double *getGainMap() {return gmap;};
+  /**
+     reads a 32 bit tiff file of the size of the detector and sets its values as gain map for the detector. If file does not exist returns NULL, but does not change gainmap compared to previous settings.
+     \param imgname complete name of the file containing the gain map data
+     \returns pointer to current gain map is file reading succeeded, NULL is file reading didn't work.
+  */
+  double *readGainMap(const char * imgname) {
+    uint32 nnx, nny;
+    float *gm=ReadFromTiff( imgname, nny, nnx);
+    if (gm) {
+      if (gmap) delete [] gmap; 
+      gmap=new double[nnx*nny];
+      for (int ix=0; ix<nnx; ix++) {
+	for (int iy=0; iy<nny; iy++) {
+	  gmap[iy*nnx+ix]=gm[iy*nnx+ix];
+	}
+      }
+      return gmap;
+    }
+    return NULL;
+  }
+   /**
+     writes a 32 bit tiff file of the size of the detector and contaning the gain map value, if any. If file doesn'e exist or gainmap is undefined, does not do anything.
+     \param imgname complete name of the file to be written
+     \returns NULL if file writing didn't succeed, else a pointer
+  */
+  void *writeGainMap(const char * imgname) {
+    float *gm=NULL;
+    void *ret;
+    if (gmap)  {
+      gm=new float[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	  gm[iy*nx+ix]=gmap[iy*nx+ix];
+	}
+      }
+      ret=WriteToTiff(gm, imgname, ny, nx);   
+      delete [] gm;
+    }
+    return ret;
+  }
+  
+  
+  /** resets the pedestalSubtraction array, the commonModeSubtraction and the image data*/
+    
+  virtual void newDataSet(){
+    iframe=-1; 
+    for (int iy=0; iy<ny; iy++) 
+      for (int ix=0; ix<nx; ix++) {
+	stat[iy][ix].Clear(); 
+	image[iy*nx+ix]=0;
+      }
+    if (cmSub) cmSub->Clear(); 
+  };  
+  
+  /** resets the commonModeSubtraction and increases the frame index */
+  virtual void newFrame(){iframe++; if (cmSub) cmSub->newFrame();};
+  
+
+    /** sets the commonModeSubtraction algorithm to be used 
+	\param cm commonModeSubtraction algorithm to be used (NULL unsets) 
+	\returns pointer to the actual common mode subtraction algorithm
+    */
+    commonModeSubtraction *setCommonModeSubtraction(commonModeSubtraction *cm) {cmSub=cm; return cmSub;};
+/** 
+      gets the commonModeSubtraction algorithm to be used 
+	\returns pointer to the actual common mode subtraction algorithm
+    */
+    commonModeSubtraction *getCommonModeSubtraction() {return cmSub;};
+
+
+    /**
+       sets the sign of the data
+       \param sign 1 means positive values for photons, -1 negative, 0 gets
+       \returns current sign for the data
+    */
+    int setDataSign(int sign=0) {if (sign==1 || sign==-1) dataSign=sign; return dataSign;};
+
+    
+    /**
+       adds value to pedestal (and common mode) for the given pixel
+       \param val value to be added
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param cm 1 adds the value to common mod, 0 skips it. Defaults to 0. - not properly implemented
+    */
+    virtual void addToPedestal(double val, int ix, int iy=0){ 
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	stat[iy][ix].addToPedestal(val); 
+	if (cmSub)  {
+	  if (det) if (det->isGood(ix, iy)==0) return;
+	  cmSub->addToCommonMode(val, ix, iy);
+	};
+      };
+    }
+    
+    /**
+       gets  pedestal (and common mode)
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param cm 0 (default) without common mode subtraction, 1 with common mode subtraction (if defined)
+       \returns pedestal value
+    */
+    virtual double getPedestal(int ix, int iy, int cm=0){if (ix>=0 && ix<nx && iy>=0 && iy<ny) if (cmSub && cm>0) return stat[iy][ix].getPedestal()-cmSub->getCommonMode(); else return stat[iy][ix].getPedestal(); else return -1;};
+
+    /**
+       gets  pedestal rms (i.e. noise)
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \returns pedestal rms
+    */
+    virtual double getPedestalRMS(int ix, int iy){if (ix>=0 && ix<nx && iy>=0 && iy<ny) return stat[iy][ix].getPedestalRMS();else return -1;};
+
+   
+    /**
+       gets  pedestal (and common mode)
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param cm 0 (default) without common mode subtraction, 1 with common mode subtraction (if defined)
+       \returns pedestal value
+    */
+    virtual double* getPedestal(double *ped){
+      if (ped==NULL)
+	ped=new double[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
+	}
+      }
+      return ped;
+    };
+
+    /**
+       gets  pedestal rms (i.e. noise)
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \returns pedestal rms
+    */
+    virtual double* getPedestalRMS(double *ped=NULL){
+      if (ped==NULL)
+	ped=new double[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	  ped[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+	}
+      }
+      return ped;
+    };
+
+
+
+
+
+
+
+
+
+
+
+
+
+    
+    /**
+       sets  pedestal
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param val value to set
+       \param rms rms to be set if any, defaults to 0
+       \param m number of pedestal samples to be set or the moving stat structure is any, defaults to 0
+    */
+    virtual void setPedestal(int ix, int iy, double val, double rms=0, int m=-1){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy][ix].setPedestal(val,rms, m);};
+    
+  /**
+       sets  pedestal
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param val value to set
+       \param rms rms to be set if any, defaults to 0
+       \param m number of pedestal samples to be set or the moving stat structure is any, defaults to 0
+    */
+    virtual void setPedestal(double *ped, double *rms=NULL, int m=-1){
+      double rr=0;
+      for (int ix=xmin; ix<xmax; ix++) {
+	for (int iy=ymin; iy<ymax; iy++) {
+	  if (rms) rr=rms[iy*nx+ix];
+	  stat[iy][ix].setPedestal(ped[iy*nx+ix],rr, m);
+	};
+      };
+
+    }
+    
+
+
+
+
+    /**
+       sets  pedestal rms
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \param rms value to set
+    */
+    virtual void setPedestalRMS(int ix, int iy, double rms=0){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy][ix].setPedestalRMS(rms);};
+    
+
+
+
+    /**
+       sets  pedestal rms for all pixels
+       \param rms pointer to array of pedestal rms
+    */
+ virtual void setPedestalRMS(double *rms){
+      for (int ix=xmin; ix<xmax; ix++) {
+	for (int iy=ymin; iy<ymax; iy++) {
+	  stat[iy][ix].setPedestalRMS(rms[iy*nx+ix]);
+	};
+      };
+
+    }
+    
+
+
+     /**
+       write 32bit tiff file with detector image data
+       \param imgname file name to be written
+       \returns NULL if file writing didn't succed, otherwise a pointer
+    */
+  virtual void *writeImage(const char * imgname) {
+    float *gm=NULL;
+    void *ret;
+      gm=new float[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	    gm[iy*nx+ix]=image[iy*nx+ix];
+	}
+      }
+      ret=WriteToTiff(gm, imgname, ny, nx);   
+      delete [] gm;
+      return ret;
+  }
+   
+       /**
+       write 32bit tiff file containing the pedestals
+       \param imgname file name to be written
+       \returns NULL if file writing didn't succed, otherwise a pointer
+    */
+    
+  virtual void *writePedestals(const char * imgname) {
+    float *gm=NULL;
+    void *ret;
+      gm=new float[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	  if (cmSub) 
+	    gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode();
+	  else
+	    gm[iy*nx+ix]=stat[iy][ix].getPedestal();
+	}
+      }
+      ret=WriteToTiff(gm, imgname, ny, nx);   
+      delete [] gm;
+      return ret;
+  }
+  
+ /**
+      read 32bit tiff file containing the pedestals
+       \param imgname file name to be read
+       \returns 0 if file reading didn't succed, otherwise 1
+    */
+  int readPedestals(const char * imgname) {
+    uint32 nnx, nny;
+    float *gm=ReadFromTiff( imgname, nny, nnx);
+    if (nnx>nx) nnx=nx;
+    if (nny>ny) nny=ny;
+    
+
+
+    if (gm) {
+      for (int ix=0; ix<nnx; ix++) {
+	for (int iy=0; iy<nny; iy++) {
+	  stat[iy][ix].setPedestal(gm[iy*nx+ix],-1,-1);
+	}
+      }
+      delete [] gm;
+      return 1;
+    }
+    return NULL;
+  }
+  
+ /**
+      read 32bit tiff file containing the image data
+       \param imgname file name to be read
+       \returns 0 if file reading didn't succed, otherwise 1
+    */
+  int readImage(const char * imgname) {
+    uint32 nnx, nny;
+    float *gm=ReadFromTiff( imgname, nny, nnx);
+    if (nnx>nx) nnx=nx;
+    if (nny>ny) nny=ny;
+    
+
+
+    if (gm) {
+      for (int ix=0; ix<nnx; ix++) {
+	for (int iy=0; iy<nny; iy++) {
+	  image[iy*nx+ix]=gm[iy*nx+ix];
+	}
+      }
+      delete [] gm;
+      return 1;
+    }
+    return NULL;
+  }
+  
+   
+    /**
+      returns pointer to image data
+       \returns pointer to image data
+    */  
+  virtual int *getImage(){return image;};
+      /**
+      write 32bit tiff file containing the pedestals RMS
+       \param imgname file name to be written
+       \returns NULL if file writing didn't succed, otherwise a pointer
+    */
+  void *writePedestalRMS(const char * imgname) {
+    float *gm=NULL;
+    void *ret;
+      gm=new float[nx*ny];
+      for (int ix=0; ix<nx; ix++) {
+	for (int iy=0; iy<ny; iy++) {
+	    gm[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+	}
+      }
+      ret=WriteToTiff(gm, imgname, ny, nx);  
+      delete [] gm;
+      return ret;
+    }
+  
+   /**
+      read 32bit tiff file containing the pedestals RMS
+       \param imgname file name to be read
+       \returns 0 if file reading didn't succed, otherwise 1
+    */
+
+  int readPedestalRMS(const char * imgname) {
+    uint32 nnx, nny;
+    float *gm=ReadFromTiff( imgname, nny, nnx);
+    if (nnx>nx) nnx=nx;
+    if (nny>ny) nny=ny;
+    if (gm) {
+      for (int ix=0; ix<nnx; ix++) {
+	for (int iy=0; iy<nny; iy++) {
+	  stat[iy][ix].setPedestalRMS(gm[iy*nx+ix]);
+	}
+      }
+      delete [] gm;
+      return 1;
+    }
+    return 0;
+  }
+  
+    
+
+
+
+
+  /**
+      Adds all the data for each pixels in the selected region of interest to the pedestal
+       \param data pointer to the data
+    */
+    
+    virtual void addToPedestal(char *data) {
+      
+      
+      newFrame();
+      
+      
+      for (int ix=xmin; ix<xmax; ix++) {
+	for (int iy=ymin; iy<ymax; iy++) {
+	  
+	  
+	  addToPedestal(data,ix,iy);
+	  
+	  
+	}
+      }
+      return ;
+      
+    };
+
+
+
+  /**
+     Sets region of interest in which data should be processed
+       \param xmi minimum x. if -1 or out of range remains unchanged
+       \param xma maximum x. if -1 or out of range remains unchanged
+       \param ymi minimum y. if -1 or out of range remains unchanged
+       \param yma maximum y. if -1 or out of range remains unchanged
+    */
+
+    void setROI(int xmi=-1, int xma=-1, int ymi=-1, int yma=-1) {
+      if (xmi>=0 && xmi<=nx) xmin=xmi;
+      if (xma>=0 && xma<=nx) xmax=xma;
+      if (xmax<xmin) {
+	xmi=xmin;
+	xmin=xmax;
+	xmax=xmi;
+      }
+      
+      if (ymi>=0 && ymi<=ny) ymin=ymi;
+      if (yma>=0 && yma<=ny) ymax=yma;
+      if (ymax<ymin) {
+	ymi=ymin;
+	ymin=ymax;
+	ymax=ymi;
+      }
+      
+
+
+    };
+      /**
+     Gets region of interest in which data are processed
+       \param xmi reference to minimum x.
+       \param xma reference to maximum x. 
+       \param ymi reference to minimum y. 
+       \param yma reference to maximum y. 
+    */
+
+    void getROI(int &xmi, int &xma, int &ymi, int &yma) {xmi=xmin; xma=xmax; ymi=ymin; yma=ymax;};
+
+
+
+
+  /**
+      Adds all the data for the selected pixel to the pedestal
+       \param data pointer to the data
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+    */
+
+
+    virtual void addToPedestal(char *data, int ix, int iy=0) {
+      
+      
+      double val;
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	
+	if (det)
+	  val=dataSign*det->getValue(data, ix, iy);
+	else
+	  val=((double*)data)[iy*nx+ix];
+	
+	addToPedestal(val,ix,iy);
+      }
+      return  ;
+      
+    };
+      
+  
+  /**
+     Subtracts pedestal from the data array in the region of interest
+       \param data pointer to the data
+       \param val pointer where the pedestal subtracted data should be added. If NULL, the internal image is used
+       \returns pointer to the pedestal subtracted data
+    */
+
+        
+   virtual  double *subtractPedestal(char *data, double *val=NULL) {
+      
+      newFrame();
+
+      if (val==NULL)
+	val=new double[nx*ny];
+
+      for (int ix=xmin; ix<xmax; ix++) {
+	for (int iy=ymin; iy<ymax; iy++) {
+	  val[iy*nx+ix]+=subtractPedestal(data, ix, iy);
+	}
+      }
+      return  val;
+    };
+      
+
+
+
+ /**
+     Subtracts pedestal from the data for a selected pixel
+       \param data pointer to the data
+       \param ix pixel x coordinate
+       \param iy pixel y coordinate
+       \returns pedestal subtracted value
+    */
+
+
+
+   virtual  double subtractPedestal(char *data, int ix, int iy=0) {
+     double g=1.;
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	if (gmap) {
+	  g=gmap[iy*nx+ix];
+	  if (g==0) g=-1.;
+	}
+
+	if (det)
+	  return (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy))/g;
+	else
+	  return (((double*)data)[iy*nx+ix]-getPedestal(ix,iy))/g;
+      }
+   };
+      
+
+   /**
+      sets threshold value for conversion into number of photons
+      \param t threshold to be set 
+      \returns threshold value
+    */
+   double setThreshold(double t){thr=t; return thr;};
+     
+   /**
+      gets threshold value for conversion into number of photons
+      \returns threshold value
+    */
+   double getThreshold(){return thr;};
+     /**
+      converts the data into number of photons for the selected pixel
+      \param data pointer to the data
+      \param ix pixel x coordinate
+      \param iy pixel y coordinate
+      \returns converted number of photons. If no threshold is set, returns gain converted pedestal subtracted data.
+    */
+
+   virtual  int getNPhotons(char *data, int ix, int iy=0) {
+     int nph=0;
+     double v;
+     if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+       v=subtractPedestal(data,ix,iy);
+       if (thr>0) {
+	 v+=0.5*thr;
+	 nph=v/thr;
+	 return nph;
+       } else
+	 return v;
+     }
+     return 0;  
+   };
+   
+   /**
+      converts the data into number of photons for all pixels
+      \param data pointer to the data
+      \param nph pointer where the photons should added. If NULL,the internal image is used
+      \returns pointer to array containing the number of photons
+   */
+     int *getNPhotons(char *data,  int *nph=NULL) {
+       
+       double val;
+     if (nph==NULL)
+       nph=image;
+     newFrame();
+     for (int ix=xmin; ix<xmax; ix++) {
+       for (int iy=ymin; iy<ymax; iy++) {
+	 nph[iy*nx+ix]+=getNPhotons(data, ix, iy);
+       }
+     }
+     return nph;
+     
+   }
+
+ /**
+      clears the image array
+     
+    */
+   virtual void clearImage(){  
+     for (int ix=0; ix<nx; ix++) {
+       for (int iy=0; iy<ny; iy++) { 
+	 image[iy*nx+ix]=0;
+       }
+     }
+   };
+
+    /** sets/gets number of samples for moving average pedestal calculation
+	\param i number of samples to be set (0 or negative gets)
+	\returns actual number of samples
+    */
+    int SetNPedestals(int i=-1) {
+      int ix=0, iy=0; 
+      if (i>0) 
+	for (ix=0; ix<nx; ix++) 
+	  for (iy=0; iy<ny; iy++) 
+	    stat[iy][ix].SetNPedestals(i); 
+      return stat[0][0].SetNPedestals();
+    };
+
+ /** gets number of samples for moving average pedestal calculation
+	\returns actual number of samples
+    */
+    int GetNPedestals(int ix, int iy) {
+      if  (ix>=0 &&  ix<nx && iy>=0 && iy<ny) 
+	return stat[iy][ix].GetNPedestals(); 
+      else
+	return -1;
+    };
+
+ 
+ /** calculates the sum of photons in the specified region of interest. 
+     \param data pointer to the data
+     \param xmi minimum x for the calculation. If -1 the minimum x of the predefined region of interest is used
+     \param xma maximum x for the calculation. If -1 the maximum x of the predefined region of interest is used
+     \param ymi minimum y for the calculation. If -1 the minimum y of the predefined region of interest is used
+     \param yma maximum y for the calculation. If -1 the maximum y of the predefined region of interest is used
+     
+	\returns total number of photons in
+    */
+    virtual int getTotalNumberOfPhotons(char *data, int xmi=-1, int xma=-1, int ymi=-1, int yma=-1) {
+      int val=0;
+      if (xmi<0) xmi=xmin;
+      if (xma<0) xma=xmax;
+      if (ymi<0) ymi=ymin;
+      if (yma<0) yma=ymax;
+      
+      for (int ix=xmi; ix<xma; ix++)
+	for (int iy=ymi; iy<yma; iy++)
+	  if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
+	    val+=getNPhotons(data, ix, iy);
+      return val;
+      
+    };
+
+
+ /** 
+     calculates the image converted into number of photons. If the frame mode is pedestal, it also it to the pdedestal subtraction.
+     \param data pointer to the data to be processed
+     \param val pointer of the data to be added to. If NULL, the internal image will be used
+     \param pointer to the processed data
+     \returns 
+    */
+
+    virtual void processData(char *data,int *val=NULL) {
+      switch(fMode) {
+      case ePedestal:
+	addToPedestal(data);
+	break;
+      default:
+	getNPhotons(data,val);
+      }
+    };
+
+    virtual char *getInterpolation(){return NULL;};
+
+ /** sets the current frame mode for the detector
+     \param f frame mode to be set
+     
+     \returns current frame mode
+    */
+    frameMode setFrameMode(frameMode f) {fMode=f; return fMode;};
+    
+ /** gets the current frame mode for the detector
+     \returns current frame mode
+    */
+    frameMode getFrameMode() {return fMode;};
+    
+/** sets file pointer where to write the clusters to 
+    \param f file pointer
+    \returns current file pointer
+*/
+    FILE *setFilePointer(FILE *f){myFile=f; return myFile;};
+
+/** gets file pointer where to write the clusters to 
+    \returns current file pointer
+*/
+    FILE *getFilePointer(){return myFile;};
+    void setMutex(pthread_mutex_t *m){fm=m;};
+ protected:
+  
+    slsDetectorData<dataType> *det; /**< slsDetectorData to be used */
+    int nx; /**< Size of the detector in x direction */
+    int ny; /**< Size of the detector in y direction */
+    pedestalSubtraction **stat; /**< pedestalSubtraction class */
+    commonModeSubtraction *cmSub;/**< commonModeSubtraction class */
+    int dataSign; /**< sign of the data i.e. 1 if photon is positive, -1 if negative */
+    int iframe;  /**< frame number (not from file but incremented within the dataset every time newFrame is called */
+    double *gmap;
+    int *image;
+    int id;
+    //int xmin, xmax, ymin, ymax;  int xmin; /**< minimum x of the region of interest */
+    int xmin; /**< minimum x of the region of interest */
+    int xmax; /**< maximum x of the region of interest */
+    int ymin;/**< minimum y of the region of interest */
+    int ymax;/**< maximum y of the region of interest */
+    double thr; /**< threshold to be used for conversion into number of photons */
+    //  int nSigma; /**< number of sigma to be used for conversion into number of photons if threshold is undefined */
+    frameMode fMode; /**< current detector frame mode */
+    FILE *myFile; /**< file pointer to write to */
+    
+    pthread_mutex_t *fm;
+};
+
+#endif

slsDetectorCalibration/dataStructures/gotthardDoubleModuleDataNew.h

@@ -0,0 +1,164 @@
+#ifndef GOTTHARD2MODULEDATANEW_H
+#define  GOTTHARD2MODULEDATANEW_H
+#include "gotthardModuleDataNew.h"
+
+
+
+
+
+
+
+
+class gotthardDoubleModuleDataNew : public slsDetectorData<uint16_t> {
+
+ private:
+  const int nModules;
+  const int offset;
+  int iframe;
+    
+
+public:
+
+
+
+	/**
+     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
+     (1x1280 pixels, 2 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+	 */
+
+
+ gotthardDoubleModuleDataNew(int off=24*2, int nmod=2): slsDetectorData<uint16_t>(1280*nmod, 1, nmod*(1280*2+off)), nModules(nmod), offset(off),iframe(0) {
+    
+    
+    
+    
+
+
+		uint16_t **dMask;
+		int **dMap;
+		int ix, iy;
+		int ypixels=1;
+		int xpixels=1280*nmod;
+		int imod, ipix;
+		dMask=new uint16_t*[1];
+		dMap=new int*[1];
+		dMap[0] = new int[1280*nmod];
+		dMask[0] = new uint16_t[1280*nmod];
+
+		for(int ix=0; ix<xpixels; ix++) {
+		  imod=ix%2;
+		  if (imod==0)
+		    ipix=ix/2;
+		  else
+		    ipix=1280-1-ix/2;
+		  if (imod==0)
+		    dMap[0][ix] =ipix*2+offset;
+		  else
+		    dMap[0][ix] = 1280*2+2*offset+ipix*2;//dataSize-2-ix;//+2*offset;
+		  // dMap[0][ix] = 2*ipix+offset*(imod+1)+1280*2*imod; 
+		  dMask[0][ix] = 0x0;
+		}
+
+		setDataMap(dMap);
+		setDataMask(dMask);
+
+	};
+
+
+	  /**
+
+	     Returns the frame number for the given dataset.
+	     \param buff pointer to the dataset
+	     \returns frame number
+
+	   */
+
+
+  int getFrameNumber(char *buff){if (offset>=sizeof(sls_detector_header)) return ((sls_detector_header*)buff)->frameNumber; return iframe;};//*((int*)(buff+5))&0xffffff;};   
+
+
+
+	/**
+     gets the packets number (last packet is labelled with 0 and is replaced with 40)
+     \param buff pointer to the memory
+     \returns packet number
+
+	 */
+
+  int getPacketNumber(char *buff){if (offset>=sizeof(sls_detector_header))return ((sls_detector_header*)buff)->packetNumber;};
+
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+  
+
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/gotthardModuleDataNew.h

@@ -0,0 +1,170 @@
+#ifndef GOTTHARDMODULEDATANEW_H
+#define  GOTTHARDMODULEDATANEW_H
+#include "slsDetectorData.h"
+
+
+
+
+
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
+
+
+
+
+
+
+class gotthardModuleDataNew : public slsDetectorData<uint16_t> {
+
+ private:
+  
+  int iframe;
+  const int offset;
+
+
+public:
+
+
+
+	/**
+     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
+     (1x1280 pixels, 2 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+	 */
+
+
+    gotthardModuleDataNew(int off=24*2, int nch=1280): slsDetectorData<uint16_t>(nch, 1, nch*2+off), offset(off) {
+
+		uint16_t **dMask;
+		int **dMap;
+		int ix, iy;
+		int ypixels=1;
+		int xpixels=nch;
+
+		dMask=new uint16_t*[1];
+		dMap=new int*[1];
+		dMap[0] = new int[nch];
+		dMask[0] = new uint16_t[nch];
+
+		for(int ix=0; ix<xpixels; ix++) {
+		  dMap[0][ix] = 2*ix+offset; 
+		  dMask[0][ix] = 0x0;
+		}
+
+		setDataMap(dMap);
+		setDataMask(dMask);
+
+	};
+
+
+	  /**
+
+	     Returns the frame number for the given dataset.
+	     \param buff pointer to the dataset
+	     \returns frame number
+
+	   */
+
+
+  int getFrameNumber(char *buff){if (offset>=sizeof(sls_detector_header)) return ((sls_detector_header*)buff)->frameNumber; return iframe;};//*((int*)(buff+5))&0xffffff;};   
+
+
+
+	/**
+     gets the packets number (last packet is labelled with 0 and is replaced with 40)
+     \param buff pointer to the memory
+     \returns packet number
+
+	 */
+
+  int getPacketNumber(char *buff){if (offset>=sizeof(sls_detector_header))return ((sls_detector_header*)buff)->packetNumber;};
+
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+  
+
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03Ctb10GbT1Data.h

@@ -23,15 +23,15 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
-  
+   moench03Ctb10GbT1Data(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
 
-  //  moench03Ctb10GbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, 8208*40, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
- moench03Ctb10GbT1Data(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
 
-    int adc_nr[32]={200,225,250,275,300,325,350,375,\
-		    0,25,50,75,100,125,150,175,\
-		    175,150,125,100,75,50,25,0,\
-		    375,350,325,300,275,250,225,200};
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
     int row, col;
 
     int isample;
@@ -40,17 +40,18 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
     
     int npackets=40;
     int i;
-
+    int adc4(0);
 
     for (int ip=0; ip<npackets; ip++) {
       for (int is=0; is<128; is++) {
 
 	for (iadc=0; iadc<nadc; iadc++) {
 	  i=128*ip+is;
+	  adc4=(int)iadc/4;
 	  if (i<sc_width*sc_height) {
 	    //  for (int i=0; i<sc_width*sc_height; i++) {
 	    col=adc_nr[iadc]+(i%sc_width);
-	    if (iadc<16) {
+	    if (adc4%2==0) {
 	      row=199-i/sc_width;
 	    } else {
 	      row=200+i/sc_width;
@@ -77,10 +78,10 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	  // ii=ibyte+128*32*ipacket;
 	  isample=ii/nadc;
 	  iadc=ii%nadc;
-	
+	  adc4 = (int)iadc/4;
 	  ix=isample%sc_width;
 	  iy=isample/sc_width;
-	  if (iadc<(nadc/2)) {
+	  if (adc4%2==0) {
 	    xmap[i]=adc_nr[iadc]+ix;
 	    ymap[i]=ny/2-1-iy;
 	  } else {
@@ -101,6 +102,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
   };
     
 
+
      /**
 
      Returns the frame number for the given dataset. Purely virtual func.
@@ -174,24 +176,45 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 /*     }; */
 
 
-  	virtual char *readNextFrame(ifstream &filebin, int& fnum) {
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
 	  char *data=new char[packetSize*nPackets];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+
+  }
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
 	  char *retval=0;
-	  int np=0, nd;
-	  fnum = -1;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
 	  int  pn;
 	  char aa[8224];
 	  char *packet=(char *)aa;
+	  //  cout << packetSize*nPackets << endl;
+	  if (ff>=0)
+	    fnum=ff;
 
 	  if (filebin.is_open()) {
 
 
 
 
-	    while(filebin.read((char*)packet, 8208) && np<nPackets){
+	    while(filebin.read((char*)packet, 8208) ){
 	      pn=getPacketNumber(packet);
 	      
-	      if (pn==1 && fnum<0)
+	      if (fnum<0)
 		fnum= getFrameNumber(packet);
 	      
 	      // cout << "fn: " << fnum << "\t pn: " << pn << endl;
@@ -199,14 +222,24 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 		if (getFrameNumber(packet) !=fnum) { 
 		  
 		  if (np==0){
-		    delete [] data;
+		    // delete [] data;
 		    return NULL;
 		  } else
+		    filebin.seekg(-8208,ios_base::cur);
 		    return data;
 		}
-		
+		if (pn>nPackets) {
+		  cout << "Bad packet number " << pn << endl;
+		}
+
 		memcpy(data+(pn-1)*packetSize, packet, packetSize);
 		np++;
+
+		if (np==nPackets)
+		  break;
+
+		if (pn==nPackets)
+		  break;
 		
 	      }
 	    }
@@ -214,18 +247,34 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	  }
 
 	  if (np==0){
-	    delete [] data;
+	    // delete [] data;
 	    return NULL;
 	  }
 
-	};
+	  ff=fnum;
+	  return data;
+	  
+  };
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 
 int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
 
-  	virtual char *readNextFrame(ifstream &filebin) {
-	  int fnum;
-	  return readNextFrame(filebin, fnum);
-	};
 
 };
 

slsDetectorCalibration/dataStructures/moench03CtbData.h

@@ -4,7 +4,7 @@
 
 
 
-class moench03TCtbData : public slsDetectorData<uint16_t> {
+class moench03CtbData : public slsDetectorData<uint16_t> {
 
  private:
   
@@ -25,21 +25,24 @@ class moench03TCtbData : public slsDetectorData<uint16_t> {
   */
   
 
-  moench03TCtbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
+  moench03CtbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
 
-    
-    int adc_nr[32]={200,225,250,275,300,325,350,375,\
-		    0,25,50,75,100,125,150,175,\
-		    175,150,125,100,75,50,25,0,\
-		    375,350,325,300,275,250,225,200};
+     
     int row, col;
 
     int isample;
     int iadc;
     int ix, iy;
 
+    int adc_nr[32]={200,225,250,275,300,325,350,375,\
+		    0,25,50,75,100,125,150,175,\
+		    175,150,125,100,75,50,25,0,\
+		    375,350,325,300,275,250,225,200};
     
-
+ /* int adc_nr[32]={300,325,350,375,300,325,350,375,		\ */
+ /* 		    200,225,250,275,200,225,250,275,\ */
+ /* 		    100,125,150,175,100,125,150,175,\ */
+ /* 		    0,25,50,75,0,25,50,75}; */
 
 
     for (iadc=0; iadc<nadc; iadc++) {

slsDetectorCalibration/dataStructures/moench03T1CtbData.h

@@ -0,0 +1,158 @@
+#ifndef MOENCH03T1CTBDATA_H
+#define  MOENCH03T1CTBDATA_H
+#include "slsDetectorData.h"
+
+
+
+class moench03T1CtbData : public slsDetectorData<uint16_t> {
+
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  
+
+  moench03T1CtbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
+
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+
+    
+
+
+
+    for (iadc=0; iadc<nadc; iadc++) {
+      for (int i=0; i<sc_width*sc_height; i++) {
+	col=adc_nr[iadc]+(i%sc_width);
+	if (iadc<16) {
+	  row=199-i/sc_width;
+	} else {
+	  row=200+i/sc_width;
+	}
+	dataMap[row][col]=(nadc*i+iadc)*2;
+	if (dataMap[row][col]<0 || dataMap[row][col]>=2*400*400)
+	  cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  
+      }
+    }
+    int adc4;
+    for (int i=0; i<nx*ny; i++) {
+      isample=i/nadc;
+      iadc=i%nadc;
+      ix=isample%sc_width;
+      iy=isample/sc_width;
+      adc4 = (int)iadc/4;
+      // if (iadc<(nadc/2)) {
+      if (adc4%2==0) {
+	xmap[i]=adc_nr[iadc]+ix;
+	ymap[i]=ny/2-1-iy;
+      } else {
+	xmap[i]=adc_nr[iadc]+ix;
+	ymap[i]=ny/2+iy;
+      }
+
+
+    }
+
+
+
+    
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+
+    virtual  int getFrameNumber(char *buff){(void)buff; return iframe;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+  virtual int getPacketNumber(char *buff)=0;
+
+  */
+
+   /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+
+  */
+    virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
+
+
+   /**
+
+     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
+     \param filebin input file stream (binary)
+     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
+
+  */
+    virtual char *readNextFrame(ifstream &filebin){
+      //	int afifo_length=0;  
+      uint16_t *afifo_cont; 
+      int ib=0;
+      if (filebin.is_open()) {
+	afifo_cont=new uint16_t[dataSize/2];
+ 	while (filebin.read(((char*)afifo_cont)+ib,2)) {
+	  ib+=2;
+	  if (ib==dataSize) break;
+	}
+	if (ib>0) {
+	  iframe++;
+	  // cout << ib << "-" << endl;
+	  return (char*)afifo_cont;
+	} else {
+	  delete [] afifo_cont;
+	  return NULL;
+	}
+      }     
+      return NULL;
+    };
+
+
+  
+
+};
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ReceiverData.h

@@ -0,0 +1,285 @@
+#ifndef MOENCH03T1ZMQDATA_H
+#define  MOENCH03T1ZMQDATA_H
+#include "slsDetectorData.h"
+
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
+
+
+class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nPackets; /**<number of UDP packets constituting one frame */
+  const int packetSize; /**< size of a udp packet */
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+    moench03T1ReceiverData(int npackets=40, int ps=8192): slsDetectorData<uint16_t>(400, 400, ps*npackets+sizeof(sls_detector_header)), packetSize(ps), nPackets(npackets) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    int adc4(0);
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=8192*40)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    int off=sizeof(sls_detector_header)/2;
+    for (ipacket=0; ipacket<npackets; ipacket++) {
+      for (ibyte=0;  ibyte< 8192/2; ibyte++) {
+	i=ipacket*8208/2+ibyte;
+	  isample=ii/nadc;
+	  iadc=ii%nadc;
+	  adc4 = (int)iadc/4;
+	  ix=isample%sc_width;
+	  iy=isample/sc_width;
+	  if (adc4%2==0) {
+	    xmap[i+off]=adc_nr[iadc]+ix;
+	    ymap[i+off]=ny/2-1-iy;
+	  } else {
+	    xmap[i+off]=adc_nr[iadc]+ix;
+	    ymap[i+off]=ny/2+iy;
+	  }
+	  
+	ii++;
+	//	}
+      }
+    }
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h

@@ -0,0 +1,285 @@
+#ifndef MOENCH03T1RECDATANEW_H
+#define  MOENCH03T1RECDATANEW_H
+#include "slsDetectorData.h"
+
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
+
+
+class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+    moench03T1ReceiverDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32+sizeof(sls_detector_header)), nSamples(ns) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    int off=sizeof(sls_detector_header)/2;
+    for (ipacket=0; ipacket<npackets; ipacket++) {
+      for (ibyte=0;  ibyte< 8192/2; ibyte++) {
+	i=ipacket*8208/2+ibyte;
+	  isample=ii/nadc;
+	  if (isample<nSamples) {
+	  iadc=ii%nadc;
+	  adc4 = (int)iadc/4;
+	  ix=isample%sc_width;
+	  iy=isample/sc_width;
+	  if (adc4%2==0) {
+	    xmap[i+off]=adc_nr[iadc]+ix;
+	    ymap[i+off]=ny/2-1-iy;
+	  } else {
+	    xmap[i+off]=adc_nr[iadc]+ix;
+	    ymap[i+off]=ny/2+iy;
+	  }
+	  }
+	ii++;
+	//	}
+      }
+    }
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqData.h

@@ -0,0 +1,268 @@
+#ifndef MOENCH03T1ZMQDATA_H
+#define  MOENCH03T1ZMQDATA_H
+#include "slsDetectorData.h"
+
+
+
+class moench03T1ZmqData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nPackets; /**<number of UDP packets constituting one frame */
+  const int packetSize; /**< size of a udp packet */
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+ moench03T1ZmqData(int npackets=40, int ps=8192): slsDetectorData<uint16_t>(400, 400, ps*npackets), packetSize(ps), nPackets(npackets) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    int adc4(0);
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=8192*40)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (int ipacket=0; ipacket<npackets; ipacket++) {
+      for (int ibyte=0;  ibyte< 8192/2; ibyte++) {
+	i=ipacket*8208/2+ibyte;
+	/* if (ibyte<8) { */
+	/* //header! */
+	/*   xmap[i]=-1; */
+	/*   ymap[i]=-1; */
+	/* } else { */
+	  // ii=ibyte+128*32*ipacket;
+	  isample=ii/nadc;
+	  iadc=ii%nadc;
+	  adc4 = (int)iadc/4;
+	  ix=isample%sc_width;
+	  iy=isample/sc_width;
+	  if (adc4%2==0) {
+	    xmap[i]=adc_nr[iadc]+ix;
+	    ymap[i]=ny/2-1-iy;
+	  } else {
+	    xmap[i]=adc_nr[iadc]+ix;
+	    ymap[i]=ny/2+iy;
+	  }
+	  
+	ii++;
+	//	}
+      }
+    }
+    
+
+    
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[packetSize*nPackets];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, packetSize*nPackets) ){
+	      iframe++;
+	      ff=iframe;
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<packetSize*nPackets) ndata=dsize;
+    else ndata=packetSize*nPackets;
+    return data;
+
+  }
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h

@@ -0,0 +1,268 @@
+#ifndef MOENCH03T1ZMQDATANEW_H
+#define  MOENCH03T1ZMQDATANEW_H
+#include "slsDetectorData.h"
+
+
+
+class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nSamples;
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+ moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2), nSamples(ns) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+  
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (int ipacket=0; ipacket<npackets; ipacket++) {
+      for (int ibyte=0;  ibyte< 8192/2; ibyte++) {
+	i=ipacket*8208/2+ibyte;
+	/* if (ibyte<8) { */
+	/* //header! */
+	/*   xmap[i]=-1; */
+	/*   ymap[i]=-1; */
+	/* } else { */
+	  // ii=ibyte+128*32*ipacket;
+	  isample=ii/nadc;
+	  if (isample<nSamples) {
+	  iadc=ii%nadc;
+	  adc4 = (int)iadc/4;
+	  ix=isample%sc_width;
+	  iy=isample/sc_width;
+	  if (adc4%2==0) {
+	    xmap[i]=adc_nr[iadc]+ix;
+	    ymap[i]=ny/2-1-iy;
+	  } else {
+	    xmap[i]=adc_nr[iadc]+ix;
+	    ymap[i]=ny/2+iy;
+	  }
+	  }
+	  
+	ii++;
+	//	}
+      }
+    }
+    
+
+    
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[32*2*nSamples];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, 32*2*nSamples) ){
+	      iframe++;
+	      ff=iframe;
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<32*2*nSamples) ndata=dsize;
+    else ndata=32*2*nSamples;
+    return data;
+
+  }
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+int getPacketNumber(int x, int y) {return 0;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03TCtbData.h

@@ -4,7 +4,7 @@
 
 
 
-class moench03CtbData : public slsDetectorData<uint16_t> {
+class moench03TCtbData : public slsDetectorData<uint16_t> {
 
  private:
   
@@ -25,13 +25,9 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
   */
   
 
-  moench03CtbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
+  moench03TCtbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*2*32, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
 
-    
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
-		    200,225,250,275,200,225,250,275,\
-		    100,125,150,175,100,125,150,175,\
-		    0,25,50,75,0,25,50,75};
+   
     int row, col;
 
     int isample;
@@ -40,6 +36,17 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
 
     
 
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+   
+
+    /* int adc_nr[32]={200,225,250,275,300,325,350,375,\ */
+    /* 		    0,25,50,75,100,125,150,175,\ */
+    /* 		    175,150,125,100,75,50,25,0,\ */
+    /* 		    375,350,325,300,275,250,225,200}; */
 
 
     for (iadc=0; iadc<nadc; iadc++) {
@@ -56,12 +63,15 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
 	  
       }
     }
+    int adc4;
     for (int i=0; i<nx*ny; i++) {
       isample=i/nadc;
       iadc=i%nadc;
       ix=isample%sc_width;
       iy=isample/sc_width;
-      if (iadc<(nadc/2)) {
+      adc4 = (int)iadc/4;
+      // if (iadc<(nadc/2)) {
+      if (adc4%2==0) {
 	xmap[i]=adc_nr[iadc]+ix;
 	ymap[i]=ny/2-1-iy;
       } else {
@@ -72,6 +82,22 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
 
     }
 
+    /* for (int i=0; i<nx*ny; i++) { */
+    /*   isample=i/nadc; */
+    /*   iadc=i%nadc; */
+    /*   ix=isample%sc_width; */
+    /*   iy=isample/sc_width; */
+    /*   if (iadc<(nadc/2)) { */
+    /* 	xmap[i]=adc_nr[iadc]+ix; */
+    /* 	ymap[i]=ny/2-1-iy; */
+    /*   } else { */
+    /* 	xmap[i]=adc_nr[iadc]+ix; */
+    /* 	ymap[i]=ny/2+iy; */
+    /*   } */
+
+
+    /* } */
+
 
 
     

slsDetectorCalibration/demoCreateTree.C

@@ -1,31 +0,0 @@
-{
-
-  //.L moenchReadData.C
-
-
-
-
-
-
-  TFile *fout;
-  THStack *hs2N;
-
-  fout=new TFile("/scratch/outfile.root","RECREATE");
-
-  hs2N=moenchReadData("/data/moench_xbox_20140113/MoTarget_45kV_0_8mA_12us_120V_cds_g4_f00000%04d000_0.raw","dum",0,20,1500,-500,2500,1,0.,1,159,1,159, 0,1); 
-  hs2N->SetName("cds_g4");
-  hs2N->SetTitle("cds_g4");
-  (TH2F*)(hs2N->GetHists()->At(0))->Write();
-
- (TH2F*)(hs2N->GetHists()->At(1))->Write();
- (TH2F*)(hs2N->GetHists()->At(2))->Write();
- (TH2F*)(hs2N->GetHists()->At(3))->Write();
- (TH2F*)(hs2N->GetHists()->At(4))->Write();
-
-
-  fout->Close();
-
-
-
-}
-

slsDetectorCalibration/etaVEL/imageMacro.C

@@ -1,457 +0,0 @@
-TH2D *imageMacro(char *name) {
-
-  //TH2D *makeNorm(){
-
-  //TFile ff("/local_zfs_raid/tomcat_20160528/trees/img_blank_eta_gmap.root");
-  //TH2D *hff=(TH2D*)ff.Get("imgHR");
-    TFile *ff=new TFile("/mnt/moench_data/tomcat_20160528_img/img_blank_eta_nb25.root");
-  //  TFile ff("/local_zfs_raid/tomcat_20160528/trees/img_blank_eta_gcorr_nb25.root");
-  TH2D *hff=(TH2D*)ff->Get("blankHR");
-  hff->SetName("imgBlank");
-  TH2D *hpixel=new TH2D("hpixel","hpixel",25,0,25,25,0,25);
-  for (int ibx=10*25; ibx<hff->GetNbinsX()-10*25; ibx++) {
-    for (int iby=20*25; iby<hff->GetNbinsY()-20*25; iby++) {
-      hpixel->Fill((ibx-12)%25,(iby-12)%25,hff->GetBinContent(ibx+1,iby+1));
-    }
-  }
-  hpixel->Scale(1./hpixel->GetBinContent(13,13));
-
-  // new TCanvas();
-  // hpixel->Draw("colz"); 
-
-  //  TH2D *hraw=(TH2D*)hff->Clone("hraw");
-  TH2D *hpix=(TH2D*)hff->Clone("hpix");
-
-  for (int ibx=0; ibx<hff->GetNbinsX(); ibx++) {
-    for (int iby=0; iby<hff->GetNbinsY(); iby++) {
-      hpix->SetBinContent(ibx+1,iby+1,hpixel->GetBinContent(hpixel->GetXaxis()->FindBin((ibx-12)%25),hpixel->GetXaxis()->FindBin((iby-12)%25)));
-    }
-  }
-  //  return hpix;
-  //}
-
-  //void imageMacro(char *name,TH2D *hpix=NULL){
-  // hff->Divide(hpix);
-
-  //  new TCanvas();
-  // hff->Draw("colz");
-
-  // if (hpix==NULL)
-  //  hpix=makeNorm();
-  TH2D *hg;
-
-  char nn[1000];
-  if (strcmp(name,"blank")==NULL) {
-    hg=hff;
-  }    else {
-    
-  
-  sprintf(nn,"/mnt/moench_data/tomcat_20160528_img/img_%s_eta_nb25.root", name);
-  // if (strcmp(name,"blank"))
-    TFile *fg=new TFile(nn);
-    // else
-    // TFile fg=gDirectory;
-
-  //TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_grating_1d_eta_gmap.root");
-  //TH2D *hg=(TH2D*)fg.Get("imgHR");
-  //   TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_grating_1d_eta_nb25.root");
-  //  TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_sample_eta_nb25.root");
-  // TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_grating_1d_eta_gcorr_nb25.root");
-   sprintf(nn,"%sHR",name);
-   TH2D *hg=(TH2D*)fg->Get(nn);
-   // hg->SetName("imgGrating");
-
-  //hg->Divide(hff);
-  }
-   if (hpix)
-     hg->Divide(hpix);
-   new TCanvas();
-   hg->Draw("colz");
-
-   return hg;
-}
-
-
-void imageMacro(TH2D *hg){
-
-  Double_t imageData[200*400*25*25];
-  const int nsigma=5.;
-  int ip=0;
-  int max=0;
-  Double_t avg=0, rms=0;
-    for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-   for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-     imageData[ip]=hg->GetBinContent(ibx+1,iby+1);
-     if (imageData[ip]>max) max=imageData[ip];
-     //  if (imageData[ip]>3000) imageData[ip]=3000.;
-     avg+=((Double_t)imageData[ip])/(hg->GetNbinsY()*hg->GetNbinsX());
-     rms+=((Double_t)imageData[ip])*((Double_t)imageData[ip])/(hg->GetNbinsY()*hg->GetNbinsX());
-     ip++;
-    }
-  }  
-    rms=TMath::Sqrt(rms-avg*avg);
-    ip=0;
-    for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-      for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-     if (imageData[ip]>avg+nsigma*rms) imageData[ip]=avg+nsigma*rms;
-     //  if (imageData[ip]>3000) imageData[ip]=3000.;
-     ip++;
-    }
-  }
-    cout << "MAXIMUM IS "<< max << endl;
-    cout << "AVERAGE IS "<< avg << endl;
-    cout << "RMS IS "<< rms << endl;
-
-
- int nbx=hg->GetNbinsX();
-int nby=hg->GetNbinsY();
-Short_t *buffer=new Short_t[nbx];
-//   // cout << "Size of short int is "<<sizeof(char)<< endl;
-//   // cout << "width is "<<nbx<< endl;
-//   // cout << "height is "<<nby<< endl;
-  sprintf(nn,"%s_HR.bin", name);
- ofstream myFile (nn, ios::out | ios::binary);
- ip=0;
- for (int iy=0; iy<nby; iy++) {
-   for (int ix=0; ix<nbx; ix++) {
-     buffer[ix]=imageData[ip]*65535/nsigma/avg;
-     ip++;
-   }
-   myFile.write((char*)buffer, nbx*sizeof(Short_t));
- }
- myFile.close();
-
-
-
-
-
- TASImage *img=new TASImage 	( "img",imageData, 400*25, 200*25);//		TImagePalette *  	palette = 0 
-    new TCanvas();
-    img->SetImageCompression(0);
-    img->SetImageQuality(TAttImage::kImgBest);
-    //  img->Gray(kTRUE);
-    img->Draw();
-
-  sprintf(nn,"%s_HR.tiff", name);
-
-    img->WriteImage(nn, TImage::kTiff);	
-
-    // new TCanvas();
-    // hg->SetMaximum(3000);
-    // hg->DrawCopy("colz");
-
-
-    hg->Rebin2D(25,25);
-
-    Double_t imageDataLR[200*400];
-
-    ip=0; max=0;avg=0; rms=0;
-    for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-   for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-     imageDataLR[ip]=hg->GetBinContent(ibx+1,iby+1);
-     if (imageDataLR[ip]>max) max=imageDataLR[ip];
-     avg+=((Double_t)imageDataLR[ip])/(hg->GetNbinsY()*hg->GetNbinsX());
-     rms+=((Double_t)imageDataLR[ip])*((Double_t)imageDataLR[ip])/(hg->GetNbinsY()*hg->GetNbinsX());
-     ip++;
-    }
-    }
-    rms=TMath::Sqrt(rms-avg*avg);
-    ip=0;
-    for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-      for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-     if (imageDataLR[ip]>avg+nsigma*rms) imageDataLR[ip]=avg+nsigma*rms;
-     //  if (imageData[ip]>3000) imageData[ip]=3000.;
-     ip++;
-    }
-  }
-    cout << "MAXIMUM IS "<< max << endl;
-    cout << "AVERAGE IS "<< avg << endl;
-    cout << "RMS IS "<< rms << endl;
-
-    TASImage *imgLR=new TASImage 	( "imgLR",imageDataLR, 400, 200);//		TImagePalette *  	palette = 0 
-    new TCanvas();
-    imgLR->SetImageCompression(0);
-    imgLR->SetImageQuality(TAttImage::kImgBest);
-    // imgLR->Gray(kTRUE);
-    imgLR->Draw();
-
-
-    sprintf(nn,"%s_LR.tiff", name);
-
-    imgLR->WriteImage(nn, TImage::kTiff);	
-
-
- int nbx1=hg->GetNbinsX();
-int nby1=hg->GetNbinsY();
-Short_t *buffer1=new Short_t[nbx1];
-//   // cout << "Size of short int is "<<sizeof(char)<< endl;
-//   // cout << "width is "<<nbx<< endl;
-//   // cout << "height is "<<nby<< endl;
-  sprintf(nn,"%s_LR.bin", name);
- ofstream myFile1 (nn, ios::out | ios::binary);
- ip=0;
- for (int iy=0; iy<nby1; iy++) {
-   for (int ix=0; ix<nbx1; ix++) {
-     buffer1[ix]=imageDataLR[ip]*256/nsigma/avg;
-     ip++;
-   }
-   myFile1.write((char*)buffer1, nbx1*sizeof(Short_t));
- }
- myFile1.close();
-
- cout << sizeof(Short_t) << endl;
-    //for grating2D the gratings are in the pixels (150-260)x(80-190)
-
-
-
-
-//   //  hg->Draw("colz");
-//   int off=13;
-//   // hg->Divide(hpix);
-//   int ix,iy, sbx, sby, ibx2, iby2, sbx2, sby2;
-//   TH2F *hh13b=new TH2F("hh13b","hh13b",400*24,0,400,200*24,100,300);
-//   TH2F *hh13=new TH2F("hh13","hh13",400*23,0,400,200*23,100,300);
-//   TH2F *hh=new TH2F("hh","hh",400*21,0,400,200*21,100,300);
-//   TH2F *h1=new TH2F("h1","h1",400*23,0,400,200*23,100,300);
-//   for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-//     for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-//       ix=(ibx-off)/25;
-//       iy=(iby-off)/25;
-//       sbx=(ibx-off)%25;
-//       sby=(iby-off)%25;
-//       sbx2=sbx-1;
-//       sby2=sby-1;
-//       if (sbx2<0) sbx2=0;
-//       if (sby2<0) sby2=0;
-//       if (sbx2>22) sbx2=22;
-//       if (sby2>22) sby2=22;
-//       ibx2=ix*23+(sbx2+off);
-//       iby2=iy*23+(sby2+off);
-
-//       hh13->Fill(hh13->GetXaxis()->GetBinCenter(ibx2+1),hh13->GetYaxis()->GetBinCenter(iby2+1),hg->GetBinContent(ibx+1,iby+1));
-//       //  h1->Fill(h1->GetXaxis()->GetBinCenter(ibx2+1),h1->GetYaxis()->GetBinCenter(iby2+1),hpix->GetBinContent(ibx+1,iby+1));
-
-//       off=13;
-
-//       ix=(ibx-off)/25;
-//       iy=(iby-off)/25;
-//       sbx=(ibx-off)%25;
-//       sby=(iby-off)%25;
-//       sbx2=sbx-1;
-//       sby2=sby-1;
-//       // if (sbx2<0) sbx2=0;
-//       // if (sby2<0) sby2=0;
-//       ibx2=ix*24+(sbx2+off);
-//       iby2=iy*24+(sby2+off);
-
-// 	if (sbx2<0 && sby2>=0) {
-// 	  ibx2=ix*24+(sbx2+off);
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.5*hg->GetBinContent(ibx+1,iby+1));
-// 	  ibx2=ix*24+(sbx2+off)+1;
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.5*hg->GetBinContent(ibx+1,iby+1));
-// 	} else if (sby2<0 && sbx2>=0){
-// 	  iby2=iy*24+(sby2+off);
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.5*hg->GetBinContent(ibx+1,iby+1));
-// 	  iby2=iy*24+(sby2+off)+1;
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.5*hg->GetBinContent(ibx+1,iby+1));
-// 	}  else if (sby2<0 && sbx2<0){
-// 	  iby2=iy*24+(sby2+off);
-// 	  ibx2=ix*24+(sbx2+off);
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.25*hg->GetBinContent(ibx+1,iby+1));
-// 	  iby2=iy*24+(sby2+off)+1;
-// 	  ibx2=ix*24+(sbx2+off);
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.25*hg->GetBinContent(ibx+1,iby+1));
-// 	  iby2=iy*24+(sby2+off);
-// 	  ibx2=ix*24+(sbx2+off)+1;
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.25*hg->GetBinContent(ibx+1,iby+1));
-// 	  iby2=iy*24+(sby2+off)+1;
-// 	  ibx2=ix*24+(sbx2+off)+1;
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),0.25*hg->GetBinContent(ibx+1,iby+1));
-// 	}else {
-
-
-// 	  hh13b->Fill(hh13b->GetXaxis()->GetBinCenter(ibx2+1),hh13b->GetYaxis()->GetBinCenter(iby2+1),hg->GetBinContent(ibx+1,iby+1));
-
-// 	}
-
-      
-
-//       ix=(ibx-off)/25;
-//       iy=(iby-off)/25;
-//       sbx=(ibx-off)%25;
-//       sby=(iby-off)%25;
-//       sbx2=sbx-2;
-//       sby2=sby-2;
-//       if (sbx2<0) sbx2=-1;
-//       if (sby2<0) sby2=-1;
-//       if (sbx2>20) sbx2=-1;
-//       if (sby2>20) sby2=-1;
-//       ibx2=ix*21+(sbx2+off);
-//       iby2=iy*21+(sby2+off);
-//       if (sbx2>=0 && sby2>=0)  hh->Fill(hh->GetXaxis()->GetBinCenter(ibx2+1),hh->GetYaxis()->GetBinCenter(iby2+1),hg->GetBinContent(ibx+1,iby+1));
-      
-//     }
-//   }  
-
-//   new TCanvas();
-//   hg->GetXaxis()->SetRangeUser(84,87);
-//   hg->GetYaxis()->SetRangeUser(120,124);
-//   hg->Draw("colz");
-  
-
-
-
-
-//   new TCanvas();
-//   //  hh->Divide(h1);
-//   hh->GetXaxis()->SetRangeUser(84,87);
-//   hh->GetYaxis()->SetRangeUser(120,124);
-//   hh->Draw("colz");
-
-
-//   new TCanvas();
-//   //  hh->Divide(h1);
-//   hh13b->GetXaxis()->SetRangeUser(84,87);
-//   hh13b->GetYaxis()->SetRangeUser(120,124);
-//   hh13b->Draw("colz");
-
-//   new TCanvas();
-//   //  hh->Divide(h1);
-//   hh13->GetXaxis()->SetRangeUser(84,87);
-//   hh13->GetYaxis()->SetRangeUser(120,124);
-//   hh13->Draw("colz");
-
-//   // //TFile fsg("/local_zfs_raid/tomcat_20160528/trees/img_sample_grating_1d_eta_gmap.root");
-//   // //TH2D *hsg=(TH2D*)fsg.Get("sample_grating_1dHR");
-//   // TFile fsg("/local_zfs_raid/tomcat_20160528/trees/img_sample_grating_1d_eta.root");
-//   // TH2D *hsg=(TH2D*)fsg.Get("imgHR");
-//   // hsg->SetName("imgGratingSample");
-
-
-//   // hsg->Divide(hpix);
-
-//   // Double_t nf=hff->Integral(100,hff->GetNbinsX()-100,hff->GetYaxis()->FindBin(130), hff->GetYaxis()->FindBin(140))/((hff->GetNbinsX()-200)*250);
-//   // hff->Scale(1./nf);
-
-//   // // hg->Divide(hff);
-//   // //hsg->Divide(hff);
-
-//   // Double_t ng=hg->Integral(100,hg->GetNbinsX()-100,hg->GetYaxis()->FindBin(130), hg->GetYaxis()->FindBin(140))/((hg->GetNbinsX()-200)*250);
-//   //  Double_t nsg=hsg->Integral(100,hsg->GetNbinsX()-100,hsg->GetYaxis()->FindBin(130), hsg->GetYaxis()->FindBin(140))/((hsg->GetNbinsX()-200)*250);
-
-//   //  hg->Scale(1/ng);
-//   //  hsg->Scale(1/nsg);
-
-//   //  // new TCanvas();
-//   //  // hg->SetMaximum(1.);
-//   //  // hg->Draw("colz");
-//   //  // new TCanvas();
-//   //  // hsg->SetMaximum(1.);
-//   //  // hsg->Draw("colz");
-   
-//   // //  TH1D *pg=hg->ProjectionX("pg",hg->GetYaxis()->FindBin(174.5)+1,hg->GetYaxis()->FindBin(175.5));
-//   // //  TH1D *psg=hsg->ProjectionX("psg",hsg->GetYaxis()->FindBin(174.5)+1,hsg->GetYaxis()->FindBin(175.5));
-//   // //  psg->SetLineColor(2);
-//   // // new TCanvas();
-  
-//   // // pg->Draw("l");
-//   // // psg->Draw("l same");
-  
-//   // int nbx=hg->GetNbinsX();
-//   // int nby=hg->GetNbinsY();
-//   // char buffer[nbx];
-//   // cout << "Size of short int is "<<sizeof(char)<< endl;
-//   // cout << "width is "<<nbx<< endl;
-//   // cout << "height is "<<nby<< endl;
-//   // ofstream myFile ("grating_1d.bin", ios::out | ios::binary);
-//   // for (int iy=0; iy<nby; iy++) {
-//   //   for (int ix=0; ix<nbx; ix++) {
-//   //     buffer[ix]=hg->GetBinContent(ix+1,iy+1);
-//   //   }
-//   //   myFile.write((char*)buffer, nbx*sizeof(char));
-//   // }
-//   // myFile.close();
-
-
-//   // nbx=hsg->GetNbinsX();
-//   // nby=hsg->GetNbinsY();
-
-//   // cout << "Size of short int is "<<sizeof(char)<< endl;
-//   // cout << "width is "<<nbx<< endl;
-//   // cout << "height is "<<nby<< endl;
-
-//   // ofstream myFile1 ("sample_grating_1d.bin", ios::out | ios::binary);
-//   // for (int iy=0; iy<nby; iy++) {
-//   //   for (int ix=0; ix<nbx; ix++) {
-//   //     buffer[ix]=hsg->GetBinContent(ix+1,iy+1);
-//   //   }
-//   //   myFile1.write((char*)buffer, nbx*sizeof(char));
-//   // }
-//   // myFile1.close();
-
-// // NAME
-// //        raw2tiff - create a TIFF file from a raw data
-
-// // SYNOPSIS
-// //        raw2tiff [ options ] input.raw output.tif
-
-// // DESCRIPTION
-// //        raw2tiff  converts  a  raw byte sequence into TIFF.  By default, the TIFF image is created with data samples packed (PlanarConfiguration=1), compressed with the PackBits algorithm (Compression=32773),
-// //        and with each strip no more than 8 kilobytes.  These characteristics can overridden, or explicitly specified with the options described below.
-
-// // OPTIONS
-// //        -H number
-// //               size of input image file header in bytes (0 by default). This amount of data just will be skipped from the start of file while reading.
-
-// //        -w number
-// //               width of input image in pixels (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-// //        -l number
-// //               length of input image in lines (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-// //        -b number
-// //               number of bands in input image (1 by default).
-
-// //        -d data_type
-// //               type of samples in input image, where data_type may be:
-// //               byte     8-bit unsigned integer (default),
-// //               short    16-bit unsigned integer,
-// //               long     32-bit unsigned integer,
-// //               sbyte    8-bit signed integer,
-// //               sshort   16-bit signed integer,
-// //               slong    32-bit signed integer,
-// //               float    32-bit IEEE floating point,
-// //               double   64-bit IEEE floating point.
-
-// //        -i config
-// //               type of samples interleaving in input image, where config may be:
-// //               pixel   pixel interleaved data (default),
-// //               band    band interleaved data.
-
-// //        -p photo
-// //               photometric interpretation (color space) of the input image, where photo may be:
-// //               miniswhite   white color represented with 0 value,
-// //               minisblack   black color represented with 0 value (default),
-// //               rgb          image has RGB color model,
-// //               cmyk         image has CMYK (separated) color model,
-// //               ycbcr        image has YCbCr color model,
-// //               cielab       image has CIE L*a*b color model,
-// //               icclab       image has ICC L*a*b color model,
-// //               itulab       image has ITU L*a*b color model.
-
-// //        -s     swap bytes fetched from the input file.
-
-// //        -L     input data has LSB2MSB bit order (default).
-
-// //        -M     input data has MSB2LSB bit order.
-
-// //        -c     Specify a compression scheme to use when writing image data: -c none for no compression, -c packbits for the PackBits compression algorithm (the default), -c jpeg for the baseline JPEG compres-
-// //               sion algorithm, -c zip for the Deflate compression algorithm, and -c lzw for Lempel-Ziv & Welch.
-
-// //        -r number
-// //               Write data with a specified number of rows per strip; by default the number of rows/strip is selected so that each strip is approximately 8 kilobytes.
-// //width is 10000
-// //height is 5000
-
-
-}

slsDetectorCalibration/etaVEL/imageMacroG2D.C

@@ -1,185 +0,0 @@
-{ 
-  TColor::InitializeColors();
-  const Int_t NRGBs = 5;
-  const Int_t NCont = 255;//90;
-
-  Double_t stops[NRGBs] = { 0.00, 0.34, 0.61, 0.84, 1.00 };
-  Double_t red[NRGBs]   = { 0.00, 0.00, 0.87, 1.00, 0.51 };
-  Double_t green[NRGBs] = { 0.00, 0.81, 1.00, 0.20, 0.00 };
-  Double_t blue[NRGBs]  = { 0.51, 1.00, 0.12, 0.00, 0.00 };
-  Double_t gray[NRGBs]  = { 1., 0.34, 0.61, 0.84, 1.00};
-  Double_t zero[NRGBs]  = { 0., 0.0,0.0, 0.0, 0.00};
-  //TColor::CreateGradientColorTable(NRGBs, stops, red, green, blue, NCont);
-   TColor::CreateGradientColorTable(NRGBs, stops, gray, gray, gray, NCont);
- 
-  gStyle->SetNumberContours(NCont);
-
-  gStyle->SetPadTopMargin(0);
-  gStyle->SetPadRightMargin(0);
-  gStyle->SetPadBottomMargin(0);
-  gStyle->SetPadLeftMargin(0);
-
-
-
-  gROOT->ForceStyle();
-
-  // TFile ff("/local_zfs_raid/tomcat_20160528/trees/img_blank_eta.root");
-  // TH2D *hff=(TH2D*)ff.Get("imgHR");
-  TFile ff("/mnt/moench_data/tomcat_20160528_img/img_blank_eta_nb25.root");
-  TH2D *hff=(TH2D*)ff.Get("blankHR");
-  hff->SetName("imgBlank");
-  TH2D *hpixel=new TH2D("hpixel","hpixel",25,0,25,25,0,25);
-  for (int ibx=10*25; ibx<hff->GetNbinsX()-10*25; ibx++) {
-    for (int iby=20*25; iby<hff->GetNbinsY()-20*25; iby++) {
-      hpixel->Fill((ibx-12)%25,(iby-12)%25,hff->GetBinContent(ibx+1,iby+1));
-    }
-  }
-  hpixel->Scale(1./hpixel->GetBinContent(13,13));
-
-  // new TCanvas();
-  // hpixel->Draw("colz"); 
-
-  TH2D *hraw=(TH2D*)hff->Clone("hraw");
-  TH2D *hpix=(TH2D*)hff->Clone("hpix");
-
-  for (int ibx=0; ibx<hff->GetNbinsX(); ibx++) {
-    for (int iby=0; iby<hff->GetNbinsY(); iby++) {
-      hpix->SetBinContent(ibx+1,iby+1,hpixel->GetBinContent(hpixel->GetXaxis()->FindBin((ibx-12)%25),hpixel->GetXaxis()->FindBin((iby-12)%25)));
-    }
-  }
-
-  hff->Divide(hpix);
-
-  //  new TCanvas();
-  // hff->Draw("colz");
-
-
-  // TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_grating_2d_eta.root");
-  // TH2D *hg=(TH2D*)fg.Get("imgHR");
-  TFile fg("/mnt/moench_data/tomcat_20160528_img/img_grating_2d_eta_nb25.root");
-  TH2D *hg=(TH2D*)fg.Get("grating_2dHR");
-  hg->SetName("imgGrating");
-
-  hg->Divide(hpix);
-
-
-
-  Double_t nf=hff->Integral(100,hff->GetNbinsX()-100,hff->GetYaxis()->FindBin(130), hff->GetYaxis()->FindBin(140))/((hff->GetNbinsX()-200)*250);
-  hff->Scale(1./nf);
-
-  // hg->Divide(hff);
-  //hsg->Divide(hff);
-
-  Double_t ng=hg->Integral(100,hg->GetNbinsX()-100,hg->GetYaxis()->FindBin(130), hg->GetYaxis()->FindBin(140))/((hg->GetNbinsX()-200)*250);
- 
-   hg->Scale(1/ng);
-
-   new TCanvas("c1","c1",800,800);
-   hg->SetMaximum(2.);
-   Double_t xmin=hg->GetXaxis()->GetXmin();
-   Double_t xmax=hg->GetXaxis()->GetXmax();
-   Double_t ymin=hg->GetYaxis()->GetXmin();
-   Double_t ymax=hg->GetYaxis()->GetXmax();
-   hg->SetTitle(";mm;mm;Normalized intensity (a.u.)");
-   hg->GetXaxis()->Set(hg->GetXaxis()->GetNbins(),xmin*0.025-180.*0.025+0.1,xmax*0.025-180.*0.025+0.1);
-   hg->GetYaxis()->Set(hg->GetYaxis()->GetNbins(),ymin*0.025-180.*0.025-1.5,ymax*0.025-180*0.025-1.5);
-   
-   hg->GetXaxis()->SetRangeUser(0,0.5);
-   hg->GetYaxis()->SetRangeUser(0,0.5);
-   
-   hg->Draw("col");
-   hg->SetStats(kFALSE);
-   // new TCanvas();
-   // hsg->SetMaximum(1.);
-   // hsg->Draw("colz");
-   
-  //  TH1D *pg=hg->ProjectionX("pg",hg->GetYaxis()->FindBin(174.5)+1,hg->GetYaxis()->FindBin(175.5));
-  //  TH1D *psg=hsg->ProjectionX("psg",hsg->GetYaxis()->FindBin(174.5)+1,hsg->GetYaxis()->FindBin(175.5));
-  //  psg->SetLineColor(2);
-  // new TCanvas();
-  
-  // pg->Draw("l");
-  // psg->Draw("l same");
-  
-  int nbx=hg->GetNbinsX();
-  int nby=hg->GetNbinsY();
-  char buffer[nbx];
-  cout << "Size of short int is "<<sizeof(char)<< endl;
-  cout << "width is "<<nbx<< endl;
-  cout << "height is "<<nby<< endl;
-  ofstream myFile ("grating_2d.bin", ios::out | ios::binary);
-  for (int iy=0; iy<nby; iy++) {
-    for (int ix=0; ix<nbx; ix++) {
-      buffer[ix]=hg->GetBinContent(ix+1,iy+1);
-    }
-    myFile.write((char*)buffer, nbx*sizeof(char));
-  }
-  myFile.close();
-
-
-// NAME
-//        raw2tiff - create a TIFF file from a raw data
-
-// SYNOPSIS
-//        raw2tiff [ options ] input.raw output.tif
-
-// DESCRIPTION
-//        raw2tiff  converts  a  raw byte sequence into TIFF.  By default, the TIFF image is created with data samples packed (PlanarConfiguration=1), compressed with the PackBits algorithm (Compression=32773),
-//        and with each strip no more than 8 kilobytes.  These characteristics can overridden, or explicitly specified with the options described below.
-
-// OPTIONS
-//        -H number
-//               size of input image file header in bytes (0 by default). This amount of data just will be skipped from the start of file while reading.
-
-//        -w number
-//               width of input image in pixels (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-//        -l number
-//               length of input image in lines (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-//        -b number
-//               number of bands in input image (1 by default).
-
-//        -d data_type
-//               type of samples in input image, where data_type may be:
-//               byte     8-bit unsigned integer (default),
-//               short    16-bit unsigned integer,
-//               long     32-bit unsigned integer,
-//               sbyte    8-bit signed integer,
-//               sshort   16-bit signed integer,
-//               slong    32-bit signed integer,
-//               float    32-bit IEEE floating point,
-//               double   64-bit IEEE floating point.
-
-//        -i config
-//               type of samples interleaving in input image, where config may be:
-//               pixel   pixel interleaved data (default),
-//               band    band interleaved data.
-
-//        -p photo
-//               photometric interpretation (color space) of the input image, where photo may be:
-//               miniswhite   white color represented with 0 value,
-//               minisblack   black color represented with 0 value (default),
-//               rgb          image has RGB color model,
-//               cmyk         image has CMYK (separated) color model,
-//               ycbcr        image has YCbCr color model,
-//               cielab       image has CIE L*a*b color model,
-//               icclab       image has ICC L*a*b color model,
-//               itulab       image has ITU L*a*b color model.
-
-//        -s     swap bytes fetched from the input file.
-
-//        -L     input data has LSB2MSB bit order (default).
-
-//        -M     input data has MSB2LSB bit order.
-
-//        -c     Specify a compression scheme to use when writing image data: -c none for no compression, -c packbits for the PackBits compression algorithm (the default), -c jpeg for the baseline JPEG compres-
-//               sion algorithm, -c zip for the Deflate compression algorithm, and -c lzw for Lempel-Ziv & Welch.
-
-//        -r number
-//               Write data with a specified number of rows per strip; by default the number of rows/strip is selected so that each strip is approximately 8 kilobytes.
-//width is 10000
-//height is 5000
-
-
-}

slsDetectorCalibration/etaVEL/imageMacroSample.C

@@ -1,173 +0,0 @@
-{
-  // TFile ff("/local_zfs_raid/tomcat_20160528/trees/img_blank_eta.root");
-  // TH2D *hff=(TH2D*)ff.Get("imgHR");
-  // TFile ff("/local_zfs_raid/tomcat_20160528/trees/img_blank_eta_gmap_v2.root");
-  // TH2D *hff=(TH2D*)ff.Get("blankHR");
-  // hff->SetName("imgBlank");
-  // TH2D *hpixel=new TH2D("hpixel","hpixel",25,0,25,25,0,25);
-  // for (int ibx=10*25; ibx<hff->GetNbinsX()-10*25; ibx++) {
-  //   for (int iby=20*25; iby<hff->GetNbinsY()-20*25; iby++) {
-  //     hpixel->Fill((ibx-12)%25,(iby-12)%25,hff->GetBinContent(ibx+1,iby+1));
-  //   }
-  // }
-  // hpixel->Scale(1./hpixel->GetBinContent(13,13));
-
-  // // new TCanvas();
-  // // hpixel->Draw("colz"); 
-
-  // TH2D *hraw=(TH2D*)hff->Clone("hraw");
-  // TH2D *hpix=(TH2D*)hff->Clone("hpix");
-
-  // for (int ibx=0; ibx<hff->GetNbinsX(); ibx++) {
-  //   for (int iby=0; iby<hff->GetNbinsY(); iby++) {
-  //     hpix->SetBinContent(ibx+1,iby+1,hpixel->GetBinContent(hpixel->GetXaxis()->FindBin((ibx-12)%25),hpixel->GetXaxis()->FindBin((iby-12)%25)));
-  //   }
-  // }
-
-  // hff->Divide(hpix);
-
-  // Double_t nf=hff->Integral(100,hff->GetNbinsX()-100,hff->GetYaxis()->FindBin(130), hff->GetYaxis()->FindBin(140))/((hff->GetNbinsX()-200)*250);
-  // hff->Scale(1./nf);
-
-  //  new TCanvas();
-  // hff->Draw("colz");
-
-
-  // TFile fg("/local_zfs_raid/tomcat_20160528/trees/img_grating_2d_eta.root");
-  // TH2D *hg=(TH2D*)fg.Get("imgHR");
-  TFile fg("/mnt/moench_data/tomcat_20160528_img/img_sample_eta_gmap_v2.root");
-  TH2D *hg=(TH2D*)fg.Get("sampleHR");
-  hg->SetName("imgSample");
-
-  // hg->Divide(hpix);
-
-
-
-
-  // hg->Divide(hff);
-  //hsg->Divide(hff);
-
-  Double_t ng=hg->Integral(100,hg->GetNbinsX()-100,hg->GetYaxis()->FindBin(130), hg->GetYaxis()->FindBin(140))/((hg->GetNbinsX()-200)*250);
- 
-   hg->Scale(1/ng);
-
-   // new TCanvas();
-   // hsg->SetMaximum(1.);
-   // hsg->Draw("colz");
-   
-  //  TH1D *pg=hg->ProjectionX("pg",hg->GetYaxis()->FindBin(174.5)+1,hg->GetYaxis()->FindBin(175.5));
-  //  TH1D *psg=hsg->ProjectionX("psg",hsg->GetYaxis()->FindBin(174.5)+1,hsg->GetYaxis()->FindBin(175.5));
-  //  psg->SetLineColor(2);
-  // new TCanvas();
-  
-  // pg->Draw("l");
-  // psg->Draw("l same");
-   TH2D *hpixel1=new TH2D("hpixel1","hpixel1",25,0,25,25,0,25);
-  for (int ibx=10*25; ibx<35*25; ibx++) {
-    for (int iby=25*25; iby<50*25; iby++) {
-      hpixel1->Fill((ibx-12)%25,(iby-12)%25,hg->GetBinContent(ibx+1,iby+1));
-    }
-  }
-  hpixel1->Scale(1./hpixel1->GetBinContent(13,13));
-
-  // new TCanvas();
-  // hpixel->Draw("colz"); 
-
-  TH2D *hpix1=(TH2D*)hg->Clone("hpix1");
-
-  for (int ibx=0; ibx<hg->GetNbinsX(); ibx++) {
-    for (int iby=0; iby<hg->GetNbinsY(); iby++) {
-      hpix1->SetBinContent(ibx+1,iby+1,hpixel1->GetBinContent(hpixel1->GetXaxis()->FindBin((ibx-12)%25),hpixel1->GetXaxis()->FindBin((iby-12)%25)));
-    }
-  }
-
-  hg->Divide(hpix1);
-
-  new TCanvas();
-  hg->SetMaximum(4);
-  hg->SetMinimum(0.5);
-  hg->Draw("colz");
-  
-
-  int nbx=hg->GetNbinsX();
-  int nby=hg->GetNbinsY();
-  char buffer[nbx];
-  cout << "Size of short int is "<<sizeof(char)<< endl;
-  cout << "width is "<<nbx<< endl;
-  cout << "height is "<<nby<< endl;
-  ofstream myFile ("sample.bin", ios::out | ios::binary);
-  for (int iy=0; iy<nby; iy++) {
-    for (int ix=0; ix<nbx; ix++) {
-      buffer[ix]=hg->GetBinContent(ix+1,iy+1);
-    }
-    myFile.write((char*)buffer, nbx*sizeof(char));
-  }
-  myFile.close();
-
-
-// NAME
-//        raw2tiff - create a TIFF file from a raw data
-
-// SYNOPSIS
-//        raw2tiff [ options ] input.raw output.tif
-
-// DESCRIPTION
-//        raw2tiff  converts  a  raw byte sequence into TIFF.  By default, the TIFF image is created with data samples packed (PlanarConfiguration=1), compressed with the PackBits algorithm (Compression=32773),
-//        and with each strip no more than 8 kilobytes.  These characteristics can overridden, or explicitly specified with the options described below.
-
-// OPTIONS
-//        -H number
-//               size of input image file header in bytes (0 by default). This amount of data just will be skipped from the start of file while reading.
-
-//        -w number
-//               width of input image in pixels (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-//        -l number
-//               length of input image in lines (can be guessed, see GUESSING THE IMAGE GEOMETRY below).
-
-//        -b number
-//               number of bands in input image (1 by default).
-
-//        -d data_type
-//               type of samples in input image, where data_type may be:
-//               byte     8-bit unsigned integer (default),
-//               short    16-bit unsigned integer,
-//               long     32-bit unsigned integer,
-//               sbyte    8-bit signed integer,
-//               sshort   16-bit signed integer,
-//               slong    32-bit signed integer,
-//               float    32-bit IEEE floating point,
-//               double   64-bit IEEE floating point.
-
-//        -i config
-//               type of samples interleaving in input image, where config may be:
-//               pixel   pixel interleaved data (default),
-//               band    band interleaved data.
-
-//        -p photo
-//               photometric interpretation (color space) of the input image, where photo may be:
-//               miniswhite   white color represented with 0 value,
-//               minisblack   black color represented with 0 value (default),
-//               rgb          image has RGB color model,
-//               cmyk         image has CMYK (separated) color model,
-//               ycbcr        image has YCbCr color model,
-//               cielab       image has CIE L*a*b color model,
-//               icclab       image has ICC L*a*b color model,
-//               itulab       image has ITU L*a*b color model.
-
-//        -s     swap bytes fetched from the input file.
-
-//        -L     input data has LSB2MSB bit order (default).
-
-//        -M     input data has MSB2LSB bit order.
-
-//        -c     Specify a compression scheme to use when writing image data: -c none for no compression, -c packbits for the PackBits compression algorithm (the default), -c jpeg for the baseline JPEG compres-
-//               sion algorithm, -c zip for the Deflate compression algorithm, and -c lzw for Lempel-Ziv & Welch.
-
-//        -r number
-//               Write data with a specified number of rows per strip; by default the number of rows/strip is selected so that each strip is approximately 8 kilobytes.
-//width is 10000
-//height is 5000
-
-
-}

slsDetectorCalibration/etaVEL/slsInterpolation.h

@@ -1,224 +0,0 @@
-#ifndef SLS_INTERPOLATION_H
-#define SLS_INTERPOLATION_H
-
-#include <TObject.h>
-#include <TTree.h>
-#include <TH2F.h>
-
-#ifndef DEF_QUAD
-#define DEF_QUAD
- enum quadrant {
-    TOP_LEFT=0,
-    TOP_RIGHT=1,
-    BOTTOM_LEFT=2,
-    BOTTOM_RIGHT=3,
-    UNDEFINED_QUADRANT=-1
-  };
-#endif
-
-class slsInterpolation : public TObject{
-
- public:
- slsInterpolation(int nx=40, int ny=160, int ns=25) :nPixelsX(nx), nPixelsY(ny),  nSubPixels(ns) {hint=new TH2F("hint","hint",ns*nx, 0, nx, ns*ny, 0, ny);};
- 
-  //create eta distribution, eta rebinnining etc.
-  //returns flat field image
-  virtual void prepareInterpolation(int &ok)=0;
-
-  //create interpolated image
-  //returns interpolated image
-  virtual TH2F *getInterpolatedImage(){return hint;};
-  //return position inside the pixel for the given photon
-  virtual void getInterpolatedPosition(Int_t x, Int_t y, Double_t *data, Double_t &int_x, Double_t &int_y)=0;
-
-  TH2F *addToImage(Double_t int_x, Double_t int_y){hint->Fill(int_x, int_y); return hint;};
-
-
-
-  virtual int addToFlatField(Double_t *cluster, Double_t &etax, Double_t &etay)=0;
-  virtual int addToFlatField(Double_t etax, Double_t etay)=0;
-  
-  //virtual void Streamer(TBuffer &b);
-
-  
-  static int calcQuad(Double_t *cl, Double_t &sum, Double_t &totquad, Double_t sDum[2][2]){
-    
-    int corner = UNDEFINED_QUADRANT;
-    Double_t *cluster[3];
-    cluster[0]=cl;
-    cluster[1]=cl+3;
-    cluster[2]=cl+6;
-
-    sum = cluster[0][0] + cluster[1][0] + cluster[2][0] + cluster[0][1] + cluster[1][1] + cluster[2][1] + cluster[0][2] + cluster[1][2] + cluster[2][2];
-    
-    double sumBL = cluster[0][0] + cluster[1][0] + cluster[0][1] + cluster[1][1]; //2 ->BL
-    double sumTL = cluster[1][0] + cluster[2][0] + cluster[2][1] + cluster[1][1]; //0 ->TL
-    double sumBR = cluster[0][1] + cluster[0][2] + cluster[1][2] + cluster[1][1]; //3 ->BR
-    double sumTR = cluster[1][2] + cluster[2][1] + cluster[2][2] + cluster[1][1]; //1 ->TR
-    double sumMax = 0;
-    double t, r;
-    
-    // if(sumTL  >= sumMax){
-    sDum[0][0] = cluster[0][0]; sDum[1][0] = cluster[1][0];
-    sDum[0][1] = cluster[0][1]; sDum[1][1] = cluster[1][1];
-    corner = BOTTOM_LEFT;
-    sumMax=sumBL;
-    // } 
-    
-    if(sumTL  >= sumMax){
-      sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0];
-      sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1];
-
-      corner = TOP_LEFT;
-      sumMax=sumTL;
-    } 
-
-    if(sumBR  >= sumMax){
-      sDum[0][0] = cluster[0][1]; sDum[1][0] = cluster[1][1];
-      sDum[0][1] = cluster[0][2]; sDum[1][1] = cluster[1][2];
-      
-      corner = BOTTOM_RIGHT;
-      sumMax=sumBR;
-    }
-    
-    if(sumTR  >= sumMax){
-      sDum[0][0] = cluster[1][1]; sDum[1][0] = cluster[2][1];
-      sDum[0][1] = cluster[1][2]; sDum[1][1] = cluster[2][2];
-      
-      corner = TOP_RIGHT;
-      sumMax=sumTR;
-    }
-    
-    totquad=sumMax;
-  
-    return corner;
-    
-  } 
-
-  static int calcEta(Double_t totquad, Double_t sDum[2][2], Double_t &etax, Double_t &etay){
-    Double_t t,r;
-    
-    if (totquad>0) {
-      t = sDum[1][0] + sDum[1][1];
-      r = sDum[0][1] + sDum[1][1];
-      etax=r/totquad;
-      etay=t/totquad;
-    }
-    return 0;
-    
-  } 
-
-
-  static int calcEta(Double_t *cl, Double_t &etax, Double_t &etay, Double_t &sum, Double_t &totquad, Double_t sDum[2][2]) {
-    int corner = calcQuad(cl,sum,totquad,sDum);
-    calcEta(totquad, sDum, etax, etay);
-    
-    return corner;
-  }
-
-
-  static int calcEtaL(Double_t totquad, int corner, Double_t sDum[2][2], Double_t &etax, Double_t &etay){
-    Double_t t,r, toth, totv;
-    if (totquad>0) {
-      switch(corner) {
-      case TOP_LEFT:
-	t = sDum[1][1] ;
-	r = sDum[0][1] ;
-	toth=sDum[1][1]+sDum[1][0];
-	totv=sDum[0][1]+sDum[1][1];
-	break;
-      case TOP_RIGHT:
-	t = sDum[1][0] ;
-	r = sDum[0][1] ;
-	toth=sDum[0][0]+t;
-	totv=sDum[0][0]+r;
-	break;
-      case BOTTOM_LEFT:
-	r = sDum[1][1] ;
-	t = sDum[1][1] ;
-	toth=sDum[1][0]+t;
-	totv=sDum[0][1]+r;
-	break;
-      case BOTTOM_RIGHT:
-	t = sDum[1][0] ;
-	r = sDum[1][1] ;
-	toth=sDum[1][1]+t;
-	totv=sDum[0][1]+r;
-	break;
-      default:
-	etax=-1;
-	etay=-1;
-	return 0;
-      }
-      etax=r/totv;
-      etay=t/toth;
-    }
-    return 0;
-  }
-
-  static int calcEtaL(Double_t *cl, Double_t &etax, Double_t &etay, Double_t &sum, Double_t &totquad, Double_t sDum[2][2]) {
-    int corner = calcQuad(cl,sum,totquad,sDum);
-    calcEtaL(totquad, corner, sDum, etax, etay);
-    
-    return corner;
-  }
-
-
-
-  static int calcEtaC3(Double_t *cl, Double_t &etax, Double_t &etay, Double_t &sum, Double_t &totquad, Double_t sDum[2][2]){
-    
-    int corner = calcQuad(cl,sum,totquad,sDum);
-    calcEta(sum, sDum, etax, etay);
-    return corner;
-    
-  }
-
-
-
-  static int calcEta3(Double_t *cl, Double_t &etax, Double_t &etay, Double_t &sum) {
-    Double_t l,r,t,b;
-    sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8];
-    if (sum>0) {
-      l=cl[0]+cl[3]+cl[6];
-      r=cl[2]+cl[5]+cl[8];
-      b=cl[0]+cl[1]+cl[2];
-      t=cl[6]+cl[7]+cl[8];
-      etax=(-l+r)/sum;
-      etay=(-b+t)/sum;
-    }
-    
-    return -1;
-  }
-
-
-
-  static int calcEta3X(Double_t *cl, Double_t &etax, Double_t &etay, Double_t &sum) {
-    Double_t l,r,t,b;
-    sum=cl[0]+cl[1]+cl[2]+cl[3]+cl[4]+cl[5]+cl[6]+cl[7]+cl[8];
-    if (sum>0) {
-      l=cl[3];
-      r=cl[5];
-      b=cl[1];
-      t=cl[7];
-      etax=(-l+r)/sum;
-      etay=(-b+t)/sum;
-    }
-    return -1;
-  }
-
-
-
-
-
-
- protected:
-  int nPixelsX, nPixelsY;
-  int nSubPixels;
-  TH2F *hint;
-
-
-  //  ClassDefNV(slsInterpolation,1);
-  // #pragma link C++ class slsInterpolation-;
-};
-
-#endif

slsDetectorCalibration/gMapDemo.C

@@ -1,11 +0,0 @@
-{
-  //.L energyCalibration.cpp+
-  //.L gainMap.C+
-  TFile fin("/data/moench_xbox_20140113/MoTarget_45kV_0_8mA_120V_cds_g4.root");
-  TH2F *h2=fin.Get("h2");
-  TH2F *gMap=gainMap(h2,4);
-  gMap->Draw("colz");
-
-
-
-}

slsDetectorCalibration/gainMap.C

@@ -1,228 +0,0 @@
-#define MYROOT
-#include <TH2F.h>
-#include <TSpectrum.h>
-#include <TH1D.h>
-#include <TFile.h>
-#include <TList.h>
-#include <TPolyMarker.h>
-#include <THStack.h>
-#include <TF1.h>
-#include <TGraphErrors.h>
-#include <iostream>
-#include <energyCalibration.h>
-
-using namespace std;
-
-
-#define FOPT "0"
-
-TH2F *gainMap(TH2F *h2, float g) {
-  //  int npx, npy;
-  int npx=160, npy=160;
-  // det->getDetectorSize(npx, npy);
-
-  TH2F *gMap=new TH2F("gmap",h2->GetTitle(), npx, -0.5, npx-0.5, npy, -0.5, npy-0.5);
-
-  Double_t ens[3]={0,8,17.5}, eens[3]={0.,0.1,0.1};
-  Double_t peaks[3], epeaks[3];
-
-
-
-  int ibin;
-  TH1D *px;
-
-
-  energyCalibration *enCal=new energyCalibration();
-  enCal->setPlotFlag(0);
-  // enCal->setChargeSharing(0);
-  enCal->setScanSign(1);
-
-  Double_t gain, off, egain, eoff;
-
-
-  TList *functions;
-  TPolyMarker *pm ;
-  Double_t *peakX, *peakY;
-  TSpectrum *s=new TSpectrum();
-  Double_t mypar[10], emypar[10];
-  Double_t prms, np;
-  int iit=0;
-  TGraph *glin;
-  Double_t peakdum, hpeakdum;
-
-  for (int ix=1; ix<npx-1; ix++) {
-    for (int iy=1; iy<npy-1; iy++) {
-      // cout << ix << " " << iy << " " << ibin << endl;
-      ibin=ix*npy+iy;
-      px=h2->ProjectionX("px",ibin+1,ibin+1);
-      prms=10*g;
-      iit=0;
-      np=s->Search(px,prms,"",0.2);
-      while (np !=2) {
-	if (np>2)
-	  prms+=0.5*prms;
-	else
-	  prms-=0.5*prms;
-	iit++;
-	if (iit>=10)
-	  break;
-	np=s->Search(px,prms,"",0.2);
-      }
-      if (np!=2)
-	cout << "peak search could not converge " << ibin << endl;
-      if (np==2) {
-	pm=NULL;
-	functions=px->GetListOfFunctions();
-	if (functions)
-	  pm = (TPolyMarker*)functions->FindObject("TPolyMarker");
-	if (pm) {
-	  peakX=pm->GetX();
-	  peakY=pm->GetY();
-
-
-	  if (peakX[0]>peakX[1]) {
-	    peakdum=peakX[0];
-	    hpeakdum=peakY[0];
-	    peakX[0]= peakX[1];
-	    peakY[0]= peakY[1];
-	    peakX[1]= peakdum;
-	    peakY[1]= hpeakdum;
-	    
-	  }
-
-	  cout << "("<< ix << "," << iy << ") "  << endl;
-	  for (int ip=0; ip<np; ip++) {
-	    //  cout << ip << " " << peakX[ip] << " " << peakY[ip] << endl;
-	    
-	    enCal->setFitRange(peakX[ip]-10*g,peakX[ip]+10*g);
-	    mypar[0]=0;
-	    mypar[1]=0;
-	    mypar[2]=peakX[ip];
-	    mypar[3]=g*10;
-	    mypar[4]=peakY[ip];
-	    mypar[5]=0;
-	    
-
-
-	    enCal->setStartParameters(mypar);
-	    enCal->fitSpectrum(px,mypar,emypar);
-
-	    
-	    peaks[ip+1]=mypar[2];
-	    epeaks[ip+1]=emypar[2];
-	  }
-	  
-	  peaks[0]=0;
-	  epeaks[0]=1;
-
-	  //	  for (int i=0; i<3; i++) cout << i << " " << ens[i] << " " << eens[i]<< " "<< peaks[i]<< " " << epeaks[i] << endl;
-
-	  glin= enCal->linearCalibration(3,ens,eens,peaks,epeaks,gain,off,egain,eoff);
-
-	  //  cout << "Gain " << gain << " off " << off << endl;
-	  if (off>-10 && off<10) {
-	    gMap->SetBinContent(ix+1,iy+1,gain);
-	    gMap->SetBinError(ix+1,iy+1,egain);
-	  }
-	  if (glin)
-	    delete glin;
-	}
-      }
-
-
-    }
-  }
-
-  return gMap;
-}
-
-
-TH2F *noiseMap(TH2F *h2) {
-  //  int npx, npy;
-  int npx=160, npy=160;
-  // det->getDetectorSize(npx, npy);
-
-  TH2F *nMap=new TH2F("nmap",h2->GetTitle(), npx, -0.5, npx-0.5, npy, -0.5, npy-0.5);
-
-  int ibin;
-  TH1D *px;
-
-  for (int ix=0; ix<npx; ix++) {
-    for (int iy=0; iy<npy; iy++) {
-      cout << ix << " " << iy << " " << ibin << endl;
-      ibin=ix*npy+iy;
-      px=h2->ProjectionX("px",ibin+1,ibin+1);
-      px->Fit("gaus", FOPT);
-      if (px->GetFunction("gaus")) {
-	nMap->SetBinContent(ix+1,iy+1,px->GetFunction("gaus")->GetParameter(2));
-      }
-      // delete px;
-    }
-  }
-
-  return nMap;
-}
-
-
-THStack *noiseHistos(char *tit) {
-  char fname[10000];
-
-  sprintf(fname,"/data/moench_xbox_20140116/noise_map_%s.root",tit);
-  TFile *fn=new TFile(fname);
-  TH2F *nmap=(TH2F*)fn->Get("nmap");
-
-  if (nmap==NULL) {
-    cout << "No noise map in file " << fname << endl;
-
-    return NULL;
-  }
-
-  sprintf(fname,"/data/moench_xbox_20140113/gain_map_%s.root",tit);
-  TFile *fg=new TFile(fname);
-  TH2F *gmap=(TH2F*)fg->Get("gmap");
-
-  if (gmap==NULL) {
-    cout << "No gain map in file " << fname << endl;
-
-    return NULL;
-  }
-
-  nmap->Divide(gmap);
-  nmap->Scale(1000./3.6);
-
-  THStack *hs=new THStack(tit,tit);
-  hs->SetTitle(tit);
-
-  TH1F *h;
-  char hname[100];
-
-    cout << tit << endl;
-  for (int is=0; is<4; is++) {
-    sprintf(hname,"h%ds",is+1);
-
-    h=new TH1F(hname,tit,500,0,500);
-    hs->Add(h);
-    //  cout << hs->GetHists()->GetEntries() << endl;
-    for (int ix=40*is+2; ix<40*(is+1)-2; ix++) {
-
-      for (int iy=2; iy<158; iy++) {
-	if (ix<100 || ix>120)
-	  h->Fill(nmap->GetBinContent(ix+1,iy+1));
-      }
-    } 
-    cout << is+1 << "SC: " <<  "" << h->GetMean() << "+-" << h->GetRMS();
-    h->Fit("gaus","0Q");
-    h->SetLineColor(is+1);
-    if (h->GetFunction("gaus")) {
-      h->GetFunction("gaus")->SetLineColor(is+1);
-      cout << " or " << h->GetFunction("gaus")->GetParameter(1) << "+-" << h->GetFunction("gaus")->GetParError(1);
-    }
-    cout << endl;
-  }
-
-  //  cout << hs->GetHists()->GetEntries() << endl;
-
-  return hs;
-
-
-}